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Questions related from Sachin Teotia
I have few hundreds of differentially expressed genes from a RNA-seq experiment done on rice. The genes are in RAP ID which can be converted to MSU IDs through online tools. Is there a online...
03 April 2020 4,274 0 View
There are problems germinating old transgenic rice seeds (Japonica). Some seeds are 4 years old, while others are 3. They were stored at room temperature. Can we treat them in a way to have at...
15 June 2019 5,895 3 View
I am looking for predicted direct targets of rice TFs. For Arabidopsis we have several databases and this recent paper (http://www.nature.com/articles/srep25164#s2) discusses in great detail about...
03 December 2016 2,980 2 View
What is the safe fold change to consider in a RNA-seq experiment? Fold change > 1.5, FDR < 0.05, P-value < 0.05 and 'Test status' = OK is one criteria which was taken, but I have also...
04 November 2015 3,134 12 View
We have 5 candidate genes in the wild type and the mutant in rice, each gene is about 6 kb long. We want to compare the methylation status of these 5 genes between the two samples. We are mainly...
16 October 2015 8,886 3 View
What is an effective and user friendly method for GO and pathway enrichment analysis in RNA-seq data for Arabidopsis? I saw some tools like AgriGO, Bingo, Blast2Go and the latest PlantGSEA and...
14 October 2015 4,408 5 View
While in literature there is no report, to my knowledge, to silence one transgene in Arabidopsis (under 35S promoter) using another transgene (artificial microRNA, under inducible system). I think...
27 June 2015 9,528 1 View
I have RNA-seq data of rice with some 12000 differentially expressed genes. How to make heat maps and clusters from that data?
26 June 2015 4,696 30 View
We got RNA-seq done on rice (Nipponbare). The sequencing facility aligned the reads to the reference transcriptome (Ensembl Oryza_sativa_japonica IRGSP-1.0). Ensembl database does not match...
19 June 2015 6,086 10 View
For checking root phenotype, is it must to grow rice plants hydroponically, I know for abiotic stress we do need to grow them hydroponically, is the same for root study too? Can't we grow them in...
12 May 2015 3,974 5 View
What RIN (RNA Integration Number) value is good for Illumina RNA-seq for plant samples? I am doing strand-specific polyA-based mRNA-seq and the RIN values of my mutants are above 8 while RIN...
29 April 2015 6,620 2 View
What is the difference between strand-specific and not strand-specific RNA-seq data? Is non-strand specific the regular polyA-based mRNA library? And how these two seq-libraries differ...
15 April 2015 7,438 11 View
We want to grow rice (Nipponbare) hydroponically to study root phenotype and also abiotic stress. Can anyone provide the entire protocol including the nutrient solution recipe and how many days it...
13 April 2015 7,344 13 View
I want to select transgenic Arabidopsis seeds using BASTA on MS medium. My mutant does not survive well on the soil and want to initially select the T0 seeds on BASTA in MS medium. Can anyone tell...
30 March 2015 9,193 7 View
I am preparing RNA from plant samples for RNA-seq. Is it necessary to treat the RNA with DNAse (which will be done once RNA is isolated)? My concern is, extra step of DNase treatment and then...
22 March 2015 1,186 7 View
We have seen VIGS induced silencing of PDS, GFP and many other genes in many species. Is there any report or is it possible that we can knockdown a gene expressed in germline tissues using VIGS?...
14 January 2015 3,670 3 View
Which plant binary vector has a 1X normal 35S promoter to drive the transgene and Bar as a selectable marker? I want to transform Arabidopsis plants. Thanks.
25 November 2014 489 7 View
I am regenerating transformed rice calli on MS-medium. Before this, all stages were grown in the dark. But after keeping them in light for regeneration, a lot of condensation has formed on the lid...
12 October 2014 8,424 16 View
I want to transform Arabidopsis with pTF101.1 binary vector which has a bar resistance gene. Normally people have used this vector for crops such as soybean and maize, not frequently been used for...
28 September 2014 6,985 4 View
We are thinking to manually isolate RNA using trizol or a reagent like 'Plant RNA reagent' which even uses a simpler protocol and yields high quality RNA. Please check this...
25 September 2014 9,854 3 View
I have a question for doing RNA-seq on Arabidopsis samples comparing differential gene expression between wild type and miRNA mutant lines. Just one mutant will be compared.How many replicates are...
22 August 2014 390 1 View
