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Sample GSM2736078 Query DataSets for GSM2736078
Status Public on May 17, 2018
Title ATMSC-OCHAEV-b
Sample type RNA
 
Source name ATMSC-OCHAEV
Organism Homo sapiens
Characteristics gender: female
cell type: adipose tissue-derived mesenchymal stem/stromal cells
treatment: OC HA-EVs
Treatment protocol The culture medium was removed, the wells were washed in PBS and the contents were collected for analysis.
Growth protocol AT-MSCs at passages 4-6 were seeded in 96-well plates at 2.5 * 103 cells/cm2. ls. The cells were cultured for 18 days at 37°C and 5% CO2 in a humidified atmosphere during which the medium was refreshed every 2-3 days. Each time, EVs were freshly added.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the AT-MSCs using the miRCURY™ RNA Isolation Kit (Exiqon A/S) according to the manufacturer's instructions.
Label biotin
Label protocol The starting amount of total RNA was 100 ng. 15 ug of cRNA was used for single-stranded cDNA-synthesis (sscDNA). This single-stranded DNA sample is then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the unnatural dUTP residues and breaks the DNA strand. DNA is labeled by erminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin. GeneChip® WT Plus Reagent Kit, Manual Target Preparation for GeneChip® Whole Transcript Expression Arrays, P/N 703174 Rev.5, Affymetrix.
 
Hybridization protocol A hybridization cocktail is prepared including the labeled, fragmented target and hybridization controls. The target is then hybridized to the GeneChip array in cartridge format during 16-hour incubation at 45 °C. Immediately following hybridization, the array is washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450, followed by scanning on a GeneChip® Scanner. GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 4, Affymetrix
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
Description OC HA-EVs (b)
Data processing The data were analyzed with R Statistical Software (R 3.4.0) using the Robust Multichip Average (RMA) algorithm of the oligo package as a normalization method. A modified t-statistics was calculated using the limma package. A false discovery rate (FDR) of < 0.05 was used to filter differentially expressed genes between treatments and control (EV-depleted MM).
 
Submission date Aug 09, 2017
Last update date May 17, 2018
Contact name Arjen WH Gebraad
E-mail(s) arjen.gebraad@helsinki.fi
Organization name University of Helsinki
Department Department of Oral and Maxillofacial Diseases
Lab Translational Research on Oral and Maxillofacial Sciences Group
Street address Haartmaninkatu 8, PO box 63
City Helsinki
State/province NA
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL23126
Series (1)
GSE102401 Effect of monocyte- and osteoclast-derived extracellular vesicles on adipose tissue-derived mesenchymal stem/stromal cells

Data table header descriptions
ID_REF
VALUE log 2 GC-RMA signal

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 0.676112945
AFFX-BkGr-GC04_st 0.681074651
AFFX-BkGr-GC05_st 0.64298598
AFFX-BkGr-GC06_st 0.719920763
AFFX-BkGr-GC07_st 0.725280259
AFFX-BkGr-GC08_st 0.738754305
AFFX-BkGr-GC09_st 0.76898508
AFFX-BkGr-GC10_st 0.94313185
AFFX-BkGr-GC11_st 1.024717294
AFFX-BkGr-GC12_st 1.294630412
AFFX-BkGr-GC13_st 1.530468827
AFFX-BkGr-GC14_st 1.990981886
AFFX-BkGr-GC15_st 2.475760838
AFFX-BkGr-GC16_st 3.459821622
AFFX-BkGr-GC17_st 3.813028799
AFFX-BkGr-GC18_st 4.583084433
AFFX-BkGr-GC19_st 5.203501203
AFFX-BkGr-GC20_st 5.450678338
AFFX-BkGr-GC21_st 5.798060992
AFFX-BkGr-GC22_st 6.374042499

Total number of rows: 138745

Table truncated, full table size 4075 Kbytes.




Supplementary file Size Download File type/resource
GSM2736078_11_EV_OC_HA_b_Clariom_D_Human_.CEL.gz 21.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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