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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 04, 2024 |
| Title |
B cells, B220+, CSP_HAuMT_Set2, CSP |
| Sample type |
SRA |
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| Source name |
Spleen / mLN / PPs
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen / mLN / PPs
cell type: B cell
genotype: HA-uMT
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| Extracted molecule |
protein |
| Extraction protocol |
Single cells after sorting were encapsulated in Gel beads in Emulsion (GEM) using the 10X Controller with a Chromium Next GEM Single Cell 5' Kit v3, Chromium Single Cell Mouse BCR Amplification Kit, and Chromium 5’ Feature Barcode Kit.
library preparation using Chromium GEM-X Single Cell 5' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocol. Briefly, after gel-beads in emulsion (GEMs) generation, RT-PCR, cDNA amplification, fragmentation, end repair, A-tailing and sample indexing were performed.
CITE-seq
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| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
Library name: WL-54-CSP
10x Genomics
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| Data processing |
CellRanger count and vdj to process raw fastq files into a set of seven files per each sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv v8.0.1
Assembly: GRCm39-2024-A
Supplementary files format and content: CellRanger count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj output files: all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv
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| Submission date |
Nov 28, 2024 |
| Last update date |
Dec 04, 2024 |
| Contact name |
Duane R. Wesemann |
| E-mail(s) |
DWESEMANN@BWH.HARVARD.EDU
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| Organization name |
Brigham and Women's Hospital
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| Department |
Medicine, Division of Allergy and Clinical Immunology
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE283094 |
Anitbody affinity birth through somatic hypermutation |
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| Relations |
| BioSample |
SAMN45093957 |
| SRA |
SRX26910276 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8655930_WL-54-CSP_barcodes.tsv.gz |
147.7 Kb |
(ftp)(http) |
TSV |
| GSM8655930_WL-54-CSP_features.tsv.gz |
78 b |
(ftp)(http) |
TSV |
| GSM8655930_WL-54-CSP_matrix.mtx.gz |
384.5 Kb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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