|
| Status |
Public on Jun 29, 2020 |
| Title |
Sample_NB_TET2_WT2 |
| Sample type |
SRA |
| |
|
| Source name |
Naïve B-cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: naive B-cells
tissue: spleen
genotype: TET2 Wild-Type
strain: C57BL/6
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Cells were isolated from mouse spleens
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and Qiagen Rneasy kit
Illumina's RNA-seq-TruSeq-stranded-mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were trimmed for truseq R1 adapter sequences using Flexbar.
Trimmed reads were mapped to the GRCm38.p3 reference genome using STAR (version 2.3.0e_r291) with the default parameters.
Read Counts per gene were computed using featureCounts (v1.5.1) tool from Subread package with the following parameters: -t "exon", -g "gene_name". GRCm38 Gencode was used as a reference gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: nbgcb.genecounts.txt file contain raw read counts per gene.
|
| |
|
| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Sheng Li |
| Organization name |
The Jackson Laboratory
|
| Lab |
Li Lab
|
| Street address |
10 Discovery Drive
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE132596 |
Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [RNA-seq] |
| GSE140086 |
Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells |
|
| Relations |
| BioSample |
SAMN12037563 |
| SRA |
SRX6047962 |
