 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 29, 2018 |
| Title |
Dmel_male_MLE_Input |
| Sample type |
SRA |
| |
|
| Source name |
third instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: White-eyed (w1118) Oregon-R
chip antibody: none
|
| Growth protocol |
Drosophila melanogaster were reared on a cornflour-molasses fruit fly medium [1l water, 12g agar-agar threads, 18g bakery yeast, 10g soya flour, 80g corn flour, 22g molasses, 80g malt extract, 2.4g 4-hydroxibenzoic acid methylester (Nipagin), 6.25ml propionic acid] at 25¡C, 70% relative humidity and 12 hr dark/12 hr light cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Larvae were dissected and the front part fixed at RT for 15 min with 1% or 0.2% Formaldehyde. Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using Phenol-Chloroform Extraction and Ethanol precipitation.
NEB Next Ultra II
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Paired-end 75 bp reads were mapped to dm6 with bowtie2 (Galaxy Version 2.3.0.1) using parameters: --sensitive, --end-to-end for histones and --sensitive --local for all other profiles. For Msl2 ChIP-seq, read-pairs with a minimal overlap of 10 bp were merged and Illumina adpters were trimmed using bbmerge (v7.3), resulting in small (≤140 bp) and large (>140 bp) fragments. Merged, single end reads and unmerged, paired-end reads were then mapped separately.
Peaks were called with MACS2 (Galaxy Version 2.1.1.20160309.0) on each replicated and merged using cat, BEDtools sort (Galaxy Version 2.27.0.0) followed by BEDtools merge with 10 bp option.
Coverage files were generated with deepTools2 (Galaxy Version 2.5.1.0.0) bamCompare, binsize of 2. Duplicate reads and reads with a mapping quality < 10 were removed, the X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H3, H4K16ac, H3K36me3, H4ac, H3ac; Input subtraction for Drosophila MSL2-Flag, untagged-Flag, MLE, MSL1, NSL1 (S2 cells), MSL2 (S2 cells); 1 x Coverage for Drosophila H4K16ac, H3K36me3, H3ac, H4ac shown in Figure 1d and 2a; mESC H4K16ac log2FC over H3.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigWig files of uniquely mapped reads, bed files of Msl2 peaks
|
| |
|
| Submission date |
Jan 30, 2018 |
| Last update date |
Jun 29, 2018 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23323 |
| Series (2) |
| GSE109898 |
Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [ChIP-seq Dmel] |
| GSE109901 |
Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals |
|
| Relations |
| BioSample |
SAMN08442050 |
| SRA |
SRX3632913 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
