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Questions related from Aravind Tallam
Dear All, I have RNA-Seq data from a patient cohort and for my analysis, i would like to exclude the genes and miRNAs which are specific for male and female. Hence, could you please suggest where...
08 August 2016 7,707 1 View
Hi All, After aligning to the genome, we figured out that there are lot of globin transcripts in our data due to the experimental error while isolating RNA. I am aware that we can mask specific...
03 March 2016 597 1 View
Hello all, I have several methods and tools like Biobase, Jaspar to predict transcription factors for my genes of interest (in both human and mouse), but they all are giving me too many candidates...
09 September 2014 3,857 8 View
I have been working with Human primary macrophages (differentiated from monocytes isolated from blood) and the experiments done to date with siRNA and shRNA (Nucleofection) in these cells were...
11 November 2013 3,871 0 View
I need the chemical inhibitors of the above genes and I have been searching in different papers and companies. If any of you already know the chemical inhibitors, could you please tell me? Cell...
09 September 2013 3,420 2 View
I have differentially expressed genes from my microarray data and i would like to know if there are any knowledge sources/tools with the collection of all known Transcription factors from...
09 September 2013 1,483 7 View
I have a network with 500 nodes and 400 edges. Iam interested in the pathways between 2 nodes and for that i have calculated all the shortest paths between that 2 nodes. To test experimentally, i...
08 August 2013 8,525 3 View
Dear All, I would like to have the bigwig or BAM output files after aligning my Chip-Seq data with the reference genome and then use these files for peak calling. Could you please advice me about...
07 July 2013 7,658 8 View
I have been working on the analysis of time course microarray data (Agilent, Affymetrix, Illumina and Caltech platforms). I used Limma and Timecourse packages in R till now. I would like to know...
03 March 2013 6,325 6 View
I downloaded a dataset from GEO (GSE1906) and they have only 1 sample (I mean with out any replicates/triplicates) per condition and their data files contain the measure of the abundance of a...
03 March 2013 5,018 6 View
Using GEO data and network inference methods (GRN), I have got relationships between genes from each GRN method (example, GENIE3, CLR, LASSO). For specific genes which I am interested, I have got...
03 March 2013 3,931 4 View
We have discovered the expression of a gene in humans which is annotated as a mouse homologue in the databases. We would like to get the original sequence of that gene (as the present one in the...
02 February 2013 3,287 8 View
As you might know that some of the datasets in GEO will contain the data in SOFT formatted files instead of CEL files which contains the abundance of the transcripts. Do we need to consider these...
02 February 2013 3,237 9 View
We have a gene in question and want to know if it can act as a transcription factor or not. Are there any tools which can predict this function given the gene or its sequence?
01 January 2013 5,241 11 View
Which is the state-of-art, reliable and efficient method to obtain transcriptomics data, microarray or RNA-Seq?. Also can we get both mRNA and MiRNAs from one RNA-Seq experiment which is not...
10 October 2012 8,565 6 View
I prepared mRNA and miRNA samples from Human primary monocytes and macrophages. These samples will be tested for their RIN (>7.0) and quantity (>1micro g) to be sent to microarray. In addition,...
10 October 2012 7,323 8 View
For the differentiation of human primary monocytes to macrophages, I use human serum added to RPMI. Due to some problems with the human serum, the cells isolated from a lot of blood samples...
10 October 2012 421 10 View
I will be sacrificing mice and will extract blood by cardiac puncture. I need to isolate monocytes and differentiate them into macrophages. I found some papers but they modify the protocol...
03 March 2012 9,066 13 View
