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| Status |
Public on Dec 13, 2022 |
| Title |
ChIPSeq_H3K4me1_iMEF2_input |
| Sample type |
SRA |
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| Source name |
iMEF2
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| Organism |
Mus musculus |
| Characteristics |
cell line: iMEF2
chip antibody: none
treatment: untreated
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| Treatment protocol |
At day 0 cells were treated with 5 nM 4-Hydroxytamoxifen (+HOT) (Tocris, 3412) or with vehicle (-HOT, 100% ethanol). Thereafter cells were passaged when needed to maintain subconfluency or solely supplied with new medium with the addition of HOT or vehicle as before.
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| Growth protocol |
For the generation of immoralized fibroblast cultures (iMEF) the cells were infected with a retrovirus encoding an shRNA against p19Arf and a Blasticidin resistance gene used for the initial selection of infected cells (10 µg/ml Blasticidin, Invivogen, ant-bl). MEF cells were cultivated in DMEM (ThermoFisher Scientific, 61965059) supplemented with 10% heat-inactivated fetal bovine serum (FBS, ThermoFisher Scientific, 10270106) and 1% penicillin/streptomycin (ThermoFisher Scientific, 15070063).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
iMEF cells were treated with HOT or vehicle for 5 days and cross-linked with 1% formaldehyde in cell culture medium on a shaking platform for 10 min at room temperature (RT). The cross-linking reaction was quenched by adding glycine to 125 mM and incubation for another 5 min at RT. Adherent cells were washed with PBS twice and collected in PBS by scraping the cells from the dish. Cells were centrifuged at 380 x g for 5 min at 4°C and resuspended in 1 ml Lysis Buffer B (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 0.25% (v/v) Triton X-100) per 2 x 107 cells and centrifuged. To the pellet 1 ml Lysis Buffer C (10 mM Hepes pH 6.5, 10 mM EDTA, 0.5 M EGTA, 200 mM NaCl) was added per 2 x 107 cells, followed by an incubation on ice for 10 min. After a further centrifugation step, disruption of the pelleted nuclei was performed in 200 μl lysis buffer D (50 mM Tris pH 8, 10 mM EDTA, 1% (w/v) SDS, protease inhibitor cocktail (1xPIC, Merck, P8340) per 5 x 106 MEF cells for 30 min at 15°C. 200 μl aliquots were sonicated for a minimum of 10 cycles using a Bioruptor Pico (Diagenode) with 30-second on-off-cycles to achieve DNA fragment lengths of about 800 bp or 300 bp for ChIP-qPCR or ChIP-seq, respectively. The size distribution of the resulting DNA fragments was assessed by agarose gel electrophoresis. To remove cell debris, lysates were centrifuged for 10 min at 10,000 x g (15°C), the supernatants pooled, and DNA concentrations were measured using a NanoDrop 1000 device (Peqlab). ChIP assays were performed using the OneDay ChIP Kit from Diagenode (C01010080) according to the manufacturer’s instructions. To capture protein-DNA complexes, 42 μl of Protein A beads per sample were pre-incubated in 1 x ChIP buffer for 2 hours at 4 °C with 2 μg of specific antibody or rabbit IgG (provided by the kit). The sheared chromatin (10 – 100 µg) was diluted 4.7-fold with 1 x ChIP buffer, setting aside 1/10 of the diluted chromatin for the input control, and mixed with the pre-incubated beads for 30 min at 4°C. Subsequently, the chromatin-antibody-bead complexes were washed three times with 1 x ChIP buffer and taken up in DNA purifying slurry. The diluted input control chromatin was precipitated by the addition of 5 volumes 100% ethanol and centrifuged at 16,000 x g, 4°C for 10 min. The dried pellets were resuspended in RNase-free H2O and mixed with DNA purifying slurry. The DNA of all samples was reverse crosslinked and further purified according to the manual.
The libraries were prepared using the Next Ultra II kit (New England BioLabs) and the sequencing was performed as single reads for 75 cycles with a NextSeq 500/550 High Output kit v2 (Illumina) according to the manufacturers recommendations.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Alignment by BWA
Filtering by Samtools
Narrow peaks by Macs2
BigWig files by Deeptools bamCoverage
Deseq2 for differential analysis
Assembly: mm9
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| Submission date |
May 31, 2022 |
| Last update date |
Dec 13, 2022 |
| Contact name |
Mirna Barsoum |
| E-mail(s) |
mirna.barsoum@rwth-aachen.de
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| Phone |
00492418088915
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| Organization name |
Uniklinik RWTH Aachen
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| Department |
Institute of Biochemistry and Molecular Biology
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| Lab |
Bernhard Lüscher
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| Street address |
Pauwelsstrasse 30
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| City |
Aachen |
| State/province |
North Rhine Westphalia |
| ZIP/Postal code |
52074 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE205232 |
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters [ChIP-seq H3K4me1,me3] |
| GSE205233 |
Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters. |
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| Relations |
| BioSample |
SAMN28794781 |
| SRA |
SRX15540083 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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