########### ## Title ## ########### Circular RNAs in Alzheimer Disease Brains - RNA-seq Data ############################# ## Dataset Summary ## ############################# This dataset presents the results from processing ribosomal RNA (rRNA)-depleted RNA-seq data derived from human brain tissues donated by individuals with and without Alzheimer disease (AD). At the individual-level, it includes data for circular and linear RNA counts as well as technical, clinical, and neuropathological phenotypes. At the summary statistic-level, it includes discovery, replication, and meta-analysis circular RNA (circRNA) differential expression and AD-trait correlation results. Differential expression results include comparisons of circRNA expression between: 1) controls versus AD 2) controls versus pre-symptomatic AD (PreSympAD) and controls versus symptomatic AD (SympAD) 3) controls versus autosomal dominant AD (ADAD) 4) AD versus ADAD, controlling for neuropathological severity as measured by Braak score AD is neuropathologically-diagnosed AD (includes both SympAD and PreSympAD) PreSympAD includes individuals with neuropathological evidence of AD but, at most, very mild dementia (CDR <= 0.5). SympAD includes individuals with neuropathological evidence of AD and clinical dementia (CDR >= 1) AD traits analyses for correlation with circRNA expression include: 1) Clinical dementia rating (CDR, https://knightadrc.wustl.edu/CDR/CDR.htm) - CDR is a clinical measure of cognitive impairment with a range from 0 (no dementia) to 3 (severe dementia). 2) Braak score - Braak score is a neuropathological measure of AD severity determined by the number and distribution of neurofibrillary tau tangles throughout the brain. Braak scores range from 0 (absent, at most incidental tau tangles) to 6 (severe, extensive tau tangles in neocortical areas). 3) PlaqueMean - Mean number of amyloid plaques, a neuropathological measure of AD severity Discovery dataset is derived from parietal cortex samples donated by individuals from the Knight-ADRC (https://knightadrc.wustl.edu/). Unaligned (raw) RNA-seq data (.bam files) for those discovery dataset individuals who consented for their sequence data to be shared is included in this dataset (DiscoveryRawRNAseqData). Replication dataset is the publicly-accessible Advanced Medicine Partnership for AD: Mount Sinai Brain Bank (MSBB) dataset. Unaligned (raw) RNA-seq data for replication dataset individuals is available via the Synapse portal (https://www.synapse.org/#!Synapse:syn3159438). Replication dataset regions include: BM10 - frontal pole BM22 - superior temporal gyrus BM36 - parahippocampal gyrus BM44 - inferior frontal gyrus Sequencing information derived from ADAD samples is protected and requires additional authorization from DIAN (https://dian.wustl.edu/our-research/observational-study/) for access. Methods employed to generate all data included in this dataset are described in the Online Methods of "An atlas of cortical circular RNA expression in Alzheimer disease brains demonstrates clinical and pathological associations" Dube et al., 2019. ################################ ## Filenames and Descriptions ## ################################ ==> ADADvsAD_BraakControlled_parietal_condition.txt <== circRNA differential expression between autosomal dominant Alzheimer disease (ADAD) versus Alzheimer disease (AD), controlling for Braak score in the Knight ADRC discovery parietal dataset. ==> ADADvsCO_parietal_condition.txt <== circRNA differential expression between autosomal dominant Alzheimer disease (ADAD) versus controls in the Knight ADRC discovery parietal dataset. ==> BOX_coldata_BM10.txt <== Technical, clinical, and neuropathological phenotype data for the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> BOX_coldata_BM22.txt <== Technical, clinical, and neuropathological phenotype data for the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> BOX_coldata_BM36.txt <== Technical, clinical, and neuropathological phenotype data for the replication MSBB, Brodmann Area 36 (BM36) dataset. ==> BOX_coldata_BM44.txt <== Technical, clinical, and neuropathological phenotype data for the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> BOX_coldata_parietal_externalID.txt <== Technical, clinical, and neuropathological phenotype data for the discovery Knight ADRC, parietal dataset. ==> BOX_coldata_RNAseq_data_dictionary.xlsx <== Data dictionary for Technical, clinical, and neuropathological variables included in the phenotype data files. ==> cts_circ_BM10.txt <== CircRNA count data in the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> cts_circ_BM22.txt <== CircRNA count data in the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> cts_circ_BM36.txt <== CircRNA count data in the replication MSBB, Brodmann Area 36 (BM36) dataset. ==> cts_circ_BM44.txt <== CircRNA count data in the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> cts_circ_parietal_externalID.txt <== CircRNA count data in the discovery Knight ADRC, parietal dataset. ==> cts_linear_BM10.txt <== Linear RNA count data in the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> cts_linear_BM22.txt <== Linear RNA count data in the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> cts_linear_BM36.txt <== Linear RNA count data in the replication MSBB, Brodmann Area 36 (BM26) dataset. ==> cts_linear_BM44.txt <== Linear RNA count data in the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> cts_linear_parietal_externalID.txt <== Linear RNA count data in the discovery Knight ADRC, parietal dataset. ==> Discovery_parietal_braak.txt <== circRNA correlation with Braak score in the discovery Knight ADRC parietal dataset. ==> Discovery_parietal_CDR.txt <== circRNA correlation with Clinical Dementia Rating (CDR) in the discovery Knight ADRC parietal dataset. ==> Discovery_parietal_condition.txt <== circRNA differential expression between Alzheimer disease (AD) versus controls in the discovery Knight ADRC parietal dataset. ==> meta_both_braak_BM10_table_Box.txt <== Meta-analysis of Knight ADRC parietal and MSBB Brodmann Area 10 (BM10) results of circRNA correlation with Braak score. ==> meta_both_CDR_BM10_table_Box.txt <== Meta-analysis of Knight ADRC parietal and MSBB Brodmann Area 10 (BM10) results of circRNA correlation with clinical dementia rating (CDR). ==> meta_both_condition_BM10_table_Box.txt <== Meta-analysis of Knight ADRC parietal and MSBB Brodmann Area 10 (BM10) results of circRNA differential expression between Alzheimer disease (AD) versus controls. ==> Replication_BM10_braak.txt <== circRNA correlation with Braak score in the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> Replication_BM10_CDR.txt <== circRNA correlation with Clinical Dementia Rating (CDR) in the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> Replication_BM10_condition.txt <== circRNA differential expression between Alzheimer disease (AD) versus controls in the replication MSBB, Brodmann Area 10 (BM10) dataset. ==> Replication_BM10_PlaqueMean.txt <== circRNA correlation with mean number of plaques in the MSBB, Brodmann Area 10 (BM10) dataset. ==> Replication_BM22_braak.txt <== circRNA correlation with Braak score in the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> Replication_BM22_CDR.txt <== circRNA correlation with Clinical Dementia Rating (CDR) in the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> Replication_BM22_condition.txt <== circRNA differential expression between Alzheimer disease (AD) versus controls in the replication MSBB, Brodmann Area 22 (BM22) dataset. ==> Replication_BM22_PlaqueMean.txt <== circRNA correlation with mean number of plaques in the MSBB, Brodmann Area 22 (BM22) dataset. ==> Replication_BM36_braak.txt <== circRNA correlation with Braak score in the replication MSBB, Brodmann Area 36 (BM36) dataset. ==> Replication_BM36_CDR.txt <== circRNA correlation with Clinical Dementia Rating (CDR) in the replication MSBB, Brodmann Area 36 (BM36) dataset. ==> Replication_BM36_condition.txt <== circRNA differential expression between Alzheimer disease (AD) versus controls in the replication MSBB, Brodmann Area 36 (BM36) dataset. ==> Replication_BM36_PlaqueMean.txt <== circRNA correlation with mean number of plaques in the MSBB, Brodmann Area 36 (BM36) dataset. ==> Replication_BM44_braak.txt <== circRNA correlation with Braak score in the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> Replication_BM44_CDR.txt <== circRNA correlation with Clinical Dementia Rating (CDR) in the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> Replication_BM44_condition.txt <== circRNA differential expression between Alzheimer disease (AD) versus controls in the replication MSBB, Brodmann Area 44 (BM44) dataset. ==> Replication_BM44_PlaqueMean.txt <== circRNA correlation with mean number of plaques in the MSBB, Brodmann Area 44 (BM44) dataset. ==> SympADvsCO_PreSympADvsCO_BM10.txt <== circRNA differential expression between presymptomatic Alzheimer disease (PreSympAD) versus controls compared to symptomatic Alzheimer disease (SympAD) versus controls in the replication, MSBB Brodmann Area 10 (BM10) dataset. ==> SympADvsCO_PreSympADvsCO_BM22.txt <== circRNA differential expression between presymptomatic Alzheimer disease (PreSympAD) versus controls compared to symptomatic Alzheimer disease (SympAD) versus controls in the replication, MSBB Brodmann Area 22 (BM22) dataset. ==> SympADvsCO_PreSympADvsCO_BM36.txt <== circRNA differential expression between presymptomatic Alzheimer disease (PreSympAD) versus controls compared to symptomatic Alzheimer disease (SympAD) versus controls in the replication, MSBB Brodmann Area 36 (BM36) dataset. ==> SympADvsCO_PreSympADvsCO_BM44.txt <== circRNA differential expression between presymptomatic Alzheimer disease (PreSympAD) versus controls compared to symptomatic Alzheimer disease (SympAD) versus controls in the replication, MSBB Brodmann Area 44 (BM44) dataset. ==> SympADvsCO_PreSympADvsCO_parietal.txt <== circRNA differential expression between presymptomatic Alzheimer disease (PreSympAD) versus controls compared to symptomatic Alzheimer disease (SympAD) versus controls in the discovery, Knight ADRC parietal dataset.