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Sample GSM5413224 Query DataSets for GSM5413224
Status Public on Jul 26, 2021
Title 2204_UC uninflamed sigmoid colon
Sample type RNA
 
Channel 1
Source name UC uninflamed sigmoid colon
Organism Homo sapiens
Characteristics Sex: not determined
diagnosis: Ulcerative colitis
inflammation: Uninflamed
tissue: Colon
batch: 8
Extracted molecule total RNA
Extraction protocol RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.
Label Cy5
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).
 
Channel 2
Source name Universal human reference (UHR) from Stratagene
Organism Homo sapiens
Characteristics sample type: pooled human reference RNA
Extracted molecule total RNA
Extraction protocol RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.
Label Cy3
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).
 
 
Hybridization protocol Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.
Scan protocol Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.
Description SAM745536
Data processing Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.
 
Submission date Jul 01, 2021
Last update date Jul 27, 2021
Contact name Jason A Hackney
E-mail(s) hackney.jason@gene.com
Organization name Genentech, Inc.
Department Department of Bioinformatics and Computational Biology
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL6480
Series (1)
GSE179285 Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (test/reference)

Data table
ID_REF VALUE
A_24_P66027 0.525724301
A_32_P77178 1.080586934
A_23_P212522 1.696245874
A_24_P934473 0.761855152
A_24_P9671 1.412006065
A_32_P29551 0.773503821
A_24_P801451 0.60648292
A_32_P30710 0.626812784
A_32_P89523 1.009043559
A_24_P704878 0.970562666
A_32_P86028 0.5985185
A_24_P470079 0.873400733
A_23_P65830 0.820246312
A_23_P109143 0.592709946
A_24_P595567 0.780212661
A_24_P391591 1.161549031
A_24_P799245 0.979111953
A_24_P932757 0.958603818
A_24_P835500 2.258525661
A_23_P54340 0.91880563

Total number of rows: 41000

Table truncated, full table size 983 Kbytes.




Supplementary file Size Download File type/resource
GSM5413224_Agilent_251485060291_S01_GE2_107_Sep09_1_2.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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