|
| Status |
Public on Mar 26, 2019 |
| Title |
SAM24332683 Embryo C91A_D4_4OHT |
| Sample type |
SRA |
| |
|
| Source name |
C91A_D4_4OHT
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: knock-in BAP1 C91A mutant
cell type: protected BAP1 mESc
sample_id: SAM24332683
primary_tissue: Embryo
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen) and 0.5
ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The
libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
|
| |
|
| Submission date |
Sep 25, 2018 |
| Last update date |
Mar 28, 2019 |
| Contact name |
Rohit Reja |
| E-mail(s) |
rejar@gene.com
|
| Phone |
+1-650-467-7615
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE120413 |
RNAseq in protected BAP1 mESc |
| GSE120447 |
Intrinsic Apoptosis Shapes the Tumor Spectrum Linked to Inactivation of the Deubiquitinase BAP1 |
|
| Relations |
| BioSample |
SAMN10124415 |
| SRA |
SRX4736585 |
