|
| Status |
Public on Dec 31, 2013 |
| Title |
KBM7 bio rep2 |
| Sample type |
SRA |
| |
|
| Source name |
KBM7
|
| Organism |
Homo sapiens |
| Characteristics |
ploidy: haploid
cell line: KBM7
|
| Treatment protocol |
none
|
| Growth protocol |
KBM7 cell line was cultured according to standard cell culture procedures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZol (Sigma) and ribosomal RNAs were depleted using RiboZero (Epicentre).
Libraries were constructed using Illumina mRNA library construction KIT with modifications according to: Sultan et al. BBRC 2012 (PMID:22609201)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
biological replicate 1
strand specific RNA-Seq using UTP/UNG
|
| Data processing |
basecalling
alignment of both technical replicates (TopHat v2.0.3 using Bowtie 2.0.0.6)
Fusion candidate gene were identified using three software algorithms
deFuse(1) (version 0.6.1) and Tophat-Fusion (2) (version 2.0.8) were used with default parameters, for FusionMap (3) (release 2013-02-01) parameter "NonCanonicalSpliceJuncitonPenalty" was set to 2
To reduce false positives only those fusion candidates were validated that could be detected with at least 2 fusion detection software tools
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including the raw output of the fusion transcript detection tools (bio rep2)
|
| |
|
| Submission date |
May 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Florian M Pauler |
| E-mail(s) |
florian.pauler@ist.ac.at
|
| Phone |
+43 2243 9000-7434
|
| Organization name |
IST Austria
|
| Lab |
Simon Hippenmeyer
|
| Street address |
Am Campus 1
|
| City |
Klosterneuburg |
| ZIP/Postal code |
3400 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47428 |
A haploid gene-trap mutant collection enables functional genetics in human cells |
|
| Relations |
| BioSample |
SAMN02179867 |
| SRA |
SRX286829 |
