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Sample GSM503406 Query DataSets for GSM503406
Status Public on Feb 02, 2010
Title HL60, BR1, 36hr
Sample type RNA
 
Channel 1
Source name HL60 cells treated with 36 hours of vitamin D exposure
Organism Homo sapiens
Characteristics cell line: HL60
vitamin d exposure: 36hrs
Treatment protocol We stimulated cells with 0.1 microM calcitriol for 0 hours, 8 hours or 36 hours
Growth protocol We used nine cell lines (Hep-G2, HL60, K562, AG09309, AG09319, GM15084, GM12878, GM07348 and GM07019). These were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, 0.2 mM L-glutamine at 37 oC in 5% humidified CO2
Extracted molecule total RNA
Extraction protocol After harvesting, cells were lysed in 500 uL of lysis buffer (Promega). Homogenised samples were immediately stored at -80 oC
Label Hy3
Label protocol 400 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer
 
Channel 2
Source name Common reference (S1-S54)
Organism Homo sapiens
Characteristics cell line: Common reference (S1-S54)
vitamin d exposure: --
Treatment protocol We stimulated cells with 0.1 microM calcitriol for 0 hours, 8 hours or 36 hours
Growth protocol We used nine cell lines (Hep-G2, HL60, K562, AG09309, AG09319, GM15084, GM12878, GM07348 and GM07019). These were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, 0.2 mM L-glutamine at 37 oC in 5% humidified CO2
Extracted molecule total RNA
Extraction protocol After harvesting, cells were lysed in 500 uL of lysis buffer (Promega). Homogenised samples were immediately stored at -80 oC
Label Hy5
Label protocol 400 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer
 
 
Hybridization protocol The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)
Scan protocol After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA)
Description HL60 cells treated with 36 hours of vitamin D exposure
Data processing The quantified signals were background corrected (Normexp with offset value 10 [21]) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm
 
Submission date Feb 01, 2010
Last update date Feb 01, 2010
Contact name Adam Handel
E-mail(s) ahandel@doctors.org.uk
Organization name University of Oxford
Department Wellcome Trust Centre for Human Genetics
Lab Ebers Group
Street address Roosevelt Drive
City Oxford
ZIP/Postal code OX3 7BN
Country United Kingdom
 
Platform ID GPL7723
Series (1)
GSE20122 Vitamin D and microRNA Expression

Data table header descriptions
ID_REF
VALUE log2(Hy3/Hy5) - log2 of ratio between sample and reference miRNA

Data table
ID_REF VALUE
17748 0.26
17888
17749 0.18
42769 -0.11
19004 0.27
42653
46437 0.21
42505 0.73
46436 0.27
46435 -0.13
46438 -0.05
42778
9938 -0.19
19581 -2.95
31026
10919 0.20
42648 -0.81
42508 0.44
19582 0.15
17854 0.24

Total number of rows: 567

Table truncated, full table size 5 Kbytes.




Supplementary file Size Download File type/resource
GSM503406_Hy3_Exiqon_14114406_S01_Cropped.txt.gz 883.1 Kb (ftp)(http) TXT
GSM503406_Hy5_Exiqon_14114406_S01_Cropped.txt.gz 791.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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