 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 08, 2015 |
| Title |
ATR_PR-Set7_RNAi_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Kc167
|
| Organism |
Drosophila melanogaster |
| Characteristics |
experiment: early origin
chip antibody: Mouse anti-BrdU (BD Biosciences #555627)
RNAi treatment: ATR & PR-Set7
replicate: 2
|
| Growth protocol |
Drosophila Kc167 cells were cultured at 25℃ in Schneider’s Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Gemini) and 1% penicillin/streptomycin/glutamine (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In early origin experiments, chromatin was isolated and BrdU was immunoprecipted as described in (Ryba et al., Nat Protoc, 2011). H4K20me1 and γ-H2Av ChIP were performed as described in (MacAlpine et al., Genome Research, 2010).
Sequencing libraries were prepared using Illumina's TruSeq protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 30 -m 1 --best --strata -y.
RPKM (reads per thousand kb, per million mappable reads) was determined with RSamtools and GenomicRanges packages in R. For early origin and H4K20me1 experiments, genome is divided into 10 kb bins stepping every 1 kb. For γ-H2Av experiment, genome is divided into nonoverlapping 5 kb bins.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: csv files with columns chr, start,end,RPKM.
|
| |
|
| Submission date |
Oct 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Alan Belsky |
| E-mail(s) |
jason.belsky@duke.edu
|
| Organization name |
Duke University
|
| Department |
Pharmacology and Cancer Biology
|
| Lab |
David MacAlpine Lab
|
| Street address |
LSRC Room C333
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE73668 |
Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila |
|
| Relations |
| BioSample |
SAMN04126436 |
| SRA |
SRX1299930 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1900402_ATR_PR-Set7_RNAi_rep2_Sample8.csv.gz |
771.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
