|
| Status |
Public on Apr 05, 2023 |
| Title |
HSPCs_IFNα_24h, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: hematopoetic stem and progenitors
tissue: Bone Marrow
genotype: Wildtype
age: 12-14 weeks old
treatment: IFNa_24h
|
| Treatment protocol |
Mice were injected subcutaneously with 50.000 international units (IU) of recombinant mouse IFNα per 20g mouse. Recombinant mouse IFNα was diluted in PBS and control mice were injected with 100 µl PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library was performed using the Chromium Next GEM single cell 3‘ reagent kits v3.1 following the official instruction manual (https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry).Briefly, cells were super-loaded according to the manufacturer’s instructions up until the cDNA amplification step. 1 ul/sample of HTO primers was spiked into the cDNA amplification PCR, and cDNA was amplified according to the 10x Single Cell 3′ v3.1 protocol aiming for a targeted cell recovery of 500-6000 cells. Following PCR, cDNA cleanup was performed by using SPRI to separate the HTO-derived cDNAs (in the supernatant) from the mRNA-derived cDNAs (retained on beads). The cDNA fraction was processed according to the manufacturer's protocol to generate the transcriptome library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The cellranger pipeline (version 3.1.0) was used to align all reads to the mm10 genome and count the coverage of each gene in each cell. CITEseqCount v1.4.3 was used for the hashtag count matrix generation.
Assembly: mm10
Supplementary files format and content: Tab separated values files and comma separated values files
Supplementary files format and content: AnnData object and Seurat object [The data in the object is filtered (low quality genes and cells are removed), but has not been processed (no scaling, normalization, log transform etc.)]
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Apr 05, 2023 |
| Contact name |
Yasmin Essam Demerdash |
| E-mail(s) |
y.demerdash@dkfz.de
|
| Phone |
017629874903
|
| Organization name |
DKFZ
|
| Department |
Inflammatory Stress in Stem Cells
|
| Lab |
lab of Dr. Marieke Essers
|
| Street address |
Im Neunheimer Feld, 280
|
| City |
Heidelberg |
| State/province |
Germany |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE226824 |
Time series single-cell RNA sequencing of murine hematopoetic stem and progenitors (HSPCs) following in vivo IFNα treatment |
|
| Relations |
| BioSample |
SAMN33613585 |
| SRA |
SRX19582559 |
