{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2143BSOH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2143BSOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW281"
],
"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": "Measurement set [IGVFDS2143BSOH](/measurement-sets/IGVFDS2143BSOH/) has sequence file(s) [IGVFFI6060RUDC](/sequence-files/IGVFFI6060RUDC/), [IGVFFI1727DJMY](/sequence-files/IGVFFI1727DJMY/), [IGVFFI5007DWHI](/sequence-files/IGVFFI5007DWHI/), [IGVFFI9041LHWG](/sequence-files/IGVFFI9041LHWG/), [IGVFFI7614TPCO](/sequence-files/IGVFFI7614TPCO/), [IGVFFI6389SAKA](/sequence-files/IGVFFI6389SAKA/), [IGVFFI6933IHKQ](/sequence-files/IGVFFI6933IHKQ/), [IGVFFI0239MXTR](/sequence-files/IGVFFI0239MXTR/) 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/IGVFDS2143BSOH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2143BSOH](/measurement-sets/IGVFDS2143BSOH/) has sequence file(s): [IGVFFI6060RUDC](/sequence-files/IGVFFI6060RUDC/), [IGVFFI1727DJMY](/sequence-files/IGVFFI1727DJMY/), [IGVFFI5007DWHI](/sequence-files/IGVFFI5007DWHI/), [IGVFFI9041LHWG](/sequence-files/IGVFFI9041LHWG/), [IGVFFI7614TPCO](/sequence-files/IGVFFI7614TPCO/), [IGVFFI6389SAKA](/sequence-files/IGVFFI6389SAKA/), [IGVFFI6933IHKQ](/sequence-files/IGVFFI6933IHKQ/), [IGVFFI0239MXTR](/sequence-files/IGVFFI0239MXTR/) 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/IGVFDS2143BSOH/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s) [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s): [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s) [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s): [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2612LSTD/",
"accession": "IGVFDS2612LSTD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW281"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2549GCKW/",
"accession": "IGVFDS2549GCKW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW281"
],
"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": "2024-02-29T16:52:20.759243+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/IGVFFI6060RUDC/",
"accession": "IGVFFI6060RUDC",
"aliases": [
"gary-hon:LW281_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:22.632924+00:00",
"file_format": "fastq",
"file_size": 74905345,
"href": "/sequence-files/IGVFFI6060RUDC/@@download/IGVFFI6060RUDC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c5a5525c-9429-400c-a291-878e4f2c3532/IGVFFI6060RUDC.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/LW281_S19_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1727DJMY/",
"accession": "IGVFFI1727DJMY",
"aliases": [
"gary-hon:LW281_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:37.152073+00:00",
"file_format": "fastq",
"file_size": 503283129,
"href": "/sequence-files/IGVFFI1727DJMY/@@download/IGVFFI1727DJMY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d7d49603-4bce-4435-aed2-1b4e35a72fbb/IGVFFI1727DJMY.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/LW281_S19_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5007DWHI/",
"accession": "IGVFFI5007DWHI",
"aliases": [
"gary-hon:LW281_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:31.648172+00:00",
"file_format": "fastq",
"file_size": 215223274,
"href": "/sequence-files/IGVFFI5007DWHI/@@download/IGVFFI5007DWHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/55604513-018d-4ee8-8166-2b32280bbfb2/IGVFFI5007DWHI.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/LW281_S19_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9041LHWG/",
"accession": "IGVFFI9041LHWG",
"aliases": [
"gary-hon:LW281_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:14.530624+00:00",
"file_format": "fastq",
"file_size": 510779956,
"href": "/sequence-files/IGVFFI9041LHWG/@@download/IGVFFI9041LHWG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/316674a6-bc11-49c3-ba51-12ce884e0be7/IGVFFI9041LHWG.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/LW281_S19_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7614TPCO/",
"accession": "IGVFFI7614TPCO",
"aliases": [
"gary-hon:LW281_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:04.418758+00:00",
"file_format": "fastq",
"file_size": 79079512,
"href": "/sequence-files/IGVFFI7614TPCO/@@download/IGVFFI7614TPCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/57be1d3d-8040-43f0-b199-1545de15f951/IGVFFI7614TPCO.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/LW281_S19_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6389SAKA/",
"accession": "IGVFFI6389SAKA",
"aliases": [
"gary-hon:LW281_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:27.113168+00:00",
"file_format": "fastq",
"file_size": 76312078,
"href": "/sequence-files/IGVFFI6389SAKA/@@download/IGVFFI6389SAKA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d86601a8-9ffb-4d82-824b-dcca37bf56f1/IGVFFI6389SAKA.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/LW281_S19_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6933IHKQ/",
"accession": "IGVFFI6933IHKQ",
"aliases": [
"gary-hon:LW281_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:59.853043+00:00",
"file_format": "fastq",
"file_size": 75201613,
"href": "/sequence-files/IGVFFI6933IHKQ/@@download/IGVFFI6933IHKQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/edab6ebd-487a-46d3-8260-71c30073ba3d/IGVFFI6933IHKQ.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/LW281_S19_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0239MXTR/",
"accession": "IGVFFI0239MXTR",
"aliases": [
"gary-hon:LW281_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:18:08.868753+00:00",
"file_format": "fastq",
"file_size": 217365666,
"href": "/sequence-files/IGVFFI0239MXTR/@@download/IGVFFI0239MXTR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d757be89-013a-436e-b9bd-733045ec5db1/IGVFFI0239MXTR.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/LW281_S19_L001_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1588TVKF/"
],
"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/IGVFSM0956HKRJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0956HKRJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2302LCEO/",
"accession": "IGVFDS2302LCEO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"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": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW281), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-01T17:16:17.730047+00:00",
"submitter_comment": "Transcriptiome for LW281",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "77c7030f-51f9-42c0-8c20-5c13dc904794"
}