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| Status |
Public on Mar 30, 2015 |
| Title |
siSetx-GRO-t4 |
| Sample type |
SRA |
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| Source name |
A549 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
treatment: siSetx
infection: Influenza PR8ΔNS1
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| Extracted molecule |
total RNA |
| Extraction protocol |
At the stipulated times post infection, transcriptionally active nuclei from infected or untreated A549 cells were prepared after swelling for 5 minutes the cells in ice-cold swelling buffer (10mM Tris (pH = 7.5), 2mM MgCl2, 3mM CaCl2). Pelleted cells were re-suspended in 1ml lysis buffer (10mM Tris (pH = 7.5), 2mM MgCl2, 3mM CaCl2, 10% glycerol, 0.5% NP40, 2U/ml−SUPERaseIN (Ambion) and pipetted 20 times with a P1000 tip with the end cut off to reduce shearing. Volume was brought to 10 ml with lysis buffer and nuclei were pelleted at 600g for 5min. Nuclei were washed in 10ml lysis buffer and re-pelleted. A small aliquot was taken for Trypan blue staining to check that lysis occurred and nuclei were still intact. Nuclei were re-suspended in 1ml freezing buffer (50mM Tris-Cl (pH = 8.3), 40% glycerol, 5mM MgCl2, 0.1mM EDTA) using a P1000 tip with the end cut off and re-pelleted and re-suspended in 500μl of freezing buffer and aliquoted into 100μl aliquots and frozen in liquid nitrogen.
Library preparation was done following a previously published protocol (see PMID: 19056941)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
GRO-Seq profile of A549 cells treated with siSetx, 4 hours after infection with Influenza PR8ΔNS1
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| 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 5 million tags per sample.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files are in wig format and contain normalized mapped GRO-Seq read coverage
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| Submission date |
Dec 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ivan Marazzi |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Department of Microbiology
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| Street address |
1468 Madison Avenue
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| City |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE52935 |
SETX attenuates the antiviral innate immune response and controls viral biogenesis (GRO-Seq) |
| GSE52937 |
Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis |
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| Relations |
| BioSample |
SAMN02429361 |
| SRA |
SRX386238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1278357_siSetx-GRO-t4.hg19.neg.bedgraph.gz |
8.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1278357_siSetx-GRO-t4.hg19.pos.bedgraph.gz |
9.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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