|
Status |
Public on Jul 01, 2013 |
Title |
si-CHD1-flu |
Sample type |
SRA |
|
|
Source name |
A549 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: A549 transfected with: siRNA pools targeted to human CHD1 infected with: Flag-NS1 virus time post infection: 12h antibody: anti-Flag antibody vendor: Sigma antibody cat. #: A8592 molecule type: crosslinked-DNA
|
Treatment protocol |
For siRNA treatments, cells were transfected using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA pools targeted to either human PAF1 (L-020349-01, Dharmacon), CHD1 (L-008529-00, Dharmacon) or a control non-targeting pool (D-001810-10-05, Dharmacon) were transfected at a final siRNA concentration of 50 nM. Transfected cells were stimulated with the appropriate stimuli 48 hours post transfection. Gene knockdown efficiency was determined by quantitative PCR and/or Western blotting. For infections, the Flag-NS1 or Flag-∆PAF influenza virus was used at MOI 3.
|
Growth protocol |
Standard culture techniques
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
ChIP-Seq libraries were aligned to hg18 using bowtie, allowing 2 mismatches to the reference and no ambiguously mapping reads. RNA-Seq libraries were processed using TopHat/Cufflinks against hg18, allowing 20 max hits to the reference per read. GRO-Seq libraries were aligned to hg18 after being trimmed of 5' and 3' adapters, using bowtie, allowing 2 mismatches for trimmed reads and 3 for untrimmed reads. These were merged and processed in a strand-specific manner for integrated profiling Genome Build: Ivan_A549_NS1_siCHD1_plus_flu_2011_05_19.bowtie.bam.bed: hg18
|
|
|
Submission date |
Feb 13, 2012 |
Last update date |
May 15, 2019 |
Contact name |
ivan marazzi |
E-mail(s) |
imarazzi@rockefeller.edu
|
Phone |
2123278265
|
Fax |
2123278258
|
Organization name |
rockefeller univeristy
|
Lab |
epigenetic and immune signaling
|
Street address |
1230 York Avenue
|
City |
new york |
State/province |
ny |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE35268 |
Analysis of global gene expression profiles of hPAF1 deficient A549 cells |
GSE35774 |
Suppression of the antiviral response by an influenza "histone mimic" |
|
Relations |
SRA |
SRX119641 |
BioSample |
SAMN00788775 |