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Questions tagged [high-throughput]

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How to find out what biological effects a molecule has, without having a specific mechanism or pathway in mind?

I'm interested in finding what biological effects a (small) molecule has in a high-throughput and "low-assumption" way. I'm mainly interested in cell-based assays. Background: There are easy/...
Alex I's user avatar
  • 536
0 votes
1 answer

What is the dynamic range under initial conditions?

could someone help me to understand the following sentence better? It's from the book "A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery". And it's about ...
Mourinho_1's user avatar
4 votes
2 answers

Plating 96-well bacterial transformations

I need to clone 96 different inserts into the same backbone in arrayed format. I am planning to perform Gibson assembly reactions in a 96 well plate, and then do chemical transformations in a 96 well ...
khorms's user avatar
  • 81
2 votes
1 answer

qPCR : Cross-contamination while sealing plate

I'm trying to do realtime PCR on a plasmid and I have my positive and negative controls close to each other along with a no-template control. I add 1 ul of my template last into the 96 well plates (on ...
Prashant Bharadwaj's user avatar
1 vote
0 answers

Fisher's Method to melt p-values for CpG sites annotated to the same gene?

I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. ...
user35655's user avatar
0 votes
1 answer

How do you obtain specific mRNA transcript levels for comparison from a Hi-Seq dataset?

I have HiSeq data from mice exposed to two conditions. I would like to answer the following question: "Is there a significant difference in mRNA transcript levels when comparing condition A to ...
user avatar
0 votes
1 answer

How do high-throughput/NGS sequencers calculate quality scores?

I am confused as to how quality scores are actually calculated by DNA sequencers like Illumina. For each base call, some quality predictor value is computed, based on various properties of the ...
ShanZhengYang's user avatar
2 votes
0 answers

how to make plasma cells adhere to the bottom of a microplate?

I am isolating single plasma cells by FACS sorting into 384-well plates, with the intent to assay the supernatant and clone H/L chains from positive wells. The efficiency of the PCR is however low, ...
aag's user avatar
  • 131
3 votes
1 answer

Is there a photobleaching-resistant, cell-permeant viability stain in the far red part of the spectrum?

I am looking for a live-cell–impermeable dye for viability. (The cells cannot be permeabilized and fixed in this experiment.) I would prefer with excitation and emission spectra similar to Cy5, but I ...
Vebjorn Ljosa's user avatar
12 votes
1 answer

How to reduce edge effects in cell-based high-throughput experiments?

In high-throughput experiments where cells are cultured, treated, stained, and imaged in 384-well microplates, I frequently see significant edge effects. For instance, the following plot shows cell ...
Vebjorn Ljosa's user avatar