|
| Status |
Public on Nov 16, 2021 |
| Title |
PB.GSKJ4.rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ex vivo cultured B cells
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
sorting markers: magnetically enriched CD138+ cells
strain: C57BL/6J
mouse id: mouse 3
stimulation: LPS, IL-2, IL-5
drug treatment: 250nM GSK-J4
cell type: B cells
|
| Treatment protocol |
CD43- B cells were isolated from wild-type mice and cultured ex vivo in the presence of LPS, IL-2, and IL-5 with either DMSO or GSK-J4
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After 3 days of culture, total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
500ng of total RNA was used as input for the KAPA Biosystems mRNA HyperPrep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for all detected genes.
|
| |
|
| Submission date |
Sep 17, 2020 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Chris Scharer |
| E-mail(s) |
[email protected]
|
| Organization name |
Emory University
|
| Department |
Microbiology and Immunology
|
| Lab |
Chris Scharer
|
| Street address |
1510 Clifton Rd, Suite 3086A
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE158139 |
Chemical Inhibition of H3K27me3 demethylases during B cell differentiation |
|
| Relations |
| BioSample |
SAMN16198175 |
| SRA |
SRX9141767 |
