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PSON0001 Genomic Characterization of Cell Lines

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1 __'''PSON0001 Genomic Characterization of Cell Lines'''__ This study provides genomic characterization of 39 cell lines from Physical Sciences Oncology Center (PS-OC) Network Bioresource Core Facility (PBCF) through the sequencing of mRNA (!TruSeq Stranded RNA Sample Preparation Kit), miRNA (!TruSeq Small Total RNA Sample Prep Kit ) and exome ( Agilent !SureSelectXT2 Human All Exon V5 kit) and aligning to a reference genome (HG19/37 ). Software for the mRNA characterizations included: cufflinks, cuffdecoder, fastcqReports, mapsplice, tophat, transdecoder, for miRNA included: bowtie2, miRanalyzer, miTools. and for exome included bowtie2. Datasets include the output specific to these software packages, as well as more widely used bioinformatics formats: bam, bed, fasta, fastq, vcf (4.1).
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3 Download the dataset at [ftp://caftpd.nci.nih.gov/psondcc/CellLineGenomics/]
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5 -
Submission to NCBI's !BioProject database, with links to their entries at NCBI's Short Read Archive (SRA) and !BioSample databases:
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The project entries at NCBI's !BioProject database, with links to their entries at NCBI's Short Read Archive (SRA) and !BioSample databases:
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7 * miRNA sequencing !BioProject PRJNA325939 [http://www.ncbi.nlm.nih.gov/bioproject/325939]
8 * mRNA sequencing !BioProject PRJNA325938 [http://www.ncbi.nlm.nih.gov/bioproject/325938]
9 * Exome sequencing !BioProject PRJNA325935 [http://www.ncbi.nlm.nih.gov/bioproject/325935]
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11 +
The project entries at Synapse:
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* Exome characterization [https://www.synapse.org/#!Synapse:syn7248584]
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* mRNA characterization [https://www.synapse.org/#!Synapse:syn7248583]
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* miRNA characterization [https://www.synapse.org/#!Synapse:syn7248581]
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17 '''Table 1. 39 Cell lines used in PSON0001 Genomic Characterization of Cell Lines'''
18 ||Tissue||Cell line name||PBCF Catalog no. ||ATCC collection||Cell type||Disease and stage||NCBI !BioSample||NCBI SRA||
19 ||BRAIN||T98G||NCI-PBCF-CRL1690||CRL-1690||FIBROBLAST||GLIOBLASTOMA MULTIFORME ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292443 SAMN05292443]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547227 SRS1547227]||
20 ||BRAIN||U-87 MG||NCI-PBCF-HTB14||HTB-14||EPITHELIAL||GLIOBLASTOMA; ASTROCYTOMA GRADE IV||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292456 SAMN05292456]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547247 SRS1547247]||
21 ||BREAST||DU4475||NCI-PBCF-HTB123||HTB-123||EPITHELIAL||CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292453 SAMN05292453]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547241 SRS1547241]||
22 ||BREAST||HCC1937||NCI-PBCF-CRL-2336||CRL-2336||EPITHELIAL||PRIMARY DUCTAL CARCINOMA TNM STAGE IIB GRADE 3||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292445 SAMN05292445]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547266 SRS1547266]||
23 ||BREAST||HTERT-HME1||NCI-PBCF-CRL4010||CRL-4010||EPITHELIAL-LIKE||NORMAL ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292449 SAMN05292449]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547237 SRS1547237]||
24 ||BREAST||MCF-7||NCI-PBCF-HTB22||HTB-22||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292458 SAMN05292458]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547249 SRS1547249]||
25 ||BREAST||MCF10A-JSB||NCI-PBCF-1000||CRL-10317||EPITHELIAL||FIBROCYSTIC DISEASE ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292436 SAMN05292436]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547218 SRS1547218]||
26 ||BREAST||MCF7-B7-TS||NCI-PBCF-1001||HTB-22||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292459 SAMN05292459]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547217 SRS1547217]||
27 ||BREAST||MDA-MB-231||NCI-PBCF-HTB26||HTB-26||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292460 SAMN05292460]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547251 SRS1547251]||
28 ||BREAST||MDA-MB-468||NCI-PBCF-HTB132||HTB-132||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292454 SAMN05292454]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547243 SRS1547243]||
29 ||BREAST||T-47D||NCI-PBCF-HTB133||HTB-133||EPITHELIAL||DUCTAL CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292455 SAMN05292455]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547245 SRS1547245]||
30 ||BREAST||ZR-75-1||NCI-PBCF-CRL1500||CRL-1500||EPITHELIAL||DUCTAL CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292440 SAMN05292440]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547222 SRS1547222]||
31 ||COLON||CACO-2||NCI-PBCF-HTB37||HTB-37||EPITHELIAL-LIKE||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292461 SAMN05292461]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547253 SRS1547253]||
32 ||COLON||HCT116||NCI-PBCF-CCL247||CCL-247||EPITHELIAL||CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292433 SAMN05292433]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547263 SRS1547263]||
33 ||COLON||HT-29||NCI-PBCF-HTB38||HTB-38||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292462 SAMN05292462]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547254 SRS1547254]||
34 ||COLON||LOVO||NCI-PBCF-CCL229||CCL-229||EPITHELIAL||ADENOCARCINOMA GRADE IV||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292432 SAMN05292432]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547264 SRS1547264]||
35 ||COLON||SW480||NCI-PBCF-CCL228||CCL-228||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292431 SAMN05292431]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547250 SRS1547250]||
36 ||COLON||SW620||NCI-PBCF-CCL227||CCL-227||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292430 SAMN05292430]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547235 SRS1547235]||
37 ||LUNG||NCI-BL2126||NCI-PBCF-CCL256.1||CCL-256||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292435 SAMN05292435]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547262 SRS1547262]||
38 ||LUNG||NCI-H2087||NCI-PBCF-CRL5922||CRL-5922||EPITHELIAL-LIKE AND/OR ROUNDED||ADENOCARCINOMA STAGE 1||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292451 SAMN05292451]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547239 SRS1547239]||
39 ||LUNG||NCI-H2126||NCI-PBCF-CCL256||CCL-256||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292434 SAMN05292434]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547265 SRS1547265]||
40 ||LUNG||NL20||NCI-PBCF-CRL2503||CRL-2503||EPITHELIAL||NORMAL ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292446 SAMN05292446]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547230 SRS1547230]||
41 ||OVARY||CAOV-3||NCI-PBCF-HTB75||HTB-75||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292465 SAMN05292465]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547258 SRS1547258]||
42 ||OVARY||NIH: OVCAR-3||NCI-PBCF-HTB161||HTB-161||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292457 SAMN05292457]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547248 SRS1547248]||
43 ||OVARY||SKOV-3||NCI-PBCF-HTB77||HTB-77||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292466 SAMN05292466]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547259 SRS1547259]||
44 ||PANCREAS||CAPAN-1||NCI-PBCF-HTB79||HTB-79||EPITHELIAL||ADENOCARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292467 SAMN05292467]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547260 SRS1547260]||
45 ||PANCREAS||HTERT-HPNE||NCI-PBCF-CRL4023||CRL-4023||EPITHELIAL-LIKE||NORMAL ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292450 SAMN05292450]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547238 SRS1547238]||
46 ||PANCREAS||PANC-1||NCI-PBCF-CRL1469||CRL-1469||EPITHELIAL||EPITHELIOID CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292439 SAMN05292439]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547220 SRS1547220]||
47 ||PERIPHERAL BLOOD||NCI-BL2087||NCI-PBCF-CRL5965||CRL-5965||LYMPHOBLAST||NORMAL ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292452 SAMN05292452]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547240 SRS1547240]||
48 ||PROSTATE||22RV1||NCI-PBCF-CRL2505||CRL-2505||EPITHELIAL||CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292447 SAMN05292447]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547231 SRS1547231]||
49 ||PROSTATE||DU 145||NCI-PBCF-HTB81||HTB-81||EPITHELIAL||CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292468 SAMN05292468]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547261 SRS1547261]||
50 ||PROSTATE||LNCAP CLONE FGC||NCI-PBCF-CRL1740||CRL-1740||EPITHELIAL||CARCINOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292444 SAMN05292444]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547228 SRS1547228]||
51 ||PROSTATE||PC-3||NCI-PBCF-CRL1435||CRL-1435||EPITHELIAL||ADENOCARCINOMA GRADE IV||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292438 SAMN05292438]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547219 SRS1547219]||
52 ||PROSTATE||RWPE-1||NCI-PBCF-CRL11609||CRL-11609||EPITHELIAL||NORMAL ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292437 SAMN05292437]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547267 SRS1547267]||
53 ||PROSTATE||VCAP||NCI-PBCF-CRL2876||CRL-2876||EPITHELIAL||CANCER ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292448 SAMN05292448]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547233 SRS1547233]||
54 ||SKIN||A375||NCI-PBCF-CRL1619||CRL-1619||EPITHELIAL||MALIGNANT MELANOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292441 SAMN05292441]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547223 SRS1547223]||
55 ||SKIN||MEWO||NCI-PBCF-HTB65||HTB-65||FIBROBLAST||MALIGNANT MELANOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292463 SAMN05292463]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547256 SRS1547256]||
56 ||SKIN||SK-MEL-2||NCI-PBCF-HTB68||HTB-68||POLYGONAL||MALIGNANT MELANOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292464 SAMN05292464]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547257 SRS1547257]||
57 ||SKIN||WM266-4||NCI-PBCF-CRL1676||CRL-1676||EPITHELIAL||MELANOMA ||[https://www.ncbi.nlm.nih.gov/biosample/?term=SAMN05292442 SAMN05292442]||[https://www.ncbi.nlm.nih.gov/sra/?term=SRS1547225 SRS1547225]||
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63 '''Data usage policy'''
64
65 The data contained within the PS-ON DCC is based on several research projects and is intended to be rapidly and constantly updated for the research community to access and use. The NCI requests that any data users:
66 * Inform the data submitters about the intention to submit a publication that uses PS-ON DCC data.
67 * Include the following statement in any publications resulting from the use of PS-ON DCC data: ''Data used in this publication were generated by projects sponsored by the NCI Physical Sciences in Oncology Initiative.''