{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4208ZWQY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4208ZWQY",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf3_10x4"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0470ONXA/",
"accession": "IGVFDS0470ONXA",
"aliases": [
"ansuman-satpathy:multiseq_igvf3_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"creation_timestamp": "2024-07-21T23:09:38.143283+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2837BRET/",
"accession": "IGVFDO2837BRET",
"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5646WKOF/",
"accession": "IGVFFI5646WKOF",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:23:56.155437+00:00",
"file_format": "fastq",
"file_size": 1571560747,
"href": "/sequence-files/IGVFFI5646WKOF/@@download/IGVFFI5646WKOF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/0883ba32-e6df-4210-9b6c-682ae68cd08f/IGVFFI5646WKOF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6092XCSI/",
"accession": "IGVFFI6092XCSI",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:25:37.100563+00:00",
"file_format": "fastq",
"file_size": 13177367185,
"href": "/sequence-files/IGVFFI6092XCSI/@@download/IGVFFI6092XCSI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/b5a57ccd-bb05-4629-9ddc-97ffe6ceaa33/IGVFFI6092XCSI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9282AVJU/",
"accession": "IGVFFI9282AVJU",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:24:23.732072+00:00",
"file_format": "fastq",
"file_size": 6028975386,
"href": "/sequence-files/IGVFFI9282AVJU/@@download/IGVFFI9282AVJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/f7585a1d-6c2f-4891-a90f-a1fed0ec1933/IGVFFI9282AVJU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8434CRCY/",
"accession": "IGVFFI8434CRCY",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:22:24.731651+00:00",
"file_format": "fastq",
"file_size": 12804648797,
"href": "/sequence-files/IGVFFI8434CRCY/@@download/IGVFFI8434CRCY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/e5915da2-cd2f-42c7-94ce-66a114c6482a/IGVFFI8434CRCY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9647YMUP/",
"accession": "IGVFFI9647YMUP",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:21:27.429307+00:00",
"file_format": "fastq",
"file_size": 5858500796,
"href": "/sequence-files/IGVFFI9647YMUP/@@download/IGVFFI9647YMUP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/a78a6452-c7d0-4b90-94de-027b9ea6ab0e/IGVFFI9647YMUP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1924ARLM/",
"accession": "IGVFFI1924ARLM",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:23:37.952948+00:00",
"file_format": "fastq",
"file_size": 1477314678,
"href": "/sequence-files/IGVFFI1924ARLM/@@download/IGVFFI1924ARLM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/63b39bfe-6477-4065-b9cd-13712c4f0837/IGVFFI1924ARLM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0495XBDK/",
"accession": "IGVFFI0495XBDK",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:26:48.323089+00:00",
"file_format": "fastq",
"file_size": 1562230811,
"href": "/sequence-files/IGVFFI0495XBDK/@@download/IGVFFI0495XBDK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/20e484bf-6e20-49c6-a3ac-55e2bb4c92e2/IGVFFI0495XBDK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1852LGQD/",
"accession": "IGVFFI1852LGQD",
"aliases": [
"ansuman-satpathy:igvf_exp3_rna_10x4_NGS2_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T23:27:03.705977+00:00",
"file_format": "fastq",
"file_size": 1649592704,
"href": "/sequence-files/IGVFFI1852LGQD/@@download/IGVFFI1852LGQD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/b8ea9460-266d-4f8a-84af-1a57e40c0afa/IGVFFI1852LGQD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF3_McGinnis/GEX/FASTQ/GEX_4_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4224CMWK/",
"accession": "IGVFFI4224CMWK",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp3_rna_10x4_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:37:22.395949+00:00",
"file_format": "yaml",
"file_size": 1395,
"href": "/configuration-files/IGVFFI4224CMWK/@@download/IGVFFI4224CMWK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/1266a6d3-247b-4cb4-9999-05ff7cc7e84b/IGVFFI4224CMWK.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_rna_10x4_NGS1_rna_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2054SXAE/",
"accession": "IGVFFI2054SXAE",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp3_rna_10x4_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:37:26.298301+00:00",
"file_format": "yaml",
"file_size": 1392,
"href": "/configuration-files/IGVFFI2054SXAE/@@download/IGVFFI2054SXAE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/ac4fe36b-56ae-4670-860f-e547ccd32e4a/IGVFFI2054SXAE.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp3_rna_10x4_NGS2_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9170BNTS/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with MULTI-seq",
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS8466CGYE/",
"accession": "IGVFDS8466CGYE",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:11:22.515068+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8265VEJP/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8265VEJP",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf3_10x4"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001187/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HepG2"
],
"status": "released",
"summary": "HepG2",
"term_name": "HepG2"
},
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
},
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: H9 differentiated cell specimen induced to cardiac muscle cell for 15 days, female, Homo sapiens; HepG2 cell line, male, Homo sapiens grown in DMEM without serum; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-21T23:21:27.429307+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "f2a3aa64-38dd-422a-8de2-a31627c46266"
}