SnareSeq2

NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. HuBMAP is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.

Version 1 (no longer accepting data)

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘1’]	True
description	Textfield	Free-text description of this assay.		True
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	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.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	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.	[‘sequence’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘Slide-seq’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘RNA’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.	[‘Yes’, ‘No’]	True
acquisition_instrument_vendor	Textfield	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.		True
acquisition_instrument_model	Textfield	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.		True
rnaseq_assay_method	Textfield	The kit used for the RNA sequencing assay		True
library_construction_protocols_io_doi	Textfield	A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.		True
library_layout	Allowable Value	State whether the library was generated for single-end or paired end sequencing.	[‘single-end’, ‘paired-end’]	True
library_adapter_sequence	Textfield	Adapter sequence to be used for adapter trimming		True
puck_id	Textfield	Slide-seq captures RNA sequence data on spatially barcoded arrays of beads. Beads are fixed to a slide in a region shaped like a round puck. Each puck has a unique puck_id.		True
is_technical_replicate	Allowable Value	Is the sequencing reaction run in repliucate, TRUE or FALSE	[‘Yes’, ‘No’]	True
bead_barcode_read	Textfield	Which read file contains the bead barcode		True
bead_barcode_offset	Textfield	Position(s) in the read at which the bead barcode starts		True
bead_barcode_size	Textfield	Length of the bead barcode in base pairs		True
library_pcr_cycles	Numeric	Number of PCR cycles to amplify cDNA		True
library_pcr_cycles_for_sample_index	Numeric	Number of PCR cycles performed for library indexing		True
library_final_yield_value	Numeric	Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)		True
library_final_yield_unit	Allowable Value	Units of final library yield	[‘ng’]	False
library_average_fragment_size	Numeric	Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.		True
sequencing_reagent_kit	Textfield	Reagent kit used for sequencing		True
sequencing_read_format	Textfield	Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.		True
sequencing_read_percent_q30	Numeric	Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)		True
sequencing_phix_percent	Numeric	Percent PhiX loaded to the run		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.		True

Version 0

Attribute	Type	Description	Allowable Values	Required
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	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.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	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.	[‘sequence’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘Slide-seq’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘RNA’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.	[‘Yes’, ‘No’]	True
acquisition_instrument_vendor	Textfield	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.		True
acquisition_instrument_model	Textfield	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.		True
rnaseq_assay_method	Textfield	The kit used for the RNA sequencing assay		True
library_construction_protocols_io_doi	Textfield	A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”.		True
library_layout	Allowable Value	State whether the library was generated for single-end or paired end sequencing.	[‘single-end’, ‘paired-end’]	True
library_adapter_sequence	Textfield	Adapter sequence to be used for adapter trimming		True
puck_id	Textfield	Slide-seq captures RNA sequence data on spatially barcoded arrays of beads. Beads are fixed to a slide in a region shaped like a round puck. Each puck has a unique puck_id.		True
is_technical_replicate	Allowable Value	Is the sequencing reaction run in repliucate, TRUE or FALSE	[‘Yes’, ‘No’]	True
bead_barcode_read	Textfield	Which read file contains the bead barcode		True
bead_barcode_offset	Textfield	Position(s) in the read at which the bead barcode starts		True
bead_barcode_size	Textfield	Length of the bead barcode in base pairs		True
library_pcr_cycles	Numeric	Number of PCR cycles to amplify cDNA		True
library_pcr_cycles_for_sample_index	Numeric	Number of PCR cycles performed for library indexing		True
library_final_yield_value	Numeric	Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul)		True
library_final_yield_unit	Allowable Value	Units of final library yield	[‘ng’]	False
library_average_fragment_size	Numeric	Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation.		True
sequencing_reagent_kit	Textfield	Reagent kit used for sequencing		True
sequencing_read_format	Textfield	Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2.		True
sequencing_read_percent_q30	Numeric	Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …)		True
sequencing_phix_percent	Numeric	Percent PhiX loaded to the run		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.		True