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Sample GSM4191498 Query DataSets for GSM4191498
Status Public on Jan 01, 2021
Title hDF_F22Br_Control_24h_rep3
Sample type RNA
 
Source name hDF_F22Br_Control_24h
Organism Homo sapiens
Characteristics donor id: F22Br
Sex: Female
age: 22y
tissue: Breast
cell type: enzyme-derived, human dermal fibroblasts (hDF)
treatment: Control
treatment time: 24h
Treatment protocol hDF were seeded into 6-well microplates and cultured in complete DMEM for four days at 37°C in 5% CO2. hDF were equilibrated in low (1%) serum DMEM for 24h and treated with or without TGF-β1 (10 ng/ml; R&D) in low (1%) serum DMEM for a further 12h or 24h.
Growth protocol Human dermal fibroblasts (hDF) were cultured in phenol red-free, low glucose DMEM (Sigma-Aldrich) supplemented with 10% foetal bovine serum; 450 µg/ml L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich). Referred to as complete DMEM.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was measured using the Bioanalyser 2100 (Agilent) and RNA 6000 Nano kit (Agilent) according to the manufacturer’s instructions.
Label Cy3
Label protocol One colour Quick-Amp labelling kit (Agilent) was used to derive cyanine 3 (Cy3)-labelled cRNA from the extracted RNA. A one colour RNA spike-in kit (Agilent) was used to monitor sample amplification and labelling efficiency. For each sample, 300 ng total RNA was used; universal human reference RNA (Agilent) was used as a reference. The concentration of labelled cRNA was measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific).
 
Hybridization protocol Sample preparations were mixed, collected and incubated at 60°C for 30 min to fragment the cRNA using the gene expression hybridisation kit (Agilent): Cy3-labelled cRNA (600 ng) with nuclease-free water, 2X blocking agent, 1X fragmentation buffer. The fragmentation reaction was stopped by adding 1X hybridisation buffer Hi-RPM. Each SurePrint microarray (Agilent) was incubated in a rotisserie oven at 65°C for 17h to allow hybridisation. Following hybridisation, microarrays were added to gene expression wash buffer 1 (Agilent), incubated at room temperature for 1 min. Microarrays were washed in wash buffer 2 (Agilent) at 37°C for 1 min. Arrays were incubated in acetonitrile (Sigma-Aldrich) at room temperature for 10 sec, dried and covered with ozone protection covers (Agilent).
Scan protocol Arrays were imaged using the Agilent G2565BA microarray scanner system. All three experiments were run using the SurePrint G3 Human GE 8x60K V2 kit (Agilent).
Description F22Br_Control24(normalized)
Data processing Scanned images were analysed with G2567AA feature extraction software (v.9.5.1; Agilent) using default parameters (protocols GE1-v5_91_0806; grid 039494_D_F_20150612). Gene expression values were normalised using Agilent GeneSpring GX software (v.14.8).
 
Submission date Nov 25, 2019
Last update date Jan 02, 2021
Contact name Oliver J Culley
E-mail(s) oliver.culley1@gmail.com
Phone +447500 939574
Organization name King’s College London
Department Centre for Stem Cells and Regenerative Medicine
Lab Fiona M Watt
Street address Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
 
Platform ID GPL17077
Series (1)
GSE140962 Correlating functional heterogeneity of human dermal fibroblasts with differences in gene expression

Data table header descriptions
ID_REF
VALUE Normalised signal intensity.

Data table
ID_REF VALUE
GE_BrightCorner 0.76488256
DarkCorner -0.34113693
A_23_P117082 0.41926527
A_33_P3246448 -0.89749193
A_33_P3318220 -0.27910995
A_33_P3236322 1.548564
A_33_P3319925 -0.33828354
A_21_P0000509 -0.70667076
A_21_P0000744 0.25236797
A_24_P215804 -0.29881763
A_23_P110167 0.3397231
A_33_P3211513 0.17627335
A_23_P103349 -0.5320854
A_32_P61480 -0.3695693
A_33_P3788124 -0.35899973
A_33_P3414202 -0.14301944
A_33_P3316686 -0.45942545
A_33_P3300975 0.43910456
A_33_P3263061 0.25633287
A_33_P3261373 -0.4901228

Total number of rows: 50739

Table truncated, full table size 1235 Kbytes.




Supplementary file Size Download File type/resource
GSM4191498_US84700251_253949447260_S01_GE1_1200_Jun14_1_1.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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