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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 11, 2014 |
| Title |
H3S28ph_control_untreated_replicate2 |
| Sample type |
SRA |
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| Source name |
H3S28ph, Serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2
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| Organism |
Mus musculus |
| Characteristics |
cell line: Swiss 3T3
cell type: fibroblasts
antibody: H3S28ph (Sigma, cat number H9908)
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| Treatment protocol |
Serum-straved (72 h) mouse 3T3 fibroblasts we treated with 188.5 nM of anisomycin (Sigma) for 1 h.
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| Growth protocol |
Swiss 3T3 fibroblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% (vol/vol) fetal calf serum (FCS) in the presence of Penicillin and Streptomycin. The cells were serum-deprived for 72 h using DMEM containing 0.2% FCS (vol/vol).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunorecipitation was performed as described (Hauser et al., Molecular and Cellular Biology, 2002) with the following modifications: chromatin-antibody complexes were pulled down using Dynabeads® protein A or G beads (Invitrogen). The following antibodies were used in the study: H3S28ph (Sigma, cat number H9908), H3K9ac (Millipore, cat number 06-942), H3K4me3 (Millipore, cat number 07-473), RNAPIIS5ph (Bethyl, cat number A300-655A), RNAPIIS2ph (Bethyl, cat number A300-654A).
Immunoprecipitated DNA as well as input samples were subjected to library preparation protocol using NEBNext® Library Prep Reagent Set for Illumina (NEB). The following TrueSeq barcodes were used for the input samples: sample input_0h TTAGGC, sample input_1hA TGACCA.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
H3S28ph ChIP in serum-starved (72h) Swiss 3T3 fibroblasts, replicate 2
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| Data processing |
Basecalling with Bustard version 1.8.0 (samples H3S28ph_0h_rep1, H3S28ph_1hA_rep1, RNAPIIS2ph_0h_rep2, H3K9ac_0h_rep1, H3K9ac_1hA_rep1) or Bustard version 1.9.4 (samples H3K9ac_0h_rep2, H3K9ac_1hA_rep2) or RTA version 1.8.70.0 (samples RNAPIIS5ph_0h_rep1, RNAPIIS5ph_1hA_rep1, RNAPIIS2ph_0h_rep1, RNAPIIS2ph_1hA_rep1, RNAPIIS5ph_0h_rep2, RNAPIIS5ph_1hA_rep2, RNAPIIS2ph_1hA_rep2, H3K4me3_0h_rep1, H3K4me3_1hA_rep1, H3S28ph_0h_rep2, H3S28ph_1hA_rep2) or RTA version 1.13.48.0 (samples input_0h, input_1hA, H3K4me3_0h_rep2, H3K4me3_1hA_rep2).
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie version 12.5. Up to two mismatches were allowed. Reads that map to only one genomic location were retained. Reads derived from the input samples were trimmed to 36bp prior to the mapping.
Duplicated reads were removed and unique reads were extended to the length of 200 bp (average DNA fragment size of after chromatin sanitation). Then a bedgraph file (normalized to the total library size) using genomeCoverageBed -bga from BedTools was generated. Chromosome size information was downloaded from UCSC. BigWig files were generated from bedgraph files using bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: read desity at genomic positions (bigWig format)
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| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Anna Sawicka |
| E-mail(s) |
anna.sawicka@mpibpc.mpg.de
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| Organization name |
Max Planck Institure for Biophysical Chemistry
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| Department |
Dep. of Molecular Biology
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| Lab |
Cramer
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| Street address |
Am Fassberg 11
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| City |
Goettingen |
| ZIP/Postal code |
37077 |
| Country |
Germany |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE55774 |
Stress-induced signaling to the nucleosome in serum deprived mouse fibroblasts. |
| GSE55784 |
Genome-wide analysis of stress response in mouse fibroblasts |
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| Relations |
| BioSample |
SAMN02687762 |
| SRA |
SRX484309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1345930_H3S28ph_0h_rep2.bw |
51.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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