 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 19, 2016 |
| Title |
SMG6_rescue2 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa_SMG6_rescue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HeLa cells
gene kd: SMG6
gene rescue: SMG6
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).
Illumina TruSeq Stranded mRNA (chemistry v3), with polyA selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
batchA
|
| Data processing |
quality trimming with Trimmomatic
mapping with TopHat, GTF: Ensembl release 84
counting with HTSeq: reverse strand, union mode
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_counts.csv contains the number of mapped reads assigned to every gene in each condition
|
| |
|
| Submission date |
Aug 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Oliver Muehlemann |
| Organization name |
University of Bern
|
| Street address |
Freiestrasse 6
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE86148 |
RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells. |
|
| Relations |
| SRA |
SRX2059685 |
| BioSample |
SAMN05713062 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
