|
| Status |
Public on Apr 23, 2018 |
| Title |
m1_Pb_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
ex vivo cultured B cells
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
sorting markers: CD138+
strain: C57BL/6J
stimulation: LPS, Il2, Il5
drug treatment: DMSO
cell type: Plasmablasts
|
| Treatment protocol |
CD43- B cells were isolated from wild-type mice by CD43 depletion on a MACS column and cultured ex vivo in the presence of LPS, Il2, and Il5 with either DMSO or GSK343.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each cell type total RNA was extracted using the Qiagen RNeasy Kit
500 ng of total RNA was used as input for the KAPA Biosystems Stranded mRNA-seq kit with polyA selection beads.
|
| |
|
| 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 RefSeq gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for each gene for each sample.
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Apr 24, 2018 |
| 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 (2) |
| GSE97696 |
Chemical Inhibition of Ezh2 Alters Ex Vivo B cell Differentiation and Gene Expression Dynamics |
| GSE97698 |
Epigenetic regulation of in vivo B cell Differentiation |
|
| Relations |
| BioSample |
SAMN08971722 |
| SRA |
SRX3989022 |
