 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 01, 2017 |
| Title |
Hi-C female 1 [Sample 1] |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryo
strain/background: y[1]w[67c23]/Dp(1;Y)y[+],P{w[+mC]=ActGFP}SH1
age: 16-18hr
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C methods. Embryo sorting (female/male) was based on a Y chromosomal GFP reporter (y[1]w[67c23]/Dp(1;Y)y[+],P{w[+mC]=ActGFP}SH1) described in (Hayashi, 2010). The flies were raised in standard cornmeal yeast extract media at 25°C. Embryos were collected in 0.03% Triton X-100, 0.4% NaCl 16-18 hr after egg laying, then de-chorionated for 5 min in fresh bleach. ~3000 GFP+ (male) and GFP- (female) embryos each were sorted with a Union Biometra COPAS Large Particle Sorter, and then processed for Hi-C as in (Sexton et al., 2012).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired-end reads were mapped separately to the reference genome (BDGP 5.74) using bowtie2 (2.0.2) with "-local" settings. Hi-C data processing and analysis steps were carried out using the Homer software package (Heinz et al., 2010). Paired-end tag directories were generated by pooling technical (sequencing) replicates. Reads were extensively filtered with the recommended parameters, i.e. "-tbp 1 -removePEbg -fragLength 500 -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5". Background models, coverage-normalized ("-simpleNorm") as well as coverage- and distance-normalized correlation matrices ("-corr") were created using various resolutions ("-res") and smoothing ("-superRes") windows, from which 10 kb resolution with 50 kb smoothing was chosen for downstream analysis. The genome was divided into two compartments based on principal component analysis of the correlation matrix ("runHiCpca.pl"), where H4K16ac regions (peaks) served as a seed to define the sign of the PC1 values (processed data file).
Genome_build: BDGP 5.74
Supplementary_files_format_and_content: Bedgraph format. Hi-C PC1 values; 4C-seq, ChIP-seq and RNA-seq signals.
|
| |
|
| Submission date |
Jan 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Straße 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE94115 |
The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment |
|
| Relations |
| BioSample |
SAMN06274391 |
| SRA |
SRX2520547 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2469422_female1.pcaOut.r10k.s50k.PC1.bedGraph.gz |
225.3 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
