|
| Status |
Public on Apr 05, 2019 |
| Title |
genome_dps_wce |
| Sample type |
SRA |
| |
|
| Source name |
ML83-63 cells
|
| Organism |
Drosophila pseudoobscura |
| Characteristics |
cell line: ML83-63 cells
treatment: None
chip antibody: None
|
| Treatment protocol |
None
|
| Growth protocol |
ML83-63 cells were cultured at 25C in M3+BPYE + 10% FCS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 250~500 bp. ~ 10 million cells was used for one ChIP-nexus.
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using NEBNext End repair module. A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
dp3 genome
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings. Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, normalized to reads per million and saved in BigWig format
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
|
| |
|
| Submission date |
Jan 11, 2019 |
| Last update date |
Apr 07, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
jbz@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Zeitlinger lab
|
| Street address |
1000 E 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL23885 |
| Series (1) |
| GSE116244 |
Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing |
|
| Relations |
| BioSample |
SAMN10724565 |
| SRA |
SRX5241034 |
