ROSMAP PCC gene expression

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.