|
| Status |
Public on Aug 29, 2014 |
| Title |
H3K9ac_HeLa_shCtr_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
stable expression of shrna: shCtr1
|
| Growth protocol |
HeLa cells were grown in 15 cm Petri-dishes (medium: DMEM, 1g/l glucose + 5%FCS + Gentamicin).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HeLa cells were fixed with formaldehyde, chromatin was extracted after sonication of nuclei and H3K9ac or H2Bub-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to the Illumina ChIP-seq protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FASTQ files have been generated using CASAVA v1.8.2.
ChIP-seq reads were aligned to the hg19 genome assembly using the Bowtie aligner 0.12.8.
Wig files were generated by WigMaker3, an in-house program developed by the microarray and sequencing platform of the IGBMC.
For each pair of ChIP-seq datasets that are compared in this study (shCtrl vs shATXN7L3 (H2Bub) and shCtrl vs shADA3 (H3K9ac)), Wig files were generated from normalized BED files with the same number of aligned reads in large intergenic regions.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files (for each sample, aligned sequences were extended to 200 bp from their 3' end, and allocated into 25 bp bins)
|
| |
|
| Submission date |
Dec 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Didier Devys |
| E-mail(s) |
devys@igbmc.fr
|
| Organization name |
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)
|
| Street address |
1 rue Laurent Fries / BP 10142
|
| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE52860 |
The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [HeLa cells] |
| GSE59370 |
The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription |
|
| Relations |
| BioSample |
SAMN02428180 |
| SRA |
SRX385545 |
