User: mahnazkiani

gravatar for mahnazkiani
mahnazkiani30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 week, 1 day ago
Joined:
3 years, 4 months ago
Email:
m**********@gmail.com

Posts by mahnazkiani

<prev • 17 results • page 1 of 2 • next >
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De novo assembly and marker development for insecticide resistance
... Hello, I have a question for designing the experiment, I am interested to design markers for insecticide resistance in an insect that its genome has not been sequenced. I am thinking to sequence the genome, do de novo assembly and then look for variants between tolerant and control insect. Is this ...
next-gen sequencing written 16 days ago by mahnazkiani30 • updated 9 days ago by h.mon8.7k
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Comment: C: Differential Gene expression analysis with two factors
... Just wondering that does it makes sense to get DEGs from two genotypes and then use venn diagram to find similar DEGs in two genotypes and go through functional analysis after that? ...
written 26 days ago by mahnazkiani30
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Differential Gene expression analysis with two factors
... Hi, I have a question about RNA-seq data analysis, I have two genotypes and 3 sampling from a different part of the plant in each genotype. I want to analyze both genotypes together using factor analysis with a genotype: stage interaction term. How I can do that? Can I use edgeR? Appreciate your h ...
rna-seq written 26 days ago by mahnazkiani30 • updated 26 days ago by Devon Ryan70k
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Comment: C: Designing the RNA-seq for plant-insect interaction
... Thank you for your comment, I have two plant genotypes, one is resistant to insect and the other one is susceptible, I want to compare the gene expression of those two plants. The plants in the pots should be uniform because they are hybrid seed. Do you still think that is better to not have techni ...
written 3 months ago by mahnazkiani30
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Designing the RNA-seq for plant-insect interaction
... Hi, I am going to design a RNA-seq plant-insect interaction. I am not sure about how I should have biological and technical reps. If I collect the samples from 3 plants that planted in the same pot, can I consider each of them as technical reps and the whole pot as one biological rep and then the s ...
biological reps technical reps rna-seq written 3 months ago by mahnazkiani30 • updated 3 months ago by WouterDeCoster21k
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RNA-seq results comparison possible or not?
... I have 2 sets of data for my plant, the first set included 3 biological reps from plants that grown in 3 different times and got the samples from 2 parts of the stem to compare cell wall genes expression, my second set of plants grown in different light condition but still have 2 biological reps. ...
rna-seq written 15 months ago by mahnazkiani30 • updated 14 months ago by Biostar ♦♦ 20
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EdgeR output normalization?
... I have mean count output data from 3 biological reps that I got from edgeR implanted in CLC, I'm interested to do network analysis using these mean count data, do I need to do normalization before that or they are already normalized with CalcNormFactors-method-TMM?   Thanks       ...
rna-seq written 2.4 years ago by mahnazkiani30
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Network analysis-next step after calculating correlation in R
... I went through the R script that was online from the http://www.pb.ethz.ch/downloads/ . ############################################################################################################### # t_GCN.r script for computing targeted gene co-expression networks                               ...
R rna-seq written 2.4 years ago by mahnazkiani30 • updated 2.4 years ago by Jean-Karim Heriche13k
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Answer: A: Do or not doing the Co-expression data analysis?
... I have 3 biological replicates. ...
written 2.4 years ago by mahnazkiani30
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Comment: C: Do or not doing the Co-expression data analysis?
... I see, at the most I have3 samples per condition (3 sections of stems considered as the condition and 2 or 3 genotypes as the sample), therefore you don't recommend that?   ...
written 2.4 years ago by mahnazkiani30

Latest awards to mahnazkiani

Popular Question 11 months ago, created a question with more than 1,000 views. For Network analysis-next step after calculating correlation in R
Popular Question 11 months ago, created a question with more than 1,000 views. For Do or not doing the Co-expression data analysis?
Popular Question 11 months ago, created a question with more than 1,000 views. For Network analysis software
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Network analysis software

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