IGVFDS4386IYQY

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS4386IYQY/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS4386IYQY",
10    "aliases": [
11        "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input_AmpliconSequencing"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0003661/",
15        "assay_slims": [
16            "CRISPR screens"
17        ],
18        "status": "released",
19        "term_name": "in vitro CRISPR screen using flow cytometry"
20    },
21    "audit": {
22        "INTERNAL_ACTION": [
23            {
24                "category": "missing publication",
25                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
26                "level": 30,
27                "level_name": "INTERNAL_ACTION",
28                "name": "audit_file_set_missing_publication",
29                "path": "/measurement-sets/IGVFDS4386IYQY/"
30            },
31            {
32                "category": "missing sequencing kit",
33                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has sequence file(s) [IGVFFI3179VNTO](/sequence-files/IGVFFI3179VNTO/), [IGVFFI6896BRQA](/sequence-files/IGVFFI6896BRQA/), [IGVFFI1289TGPO](/sequence-files/IGVFFI1289TGPO/), [IGVFFI6390KKVR](/sequence-files/IGVFFI6390KKVR/), [IGVFFI0109SYWK](/sequence-files/IGVFFI0109SYWK/), [IGVFFI9903KKNE](/sequence-files/IGVFFI9903KKNE/), [IGVFFI0838RBJP](/sequence-files/IGVFFI0838RBJP/), [IGVFFI8470LGBH](/sequence-files/IGVFFI8470LGBH/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
34                "level": 30,
35                "level_name": "INTERNAL_ACTION",
36                "name": "audit_inconsistent_sequencing_kit",
37                "path": "/measurement-sets/IGVFDS4386IYQY/"
38            },
39            {
40                "category": "missing sequence specification",
41                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has sequence file(s): [IGVFFI3179VNTO](/sequence-files/IGVFFI3179VNTO/), [IGVFFI6896BRQA](/sequence-files/IGVFFI6896BRQA/), [IGVFFI1289TGPO](/sequence-files/IGVFFI1289TGPO/), [IGVFFI6390KKVR](/sequence-files/IGVFFI6390KKVR/), [IGVFFI0109SYWK](/sequence-files/IGVFFI0109SYWK/), [IGVFFI9903KKNE](/sequence-files/IGVFFI9903KKNE/), [IGVFFI0838RBJP](/sequence-files/IGVFFI0838RBJP/), [IGVFFI8470LGBH](/sequence-files/IGVFFI8470LGBH/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
42                "level": 30,
43                "level_name": "INTERNAL_ACTION",
44                "name": "audit_missing_seqspec",
45                "path": "/measurement-sets/IGVFDS4386IYQY/"
46            },
47            {
48                "category": "mismatched status",
49                "detail": "Released in vitro system [IGVFSM3467QAZR](/in-vitro-systems/IGVFSM3467QAZR/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
50                "level": 30,
51                "level_name": "INTERNAL_ACTION",
52                "name": "audit_item_status",
53                "path": "/in-vitro-systems/IGVFSM3467QAZR/"
54            },
55            {
56                "category": "missing publication",
57                "detail": "In vitro system [IGVFSM3467QAZR](/in-vitro-systems/IGVFSM3467QAZR/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
58                "level": 30,
59                "level_name": "INTERNAL_ACTION",
60                "name": "audit_sample_missing_publication",
61                "path": "/in-vitro-systems/IGVFSM3467QAZR/"
62            }
63        ],
64        "NOT_COMPLIANT": [
65            {
66                "category": "missing control for",
67                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
68                "level": 50,
69                "level_name": "NOT_COMPLIANT",
70                "name": "audit_control_for_control_type",
71                "path": "/measurement-sets/IGVFDS4386IYQY/"
72            }
73        ],
74        "WARNING": [
75            {
76                "category": "missing auxiliary set",
77                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
78                "level": 40,
79                "level_name": "WARNING",
80                "name": "audit_missing_auxiliary_set",
81                "path": "/measurement-sets/IGVFDS4386IYQY/"
82            },
83            {
84                "category": "missing targeted genes",
85                "detail": "Measurement set [IGVFDS4386IYQY](/measurement-sets/IGVFDS4386IYQY/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
86                "level": 40,
87                "level_name": "WARNING",
88                "name": "audit_targeted_genes",
89                "path": "/measurement-sets/IGVFDS4386IYQY/"
90            }
91        ]
92    },
93    "award": {
94        "@id": "/awards/HG011972/",
95        "component": "functional characterization",
96        "contact_pi": {
97            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
98            "title": "Jesse Engreitz"
99        },
100        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
101    },
102    "construct_library_sets": [
103        {
104            "@id": "/construct-library-sets/IGVFDS2374NXLW/",
105            "accession": "IGVFDS2374NXLW",
106            "file_set_type": "guide library",
107            "status": "in progress",
108            "summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
109        }
110    ],
111    "control_file_sets": [
112        {
113            "@id": "/measurement-sets/IGVFDS4989HPTW/",
114            "accession": "IGVFDS4989HPTW",
115            "aliases": [
116                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
117            ],
118            "status": "released"
119        }
120    ],
121    "control_for": [],
122    "control_type": "unsorted FACS input",
123    "creation_timestamp": "2023-11-30T22:49:14.495052+00:00",
124    "data_use_limitation_summaries": [
125        "no certificate"
126    ],
127    "donors": [
128        {
129            "@id": "/human-donors/IGVFDO7359LVPI/",
130            "accession": "IGVFDO7359LVPI",
131            "aliases": [
132                "igvf:donor_of_THP1"
133            ],
134            "sex": "male",
135            "status": "released",
136            "taxa": "Homo sapiens"
137        }
138    ],
139    "externally_hosted": false,
140    "file_set_type": "experimental data",
141    "files": [
142        {
143            "@id": "/sequence-files/IGVFFI3179VNTO/",
144            "accession": "IGVFFI3179VNTO",
145            "aliases": [
146                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
147            ],
148            "content_type": "reads",
149            "controlled_access": false,
150            "creation_timestamp": "2023-12-05T22:29:14.708646+00:00",
151            "file_format": "fastq",
152            "file_size": 975152,
153            "href": "/sequence-files/IGVFFI3179VNTO/@@download/IGVFFI3179VNTO.fastq.gz",
154            "md5sum": "ccbe35f099df407fb8cf9e7ba983cf13",
155            "s3_uri": "s3://igvf-files/2023/12/05/fc060a24-2f46-4275-90af-a3852699d913/IGVFFI3179VNTO.fastq.gz",
156            "sequencing_platform": {
157                "@id": "/platform-terms/EFO_0008566/",
158                "status": "released",
159                "term_name": "Illumina NextSeq 550"
160            },
161            "status": "released",
162            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep2_S400_I2_001.fastq.gz",
163            "upload_status": "validated"
164        },
165        {
166            "@id": "/sequence-files/IGVFFI6896BRQA/",
167            "accession": "IGVFFI6896BRQA",
168            "aliases": [
169                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
170            ],
171            "content_type": "reads",
172            "controlled_access": false,
173            "creation_timestamp": "2023-12-05T22:28:46.708757+00:00",
174            "file_format": "fastq",
175            "file_size": 3897024,
176            "href": "/sequence-files/IGVFFI6896BRQA/@@download/IGVFFI6896BRQA.fastq.gz",
177            "md5sum": "00ca3a93e1b66237f6f56869f45db112",
178            "s3_uri": "s3://igvf-files/2023/12/05/0bb3f02e-5656-4b02-8708-1a673c4de31a/IGVFFI6896BRQA.fastq.gz",
179            "sequencing_platform": {
180                "@id": "/platform-terms/EFO_0008566/",
181                "status": "released",
182                "term_name": "Illumina NextSeq 550"
183            },
184            "status": "released",
185            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep1_S390_R1_001.fastq.gz",
186            "upload_status": "validated"
187        },
188        {
189            "@id": "/sequence-files/IGVFFI1289TGPO/",
190            "accession": "IGVFFI1289TGPO",
191            "aliases": [
192                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
193            ],
194            "content_type": "reads",
195            "controlled_access": false,
196            "creation_timestamp": "2023-12-05T22:29:24.079522+00:00",
197            "file_format": "fastq",
198            "file_size": 3590377,
199            "href": "/sequence-files/IGVFFI1289TGPO/@@download/IGVFFI1289TGPO.fastq.gz",
200            "md5sum": "81c1e4d995dbf6227737004f50ecf873",
201            "s3_uri": "s3://igvf-files/2023/12/05/5d623586-3c89-4e78-88a0-2ba7ddcd7c16/IGVFFI1289TGPO.fastq.gz",
202            "sequencing_platform": {
203                "@id": "/platform-terms/EFO_0008566/",
204                "status": "released",
205                "term_name": "Illumina NextSeq 550"
206            },
207            "status": "released",
208            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep2_S400_R1_001.fastq.gz",
209            "upload_status": "validated"
210        },
211        {
212            "@id": "/sequence-files/IGVFFI6390KKVR/",
213            "accession": "IGVFFI6390KKVR",
214            "aliases": [
215                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
216            ],
217            "content_type": "reads",
218            "controlled_access": false,
219            "creation_timestamp": "2023-12-05T22:29:33.664945+00:00",
220            "file_format": "fastq",
221            "file_size": 4262473,
222            "href": "/sequence-files/IGVFFI6390KKVR/@@download/IGVFFI6390KKVR.fastq.gz",
223            "md5sum": "2536e28871c97575abebaf77c876a5f5",
224            "s3_uri": "s3://igvf-files/2023/12/05/619bb2fd-ab29-4fa5-8755-469ee970d5f1/IGVFFI6390KKVR.fastq.gz",
225            "sequencing_platform": {
226                "@id": "/platform-terms/EFO_0008566/",
227                "status": "released",
228                "term_name": "Illumina NextSeq 550"
229            },
230            "status": "released",
231            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep2_S400_R2_001.fastq.gz",
232            "upload_status": "validated"
233        },
234        {
235            "@id": "/sequence-files/IGVFFI0109SYWK/",
236            "accession": "IGVFFI0109SYWK",
237            "aliases": [
238                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
239            ],
240            "content_type": "reads",
241            "controlled_access": false,
242            "creation_timestamp": "2023-12-05T22:28:37.206354+00:00",
243            "file_format": "fastq",
244            "file_size": 1042570,
245            "href": "/sequence-files/IGVFFI0109SYWK/@@download/IGVFFI0109SYWK.fastq.gz",
246            "md5sum": "c9406c97ed378e1159ce18bb1c2177f5",
247            "s3_uri": "s3://igvf-files/2023/12/05/d5a15a96-9e81-4516-8b76-1ce83cdf1b39/IGVFFI0109SYWK.fastq.gz",
248            "sequencing_platform": {
249                "@id": "/platform-terms/EFO_0008566/",
250                "status": "released",
251                "term_name": "Illumina NextSeq 550"
252            },
253            "status": "released",
254            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep1_S390_I2_001.fastq.gz",
255            "upload_status": "validated"
256        },
257        {
258            "@id": "/sequence-files/IGVFFI9903KKNE/",
259            "accession": "IGVFFI9903KKNE",
260            "aliases": [
261                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
262            ],
263            "content_type": "reads",
264            "controlled_access": false,
265            "creation_timestamp": "2023-12-05T22:28:56.195388+00:00",
266            "file_format": "fastq",
267            "file_size": 4639702,
268            "href": "/sequence-files/IGVFFI9903KKNE/@@download/IGVFFI9903KKNE.fastq.gz",
269            "md5sum": "c06ce4e3c4715b9ca03d40c21e47826d",
270            "s3_uri": "s3://igvf-files/2023/12/05/5be8b736-591f-4c31-888e-9213532b2ad3/IGVFFI9903KKNE.fastq.gz",
271            "sequencing_platform": {
272                "@id": "/platform-terms/EFO_0008566/",
273                "status": "released",
274                "term_name": "Illumina NextSeq 550"
275            },
276            "status": "released",
277            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep1_S390_R2_001.fastq.gz",
278            "upload_status": "validated"
279        },
280        {
281            "@id": "/sequence-files/IGVFFI0838RBJP/",
282            "accession": "IGVFFI0838RBJP",
283            "aliases": [
284                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
285            ],
286            "content_type": "reads",
287            "controlled_access": false,
288            "creation_timestamp": "2023-12-05T22:28:27.958354+00:00",
289            "file_format": "fastq",
290            "file_size": 993450,
291            "href": "/sequence-files/IGVFFI0838RBJP/@@download/IGVFFI0838RBJP.fastq.gz",
292            "md5sum": "ebd7e3ea2f10a9829cfe47d818104995",
293            "s3_uri": "s3://igvf-files/2023/12/05/f94cfd38-1403-4364-90fe-2e7c94fcf183/IGVFFI0838RBJP.fastq.gz",
294            "sequencing_platform": {
295                "@id": "/platform-terms/EFO_0008566/",
296                "status": "released",
297                "term_name": "Illumina NextSeq 550"
298            },
299            "status": "released",
300            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep1_S390_I1_001.fastq.gz",
301            "upload_status": "validated"
302        },
303        {
304            "@id": "/sequence-files/IGVFFI8470LGBH/",
305            "accession": "IGVFFI8470LGBH",
306            "aliases": [
307                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
308            ],
309            "content_type": "reads",
310            "controlled_access": false,
311            "creation_timestamp": "2023-12-05T22:29:05.486345+00:00",
312            "file_format": "fastq",
313            "file_size": 1018711,
314            "href": "/sequence-files/IGVFFI8470LGBH/@@download/IGVFFI8470LGBH.fastq.gz",
315            "md5sum": "5103b9eead5fc5d0348867c0cab7050d",
316            "s3_uri": "s3://igvf-files/2023/12/05/adc14f7b-4031-4b6a-8295-6a100c446a45/IGVFFI8470LGBH.fastq.gz",
317            "sequencing_platform": {
318                "@id": "/platform-terms/EFO_0008566/",
319                "status": "released",
320                "term_name": "Illumina NextSeq 550"
321            },
322            "status": "released",
323            "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinAll-PCRrep2_S400_I1_001.fastq.gz",
324            "upload_status": "validated"
325        }
326    ],
327    "input_for": [
328        "/analysis-sets/IGVFDS5031MNRR/"
329    ],
330    "lab": {
331        "@id": "/labs/jesse-engreitz/",
332        "title": "Jesse Engreitz, Stanford"
333    },
334    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
335    "preferred_assay_title": "Variant-EFFECTS",
336    "protocols": [
337        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
338    ],
339    "release_timestamp": "2023-12-20T23:07:01.730150+00:00",
340    "samples": [
341        {
342            "@id": "/in-vitro-systems/IGVFSM3467QAZR/",
343            "@type": [
344                "InVitroSystem",
345                "Biosample",
346                "Sample",
347                "Item"
348            ],
349            "accession": "IGVFSM3467QAZR",
350            "aliases": [
351                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input"
352            ],
353            "classifications": [
354                "cell line"
355            ],
356            "institutional_certificates": [],
357            "modifications": [
358                {
359                    "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
360                    "modality": "prime editing",
361                    "status": "released"
362                }
363            ],
364            "sample_terms": [
365                {
366                    "@id": "/sample-terms/EFO_0001253/",
367                    "@type": [
368                        "SampleTerm",
369                        "OntologyTerm",
370                        "Item"
371                    ],
372                    "aliases": [
373                        "igvf:THP-1"
374                    ],
375                    "status": "released",
376                    "summary": "THP-1",
377                    "term_name": "THP-1"
378                }
379            ],
380            "status": "released",
381            "summary": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
382            "taxa": "Homo sapiens"
383        }
384    ],
385    "schema_version": "26",
386    "status": "released",
387    "submitted_by": {
388        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
389        "title": "Michael Montgomery"
390    },
391    "submitted_files_timestamp": "2023-12-05T22:28:27.958354+00:00",
392    "summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
393    "uuid": "1f8728be-bc45-4b1b-9fe3-fc831e64b499"
394}