|
Status |
Public on Mar 13, 2023 |
Title |
Pete_Sp_PC_GEX |
Sample type |
SRA |
|
|
Source name |
ASCs from spleen
|
Organism |
Mus musculus |
Characteristics |
strain: Prdm1-eYFP (The Jackson Laboratory, Strain # 008828) Sex: Female background: C57BL/6 tissue: spleen cell type: antibody-secreting cells (ASCs)
|
Extracted molecule |
total RNA |
Extraction protocol |
ASCs from the bone marrow, spleen and thymus of 3 months old female and male Prdm1-eYFP mice were sorted on a BD Melody instrument. Each sort consisted of a pool of 3 mice and ASCs were gated as B220+/- CD138HI IgD- CD90.2- Prdm1-eYFP+. Sorted ASCs from each sex and organ were processed in individual GEM wells as separate samples on a 10x Genomics Chromium Controller. 5' Gene Expression (GEX) Libraries and VDJ Libraries were constructed following the manufacturer's guidelines using the Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 (Catolog # 1000165) and Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell (Catolog # 1000072). VDJ Libraries were sequenced on an Illumina MiSeq. GEX Libraries were sequenced on a NovaSeq.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
Gene Expression Library.
|
Data processing |
cellranger count (v6.0.2) using the 'refdata-gex-mm10-2020-A' reference provided by 10x. cellranger vdj (v6.0.2) using the 'refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0' reference provided by 10x. Genome_build: mm10
|
|
|
Submission date |
Jan 14, 2022 |
Last update date |
Mar 13, 2023 |
Contact name |
Peter Dion Pioli |
E-mail(s) |
peter.pioli@usask.ca
|
Phone |
1-639-994-8478
|
Organization name |
University of Saskatchewan
|
Department |
Biochemistry, Microbiology and Immunology
|
Street address |
107 Wiggins Rd
|
City |
Saskatoon |
State/province |
SK |
ZIP/Postal code |
S7N 5E5 |
Country |
Canada |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE193701 |
Single cell transcriptomic and VDJ sequencing of antibody-secreting cells (ASCs) from the bone marrow, spleen and thymus of young (3 months old) female and male mice. |
|
Relations |
BioSample |
SAMN24979215 |
SRA |
SRX13789723 |