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Sample GSM4207090 Query DataSets for GSM4207090
Status Public on Nov 06, 2020
Title epididyme_50ans_section2-replicat 2
Sample type RNA
 
Source name Efferent duct intermediate segment
Organism Homo sapiens
Characteristics tissue: Efferent duct intermediate segment
donor number: 2
donor age: 50
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from each segment of caput, corpus and the cauda epididymal regions of human epidydimis from 3 healthy patients. Frozen tissues were powdered with a pestle and mortar on dry ice, and homogenized in RLT lysis buffer (Qiagen). RNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). RNA quality was assessed with the Agilent RNA 6000 pico and Agilent RNA nano kits on a 2100 Bioanalyzer from the transcriptomic Core facility of the CHUQ (Agilent). Samples were stored at −80°C until use.
Label Biotin
Label protocol For each sample, 400 ng of total RNA were labeled with the FlashTag Biotin HSR Labeling Kit (Affimetrix, Santa Clara, USA). Microarray analyses were carried out using an Affymetrix GeneChip Human Clariom S array (Affymetrix, CA, USA).
 
Hybridization protocol Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.
Scan protocol The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.
Data processing Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003).
 
Submission date Dec 06, 2019
Last update date Nov 06, 2020
Contact name Ezequiel L Calvo
E-mail(s) cezequiel@yahoo.com
Organization name CRCHUL
Department Molecular Endocrinilogy
Lab Microarrays
Street address 2705 Boul. Laurier
City Quebec
State/province Quebec
ZIP/Postal code G1V 4G2
Country Canada
 
Platform ID GPL23159
Series (1)
GSE141568 Differential gene expression profiles of human efferent ducts and epididymis

Data table header descriptions
ID_REF
VALUE Log2 RMA signal (Expression Console probe summarization output: sst-rma-gene-full-Signal).

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 7.927665
AFFX-BkGr-GC04_st 7.806894
AFFX-BkGr-GC05_st 7.810775
AFFX-BkGr-GC06_st 7.696904
AFFX-BkGr-GC07_st 7.236397
AFFX-BkGr-GC08_st 4.853675
AFFX-BkGr-GC09_st 4.116458
AFFX-BkGr-GC10_st 3.864072
AFFX-BkGr-GC11_st 3.599871
AFFX-BkGr-GC12_st 3.518134
AFFX-BkGr-GC13_st 3.350833
AFFX-BkGr-GC14_st 3.363212
AFFX-BkGr-GC15_st 3.333005
AFFX-BkGr-GC16_st 3.499457
AFFX-BkGr-GC17_st 3.649687
AFFX-BkGr-GC18_st 3.99889
AFFX-BkGr-GC19_st 7.334213
AFFX-BkGr-GC20_st 7.17606
AFFX-BkGr-GC21_st 7.44791
AFFX-BkGr-GC22_st 7.599898

Total number of rows: 24351

Table truncated, full table size 659 Kbytes.




Supplementary file Size Download File type/resource
GSM4207090_RS-10_epididyme2_50ans_section2_Clariom_S_Human_1_.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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