|
| Status |
Public on Mar 22, 2021 |
| Title |
PANC1_1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas cancer derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC1
sirna: parental cell line
passages: harvested 48h upon seeding
|
| Treatment protocol |
A549, ES2, MV3, PANC1 and HepG2 cells were harvested for RNA extraction 48 hours upon seeding. BE(2)C cells were harvested 24 hours upon seeding for RNA extraction.
|
| Growth protocol |
A549, ES2, MV3, PANC1 and 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 |
total RNA |
| Extraction protocol |
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
For A549, ES2, MV3 and PANC1 cells, 50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Small RNA-seq libraries for HepG2 and B(E)2C cells were prepared by Novogene (Hong Kong).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PANC1_WT_miRNA_CPM.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 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters -p 6 -N 1 --un-gz
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and CPM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file containing CPM values
|
| |
|
| 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 |
GPL11154 |
| Series (2) |
| GSE161099 |
IGF2BP1, a conserved regulator of RNA turnover in cancer [miRNA-seq] |
| GSE161101 |
IGF2BP1, a conserved regulator of RNA turnover in cancer |
|
| Relations |
| BioSample |
SAMN16709481 |
| SRA |
SRX9461673 |
