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Search: Posts Made By: Kaizen
Forum: Bioinformatics 02-26-2019, 11:33 PM
Replies: 0
Views: 783
Posted By Kaizen
Recommended read depth for low input bulk rna-seq

Hi,
I'm wandering what is the sequencing depth recommended for low inupt bulk RNAseq, let's say 1000 cells.
I found on the Immgen website that they keep samples with a least 1 million mapped reads...
Forum: Sample Prep / Library Generation 10-18-2018, 12:00 AM
Replies: 3
Views: 2,625
Posted By Kaizen
Do you have any experience using Smartseq2 for...

Do you have any experience using Smartseq2 for bulk samples? from 1000-10000 immune cells.
I would like to know what's the maximum number of cells that you can process in a 96 well plate using bead...
Forum: Bioinformatics 09-12-2018, 05:46 AM
Replies: 3
Views: 2,564
Posted By Kaizen
but in that case, if you have a read mapping both...

but in that case, if you have a read mapping both to the transgene sequence and to the sequence upstream of downstream of it would lead to incorrect mapping and therefore will be lost, right?
Forum: Bioinformatics 06-29-2018, 04:47 AM
Replies: 3
Views: 2,564
Posted By Kaizen
How to add GFP sequence to mouse genome for mapping

Hi guys,
I was wandering what is the right way to add the sequence of GFP reporter to a mouse genom. Basically instead of "geneA" in the genome the modified mouse has "geneA-IRES-GFP".
I guess...
Forum: Sample Prep / Library Generation 07-31-2017, 12:00 AM
Replies: 0
Views: 1,809
Posted By Kaizen
Using Clean NGS from proteigene for RNA clean up of single cell

Hello,
Does anyone have some experience using Clean NGS beads from proteigene instead of RNA clean XP beads from Beckman for single cell application?
Thanks
Forum: Sample Prep / Library Generation 07-09-2017, 11:12 PM
Replies: 16
Views: 31,032
Posted By Kaizen
Hi kcchan, Could you please share your oligo...

Hi kcchan,
Could you please share your oligo sequences? I've tried paired end multiplexing of 384 samples with custom oligos from Sigma and some of them (100 oligos) seem to not work as good as the...
Forum: Sample Prep / Library Generation 03-27-2017, 12:23 AM
Replies: 1
Views: 1,762
Posted By Kaizen
Hi, Did you get an answer elsewhere?

Hi,
Did you get an answer elsewhere?
Forum: RNA Sequencing 01-25-2017, 05:27 AM
Replies: 0
Views: 1,759
Posted By Kaizen
Concentration Illumina Index adapters

Hi,
Does anyone of you know the concentration of Illumina index adapters in this kit FC-121-101?
Thanks
Forum: Bioinformatics 10-24-2016, 10:50 PM
Replies: 1
Views: 1,116
Posted By Kaizen
Anyone? thanks

Anyone? thanks
Forum: Bioinformatics 10-24-2016, 06:27 AM
Replies: 1
Views: 1,116
Posted By Kaizen
Finding differentially expressed genes from scRNA-seq

Hi guys,
I am looking for a program that can look for DEG accross single cells but in one sample only of ~90 cells. Want I want to know is if there any heterogeneity in my population that seem to be...
Forum: Bioinformatics 10-19-2016, 04:16 AM
Replies: 1
Views: 1,068
Posted By Kaizen
Advantage of Full length in scRNAseq

Hi guys,
Can someone please tell me what are the advantages of full length scRNAseq? I was wondering because the cDNA would anyway be fragmented during the library preparation.
Thanks for your help
Forum: Bioinformatics 09-09-2016, 12:17 AM
Replies: 3
Views: 1,622
Posted By Kaizen
Thanks for your answer. Just for precision, we...

Thanks for your answer. Just for precision, we ran 2*50bp sequencing and we wanted to copare with 1*50bp sequencing.
Cheers
Forum: Bioinformatics 09-08-2016, 06:34 AM
Replies: 3
Views: 1,622
Posted By Kaizen
Question Retrieving single and reads from paired end read sequencing run

Hi everyone,
As a first single cell RNAseq experiment, we would like to compare between single end and paired end sequencing. So at the beggining we wanted to perform the two sequencing on the same...
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