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Sample GSM485685 Query DataSets for GSM485685
Status Public on Mar 22, 2010
Title GM12892_RNA-SEQ_induced_Rep1
Sample type SRA
 
Source name Lymphoblastoid Cells
Organism Homo sapiens
Characteristics cell type: Lymphoblastoid cell
cell line: GM12892
treatment: TNF-alpha induced (6h)
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12892
Treatment protocol Cells were treated with 25 ng/mL human recombinant TNF-alpha (eBioscience #14-8329) for six hours at 37°C, 5% CO2.
Growth protocol Lymphoblastoid cell lines were grown in RPMI-1640 Medium, supplemented with glutamine, 15% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 6-8 x10^5 cells/ml.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from lymphoblastoid cell lines, purified and then poly(A)-enriched using two cycles of selection with oligo(dT) cellulose. The Poly(A)-RNA was fragmented and subsequently converted into doublestranded cDNA priming with random hexamers. For construction of sequencing libraries cDNA was purified, size-seledcted on 2% agarose gel, end-repaired and phosphorylated with the End-It kit from. After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). DNA was amplified with Illumina genomic DNA primers 1.1 and 2.1 for 15 cycles by using the following program: 1. 30 s at 98 °C, 2. 15 cycles of 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C, and 3. a 5-min extension at 72 °C. The product was run on 2% agarose E-gels (Invitrogen) to isolate the libraries from residual primers and adapters. Purified library DNA was captured on an Illumina flowcell for cluster generation and sequenced on an Illumina Genome Analyzer II following the manufacturer’s protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description RNA-Seq of PolyA RNA
Data processing FASTQ files are either the sequence.txt files from the Illumnia pipeline (which exclude low quality reads) or, when available, are generated from the Illumina export.txt files which include all reads. Both types of alignment files, eland_result.txt and eland_multi.txt, are directly out of the Illumnia pipeline and unmodified. The narrowPeak files are the scored results generated from the PeakSeq pipeline (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/19122651?dopt=Abstract) and formatted in the UCSC narrowPeak format.
 
Submission date Dec 15, 2009
Last update date May 15, 2019
Contact name Flora Vaccarino
Organization name Yale University
Department Child Study Center
Lab Vaccarino
Street address 230 South Frontage Road
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL9115
Series (2)
GSE19481 Human variation in PolII and NF-KappaB binding (RNA-seq study with TNF-alpha induced)
GSE19486 Human variation in PolII and NF-KappaB binding
Relations
SRA SRX017931
BioSample SAMN00010308

Supplementary file Size Download File type/resource
GSM485685_GM12892_RNAseq_rep1_FC42F1AHM_20090722_s_2_eland_multi.txt.gz 525.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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