|
| Status |
Public on Jun 11, 2018 |
| Title |
WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293T
genotype: WT
passage: 10-15
transfection: control(empty vector)
|
| Treatment protocol |
HEK293T cells were transfected with empty vector or tRNA expression plasmids 4 times in two days intervals.
|
| Growth protocol |
complete medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified with Qiagen RNeasy kit
1 ug of total RNA from pcDNA3(empty vector), tRNA LeuAAG (tRF-3003) and tRNA LeuTAA (tRF-3009) overexpressing cells were used for library preparation. Libraries were prepared using NEBNext Ultra directional RNA library prep kit with NEBNext Poly(A) mRNA Magnetic Isolation Module for Illumina. The libraries were indexed using NEBNext Multiplex oligos for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate1
|
| Data processing |
We received on an average 30 million 50 bases long paired end reads for each of the replicates and had two replicates for each condition. The transcript (RefSeq genes) sequences for the genome build hg38 were downloaded from UCSC table browser on Dec 10, 2016 (http://genome.ucsc.edu). We used default parameters of Kallisto (Bray, Pimentel et al. 2016) to build an index for the above transcript sequence and then quantified abundances of the transcripts from the paired end RNAseq fastq reads (Bray, Pimentel et al. 2016). The DESeq2 (Love, Huber et al. 2014) package in R was used for differential expression analysis of the quantified data obtained from Kallisto. The normalized count data from DESeq2 was used for all other downstream analysis.
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anindya Dutta |
| E-mail(s) |
ad8q@virginia.edu, pk7z@virginia.edu
|
| Phone |
434 - 924 - 2466
|
| Organization name |
University of Virginia
|
| Department |
MD-BIOC BC/Mole Genetics~School of medicine
|
| Lab |
Anindya dutta lab
|
| Street address |
Room no. 1232, Jordan Hall
|
| City |
Charlottesville, |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE99769 |
Global gene repression by Dicer-independent tRNA fragments |
|
| Relations |
| BioSample |
SAMN07203122 |
| SRA |
SRX2892794 |
