|
Status |
Public on Dec 01, 2014 |
Title |
siGL2+siXRN1 Bio1 C-PARE |
Sample type |
SRA |
|
|
Source name |
HeLa+TCRβ68
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa stably transfected reporter: TCRβ68 transient transfection: siGL2 and siXRN1 library strategy: C-PARE
|
Treatment protocol |
transfected with siRNAs targeting GL2 and XRN1
|
Extracted molecule |
polyA RNA |
Extraction protocol |
C-PARE Libraries were constructed from poly(A)+ mRNA isolated from 300 μg of total RNA as starting material dephosphorylated with calf intestinal alkaline phosphatase (Invitrogen) treatment at 37°C for 1 hr. After terminating the reaction with phenol/chloroform extraction and ethanol precipitation, mRNA was decapped using tobacco acid pyrophosphatase (Epicenter) at 37°C for 1 hr and cleaned with phenol/chloroform extraction and ethanol precipitation.m RNA was used for PARE library construction as previously described.
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|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
C-PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siGL2 and siXRN1 library strategy: C-PARE
|
Data processing |
[All] base calling was done using bcl2fastq_1.8.3 [RNA-Seq] Sequenced reads were trimmed for adapter sequence and mapped to hg19 whole genome using Tophat v2.0.11, with 1 mismatch, gtf file gencode.v11.annotation.gtf, --no-novel-juncs [RNA-Seq] Transcript abundance (fpkm) was calculated using Cufflinks V2.2.0 using compatible hits normalization [PARE, SPARE, C-PARE] Sequenced reads were trimmed for adapter sequence and raw abundance was counted Genome_build: hg19 Supplementary_files_format_and_content: Transcript abundance (fpkm) reported for RNA-Seq samples. Trimmed sequence and sequence abundance reported for PARE, SPARE, C-PARE samples.
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|
|
Submission date |
Sep 13, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Pamela J Green |
Organization name |
University of Delaware
|
Department |
Delaware Biotechnology Institute
|
Street address |
15 Innovation Way
|
City |
Newark |
State/province |
DE |
ZIP/Postal code |
19711 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE61398 |
Direct identification of endogenous SMG6 targets and a preferred motif spanning SMG6 cleavage sites by parallel analysis of RNA ends in human cells |
|
Relations |
BioSample |
SAMN03067829 |
SRA |
SRX700547 |