|
| Status |
Public on Feb 16, 2024 |
| Title |
pbmc scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
|
| Growth protocol |
PBMCs were thawed in RPMI 1640 with 5% FBS, and incubated at 37°C for 1 hr for recovery to ground state. 3x105 cells were set aside for scRNA-sequencing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells allocated for scRNA-seq were strained and washed with PBS containing 0.4% BSA, before strained through a 40 uM cell strainer.
Sample barcoding and library preparation was carried out using the 10x sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing alignment to the hg19 reference genome was performed using CellRanger (version 2.1.0), and spliced, unspliced, and ambiguous read counts were extracted using Velocyto.
Normalization, log transformation, and other data processing carried out in Scanpy (version 1.8.2; Wolf et al., 2018).
Assembly: hg19
Supplementary files format and content: Processed data, including cluster assignments, provided in h5ad format. Raw counts of full data available in the .raw attribute of the AnnData structure: Raw counts stored in .raw.X; Cell names are stored in .raw.obs_names; Gene names are stored in .raw.var_names.
|
| |
|
| Submission date |
Feb 16, 2023 |
| Last update date |
Feb 16, 2024 |
| Contact name |
Patrick Cahan |
| E-mail(s) |
patrick.cahan@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
ICE and Biomedical Engineering
|
| Lab |
Cahan Lab
|
| Street address |
733 North Broadway, MRB 653
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE225431 |
Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells |
|
| Relations |
| BioSample |
SAMN33325343 |
| SRA |
SRX19390862 |
