|
| Status |
Public on Aug 01, 2016 |
| Title |
S2_C646_10minCBPIn |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: cell culture
assay: PRO-seq
chip antibody: N/A
|
| Extracted molecule |
other |
| Extraction protocol |
Nuclei were isolated for PRO-seq and run-on reactions were performed with biotinylated nucleotides.
PRO-seq libraries were performed according to the paper: Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. PMID: 23430654.
OTHER (PRO-seq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nascent RNA
|
| Data processing |
PRO-seq: adapters were removed and the reads were trimmed to 36bp. Reverse complement of reads were generated.
PRO-seq: reads were first mapped to ribosomal genome and anything that did not map to ribosomal genome were mapped to rest of the genome using mm10. The bedgraph files were normalized with the custom normalization approach as discribed in the paper and the bigWig files were generated from the normalized bedgraph files.
Genome_build: dm3
Supplementary_files_format_and_content: bigWig for PRO-seq
|
| |
|
| Submission date |
May 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dig Bijay Mahat |
| E-mail(s) |
[email protected]
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology & Genetics
|
| Lab |
John Lis
|
| Street address |
526 campus Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE81649 |
CBP regulates promoter-proximal RNA polymerase II |
|
| Relations |
| BioSample |
SAMN05064365 |
| SRA |
SRX1775534 |
