|
| Status |
Public on Mar 14, 2017 |
| Title |
mRNA_Panc1_siKLF10+TGFb_C |
| Sample type |
SRA |
| |
|
| Source name |
Panc1
|
| Organism |
Homo sapiens |
| Characteristics |
immortalization type: SV40 large T antigen immortalized
cell line: Panc1
|
| Treatment protocol |
A549 and Panc1 cells were treated with 5 ng/ml TGFβ (R&D systems) for 72 hours.
|
| Growth protocol |
A549 and Panc1 cells were maintained in phenol red-free Dulbecco’s Modified Eagle’s Media/F12 (DMEM/F12; Invitrogen) supplemented with 10% fetal bovine serum and 1x penicillin/streptomycin (Sigma-Aldrich) at 37°C under 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total cell RNA was isolated with standard TRIzol extraction protocol.
For mRNA-Seq, 1 µg of total cell RNA was subjected to mRNA enrichment by NEXTflex Poly(A) Beads Protocol which was then used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The FASTQ files were mapped to the human genome (assembly hg19) using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings on Galaxy Platform (Version 0.9). The read counting was performed via HTSeq (version 0.6.0) with following parameters: -f bam -r pos -s reverse -a 10 -t exon -m union. The count files were subsequently subjected for differential analysis using the DESeq2 Package on R (Bioconductor version 3.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files in .csv format represent the differential gene expression analysis results obtained by DESeq2.
|
| |
|
| Submission date |
Nov 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A. Johnsen |
| Organization name |
University Medical Center Goettingen
|
| Department |
Department of General, Visceral and Pediatric Surgery
|
| Lab |
AG Johnsen/Tumorepigenetics
|
| Street address |
Robert-Koch-Straße 40
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE90566 |
Krüppel-like Transcription Factor-10 (KLF10) Provides a Negative Feedback Mechanism to Suppress TGFβ-Induced Epithelial-to-Mesenchymal Transition [RNA-Seq] |
| GSE90567 |
Krüppel-like Transcription Factor-10 (KLF10) Provides a Negative Feedback Mechanism to Suppress TGFβ-Induced Epithelial-to-Mesenchymal Transition |
|
| Relations |
| BioSample |
SAMN06062150 |
| SRA |
SRX2378844 |
