Does cDNA library size have any effect on sequencing or downstream differential gene expression analysis?

03 November 2021 1 5K Report

I have prepared cDNA libraries. Library size is large in a few of my samples (680-777 bp, including adapters), does large library size have any effect on RNAseq (NovaSeq) or downstream analysis? I plan to do differential gene expression analysis.

Soner Öner-Sieben

Hi Mousumi,

size shouldn't be an issue.

Best

Soner

Badges
Science topic

More Mousumi Mary's questions See All

How to interpret MIC values in microplate reader?

Good day! I am currently testing my sample for MIC, may you help me how to interpret the results at OD630? how would I know if there is growth or not based on the values given by the microplate...

01 June 2024 7,920 3 View

Why do you translate my name?

My name is Mary Elizabeth C. Bernardes -de-Oliveira or M.E.C. Bernardes-de-Oliveira. But, Maria there isn't! Please correct this for me.

27 May 2024 8,228 2 View

What are your free yet efficient go-tos tools for meta-analysis?

Need advice on user-friendly tools to ease meta-analysis process of selecting eligible and fugitive studies

02 May 2024 2,332 3 View

What cut off values should I use for my phylogenetic tree?

Hi, I am currently constructing a phylogenetic tree involving heterokonts, specifically of marine diatoms and dinoflagellates. Looking at the BLASTn results of my query sequence, I am wondering...

30 April 2024 4,239 2 View

Why do i have 2 bands in γ-tubulin in tissue?

The γ-tubulin Ab i got gives me a 48kDa band in hepa cell samples but when i try it in mouse liver tissue samples i get a weird band at 48 and another one at almost 70kDa. Ive tried a different Ab...

23 April 2024 9,475 0 View

How to respond to request for copy of article?

Someone has requested a copy of an article I co-authored but I don't see options to respond. When I clicked on "View Request," it took me to a page with information about the article but not...

19 April 2024 6,368 1 View

Can the XRD intensity peak of magnesium doped ZnO be more than the undoped ZnO?

Can the reasons for such an incident be detailed?

13 February 2024 2,795 4 View

What is AI? And how does AI relate to the Law?

Kindly research on how AI is going to impact on legal sevices and in particular arbitraration.Right now some firms have started using AI for research,due diligence and data analytics.

12 February 2024 4,005 5 View

Is it possible to obtain reduced graphene oxide through utilizing the Modified Hummer method?

Our goal is to synthesize graphene oxide (GO) utilizing biomass graphite through a modified Hummers method. However, we get rGO straight away. How is rGO produced in the absence of a reducing...

01 February 2024 7,346 3 View

Aside from Starch Casein Agar, what media is used to isolate Actinomycetes?

There is no available sca here in the PH, and we need to isolate Actinomycetes. Thank you in advance!

20 January 2024 4,713 2 View

Where to find a gene list for CRISPRa/i library screening of regulatory factors that affect pathogenic Th17 differentiation in PBMC?

I want to perform a CRISPRa/i library screening for candidate regulatory factors that affect pathogenic Th17 differentiation in PBMC. But I am wondering how to define the size of gene library, so...

31 July 2024 2,150 0 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

Can I please ask why my samples from anaerobic bioreactor giving me different size PCR product even after multiple runs?

Hi everyone, I have extracted DNA from a biogas bioreactor using Qiagen kit and prep cDNA library then used this library as template to optimize primers for qPCR (taken from papers). Some of the...

23 July 2024 1,329 5 View

How to fix install package meta in R?

> library(meta) Error: package or namespace load failed for ‘meta’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘numDeriv’

18 July 2024 3,536 0 View

Can I use DNA a ladder for RNA samples in agarose electrophoresis? Or It is preferable to use cDNA amplified from RT-qPCR for the same samples?

I performed a nucleic acid extraction using 2 protocols for RNA extraction (Dengue Virus) and one parameter I need to evaluate is the integrity of my RNA samples. In this case, I can't use a RNA...

09 July 2024 4,857 2 View

Hi all, what is the interpretation of the results of this gel electrophoresis image?

We aim to measure the RNA expression of p53 and K-RAS biomarkers in colon cancer samples. We extracted the RNA from Rneasy FFPE kit and converted the it to cDNA and did real-time PCR using Cyber...

08 July 2024 7,781 6 View

How to properly dilute RNA for cDNA?

Hi all, I have a question regarding proper dilutions and conversions of my RNA. According to my protocol, my cDNA kit is optimized for 1ug of RNA and calls for this amount. I would like to...

07 July 2024 9,206 4 View

Sybergreen qpcr troublshoulting?

500 ng RNA is converted to cDNA to be genetically expressed by qpcr sybergreen dye, 1 ul primer F, 1 ul primer R, 10 ul master mix, 1 ul cdna template, and instead of a complete total volume...

06 July 2024 5,478 4 View

Why is my HPRT1 housekeeping gene not coming at same Ct in qPCR?

I am doing qPCR but my HPRT1 Ct is not coming at the same point. I see a 2 cycle spread in Ct. I have checked my RNA quality A260/280, 230/280 values, did ethidium bromide gel. I used superscript...

04 July 2024 5,605 3 View

How to amplify NCF1 with real time PCR without amplifying its pseudogenes NCF1B, NCF1C ?

I've been trying to design primers for qPCR to detect NCF1 cDNA using Primer3Plus and NCBI Primer-BLAST, but I couldn't find primers that are specific to the gene. Any help ? Thanks !

04 July 2024 3,068 3 View