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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 09, 2015 |
| Title |
RNAseq G9aCntr4 |
| Sample type |
SRA |
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| Source name |
Epiblast E6.25
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| Organism |
Mus musculus |
| Characteristics |
background: mixed background
age: E6.25 dpc
genotype: G9a+/+
tissue/cell type: epiblast
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| Treatment protocol |
no treatment
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| Growth protocol |
see extra colum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single E6.25 epiblast were dissected as previously described (Tesar et al., 2007).
750 pg of RNA from each sample was amplified using Ovation RNA-seq System V2 (Nugen). Quality of cDNA was confirmed by measuring the expression of G9a, Ezh2, Oct4 and Nanog by qPCR . For every sample 1.5 μg of cDNA was sheared to ~230 bp using S220 Focused-ultrasonicator (Covaris). Fragmented cDNA was then concentrated using Qiagen Reaction Clean Up Kit (MinElute). 500 ng of each sample was used as input for library preparation using Encore Rapid DR Multiplex Library System (Nugen).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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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 |
GPL17021 |
| 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 |
SAMN03799368 |
| SRA |
SRX1074941 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1725722_G9a.cntr.4.counts.txt.gz |
312.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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