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Search: Posts Made By: Alex Clop
Forum: General 10-22-2014, 08:33 AM
Replies: 0
Views: 845
Posted By Alex Clop
TargetScan input files

Hi there,

I want to identify conserved miRNA target sites in the pig (Sus scrofa) using TargetScan. This tool requires (i) a list of miRNAs and (ii) a list of aligned 3'UTR sequences from many...
Forum: Epigenetics 01-11-2012, 04:37 AM
Replies: 6
Views: 4,922
Posted By Alex Clop
Hi Jon As I am interested in histone...

Hi Jon

As I am interested in histone modifications, I am doing micrococcal digestion on native chromatin so that my major fraction correspond to mono-nucleosomal bands (150bp) with very weak di-...
Forum: Epigenetics 01-11-2012, 03:14 AM
Replies: 6
Views: 4,922
Posted By Alex Clop
Hi Jon As I am interested in histone...

Hi Jon

As I am interested in histone modifications, I am doing micrococcal digestion on native chromatin so that my major fraction correspond to mono-nucleosomal bands (150bp) with very weak di-...
Forum: Epigenetics 01-09-2012, 09:49 AM
Replies: 6
Views: 4,922
Posted By Alex Clop
Indexing ChIPseq libraries using Illumina's TruSeq and ChIPseq kits

Hi there,

I have prepared five indexed libraries from two ChIP samples and three different non immunoprecipitated chromatins (inputs) consisting in mono-nucleosomal bands (150bp long). The samples...
Forum: Epigenetics 03-18-2011, 01:31 PM
Replies: 0
Views: 2,108
Posted By Alex Clop
Chromatin micrococcal digestion

Dear all,

I want to do a ChIP-seq experiment using a H3K4me1 antibody and have put in place a native chromatin extraction protocol with micrococcal nuclease digestion. With this protocol one ends...
Forum: Epigenetics 03-10-2011, 11:38 AM
Replies: 22
Views: 9,523
Posted By Alex Clop
Thanks Ethan for sharing. I will keep you...

Thanks Ethan for sharing.

I will keep you posted with my own optimizations.

Cheers
Forum: Epigenetics 03-10-2011, 09:13 AM
Replies: 22
Views: 9,523
Posted By Alex Clop
Hi all, ETHANol, I am also using the...

Hi all,

ETHANol,

I am also using the epigenome protocol for native chromatin with micrococcal digestion but don't know how to get to highest amount of chromatin together with only...
Forum: Epigenetics 03-09-2011, 07:58 AM
Replies: 9
Views: 7,232
Posted By Alex Clop
Thanks for all your replies, really. I...

Thanks for all your replies, really.

I considered the option of selecting the mononucleosomes but I was resilient as a lot of precious chromatin would then be discarded and the starting amount...
Forum: Epigenetics 03-08-2011, 07:05 AM
Replies: 9
Views: 7,232
Posted By Alex Clop
ChIPseq for histone modifications

Hello there,

I want to do ChIP-seq for H3K4me modified histone and have a native chromatin extraction protocol with micrococcal nuclease step in place. I plan to use the Illumina HiSeq200 for...
Forum: Bioinformatics 08-12-2010, 05:31 AM
Replies: 1
Views: 2,636
Posted By Alex Clop
Mapping 454 reads using Galaxy online.

Dear all,

We have been trying to do Mapping assemby of 454 reads using the Galaxy webbased tool (http://main.g2.bx.psu.edu/) but we are finding problems in converting from SAM format to BAM...
Forum: 454 Pyrosequencing 11-19-2008, 02:23 AM
Replies: 5
Views: 4,394
Posted By Alex Clop
454: Unmapped contigs after Reference Assembly

Dear all,

We have sequenced human BAC clones using 454 sequencing technology. During the assembling process into a consensus sequence (CONS) using in parallel two reference sequences, many reads...
Forum: 454 Pyrosequencing 11-19-2008, 01:55 AM
Replies: 9
Views: 7,502
Posted By Alex Clop
454 sequences by Pyrosequencing. As defined by...

454 sequences by Pyrosequencing. As defined by Nature Reviews Genetics Glossary, Pyrosequencing is A DNA sequencing technique that relies on detection of pyrophosphate release on nucleotide...
Forum: Bioinformatics 10-14-2008, 03:54 AM
Replies: 8
Views: 4,006
Posted By Alex Clop
Dear Colin Thanks very much for the info. I...

Dear Colin

Thanks very much for the info. I will have a look now.

I am currently testing the CLC Genomics Workbench from CLC Bio. It seems quite good up to now, but I am still testing it.
...
Forum: Bioinformatics 09-17-2008, 02:11 AM
Replies: 8
Views: 4,006
Posted By Alex Clop
re: finding polymorphisms by large sequence alignments

Thanks for your replies.

Yes, there is Newbler which is supplied by Roche with the 454 machine. We do not have this facility here so don't have access to the software. We are thinking about...
Forum: Bioinformatics 09-12-2008, 10:21 AM
Replies: 8
Views: 4,006
Posted By Alex Clop
finding polymorphisms by large sequence alignments

Hello all

I just registered to SEQanswers after a friends recommendation. I work in molecular genomics since 1996, starting in livestock genomics in Barcelona and currently working in the genetics...
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