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Sample GSM3440012 Query DataSets for GSM3440012
Status Public on Apr 07, 2021
Title G2-9: Colon, AOM+DSS treated, Cardamonin simultaneous treatment, biol.rep.3
Sample type RNA
 
Source name Colon, AOM, Cardamonin simultaneous
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Colon
treatment regime: Treated - Cardamonin simultanoeus
Treatment protocol Azoxymethane (AOM) was given a single (10mg/kg B.wt) intraperitonielly at day 0 and three bouts of 5% DSS at days 5-10, 25-30, 45-50. At day 140, the mice were sacrificed. Cardamonin was administered orally, at a dose of 10mg/kg, 5 times every week for simultaneous group. And treatment started at a dose of 10mg/kg, 5times every week from 16th week to 30th week for the ''after tumor formation''group.
Growth protocol Colon collected from mice treated with AOM+DSS, followed by Cardamonin simultaneously treated or after tumor development. Colon from normal, healthy mice were used as control.
Extracted molecule total RNA
Extraction protocol Colon dissected and rinsed in 1X PBS, followed by snap freezing in liquid nitrogen. This was ground in liquid nitrogen, and mirVana miRNA isolation kit was used for the subsequent steps.
Label Biotin
Label protocol Total RNA was used for the reaction, Poly(A) tailing was performed followed by biotin labelling of the RNA. This was done by Flash Tag Biotin HSR labelling kit by Affymetrix
 
Hybridization protocol Samples were hybridised using Affymetrix hybridisation kit. Briefly, biotin labelled sample and hybridisation master mix were incubated at 99oC for 5 mins, then at 45oC for 5 mins. 130ul was injected into the array and both septa covered with tough spots. Loaded into hybridisation oven and incubated at 48oC, 60rpm for 16-18hrs
Scan protocol The chips were then scanned with an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, California, United States).
Description miRNA expression from AOM and cardamonin treated samples
Data processing The Data generated from the scan was then analyzed using the Bioconductor packages (Oligo, limma)
 
Submission date Oct 22, 2018
Last update date Apr 07, 2021
Contact name Dr. Harikumar K B
E-mail(s) harikumar@rgcb.res.in
Phone +91-471-2529-596
Organization name Rajiv Gandhi centre for Biotechnology
Department Cancer Research Program
Lab CRP-7
Street address Poojappura
City Thycaud
State/province Kerala
ZIP/Postal code 695 014
Country India
 
Platform ID GPL19117
Series (1)
GSE121608 Cardamonin repel colitis and its associated colorectal cancer

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
14q0_st 1.011869886
14qI-1_st 0.991312915
14qI-1_x_st 1.400119171
14qI-2_st 0.892672284
14qI-3_x_st 1.740537077
14qI-4_st 0.889455901
14qI-4_x_st 0.732160811
14qI-5_st 1.341356935
14qI-6_st 0.754016278
14qI-7_st 1.429207038
14qI-8_st 1.200291759
14qI-8_x_st 1.189287008
14qI-9_x_st 0.904293212
14qII-1_st 1.685765677
14qII-1_x_st 1.511289187
14qII-10_st 1.157728134
14qII-11_st 2.037532965
14qII-12_st 1.069858535
14qII-12_x_st 2.042810788
14qII-13_st 0.88263198

Total number of rows: 36353

Table truncated, full table size 983 Kbytes.




Supplementary file Size Download File type/resource
GSM3440012_G2-9_miRNA-4_0.CEL.gz 699.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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