|
| Status |
Public on Dec 16, 2014 |
| Title |
RNA-seq in KB cells (control) |
| Sample type |
SRA |
| |
|
| Source name |
KB cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
|
| Treatment protocol |
IL-1 alpha was added directly to the cell culture medium
|
| Growth protocol |
cells were cultured in DMEM, 10% FCS, to subconfluency
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIZOL
Single-end sequencing libraries were prepared from purified polyA-mRNA isolated from non-treated or IL-1 treated KB cells using ScriptSeqTM v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-seq
KB cells control
|
| Data processing |
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Read mapping was done with Bowtie2 called from TopHat
The aligned reads were analyzed with Cufflinks and Cuffdiff in order to obtain gene expression measures and to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Gene model specific output from cuffdiff analysis
|
| |
|
| Submission date |
Dec 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE64185 |
The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 [RNA-Seq] |
| GSE64224 |
The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 |
|
| Relations |
| BioSample |
SAMN03265667 |
| SRA |
SRX810467 |
