|
| Status |
Public on Oct 25, 2016 |
| Title |
RNA-seq data from HEK293 cell lines overexpressing GFP-tagged ZNF684 [ZNF684_rep1] |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells expressing GFP-tagged protein
|
| Organism |
Homo sapiens |
| Characteristics |
uniprotkb id: Q5T5D7
cell line: HEK293
library type: mRNA V2
|
| Treatment protocol |
Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting.
|
| Growth protocol |
HEK293 cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum and antibiotics. Gateway-compatible entry clones were cloned into the pDEST pcDNA5/FRT/TO-eGFP vector according to the manufacturer's instructions and co-transfected into Flp-In T-REx 293 cells together with the pOG44 Flp recombinase expression plasmid. Cells were selected for FRT site-specific recombination into the genome, following instructions by the manufacturer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from lysates using Trizol (Thermo Fisher Scientific) as described by the manufacturer.
Sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were mapped to the annotated human transcriptome using TopHat2, based on annotations from GENCODE v19.
Gene-level read counts were then quantified using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq-count output, indicating the number of reads mapping to each gene.
Supplementary_files_format_and_content: OE.vsd_normalized.log2.txt: Tab-delimited text file includes normalized gene expression matrix.
|
| |
|
| Submission date |
Jan 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hamed S Najafabadi |
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Lab |
Computational and Statistical Genomics Lab
|
| Street address |
740 Dr. Penfield Avenue, Room 7202
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0G1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE76495 |
Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq] |
| GSE76496 |
Multiparameter functional diversity of human C2H2 zinc finger proteins |
|
| Relations |
| BioSample |
SAMN04383103 |
| SRA |
SRX1515162 |
