ROSMAP PCC alternative splicing#

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:

  • Leafcutter ratio output/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/leafcutter_output/batch_all/batch_all_bam_no_ext_no_outlier_intron_usage_perind.counts.gz:
  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)
  • Leafcutter counts output/restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/leafcutter_output/batch_all/batch_all_bam_no_ext_no_outlier_intron_usage_perind_numers.counts.gz:
  1. Columns are sample names and rows are introns. Contains each type of intron usage count under each sample (#particular intron in a sample).
  2. 535 columns (including index) and 389332 rows (including header)

Other key data files#

  • PCC splicing data from Zhang Lab, /restricted/projectnb/casa/frank/xqtl_project/ROSMAP_PCC/:
$ 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: