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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 26, 2016 |
| Title |
Control ATAC-seq replicate 4 |
| Sample type |
SRA |
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| Source name |
Control ATAC-seq, ESC
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| Organism |
Mus musculus |
| Characteristics |
strain: 46C (129/Ola strain)
cell line: ESC line 46C
transfection: control shRNA vector, 48h timepoint, replicate 2
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| Treatment protocol |
described in the SAMPLES section (experimental conditions)
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| Growth protocol |
Embryonic stem cells were cultured at 37°C, 5% CO2, on mitomycin C-inactivated mouse embryonic fibroblasts, in DMEM (Sigma) with 15% foetal bovine serum and leukemia inhibitory factor (LIF).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were collected, washed with cold PBS and resuspended in 50ul of ES buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2). Permeabilized cells were resuspended in 50 ul Transposase reaction (1X Tagmentation buffer, 1.0-1.5 ul Tn5 transposase enzyme (Illumina)) and incubated for 30min at 37°C. Subsequent steps of the protocol were performed as described in PMID: 24097267.
Transposed DNA was subjected to several round of amplification with Ad2 primer pairs (the reverse primer contains the index allowing subsequent multiplexing. Oligonucleotide sequences are available in PMID: 24097267). Libraries were next purified using a Qiagen MinElute kit and Ampure XP magnetic beads (1:1.6 ratio) to remove remaining non ligated adapters.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
library strategy: ATAC-seq
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| Data processing |
Basecalling was performed with RTA 1.18.64. Bcl conversions into Fastq and demultiplexing were performed using bcl2fastq version 1.8.3, Sequenced reads were trimmed for adaptor sequence and masked for low-complexity/low-quality sequence with Trimmomatic 0.32, then mapped to mm9 whole genome using bowtie v0.12.7 with parameters -a -m1 --best --strata -v2 p3
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using WigMaker 3 with default parameters; Scores represent the maximum number of reads overlapping in a 25 bp bin
Supplementary_files_format_and_content: BIGWIG files were generated with UCSC tools (v4) using WigToBigWig program
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| Submission date |
Nov 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthieu GERARD |
| E-mail(s) |
matthieu.gerard@cea.fr
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| Organization name |
CEA
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| Department |
I2BC
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| Lab |
Mammalian Epigenomics
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| Street address |
SBIGeM bldg 142
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91191 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE64825 |
Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells |
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| Relations |
| BioSample |
SAMN04271245 |
| SRA |
SRX1433598 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1941488_ATAC-seq_control_transfection_48h_timepoint_replicate_2_B00H5QM_shuf33M.bw |
332.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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