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Sample GSM8150437 Query DataSets for GSM8150437
Status Public on Apr 25, 2024
Title CB-D4_cDC1_pool_S19
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: pooled b1 and b2
donor: d4
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, pooled from donor 3 and donor 4, 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 SAMN40475391
SRA SRX23964743

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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