|
| Status |
Public on Feb 09, 2013 |
| Title |
ChIP-seq input Tj-GAL4->piwi |
| Sample type |
SRA |
| |
|
| Source name |
ChIP-seq input Tj-GAL4->piwi
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovaries
age: 3-5 days
chip antibody: none (input)
|
| Treatment protocol |
ovaries were dissected on ice
|
| Growth protocol |
flies were kept at 25 degrees
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: chromatin from 50 ovaries was fragmented on Bioruptor during 14 min (2 cycles, 7 min each), an aliquot was kept as "input", the rest was used for ChIP with H3K9me-ab. The detailed protocols can be found in the Rozhkov et al, 2013
The detailed methods described in the Rozhkov et al. 2013
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For ChIPseq libraries, peaks were identified using SICER (version 1.1) and the following parameters: redundancy threshold =1, fragment size = 250, window size = 500, gap size = 500, FDR = 0.05, effective genome size = 0.72
Genome_build: dm3
|
| |
|
| Submission date |
Jan 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Nikolay V Rozhkov |
| E-mail(s) |
nik.rozhkov@gmail.com, rozhkov@cshl.edu
|
| Organization name |
CSHL
|
| Lab |
Hannon
|
| Street address |
1 Bungtown Rd.
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE43360 |
Multiple roles for Piwi in silencing Drosophila transposons |
|
| Relations |
| SRA |
SRX215625 |
| BioSample |
SAMN01883287 |
