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Sample GSM1492703 Query DataSets for GSM1492703
Status Public on Apr 28, 2016
Title Input
Sample type SRA
Source name MCF7 cell line
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: breast cancer cells
Treatment protocol For H2A.Z knockdown experiments, 10umol/l scramble and H2A.Z siRNA were used to transfect MCF7.
Growth protocol MCF7 was cultured in DMEM with 10% FBS
Extracted molecule genomic DNA
Extraction protocol MCF7 were crosslinked with 1% formaldehyde for 10min and then incubated with nuclear extraction buffer (20mM Hepes-KOH ph7.5, 10mM KCl, 1mM EDTA, 0.2% NP40, 1mM DTT and 10% glycerol) to isolate nuclei. The nulei in sonication buffer (20mM Tris-HCl pH8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% TritonX-100) was sheared in Misonix Sonicator. The further chromatin immunoprecipitation was implimented with RNAP2 antibody (05-623 Millipore) .
The library construction followed the protocol in kit of NEBNext® ChIP-Seq Library Prep Reagent Set (E6200, New England Biolab) with the modfication that single index primer in place of dual primers was used in the final step of PCR amplication.
The libraries were indexed with Illumina barcode. Five indexed libraries were finally pooled into one lane and sequenced in Hiseq2500.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description Cross-linked, sonicated genomic input DNA
Data processing First the reads with aligned to hg19 using bowtie2 with -M 1 option.
Aligned reads were processed and filtered using the spp R package to filter out low quality reads.
ChIP-seq and input reads were mapped to RefSeq annotated genes calculating the background-subtracted RNA Polymerase II density at the TSS and gene body of each gene
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated files (CSV) of each RefSeq isoform with library-size and length normalized read density of ChIP or Input reads mapping to the TSS or gene body of each annotated isoform
Submission date Aug 28, 2014
Last update date May 15, 2019
Contact name Peter J Park
Phone 617-432-7373
Organization name Harvard Medical School
Department Center for Biomedical Informatics
Street address 10 Shattuck St
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL16791
Series (1)
GSE60872 The functional impact of RNA Polymerase II pausing across multiple mamamlian cell types
BioSample SAMN03010665
SRA SRX689185

Supplementary file Size Download File type/resource
GSM1492703_MCF7-input-density.csv.gz 296.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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