ROSMAP AC alternative splicing QTL #
Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing. 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.
| Brain | Description |
|---|---|
| Batch 1 | 638 |
| Batch 2 | 252 (117 for PolyA selection & 135 for rRNA depletion) |
| Batch 3 | 251 |
| Total | 1141 |
| 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
sQTL analysis performed by Gao Wang’s Lab and Xiaoling Zhang’s lab #
Analyst #
Shrishtee Kandoi, Xuanhe Chen
Analysis Description #
Brain multi-region RNA-seq data was proccessed with the xQTL-pipeline, for analysis detial please check records here: sQTL
- 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 #
In this analysis we performed two methods: leafcutter and psichomics.
leafcutter #
- Output summary statistics are uploaded to the FTP server:
/ftp_fgc_xqtl/projects/rna-seq/BU/ROSMAP_DLPFC/sQTL/association_scan/
psichomics #
- data generation using psichomics still in progress