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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 20, 2012 |
| Title |
Input DNA |
| Sample type |
SRA |
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| Source name |
input DNA
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| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
age: 30 days old
organ: testes
cell type: spermatids
chip-antibody: none
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| 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.
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| 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 ⼠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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
ANU/JCSMR/BRF facility
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| 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)
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| Submission date |
Jun 13, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Rohan Williams |
| E-mail(s) |
rohan.williams@anu.edu.au
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| Organization name |
ANU
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| Street address |
Garran Rd ACTON
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| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| 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 |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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