Sequence Assays
scRNAseq-10xGenomics-v2 / scRNAseq-10xGenomics-v3 / snRNAseq-10xGenomics-v2 / snRNAseq-10xGenomics-v3 / scRNAseq / sciRNAseq / snRNAseq / SNARE2-RNAseq
Related files:
-
🔬 Background doc: More details about this type.
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
This schema is for single cell RNA sequencing (scRNAseq). v3 adds umi_* fields.
Metadata schema
Version 3 (use this one)
Shared by all types
version
description
donor_id
tissue_id
execution_datetime
protocols_io_doi
operator
operator_email
pi
pi_email
assay_category
assay_type
analyte_class
is_targeted
acquisition_instrument_vendor
acquisition_instrument_modelUnique to this type
sc_isolation_protocols_io_doi
sc_isolation_entity
sc_isolation_tissue_dissociation
sc_isolation_enrichment
sc_isolation_quality_metric
sc_isolation_cell_number
rnaseq_assay_input
rnaseq_assay_method
library_construction_protocols_io_doi
library_layout
library_adapter_sequence
library_id
is_technical_replicate
cell_barcode_read
umi_read
umi_offset
umi_size
cell_barcode_offset
cell_barcode_size
expected_cell_count
library_pcr_cycles
library_pcr_cycles_for_sample_index
library_final_yield_value
library_final_yield_unit
library_average_fragment_size
sequencing_reagent_kit
sequencing_read_format
sequencing_read_percent_q30
sequencing_phix_percent
contributors_path
data_path
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 3 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | sequence |
| required | True |
assay_type
The UMI sequence length in the 10xGenomics-v2 kit is 10 base pairs and the length in the 10xGenomics-v3 kit is 12 base pairs.
| constraint | value |
|---|---|
| enum | scRNAseq-10xGenomics-v2, scRNAseq-10xGenomics-v3, snRNAseq-10xGenomics-v2, snRNAseq-10xGenomics-v3, scRNAseq, sciRNAseq, snRNAseq, or SNARE2-RNAseq |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | RNA |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
sc_isolation_protocols_io_doi
Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
sc_isolation_entity
The type of single cell entity derived from isolation protocol.
| constraint | value |
|---|---|
| enum | whole cell, nucleus, cell-cell multimer, or spatially encoded cell barcoding |
| required | True |
sc_isolation_tissue_dissociation
The method by which tissues are dissociated into single cells in suspension.
| constraint | value |
|---|---|
| required | True |
sc_isolation_enrichment
The method by which specific cell populations are sorted or enriched.
| constraint | value |
|---|---|
| enum | none or FACS |
| required | True |
sc_isolation_quality_metric
A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level.
| constraint | value |
|---|---|
| required | True |
sc_isolation_cell_number
Total number of cell/nuclei yielded post dissociation and enrichment.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_input
Number of cell/nuclei input to the assay.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_method
The kit used for the RNA sequencing assay.
| constraint | value |
|---|---|
| required | True |
library_construction_protocols_io_doi
A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
library_layout
State whether the library was generated for single-end or paired end sequencing.
| constraint | value |
|---|---|
| enum | single-end or paired-end |
| required | True |
library_adapter_sequence
Adapter sequence to be used for adapter trimming. Example: CTGTCTCTTATACACATCT.
| constraint | value |
|---|---|
| pattern (regular expression) | [ATCG]+(\+[ATCG]+)? |
| required | True |
library_id
A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.
| constraint | value |
|---|---|
| required | True |
is_technical_replicate
Is the sequencing reaction run in replicate, TRUE or FALSE.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
cell_barcode_read
Which read file(s) contains the cell barcode. Multiple cell_barcode_read files must be provided as a comma-delimited list (e.g. file1,file2,file3). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
umi_read
Which read file(s) contains the UMI (unique molecular identifier) barcode. Example: R1.
| constraint | value |
|---|---|
| pattern (regular expression) | [^/]+ |
| required | True |
umi_offset
Position in the read at which the umi barcode starts.
| constraint | value |
|---|---|
| type | integer |
| required | True |
umi_size
Length of the umi barcode in base pairs.
| constraint | value |
|---|---|
| type | integer |
| required | True |
cell_barcode_offset
Position(s) in the read at which the cell barcode starts. Leave blank if not applicable. Example: 0,0,38,76.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | \d+(,\d+)* |
cell_barcode_size
Length of the cell barcode in base pairs. Leave blank if not applicable. Example: 16,8,8,8.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | \d+(,\d+)* |
expected_cell_count
How many cells are expected? This may be used in downstream pipelines to guide selection of cell barcodes or segmentation parameters. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | integer |
| required | False |
library_pcr_cycles
Number of PCR cycles to amplify cDNA.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_pcr_cycles_for_sample_index
Number of PCR cycles performed for library indexing.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_final_yield_value
Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)
| constraint | value |
|---|---|
| type | number |
| required | True |
library_final_yield_unit
Units of final library yield. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | ng |
| required | False |
| required if | library_final_yield_value present |
library_average_fragment_size
Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.
| constraint | value |
|---|---|
| type | integer |
| required | True |
sequencing_reagent_kit
Reagent kit used for sequencing.
| constraint | value |
|---|---|
| required | True |
sequencing_read_format
Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(/\d+)+ |
| required | True |
sequencing_read_percent_q30
Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
sequencing_phix_percent
Percent PhiX loaded to the run.
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 2
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 2 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | sequence |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | scRNAseq-10xGenomics-v2, scRNAseq-10xGenomics-v3, snRNAseq-10xGenomics-v2, snRNAseq-10xGenomics-v3, scRNAseq, sciRNAseq, snRNAseq, or SNARE2-RNAseq |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | RNA |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
sc_isolation_protocols_io_doi
Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
sc_isolation_entity
The type of single cell entity derived from isolation protocol.
| constraint | value |
|---|---|
| enum | whole cell, nucleus, cell-cell multimer, or spatially encoded cell barcoding |
| required | True |
sc_isolation_tissue_dissociation
The method by which tissues are dissociated into single cells in suspension.
| constraint | value |
|---|---|
| required | True |
sc_isolation_enrichment
The method by which specific cell populations are sorted or enriched.
| constraint | value |
|---|---|
| enum | none or FACS |
| required | True |
sc_isolation_quality_metric
A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level.
| constraint | value |
|---|---|
| required | True |
sc_isolation_cell_number
Total number of cell/nuclei yielded post dissociation and enrichment.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_input
Number of cell/nuclei input to the assay.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_method
The kit used for the RNA sequencing assay.
| constraint | value |
|---|---|
| required | True |
library_construction_protocols_io_doi
A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
library_layout
State whether the library was generated for single-end or paired end sequencing.
| constraint | value |
|---|---|
| enum | single-end or paired-end |
| required | True |
library_adapter_sequence
Adapter sequence to be used for adapter trimming. Example: CTGTCTCTTATACACATCT.
| constraint | value |
|---|---|
| pattern (regular expression) | [ATCG]+(\+[ATCG]+)? |
| required | True |
library_id
A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.
| constraint | value |
|---|---|
| required | True |
is_technical_replicate
Is the sequencing reaction run in replicate, TRUE or FALSE.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
cell_barcode_read
Which read file(s) contains the cell barcode. Multiple cell_barcode_read files must be provided as a comma-delimited list (e.g. file1,file2,file3). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
cell_barcode_offset
Position(s) in the read at which the cell barcode starts. Leave blank if not applicable. Example: 0,0,38,76.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | \d+(,\d+)* |
cell_barcode_size
Length of the cell barcode in base pairs. Leave blank if not applicable. Example: 16,8,8,8.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | \d+(,\d+)* |
expected_cell_count
How many cells are expected? This may be used in downstream pipelines to guide selection of cell barcodes or segmentation parameters. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | integer |
| required | False |
library_pcr_cycles
Number of PCR cycles to amplify cDNA.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_pcr_cycles_for_sample_index
Number of PCR cycles performed for library indexing.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_final_yield_value
Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)
| constraint | value |
|---|---|
| type | number |
| required | True |
library_final_yield_unit
Units of final library yield. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | ng |
| required | False |
| required if | library_final_yield_value present |
library_average_fragment_size
Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.
| constraint | value |
|---|---|
| type | integer |
| required | True |
sequencing_reagent_kit
Reagent kit used for sequencing.
| constraint | value |
|---|---|
| required | True |
sequencing_read_format
Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(/\d+)+ |
| required | True |
sequencing_read_percent_q30
Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
sequencing_phix_percent
Percent PhiX loaded to the run.
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 1
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 1 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | sequence |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | scRNAseq-10xGenomics, snRNAseq-10xGenomics-v2, snRNAseq-10xGenomics-v3, scRNAseq, sciRNAseq, snRNAseq, or SNARE2-RNAseq |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | RNA |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
sc_isolation_protocols_io_doi
Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
sc_isolation_entity
The type of single cell entity derived from isolation protocol.
| constraint | value |
|---|---|
| enum | whole cell, nucleus, cell-cell multimer, or spatially encoded cell barcoding |
| required | True |
sc_isolation_tissue_dissociation
The method by which tissues are dissociated into single cells in suspension.
| constraint | value |
|---|---|
| required | True |
sc_isolation_enrichment
The method by which specific cell populations are sorted or enriched.
| constraint | value |
|---|---|
| enum | none or FACS |
| required | True |
sc_isolation_quality_metric
A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level.
| constraint | value |
|---|---|
| required | True |
sc_isolation_cell_number
Total number of cell/nuclei yielded post dissociation and enrichment.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_input
Number of cell/nuclei input to the assay.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_method
The kit used for the RNA sequencing assay.
| constraint | value |
|---|---|
| required | True |
library_construction_protocols_io_doi
A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
library_layout
State whether the library was generated for single-end or paired end sequencing.
| constraint | value |
|---|---|
| enum | single-end or paired-end |
| required | True |
library_adapter_sequence
Adapter sequence to be used for adapter trimming. Example: CTGTCTCTTATACACATCT.
| constraint | value |
|---|---|
| pattern (regular expression) | [ATCG]+(\+[ATCG]+)? |
| required | True |
library_id
A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.
| constraint | value |
|---|---|
| required | True |
is_technical_replicate
Is the sequencing reaction run in repliucate, TRUE or FALSE.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
cell_barcode_read
Which read file contains the cell barcode.
| constraint | value |
|---|---|
| required | True |
cell_barcode_offset
Position(s) in the read at which the cell barcode starts. Example: 0,0,38,76.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(,\d+)* |
| required | True |
cell_barcode_size
Length of the cell barcode in base pairs. Example: 16,8,8,8.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(,\d+)* |
| required | True |
library_pcr_cycles
Number of PCR cycles to amplify cDNA.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_pcr_cycles_for_sample_index
Number of PCR cycles performed for library indexing.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_final_yield_value
Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)
| constraint | value |
|---|---|
| type | number |
| required | True |
library_final_yield_unit
Units of final library yield. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | ng |
| required | False |
| required if | library_final_yield_value present |
library_average_fragment_size
Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.
| constraint | value |
|---|---|
| type | integer |
| required | True |
sequencing_reagent_kit
Reagent kit used for sequencing.
| constraint | value |
|---|---|
| required | True |
sequencing_read_format
Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(/\d+)+ |
| required | True |
sequencing_read_percent_q30
Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
sequencing_phix_percent
Percent PhiX loaded to the run.
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 0
Shared by all types
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)? |
| required | True |
execution_datetime
Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
assay_category
Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.
| constraint | value |
|---|---|
| enum | sequence |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | scRNAseq-10xGenomics, snRNAseq-10xGenomics-v2, snRNAseq-10xGenomics-v3, scRNAseq, sciRNAseq, snRNAseq, or SNARE2-RNAseq |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | RNA |
| required | True |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
acquisition_instrument_vendor
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
| constraint | value |
|---|---|
| required | True |
acquisition_instrument_model
Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.
| constraint | value |
|---|---|
| required | True |
Unique to this type
sc_isolation_protocols_io_doi
Link to a protocols document answering the question: How were single cells separated into a single-cell suspension?
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
sc_isolation_entity
The type of single cell entity derived from isolation protocol.
| constraint | value |
|---|---|
| required | True |
sc_isolation_tissue_dissociation
The method by which tissues are dissociated into single cells in suspension.
| constraint | value |
|---|---|
| required | True |
sc_isolation_enrichment
The method by which specific cell populations are sorted or enriched. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
sc_isolation_quality_metric
A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level.
| constraint | value |
|---|---|
| required | True |
sc_isolation_cell_number
Total number of cell/nuclei yielded post dissociation and enrichment.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_input
Number of cell/nuclei input to the assay.
| constraint | value |
|---|---|
| type | integer |
| required | True |
rnaseq_assay_method
The kit used for the RNA sequencing assay.
| constraint | value |
|---|---|
| required | True |
library_construction_protocols_io_doi
A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
library_layout
State whether the library was generated for single-end or paired end sequencing.
| constraint | value |
|---|---|
| enum | single-end or paired-end |
| required | True |
library_adapter_sequence
Adapter sequence to be used for adapter trimming.
| constraint | value |
|---|---|
| required | True |
library_id
A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.
| constraint | value |
|---|---|
| required | True |
is_technical_replicate
Is the sequencing reaction run in repliucate, TRUE or FALSE.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
cell_barcode_read
Which read file contains the cell barcode.
| constraint | value |
|---|---|
| required | True |
cell_barcode_offset
Position(s) in the read at which the cell barcode starts.
| constraint | value |
|---|---|
| required | True |
cell_barcode_size
Length of the cell barcode in base pairs.
| constraint | value |
|---|---|
| required | True |
library_pcr_cycles
Number of PCR cycles to amplify cDNA.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_pcr_cycles_for_sample_index
Number of PCR cycles performed for library indexing.
| constraint | value |
|---|---|
| type | integer |
| required | True |
library_final_yield_value
Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)
| constraint | value |
|---|---|
| type | number |
| required | True |
library_final_yield_unit
Units of final library yield. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | ng |
| required | False |
| required if | library_final_yield_value present |
library_average_fragment_size
Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.
| constraint | value |
|---|---|
| type | integer |
| required | True |
sequencing_reagent_kit
Reagent kit used for sequencing.
| constraint | value |
|---|---|
| required | True |
sequencing_read_format
Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56.
| constraint | value |
|---|---|
| pattern (regular expression) | \d+(/\d+)+ |
| required | True |
sequencing_read_percent_q30
Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
sequencing_phix_percent
Percent PhiX loaded to the run.
| constraint | value |
|---|---|
| type | number |
| required | True |
| minimum | 0 |
| maximum | 100 |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Directory schemas
| pattern | required? | description |
|---|---|---|
[^/]+\.fastq\.gz |
✓ | Compressed FastQ file |
extras\/.* |
Folder for general lab-specific files related to the dataset. [Exists in all assays] |