|
| Status |
Public on Apr 25, 2024 |
| Title |
HDF51_CD14_neg_DC2_b1_S5 |
| Sample type |
SRA |
| |
|
| Source name |
HDF51
|
| Organism |
Homo sapiens |
| Characteristics |
sample source: induced pluripotent stem cell
cell line: HDF51
cell type: dendritic cell type two (CD1c-positive CD14-negative) differentiated from induced pluripotent stem cell
phenotype: HLA-DR+ CD11c+ CD1c+ CD14-
batch: b1
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 |
induced pluripotent stem cell (iPSC) HDF51 line, replicate 1, batch 1, differentiated to CD14-negative cDC2 in a three dimentional (embryoid body) culture.
|
| 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 |
SAMN40475387 |
| SRA |
SRX23964747 |
