 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 03, 2016 |
| Title |
setx_ChIP_t0 |
| Sample type |
SRA |
| |
|
| Source name |
A549 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
chip antibody: SETX
infection: uninfected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Previously described protocols (see PMID: 17512414 and PMID: 17406303) with minor modifications were used: (i) Sonication: A refrigerated Bioruptor (Diagenode) was used . Sonication conditions were optimized to generate DNA fragments of approximately 200-500 bp. (ii) Antibodies (Ab) were coupled with Invitrogen Dynabeads anti-mouse M-280 #112-02, or Dynabeads anti-rabbit M-280 #112-04 for 6hours. Ab-beads and chromatin were then immunoprecipitated overnight. (iii) After the wash steps, reverse crosslinking was carried out at 65°C for 2 hours in a thermomixer programmed for mixing at 700 rpm 2 min on/ min off. ChIP DNA was then isolated, after RNase digestion and proteinase K digestion, using QIAGEN MinElute kit (28004).
For library preparation, 30 ul of ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies, cat# ER0720), and purified end-repaired DNA using the QIAGEN PCR purification kit (28104). DNA END Repair was done using Klenow Fragment (NEB M0212L), and purified DNA was collected with QIAGEN MinElute kit. Ligation of Illlumina/Solexa adapters (#FC-102-1003) to DNA fragments overnight was achieved using T4 DNA ligase (NEB M0202L). Adaptor-ligated DNA fragments were purified with the QIAGEN MinElute kit. 18 cycles of PCR was performed with the Illumina/Solexa primers 1.0 and 2.0, and an aliquot of material was used to check the fragment size on agarose gel. The remaining DNA was column purified and bio-analyzed before sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SETX ChIP-Seq profile in uninfected A549 cells
|
| Data processing |
Following adapter trimming and quality filtering, reads were mapped to the human reference genome (GRCh37, hg19) using bowtie v0.12.9 (see PMID: 19261174). Unique best matches were kept and normalized to a total level of 44M tags per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in wig format and contain normalized mapped ChIP-Seq read coverage
|
| |
|
| Submission date |
Dec 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ivan Marazzi |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Department of Microbiology
|
| Street address |
1468 Madison Avenue
|
| City |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE52936 |
SETX attenuates the antiviral innate immune response and controls viral biogenesis (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN02429363 |
| SRA |
SRX386239 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1278358_setx_ChIP_t0.bedgraph.gz |
473.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
