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| Status |
Public on Mar 22, 2010 |
| Title |
GM12892_RNA-SEQ_induced_Rep1 |
| Sample type |
SRA |
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| Source name |
Lymphoblastoid Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphoblastoid cell
cell line: GM12892
treatment: TNF-alpha induced (6h)
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| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12892
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| Treatment protocol |
Cells were treated with 25 ng/mL human recombinant TNF-alpha (eBioscience #14-8329) for six hours at 37°C, 5% CO2.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
RNA-Seq of PolyA RNA
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| 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://www.ncbi.nlm.nih.gov/pubmed/19122651?dopt=Abstract) and formatted in the UCSC narrowPeak format.
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| Submission date |
Dec 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Flora Vaccarino |
| Organization name |
Yale University
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| Department |
Child Study Center
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| Lab |
Vaccarino
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| Street address |
230 South Frontage Road
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| 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 |
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| 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 Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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