FunGen-xQTL Resources

ROSMAP PCC Expression QTL

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

Please refer to this document for an overview of the ROSMAP project.

Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Modality
eQTLQTL results
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
Source data
ROSMAP PCC Expression
Open syn69670592 in Synapse ↗ Query associations in the xQTL Atlas ↗

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
Synapsesyn69670592ControlledResults described below

Other Synapse IDs on this page syn69670600 syn69670611 syn69670597 syn69865816 syn69670630

shell
pip install synapseclient
synapse login
synapse get -r syn69670592

Contact

Frank Grenn

Study Overview

In progress

  • Sample information: ####/####_sample_attributes.csv.
  • Lab protocol: ####/####_lab_protocol.csv.
  • Computational protocol: ####/####_computational_protocol.csv.
  • QTL summary statistics output: ####/####.qtl_results.csv.
  • Fine-mapping results individual level data model: ####/####.susie.csv.
  • Fine-mapping results summary statistics model: ####/####.susie_rss.csv.
  • Colocalization with AD GWAS: ####/####.susie_coloc.csv.

Analysis Status

TransQTL association: Need to be performed.

Dataset Details

Path(s) to QTL results

text
$ ls -lh | head
total 35G
-rw-r--r-- 1 fgrennjr casa  529M Mar 17 16:02 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet
-rw-r--r-- 1 fgrennjr casa   285 Mar 17 17:06 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet.stderr
-rw-r--r-- 1 fgrennjr casa  173K Mar 17 17:06 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.cis_qtl_pairs.1.parquet.stdout
-rw-r--r-- 1 fgrennjr casa  555K Mar 17 17:06 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 fgrennjr casa  2.6G Mar 17 16:04 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.1.norminal.cis_long_table.txt
-rw-r--r-- 1 fgrennjr casa  253M Mar 17 16:00 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet
-rw-r--r-- 1 fgrennjr casa   285 Mar 17 16:31 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet.stderr
-rw-r--r-- 1 fgrennjr casa   72K Mar 17 16:31 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.cis_qtl_pairs.10.parquet.stdout
-rw-r--r-- 1 fgrennjr casa  234K Mar 17 16:31 PCC_samples_list.rnaseqc.gene_tpm.low_expression_filtered.outlier_removed.tmm.expression.bed.per_chrom_pcc_batch_all.rnaseqc.ROSMAP_covariates.ROSMAP_NIA_WGS.pca.PEER.txt.10.emprical.cis_sumstats.txt

Path(s) to cis-QTL association testing

output of TensorQTL.ipynb

Path(s) to fine-mapping with SuSiE RSS model

Fine-mapping model objects (SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).

Path(s) to TWAS models

Pre-trained TWAS weight models for this context: syn69670600

Quantile TWAS (qTWAS) models: syn69670611

Path(s) to colocalization with SuSiE-coloc / ColocBoost

Multi-context colocalization models (ColocBoost): syn69670597

AD GWAS–xQTL colocalization results: syn69865816

AD GWAS–xQTL colocalization models: syn69670630

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.

Wang lab:

  • TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
  • ROSMAP_CUIMC1_bulk_eQTLprovides information about the input files for AC/DLPFC/PCC TensorQTL cis association in the base_params variable in [generate_command_1].

Analyses

  • cis-QTLDone
  • cTWASDone

Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.