|
| Status |
Public on Oct 15, 2021 |
| Title |
76w2_257_S1_L001 |
| Sample type |
SRA |
| |
|
| Source name |
hematopoietic system
|
| Organism |
Heterocephalus glaber |
| Characteristics |
strain: Naked mole-rat
tissue: bone marrow
age: 2-4 years
genotype: wildtype
recipient strain: NSGS [Jax #013062]
recipient facs population: NOT Thy1.1-/CD34-
donor facs population: CP1
immunophenotype: LIN+/Thy1.1int/CD34+
molecule subtype: 3' mRNA UMI
|
| Treatment protocol |
Cells were processed for TotalSeq™ CITE reagents according to the manufacturers instructions (BioLegend), using both human and mouse Fc blocking reagents (BioLegend)
|
| Growth protocol |
Naked mole-rat sorted HSPC populations (CP1 vs LTC) from donors aged 2-4 years were i.v. transplanted into preconditioned NSGS recipients and extracted from marrow 4 weeks post TX
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted as viable xenograft according to FACS staining
Chromium Single-Cell 3′ Library & Gel Bead Kit v3 (10X Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
library strategy: single-cell CITE-Seq
Cellranger 3.1.0 was used to generate count matrices from both an ENSEMBL94 mouse reference and FRAMA for the same library
RNA features from each reference were labelled with a species tag
RNA features were uniquefied using data.table by sum-up each duplicate
ADT features from each sample were concatenated
Annotation of features, molecules/cells and samples was indexed against the feature matrices
Supplementary_files_format_and_content: R workspace containing RNA count matrix, ADT count matrix and cell annotation
|
| |
|
| Submission date |
Oct 12, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Stephan Emmrich |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Rochester
|
| Street address |
213 Hutchison Hall, River Campus
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14627 |
| Country |
USA |
| |
|
| Platform ID |
GPL30845 |
| Series (2) |
| GSE185722 |
Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [Xeno] |
| GSE185724 |
Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats. |
|
| Relations |
| BioSample |
SAMN22225133 |
| SRA |
SRX12576796 |
