rneasy minikit  (Qiagen)

Journal: The FASEB Journal

Article Title: Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons

doi: 10.1096/fj.201802646R

Figure Lengend Snippet: Experimental design of the study. ChIP-seq analysis was performed for open chromatin extracted from neuronal nuclei of post mortem PFC of multiple human subjects. Sample subsets from unaffected individuals and patients with psychiatric disorders were also used for WGS and RNA-seq analysis of total PFC tissue or white and gray matter of PFC. The arrows indicate the individual samples used in each analysis. FACS, fluorescence-activated cell sorting; FITC, fluorescein isothiocyanate; NeuN, neuronal nuclei.

Article Snippet: RNA (∼50 ng) was used to prepare indexed libraries with the ScriptSeq v.2 RNA Sequencing (RNA-Seq) Library Kit (Illumina).

Techniques: ChIP-sequencing, RNA Sequencing Assay, Fluorescence, FACS

Journal: The FASEB Journal

Article Title: Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons

doi: 10.1096/fj.201802646R

Figure Lengend Snippet: Integration of H3K4me3 and RNA-seq data identified novel protein-coding and noncoding neuronal genes active in the human brain. A) Novel unannotated ncRNA gene with TSS mapped to the H3K4me3-marked region also harboring a promoter and TSS for the CCHC-type zinc finger nucleic acid binding protein gene. B) A novel ncRNA multiexonic gene with widely variable neuronal H3K4me3 abundance and expression in neurons from different individuals. C) Relative proportion of H3K4me3-marked promoter regions for previously annotated genes. D) Proportion of novel genes with notable protein-coding potential. Sample prefix indicates disease status; suffix indicates tissue for RNA-seq samples. H3K4me3 peaks are color-coded (red, schizophrenia; purple, autism; blue, control). A, autism; C, control; G, cortical gray matter; S, schizophrenia; W, cortical white matter; STG, superior temporal gyrus. For RNA-seq, blue lines show the connection of exons in spliced transcript reads.

Article Snippet: RNA (∼50 ng) was used to prepare indexed libraries with the ScriptSeq v.2 RNA Sequencing (RNA-Seq) Library Kit (Illumina).

Techniques: RNA Sequencing Assay, Binding Assay, Expressing

Journal: The FASEB Journal

Article Title: Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons

doi: 10.1096/fj.201802646R

Figure Lengend Snippet: Single nucleotide substitutions in the promoter are associated with induction of open chromatin and neuronal transcription activation of the testis-specific gene NUP21OL. A) Linkage of the rs114697636 SNP G allele, located near a start codon, and the rs11264875 SNP A allele, located at an exonic region of NUP210L. Monoallelic expression is demonstrated by direct Sanger sequencing of brain transcript cDNA from heterozygous carriers. B) Presence of the G allele at rs114697636 was strongly associated with an emerging H3K4me3 peak at the NUP210L promoter in all carriers. Asterisks denote the presence of the G allele in heterozygous (C28 and S14) and homozygous (A5) individuals. C) RT-PCR analysis of NUP210L relative to ubiquitin C (UBC) gene shows that NUP210L expression occurs in carriers of the rs114697636-G allele variant only (see also Supplemental Fig. S8). D) In general, NUP210L was characterized by testis-specific transcription and an active chromatin state of the promoter. ChIP-seq of testis (68) and RNA-seq of a panel of tissues from the Illumina BodyMap project are shown. A, autism; C, control; S, schizophrenia.

Article Snippet: RNA (∼50 ng) was used to prepare indexed libraries with the ScriptSeq v.2 RNA Sequencing (RNA-Seq) Library Kit (Illumina).

Techniques: Activation Assay, Expressing, Sequencing, Reverse Transcription Polymerase Chain Reaction, Variant Assay, ChIP-sequencing, RNA Sequencing Assay