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Sample GSM4240555 Query DataSets for GSM4240555
Status Public on Dec 30, 2020
Title HNSCC, untreated, patient 8 rep 1
Sample type RNA
 
Source name HNSCC
Organism Homo sapiens
Characteristics cell type: mesenchymal stromal cells
treatment: NONE
tissue: HNSCC
patient: 8
ChIP: 4
Treatment protocol Cells were analyzed either resting either after 16 hours stimulation with IFNg and TNFa.
Growth protocol Cells were kept in culture in DMEM medium supplemented with 10% FCS.
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNeasy Micro Kit - QIAGEN following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer
Label Cy3
Label protocol Labelling was performed with the one color (Cyanine 3-CTP) Low Input Quick Amp Labeling Kit (Agilent Technologies) accordinf to manufacturer protocol.
 
Hybridization protocol Hybridization was performed according to specifications in One-Color Microarray-Based Gene Expression Analysis Protocol
Scan protocol The data was extracted using Agilent Feature Extraction Software version 10.7.3.1 with default parameters of protocol GE1_107_Sep09.
Description H_8_1
Data processing Data preprocessing was performed using R/Bioconductor (version 3.6) limma (version 3.34.9) package. Briefly, raw Feature Extractor data was loaded into R and further background corrected (method=”minimum”), normalized (method=”quantile”) and filtered to remove control probes.
 
Submission date Jan 01, 2020
Last update date Dec 31, 2020
Contact name Matteo Ramazzotti
E-mail(s) matteo.ramazzotti@unifi.it
Organization name University of Florence
Department Experimental and Clinical Biomedical Sciences
Street address viale Morgagni 50
City Firenze
ZIP/Postal code 50134
Country Italy
 
Platform ID GPL17077
Series (1)
GSE142816 Microarray gene expression analysis of HNSCC- and BM- derived mesenchymal stromal cells

Data table header descriptions
ID_REF
VALUE Values are defined as log2 transformed intensity values as resulting from preprocessing procedures

Data table
ID_REF VALUE
A_23_P117082 12.16580191
A_33_P3246448 9.073744098
A_33_P3318220 5.261507309
A_33_P3236322 5.510269671
A_33_P3319925 6.075144844
A_21_P0000509 13.97763629
A_21_P0000744 9.295033483
A_24_P215804 5.582141982
A_23_P110167 9.45604668
A_33_P3211513 7.22136055
A_23_P103349 5.442208978
A_32_P61480 5.224604682
A_33_P3788124 5.67507492
A_33_P3414202 7.075312006
A_33_P3316686 7.382691567
A_33_P3300975 5.718532876
A_33_P3263061 11.00437959
A_33_P3261373 5.366868586
A_24_P278460 7.075312006
A_21_P0013109 5.63571812

Total number of rows: 50599

Table truncated, full table size 1254 Kbytes.




Supplementary file Size Download File type/resource
GSM4240555_US90403629_253949411100_S01_GE1_105_Dec08_2_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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