|
| Status |
Public on Oct 09, 2014 |
| Title |
HeLa_rep2_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: cervical epithelial
|
| Treatment protocol |
For Drosha RNAi, 5x10^5 cells were seeded per 10cm dish, transfected after 24h with 60nM siRNA, harvested by trypsinization 72h after transfection.
|
| Growth protocol |
Hela, A549 and HEK293 cells were maintained under standard conditions at 37°C and 5% CO2 in DMEM containing 10% FCS and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The chromatin fraction was isolated as in Bhatt et al. (Cell 2012), and associated total RNA was isolated using Trizol.
The library was constructed using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold extraction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file contains RPKM for primiRNA abundance measurements
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for repeats or low-quality sequence, then mapped to hg19 whole genome using TopHat 2 and default parameters
Reads in the 100 bp regions upstream and downstream of the premiRNA Drosha cutting sites we counted by means of the HTSeq software v0.5.4p2
Reads per Kilobase per Milion reads were calculated for each miRNA primary transcript according to the definition in Mortazavi et al., Nat Methods 2008, averaging the two rpkm values from the regions upstream and downstream of each miRNA precursor.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample
|
| |
|
| Submission date |
Apr 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Annalisa Marsico |
| E-mail(s) |
marsico@molgen.mpg.de
|
| Organization name |
Max Planck Institute for Molecular Genetics
|
| Department |
Computational Biology
|
| Street address |
Ihnestraße 63-73
|
| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE56862 |
Genome-wide quantification of microRNA processing efficiency from RNA-seq data |
|
| Relations |
| BioSample |
SAMN02729038 |
| SRA |
SRX518813 |
