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Sample GSM984966 Query DataSets for GSM984966
Status Public on Apr 30, 2014
Title Sample immunoprecipitate 1
Sample type SRA
Source name E14 mESCs
Organism Mus musculus
Characteristics genetic background: 129/Ola
genotype: wt
sample type: Brf1 and Brf2 immunoprecipitated complexes
antibody: anti-Brf1/2 antibody
antibody manufacturer: Cell Signaling Technologies
antibody catalog #: 2119
cell type: E14 mESCs
Growth protocol E14 mESCs were cultured in 15% FBS, DMEM + 1000U/ml LIF.
Extracted molecule total RNA
Extraction protocol Cytoplasmic extracts were prepared via cold hypotonic lysis, and RNA/RNA binding protein complexes were immunoprecipitated (RIP) followed by extraction of co-isolated RNAs. As a control, RIP procedure was conducted using a non-specific rabbit IgG. Two E14 Total RNA preparations were sequenced to gauge gene expression levels prior to RIP. Isolated RNAs were processed according to manufacturer's instructions for Illumina's TruSeq RNA Prep kit. Briefly, RNA is fragmented at 94C to generate lengths of approximately 200nts. The fragments are reverse transcribed to double stranded DNA using random hexamer primers. Ends were blunted, adenylated and ligated to Illumina adapters. Fragments were gel separated and bands corresponding to 350bps were isolated for sequencing.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Basecaller software: RTA, Pipeline and conversion to FASTQ format: CASAVA 1.8.2
Sequencing reads were trimmed of first 13nts to remove random hexamer priming bias
Trimmed reads were aligned to a mm9 transcript annotation containing only protein coding genes using Bowtie (v. 1.1.2) using default paramters
FPKM measurements were generated by eXpress (v. 1.1.1) using default parameters (see Roberts A. and Pachter L., in submission)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and other abundance statistics for each transcript annotation
Submission date Aug 14, 2012
Last update date May 15, 2019
Contact name Frederick E Tan
Phone 626-395-5969
Organization name California Institute of Technology
Department Biology and Applied Physics
Lab Michael Elowitz
Street address 1200 E. California Blvd, M/C 114-96
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
Platform ID GPL13112
Series (1)
GSE40104 High-throughput sequencing of Brf1 (Zfp36l1) and Brf2 (Zfp36l2) targets
SRA SRX176592
BioSample SAMN01113182

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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