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Sample GSM4240544 Query DataSets for GSM4240544
Status Public on Dec 30, 2020
Title Bone marrow, untreated, patient 5 rep 2
Sample type RNA
 
Source name BONE MARROW
Organism Homo sapiens
Characteristics cell type: mesenchymal stem cell line
treatment: NONE
tissue: BONE MARROW
patient: 5
ChIP: 3
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 B_5_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 11.96217308
A_33_P3246448 7.974459404
A_33_P3318220 5.529918528
A_33_P3236322 5.982993575
A_33_P3319925 5.779308974
A_21_P0000509 12.9685543
A_21_P0000744 9.893431895
A_24_P215804 5.607792642
A_23_P110167 8.374257511
A_33_P3211513 7.096797498
A_23_P103349 5.320572221
A_32_P61480 5.443461612
A_33_P3788124 5.769011321
A_33_P3414202 7.207624468
A_33_P3316686 7.160422961
A_33_P3300975 9.62716336
A_33_P3263061 10.7162434
A_33_P3261373 5.696098171
A_24_P278460 7.294046313
A_21_P0013109 5.791569912

Total number of rows: 50599

Table truncated, full table size 1255 Kbytes.




Supplementary file Size Download File type/resource
GSM4240544_US90403629_253949411101_S01_GE1_105_Dec08_1_2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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