Is there a gene/mRNA/miRNA list with the sex specificity so that they could be expressed only in men or women?

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...

07 August 2016 7,640 1 View

How to do "in silico" globin exclusion of transcripts during genome alignment for RNA-Seq (masking)?

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...

02 March 2016 539 1 View

How can I predict the transcription factor for a single gene?

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...

08 September 2014 3,799 8 View

Are there any well known/successful chemical inhibitors for STAT1, STAT3, c-JUN, JUNB, NFkB, CEBPA, CEBPB, CEBPD , IRF1 and Prdm1?

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...

08 September 2013 3,365 2 View

How can we know whether a gene is a Transcription factor or not?

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...

08 September 2013 1,426 7 View

How to deduce important paths between two given nodes in a network?

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...

07 August 2013 8,455 3 View

Chip-Seq Data anaylsis : BAM and BigWig output files

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...

06 July 2013 7,591 8 View

How to combine Network predictions from literature and Network inference methods?

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...

02 March 2013 3,880 4 View

How to identify significant differentially expressed genes from samples with out replicates?

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...

02 March 2013 4,962 6 View

Suggestions to analyse microarray time course expression data.

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...

02 March 2013 6,231 6 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

Can linear DNA be used as template for site-directed mutagenesis?

Is it possible to induce site-directed substitution mutation by quick-change method on linear dsDNA? or it has to be cloned in some vector? If yes, should it be treated with the Dpn1 enzyme...

03 March 2021 401 4 View

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02 March 2021 3,060 3 View

Does anyone have a recommendation for yeast reporter gene plasmid/protocol?

Hi, could anyone recommend a plasmid and/or protocol for reporter gene assay in S. cerevisiae? I want to assess the effect of growth conditions on a transcription factor, so I want to clone it`s...

01 March 2021 210 1 View

Issues with Permeabilization during Flow Cytometry?

Hello Everyone. Currently I am working to characterize macrophages in the myocardium after ischemia-reperfusion injury in rats. Due to the low total cell number isolated from rat hearts I can...

01 March 2021 3,867 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Can someone suggest a way to prepare slides to observe under confocal microscope for observing fluorescent tagged proteins??

I am growing the cells on coverslips and transfecting the fluorescent tagged protein directly on them. Then i want to observe these cells under confocal microscope. Currently i am just using...

01 March 2021 6,142 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View