|
| Status |
Public on Aug 31, 2021 |
| Title |
RPS19DBA3 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ Lin- bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell type: CD34 enriched bone marrow
disease state: DBA
mutation: RPS19
|
| Treatment protocol |
Frozen bone marrow aspirates were thawed and 12,000 - 15,000 CD34+ Lineage negative cells were isolated by FACS.
|
| Growth protocol |
NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated and cDNA constructed using the 10x Genomics Single cell 3' Library and Gel Bead Kit according to the manufacturer's protocol.
Libraries were constructed using Chromium Single Cell 3’ library and Gel Bead Kits (10x Genomics) and sequencing performed either a NextSeq 550 (with a 26 base read for cell and molecule barcodes, an 8 base library index read, and a 98 base insert read) or a NovaSeq 6000 (with a 28 base read for cell and molecule barcodes, an 8 base library index read, and a 91 base insert read)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing data was demultiplexed and aligned to the GRCh38 3.0.0 using the 10x Genomics Cell Ranger software (v3.0.1).
Cells meeting minimum unique molecular identifier (UMI) and detectable numbers of genes, as well as a maximum percentage of mitochondrial gene expression, were included. Genes expressed in at least 10 cells were included.
Batch correction, expression matrix construction, dimensionality reduction, and k-nearest neighbor clustering was performed in R.
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: UMI counts
|
| |
|
| Submission date |
Aug 18, 2020 |
| Last update date |
Nov 20, 2024 |
| Contact name |
Jens Lichtenberg |
| E-mail(s) |
lichtenbergj@mail.nih.gov
|
| Phone |
7402749495
|
| Fax |
3014024929
|
| Organization name |
National Institutes of Health
|
| Department |
National Human Genome Research Institute
|
| Street address |
49 Convent Dr 3A19
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE156441 |
Mechanisms of failing erythropoiesis in Diamond-Blackfan anemia revealed by single cell profiling of human bone marrow progenitors |
|
| Relations |
| BioSample |
SAMN15850743 |
| SRA |
SRX8965967 |
