|
| Status |
Public on Jan 12, 2023 |
| Title |
human blood (PBMC), HTO-derived cDNA, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: PBMC (AllCells PBMC lot #3052467)
library type: HTO
antibodies/tags: TotalSeq-A anti-human antibody hash A0253
|
| Treatment protocol |
N/A
|
| Growth protocol |
PBMCs (AllCells Lot #3082436) were thawed from a cryolot at 37C for 2 mins, then resuspended in RPMI-1640 (Thermofisher #11875093) supplemented with 10% FBS (ThermoFisher #A3840001) at 37C.
|
| Extracted molecule |
protein |
| Extraction protocol |
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Cell Hashing library: read1 file contains cell barcode and molecular index; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TS20220816_HTO_FR_5
|
| Data processing |
Barcode error correction on RNA and HTO FASTQs performed with PIPseeker V1.0.0, along with RNA matrix generation. HTO count matrices were generated using CITE-seq Count (v1.4.3). Background barcodes were excluded from the RNA matrices.
Further processing was done with Seurat v4.1.0 (demultiplexing, hashtag identification, clustering).
Assembly: GRCh38.p13
Supplementary files format and content: Zipped folders containing filtered gene expression (RNA) and hashtag oligonucleotide (HTO) matrices, consisting of: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: Single-cell RNA-Seq with hashtag oligonucleotide (HTO) workflow
|
| |
|
| Submission date |
Oct 10, 2022 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Iain Christopher Clark |
| Organization name |
University of California, Berkeley
|
| Street address |
374 Stanley Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE202919 |
Microfluidics-free single-cell genomics with templated emulsification |
| GSE215165 |
Analysis of hashing quality in a PBMC sample |
|
| Relations |
| BioSample |
SAMN31230553 |
| SRA |
SRX17842172 |
