|
| Status |
Public on Dec 01, 2019 |
| Title |
4C-seq: gfp RNAi CES viewpoint1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
4C-seq: gfp RNAi CES viewpoint1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line background: S2
genotype/variation: gfp RNAi
primary restriction enzyme: DpnII
secondary restriction enzyme: NlaIII
|
| Treatment protocol |
RNAi treatment for 6 days at 25C
|
| Growth protocol |
S2 cells were maintained at 25C in Gibco Schneider's media supplemnted with 10% heat-inactivated FBS and 1.4X antibiotic-antimycotic
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C-seq was carried out as described by Helm et al (2014) with few modifications.
4C-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3_GFP_CES1_preprocessed_rep1
|
| Data processing |
Library strategy: 4C-seq
Sequencing reads corresponding to the reading primer were aligned to a reduced genome derived from dm6 unique sequences adjacent to restriction enzyme sites using Bowtie2 with the following parameters: -N 0 -5 24 -3 101 --very-sensitive.
Aligned reads were then processed as described in Raviram et al (2016) for use with the 4C-Ker pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bedGraph files contain normalized read counts (cis)
|
| |
|
| Submission date |
May 01, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Erica Larschan |
| E-mail(s) |
Erica_Larschan@brown.edu
|
| Organization name |
Brown University
|
| Street address |
185 Meeting St.
|
| City |
Providence |
| ZIP/Postal code |
02912 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE130544 |
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome [4C-seq] |
| GSE130546 |
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome |
|
| Relations |
| BioSample |
SAMN11547188 |
| SRA |
SRX5773202 |
