How to get data from SRA for gene expression analysis?

More Tanvir Hossain Emon's questions See All

How to derive equations for a resonant buck converter with ZVS?

I am not understanding how each author is deriving the equations and the working principle. Individual authors are giving their own working principle explanation for different circuit topology....

12 February 2021 496 1 View

Is there any website where I can find daily COVID-19 confirmed cases and deaths according to age and sex for Sri Lanka?

I need to calculate CFR based on age group and sex. For this, I need daily COVID-19 confirmed cases and deaths according to age and sex for Sri Lanka. Where can I find this?

13 December 2020 8,287 2 View

Is it possible to plot the graph between friction coefficient vs time during wear testing of FSW samples ?

I wonder in the literature that, many of the researchers keep time in seconds at very different levels. Like some may run the wear test for 3500 sec and others may run for 50000 sec. I want to...

10 October 2020 7,093 11 View

What are the basic guidelines that we have to follow while writing the scientific article?

Writing of article especially for a good journal is very challenging. This required careful assessment of all things right from the aim of the article to the finishing that includes the...

04 October 2020 8,915 72 View

How heat input intensity influence the materials grain structure?

As the excessive as well the insufficient heat lead to complex changes in the microstructure as well the grain structure of the base material due to which the materials property were affected. How...

23 September 2020 9,752 20 View

How the advancement in the technology affects the traditional way of work?

As due to the huge advancement in the technology the work done is more easier than the traditional way of doing it. But as the advancement in the technology may also lead to some negative aspects...

23 September 2020 5,584 53 View

What is the difference between Micro-Electro-Mechanical Systems, or MEMS and Nano-Electro-Mechanical system or NEMS?

As the technology is growing at very fast pace with many latest advancements. For which the micro level objects were transferred to nanoscale that provides enormous applications. Inspite of all...

26 August 2020 7,172 16 View

How Zener-pinning effect and Orowan strengthening mechanisms are correlated to each other?

According to the metallurgy point of view, how these mechanisms help into affects the behavior of materials' intrinsic property?

22 August 2020 8,087 6 View

How to fix atoms with same coordinate error?

I am getting a fatal error in gromacs while creating a GRO file and ligand topology file under the amber force field. The acype of python providing the error message. Parameter was: Charge =...

29 July 2020 3,347 4 View

In case of metal matrix nanocomposites how we can control the size of the particle to make significant changes in the properties?

Is there any method that we can use to control them, kindly share your experience.

22 July 2020 7,083 15 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 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

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

What is the best concentration of cDNA to be used for qPCR?

I have synthesised cDNA from 500ng/ul of RNA. The concentration of the cDNA Is about 5000ng/ul. Should I dilute my cDNA or just use it as it is for my qPCR? I usually use 2ul of cDNA for a 20ul...

24 February 2021 8,618 3 View

Recommendations on homogenizers for RNA isolation?

I will be performing RNA isolation with frozen lung biopsy samples and am in the market for a tissue homogenizer. I am wanting a homogenizer that will fit in a 1.5ml tube. I was looking at the...

24 February 2021 3,623 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Is it efficient to do liquid biopsy to investigate the gene expressions of the tumor?

To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...

23 February 2021 7,326 5 View

Matthew Edward Thornton

Hello! It is easiest to use SRAtools and "fastq-dump" I add "--split-3" this should give you R1 and R2 if it was paired sequencing. Good luck!

Rohit Kumar Verma

To get data from the Sequence Read Archive (SRA) for gene expression analysis, first, identify the relevant dataset using keywords or accession numbers. Access the SRA website or use SRA Toolkit to download and convert the raw sequencing data (FASTQ files) to a compatible format for analysis with bioinformatics tools.

Jan Oppelt

If you don't want to use sra-tools, you can search for the SRA id at https://www.ebi.ac.uk/ena/browser/ and download the fastq files directly.