|
| Status |
Public on Feb 01, 2014 |
| Title |
Beaf-32 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Late embryonic derived S2 cells
chip antibody: anti-Beaf32
|
| Treatment protocol |
S2 cells were treated with formaldehyde followed by standard sonication procedures
|
| 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 |
Standard chromatin extraction procedures were utilized for ChIP analysis using anti-Beaf32 or anti-IgG control antibodies. Antibodies were generated in the lab (Affinity purified, rabbit antibodies raised against 18AA-long C-terminal peptides.
ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 1.2 ng of starting precipitated DNA to generate sequencing libraries
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 1
|
| 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 IgG control.
Genome_build: Flybase release 5.41 GCA_000001625.2
|
| |
|
| Submission date |
Dec 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Olivier Cuvier |
| E-mail(s) |
olivier.cuvier@gmail.com
|
| 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 |
GPL9061 |
| Series (2) |
| GSE52887 |
Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins |
| GSE52962 |
Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq] |
|
| Relations |
| BioSample |
SAMN02434686 |
| SRA |
SRX386677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1278639_ChIPseq_beaf32_2L.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_2LHet.wig.gz |
6.8 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_2R.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_2RHet.wig.gz |
56.6 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_3L.wig.gz |
1.9 Mb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_3LHet.wig.gz |
47.0 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_3R.wig.gz |
2.3 Mb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_3RHet.wig.gz |
41.2 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_4.wig.gz |
92.5 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_U.wig.gz |
54.3 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_Uextra.wig.gz |
46.2 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_X.wig.gz |
1.3 Mb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_XHet.wig.gz |
5.0 Kb |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_YHet.wig.gz |
773 b |
(ftp)(http) |
WIG |
| GSM1278639_ChIPseq_beaf32_dmel_mitochondrion_genome.wig.gz |
1.3 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
