|
| Status |
Public on Sep 14, 2016 |
| Title |
Pc_ChIP-seq_in_wild-type_cells_replicate1 [part 3] |
| Sample type |
SRA |
| |
|
| Source name |
Cultured cells, WT, Pc ChIP
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Ras3
mutation: none
chip antibody: Pc from Poux et al., 2001
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP was done as described in Schwartz et al., 2006.
Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (New England BioLabs) following the manufacturer instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Base calling and quality score assignment were done with built-in Real-time analysis (RTA) software (Illumina).
ChIP-seq reads were aligned to the dm3 genome assembly using bowtie2 using the default parameters.
The SAM files with aligned reads were tested for strand cross-correlation using pyicos.
The SAM files were converted to wig format using pyicos. During conversion, the reads were extended based on the results of the above cross-correlation analysis.
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated using pyicos; Scores represent the number of reads overlapping each genomic position.
|
| |
|
| Submission date |
Jun 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuri B Schwartz |
| Organization name |
Umeå University
|
| Street address |
Byggnad 6L, NUS
|
| City |
Umeå |
| ZIP/Postal code |
90187 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16479 |
| Series (2) |
| GSE83247 |
Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 3) |
| GSE83248 |
Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements |
|
| Relations |
| BioSample |
SAMN05231713 |
| SRA |
SRX1837979 |
