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| Status |
Public on Nov 29, 2009 |
| Title |
ES_Illumina.WCE |
| Sample type |
SRA |
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| Source name |
V6.5 embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
gender: male
genotype: 129SvJaexC57BL/6
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| Growth protocol |
Mouse ES cells (V6.5; male; genotype 129SvJaexC57BL/6; passages 10–15) were cultivated in 5% CO2 at 37 °C on irradiated MEFs in DMEM containing 15% FCS, ESGRO, penicillin/streptomycin, Glutamax, non-essential amino acids and 2-mercaptoethanol. ES Cells were passaged two to three times on 0.2% gelatin-coated plates to remove MEF contamination.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
whole cell extract
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| Data processing |
Alignment: Sequences were aligned to the mm8 reference genome using ARACHNE (Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome research 12, 177-189 (2002)), as described previously (Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007)). Sequences with more than a single best match in the reference genome were discarded. We also created a map of ‘unalignable’ genomic positions to which no unique 36 base read could be uniquely aligned due inherent sequence redundancy for consideration in downstream processing
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| Submission date |
Oct 27, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Alon Goren |
| E-mail(s) |
alon_g@mit.edu
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| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142-1401 |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE18699 |
Chromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA |
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| Relations |
| SRA |
SRX014809 |
| BioSample |
SAMN00006990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM465677_ES_Illumina.WCE.aligned.txt.gz |
53.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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