{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9572XHUR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9572XHUR",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW262"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0347EJHA](/auxiliary-sets/IGVFDS0347EJHA/) has sequence file(s) [IGVFFI8305CWBO](/sequence-files/IGVFFI8305CWBO/), [IGVFFI7869XBZC](/sequence-files/IGVFFI7869XBZC/), [IGVFFI8441KFWQ](/sequence-files/IGVFFI8441KFWQ/), [IGVFFI8745GJAF](/sequence-files/IGVFFI8745GJAF/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0347EJHA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0347EJHA](/auxiliary-sets/IGVFDS0347EJHA/) has sequence file(s): [IGVFFI8305CWBO](/sequence-files/IGVFFI8305CWBO/), [IGVFFI7869XBZC](/sequence-files/IGVFFI7869XBZC/), [IGVFFI8441KFWQ](/sequence-files/IGVFFI8441KFWQ/), [IGVFFI8745GJAF](/sequence-files/IGVFFI8745GJAF/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0347EJHA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has sequence file(s) [IGVFFI8976QYEF](/sequence-files/IGVFFI8976QYEF/), [IGVFFI3235DXAM](/sequence-files/IGVFFI3235DXAM/), [IGVFFI4121BOED](/sequence-files/IGVFFI4121BOED/), [IGVFFI5785IYYQ](/sequence-files/IGVFFI5785IYYQ/), [IGVFFI7098IHKC](/sequence-files/IGVFFI7098IHKC/), [IGVFFI5235FUDZ](/sequence-files/IGVFFI5235FUDZ/), [IGVFFI1183HLRI](/sequence-files/IGVFFI1183HLRI/), [IGVFFI4170MZRR](/sequence-files/IGVFFI4170MZRR/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has sequence file(s): [IGVFFI8976QYEF](/sequence-files/IGVFFI8976QYEF/), [IGVFFI3235DXAM](/sequence-files/IGVFFI3235DXAM/), [IGVFFI4121BOED](/sequence-files/IGVFFI4121BOED/), [IGVFFI5785IYYQ](/sequence-files/IGVFFI5785IYYQ/), [IGVFFI7098IHKC](/sequence-files/IGVFFI7098IHKC/), [IGVFFI5235FUDZ](/sequence-files/IGVFFI5235FUDZ/), [IGVFFI1183HLRI](/sequence-files/IGVFFI1183HLRI/), [IGVFFI4170MZRR](/sequence-files/IGVFFI4170MZRR/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has a sequence file [IGVFFI4121BOED](/sequence-files/IGVFFI4121BOED/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has a sequence file [IGVFFI5785IYYQ](/sequence-files/IGVFFI5785IYYQ/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has a sequence file [IGVFFI1183HLRI](/sequence-files/IGVFFI1183HLRI/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has a sequence file [IGVFFI4170MZRR](/sequence-files/IGVFFI4170MZRR/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) 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/IGVFDS9572XHUR/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS9572XHUR](/measurement-sets/IGVFDS9572XHUR/) has an `assay_term` of in vitro CRISPR screen using single-cell RNA-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS9572XHUR/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6297HIRK](/auxiliary-sets/IGVFDS6297HIRK/) has sequence file(s) [IGVFFI9439HYMB](/sequence-files/IGVFFI9439HYMB/), [IGVFFI0670UYEB](/sequence-files/IGVFFI0670UYEB/), [IGVFFI7106GVUQ](/sequence-files/IGVFFI7106GVUQ/), [IGVFFI4559INCO](/sequence-files/IGVFFI4559INCO/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS6297HIRK/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6297HIRK](/auxiliary-sets/IGVFDS6297HIRK/) has sequence file(s): [IGVFFI9439HYMB](/sequence-files/IGVFFI9439HYMB/), [IGVFFI0670UYEB](/sequence-files/IGVFFI0670UYEB/), [IGVFFI7106GVUQ](/sequence-files/IGVFFI7106GVUQ/), [IGVFFI4559INCO](/sequence-files/IGVFFI4559INCO/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS6297HIRK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6297HIRK/",
"accession": "IGVFDS6297HIRK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW262"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0347EJHA/",
"accession": "IGVFDS0347EJHA",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW262"
],
"file_set_type": "gRNA 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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4543YHDW/",
"accession": "IGVFFI4543YHDW",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-02-15T23:43:21.753377+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/IGVFFI8976QYEF/",
"accession": "IGVFFI8976QYEF",
"aliases": [
"gary-hon:LW262_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:50:36.959647+00:00",
"file_format": "fastq",
"file_size": 462730226,
"href": "/sequence-files/IGVFFI8976QYEF/@@download/IGVFFI8976QYEF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c82da3e7-50d7-4fb3-b453-159dfaa49af6/IGVFFI8976QYEF.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3235DXAM/",
"accession": "IGVFFI3235DXAM",
"aliases": [
"gary-hon:LW262_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:50:45.121143+00:00",
"file_format": "fastq",
"file_size": 542790287,
"href": "/sequence-files/IGVFFI3235DXAM/@@download/IGVFFI3235DXAM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/95294977-5de9-4fbb-a1cc-3eee79d90d2d/IGVFFI3235DXAM.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4121BOED/",
"accession": "IGVFFI4121BOED",
"aliases": [
"gary-hon:LW262_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:50:53.800640+00:00",
"file_format": "fastq",
"file_size": 1620354709,
"href": "/sequence-files/IGVFFI4121BOED/@@download/IGVFFI4121BOED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e54b63a4-161d-4910-b0c1-5534d03ec145/IGVFFI4121BOED.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5785IYYQ/",
"accession": "IGVFFI5785IYYQ",
"aliases": [
"gary-hon:LW262_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:51:11.729711+00:00",
"file_format": "fastq",
"file_size": 4000651065,
"href": "/sequence-files/IGVFFI5785IYYQ/@@download/IGVFFI5785IYYQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/3efe103f-0bc2-431f-b8b4-1a9d47945c5e/IGVFFI5785IYYQ.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7098IHKC/",
"accession": "IGVFFI7098IHKC",
"aliases": [
"gary-hon:LW262_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:51:50.061260+00:00",
"file_format": "fastq",
"file_size": 427472438,
"href": "/sequence-files/IGVFFI7098IHKC/@@download/IGVFFI7098IHKC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/31da9f8f-a5f0-48e4-84e3-9b4cd9e7cd50/IGVFFI7098IHKC.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5235FUDZ/",
"accession": "IGVFFI5235FUDZ",
"aliases": [
"gary-hon:LW262_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:51:58.114289+00:00",
"file_format": "fastq",
"file_size": 493688590,
"href": "/sequence-files/IGVFFI5235FUDZ/@@download/IGVFFI5235FUDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c68f4668-cf0c-41db-bc43-38df3c59c9f2/IGVFFI5235FUDZ.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1183HLRI/",
"accession": "IGVFFI1183HLRI",
"aliases": [
"gary-hon:LW262_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:52:06.513093+00:00",
"file_format": "fastq",
"file_size": 1487561417,
"href": "/sequence-files/IGVFFI1183HLRI/@@download/IGVFFI1183HLRI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/f7cd578c-ba1f-4592-8dc0-5700c7d4307f/IGVFFI1183HLRI.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4170MZRR/",
"accession": "IGVFFI4170MZRR",
"aliases": [
"gary-hon:LW262_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:52:23.595115+00:00",
"file_format": "fastq",
"file_size": 3748111521,
"href": "/sequence-files/IGVFFI4170MZRR/@@download/IGVFFI4170MZRR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/1a23355d-149b-4b7a-9b02-8e6b8fd961c1/IGVFFI4170MZRR.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW262_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4003HZAB/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0248SELV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0248SELV",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW262"
],
"cellular_sub_pool": "subpool_LW262",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW262) modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-20T17:50:36.959647+00:00",
"submitter_comment": "Transcriptiome for LW262'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "71a0ce20-b336-46e8-9615-dd72d36c57fd"
}