|
| Status |
Public on Jul 27, 2021 |
| Title |
Single cell thymic CD19+CD21-CD35- [HE007] |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Homo sapiens |
| Characteristics |
age: 4 months
|
| Treatment protocol |
B cells were isolated by magnetic cell sorting with EasySep Human B Cell Enrichment Kit (Stem Cell Technologies) following the manufacturer’s instructions and stained in PBS with 2% FCS for 45min with the fluorochrome conjugated antibodies
|
| Growth protocol |
B cells were obtained from neonatal thymuses
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions
The libraries were quantified using KAPA hgDNA Quantification and QC Kit (Kapa Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Single cell thymic CD19+CD21-CD35-
|
| Data processing |
The sequencing was done using Chromium Single Cell 3′ Reagent Kits v2 (10X Genomics) according to the manufacturer’s instructions via NovaSeq 6000
The raw data from each sample were demultiplexed, aligned to the GRCh38-1.2.0. human reference genome.
UMI counts were quantified using the 10X Genomics Cell Ranger pipeline (v2.1.1, 10X Genomics).
Data analysis with the filtered barcode matrix files was done by using the Seurat package version 3.0 (Butler et al., 2018)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell
|
| |
|
| Submission date |
Jul 26, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Hector Cordero |
| E-mail(s) |
hc3023@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
650W 168th Street
|
| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE153117 |
Single cell transcriptomic profile of thymic CD21-CD35- B cells in human neonates |
|
| Relations |
| BioSample |
SAMN20399212 |
| SRA |
SRX11555044 |
