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| Status |
Public on Jul 01, 2017 |
| Title |
ChIP MSL2 S2 rep1 [Sample 86] |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2
gender: male
chip antibody: anti-MSL2 (Becker lab)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments (Covaris) were performed according to (Schauer et al., 2013) adapted to cell lines (Villa et al., 2016). Briefly, cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine, the cells were collected, washed and sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 min. MSL2 antibody was previously described in (Villa et al., 2012) and H4K16ac was acquired from Active Motif (#39167).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
ChIP-seq reads were mapped to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with default settings. Tag directories were generated by the Homer software package (Heinz et al., 2010). Coverage and Input normalized Bedgraph files were obtained using the "makeUCSCfile" tool with default settings.
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.
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| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
[email protected]
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| Organization name |
Helmholtz Zentrum München
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| Department |
Institute of Epigenetics and Stem Cells
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| Street address |
Feodor-Lynen-Straße 21
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| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
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| Platform ID |
GPL19951 |
| Series (1) |
| GSE94115 |
The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment |
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| Relations |
| BioSample |
SAMN06274356 |
| SRA |
SRX2520632 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2469507_141031_SL2Z_3d_MSL2.norm.bedGraph.gz |
4.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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