|
| Status |
Public on Sep 21, 2020 |
| Title |
siCtrl1 TNFa 30 min Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PANC-1 (Pancreatic ductal adenocarcinoma cell line)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC-1
treatment: TNF treatment 30min
transfection: control siRNA
|
| Treatment protocol |
Cells were transfected with RNAimay for 72h afterwards, rHuTNF-alpha was added
|
| Growth protocol |
DMEM 10%FCS 1% P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Mini Kit (Qiagen) was used according to manufacturer´s instructions, including DNase I digestion.
Library was generated using the ScriptSeq Complete Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
replicate 1
|
| Data processing |
1. Alignment of PE fastq files using STAR (2.05b) using GRCh38 and the following options: STAR --runThreadN 10 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outReadsUnmapped Fastq --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outWigType bedGraph --outWigStrand Stranded
2. EdgeR analysis of combined STAR-derived read count tables, including batch effects.
Genome_build: GRCh38
|
| |
|
| Submission date |
Sep 21, 2017 |
| Last update date |
Sep 21, 2020 |
| Contact name |
Claudia GEBHARD |
| E-mail(s) |
claudia.gebhard@gmail.com
|
| Organization name |
UNIVERSITY HOSPITAL REGENSBURG
|
| Street address |
FRANZ-JOSEF-STRAUSS ALLEE 11
|
| City |
REGENSBURG |
| ZIP/Postal code |
93042 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE104112 |
Validation of AS1 as novel regulator of tumor resistance to immune cell attack |
| GSE202305 |
RNA-seq and ATAC-seq of tumor resistance to immune cell attack |
|
| Relations |
| BioSample |
SAMN07682423 |
| SRA |
SRX3203949 |
