|
| Status |
Public on May 14, 2020 |
| Title |
BXD2-p19-/-_#2_single_cell_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
B cells and T cells from spleen of BXD2-p19-/-_#2
|
| Organism |
Mus musculus |
| Characteristics |
genotype: BXD2-p19-/-
gender: Female
tissue: spleen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells and beads containing barcoded DNA oligos were captured into oil droplets by 10xChromium controller using 10xGenomics 5' VDJ reagent kits. Individual cells were lyzed immediately, mRNA were released, and reverse transcription was performed by plyT primers according to 10xGenomics 5' VDJ standard protocol. Single-stranded cDNA was then captured in the each oil droplet by the barcoded DNA oligos carried by the beads.
Barcoded single cell cDNA were pooled and preamplified, 5' biased transcriptome libraries and BCR libraries were constructed according to the standard protocol of 10xGenomics 5' VDJ reagent kits.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B cells and T cells from spleen of BXD2-p19-/-_#2
|
| Data processing |
Raw data were processed with the Cell Ranger pipeline(v.3.0.2).
Sequencing reads were aligned using STAR aligner
The cellranger-vdj pipeline was applied for single cell V(D)J BCR data
Genome_build: mm10
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
May 14, 2020 |
| Contact name |
Min Gao |
| E-mail(s) |
mgao@uabmc.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1900 University Blvd, THT Building Suite #130G
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE145922 |
IL-23 promotes a coordinated B-cell germinal center program for class-switch recombination to IgG2b in BXD2 mice |
|
| Relations |
| BioSample |
SAMN14207646 |
| SRA |
SRX7802217 |
