|
| Status |
Public on Apr 25, 2024 |
| Title |
CB-D6_cDC1_b3_S12 |
| Sample type |
SRA |
| |
|
| Source name |
dendritic cell type one (CD141-positive) differentiated from cord blood CD34-positive hematopoietic stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
sample source: CD34-positive hematopoietic precursor cell isolated from cord blood
cell type: dendritic cell type one (CD141-positive) differentiated from cord blood CD34-positive hematopoietic stem cell
phenotype: HLA-DR+ CD11c+ CD141+ CLEC9A+
batch: b3
donor: d6
treatment: in vitro differentiation
|
| Treatment protocol |
Expanded progenitors from both sources were differentiated in RPMI 1640 supplemented with heat-inactivated FCS (10%), L-glutamine, sodium pyrovate, FLT3L (100 ng/ml), SCF (20 ng/ml), TPO (20ng/ml), GM-CSF (5 ng/mL) and IL-4 (5 ng/mL).
|
| Growth protocol |
Progenitors were expanded in RPMI supplemented with heat-inactivated FCS (10%), L-glutamine, sodium pyrovate, FLT3L (100 ng/ml), SCF (100 ng/ml), TPO (50ng/ml), IL3 (20ng/ml) and SR1 (1µM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiagen RNeasy® Plus micro Kit (Qiagen, cat#74034)
Multiplex RNA-Seq libraries were processed starting with 10ng of total RNA. The libraries were made by individual first strand synthesis to add the i7 index sequences. Samples were then pooled for subsequent processing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
CD34+ hematopoietic stem cell (HSC) isolated from fresh or frozen cord blood, donor 6, differentiated to cDC1
|
| Data processing |
Reads were aligned to GRCh38.91 Rsubread (2.10.5)
Raw counts were analysed using Limma package. Low-count genes were filtered using the default settings of filterByExpr() from EdgeR while counting for the variance between biological groups. Filtered counts were normalised to logCPM and were used for further analysis.
Assembly: Homo_sapiens.GRCh38.91
Supplementary files format and content: tab-delimited text file including raw counts for each sample
|
| |
|
| Submission date |
Mar 15, 2024 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Stemformatics . |
| Organization name |
The University of Melbourne
|
| Street address |
30 Royal Parade
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE261731 |
Gene expression profile of in-vitro differentiated Dendritic Cells (DCs) from induced pluripotent stem cell (iPSC) and cord blood sources |
|
| Relations |
| BioSample |
SAMN40475388 |
| SRA |
SRX23964746 |
