|
| Status |
Public on Feb 01, 2014 |
| Title |
CP190-WT1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: wild type Beaf
cell line: S2
chip antibody: CP190
|
| Treatment protocol |
S2 cells were stably transfected after precipitation with calcium of serial vectors (pUWG) carrying the neomycin resistance gene together with mutant-Beaf gene as compared to WT. G418 resistant colonies were taken after about 10 days under selection and then grown under normal conditions.
|
| Growth protocol |
S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/streptomycin (GIBCO, Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
S2 cells were treated with formaldehyde (0.8% final, 15 min) followed by standard sonication and extraction procedures of chromatin for ChIP analysis
ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 100 ng of starting precipitated DNA to generate sequencing libraries
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Late embryonic derived S2 cells from Drosophila melanogaster
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
ChIP peaks were analyzed using MACS (Feng et al., 2012) with respect to input control.
Genome_build: Flybase release 5.41 GCA_000001625.2
|
| |
|
| Submission date |
Dec 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Olivier Cuvier |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
LBME
|
| Lab |
Chromatin Dynamics & Cell proliferation
|
| Street address |
118 route de Narbonne
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE52886 |
Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq] |
| GSE52887 |
Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins |
|
| Relations |
| BioSample |
SAMN02429100 |
| SRA |
SRX385807 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1277517_ctrl_1_2L.wig.gz |
5.9 Mb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_2LHet.wig.gz |
48.7 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_2R.wig.gz |
5.5 Mb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_2RHet.wig.gz |
433.7 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_3L.wig.gz |
6.3 Mb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_3LHet.wig.gz |
405.1 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_3R.wig.gz |
7.4 Mb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_3RHet.wig.gz |
403.9 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_4.wig.gz |
318.4 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_U.wig.gz |
593.0 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_Uextra.wig.gz |
657.1 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_X.wig.gz |
5.3 Mb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_XHet.wig.gz |
31.0 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_YHet.wig.gz |
2.2 Kb |
(ftp)(http) |
WIG |
| GSM1277517_ctrl_1_dmel_mitochondrion_genome.wig.gz |
4.1 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
