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

Can anyone suggest a protocol for siRNA/shRNA inhibition in human primary macrophages or is there a human primary macrophage cell line?

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...

10 November 2013 3,789 0 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

Which of the Covid-19 Vaccines would elicit the best immunoprotection and why?

I want to know which of the available Covid-19 Vaccines would elicit the best immunological response and why

02 March 2021 1,388 3 View

New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before?

Question to you and THEM, the New Journal, "Integrative Psychological and Behavioral Science" -- do you not know, and have you not seen, this done before? There appears to be a core problem for...

02 March 2021 3,024 2 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Unknown debris sheets observed in cell culture flasks?

Hi, We culture neural progenitor cells in T175 culture flasks coated with PLO-Laminin. We have successfully grown these cells with our protocol for months. Recently, we observed large sheets...

25 February 2021 3,443 4 View

Experimental Design: How deal with pseudreplicates with immunological and clinical-chemical paramaeters?

Hello everybody, I am investigating the influence of a toxinon various clinical-chemical and haematological parameters in fish. I have three treatments (control, low dose, high dose) in my...

24 February 2021 1,243 1 View

Standard curve shifting over time. How do I stabilise the ELISA?

24 February 2021 1,365 3 View

Can we recognize signs of the "volatility clustering" property of a time series in its time domain plot?

My purpose is to recognize the volatility clustering property without statistical tests such as The Lagrange Multiplier (LM) test.

24 February 2021 4,150 3 View

How to run repeated measures in mvabund?

I have a dataset of fish species abundances collected from 6 different habitats over the course of 30 years. Fish were collected multiple times per year and environmental variables were recorded...

21 February 2021 3,838 1 View

Looking for advices and tips to improve the staining and the gating strategy in human blood?

Hi, I am staining a human blood with CD19, CD3,CD14 and CD16. My gating strategy in FlowJo goes like this: - First, I gate a general population SSC-A VS FSC-A => Then gate for single cells, =>...

21 February 2021 5,724 4 View

How T cells recognise non-peptide antigens?

This might sound very basic question, but please share with me an explanation of how the T cell is activated when the antigen is not a peptide? What happens? And what are the molecules involved in...

21 February 2021 564 3 View