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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 16, 2015 |
| Title |
NRF1_CHIP_toSerum_2 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 159 (mixed 129-C57Bl/6)
genotype: WT
growth condition: adaptation from 2i back to serum (3 weeks)
chip antibody: NRF1 (Abcam, ab55744)
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| Growth protocol |
Mouse embryonic stem cells were cultivated without feeders on 0.2% gelatine-coated dishes in DMEM, supplemented with 15% fetal calf serum, 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol (37°C, 7% CO2). Serum-free cultivation was performed in N2B27 medium, supplemented with 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol as well as MEK inhibitor PD0325901 (1 µM) and GSK3 inhibitor CHIR99021 (3 µM), together known as 2i. For reversal between culturing conditions, cells were cultured for at least three weeks under the new conditions prior to performing downstream experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014).
Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata.
Bigwig files were generated by extending the reads to 200bp and calculating for each genomic position the read density normalized to one million reads in the library.
Genome_build: mm9
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| Submission date |
Apr 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anais Flore Bardet |
| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE67867 |
Competition between DNA methylation and transcription factors determines binding of NRF1 |
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| Relations |
| BioSample |
SAMN03482405 |
| SRA |
SRX994814 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1657382_NRF1_CHIP_toSerum_2.bw |
309.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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