|
| Status |
Public on Dec 01, 2014 |
| Title |
siSMG6+siXRN1 Bio2 PARE |
| Sample type |
SRA |
| |
|
| Source name |
HeLa+TCRβ68
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
stably transfected reporter: TCRβ68
transient transfection: siSMG6 and siXRN1
library strategy: PARE
|
| Treatment protocol |
transfected with siRNAs targeting SMG6 and XRN1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PARE Libraries were constructed from poly(A)+ mRNA isolated from 300 μg of total RNA starting material using Absolute mRNA purification kit (Agilent Technologies). PARE libraries were constructed as previously described (German et al., 2008; German et al., 2009) as modified for Illumina HiSeq platform (Jeong and Green, 2012)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PARE libraries from HeLa cells stably transfected with TCRβ68 and transiently transfected with siRNAs targeting siSMG6 and siXRN1
library strategy: 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.
|
| |
|
| 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 |
SAMN03067833 |
| SRA |
SRX700551 |
