{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI4818IAJW/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI4818IAJW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_local"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) has `upload_status` invalidated. Validation error detail: {\"md5sum\": \"original md5sum b3204244c4d15daf18f7ab6134f3e35c does not match newly calculated md5sum 978542c9bae8ae009257e9e42aea5576.\"}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI4818IAJW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI4818IAJW](/tabular-files/IGVFFI4818IAJW/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI4818IAJW/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"barcode_map_for": [],
"content_md5sum": "6ca410be7be8a3da6d39934cf9704a60",
"content_type": "unfiltered local differential expression",
"controlled_access": false,
"creation_timestamp": "2024-12-18T19:30:50.456623+00:00",
"file_format": "csv",
"file_set": {
"@id": "/analysis-sets/IGVFDS4389OUWU/",
"accession": "IGVFDS4389OUWU",
"file_set_type": "principal analysis",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7513BJDT/",
"accession": "IGVFSM7513BJDT",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW277), male, Homo sapiens 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"
},
{
"@id": "/in-vitro-systems/IGVFSM0559UNMK/",
"accession": "IGVFSM0559UNMK",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, Homo sapiens 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"
},
{
"@id": "/in-vitro-systems/IGVFSM0604KDJF/",
"accession": "IGVFSM0604KDJF",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW280), male, Homo sapiens 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"
},
{
"@id": "/in-vitro-systems/IGVFSM7499ZWUW/",
"accession": "IGVFSM7499ZWUW",
"classifications": [
"differentiated cell specimen"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW278), male, Homo sapiens 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"
}
],
"status": "preview",
"summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
},
"file_size": 6798,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI4818IAJW/@@download/IGVFFI4818IAJW.csv.gz",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"loci_list_for": [],
"md5sum": "b3204244c4d15daf18f7ab6134f3e35c",
"s3_uri": "s3://igvf-files/2024/12/18/4a810dea-e270-4cff-a8c7-b295f23be862/IGVFFI4818IAJW.csv.gz",
"schema_version": "13",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_file_name": "/project/GCRB/Hon_lab/s215194/IGVF/data_submission/reference_files/TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis_DE_local.csv.gz",
"summary": "unfiltered local differential expression",
"upload_status": "invalidated",
"uuid": "4a810dea-e270-4cff-a8c7-b295f23be862",
"validation_error_detail": "{\"md5sum\": \"original md5sum b3204244c4d15daf18f7ab6134f3e35c does not match newly calculated md5sum 978542c9bae8ae009257e9e42aea5576.\"}"
}