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Sample GSM810673 Query DataSets for GSM810673
Status Public on Oct 06, 2011
Title Spermatocyte_input
Sample type SRA
Source name Spermatocyte
Organism Mus musculus
Characteristics cell type: Spermatocyte
antibody: None
Extracted molecule genomic DNA
Extraction protocol ChIP-seq for histone Kcr or Kac was carried out as previously described with 500 μg IMR90 chromatin (or 100 μg of fractionated germ cells chromatin) and 5 μg pan anti-Kcr or anti-Kac antibody (Hawkins et al., 2010). ChIP-seq libraries for sequencing were prepared following Illumina protocols (Illumina, San Diego, CA) with minor modifications. Libraries for input samples were generated using 20 ng corresponding input chromatin. Briefly, ChIPed DNA was first blunted with END-IT DNA repair kit (Epicenter Biotechnology, Madison, WI) and then incubated with Klenow (exo-) (New England Biolabs, MA) and dATP to generate single base 3′-dA overhang. Illumina sequencing adaptor was then ligated to the resulting DNA, and followed by size selection (180-400bp) from a 8% acrylamide gel. This size-selection step was repeated after PCR amplification with DNA primers supplied by Illumina. Libraries were sequenced using Illumina GAII or HiSeq machine as per manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Spc_input
Data processing Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 (for IMR90 data) or mouse mm9 (for sperm cell data) genome build with a bowtie software package. Total mapped tags were paired down to unique, monoclonal tags. These are tags that mapped to one location in the genome and each sequence is represented once.
Submission date Oct 06, 2011
Last update date May 15, 2019
Contact name Fulai Jin
Phone 2163681811
Organization name Case Western Reserve University
Lab Fulai Jin
Street address 10900 Euclid Avenue
City Cleveland
State/province OH - OHIO
ZIP/Postal code 44106
Country USA
Platform ID GPL11002
Series (1)
GSE32663 Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification
SRA SRX099892
BioSample SAMN00737731
Named Annotation GSM810673_Spc.input.monoclonal.bed.gz

Supplementary file Size Download File type/resource
GSM810673_Spc.input.monoclonal.bed.gz 180.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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