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Forum: Core Facilities 04-18-2016, 10:08 AM
Replies: 1
Views: 2,894
Posted By Arvind Bhagwat
Forward-reverse read counts don't match

This is 16S metagenomic seq data, sent to service provider for MiSeq but they did HiSeq and 1/16th lane, 300 PE.
However, now CLC Workbench is flagging at the import paired-end read stage, saying:...
Forum: Metagenomics 01-13-2016, 10:00 AM
Replies: 2
Views: 1,466
Posted By Arvind Bhagwat
Experimental design

We want to investigate if certain treatment (nutrition supplement) changes mouse fecal microbiome, and if it does then how long does it take to change the biome? We have sample from -3 days to 21...
Forum: Sample Prep / Library Generation 11-10-2015, 10:03 AM
Replies: 2
Views: 710
Posted By Arvind Bhagwat
Non-Microbial DNA in feces

To perform microbiome DNA shotgun sequencing from mouse feces, does one need to worry about non-microbial DNA i.e. mouse/plant? I would use NEB-microbiome enrichment kit if I have too, i.e. if...
Forum: Sample Prep / Library Generation 08-17-2012, 03:07 PM
Replies: 2
Views: 1,462
Posted By Arvind Bhagwat
Poor quality bacterial RNA, need help!

Dear Friends, I am stuck on step '0' on my bacterial RNAseq project, i.e. poor quality RNA.
My Experion runs look like this (see attached file). :confused::confused:

I am using, ~10^8 cells, in...
Forum: Sample Prep / Library Generation 06-21-2012, 09:04 AM
Replies: 6
Views: 2,850
Posted By Arvind Bhagwat
Organism is Salmonella, yields are measured using...

Organism is Salmonella, yields are measured using BioRad Expirion Hi sens chip.
Forum: Sample Prep / Library Generation 06-21-2012, 08:28 AM
Replies: 6
Views: 2,850
Posted By Arvind Bhagwat
Red face New RiboZero Magnetic kit recommends purification...

New RiboZero Magnetic kit recommends purification (post rRNA removal) by a modified Qiagen RNeasy MiniElute. Here they recommend adding 2 x vol of EtOH than recommended by Qiagen. i.e. 100 ul -rRNA...
Forum: Sample Prep / Library Generation 06-15-2012, 08:32 AM
Replies: 1
Views: 1,250
Posted By Arvind Bhagwat
Optimal fragmentation of bacterial mRNA

Would any one please share conditions used for fragmenting bacterial mRNA? I am shooting for ~200 nt and starting mRNA conc. is ~75-100 ng/. I am using NEB Next mRNA library kit. They recommend 5 min...
Forum: Introductions 04-25-2012, 01:03 PM
Replies: 1
Views: 942
Posted By Arvind Bhagwat
Exclamation Bacterial RNASeq Expression profiles and genome size

Would some one guide me on how many million reads (50 bp, no pair ends) would be considered as 'safe' if objective is to get expression profile of the entire genome of Salmonella strain (~4.5 Mbp...
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