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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
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 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
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 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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