{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4852MAUM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4852MAUM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW280"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5228AHGR](/auxiliary-sets/IGVFDS5228AHGR/) has sequence file(s) [IGVFFI3880AUGY](/sequence-files/IGVFFI3880AUGY/), [IGVFFI3453EWPB](/sequence-files/IGVFFI3453EWPB/), [IGVFFI0680SUCW](/sequence-files/IGVFFI0680SUCW/), [IGVFFI1694KFBX](/sequence-files/IGVFFI1694KFBX/), [IGVFFI3489PXOT](/sequence-files/IGVFFI3489PXOT/), [IGVFFI5218TWQD](/sequence-files/IGVFFI5218TWQD/), [IGVFFI2754LNUW](/sequence-files/IGVFFI2754LNUW/), [IGVFFI3423UPCF](/sequence-files/IGVFFI3423UPCF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5228AHGR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5228AHGR](/auxiliary-sets/IGVFDS5228AHGR/) has sequence file(s): [IGVFFI3880AUGY](/sequence-files/IGVFFI3880AUGY/), [IGVFFI3453EWPB](/sequence-files/IGVFFI3453EWPB/), [IGVFFI0680SUCW](/sequence-files/IGVFFI0680SUCW/), [IGVFFI1694KFBX](/sequence-files/IGVFFI1694KFBX/), [IGVFFI3489PXOT](/sequence-files/IGVFFI3489PXOT/), [IGVFFI5218TWQD](/sequence-files/IGVFFI5218TWQD/), [IGVFFI2754LNUW](/sequence-files/IGVFFI2754LNUW/), [IGVFFI3423UPCF](/sequence-files/IGVFFI3423UPCF/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5228AHGR/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6861GRJI](/auxiliary-sets/IGVFDS6861GRJI/) has sequence file(s) [IGVFFI7902JDLP](/sequence-files/IGVFFI7902JDLP/), [IGVFFI5920ILPO](/sequence-files/IGVFFI5920ILPO/), [IGVFFI0148GGAF](/sequence-files/IGVFFI0148GGAF/), [IGVFFI9772UXBJ](/sequence-files/IGVFFI9772UXBJ/), [IGVFFI5059JEYE](/sequence-files/IGVFFI5059JEYE/), [IGVFFI4378HMYC](/sequence-files/IGVFFI4378HMYC/), [IGVFFI7335PJUM](/sequence-files/IGVFFI7335PJUM/), [IGVFFI2706WHPV](/sequence-files/IGVFFI2706WHPV/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS6861GRJI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6861GRJI](/auxiliary-sets/IGVFDS6861GRJI/) has sequence file(s): [IGVFFI7902JDLP](/sequence-files/IGVFFI7902JDLP/), [IGVFFI5920ILPO](/sequence-files/IGVFFI5920ILPO/), [IGVFFI0148GGAF](/sequence-files/IGVFFI0148GGAF/), [IGVFFI9772UXBJ](/sequence-files/IGVFFI9772UXBJ/), [IGVFFI5059JEYE](/sequence-files/IGVFFI5059JEYE/), [IGVFFI4378HMYC](/sequence-files/IGVFFI4378HMYC/), [IGVFFI7335PJUM](/sequence-files/IGVFFI7335PJUM/), [IGVFFI2706WHPV](/sequence-files/IGVFFI2706WHPV/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS6861GRJI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4852MAUM](/measurement-sets/IGVFDS4852MAUM/) has sequence file(s) [IGVFFI2029JXNO](/sequence-files/IGVFFI2029JXNO/), [IGVFFI5968EMNM](/sequence-files/IGVFFI5968EMNM/), [IGVFFI5279XVPR](/sequence-files/IGVFFI5279XVPR/), [IGVFFI0247GQRZ](/sequence-files/IGVFFI0247GQRZ/), [IGVFFI2258YBMU](/sequence-files/IGVFFI2258YBMU/), [IGVFFI7405MHEB](/sequence-files/IGVFFI7405MHEB/), [IGVFFI5720TGFT](/sequence-files/IGVFFI5720TGFT/), [IGVFFI0310AMSG](/sequence-files/IGVFFI0310AMSG/), [IGVFFI8440RLPZ](/sequence-files/IGVFFI8440RLPZ/), [IGVFFI1271VSVP](/sequence-files/IGVFFI1271VSVP/), [IGVFFI7057FLEI](/sequence-files/IGVFFI7057FLEI/), [IGVFFI0651DPFO](/sequence-files/IGVFFI0651DPFO/), [IGVFFI7829KDAL](/sequence-files/IGVFFI7829KDAL/), [IGVFFI0744RUTL](/sequence-files/IGVFFI0744RUTL/), [IGVFFI3192CBTL](/sequence-files/IGVFFI3192CBTL/), [IGVFFI2497DBTZ](/sequence-files/IGVFFI2497DBTZ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS4852MAUM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4852MAUM](/measurement-sets/IGVFDS4852MAUM/) has sequence file(s): [IGVFFI2029JXNO](/sequence-files/IGVFFI2029JXNO/), [IGVFFI5968EMNM](/sequence-files/IGVFFI5968EMNM/), [IGVFFI5279XVPR](/sequence-files/IGVFFI5279XVPR/), [IGVFFI0247GQRZ](/sequence-files/IGVFFI0247GQRZ/), [IGVFFI2258YBMU](/sequence-files/IGVFFI2258YBMU/), [IGVFFI7405MHEB](/sequence-files/IGVFFI7405MHEB/), [IGVFFI5720TGFT](/sequence-files/IGVFFI5720TGFT/), [IGVFFI0310AMSG](/sequence-files/IGVFFI0310AMSG/), [IGVFFI8440RLPZ](/sequence-files/IGVFFI8440RLPZ/), [IGVFFI1271VSVP](/sequence-files/IGVFFI1271VSVP/), [IGVFFI7057FLEI](/sequence-files/IGVFFI7057FLEI/), [IGVFFI0651DPFO](/sequence-files/IGVFFI0651DPFO/), [IGVFFI7829KDAL](/sequence-files/IGVFFI7829KDAL/), [IGVFFI0744RUTL](/sequence-files/IGVFFI0744RUTL/), [IGVFFI3192CBTL](/sequence-files/IGVFFI3192CBTL/), [IGVFFI2497DBTZ](/sequence-files/IGVFFI2497DBTZ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4852MAUM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6861GRJI/",
"accession": "IGVFDS6861GRJI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW280"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5228AHGR/",
"accession": "IGVFDS5228AHGR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW280"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-02-21T21:07:20.687558+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2029JXNO/",
"accession": "IGVFFI2029JXNO",
"aliases": [
"gary-hon:LW280_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:36.295318+00:00",
"file_format": "fastq",
"file_size": 80411976,
"href": "/sequence-files/IGVFFI2029JXNO/@@download/IGVFFI2029JXNO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0374b758-d7e2-4328-927d-a2f3249375c7/IGVFFI2029JXNO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW280_S18_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5968EMNM/",
"accession": "IGVFFI5968EMNM",
"aliases": [
"gary-hon:LW280_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:40.808617+00:00",
"file_format": "fastq",
"file_size": 215956934,
"href": "/sequence-files/IGVFFI5968EMNM/@@download/IGVFFI5968EMNM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ffbbf697-3201-44af-b2d4-8c7a7c270d30/IGVFFI5968EMNM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5279XVPR/",
"accession": "IGVFFI5279XVPR",
"aliases": [
"gary-hon:LW280_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:09.462622+00:00",
"file_format": "fastq",
"file_size": 507523618,
"href": "/sequence-files/IGVFFI5279XVPR/@@download/IGVFFI5279XVPR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/323068f9-7d50-4677-b504-32c2981d4868/IGVFFI5279XVPR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW280_S18_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0247GQRZ/",
"accession": "IGVFFI0247GQRZ",
"aliases": [
"gary-hon:LW280_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:31.856599+00:00",
"file_format": "fastq",
"file_size": 79028496,
"href": "/sequence-files/IGVFFI0247GQRZ/@@download/IGVFFI0247GQRZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6bfcfcf5-23f4-4b1a-a3a3-ab13ce531112/IGVFFI0247GQRZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW280_S18_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2258YBMU/",
"accession": "IGVFFI2258YBMU",
"aliases": [
"gary-hon:LW280_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:46.549984+00:00",
"file_format": "fastq",
"file_size": 505690860,
"href": "/sequence-files/IGVFFI2258YBMU/@@download/IGVFFI2258YBMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/32a9d93f-3b4d-4ddf-8679-43b79cfa0fa9/IGVFFI2258YBMU.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW280_S18_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7405MHEB/",
"accession": "IGVFFI7405MHEB",
"aliases": [
"gary-hon:LW280_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:54.736337+00:00",
"file_format": "fastq",
"file_size": 79552630,
"href": "/sequence-files/IGVFFI7405MHEB/@@download/IGVFFI7405MHEB.fastq.gz",
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"status": "released",
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},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW280_S18_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5720TGFT/",
"accession": "IGVFFI5720TGFT",
"aliases": [
"gary-hon:LW280_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:59.211450+00:00",
"file_format": "fastq",
"file_size": 81939339,
"href": "/sequence-files/IGVFFI5720TGFT/@@download/IGVFFI5720TGFT.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0310AMSG/",
"accession": "IGVFFI0310AMSG",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:03.763399+00:00",
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"href": "/sequence-files/IGVFFI0310AMSG/@@download/IGVFFI0310AMSG.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8440RLPZ/",
"accession": "IGVFFI8440RLPZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:54:42.619937+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1271VSVP/",
"accession": "IGVFFI1271VSVP",
"aliases": [
"gary-hon:LW280_2_I1_2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:57:04.950406+00:00",
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"href": "/sequence-files/IGVFFI1271VSVP/@@download/IGVFFI1271VSVP.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7057FLEI/",
"accession": "IGVFFI7057FLEI",
"aliases": [
"gary-hon:LW280_2_I2_2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:57:16.809970+00:00",
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"term_name": "Illumina NextSeq 2000"
},
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"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-02-McDermott-NextSeq.10X/2023-10-02/outs/fastq_path/AAC5W2WHV/LW280_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0651DPFO/",
"accession": "IGVFFI0651DPFO",
"aliases": [
"gary-hon:LW280_1_I2_2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:54:54.309396+00:00",
"file_format": "fastq",
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},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-02-McDermott-NextSeq.10X/2023-10-02/outs/fastq_path/AAC5W2WHV/LW280_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7829KDAL/",
"accession": "IGVFFI7829KDAL",
"aliases": [
"gary-hon:LW280_1_R2_2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:55:54.773048+00:00",
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