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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 11, 2022 |
| Title |
BALBc-2 |
| Sample type |
SRA |
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| Source name |
spleen, draining lymph nodes, and bone marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
cell enrichment: CD138+ B cells
immunization: RBD-His-tag
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The enriched CD138+ plasma cells and progenitor B cells were loaded on a 10X Chromium Next GEM Chip G. The target cell number was 10,000 cells per sample. Single-cell lysis and RNA first-strand synthesis were performed using Chromium Next GEM Single Cell 5’ Gel Bead V3.1 according to the manufacturer’s protocol.
The following RNA and V(D)J library preparation was performed according to the manufacturer’s protocol (Chromium Next GEM Single Cell V(D)J reagent kit, mouse BCR). The resulting VDJ-enriched libraries were sequenced following the reading mode recommended by 10x Genomics. Sequencing was performed on a NovaSeq targeted for 10,000 reads/cell, with a total of 100 million reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x 5' single cell VDJ sequencing
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| Data processing |
Raw sequencing data were processed using Cell Ranger v3.1.0 with default settings, aligning the reads to the GRCm38 mouse VDJ reference. Outputs from Cell Ranger were then visualized using the Loupe V(D)J Browser for quality control assessment and to identify the top enriched clonotypes. The consensus amino acid sequences for the top-ranked heavy/light chain pairs in each sample were then extracted and codon-optimized for human expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: VDJ gene usage, population frequency, and CDR3 sequences for clonotypes called by CellRanger
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| Submission date |
May 18, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Ryan D Chow |
| E-mail(s) |
ryan.chow@yale.edu
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| Organization name |
Yale University
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| Street address |
850 West Campus Drive
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| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE174635 |
Development, Cryo-EM structure and function of potent monospecific and bispecific monoclonal antibodies that neutralize SARS-CoV-2 and variant B.1.351 |
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| Relations |
| BioSample |
SAMN19242330 |
| SRA |
SRX10920563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5320853_Balbc-r2-clonotypes.csv.gz |
36.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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