ROSMAP AC gene expression QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression.

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

Contact#

Frank Grenn

Data Descriptions#

Verifying current avaliable location for the dataset now

Samples were extracted using Qiagen’s miRNeasy mini kit (cat. no. 217004) and the RNase free DNase Set (cat. no. 79254), and quantified by Nanodrop and quality was evaluated by Agilent Bioanalyzer.

Notes regarding sample naming: Sequencing samples that were sequenced more than once include the sequencing batch number as the last 2 digits of the id. For example, sample 123_456789_02 is sample “123_456789”, from batch 2. The sample IDs are otherwise randomly-assigned identifiers. Some samples were re-sequenced due to poor quality or low output, they may have “redo” in the sample identifier.

eQTL analysis performed by Gao Wang’s Lab and Xiaoling Zhang’s lab#

Analyst#

Shrishtee Kandoi, Hao Sun

Analysis Status#

TransQTL association: Need to be performed.

Analysis Description#

Brain multi-region RNA-seq data was proccessed with the xQTL-pipeline, for analysis detial please check records here: eQTL eQTL_susie_result_analysis

• Genotype used in this analysis on BU cluster: /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/genotype_partition/ROSMAP_NIA_WGS.leftnorm.filtered.filtered.plink_files_list.txt

• Covariates used in this analysis on BU cluster: /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/reference_data/ROSMAP_xqtl_covariates_sex_death_pmi_study.tsv

Results#

• Output summary statistics are uploaded to the FTP server: /ftp_fgc_xqtl/projects/rna-seq/BU/ROSMAP_DLPFC/eQTL/association_scan

Association scan using TensorQTL and summary statistics standardization#

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

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

• s3://statfungen/ftp_fgc_xqtl/analysis_result/cis_association/ROSMAP/eQTL/AC/