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Targeted RNA-seq of FTLD-TDP brain samples

ABSTRACT: UNC13A features a cryptic exon which is expressed upon loss of nuclear TDP-43. Here, we perform targeted RNA-seq on RNA extracted from 10 FTLD-TDP brain samples, and four control samples, enriching for the cryptic exon via nested PCR. Each FTLD-TDP sample is heterozygous for rs12973192. There are two fastqs for each sample. One uses a sequence-specific reverse transcription primer, and detects both the cryptic-containing and correctly spliced isoforms. The second uses random hexamer primer (with specificity derived from downstream PCR and second strand synthesis) - this approach only detects the isoform containing the cryptic. The fastq files provided are demultiplexed and adaptor trimmed. Unique molecular identifiers have been moved to each read name, after \"rbc:\" (random barcode).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Oscar Wilkins

PROVIDER: E-MTAB-10237 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Differential gene expression study in brain samples from patients suffering distinct frontotemporal lobar degeneration (FTLD) conditions.

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