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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 09, 2015 |
| Title |
ESC Input nChIPseq1 |
| Sample type |
SRA |
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| Source name |
ESC
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| Organism |
Mus musculus |
| Characteristics |
background: mixed background
genotype: deltaPE-Oct4-EGFP
tissue/cell type: 2i/LIF embryonic stem cells
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| Treatment protocol |
no treatment
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| Growth protocol |
see extra colum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cultured in N2B27 2i/LIF conditions on gelatin (Ying et al., 2008) supplemented with 1% KSR.
20 ng of immunoprecipitated or input DNA was used for library preparation using Ovation Ultralow DR Multiplex System (0331, Nugen). Once prepared library DNA was resolved on a 2% agarose gel and the mononucleosome fractions were isolated
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
ChIP-seq reads were extended to 250nt for lcChIP and 150nt or 300nt for H3K27me3 and H3K9me2 nChIP respectively. Reads were aligned to the mouse reference genome (GRCm38/mm10) using bowtie with parameters –m 2 –v 0 (Langmead et al., 2009). Genome-wide ChIP vs. Input profiles were normalized by the total number of mapped reads per 200 nt (RPKM). In analogy, ChIP-seq vs. Input counts on promoters or gene bodies were normalized by the total number of mapped reads and by size (RPKM).
RNA-seq reads were all trimmed to 40nt and then adapter- and quality-trimmed, and aligned with Tophat2 (Kim et al., 2013) against the mouse reference (GRCm38/mm10) genome. Read counts per ENSEMBL were obtained by htseq-count (Anders et al., 2014).
Genome_build: GRCm38/mm10
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| Submission date |
Jun 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
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| Department |
Gurdon Institute
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE70355 |
Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development |
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| Relations |
| BioSample |
SAMN03799372 |
| SRA |
SRX1074945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1725726_ESC.H3K27me3.nchip.input.1.bedgraph.gz |
151.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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