|
| Status |
Public on Mar 22, 2021 |
| Title |
BE2C_siI1_1 |
| Sample type |
SRA |
| |
|
| Source name |
neuroblastoma derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE(2)C
sirna: siRNA pool against IGF2BP1
passages: harvested 72h upon transfection
|
| Treatment protocol |
72 hours upon transfection cells were harvested for RNA extraction.
|
| Growth protocol |
HepG2 cells were cultured in DMEM supplemented with 10% FBS. BE(2)-C cells were cultured in EMEM:DMEM/F12 (1:1) medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second strand synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DE_BE2C_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 |
GPL24676 |
| Series (2) |
| GSE161086 |
IGF2BP1, a conserved regulator of RNA turnover in cancer [polyA RNA] |
| GSE161101 |
IGF2BP1, a conserved regulator of RNA turnover in cancer |
|
| Relations |
| BioSample |
SAMN16709218 |
| SRA |
SRX9461500 |
