|
| Status |
Public on Jul 01, 2013 |
| Title |
GRO-Seq 0h |
| Sample type |
SRA |
| |
|
| Source name |
A549 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
infected with: none (uninfected)
time post infection: 0h
antibody: anti-deoxyBrU
molecule type: Nuclear-Run On RNA
|
| 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 |
total RNA |
| 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Global Run-On (GRO) Sequencing
|
| 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:
GroSeq_sample1_rmdup_merged.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 |
SRX119647 |
| BioSample |
SAMN00788781 |
