FunGen-xQTL Resources

ROSMAP PCC alternative splicing

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Data type
SplicingOmics data
Tissue or cell type
PCC
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Frank GrennSelect a name to email them
QTL results
ROSMAP PCC sQTL
Open syn3157322 in Synapse ↗

Access

Controlled access. Request data access for ROSMAP on the AD Knowledge Portal; you need a Synapse account. See How to get the data.

WhereIDAccessWhat you get
Synapsesyn3157322ControlledFiles described below

Other Synapse IDs on this page syn3388564 syn69670592 syn69670597 syn69670600 syn69670611 syn69670630 syn69865816

shell
pip install synapseclient
synapse login
synapse get -r syn3157322

Contact

Frank Grenn

Study Overview

Dataset Details

Raw data

Path(s) on HPC:

text
$ ls -lh rnaseqc_call_PCC/*.bam | head
-rw-r--r-- 1 skandoi casa 4.0G Dec 11 18:27 1000-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 3.5G Dec  9 15:22 1000-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.5G Dec 11 18:35 1001-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 4.1G Dec  9 15:25 1001-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 4.5G Dec 11 18:29 1002-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 4.2G Dec  9 15:23 1002-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.1G Dec 11 18:33 1003-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 1.5G Dec  9 15:22 1003-PCC.bam.Aligned.toTranscriptome.out.bam
-rw-r--r-- 1 skandoi casa 5.5G Dec 11 18:39 1004-PCC.bam.Aligned.sortedByCoord.out.md.bam
-rw-r--r-- 1 skandoi casa 1.1G Dec  9 15:22 1004-PCC.bam.Aligned.toTranscriptome.out.bam

Molecular phenotype matrices

Path(s) on HPC:

  1. Columns are sample names and rows are introns. Contains each type of intron usage ratio under each sample (#particular intron in a sample / #total introns classified in the same cluster in a sample).

  2. 535 columns (including index) and 389332 rows (including header)

  3. Columns are sample names and rows are introns. Contains each type of intron usage count under each sample (#particular intron in a sample).

  4. 535 columns (including index) and 389332 rows (including header)

Other key data files

text
$ ls -lh leafcutter_output
total 1.4G
drwxr-sr-x 2 fgrennjr casa 256K Mar  6 14:17 batch_all
-rw-r--r-- 1 fgrennjr casa 2.0M Mar  6 17:36 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz.leafcutter.clusters_to_genes.txt
-rw-r--r-- 1 fgrennjr casa 1.3G Mar  8 14:14 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.gz
-rw-r--r-- 1 fgrennjr casa 232K Mar  8 14:15 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.gz.tbi
-rw-r--r-- 1 fgrennjr casa 2.5K Mar  6 17:41 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.stderr
-rw-r--r-- 1 fgrennjr casa  272 Mar  8 14:16 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.stdout
-rw-r--r-- 1 fgrennjr casa  19M Mar  8 14:16 batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz_raw_data.qqnorm.phenotype_group.txt
drwxr-sr-x 2 fgrennjr casa 4.0K Mar  5 11:43 normalize

Analysis notebook generation in progress and will be uploaded to https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Zhang_BU/PCC_AC. Steps will be similar to what is found in https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Zhang_BU/ROSMAP_DLPFC.

Study Metadata

  • PI: David A. Bennett (Rush University Medical Center, Chicago, IL, USA)
  • Grant numbers: U01AG046152, R01AG048015, U01AG061356, R01AG15819, U01AG061359
  • Publication: PMID: 30084846
  • Genetics publication: PMID: 40407102
  • Acknowledgement: Study data were generated from postmortem brain tissue provided by the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) cohort at Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago.
  • Omics data: syn3388564
  • Genetics data: ng00067

QTL Analysis

QTL analysis for this dataset is documented in ../../qtl/sQTL/ROSMAP_PCC_splicing_qtl.md.

Flagship paper analyses: