|
| Status |
Public on Aug 04, 2015 |
| Title |
RAG2ko_thy_mm_CD3_RNAseq Q1 |
| Sample type |
SRA |
| |
|
| Source name |
thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: thymocytes
genotype: Rag2: -/-
strain: C57BL/6
age: 4 weeks
Sex: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total thymocyte RNA was isolated using Trizol (Invitrogen),
RNA-seq libraries were prepared using the Illumina Tru-seq RNA sample prep kit V2 following manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Q1
|
| Data processing |
The short reads were aligned to the mm9 genome with GSNAP (version 2012-07-20) (Wu and Nacu, 2010), allowing known splice junctions extracted from RefSeq GTF (June 2013).
After sorting of the alignment files, htseq-count (Htseq version 0.5.4) (Anders et al., 2014) was used to count the number of reads fitting each gene model in the RefSeq GTF (after removing small RNAs).
Counts for each gene were then read into R (version 3.1, http://www.R-project.org) and analyzed with DESeq (version 1.16) (Anders and Huber, 2010).
Genome_build: GRCm37/mm9
|
| |
|
| Submission date |
Jun 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaakov Maman |
| Organization name |
Bar-Ilan University
|
| Department |
Azrieli Faculty of Medicine
|
| Lab |
Genome Instability & Cancer
|
| Street address |
Henrietta Szold 8
|
| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE69473 |
RAG Represents a Widespread Threat to the Lymphocyte Genome - (RNA-seq) |
| GSE69478 |
RAG Represents a Widespread Threat to the Lymphocyte Genome |
|
| Relations |
| BioSample |
SAMN03757524 |
| SRA |
SRX1046518 |
