|
| Status |
Public on Aug 20, 2023 |
| Title |
93-0 [ssBCR-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
single-cell BCR-seq of human: adult female PBMC pre-vaccination
|
| Organism |
Homo sapiens |
| Characteristics |
timepoint: pre-vaccination
tissue: PBMC
cell type: B-cell
Sex: female
age: 92
ethnicity: Not Hispanic or Latino
race: White
library type: scBCR-seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
B cells were isolated from PBMCs using the EasySepTM Human Pan-B cell Enrichment Kit (immunomagnetic negative selection kit, StemCell) per the manufacturer’s instructions.
Single-cell emulsions and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol using the Chromium Controller (10x Genomics). The NovaSeq 6000 with 150x150 paired-end reads was used to sequence gene expression libraries.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: scBCR-seq
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Quality control was performed removing sequences with nonproductive arrangements, lacking valid V or J gene annotation. Cells were further filtered that have exactly one heavy chain sequence.
B cell clones were inferred based on heavy chain sequences using hierarchical clustering with single-linkage (Gupta 2017) for each subject with day 0 and day 7 cells combined. Sequences were first partitioned based on common V and J gene annotations and junction lengths. Within each partition, sequences whose junction sequences were within 0.12 normalized Hamming distances between each other were clustered as clones. The cutoff was chosen based on manual inspection of the bimodal distance-to-nearest distribution.
Somatic hypermutation frequency was computed using the “calcObservedMutations” function from SHazaM v1.0.2 package (Gupta 2015) and was the number of nucleotide mismatches from the germline sequences of the heavy chain variable segments leading up to the CDR3.
Genome_build: GRCh38
Supplementary_files_format_and_content: BCR-seq results were saved in AIRR-tsv format and gzip compressed.
Supplementary_files_format_and_content: Tar archives include cell ranger output files.
|
| |
|
| Submission date |
May 25, 2021 |
| Last update date |
May 10, 2024 |
| Contact name |
Steven Kleinstein |
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
Kleinstein
|
| Street address |
300 George St.
|
| City |
New Haven |
| State/province |
Ct |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE175523 |
High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults (single-cell BCR) |
| GSE175524 |
High-throughput Single-cell Profiling of B cell Responses Following Inactivated Influenza Vaccination in Young and Older Adults |
|
| Relations |
| BioSample |
SAMN19189503 |
| SRA |
SRX10918220 |
