|
| Status |
Public on Mar 13, 2020 |
| Title |
input DNA Dicer2 kd H3K9me3 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: input
genotype/variation: Dicer2 kd
cell line: S2 cells
passages: E20-24h
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP sequencing, DNA libraries were constructed using the NEBNext® UltraTM II DNA Library Prep kit (NEB, USA) following manufacturer’s recommendations. After end Repair, 5 ́ phosphorylation and dA-Tailing of purified DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated and he library fragments were purified with SPRIselect sample purification beads (NEB, USA). At last, PCR products were purified, and library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced at the Annoroad Gene Technology (Beijing, China) on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Clean reads were mapped to the reference Drosophila genome (dm6) using Bowtie2.
Enriched peaks were detected by MACS2 with input data as control using the parameters -f BAMPE --nomodel --keep-dup all --broad.
The wig files of each chromatin mark ChIP-seq dataset was obtained by using bamCoverage tools from Deeptools with the parameters: --binSize 1000, --normalizeTo1x 142573017 and --ignoreForNormalization chrM.
Genome_build: dm6
|
| |
|
| Submission date |
Jul 15, 2019 |
| Last update date |
Mar 14, 2020 |
| Contact name |
Yajing Hao |
| E-mail(s) |
yahao@health.ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Dept. of Cellular and Molecular Medicine
|
| Lab |
Professor of Xiang-Dong Fu
|
| Street address |
George Palade Laboratories 9500 Gilman Drive, Room 217
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL23702 |
| Series (1) |
| GSE134307 |
Global studies of repeat RNAs on heterochromatin regions in Drosophila S2 cells |
|
| Relations |
| BioSample |
SAMN12277194 |
| SRA |
SRX6448061 |
