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Sample GSM4094339 Query DataSets for GSM4094339
Status Public on Mar 01, 2021
Title CRC 351 RHAMM+ CD44+
Sample type RNA
Source name primary human colorectal cancer
Organism Homo sapiens
Characteristics tissue: colorectal cancer
patient id: 351
cell markers: RHAMM+ CD44+
Growth protocol 5000-10000 numbers of cells from freshly isolated colorectal cancer tissues were directly sorted into RNA extraction dilution by FACS.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Thermo Fisher Scientific; catalog # 15596026), in accordance with the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Sep 24, 2019
Last update date Mar 02, 2021
Contact name Michitaka Nakano
Organization name Kyushu University
Department Department of Medicine and Biosystemic Sciences
Street address 3-1-1, Maidashi, Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL17077
Series (1)
GSE137919 RHAMM marks proliferative subpopulation within CD44+ human colorectal cancer stem cells

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 7.313981
DarkCorner -5.593169
A_23_P117082 3.694087
A_33_P3246448 -5.65296
A_33_P3318220 -5.6520267
A_33_P3236322 -2.5773363
A_33_P3319925 -3.9714155
A_21_P0000509 8.158778
A_21_P0000744 -2.1269937
A_24_P215804 -1.8270855
A_23_P110167 4.3082924
A_33_P3211513 3.3880749
A_23_P103349 -5.264561
A_32_P61480 -5.5002985
A_33_P3788124 -3.0286756
A_33_P3414202 -0.41743088
A_33_P3316686 0.825222
A_33_P3300975 -4.984236
A_33_P3263061 3.5887394
A_33_P3261373 -5.202281

Total number of rows: 50739

Table truncated, full table size 1191 Kbytes.

Supplementary file Size Download File type/resource
GSM4094339_SG13284322_253949440299_S001_GE1_1105_Oct12_2_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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