{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI2200CONX/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI2200CONX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinD-PCRrep2_I2"
],
"assay_titles": [
"Variant FlowFISH"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released sequence file [IGVFFI2200CONX](/sequence-files/IGVFFI2200CONX/) has in progress subobject auxiliary set [IGVFDS0253FYBC](/auxiliary-sets/IGVFDS0253FYBC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/sequence-files/IGVFFI2200CONX/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"content_md5sum": "5f2673ae6f9a1e76bb90860c793eb410",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:31:36.353598+00:00",
"file_format": "fastq",
"file_set": {
"@id": "/auxiliary-sets/IGVFDS0253FYBC/",
"accession": "IGVFDS0253FYBC",
"file_set_type": "variant sequencing",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4221WRQS/",
"accession": "IGVFSM4221WRQS",
"classifications": [
"cell line"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"term_name": "Jurkat"
}
],
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with a guide library",
"taxa": "Homo sapiens"
}
],
"summary": "variant sequencing for prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
"file_size": 3251108,
"gene_list_for": [],
"href": "/sequence-files/IGVFFI2200CONX/@@download/IGVFFI2200CONX.fastq.gz",
"illumina_read_type": "I2",
"index": "TCTCGGTC:ACTG",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"loci_list_for": [],
"maximum_read_length": 4,
"md5sum": "f215df5eadddde76dc9d57ca0e3b931f",
"mean_read_length": 4,
"minimum_read_length": 4,
"read_count": 409698,
"release_timestamp": "2023-12-20T23:44:39.443330+00:00",
"s3_uri": "s3://igvf-files/2023/12/05/010a78f6-fc3b-4f36-8681-580e578645d8/IGVFFI2200CONX.fastq.gz",
"schema_version": "14",
"seqspecs": [],
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"sequencing_run": 1,
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S15-BioRep2-FFRep1-BinD-PCRrep2_S187_I2_001.fastq.gz",
"summary": "I2 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "010a78f6-fc3b-4f36-8681-580e578645d8"
}