|
| Status |
Public on Jan 28, 2019 |
| Title |
Kc167_dsclamp_clamp-abcam_11 |
| Sample type |
SRA |
| |
|
| Source name |
Kc167 cells, dsCLAMP, clamp-abcam ChIP
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc167
treatment: dsCLAMP
chip antibody: clamp-abcam
|
| Treatment protocol |
10 million Kc167 cells were transfected with 5 ug of dsRNA (DRSC 29935) against Clamp by using Amexa cell line Nucleofector kit V (Lonza) and incubated 6 days at 25°C to obtain significant knockdown of Clamp.
|
| Growth protocol |
Kc167 cells-derived from Drosophila embryo were routinely maintained in CCM3 (Thermo Scientific HyClone, Logan, UT). The cells were maintained in monolayer at 25°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed as described previously (Matzat et al., 2012).
ChIP antibodies: clamp: Rabbit anti-CLAMP antibody (sdix, Cat no# 4988.00.02); clamp-abcam: Rabbit anti-CLAMP antibody (made through Abcam by Erica N. Larschan, Brown University); suhw: Guinea pig serum against Su(Hw) (Moshkovich and Lei, 2010 PMID: 21852534); mod: Rabbit serum against Mod(mdg4)2.2 (Van Bortle et al., 2012, PMID: 22722341); cp190: Rabbit serum against CP190 (Pai et al. 2004, PMID: 15574329).
ChIP-seq library was prepared as described previously (Matzat et al., 2012).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ib47_dsclamp_clamp-abcam
Processed data file: dsclamp_clamp-abcam.narrowPeak
|
| Data processing |
Reads were trimmed using cutadapt v1.8.1 with arguments --quality-cutoff 20 -a AGATCGGAAGAGC --minimum-length 25 --overlap 10
Trimmed reads were mapped with bowtie2 v2.2.9 with default arguments to the dm6 assembly.
Multimappers were removed from aligned reads with samtools v1.2 vew command with argument -q 20.
Duplicates were removed from mapped, uniquely-mapping reads with picard MarkDuplicates v2.9.2.
Macs2 v2.1.0.20150731 was used to call peaks by providing replicate Ips and inputs as multiple BAMs, effectively calling peaks on pooled samples, and using additional arguments -f BAM --gsize=dm
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: narrowPeak files of called peaks as output from macs2 peak-calling.
|
| |
|
| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Cameron Palmer |
| E-mail(s) |
palmercd@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Diabetes and Digestive and Kidney Diseases
|
| Lab |
Laboratory of Cellular and Developmental Biology
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE103601 |
The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: ChIP-seq of CP190, Su(Hw), Mod(mdg4) for genome-wide overlap with CLAMP |
| GSE118700 |
The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila |
|
| Relations |
| BioSample |
SAMN07614938 |
| SRA |
SRX3167261 |
