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Sample GSM4240554 Query DataSets for GSM4240554
Status Public on Dec 30, 2020
Title HNSCC, treated, patient 7 rep 2
Sample type RNA
 
Source name HNSCC
Organism Homo sapiens
Characteristics cell type: mesenchymal stromal cells
treatment: IFNG+TNFA
tissue: HNSCC
patient: 7
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 HIT_7_2
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 12.54166924
A_33_P3246448 7.89675811
A_33_P3318220 5.340406491
A_33_P3236322 5.852139328
A_33_P3319925 5.916999049
A_21_P0000509 13.75672896
A_21_P0000744 8.57204883
A_24_P215804 5.642503029
A_23_P110167 8.868350882
A_33_P3211513 7.102057715
A_23_P103349 5.287967841
A_32_P61480 5.676838606
A_33_P3788124 5.47370575
A_33_P3414202 6.478264032
A_33_P3316686 7.341796772
A_33_P3300975 7.527232626
A_33_P3263061 10.89174811
A_33_P3261373 5.47370575
A_24_P278460 6.242876367
A_21_P0013109 5.37340896

Total number of rows: 50599

Table truncated, full table size 1253 Kbytes.




Supplementary file Size Download File type/resource
GSM4240554_US90403629_253949411100_S01_GE1_105_Dec08_1_4.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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