|
| Status |
Public on Jan 08, 2018 |
| Title |
Dsim_CidM_10m_long_(20151015_PT_Ds_ML82_10m_input) |
| Sample type |
SRA |
| |
|
| Source name |
ML82-19a cells
|
| Organism |
Drosophila simulans |
| Characteristics |
cell type: ML82-19a cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila_ChIP_protocol.rtf
PMID 25827087
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP Drosophila simulans chromatin 10 min
|
| Data processing |
1. We trimmed the 250bp single-end reads with trim_galore/cutadapt using parameters "-f fastq -e 0.1 -q 20 -o 3 -a AGATCGGAAGAGC". The supplementary fasta file contains the trimmed reads. 2. We clustered the trimmed reads with cdhit. 3. We looked for short specific alpha satellite sequences in the trimmed reads with grep.
|
| |
|
| Submission date |
Oct 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL22293 |
| Series (1) |
| GSE105100 |
Simple and Complex Centromeric Satellites in Drosophila Sibling Species |
|
| Relations |
| BioSample |
SAMN07796393 |
| SRA |
SRX3293415 |
