FunGen-xQTL Resources

ROSMAP AC gene expression

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.

Cohort
ROSMAPReligious Orders Study and Rush Memory and Aging Project
Data type
ExpressionOmics data
Tissue or cell type
AC
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
QTL results
ROSMAP AC eQTL
Open syn3388564 in Synapse ↗

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
Synapsesyn3388564ControlledFiles described below

Other Synapse IDs on this page syn69670592 syn69670597 syn69670600 syn69670611 syn69670630 syn69865816

shell
pip install synapseclient
synapse login
synapse get -r syn3388564

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.

BrainDescription
Batch 1638
Batch 2252 (117 for PolyA selection & 135 for rRNA depletion)
Batch 3251
Total1141

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 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

Results

Output files: see the Synapse IDs listed on this page.

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

Results

In this analysis we performed two methods: leafcutter and psichomics.

leafcutter

Output files: see the Synapse IDs listed on this page.

psichomics

  • data generation using psichomics still in progress

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/eQTL/ROSMAP_AC_expression_qtl.md.

Flagship paper analyses: