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| Status |
Public on Feb 07, 2014 |
| Title |
Polio-Infected / M25 HeLa cells / 2 hpa |
| Sample type |
SRA |
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| Source name |
Polio-Infected / M25 HeLa cells / 2 hpa
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| Organism |
Homo sapiens |
| Characteristics |
strain: M25 HeLa / dominant-negative mutant RNase L
experimental condition: Polio-Infected / M25 HeLa cells / 2 hpa
exptl time: 2 hr post-adsorption (hpa)
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 2 hpa
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| 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]
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| Submission date |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daphne A. Cooper |
| Organization name |
University of Colorado
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| Department |
Department of Microbiology
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| Lab |
David J. Barton
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| Street address |
12800 E. 19th Ave.
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE52489 |
Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs |
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| Relations |
| BioSample |
SAMN02412362 |
| SRA |
SRX378922 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1267808_dinuc.M25.PV.18S.2hpa.txt.gz |
11.0 Kb |
(ftp)(http) |
TXT |
| GSM1267808_dinuc.M25.PV.28S.2hpa.txt.gz |
17.5 Kb |
(ftp)(http) |
TXT |
| GSM1267808_dinuc.M25.PV.5.8S.2hpa.txt.gz |
754 b |
(ftp)(http) |
TXT |
| GSM1267808_dinuc.M25.PV.5S.2hpa.txt.gz |
633 b |
(ftp)(http) |
TXT |
| GSM1267808_dinuc.M25.PV.PV.2hpa.txt.gz |
936 b |
(ftp)(http) |
TXT |
| GSM1267808_dinuc.M25.PV.U6.2hpa.txt.gz |
287 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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