|
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 |