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Sample GSM2747733 Query DataSets for GSM2747733
Status Public on Aug 01, 2019
Title B16F0 cells cultured for 24 hr in serum-free media, rep 4
Sample type RNA
 
Source name B16F0 cells
Organism Mus musculus
Characteristics tag: B16F0
Treatment protocol not applicable
Growth protocol Cultured for 24 hours in serum-free media
Extracted molecule total RNA
Extraction protocol Total RNA isolated from B16F0 exosomes and cells by RNeasy kit (Qiagen) was quantified using Nanodrop and analyzed by on-chip-electrophoresis using the Agilent Bioanalyzer.
Label biotin
Label protocol Four hundred nanograms of each miRNA sample was biotin labeled using the Genisphere FlashTag HSR Kit according to the manufacturer's instructions. The labeling of RNA was confirmed by Enzyme Linked Oligosorbent Assay (ELOSA) according Genisphere FlashTag HSR protocol.
 
Hybridization protocol The 21.5 microl of biotin-labeled RNA with added hybridization controls was hybridized to the GeneChip miRNA 2.0 Arrays (Affymetrix) at 48oC and 60 rpm for 16 hours in GeneChip Hybridization Oven 640 (Affymetrix).The entire reaction of fragmented and biotin-labeled cDNA (50 mu) with added hybridization controls was hybridized to the mouse GeneChip 1.0 ST Exon Arrays (Affymetrix) at 45oC for 17 hours in GeneChip Hybridization Oven 640 (Affymetrix).
Scan protocol GeneChip miRNA 2.0 Arrays were stained using FS 450_0003 protocol in Affymetrix GeneChip Fluidics Station 450. Briefly, biotin-labeled RNA was reacted using washes with a solution containing a streptavidin-phycoerythrin complex, with an intermediate treatment of biotin-labeled anti-streptadvidin antibody to amplify the signal. Phycoerythrin labeling was detected within the Affymetrix GeneChip Scanner 3000 7G plus using 532 nm light and detected by a photomultiplier tube.
Data processing A miRNA QC Tool software (Affymetrix) was used to check quality controls of hybridized chips. All chips that passed quality controls were RMA normalized using miRNA QC Tool.
 
Submission date Aug 21, 2017
Last update date Aug 01, 2019
Contact name David John Klinke
E-mail(s) David.Klinke@mail.wvu.edu
Phone 304-293-9346
Organization name West Virginia University
Department Chemical Engineering
Street address P.O. Box 6102
City Morgantown
State/province WV
ZIP/Postal code 26506-6102
Country USA
 
Platform ID GPL14613
Series (2)
GSE102883 Expression data of miRNA from parental B16F0 cells and B16F0 exosomes [miRNA]
GSE102951 Expression data from parental B16F0 cells and B16F0 exosomes

Data table header descriptions
ID_REF
VALUE RMA signal estimates from Expression Console Software
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
cel-let-7_st 11.97735 8.72E-16
cel-let-7-star_st 3.867929 0.9439553
cel-lin-4_st 4.164014 0.1193154
cel-lin-4-star_st 3.777044 0.592277
cel-miR-1_st 4.085317 0.1896764
cel-miR-2_st 3.97813 0.6105955
cel-miR-34_st 3.923711 0.4255806
cel-miR-34-star_st 4.247579 0.1165753
cel-miR-35_st 3.839018 0.6829782
cel-miR-36_st 4.031512 0.1963271
cel-miR-37-star_st 3.911351 0.9447872
cel-miR-37_st 3.699793 0.8170468
cel-miR-38_st 3.959168 0.5613415
cel-miR-39_st 4.128136 0.3297949
cel-miR-40_st 4.083018 0.536665
cel-miR-41_st 3.769105 0.6566804
cel-miR-42-star_st 3.984671 0.8763427
cel-miR-42_st 4.115679 0.3241621
cel-miR-43_st 4.048696 0.4899638
cel-miR-44_st 3.976091 0.6791865

Total number of rows: 20180

Table truncated, full table size 700 Kbytes.




Supplementary file Size Download File type/resource
GSM2747733_4_cell_24h_miRNA-2_0_.CEL.gz 616.2 Kb (ftp)(http) CEL
Processed data included within Sample table

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