|
Status |
Public on Dec 01, 2014 |
Title |
siUPF1+siXRN1 Bio1 RNA-seq |
Sample type |
SRA |
|
|
Source name |
HeLa+TCRβ68
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa stably transfected reporter: TCRβ68 transient transfection: siUPF1 and siXRN1
|
Treatment protocol |
transfected with siRNAs targeting UPF1 and XRN1
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNAseq libraries were constructed from poly(A)+ RNA using TruSeq RNA sample prep kit (Illumina)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
RNA-Seq libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siUPF1 and siXRN1 Processed data file: isoform_expression.txt
|
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 |
SAMN03067840 |
SRA |
SRX700558 |