RNA-Seq (polyA+) analysis of DLBCL cell line HS0798 - SRA

SRX079566: RNA-Seq (polyA+) analysis of DLBCL cell line HS0798
2 ILLUMINA (Illumina Genome Analyzer IIx) runs: 16.9M spots, 1.2G bases, 1.1Gb downloads

Design: PolyA+ RNA was purified using the MACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany), from 5-10ug of DNaseI-treated total RNA as per the manufacturer's instructions. Double-stranded cDNA was synthesized from the purified polyA+RNA using the Superscript Double-Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA, USA) and random hexamer primers (Invitrogen) at a concentration of 5uM. The cDNA was fragmented by sonication and a paired-end sequencing library prepared following the Illumina paired-end library preparation protocol (Illumina, Hayward, CA, USA).

Submitted by: BC Cancer Agency Michael Smith Genome Sciences Centre (BCCAGSC)

Study: CGCI: Non-Hodgkin Lymphoma (NHL)

PRJNA172563 • SRP020237 • All experiments • All runs

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The Office of Cancer Genomics (OCG) at the National Cancer Institute sponsored a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel emerging sequencing technologies in cancer. The CGCI program included comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors. CGCI characterized a number of B-cell non-Hodgkin lymphomas (including diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and adult and pediatric Burkitt lymphomas). All data from these projects is available at the NCI Genomic Data Commons. In combination, the lymphoid cancers (non-Hodgkin lymphoma, Hodgkin lymphoma, myeloma and chronic lymphocytic leukemia), constitute the fourth most common malignancy in both men and... (for more see dbGaP study page.)

Sample: human B cell lymphoma cell line DB

SAMN00630374 • SRS212581 • All experiments • All runs

Organism: Homo sapiens

Library:

Name: HS0798

Instrument: Illumina Genome Analyzer IIx

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Spot descriptor:

1 forward37 reverse

Pipeline: show...hide...

Name	Step	Prev Step	Program	Version
BASE_CALLS	1	NIL	Bustard	1.9.5
QUALITY_SCORES	2	1	Bustard	1.9.5

Runs: 2 runs, 16.9M spots, 1.2G bases, 1.1Gb

Run	# of Spots	# of Bases	Size	Published
SRR292241	9,721,384	699.9M	956.3Mb	2011-06-24
SRR390728	7,178,576	516.9M	186.1Mb	2011-12-21

ID:: 90134

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