|
| Status |
Public on Jul 23, 2013 |
| Title |
Nsun_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK292_SiNsun2_RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: Human Embryonic Kidney cells
transfected with: siRNA against Nsun2
|
| Treatment protocol |
HEK293 cells were transfected with siRNAs directed against NSUN2 or otherwise a scrambled control sequence as a negative control. 48 hours post-transfection, cells were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained using the standard Trizol extraction protocol and the mRNA fraction was subsequently purified using oligodT magnetic dynabeads.
Libraries were prepared using the Illumina TruSeq mRNA library prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads were aligned to the human reference genome (GRCh37/hg19) using tophat (version 2.0.4). Only the reads uniquely aligning to the genome and aligning without mismatch were considered for further analysis. Fragment counts were normalized and differential abundance of fragments was evaluated with the Bioconductor DESeq package (http://www-huber.embl.de/users/anders/DESeq).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample
|
| |
|
| Submission date |
Feb 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Dietmann |
| Organization name |
Washington University School of Medicine
|
| Street address |
4565 McKinley Avenue
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE44384 |
NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [RNA-seq] |
| GSE44386 |
NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs |
|
| Relations |
| SRA |
SRX243940 |
| BioSample |
SAMN01924100 |
