Sequence Assays

bulkATACseq

Related files:

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

This schema is for Assay for Transposase-Accessible Chromatin by sequencing (ATACseq)of bulk sample.

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

bulk_transposition_input_number_nuclei
bulk_atac_cell_isolation_protocols_io_doi
is_technical_replicate
library_adapter_sequence
library_average_fragment_size
library_concentration_value
library_concentration_unit
library_construction_protocols_io_doi
library_creation_date
library_final_yield_value
library_final_yield_unit
library_id
library_layout
library_pcr_cycles
library_preparation_kit
sample_quality_metric
sequencing_phix_percent
sequencing_read_format
sequencing_read_percent_q30
sequencing_reagent_kit
transposition_kit_number
transposition_method
transposition_transposase_source
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	`bulkATACseq`
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

`bulk_transposition_input_number_nuclei`

A number (no comma separators)

constraint	value
required	`True`

`bulk_atac_cell_isolation_protocols_io_doi`

Link to a protocols document answering the question: How was tissue stored and processed for cell/nuclei isolation.

constraint	value
required	`True`
pattern (regular expression)	`10\.17504/.*`
url	prefix: `https://dx.doi.org/`

`is_technical_replicate`

Is this a sequencing replicate?

constraint	value
type	`boolean`
required	`True`

`library_adapter_sequence`

Adapter sequence to be used for adapter trimming.

constraint	value
required	`True`

`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`

`library_concentration_value`

The concentration value of the pooled library samples submitted for sequencing.

constraint	value
type	`number`
required	`True`

`library_concentration_unit`

Unit of library_concentration_value. Leave blank if not applicable.

constraint	value
enum	`nM`
required	`False`
required if	`library_concentration_value` present

`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_creation_date`

date and time of library creation. YYYY-MM-DD, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s. Leave blank if not applicable.

constraint	value
type	`datetime`
format	`%Y-%m-%d`
required	`False`

`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_id`

A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked.

constraint	value
required	`True`

`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_pcr_cycles`

Number of PCR cycles performed in order to add adapters and amplify the library. Usually, this includes 5 pre-amplificationn cycles followed by 0-5 additional cycles determined by qPCR.

constraint	value
type	`integer`
required	`True`

`library_preparation_kit`

Reagent kit used for library preparation.

constraint	value
required	`True`

`sample_quality_metric`

This is a quality metric by visual inspection. This should answer the question: Are the nuclei intact and are the nuclei free of significant amounts of debris? This can be captured at a high level, “OK” or “not OK”.

constraint	value
required	`True`

`sequencing_phix_percent`

Percent PhiX loaded to the run.

constraint	value
type	`number`
required	`True`
minimum	`0`
maximum	`100`

`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_reagent_kit`

Reagent kit used for sequencing.

constraint	value
required	`True`

`transposition_kit_number`

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

constraint	value
required	`False`

`transposition_method`

Modality of capturing accessible chromatin molecules. The kit used, for example.

constraint	value
required	`True`

`transposition_transposase_source`

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

constraint	value
required	`True`

`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