Sequence Assays

SNARE-seq2 / sciATACseq / snATACseq

Related files:

🔬 Background doc: More details about this type.
📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

This schema is for the single nucleus Assay for Transposase Accessible Chromatin by sequencing (snATACseq).

Metadata schema

Version 1 (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_model

Unique to this type

is_technical_replicate
library_id
sc_isolation_protocols_io_doi
sc_isolation_entity
sc_isolation_tissue_dissociation
sc_isolation_enrichment
sc_isolation_quality_metric
sc_isolation_cell_number
transposition_input
transposition_method
transposition_transposase_source
transposition_kit_number
library_construction_protocols_io_doi
library_layout
library_adapter_sequence
cell_barcode_read
cell_barcode_offset
cell_barcode_size
library_pcr_cycles
library_pcr_cycles_for_sample_index
library_final_yield
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	`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`

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	`SNARE-seq2`, `sciATACseq`, or `snATACseq`
required	`True`

`analyte_class`

Analytes are the target molecules being measured with the assay.

constraint	value
enum	`DNA`
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

`is_technical_replicate`

If TRUE, fastq files in dataset need to be merged.

constraint	value
type	`boolean`
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`

`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. “OK” or “not OK”, or with more specificity such as “debris”, “clump”, “low clump”.

constraint	value
required	`True`

`sc_isolation_cell_number`

Total number of cell/nuclei yielded post dissociation and enrichment.

constraint	value
type	`integer`
required	`True`

`transposition_input`

Number of cell/nuclei input to the assay.

constraint	value
type	`number`
required	`True`

`transposition_method`

Modality of capturing accessible chromatin molecules.

constraint	value
enum	`SNARE-Seq2-AC`, `bulkATACseq`, `snATACseq`, or `sciATACseq`
required	`True`

`transposition_transposase_source`

The source of the Tn5 transposase and transposon used for capturing accessible chromatin.

constraint	value
enum	`10X snATAC`, `In-house`, `Nextera`, or `10X multiome`
required	`True`

`transposition_kit_number`

If Tn5 came from a kit, provide the catalog number. Leave blank if not applicable.

constraint	value
required	`False`

`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”. 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/`

`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`

`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). This field is not required for barcoding by single-cell combinatorial indexing. Leave blank if not applicable.

constraint	value
required	`False`

`cell_barcode_offset`

Positions in the read at which the cell barcodes start. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences (the offsets). First barcode at position 0, then 38, then 76. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.) 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. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences, the offsets. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.) Leave blank if not applicable. Example: 16,8,8,8.

constraint	value
required	`False`
pattern (regular expression)	`\d+(,\d+)*`

`library_pcr_cycles`

Number of PCR cycles to enrich for accessible chromatin fragments.

constraint	value
type	`integer`
required	`True`

`library_pcr_cycles_for_sample_index`

Number of PCR cycles performed for library generation (figure in Descriptions section)

constraint	value
type	`integer`
required	`True`

`library_final_yield`

Total ng of library after final pcr amplification step.

constraint	value
type	`number`
required	`True`

`library_final_yield_unit`

Units for library_final_yield. Leave blank if not applicable.

constraint	value
enum	`ng`
required	`False`
required if	`library_final_yield` 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