|
| Status |
Public on Sep 05, 2017 |
| Title |
Differentiation replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
lif removal: minusLIF 3 days
genotype: haploid murine ES cells
|
| Treatment protocol |
RNA was harvested by direct lysis on cell culture dishes using RLT buffer (Qiagen)
|
| Growth protocol |
see www.haplobank.at
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see www.haplobank.at
Illumina TrueSeq RNA library Prep kit V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Mus musculus genome (mm10); a maximum of 6 mismatches were allowed. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC RefSeq mm10). rRNA loci are masked on the genome for downstream analysis. Transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator. The mean FPKM was calculated over the replicates.
Aligned reads were subjected to FPKM measurements with Cufflinks (v1.3.0). Furthermore, only those fragments compatible with UCSC RefSeq annotation (mm10) of genes with at least one protein coding transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator. The mean FPKM was calculated over the replicates.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated text file (standard Cufflinks output)
|
| |
|
| Submission date |
Jul 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Rainer Burkard |
| E-mail(s) |
thomas.burkard@imba.oeaw.ac.at
|
| Organization name |
IMBA
|
| Street address |
Dr. Bohrgasse 7
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE84050 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [RNA-Seq] |
| GSE84090 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets |
|
| Relations |
| BioSample |
SAMN05360290 |
| SRA |
SRX1898017 |
