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Sample GSM6892085 Query DataSets for GSM6892085
Status Public on May 31, 2023
Title CD34+ SC_1 (CM245-01)
Sample type RNA
 
Source name human umbilical cord blood
Organism Homo sapiens
Characteristics tissue: umbilical cord blood
cell type: CD34+ stem cells
Treatment protocol cells were treated on days 1 and 2 with valproic acid (VPA) and 5-azacytidine (5’AZA), respectively. From day 3, the medium was renewed 3 times per week with previous medium containing ascorbic acid and TGF-β1 until day 14.
Growth protocol Human umbilical cord blood (Hu-UCB) samples were obtained from healthy, consenting donors undergoing normal deliveries. The cells were incubated in Iscove’s modified medium (IMDM) supplemented with 12.5% fetal bovine serum, 2.5% horse serum, 2 mM L-glutamine,, 7 μM 1-thioglycerol , 1% penicillin/streptomycin, BMP2, bFGF, VEGF, IGF1), and BMP4
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from UCB-CD34+- and UCB-CD34+-treated cells and, at different stages of differentiation, cardiac progenitors (CMPCs) and cardiomyocytes (4 pools of quadruplets).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp WT Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25× Agilent Fragmentation Buffer and 10x Agilent Gene Expression Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by very slow removing.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in CD34+ stem cells from blood cord
Data processing The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.
The data were filtered and normalized using Agilent Genespring GX software
 
Submission date Dec 23, 2022
Last update date May 31, 2023
Contact name Anne ARIES
E-mail(s) ariesa@ghrmsa.fr
Organization name IRHT
Street address 87 Av d'Alkirch
City Mulhouse
ZIP/Postal code 68100
Country France
 
Platform ID GPL17077
Series (1)
GSE221650 Deciphering the cardiovascular potential of human CD34+ stem cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 -0.42393255
A_33_P3246448 -1.3661175
A_33_P3319925 -0.15721726
A_21_P0000509 -5.2799807
A_21_P0000744 2.4062777
A_24_P215804 -0.18930125
A_23_P110167 0.23954487
A_33_P3211513 2.0835974
A_23_P103349 1.2734208
A_33_P3414202 1.4223602
A_33_P3316686 0.48010254
A_33_P3300975 -0.332273
A_33_P3263061 -0.032983065
A_24_P278460 0.03954625
A_21_P0014651 1.3610585
A_24_P286898 0.2732339
A_23_P340890 0.06672573
A_21_P0010885 0.023465157
A_23_P89762 1.7263148
A_33_P3379396 0.6617241

Total number of rows: 28008

Table truncated, full table size 666 Kbytes.




Supplementary file Size Download File type/resource
GSM6892085_CM245-01.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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