|
| Status |
Public on Oct 09, 2014 |
| Title |
A549_repA_smallRNASeq |
| Sample type |
SRA |
| |
|
| Source name |
Adenocarcinomic human alveolar basal epithelial cells (A549 cells)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: Adenocarcinomic human alveolar basal epithelial cells
|
| 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 extraction.
The libraries for sequencing small RNAs were constructed using the Illumina TrueSeq small RNA kit.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file contains RPKM for mature miRNA abundance measurements
|
| Data processing |
Sequenced reads were trimmed forthree-prime adaptor sequence, masked for low-quality and short sequences, then mapped to hg19 whole genome using the short-read aligner Bowtie2. Reads that mapped perfectly to nucleotide position 1 to 18 of each annotated miRNA were used to quantify miRNA expression.
Reads per Kilobase per Milion reads were calculated for each mature miRNA according to the definition in Mortazavi et al., Nat Methods 2008, averaging the two rpkm values from the two replicates for each cell line.
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 |
SAMN02729033 |
| SRA |
SRX518819 |
