FunGen-xQTL Resources

ROSMAP PCC gene expression

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
ExpressionOmics 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 eQTL
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 genes.

  2. 560 columns (including index) and 60669 rows (including header)

  3. Columns are sample names and rows are genes.

  4. 560 columns (including index) and 60669 rows (including header)

Other key data files

  • Gene expression matrices after QC and normalization filters from Zhang Lab
text
$ ls -lh
total 45M
-rw-r--r-- 1 fgrennjr casa  45M Mar 16 19:25 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.gz
-rw-r--r-- 1 fgrennjr casa 236K Mar 16 19:25 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.gz.tbi
-rw-r--r-- 1 fgrennjr casa  330 Mar 16 19:25 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.stderr
-rw-r--r-- 1 fgrennjr casa  203 Mar 16 19:25 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.stdout

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/eQTL/ROSMAP_PCC_expression_qtl.md.

Flagship paper analyses: