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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 09, 2011 |
| Title |
NP_H3K4me1_ChIPseq |
| Sample type |
SRA |
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| Source name |
Neural progenitor cells
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| Organism |
Mus musculus |
| Characteristics |
strain: Mixed (129-C57Bl/6)
cell type: ES-derived neural progenitor cells
antibody: H3K4me1
antibody vendor: Abcam
antibody catalog#: ab8895
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| Growth protocol |
Wild-type embryonic stem cells (129-C57Bl/6) were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) assay for CTCF was performed according to the Upstate protocol. ChIP assay for REST was performed as previously described (Koch et al., 2007). ChIP experiments for Pax6, PolII and monomethylated H3K4 (H3K4me1) were performed as previously described (Weber et al., 2007). The antibodies used were: anti-monomethyl-H3K4(Abcam #ab8895), anti-CTCF(SantaCruz #15914), anti-PolII(), anti-REST (Santa Cruz #H-290)., anti-Pax6(Covance PRB-278P). ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/80 of ChIP or 20ng of input chromatin per PCR reaction. H3K4me1, CTCF, PolII and REST ChIP-seq libraries for Illumina sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illuminaâs instructions and sequenced on the Genome Analyzer 2 following the manufacturerâs protocols. Pax6 ChIP samples were amplified using the WGA2 kit (Sigma) and hybridized to a custom tiling microarray (NimbleGen Systems Inc.).
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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 |
Chromatin IP against H3K4me1
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| Data processing |
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
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| Submission date |
Sep 01, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE30203 |
DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP-seq]. |
| GSE30206 |
DNA binding factors shape the mouse methylome at distal regulatory regions. |
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| Relations |
| SRA |
SRX095620 |
| BioSample |
SAMN00715288 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM789450_ChIPseq_H3K4me1_NP.wig.gz |
24.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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