|
| Status |
Public on Apr 17, 2017 |
| Title |
TFIIA ChIP-seq Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Kc167 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc167 cells
chip antibody: anti-TFIIA rabbit polyclonal, Kadonaga lab
illumina multiplex barcode: TGACCA
|
| Growth protocol |
grown at 25C in HyClone SFX-Insect Cell Culture Media
|
| 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 300~500 bp. ~ 20 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 HiSeq 2500 |
| |
|
| Data processing |
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
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
|
| |
|
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17275 |
| Series (2) |
| GSE85740 |
Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-Seq] |
| GSE85741 |
Paused RNA polymerase II inhibits new transcriptional initiation |
|
| Relations |
| BioSample |
SAMN05583750 |
| SRA |
SRX2033489 |
