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Sample GSM763959 Query DataSets for GSM763959
Status Public on Jul 19, 2011
Title serum_1_RNAseq
Sample type SRA
Source name HCT-116
Organism Homo sapiens
Characteristics cell line: HCT-116
passages: passage 4-15
treatment: serum-induced
Treatment protocol For serum stimulation, cells were first starved by washing cells 2x in PBS, then culturing for 40 hours in McCoy’s 5A without serum. Cells were then either left untreated or treated with serum for 30 minutes before harvesting.
Growth protocol HCT-116 cells were grown in McCoy’s 5A medium supplemented with 10% FBS.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from serum-treated and untreated HCT-116 cells with RNeasy kit following manufacturer's protocol. And 2 ug of total RNA from each sample was used to prepare the libraries with the Illumina mRNA-Seq Sample Prep Kit (RS-100-0801) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description serum mRNA
Data processing Alignment: Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the human genome (UCSC hg19) using the tophat (Trapnell et al. 2009) alignment tool, version 1.2.0, allowing unique matches only, and the full human ENSEMBL 59 GTF.
Submission date Jul 19, 2011
Last update date May 15, 2019
Contact name Alexander (Garrett) Garruss
Organization name Stowers Institute for Medical Research
Lab Shilatifard
Street address 1000 East 50th Street
City Kansas CIty
State/province Missouri
ZIP/Postal code 64110
Country USA
Platform ID GPL10999
Series (2)
GSE30268 Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).
GSE30786 Determination of transcript abundance before and after serum induction in human HCT-116 colon cancer cell line.
SRA SRX084348
BioSample SAMN00672477

Supplementary file Size Download File type/resource
GSM763959_serum_1_aligned.txt.gz 314.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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