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Sample GSM1154728 Query DataSets for GSM1154728
Status Public on Feb 09, 2017
Title PBL from Minimal ImmunoSuppression 7
Sample type RNA
 
Channel 1
Source name Total RNA from 20 pooled cell lines
Organism Homo sapiens
Characteristics sample type: pool of 20 cell lines from Pat Brown's lab
Extracted molecule total RNA
Extraction protocol Patient peripheral blood (10 ml) was harvested in EDTA tubes from a peripheral vein or arterio-venous fistula. Peripheral blood leukocytes (PBL) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and 10 million cells were frozen in Trizol reagent (Invitrogen,Life Technologies, San Diego, CA) for RNA extraction.
Label Cy3
Label protocol Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method described by Wang et al. (Nat Biotechnol, 2000).
 
Channel 2
Source name Total RNA from Peripheral Blood Leukocytes (PBL), MIS7
Organism Homo sapiens
Characteristics sample type: PBL from MIS7
cell type: Peripheral blood leukocytes
treatment: renal transplant
response: Minimal ImmunoSuppression
Extracted molecule total RNA
Extraction protocol Patient peripheral blood (10 ml) was harvested in EDTA tubes from a peripheral vein or arterio-venous fistula. Peripheral blood leukocytes (PBL) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and 10 million cells were frozen in Trizol reagent (Invitrogen,Life Technologies, San Diego, CA) for RNA extraction.
Label Cy5
Label protocol Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method described by Wang et al. (Nat Biotechnol, 2000).
 
 
Hybridization protocol cDNA microarrays, containing ~32,000 cDNA clones (12,400 known unique genes), were processed using established protocols, using 2 μg RNA in each channel against a “common reference” RNA pool.
Scan protocol Hybridized microarrays were scanned using GenePix 4000 (Axon Instruments, Union City, CA) and fluorescent images were analyzed with the GenePix Pro software package.
Description Minimal ImmunoSuppression, Biological replicate 7 of 10
Data processing Defective spots were flagged and removed. Defective spots were flagged and removed, generating a data file with 11,820 clones under low stringency retrieval settings (80% representative data, signal/noise ratio of expression measurements > 1.5, signal >200 in both channels and expression cut-off of 2-fold in one or more array). Data were centered prior to statistical analysis.
 
Submission date Jun 05, 2013
Last update date Feb 09, 2017
Contact name Daniel BARON
E-mail(s) daniel.baron@univ-nantes.fr
Organization name Institut national de la santé et de la recherche médicale-INSERM
Department UMR1064 - Centre de Recherche en Transplantation & Immunologie
Lab Tolerance et regulation lymphocytaire
Street address 30 Bd Jean Monnet
City Nantes
State/province Loire-Atlantique (44)
ZIP/Postal code 44093
Country France
 
Platform ID GPL6271
Series (1)
GSE47683 Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance
Relations
Reanalyzed by GSE49198

Data table header descriptions
ID_REF
VALUE Normalized log ratio Channel 2 (Red)/Channel 1 (Green)

Data table
ID_REF VALUE
1 -0.568387946
2 -0.881609008
3 0.106237559
4 -0.604160008
5 0.826948898
6 -1.332612796
7 -0.454646012
8 0.097088475
9 0.210797224
10 0.293501524
11 0.054478373
12 -0.499718958
13 -0.099129034
14 0.037346086
15 -0.133302317
16 -0.749536738
17 -0.371466809
18 -0.480172635
19 -0.291477066
20 -0.647482768

Total number of rows: 37632

Table truncated, full table size 658 Kbytes.




Supplementary file Size Download File type/resource
GSM1154728_Exptid-38027_Name-74MIS.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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