|
| Status |
Public on Jun 01, 2024 |
| Title |
Lin- cells_scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks old
genotype: wild type
tissue: bone marrow
cell type: LSK
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lin- cells were enriched from C57/B6 mice according to the EasySep™ Mouse Hematopoietic Progenitor Cell Isolation Kit.
Library was performed according to che manufacter's instrucions (Single Cell 3′ library and Gel Bead Kit v.3 protocol,10 Genomics ). Briefly, Lin- cells Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol. Qubit was used for library quantification before pooling.The final library pool was sequenced on the Illumina Nova6000 instrument using 150-base-pair paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10XGenomics
|
| Data processing |
Differential expression of each cluster was calculated using the ‘bimod’ test as implemented in Seurat FindMarkers function.Genes with a log2 average expression difference 0.585 and P < 0.05 were identified as marker genes. Cell clusters were annotated using canonical markers of known cell types.
Seurat-Bimod statistical test was used to find differentially expressed genes between each group of cells and other groups of cells (FDR <= 0.05 and |log2 Fold Change| >= 1.5)
Assembly: mm10
|
| |
|
| Submission date |
Nov 26, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
CHENGFANG ZHOU |
| E-mail(s) |
chengfangzhou47@gmail.com
|
| Phone |
(86)13368348471
|
| Organization name |
Chongqing Medical University
|
| Department |
Institute of Life Sciences
|
| Street address |
No. 1, Medical College Road
|
| City |
Chongqing |
| ZIP/Postal code |
400032 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE248638 |
Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening (scRNA-Seq) |
| GSE248639 |
Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening. |
|
| Relations |
| BioSample |
SAMN38440432 |
| SRA |
SRX22643591 |
