|
Status |
Public on Sep 21, 2020 |
Title |
siAS1 TNFa 30 min Rep2 |
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: SIK3 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 2
|
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 |
SAMN07682420 |
SRA |
SRX3203952 |