|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 07, 2014 |
Title |
Polio-Infected / W12 HeLa cells / 0 hpa |
Sample type |
SRA |
|
|
Source name |
Polio-Infected / W12 HeLa cells / 0 hpa
|
Organism |
Homo sapiens |
Characteristics |
strain: W12 HeLa / wildtype RNase L experimental condition: Polio-Infected / W12 HeLa cells / 0 hpa exptl time: 0 hr post-adsorption (hpa)
|
Extracted molecule |
total RNA |
Extraction protocol |
Total cellular RNA was extracted using 4M guanidine thiocyanate with acid phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Illumina TruSeq RNA linker with 8-base Unique Molecular Identifier (UMI) was attached with Arabidopsis thaliana tRNA ligase (recognizes RNAs with terminal 2', 3'-cyclic phosphates). cDNA was generated using a DNA primer specific to the Illumina linker, and the IDT miRNA cloning linker 1 was attached to the 3'-end of the cDNA. cDNAs were PCR amplified, pooled, and sequenced. 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing were used to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
|
|
Description |
Total RNA from polio-infected W12 HeLa cells 2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / W12 HeLa cells / 0 hpa
|
Data processing |
Reads were trimmed for contaminating linker sequence. Reads were aligned using Bowtie with -m1 --best --strata options The 8-base UMI at the 5'-end of the raw read was counted to remove PCR over-amplification bias. Signal from No 2-5A and No RNase A timepoints was subtracted from 0, 2.5, 5, 10, and 20 minute timepoints in RNase L and RNase A data (except for PV RNase L), these processed data samples include "baseline" in the file name. The 3'-dinucleotide from the read was obtained to characterize RNase specificity, and # of UMI reads were plotted against genome postion using R to map cleavage sites across the genome/sequence. Genome_build: HCV: Hepatits C virus subtype 1A polyprotein gene complete cds (AF009606.1) Genome_build: PV: Human poliovirus 1 Mahoney, complete genome (V01149.1) Genome_build: 28S: Homo sapiens RNA, 28S ribosomal 1 (RN28S1), ribosomal RNA (NR_003287.2) Genome_build: 18S: Homo sapiens RNA, 18S ribosomal 1 (RN18S1), ribosomal 1 (NR_003286.2), Genome_build: 5.8S: Homo sapiens RNA, 5.8S ribosomal 1 (RN5-8S1), ribosomal RNA (NR_003285.2) Genome_build: 5S: Homo sapiens RNA, 5S ribosomal 9 (RN5S9), ribosomal RNA (NR_023371.1) Genome_build: U6: Homo sapiens RNA, U6 small nuclear 33 (RNU6-33), small nuclear RNA (NR_046491.1) Supplementary_files_format_and_content: text files include tab delimited columns [genome, cleavage site, cleavage site+1, # of UMI reads, and dinucleotide]
|
|
|
Submission date |
Nov 19, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Daphne A. Cooper |
Organization name |
University of Colorado
|
Department |
Department of Microbiology
|
Lab |
David J. Barton
|
Street address |
12800 E. 19th Ave.
|
City |
Aurora |
State/province |
CO |
ZIP/Postal code |
80045 |
Country |
USA |
|
|
Platform ID |
GPL15520 |
Series (1) |
GSE52489 |
Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs |
|
Relations |
BioSample |
SAMN02412393 |
SRA |
SRX378914 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1267800_dinuc.W12.PV.18S.0hpa.txt.gz |
6.0 Kb |
(ftp)(http) |
TXT |
GSM1267800_dinuc.W12.PV.28S.0hpa.txt.gz |
6.4 Kb |
(ftp)(http) |
TXT |
GSM1267800_dinuc.W12.PV.5.8S.0hpa.txt.gz |
321 b |
(ftp)(http) |
TXT |
GSM1267800_dinuc.W12.PV.5S.0hpa.txt.gz |
319 b |
(ftp)(http) |
TXT |
GSM1267800_dinuc.W12.PV.PV.0hpa.txt.gz |
432 b |
(ftp)(http) |
TXT |
GSM1267800_dinuc.W12.PV.U6.0hpa.txt.gz |
159 b |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|