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Sample GSM2099099 Query DataSets for GSM2099099
Status Public on Jul 17, 2016
Title CX3CR1high cells vs. Ly6c+ CD11b+ monocytes
Sample type RNA
 
Channel 1
Source name Pooled CX3CR1high CD11b+ CD11c+ cells derived from CX3CR1gfp/+ mice
Organism Mus musculus
Characteristics strain/background: CX3CR1gfp/+ (PMID: 22403066)
tissue source: intestinal lamina propria
cell type: CX3CR1high CD11b+ CD11c+ cells
sample type: pooled
Treatment protocol Murine large intestinal lamina propria cells were isolated from CX3CR1gfp/+ mice as previously described (PMID: 22403066).
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 Cy5
Label protocol 25 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent). In brief, cDNA was reverse transcribed from 25 ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent).
 
Channel 2
Source name Pooled blood Ly6c+ CD11b+ monocytes derived from C57BL/6J mice
Organism Mus musculus
Characteristics strain/background: C57BL/6J
tissue source: blood
cell type: Ly6c+ CD11b+ monocytes
sample type: pooled
Treatment protocol Murine large intestinal lamina propria cells were isolated from CX3CR1gfp/+ mice as previously described (PMID: 22403066).
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 25 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent). In brief, cDNA was reverse transcribed from 25 ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent).
 
 
Hybridization protocol Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent). 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 G2565AA DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Description Cy3-blood vs Cy5-colon
Data processing Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization. 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 GPL10333
Series (2)
GSE79628 Microarray analysis of CX3CR1high CD11b+ CD11c+ cells in murine 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 Normalized log10 ratio (CX3CR1high CD11b+ CD11c+/Blood Ly6c+ CD11b+ monocyte) representing test/reference

Data table
ID_REF VALUE
1 0.106772919
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 -0.110910363
13 0
14 1.72324291
15 0.993974996
16 -0.266453983
17 -0.517283378
18 0
19 0.176755886
20 0.789468818

Total number of rows: 44397

Table truncated, full table size 701 Kbytes.




Supplementary file Size Download File type/resource
GSM2099099_1_cy3-blood_vs_cy5-colon_1_1.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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