ROSMAP PCC gene expression#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.

Contact#

Frank Grenn

Study Overview#

Dataset Details#

Raw data#

Path(s) on HPC:

  • PCC RNASeq data from Zhang Lab, /restricted/projectnb/casa/skandoi/ROSMAP_PCC_AC:
$ 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:

  • TPM (before QC or normalization filters) /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/rnaseqc_call/PCC_samples_list.rnaseqc.gene_tpm.subset.gct.gz:
  1. Columns are sample names and rows are genes.
  2. 560 columns (including index) and 60669 rows (including header)
  • Counts (before QC or normalization fitlers):/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/rnaseqc_call/PCC_samples_list.rnaseqc.gene_readsCount.subset.gct.gz:
  1. Columns are sample names and rows are genes.
  2. 560 columns (including index) and 60669 rows (including header)

Other key data files#

  • Gene expression matrices after QC and normalization filters from Zhang Lab, /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/rnaseqc_call/normalize:
$ 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: