|
| Status |
Public on Dec 08, 2020 |
| Title |
B3-I |
| Sample type |
SRA |
| |
|
| Source name |
activated B cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: 3 hours after LPS treatment
|
| Treatment protocol |
Naïve B cells were negatively isolated (Miltenyi, 130-090-862), CTV labelled and stimulated with 25μg/ml LPS (Salmonella typhosa origin, Sigma)
|
| Growth protocol |
B lymphocytes were cultured in RPMI 1640 with 2mM GlutaMAX, 50 μM β-mercaptoethanol and 10% heat-inactivated fetal calf serum
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using NucleoSpin RNA Plus (Macherey-Nagel) from sorted naïve/activated/differentiated B cell populations
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base-calling was performed using Illumina Casava v1.8.2
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.
|
| |
|
| Submission date |
Mar 24, 2020 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE147496 |
RNA-seq of primary mouse B cell progenitor populations after activation with LPS |
| GSE147497 |
RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS |
|
| Relations |
| BioSample |
SAMN14443804 |
| SRA |
SRX7988775 |
