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Sample GSM1129328 Query DataSets for GSM1129328
Status Public on May 13, 2013
Title OCI-Ly1 shEZH2 2
Sample type SRA
 
Source name OCI-Ly1 cell line
Organism Homo sapiens
Characteristics cell type: OCI-Ly1 cell line
treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days
Extracted molecule total RNA
Extraction protocol RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturer’s protocol.
ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iTâ„¢ dsDNA HS Assay (Life Technologies)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing genome build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml)
 
Submission date Apr 25, 2013
Last update date May 15, 2019
Contact name Matt Teater
E-mail(s) mrt2001@med.cornell.edu
Organization name Weill Cornell Medical College
Street address 445 E 69th St
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL11154
Series (1)
GSE45982 EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation
Relations
BioSample SAMN02056273
SRA SRX271824

Supplementary file Size Download File type/resource
GSM1129328_Sample_22_OCILy1_shEZH2_2_RefSeq_FPKM.txt.gz 734.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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