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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 09, 2015 |
Title |
EpiLC Input nChIPseq1 |
Sample type |
SRA |
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Source name |
EpiLC
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Organism |
Mus musculus |
Characteristics |
background: mixed background age: 2 days post induction genotype: deltaPE-Oct4-EGFP tissue/cell type: epiblast-like 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 |
EpiLCs were induced for 48h from 2i/LIF ESCs as previously described (Hayashi et al., 2011). 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 2000 |
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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 |
GPL13112 |
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 |
SAMN03799334 |
SRA |
SRX1074907 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1725688_EpiLC.H3K27me3.nchip.input.1.bedgraph.gz |
232.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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