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Sample GSM5818961 Query DataSets for GSM5818961
Status Public on Mar 13, 2023
Title Kim_BM_PC_GEX
Sample type SRA
 
Source name ASCs from bone marrow
Organism Mus musculus
Characteristics strain: Prdm1-eYFP (The Jackson Laboratory, Strain # 008828)
Sex: Male
background: C57BL/6
tissue: bone marrow
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 SAMN24979217
SRA SRX13789725

Supplementary file Size Download File type/resource
GSM5818961_Kim_BM_PC_filtered_barcodes.tsv.gz 24.5 Kb (ftp)(http) TSV
GSM5818961_Kim_BM_PC_filtered_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM5818961_Kim_BM_PC_filtered_matrix.mtx.gz 19.2 Mb (ftp)(http) MTX
GSM5818961_Kim_BM_PC_raw_barcodes.tsv.gz 2.1 Mb (ftp)(http) TSV
GSM5818961_Kim_BM_PC_raw_features.tsv.gz 254.1 Kb (ftp)(http) TSV
GSM5818961_Kim_BM_PC_raw_matrix.mtx.gz 92.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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