|
| Status |
Public on Mar 22, 2021 |
| Title |
MV3_siI1_3 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MV3
sirna: siRNA pool against IGF2BP1
passages: harvested 72h upon transfection
|
| Treatment protocol |
72 (A-549, ES-2, MV-3) or 96 (PANC-1) hours upon transfection cells were harvested for RNA extraction.
|
| Growth protocol |
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.
1µg of total RNA served as input for rRNA depletion using RiboCop v1.2 (Lexogen). NEBNext Ultra Directional RNA Library kit (NEB) was used for library generation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DE_MV3_C_vs_I1_all.csv
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample
|
| |
|
| Submission date |
Nov 09, 2020 |
| Last update date |
Mar 22, 2021 |
| 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 |
GPL18573 |
| Series (2) |
| GSE161087 |
IGF2BP1, a conserved regulator of RNA turnover in cancer [total RNA] |
| GSE161101 |
IGF2BP1, a conserved regulator of RNA turnover in cancer |
|
| Relations |
| BioSample |
SAMN16709245 |
| SRA |
SRX9461560 |
