{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7266YGXS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7266YGXS",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7266YGXS](/measurement-sets/IGVFDS7266YGXS/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS7266YGXS/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS7266YGXS](/measurement-sets/IGVFDS7266YGXS/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS7266YGXS/"
}
]
},
"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": [],
"controlled_access": true,
"creation_timestamp": "2025-03-05T19:51:00.326555+00:00",
"data_use_limitation_summaries": [
"GRU-PUB"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7212RCQM/",
"accession": "IGVFDO7212RCQM",
"aliases": [
"leif-ludwig:donor2308915002"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI9183QZJU/",
"accession": "IGVFFI9183QZJU",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_L007_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T16:10:49.945617+00:00",
"file_format": "yaml",
"file_size": 1492,
"href": "/configuration-files/IGVFFI9183QZJU/@@download/IGVFFI9183QZJU.yaml.gz",
"md5sum": "1e4c6dcd60c0a19cfc39f83062f840c8",
"s3_uri": "s3://igvf-files/2025/03/19/3b1f174b-ed15-4085-80b2-aeea2a44ca87/IGVFFI9183QZJU.yaml.gz",
"status": "preview",
"submitted_file_name": "/Users/fermel/work/IGVF/seqspecs_samples_6-15/measurement2308915002_scRNA_L007.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1290CMGG/",
"accession": "IGVFFI1290CMGG",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_L006_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T16:10:47.386169+00:00",
"file_format": "yaml",
"file_size": 1489,
"href": "/configuration-files/IGVFFI1290CMGG/@@download/IGVFFI1290CMGG.yaml.gz",
"md5sum": "5e59464cd56e2b9d6674b4401d100592",
"s3_uri": "s3://igvf-files/2025/03/19/b430a7ef-b036-4c9e-8538-07af0418e4eb/IGVFFI1290CMGG.yaml.gz",
"status": "preview",
"submitted_file_name": "/Users/fermel/work/IGVF/seqspecs_samples_6-15/measurement2308915002_scRNA_L006.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4224ZTTQ/",
"accession": "IGVFFI4224ZTTQ",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_L004_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T16:10:48.587434+00:00",
"file_format": "yaml",
"file_size": 1491,
"href": "/configuration-files/IGVFFI4224ZTTQ/@@download/IGVFFI4224ZTTQ.yaml.gz",
"md5sum": "eb8a6b1a3bcbc95e5a1c0476379a1c9a",
"s3_uri": "s3://igvf-files/2025/03/19/aa6a2c27-7def-4383-a1b0-54ba6c51f515/IGVFFI4224ZTTQ.yaml.gz",
"status": "preview",
"submitted_file_name": "/Users/fermel/work/IGVF/seqspecs_samples_6-15/measurement2308915002_scRNA_L004.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3563ZXOD/",
"accession": "IGVFFI3563ZXOD",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_L005_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-19T16:10:51.555367+00:00",
"file_format": "yaml",
"file_size": 1489,
"href": "/configuration-files/IGVFFI3563ZXOD/@@download/IGVFFI3563ZXOD.yaml.gz",
"md5sum": "a00d1d7bd1bea81be01914b21afe4488",
"s3_uri": "s3://igvf-files/2025/03/19/da0e500d-b4a6-4aea-9613-5024abb0f8e9/IGVFFI3563ZXOD.yaml.gz",
"status": "preview",
"submitted_file_name": "/Users/fermel/work/IGVF/seqspecs_samples_6-15/measurement2308915002_scRNA_L005.spec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4854HPIG/",
"accession": "IGVFFI4854HPIG",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R1_006"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:24:10.227753+00:00",
"file_format": "fastq",
"file_size": 1716130731,
"href": "/sequence-files/IGVFFI4854HPIG/@@download/IGVFFI4854HPIG.fastq.gz",
"md5sum": "27f50b0b9f3352d7d8443b85d93028f2",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/24867bef-79b3-4d32-8b86-c3de277cc38c/IGVFFI4854HPIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9080GRHE/",
"accession": "IGVFFI9080GRHE",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R1_004"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:24:50.522847+00:00",
"file_format": "fastq",
"file_size": 1678180159,
"href": "/sequence-files/IGVFFI9080GRHE/@@download/IGVFFI9080GRHE.fastq.gz",
"md5sum": "d613cba6f3e440a19a266394489e1ea0",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/a83b78eb-f392-4b05-945f-70b49cb01a73/IGVFFI9080GRHE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7040SJOH/",
"accession": "IGVFFI7040SJOH",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R1_007"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:25:26.769094+00:00",
"file_format": "fastq",
"file_size": 1699906363,
"href": "/sequence-files/IGVFFI7040SJOH/@@download/IGVFFI7040SJOH.fastq.gz",
"md5sum": "a50c9dd75a8c1b5b69571aa0d51bb62f",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/386a97c0-c922-43c0-ad6b-bc568559eca2/IGVFFI7040SJOH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3794VNHW/",
"accession": "IGVFFI3794VNHW",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R1_005"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:26:02.835240+00:00",
"file_format": "fastq",
"file_size": 1703339139,
"href": "/sequence-files/IGVFFI3794VNHW/@@download/IGVFFI3794VNHW.fastq.gz",
"md5sum": "ca48ee9d8069c8d2c2564c203d0bf0a2",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/70de5558-2822-4d6b-aa8b-7886942e08fd/IGVFFI3794VNHW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5653LXXY/",
"accession": "IGVFFI5653LXXY",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R2_007"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:26:42.940054+00:00",
"file_format": "fastq",
"file_size": 3454181764,
"href": "/sequence-files/IGVFFI5653LXXY/@@download/IGVFFI5653LXXY.fastq.gz",
"md5sum": "68dd85c9cc487e4dbf45a30469644131",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/26da2fa8-6d73-433b-bd01-0fb24ef0f6c4/IGVFFI5653LXXY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7702OGRU/",
"accession": "IGVFFI7702OGRU",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R2_005"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:27:45.347840+00:00",
"file_format": "fastq",
"file_size": 3473378020,
"href": "/sequence-files/IGVFFI7702OGRU/@@download/IGVFFI7702OGRU.fastq.gz",
"md5sum": "bd849b0e444cbe1b213c5dc4a625104b",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/3bb3400e-049e-4360-b1fe-0c689439ae87/IGVFFI7702OGRU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4232EFWJ/",
"accession": "IGVFFI4232EFWJ",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R2_004"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:29:20.909062+00:00",
"file_format": "fastq",
"file_size": 3427967039,
"href": "/sequence-files/IGVFFI4232EFWJ/@@download/IGVFFI4232EFWJ.fastq.gz",
"md5sum": "f2df2179750d6020c569ffc6ba2dfe8b",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/e6cae143-5ab3-44b3-8a2c-639dbad466bb/IGVFFI4232EFWJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5771OWPC/",
"accession": "IGVFFI5771OWPC",
"aliases": [
"leif-ludwig:measurement2308915002_scRNA_R2_006"
],
"content_type": "reads",
"controlled_access": true,
"creation_timestamp": "2025-03-07T15:30:25.997505+00:00",
"file_format": "fastq",
"file_size": 3498369213,
"href": "/sequence-files/IGVFFI5771OWPC/@@download/IGVFFI5771OWPC.fastq.gz",
"md5sum": "92070f9302291c9fdbba5340f0b90fcc",
"s3_uri": "s3://igvf-restricted-files/2025/03/07/97b342c3-1a47-4c72-be8d-5520d0f56af4/IGVFFI5771OWPC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/data/cephfs-1/work/groups/ludwig/A5024_20250213/250204_LH00253_0201_A22V5T7LT3_A5024_FASTQ/hPBMC_2308915002_Multiome_GEX_905_S11_L006_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/leif-ludwig/",
"title": "Leif Ludwig, MDC"
},
"multiome_size": 2,
"notes": "This measurement set previously used scMito-seq as a preferred_assay_title, but this enum is now replaced with 10x multiome with scMito-seq.",
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome with scMito-seq",
"protocols": [
"https://www.protocols.io/view/mtscmultiome-atac-gex-protocol-d554888w"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS6604PKVN/",
"accession": "IGVFDS6604PKVN",
"status": "preview"
}
],
"samples": [
{
"@id": "/primary-cells/IGVFSM0159TYAA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0159TYAA",
"aliases": [
"leif-ludwig:sample2308915002"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/426307fa-9064-4824-a88a-2e033218fc6c/",
"certificate_identifier": "IP115-11",
"controlled_access": true,
"data_use_limitation": "GRU",
"data_use_limitation_modifiers": [
"PUB"
],
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_2000001/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "peripheral blood mononuclear cell",
"term_name": "peripheral blood mononuclear cell"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 23 years) peripheral blood mononuclear cell",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/8164e524-79d5-4407-8a75-c0ea353d28ea/",
"title": "Ludwig Lab"
},
"submitted_files_timestamp": "2025-03-07T15:24:10.227753+00:00",
"summary": "10x multiome with scMito-seq",
"uuid": "8955e2f1-f6f0-4f4d-b78f-60aa55458c1d"
}