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Sample GSM740676 Query DataSets for GSM740676
Status Public on Jan 20, 2012
Title Input DNA
Sample type SRA
Source name input DNA
Organism Mus musculus
Characteristics strain: Balb/c
age: 30 days old
organ: testes
cell type: spermatids
chip-antibody: none
Growth protocol Testis tubules from wild type Balb/c mice were placed in 1-2 ml of ice-cold PBS-GL buffer (PBS supplemented with 5.6mM D-glucose, 5.4mM DL-lactate, 0.5mM DTT, 0.2mM PMSF, and protease inhibitor cocktail (Roche)) and dissected with scissors followed by homogenisation with 3-4 strokes in a Dounce homogeniser (pestle type A, cell integrity monitored by microscopy). The cellular mixture was filtered through a 70µm cell strainer to obtain a single cell suspension.
Extracted molecule genomic DNA
Extraction protocol The nuclear extract was digested for 55-65 minutes at 37°C with Micrococcal nuclease (New England Biolabs; 30 units per 220 μl of extract) to obtain ∼ 80% mononucleosomes. Following centrifugation at 10,000g for 5 min, the supernatant (S1) and the resuspended pellet (S2) were dialysed against 10mM Tris, 1mM EDTA, 0.5mM EGTA, pH 7.6, overnight at 4°C. The S1 and S2 supernatants were combined and dialysed against 10mM Tris, 1mM EDTA, 0.5mM EGTA, 4% glycerol, pH 7.6, aliquoted and stored at -80°C. Histone-DNA complexes were isolated with antibody.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description ANU/JCSMR/BRF facility
Data processing A custom pipeline for processing Illumina sequence data is employed, referred to as ChipPy and implemented in the Python programming language (version 2.7), as an extension of the PyCogent genomic biology library. Critical key components of this pipeline were external alignment algorithms (Bowtie version 0.12.5, 64-bit) and database engines (ENSEMBL release 58). All software is available on request from the authors. (Processed data genome build : NCBI m37)
Submission date Jun 13, 2011
Last update date May 15, 2019
Contact name Rohan Williams
Organization name ANU
Street address Garran Rd ACTON
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
Platform ID GPL11002
Series (2)
GSE29913 Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]
GSE29916 Functional studies of a H2A.Bbd-like histone variant in mouse spermatogenesis
SRA SRX076065
BioSample SAMN00627018

Supplementary file Size Download File type/resource
GSM740676_30do_Input_processed.tar.gz 47.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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