|
| Status |
Public on Mar 19, 2018 |
| Title |
siI3_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ovarian cancer derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ovarian cancer derived cell line
cell line: ES-2
sirna: siRNA pool against IGF2BP3
|
| Treatment protocol |
Parental ES-2 cells were seeded for RNA extraction.
|
| Growth protocol |
ES-2 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
500 ng of total RNA was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer. The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 51 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
small RNA
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.6) with parameters -q 10 -m 15
Trimmed reads were mapped against the human genome (hg19 UCSC) using Bowtie2 (v 2.2.4) with parameters -N 0
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -M -t miRNA -g ID and annotated using miRBase (v 20)
Differential gene expression was assessed using R/edgeR (v 3.12) using TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including CPM, log2 fold change and false discovery rate values for each sample
|
| |
|
| Submission date |
Jan 26, 2018 |
| Last update date |
Mar 19, 2018 |
| Contact name |
Markus Glaß |
| E-mail(s) |
markus.glass@medizin.uni-halle.de
|
| Organization name |
Martin Luther University Halle-Wittenberg
|
| Department |
Institute of Molecular Medicine
|
| Lab |
Huettelmaier Lab
|
| Street address |
Kurt-Mothes-Str. 3a
|
| City |
Halle |
| ZIP/Postal code |
06120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE109422 |
IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors [small RNA] |
|
| Relations |
| BioSample |
SAMN08407913 |
| SRA |
SRX3603939 |
