|
| Status |
Public on Aug 01, 2013 |
| Title |
PolII ChIP-seq from Control-KD |
| Sample type |
SRA |
| |
|
| Source name |
EGFP-KD_PolII ChIP-seq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
transfected with: siRNA against EGFP
chip antibody: anti-Pol II antibody 8WG16
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-56767
chip antibody lot #: A1712
|
| Treatment protocol |
OSC were transfected once with siRNAs and analyzed after 2 days
|
| Growth protocol |
Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinking chomatin was sheared to 200bp using a Covaris S2 ultrasonicators, immunoprecipitated using anti-Pol II antibody 8WG16 (Santa Cruz). After reversing the cross-linking, samples were treated with RNase A and then DNA was recovered.
The deep sequencing libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Sample 7
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence using cutadapt software, then mapped to dm3 whole genome and repbase transposable elements using bowtie2 v2.0.0 with default parameters
For calculation of Reads Per Million mapped reads (RPM) of transposable elements, dm3 genome and repbase transposable element mapping result was processed using in-house perl script. In short, number of reads falling in the transposable elements were counted and normalized by the count of genome mapped reads.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files include tag density for each transposable element (normalized by Reads Per Million mapped reads (RPM))
|
| |
|
| Submission date |
Jun 26, 2013 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Molecular Biology
|
| Lab |
Siomi Lab
|
| Street address |
35 Shinanomachi, Shinjuku-ku,
|
| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE47006 |
Expression profile and RNA Polymerase II occupancy of transposable elements among knock down of the piRNA pathway components in OSCs |
|
| Relations |
| BioSample |
SAMN02213900 |
| SRA |
SRX315132 |
