|
| Status |
Public on Sep 06, 2018 |
| Title |
1703_nB_pos [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: naive B cells
gender: female
sorting markers: Thy1.1- F4/80- CD11c- B220+ GL7- CD138-
strain: C57BL/6J
tissue: spleen
stimulation: LPS
lsd1 status: knockout
|
| Treatment protocol |
Three days following LPS stimulation, cells were FACS-purified from the spleens of wild-type and LSD1-knockout mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
All RNA from 50,000 cells per sample 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 HOMER package v4.8.2.
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing mRNA/cell (FPKM normalized to ERCC spike-in transcripts) normalized read counts for each sample.
|
| |
|
| Submission date |
May 22, 2018 |
| Last update date |
Sep 06, 2018 |
| Contact name |
Jeremy Matthew Boss |
| E-mail(s) |
[email protected]
|
| Organization name |
Emory University
|
| Department |
Microbiology and Immunology
|
| Lab |
Dr. Jeremy M. Boss
|
| Street address |
1510 Clifton Rd NE, Room 3120
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE114775 |
LSD1 regulates the plasmablast transcriptome |
| GSE114777 |
LSD1 regulates plasmablast chromatin accessibility and transcriptome |
|
| Relations |
| BioSample |
SAMN09238001 |
| SRA |
SRX4112887 |
