GSE107896
GSE GEOWidespread RNA editing dysregulation in Autism Spectrum Disorders
Organism:
Homo sapiens
Platform:
GPL20301
Samples:
12
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Dec 11 2017
Last Updated:
May 15 2019
Status:
Public on Dec 14 2018
Contact:
Grace,,Xiao (UCLA)
Relations
SuperSeries of: GSE107867
SuperSeries of: GSE107895
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421887
Summary
This SuperSeries is composed of the SubSeries listed below.
Overall Design
Refer to individual Series
Analysis (14 steps)
View Data Processing
Processing steps for GSE107896
- Map fastq reads with HISAT2 hisat2 -q --phred64 -x grch37_tran/genome_tran --no-unal --reorder --no-mixed
- Extract uniquely mapped reads from SAM files
- Remap unmapped reads with hyperediting pipeline.
- In brief, convert all adenosines to guanosines and align to modified hg19 genome where adenosines are also substituted by guanosines.
- Obtain uniquely mapped reads pairs from hyperediting pipeline and combine with uniquely mapped reads from first round of read mapping
- Identify RNA-DNA differences between mapped reads and hg19 reference genome.
- Apply log-likelihood test to determine whether RDD is likely resulted from sequencing error (Bahn et. al.
- PMID: 21960545)
Showing first 8 steps.
Supplementary Files (1)
GSE107896_RAW.tar
Download
Dataset Citations (1)
Widespread RNA editing dysregulation in brains from autistic individuals.
PMID 30559470
· 2019
· Nature neuroscience
Stephen S Tran, Hyun-Ik Jun, Jae Hoon Bahn, Adel Azghadi, Gokul Ramaswami, Eric L Van Nostrand, Thai B Nguyen, Yun-Hua E Hsiao, Changhoon Lee, Gabriel A Pratt, Verónica Martínez-Cerdeño, Randi J Hagerman, Gene W Yeo, Daniel H Geschwind, Xinshu Xiao
Linked Publications (1)
Widespread RNA editing dysregulation in brains from autistic individuals.
Nature neuroscience · 2019