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NicoBxl's Content

There have been 23 items by NicoBxl (Search limited from 13-November 18)


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#125788 checking whther there is any miRNA in introns of a specific gene.

Posted by NicoBxl on 20 December 2011 - 06:18 AM in siRNA, microRNA and RNAi

go to mirbase website. Download the gff file ( coordinates of each pre-miRNA). Check if they are in intron by overlapping with the intron coordinates. You can have the coordinates of exons (so introns too) in ensembl (biomart). Enjoy



#122962 how to know introns of a gene

Posted by NicoBxl on 03 November 2011 - 06:37 AM in Bioinformatics and Biostatistics

check ensembl



#121353 How to predict targets from a novel miRNA

Posted by NicoBxl on 12 October 2011 - 02:45 AM in siRNA, microRNA and RNAi

http://www.protocol-...-and-softwares/



#120888 Software for selection genes related to concrete cell processes

Posted by NicoBxl on 05 October 2011 - 05:31 AM in Bioinformatics and Biostatistics

take a look at Gene Ontology : http://www.geneontology.org/ or kegg : http://www.genome.jp/kegg/



#120222 Targets of mirna*

Posted by NicoBxl on 23 September 2011 - 12:14 AM in siRNA, microRNA and RNAi

from mirbase blog : http://www.mirbase.o...hats-in-a-name/



#120221 Bioinformatic tools for novel miRNA target prediction

Posted by NicoBxl on 23 September 2011 - 12:10 AM in Bioinformatics and Biostatistics

miRanda or targetscan



#114351 3'UTR sequence of a gene

Posted by NicoBxl on 06 July 2011 - 03:17 AM in siRNA, microRNA and RNAi

ensembl biomart ;)



#113879 What kind of statistics to use?

Posted by NicoBxl on 30 June 2011 - 03:48 AM in Bioinformatics and Biostatistics

for post-hoc use a wilcoxson test



#113333 simple heat map

Posted by NicoBxl on 23 June 2011 - 01:48 AM in Bioinformatics and Biostatistics

http://www2.warwick....cock/r/heatmap/



#110227 How can I find genomic sequence of a transcript

Posted by NicoBxl on 19 May 2011 - 12:04 AM in Bioinformatics and Biostatistics

use ensembl biomart

http://www.ensembl.o...9a2e33876767c0d



#110226 BLASTing a limited database

Posted by NicoBxl on 19 May 2011 - 12:03 AM in Bioinformatics and Biostatistics

You've to create an another DB with your subset sequences ( with formatdb )

and then blast your sequences against



#110036 Heatmap from excel file

Posted by NicoBxl on 17 May 2011 - 01:36 AM in Bioinformatics and Biostatistics

you can use R

to import your data in R from excel, you've to export your sheet in csv format (tab delimited)

in R :

A <- read.table("your file.csv",header=TRUE,row.names=TRUE,sep="\t")
heatmap(as.matrix(A))

here's more info and examples : http://www2.warwick....cock/r/heatmap/



#107977 RT-PCR t-test, and ANOVA

Posted by NicoBxl on 26 April 2011 - 06:28 AM in PCR, RT-PCR and Real-Time PCR

I read that the Wilcoxon test is better than the t-test for this kind of data . Is it true ?



#107619 RT-PCR t-test, and ANOVA

Posted by NicoBxl on 21 April 2011 - 11:44 PM in PCR, RT-PCR and Real-Time PCR

Hi,

Can you help me to analyze my RT-PCR data. I've the CT for all my samples and I've compute the dCT. I've four groups of samples ( one group per condition) and I want to perform ANOVA. How can I do that ? in R ?

Here's a example of my dCT matrix
        ctrl1  ctrl2  ctrl3     A1     A2     A3     B1     B2     B3
gene1   7.307  0.237  0.611  9.640  8.705  8.870  7.307  0.611  0.237
gene2   9.061 10.111 11.016 12.025 11.482 10.982  9.061 11.016 10.111
gene3   7.903 12.048 11.911 10.796 10.931 10.648  7.903 11.911 12.048
gene4  11.731 17.809 15.951 19.682 16.964 14.036 11.731 15.951 17.809
gene5   9.464  8.955  9.351 11.730 10.652 11.009  9.464  9.351  8.955
gene6   5.737  6.539  7.557  9.279  8.057  8.115  5.737  7.557  6.539
gene7  12.971 10.800 11.314 14.235 13.043 12.999 12.971 11.314 10.800
gene8   6.756  6.060  6.297  8.254  7.907  7.680  6.756  6.297  6.060
gene9  20.093 21.098 21.488 23.132 22.913 23.040 20.093 21.488 21.098
gene10 11.943 13.582 14.404 15.425 15.627 13.367 11.943 14.404 13.582

Thanks,

N.



#107316 pri-miRNA sequencing

Posted by NicoBxl on 20 April 2011 - 12:17 AM in siRNA, microRNA and RNAi

I'm not looking after pre-miR but at pri-miR ( the first step in the life of the miRNA )



#106508 miRNA LNA

Posted by NicoBxl on 12 April 2011 - 03:26 AM in siRNA, microRNA and RNAi

Hi,

Before testing my antimir LNA, I've to design a scramble LNA ( for the control ). How can I know wich sequence to use for the scramble control ? Is it a pure random sequence ? a permutation of my miRNA to inhibit ?

Thanks,

N.



#105694 pri-miRNA sequencing

Posted by NicoBxl on 04 April 2011 - 04:29 AM in siRNA, microRNA and RNAi

Hi,

Is it possible to detect pri-miRNA from RNA-seq data ? Is there any studies on this subject?

Thanks,

N.



#103537 Adapters

Posted by NicoBxl on 14 March 2011 - 06:17 AM in siRNA, microRNA and RNAi

can you tell us which sequencing plateform (illumina, 454, ... ) did you use ?



#103300 How BLAST

Posted by NicoBxl on 11 March 2011 - 02:27 AM in Bioinformatics and Biostatistics

to specify the strand in the blast program use the -S param

-S N (bl2seq, blast2, blastall, blastall_old, blastcl3,
megablast) Query strands to search against database for blastn,
blastx, tblastx:
1 top
2 bottom
3 both (default)



#103100 predict union between microRNAs and genes

Posted by NicoBxl on 09 March 2011 - 03:41 AM in siRNA, microRNA and RNAi

targetscan, miRanda, PITA, pictar,...

there's a lot of miRNA target prediction tools.



#103098 pri-miRNA transcript characterization

Posted by NicoBxl on 09 March 2011 - 03:38 AM in siRNA, microRNA and RNAi

Since it is pretty hard to detect precursor miRNA, if you have cloned and know the mature miRNA sequence, you should blast the genome to find where it is derived, then use the sequence from that region to predict secondary structure of RNA to see if stem-loop structure can be formed by the sequence.



I already did that (prediction with miRDeep ans sRNAloop and experimentaly by custom stemloop RT-PCR )

Now we want to know the pri-miRNA (not the pre-miRNA)



#103019 pri-miRNA transcript characterization

Posted by NicoBxl on 08 March 2011 - 01:15 AM in siRNA, microRNA and RNAi

Hi,

I'm looking for a way to characterize the pri-miRNA of a miRNA. The problem is that we just discover this miRNA and don't know where the pri-miRNA starts.

Anyone knows how to do such a thing ?

Thanks

N.



#99220 Relative quantification analysis Ct values & 2-ΔΔCT method

Posted by NicoBxl on 01 February 2011 - 01:38 AM in PCR, RT-PCR and Real-Time PCR

I've a similar problem

I want to analyze two samples A and B.

For some genes, I've a CT of 40(so undetected) in A and 30 in B.

How can I calculate a foldchange for this ?

If it's impossible how can I present the data

Thanks




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