Forum: RNA Sequencing
07-11-2016, 08:55 AM
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Replies: 1
Views: 1,100
Agilent small RNA chip ladder giving error
The ladder on the small RNA chip is giving error. We repeated a few times, but still the same. Why is that happening. The kit is not expired and ladder is not old either.
Please advise.
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Forum: Illumina/Solexa
06-20-2016, 10:37 AM
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Replies: 0
Views: 919
Has anyone done Zebrafish RNA-Seq?
I have attached RNA seq alignment results for Zebrafish and the % aligned is 65% (and I get 95% alignment with Human samples).
I wanted to know if you have done Zebrafish RNA-Seq and if you get...
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Forum: Sample Prep / Library Generation
06-17-2016, 08:17 AM
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Replies: 9
Views: 2,355
message
I just send you a message asking a question. Please let me know.
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Forum: Sample Prep / Library Generation
06-17-2016, 07:43 AM
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Replies: 0
Views: 851
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Forum: Illumina/Solexa
06-10-2016, 12:28 PM
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Replies: 6
Views: 3,963
I quantify each library with Qubit, in...
I quantify each library with Qubit, in triplicates and take average. Then calculate how much you need for a 70 ng pool (for example). Change the pool concentration if needed to adjust final volume of...
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Forum: Illumina/Solexa
06-10-2016, 12:14 PM
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Replies: 4
Views: 2,233
Yes that is correct, ideally is 850 to 1000. I...
Yes that is correct, ideally is 850 to 1000. I agree with Genomax that clustering also depends on the sample type, library etc. Libraries do perform differently, so clustering will differ. Do not...
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Forum: Sample Prep / Library Generation
06-10-2016, 08:38 AM
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Replies: 9
Views: 2,355
small RNA library
See attached. Sample was purified when given to me and hence checked on smallRNA chip and BioA conc. was close to the conc. by Qubit microRNA assay. I used a human brain total RNA as control while...
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Forum: Illumina/Solexa
06-10-2016, 08:24 AM
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Replies: 2
Views: 1,041
HiSeq run results
Attached is a picture of the HiSeq 2500 run I recently did. The data looks really good. But the user says "I haven’t mapped to the reference genome, but it does not look good. See the sequence...
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Forum: Sample Prep / Library Generation
06-10-2016, 08:07 AM
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Replies: 9
Views: 2,355
TruSeq smallRNA libraries
I am doing a TruSeq smallRNA library prep. When I was doing Ligate 3' adapter, and came to adding the STP step, the tube in the kit was empty (Illumina glitch). Illumina said to keep samples at -80...
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Forum: Sample Prep / Library Generation
05-27-2016, 06:21 AM
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Replies: 0
Views: 1,002
TruSeq smallRNA and chip-Seq libraries
1. I will be preparing smallRNA libraries using Illumna TruSeq kit. This is my first time and I was wondering if anyone has any feedback tips for the same. There is a gel excision part which I am not...
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Forum: Sample Prep / Library Generation
05-12-2016, 02:35 PM
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Replies: 2
Views: 1,088
How to get library size
Do my libraries look OK? Are they overloaded. How to I get the library size, I cant seem to adjust the upper and lower marker. Attached is the bioanalyzer profile. I called Agilent and they said...
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Forum: Sample Prep / Library Generation
04-12-2016, 12:12 PM
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Replies: 1
Views: 970
Bioanalyzer smallRNA results
Please see attached bioanalyzer profile for a smallRNA chip. I ran the same samples twice, but the ladder is giving some problem. I prepared the gel two times separately thinking that the gel might...
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Forum: Illumina/Solexa
04-04-2016, 01:48 PM
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Replies: 7
Views: 2,413
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Forum: Illumina/Solexa
04-04-2016, 11:51 AM
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Replies: 3
Views: 2,160
16S metagenomics on MiSeq
I will be doing MiSeq run for 16S metagenomics. it will be my first time. Recently some MiSeq v3 300 PE runs gave me trouble and hence I am worried. Are there any things I should do differently from...
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Forum: Illumina/Solexa
04-04-2016, 11:45 AM
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Replies: 7
Views: 2,413
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Forum: Illumina/Solexa
04-04-2016, 08:51 AM
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Replies: 7
Views: 2,413
I think the libraries were prepared using...
I think the libraries were prepared using Nextera. I did not make them, it was another user running on our machine. The run failed three time at the 300 cycle. I think he spiked 5%. He has had...
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Forum: Illumina/Solexa
04-04-2016, 06:35 AM
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Replies: 7
Views: 2,413
MiSeq v3 PE 300 run and Illumina's service
MiSeq v3 PE 300 run failed the 3rd time for me. First time Illumina claimed that the software needs downgrading which we did. Second time they said problem is system fluidics, I checked that and it...
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Forum: Sample Prep / Library Generation
03-15-2016, 01:33 PM
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Replies: 7
Views: 3,282
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Forum: Sample Prep / Library Generation
03-15-2016, 06:35 AM
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Replies: 7
Views: 3,282
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Forum: Sample Prep / Library Generation
03-10-2016, 12:39 PM
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Replies: 7
Views: 3,282
Clontech Smart Seq v4 Ultra Low RNA Input
Have you used this kit? if you have used it what kind of RNA samples did you use. I have doing some initial experimentation and wondering which RNA would be suitable: RNA from paraffin (FFPE...
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Forum: Sample Prep / Library Generation
03-04-2016, 12:14 PM
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Replies: 2
Views: 2,847
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Forum: Sample Prep / Library Generation
03-04-2016, 12:04 PM
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Replies: 1
Views: 1,238
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Forum: Sample Prep / Library Generation
02-16-2016, 09:25 AM
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Replies: 2
Views: 1,669
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Forum: Sample Prep / Library Generation
02-11-2016, 12:11 PM
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Replies: 2
Views: 1,669
EBT solution
I don't know if this is the right forum to ask. But I wanted to know the recipe for EBT solution using Tween. It cannot be ordered on it own from Illumina and I would to like to make it myself for...
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Forum: Illumina/Solexa
01-07-2016, 12:35 PM
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Replies: 1
Views: 1,007
HiSeq 2500 computer
I am trying to turn on the computer and its says no signal detected. This is stupid question but I am really new to this machine. How to start the computer.
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