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Sample GSM2563691 Query DataSets for GSM2563691
Status Public on Feb 12, 2019
Title Control shRNA
Sample type RNA
Source name Control shRNA
Organism Homo sapiens
Characteristics cell line: Hepatocellular carcinoma cell line MHCC-97H
genotype/variation: control
Treatment protocol transfection with shRNA for 7 days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).
Hybridization protocol Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.
Description shN_NS
Perform human gene expression microarray after transfection with shRNA for 7 days
Data processing Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.
Fold Change (linear) =< 0.5 or Fold Change (linear) >= 2, T-test p-value < 0.05
Submission date Apr 04, 2017
Last update date Feb 12, 2019
Contact name Shuqiang Liu
Organization name Guangzhou University of Chinese Medicine
Street address Outer ring road No. 232
City Guangzhou
State/province Guangdong
ZIP/Postal code 510006
Country China
Platform ID GPL21185
Series (1)
GSE97387 Whole-genome gene expression profiling of UGT2B15 Knockdown/Negative Control MHCC-97H Cell Line

Data table header descriptions
VALUE Quantile-normalized signal

Data table
A_22_P00020853 2.089107142
A_24_P386334 6.907832448
A_24_P168760 8.803031852
A_21_P0014056 2.093988842
A_23_P302094 11.0278673
A_33_P3242064 3.395050228
A_24_P10214 4.435022455
A_21_P0005599 1.701291618
A_33_P3328251 2.03376081
A_23_P57007 2.552648238
A_21_P0001678 2.557053202
A_33_P3241046 1.764769491
A_21_P0014264 2.092261121
A_22_P00024989 1.908822769
A_21_P0004162 1.901328525
A_23_P255389 3.194322017
A_33_P3235841 3.912157067
A_23_P44867 3.407239434
A_23_P92543 8.783009563
A_23_P30204 8.729991594

Total number of rows: 58341

Table truncated, full table size 1463 Kbytes.

Supplementary file Size Download File type/resource
GSM2563691_shN_257236313802_S01_GE1_107_Sep09_2_2.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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