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PSON0001 Genomic Characterization of Cell Lines

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).

Download the dataset at ftp://caftpd.nci.nih.gov/psondcc/CellLineGenomics/

The project entries at NCBI’s BioProject database, with links to their entries at NCBI’s Short Read Archive (SRA) and BioSample databases:

The project entries at Synapse:


Table 1. 39 Cell lines used in PSON0001 Genomic Characterization of Cell Lines

Tissue Cell line name PBCF Catalog no. ATCC collection Cell type Disease and stage NCBI BioSample NCBI SRA
BRAIN T98G NCI-PBCF-CRL1690 CRL-1690 FIBROBLAST GLIOBLASTOMA MULTIFORME SAMN05292443 SRS1547227
BRAIN U-87 MG NCI-PBCF-HTB14 HTB-14 EPITHELIAL GLIOBLASTOMA; ASTROCYTOMA GRADE IV SAMN05292456 SRS1547247
BREAST DU4475 NCI-PBCF-HTB123 HTB-123 EPITHELIAL CARCINOMA SAMN05292453 SRS1547241
BREAST HCC1937 NCI-PBCF-CRL-2336 CRL-2336 EPITHELIAL PRIMARY DUCTAL CARCINOMA TNM STAGE IIB GRADE 3 SAMN05292445 SRS1547266
BREAST HTERT-HME1 NCI-PBCF-CRL4010 CRL-4010 EPITHELIAL-LIKE NORMAL SAMN05292449 SRS1547237
BREAST MCF-7 NCI-PBCF-HTB22 HTB-22 EPITHELIAL ADENOCARCINOMA SAMN05292458 SRS1547249
BREAST MCF10A-JSB NCI-PBCF-1000 CRL-10317 EPITHELIAL FIBROCYSTIC DISEASE SAMN05292436 SRS1547218
BREAST MCF7-B7-TS NCI-PBCF-1001 HTB-22 EPITHELIAL ADENOCARCINOMA SAMN05292459 SRS1547217
BREAST MDA-MB-231 NCI-PBCF-HTB26 HTB-26 EPITHELIAL ADENOCARCINOMA SAMN05292460 SRS1547251
BREAST MDA-MB-468 NCI-PBCF-HTB132 HTB-132 EPITHELIAL ADENOCARCINOMA SAMN05292454 SRS1547243
BREAST T-47D NCI-PBCF-HTB133 HTB-133 EPITHELIAL DUCTAL CARCINOMA SAMN05292455 SRS1547245
BREAST ZR-75-1 NCI-PBCF-CRL1500 CRL-1500 EPITHELIAL DUCTAL CARCINOMA SAMN05292440 SRS1547222
COLON CACO-2 NCI-PBCF-HTB37 HTB-37 EPITHELIAL-LIKE ADENOCARCINOMA SAMN05292461 SRS1547253
COLON HCT116 NCI-PBCF-CCL247 CCL-247 EPITHELIAL CARCINOMA SAMN05292433 SRS1547263
COLON HT-29 NCI-PBCF-HTB38 HTB-38 EPITHELIAL ADENOCARCINOMA SAMN05292462 SRS1547254
COLON LOVO NCI-PBCF-CCL229 CCL-229 EPITHELIAL ADENOCARCINOMA GRADE IV SAMN05292432 SRS1547264
COLON SW480 NCI-PBCF-CCL228 CCL-228 EPITHELIAL ADENOCARCINOMA SAMN05292431 SRS1547250
COLON SW620 NCI-PBCF-CCL227 CCL-227 EPITHELIAL ADENOCARCINOMA SAMN05292430 SRS1547235
LUNG NCI-BL2126 NCI-PBCF-CCL256.1 CCL-256 EPITHELIAL ADENOCARCINOMA SAMN05292435 SRS1547262
LUNG NCI-H2087 NCI-PBCF-CRL5922 CRL-5922 EPITHELIAL-LIKE AND/OR ROUNDED ADENOCARCINOMA STAGE 1 SAMN05292451 SRS1547239
LUNG NCI-H2126 NCI-PBCF-CCL256 CCL-256 EPITHELIAL ADENOCARCINOMA SAMN05292434 SRS1547265
LUNG NL20 NCI-PBCF-CRL2503 CRL-2503 EPITHELIAL NORMAL SAMN05292446 SRS1547230
OVARY CAOV-3 NCI-PBCF-HTB75 HTB-75 EPITHELIAL ADENOCARCINOMA SAMN05292465 SRS1547258
OVARY NIH: OVCAR-3 NCI-PBCF-HTB161 HTB-161 EPITHELIAL ADENOCARCINOMA SAMN05292457 SRS1547248
OVARY SKOV-3 NCI-PBCF-HTB77 HTB-77 EPITHELIAL ADENOCARCINOMA SAMN05292466 SRS1547259
PANCREAS CAPAN-1 NCI-PBCF-HTB79 HTB-79 EPITHELIAL ADENOCARCINOMA SAMN05292467 SRS1547260
PANCREAS HTERT-HPNE NCI-PBCF-CRL4023 CRL-4023 EPITHELIAL-LIKE NORMAL SAMN05292450 SRS1547238
PANCREAS PANC-1 NCI-PBCF-CRL1469 CRL-1469 EPITHELIAL EPITHELIOID CARCINOMA SAMN05292439 SRS1547220
PERIPHERAL BLOOD NCI-BL2087 NCI-PBCF-CRL5965 CRL-5965 LYMPHOBLAST NORMAL SAMN05292452 SRS1547240
PROSTATE 22RV1 NCI-PBCF-CRL2505 CRL-2505 EPITHELIAL CARCINOMA SAMN05292447 SRS1547231
PROSTATE DU 145 NCI-PBCF-HTB81 HTB-81 EPITHELIAL CARCINOMA SAMN05292468 SRS1547261
PROSTATE LNCAP CLONE FGC NCI-PBCF-CRL1740 CRL-1740 EPITHELIAL CARCINOMA SAMN05292444 SRS1547228
PROSTATE PC-3 NCI-PBCF-CRL1435 CRL-1435 EPITHELIAL ADENOCARCINOMA GRADE IV SAMN05292438 SRS1547219
PROSTATE RWPE-1 NCI-PBCF-CRL11609 CRL-11609 EPITHELIAL NORMAL SAMN05292437 SRS1547267
PROSTATE VCAP NCI-PBCF-CRL2876 CRL-2876 EPITHELIAL CANCER SAMN05292448 SRS1547233
SKIN A375 NCI-PBCF-CRL1619 CRL-1619 EPITHELIAL MALIGNANT MELANOMA SAMN05292441 SRS1547223
SKIN MEWO NCI-PBCF-HTB65 HTB-65 FIBROBLAST MALIGNANT MELANOMA SAMN05292463 SRS1547256
SKIN SK-MEL-2 NCI-PBCF-HTB68 HTB-68 POLYGONAL MALIGNANT MELANOMA SAMN05292464 SRS1547257
SKIN WM266-4 NCI-PBCF-CRL1676 CRL-1676 EPITHELIAL MELANOMA SAMN05292442 SRS1547225

Data usage policy

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:

  • Inform the data submitters about the intention to submit a publication that uses PS-ON DCC data.
    • 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.

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