|
| Status |
Public on Nov 27, 2019 |
| Title |
Wagner_Dmel_DL1_Input_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila DL1 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: DL1 cells
treatment: untreated
chip antibody: none
|
| Treatment protocol |
ChIP-seq experiments: ChIP-seq libraries were prepared as described in (Henriques et al. 2018) using the NEBNext Ultra II DNA library kit (NEB) following manufacturer's instructions.
|
| Growth protocol |
Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq experiments: Sonicated genomic DNA was extracted after IP with respective antibody, Phenol-Chloform extracted and ethanol precipitated.
ChIP-seq experiments: NEBNext Ultra II DNA library kit (NEB) on IPed genomic DNA following manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
ChIPseq read pairs containing one or more members with mean quality score <20 were filtered
ChIP-seq mapped using bowtie 1.2.2 retaining uniquely mapped pairs only, allowing 2 mismatches
ChIP-seq bedGraphs were generated by filtering fragments of length <75 and >500, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3
Supplementary_files_format_and_content: ChIP-seq: bedGraph containing combined count of fragment centers for all replicates
|
| |
|
| Submission date |
Apr 10, 2019 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Karen Adelman |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard Medical School
|
| Department |
Biological Chemistry and Molecular Pharmacology
|
| Street address |
45 Shattuck St. LHRRB-201a
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE114467 |
The Integrator complex terminates promoter-proximal transcription at protein-coding genes |
|
| Relations |
| BioSample |
SAMN11391707 |
| SRA |
SRX5664976 |
