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Sample GSM4240535 Query DataSets for GSM4240535
Status Public on Dec 30, 2020
Title HNSCC, treated, patient 1 rep1
Sample type RNA
Source name HNSCC
Organism Homo sapiens
Characteristics cell type: mesenchymal stromal cells
treatment: IFNG+TNFA
tissue: HNSCC
patient: 1
ChIP: 2
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 with default parameters of protocol GE1_107_Sep09.
Description HIT_1_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
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
VALUE Values are defined as log2 transformed intensity values as resulting from preprocessing procedures

Data table
A_23_P117082 12.32392378
A_33_P3246448 6.25044647
A_33_P3318220 5.718532876
A_33_P3236322 5.765700488
A_33_P3319925 6.322209844
A_21_P0000509 12.66288738
A_21_P0000744 8.340719421
A_24_P215804 5.841957399
A_23_P110167 8.510969068
A_33_P3211513 7.088788239
A_23_P103349 5.384601384
A_32_P61480 5.357552005
A_33_P3788124 5.916999049
A_33_P3414202 6.186578552
A_33_P3316686 7.68101874
A_33_P3300975 5.244958393
A_33_P3263061 11.85682063
A_33_P3261373 5.636624621
A_24_P278460 6.578254742
A_21_P0013109 5.522091069

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM4240535_US90403629_253949411048_S01_GE1_105_Dec08_1_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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