|
| Status |
Public on Feb 05, 2014 |
| Title |
NB1 shSCR KIF1Bbeta biol repl A |
| Sample type |
SRA |
| |
|
| Source name |
NB1 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: scrambled control
plasmid: KIF1Bbeta(600-1400)
cell line: NB1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen)
Illumina TruSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NB1 cells expressing shSCR and KIF1Bbeta(600-1400) construct, replicate A
|
| Data processing |
Alignment by bowtie version 0.12.7 (option --best) to genome (excluding small contigs in _random files) and exon-exon junctions (http://sandberg.cmb.ki.se/media/data/rnaseq/hg19_junctions_100.fa.gz)
Conversion of junction coordinates to genome coordinates for reads overlapping a junction
Gene expression values from rpkmforgenes (http://sandberg.cmb.ki.se/rnaseq/) version 3 May 2011
Genome_build: hg19
Supplementary_files_format_and_content: BED (aligned reads) and tab-delimited text (gene expression values)
|
| |
|
| Submission date |
Feb 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Ramsköld |
| E-mail(s) |
daniel.ramskold@ki.se
|
| Organization name |
Karolinska Institutet
|
| Lab |
Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
|
| Street address |
Nobels väg 3
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44585 |
RNA helicase A is necessary for KIF1Bβ tumor suppression in neuroblastoma |
|
| Relations |
| SRA |
SRX244314 |
| BioSample |
SAMN01924443 |
