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| Status |
Public on Apr 18, 2019 |
| Title |
ATAC_addbackMut_2 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 129S6/SvEvTac
tissue: mouse embryonic stem cells
genotype: Snf2h ko, Snf2h mutant add-back
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| Treatment protocol |
To induce deletion of Brg1 (Brg1 fl/fl ECSs), cells were treated with 1μM 4-hydroxytamoxifen for 72h. Correct depletion of Brg1 was checked by genotyping and Western Blot.
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| Growth protocol |
We cultured mouse ES cells as previously described (Mohn et al., 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and Non-essential amino acids (Gibco), beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). Differentiation of ES cells to neuronal progenitors was performed as previously described (Bibel et al., 2004; Mohn et al., 2008). Cell were grown on plates coated with 0.2% gelatin (Sigma), with the exception of Snf2h ko and ATPase mutant re-expression cell line. Those were grown on MEF feeder cells for (at least) first two passages after thawing. Brg1fl/fl ESCs were previously described (Ho et al., Nat. Cell Biol. 2011).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed according to the previously described protocol (Buenrostro et al., 2015) with modifications. Briefly, 50,000 cells were washed with cold PBS and resuspended in lysis buffer to extract nuclei. The nuclei were cold-centrifuged at 500 x g for 10 min. The nuclei pellet was incubated with transposition reaction buffer for 30 min. at 37 °C. The DNA was purified using the PCR Purification Kit (Qiagen).
The eluted transposed DNA was submitted to the PCR using Q5 High-Fidelity Polymerase (NEB). DNA was amplified with 12 cycles of PCR.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (NextSeq 500) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Paired ATAC-seq reads were first trimmed to remove adaptor sequences using cutadapt version 1.15 (Marcel Martin. EMBnet.journal, 17(1):10-12, 2011) with -a CTGTCTCTTATA -m 10 --length=51. Trimmed reads were aligned to the genome using bowtie2 version 2.3.0 ( Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359). with --sensitive-local --minins 0 --maxins 1000 –dovetail and converted to bam format.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig files were generated using the qExportWig function from the QuasR package (Gaidatzis et al, Bioinformatics 2015) version 1.18.0 with default parameters except scaling=1e6, binsize=100 and pairedAsSingle=TRUE. The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.
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| Submission date |
Mar 21, 2018 |
| Last update date |
Apr 18, 2019 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE112130 |
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ATAC-seq data sets) |
| GSE112136 |
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors |
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| Relations |
| BioSample |
SAMN08765543 |
| SRA |
SRX3827025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3058318_ATAC_addbackMut_2.scaled_0100.wig.gz |
11.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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