|
| Status |
Public on Jun 05, 2018 |
| Title |
WT3 non-stim d1 |
| Sample type |
SRA |
| |
|
| Source name |
WT3 non-stim d1
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
strain: C57BL/6
|
| Treatment protocol |
Cells were harvested and resuspend in RNAlater (Qiagen)
|
| Growth protocol |
Murine B cells were grown in RPMI 1640 supplemeted with 10 % FCS and 1x Glutamax. Non-stim samples are cells cultured for 1 day in complete RPMI supplemented with IL-4. Stimulated samples were cultured for 2 days in complete RPMI supplemented with LPS + IL-4 + IL-5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion MagMAX-96 Total RNA Isolation kit was used and manufacturer's protocol was followed
KAPA Stranded RNA-Seq Kit with RiboErase (HMR) from KAPA Biosystems
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TSU687A3_WT1_non-stim_d2_S25_L003
WT3 non-stim d1
|
| Data processing |
Read trimming and adapter removal were performed using Trim Galore! (version 0.4.2)
The RSEM package (version 1.2.31), and Bowtie2 (version 2.2.9) were used to align reads to the mouse genome (Ensembl GRCm38 release 85) and to obtain gene level counts. For RSEM, all parameters were run as default except “--forward-prob” that was set to “0”.
Differential expression analysis was carried out with DESeq2 package (version 1.14.1) within R version 3.3.2
TPM values were obtained from RSEM (genes.results files)
Genome_build: Ensembl GRCm38 release 85
Supplementary_files_format_and_content: Tab-delimited text include TPM values for each gene on each sample
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Jun 05, 2018 |
| Contact name |
Carlson Tsui |
| E-mail(s) |
carlson.tsui@crick.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE111702 |
The role of PKC-beta in B cell activation |
|
| Relations |
| BioSample |
SAMN08687149 |
| SRA |
SRX3782152 |
