Journal: Scientific Reports

Article Title: Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

doi: 10.1038/srep33616

Figure Lengend Snippet: Characteristics of an inter-specific chickpea genetic linkage (transcript) map comprising eight chromosomes constructed using a RIL mapping population (ICC 4958 × ICC 17163).

Article Snippet: The genotyping data of drought-responsive root-specific differentially expressed gene-derived SSR (genotyped by gel-based assay) and SNP (Sequenom MALDI-TOF MassARRAY) markers revealing polymorphism between mapping parental accessions (ICC 4958 and ICC 17163) was utilized to generate an inter-specific genetic linkage map (transcript map) at a higher LOD (logarithm of odds) threshold (>4.0) with Kosambi mapping function following Saxena et al . and Bajaj et al . .

Techniques: Construct

Journal: Scientific Reports

Article Title: Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

doi: 10.1038/srep33616

Figure Lengend Snippet: A left-side scale bar spanning 5 cM uniform genetic distance interval represents the genetic distance (cM) of SSR and SNP marker loci mapped on the eight LGs/chromosomes. The identity of the marker loci integrated on the chromosomes are represented on the right side of the chromosomes. The details of markers flanking and tightly linked to the major drought yield QTLs are mentioned in the . Orange and blue boxes indicate the QTLs governing yield per plant and harvest-index, respectively mapped on the chromosomes of a high-density transcript map. The SNPs used as anchor markers to construct a transcript map are illustrated with black colour lines. The non-synonymous/regulatory and synonymous SNPs derived from the differentially expressed genes are indicated with red and blue colour lines, respectively.

Article Snippet: The genotyping data of drought-responsive root-specific differentially expressed gene-derived SSR (genotyped by gel-based assay) and SNP (Sequenom MALDI-TOF MassARRAY) markers revealing polymorphism between mapping parental accessions (ICC 4958 and ICC 17163) was utilized to generate an inter-specific genetic linkage map (transcript map) at a higher LOD (logarithm of odds) threshold (>4.0) with Kosambi mapping function following Saxena et al . and Bajaj et al . .

Techniques: Marker, Construct, Derivative Assay

Journal: BMC Medical Genomics

Article Title: DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot

doi: 10.1186/1755-8794-6-46

Figure Lengend Snippet: Median methylation levels for NKX2-5 in TOF patients and controls. (A) The schematic represents the distribution of the CpG site and CpG island in the NKX2-5 gene; (B) NKX2-5 _M1 median methylation level; (C) NKX2-5 _M2 median methylation level; (D) NKX2-5 _M3 median methylation level. All of the values represent the median with the interquartile range. TSS, Transcription Start Sites; red vertical line, CpG sites; red thick bars, CpG islands; M,MassARRAY amplicon; The region between arrows, target amplicon. * p < 0.05, ** p < 0.01, *** p < 0.001 (Mann–Whitney test).

Article Snippet: The accuracy of the methylation analysis results from the MALDI-TOF MassARRAY (Sequenom) were confirmed by pyrosequencing and bisulfite sequencing PCR (BSP) [ ].

Techniques: Methylation, Amplification, MANN-WHITNEY

Journal: BMC Medical Genomics

Article Title: DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot

doi: 10.1186/1755-8794-6-46

Figure Lengend Snippet: Median methylation levels for GATA4 in TOF patients and controls. (A) The schematic represents the distribution of the CpG site and CpG island in the GATA4 gene; (B) The sequence shown represents a 500 base pair fragment (positions -392 – 107) in the 5′-UTR of GATA4 ; (C) GATA4 _M median methylation level. All of the values represent the median with the interquartile range. TSS, Transcription Start Sites; red vertical line, CpG sites; red thick bars, CpG islands; M,MassARRAY amplicon; The region between arrows, target amplicon. * p < 0.05, ** p < 0.01, *** p < 0.001 (Mann–Whitney test).

Article Snippet: The accuracy of the methylation analysis results from the MALDI-TOF MassARRAY (Sequenom) were confirmed by pyrosequencing and bisulfite sequencing PCR (BSP) [ ].

Techniques: Methylation, Sequencing, Amplification, MANN-WHITNEY

Journal: BMC Medical Genomics

Article Title: DNA methylation status of NKX2-5, GATA4 and HAND1 in patients with tetralogy of fallot

doi: 10.1186/1755-8794-6-46

Figure Lengend Snippet: Median methylation levels for HAND1 in TOF patients and controls. (A) The schematic represents the distribution of the CpG site and CpG island in the HAND1 gene; (B) HAND1 _M1 median methylation level; (C) HAND1 _M2 median methylation level; (D) HAND1 _M3 median methylation level. All of the values represent the median with the interquartile range. TSS, Transcription Start Sites; red vertical line, CpG sites; red thick bars, CpG islands; M,MassARRAY amplicon; The region between arrow, target amplicon. * p < 0.05, ** p < 0.01, *** p < 0.001 (Mann–Whitney test).

Article Snippet: The accuracy of the methylation analysis results from the MALDI-TOF MassARRAY (Sequenom) were confirmed by pyrosequencing and bisulfite sequencing PCR (BSP) [ ].

Techniques: Methylation, Amplification, MANN-WHITNEY