|
| Status |
Public on Apr 01, 2024 |
| Title |
WT Lineage depleted cells1 |
| Sample type |
SRA |
| |
|
| Source name |
BM
|
| Organism |
Mus musculus |
| Characteristics |
organ: BM
genotype: WT
|
| Treatment protocol |
LSK cells were sorted and co-cultured with E4orf1 vascular niche cells in StemSpan serum free media supplemented with SCF, Flt3, and TPO and with knockout serum replacement media, Fli-1 alleles deletion was induced using 4-OHT, then cells were resorted and transplanted into recipient mice and isolated following 4 months of engraftment.
|
| Growth protocol |
Cells were isolated from in vivo BM and depleted from lineage positive populations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lineage negative CD45.2 positive HSPCs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using Arcturus PicoPure RNA isolation kit (Applied Biosystems).
RNA-seq cDNA libraries were constructed using the 10X Chromium single-cell 3′ Library Kit according to the manufacturer’s original protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Control1
Polyadenylated mRNA
single-cell RNAseq
Control.tar
|
| Data processing |
FastQC (v0.11.8) to check FASTQ quality.
Single cell feature counts were generated using cellranger (v3.0.2).
Monocole 3 (v.3_0.2.3.0) for downstream analysis.
Batchelor (v.1.2.4) to project data and remove batch effects.
Garnette (v.0.2.15) for cell type specification.
ggplo2 (v3.3.2) for generation of violin plots comparing gene-set scores.
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: *.tar: Filtered feature-barcode matrix; barcodes.tsv, features.tsv, matrix.mtx files
|
| |
|
| Submission date |
Mar 29, 2021 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Tomer Itkin |
| E-mail(s) |
toi2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Medicine
|
| Lab |
Rafii
|
| Street address |
1300 York Avenue, A-869
|
| City |
NY |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE169431 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing |
| GSE171113 |
Transcriptional Activation of Regenerative Haematopoiesis via Niche Sensing [scRNA-seq engrafted HSPCs] |
|
| Relations |
| BioSample |
SAMN18530008 |
| SRA |
SRX10471242 |
