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Sample GSM3592441 Query DataSets for GSM3592441
Status Public on Feb 07, 2019
Title human mono.3
Sample type RNA
 
Source name human mono
Organism Homo sapiens
Characteristics subject status: healthy donor 3
cell type: Peripheral blood stem cells (PBSCs)
cell subtype: conventional monocytes (con-mono, Lin-CD34-CD33+CD14+CD11b+ cells)
treatment: mobilized by G-CSF
Extracted molecule total RNA
Extraction protocol From cryopreserved PBSC grafts of three donors, approximately 1x10^4 CD34+mono cells, 3x10^5 CD34-positive cells (CD34+cells, Lin-CD34highCD33-CD14-CD11b- cells), and 3x10^5 conventional monocytes (con-mono, Lin-CD34-CD33+CD14+CD11b+ cells) were directly sorted into tubes using FACSAriaTM II (BD Biosciences). After the collection of individual cell types, total RNA extraction was immediately performed with an RNeasyPlus Micro kit (QIAGEN) according to the manufacturer’s instructions. Thereafter, electrophoresis analyses were performed to examine the quality of the extracted RNAs using an Agilent 2100 Bioanalyzer (Agilent Technologies) with RNA Pico Chips (Agilent Technologies).
Label biotin
Label protocol Using 6ng of the extracted RNA in each sample with a GeneChip™ 3' IVT Pico Kit (Thermo Fisher Scientific), cDNA was made by reverse transcription, and cRNA was then synthesized and amplified by in vitro transcription. After the quality assessments, the cRNA was converted to biotinylated double-stranded cDNA hybridization targets.
 
Hybridization protocol The product of cDNA was then hybridized into a human Clariom™ S Assay (Thermo Fisher Scientific) with a GeneChip™ Hybridization, Wash, and Stain Kit, and a GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific) via incubation at 45°C with rotation at 60 rpm for 16 hours.
Scan protocol The arrays were automatically stained and read using a GeneChip™ Fluidics Station 450 and a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific), according to the protocol provided by the manufacturer.
Data processing The raw data were analysed according to the algorithm of a Transcriptome Analysis Console (Thermo Fisher Scientific).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Human
program-name = Expression Console
program-version = 1.4.1.46
 
Submission date Feb 06, 2019
Last update date Feb 07, 2019
Contact name Hideki Nakasone
E-mail(s) nakasone-tky@umin.ac.jp
Organization name Jichi Medical University Saitama Medical Center
Department Hematology
Street address 1-847, Amanuma-cho, Omiya-ku
City Saitama
ZIP/Postal code 330-8503
Country Japan
 
Platform ID GPL23159
Series (1)
GSE126160 CD34mono GEP

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 7.58672
AFFX-BkGr-GC04_st 6.54994
AFFX-BkGr-GC05_st 6.34554
AFFX-BkGr-GC06_st 6.30136
AFFX-BkGr-GC07_st 5.83045
AFFX-BkGr-GC08_st 3.83311
AFFX-BkGr-GC09_st 3.39402
AFFX-BkGr-GC10_st 3.14539
AFFX-BkGr-GC11_st 3.03885
AFFX-BkGr-GC12_st 2.8153
AFFX-BkGr-GC13_st 2.62015
AFFX-BkGr-GC14_st 2.55304
AFFX-BkGr-GC15_st 2.52114
AFFX-BkGr-GC16_st 2.56743
AFFX-BkGr-GC17_st 2.67189
AFFX-BkGr-GC18_st 2.75347
AFFX-BkGr-GC19_st 5.72269
AFFX-BkGr-GC20_st 5.78209
AFFX-BkGr-GC21_st 5.91102
AFFX-BkGr-GC22_st 5.95151

Total number of rows: 24351

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM3592441_EA1615_04.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM3592441_EA1615_04.sst-rma-gene-full.chp.gz 173.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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