Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from progeria patients used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques: Sample Prep

Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from adult controls used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques:

Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from children controls used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques: Sample Prep

Journal: Scientific Reports

Article Title: Allele-specific expression in a family quartet with autism reveals mono-to-biallelic switch and novel transcriptional processes of autism susceptibility genes

doi: 10.1038/s41598-018-22753-4

Figure Lengend Snippet: Distinct patterns of allele-specific gene expression in postmortem prefrontal cortex (PFC) of the offspring without and with ASD. ( a ) Parental expression patterns from the PFC of the offspring without ASD (top) and with ASD (bottom) analyzed on a genome-wide scale with RNA-Seq. ( b ) Heatmap analyses showing allele-specific gene expression profiles in the offspring without and with ASD. ( c ) Sanger sequencing validated the allele-specific expression of LRP2BP from the two offspring. Expression levels of LRP2BP from the PFC of the offspring without ASD (open bar) and with ASD (black bar) were quantified by qPCR. ( d ) Sanger sequencing validated the allele-specific expression of ZNF407 from the two offspring. Expression levels of ZNF407 from the PFC of the offspring without ASD (open bar) and with ASD (black bar) were quantified by qPCR. The offspring with and without ASD each had unique SNPs for ZNF407 : G/A for the offspring without ASD and T/A for the offspring with ASD. ( e ) Venn diagram showing overlapped Simons Foundation Autism Research Initiative (SFARI) genes with known human imprinted genes. ( f , g ) The imprinting status of seven of the 19 overlapped genes was verified by Sanger sequencing. NA, the offspring without ASD; A, the offspring with ASD; B, bi-allelic; M, maternal; p, paternal. *Gene could not be validated due to lack of availability of SNPs or low gene expression levels. SNP information was shown as (paternal allele/maternal allele). Euclidean distance was used to generate the heatmap plots.

Article Snippet: Purified RNA was then amplified and prepared for sequencing with a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

Techniques: Expressing, Genome Wide, RNA Sequencing Assay, Sequencing

Journal: Scientific Reports

Article Title: Allele-specific expression in a family quartet with autism reveals mono-to-biallelic switch and novel transcriptional processes of autism susceptibility genes

doi: 10.1038/s41598-018-22753-4

Figure Lengend Snippet: Distinct patterns of allele-specific miRNAs in the postmortem prefrontal cortex (PFC) of offspring without and with ASD. ( a ) Parental expression pattern of miRNAs was analyzed on a genome-wide scale with RNA-Seq in the PFC of both offspring. ( b ) Heatmap analyses of allele-specific expression profiles for miRNAs with fold changes of >0.5 or <−0.5 on a base-10 logarithmic scale between the offspring without and with ASD. ( c , d ) Allele-specific expression was validated for the miRNAs in ( b ) from the two offspring by Sanger sequencing. SNP information is shown as (paternal allele/maternal allele). Euclidean distance was used to generate the heatmap plots.

Article Snippet: Purified RNA was then amplified and prepared for sequencing with a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

Techniques: Expressing, Genome Wide, RNA Sequencing Assay, Sequencing

Journal: Scientific Reports

Article Title: Allele-specific expression in a family quartet with autism reveals mono-to-biallelic switch and novel transcriptional processes of autism susceptibility genes

doi: 10.1038/s41598-018-22753-4

Figure Lengend Snippet: Identification of noncanonical imprinting in the PFC of the offspring without and with ASD and editing of KMT2C transcript in human PFC. ( a ) Sanger sequencing was used to analyze noncanonical imprinting of NOS1 in the PFC of the offspring without and with ASD. “M*” stands for maternally-biased expression. ( b ) Schematic diagram of the genomic locus of human KMT2C . Arrows indicate the direction of transcription. ( c ) Sanger sequencing was performed to analyze RNA editing for KMT2C in the PFC of the offspring without and with ASD, fetal PFC, and blood from parents of the fetus. ( d ) Schematic diagram of the genomic locus of mouse Kmt2c . Arrows indicate the direction of transcription. ( e ) Sanger sequencing was performed to analyze RNA editing for Kmt2c in PFC and blood from postnatal day 28 (P28) mice and PFC from embryonic day 15.5 (E15.5) mice. SNP information is shown as (paternal allele/maternal allele).

Article Snippet: Purified RNA was then amplified and prepared for sequencing with a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

Techniques: Sequencing, Expressing