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Sample GSM2099095 Query DataSets for GSM2099095
Status Public on Jul 17, 2016
Title CD14+ CD163low, rep1
Sample type RNA
 
Source name Intestinal lamina propria CD14+ CD163low cells
Organism Homo sapiens
Characteristics tissue source: intestinal lamina propria
cell type: CD14+ CD163low
sample type: pooled
Treatment protocol Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, CD163 and CD160 using flow cytometry.
Growth protocol None
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using an miRNeasy Mini kit according to the manufacturer’s instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit on the Agilent 2100 Bioanalyzer (Agilent).
Label Cy3
Label protocol 50 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).
 
Hybridization protocol Before hybridization, 825 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.
Scan protocol The array was scanned with 5µm resolution using an Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Description CD163low_1
Data processing Data were analyzed using the bioinformatics software GeneSpring 13.0 (Agilent).
 
Submission date Mar 25, 2016
Last update date Jul 17, 2016
Contact name Daisuke Okuzaki
E-mail(s) dokuzaki@biken.osaka-u.ac.jp
Phone +81-6-6879-4935
Organization name Osaka univ.
Department Immunology Frontier Research Center
Lab Human Immunology (Single Cell Genomics)
Street address Yamadaoka 3-1
City Suita
State/province Osaka
ZIP/Postal code 565-0871
Country Japan
 
Platform ID GPL4133
Series (2)
GSE79627 Microarray analysis of CD14+ CD163high CD160high cells in human intestinal lamina propria
GSE79629 Microarray analysis of CD14+ CD163high CD160high cells in human intestinal lamina propria and CX3CR1high CD11b+ CD11c+ cells in murine intestinal lamina propria

Data table header descriptions
ID_REF
VALUE Processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
ID_REF VALUE
1 1.623927e+005
2 1.480221e+001
3 1.392315e+001
4 1.308006e+001
5 1.236571e+001
6 1.172129e+001
7 1.115437e+001
8 1.062072e+001
9 1.016165e+001
10 9.743406e+000
11 9.374263e+000
12 1.068634e+003
13 8.733533e+000
14 7.704992e+001
15 2.660289e+001
16 1.185859e+004
17 1.631295e+001
18 3.465517e+001
19 5.377308e+004
20 7.301071e+000

Total number of rows: 45015

Table truncated, full table size 868 Kbytes.




Supplementary file Size Download File type/resource
GSM2099095_1.163Low_1_1.txt.gz 7.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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