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Sample GSM5765021 Query DataSets for GSM5765021
Status Public on Mar 14, 2022
Title scBCR-seq mouse 232
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: CD45+
chimera condition: WT
Sex: M
Extracted molecule total RNA
Extraction protocol CD45 cells were enriched using MACS and captured in droplets according to 10X Genomics protocols.
Gene expression or VDJ libraries were prepared following reverse transcription according to 10X Genomics protocols.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description VDJ enriched
Data processing Library strategy: BCR-Seq
Cellranger (v5.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v4.0.0) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 200-3000 genes detected, more than 1000 reads detected, less than 5% mitochondrial RNA content, less than 25% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v4.0.0)
BCRs were filtered for cell barcodes with productive heavy and light chain sequences
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with BCR and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)
 
Submission date Dec 29, 2021
Last update date Mar 14, 2022
Contact name Elliot Akama-Garren
Organization name Harvard Medical School
Street address 200 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24247
Series (1)
GSE192762 Lupus susceptibility loci predispose mice to clonal lymphocytic responses and myeloid expansion
Relations
BioSample SAMN24499104
SRA SRX13553921

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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