Welcome to Brain 3′aTWAS hub!
This resource provides brain 3'aTWAS models and summary statistics of 3' untranslated region (3'UTR) alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) based on 17,300 RNA-seq samples across 13 brain tissues and 36 non-brain tissues from 2,937 individuals. Data underlying this project were generated from the ROS/MAP (available through Synapse), PsychENCODE and GTEx v8 cohorts.
Reference
If you use the 3′aQTLs or 3′aTWAS models in this wetsite, please cite the following papers (Other APA-related articles from our lab):
Alternative polyadenylation-wide association study (3′aTWAS) identifies novel APA-linked susceptibility genes in brain disorders
Ya Cui1,†, Frederick J. Arnold2,†, Leslie M. Thompson3, Eric J. Wagner4, Albert R. La Spada2,*, and Wei Li1,* (Submmited, 2021).
An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability
Lei Li1, Ya Cui1, ..., Eric J. Wagner2,*, and Wei Li1,* (Nature Genetics, 2021).
Downloads
1. Download 3′aQTL summary statistics
2. Download 3′aTWAS models
| Tissue | Main Sampling Site | Sample Size | 3′aTWAS Moldes File Name |
|---|---|---|---|
| Adipose - Subcutaneous | Subcutaneous tissue beneath the leg's skin sample. | 581 | Adipose_Subcutaneous.3aTWAS.gz |
| Adipose - Visceral (Omentum) | Adipose tissue on the large fold of parietal peritoneum that hangs down from the greater curvature of the stomach, passing in front of the small intestines. | 469 | Adipose_Visceral_Omentum.3aTWAS.gz |
| Adrenal Gland | Left, followed by the right if necessary for sufficient aliquots. | 233 | Adrenal_Gland.3aTWAS.gz |
| Artery - Aorta | Ascending aorta or other thoracic regions (nonatherosclerotic). | 387 | Artery_Aorta.3aTWAS.gz |
| Artery - Coronary | Left and right, noncalcific regions only. | 213 | Artery_Coronary.3aTWAS.gz |
| Artery - Tibial | Left Tibial. Peripheral tibial artery from gastrocnemius region | 584 | Artery_Tibial.3aTWAS.gz |
| Brain - Amygdala | Amygdala (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 129 | Brain_Amygdala.3aTWAS.gz |
| Brain - Anterior cingulate cortex (BA24) | Anterior cingulate cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 147 | Brain_Anterior_cingulate_cortex_BA24.3aTWAS.gz |
| Brain - Caudate (basal ganglia) | Caudate (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 194 | Brain_Caudate_basal_ganglia.3aTWAS.gz |
| Brain - Cerebellar Hemisphere | Cerebellar hemisphere (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 175 | Brain_Cerebellar_Hemisphere.3aTWAS.gz |
| Brain - Cerebellum | Right cerebellum (sampled at donor collection site and preserved in PAXgene fixative). | 209 | Brain_Cerebellum.3aTWAS.gz |
| Brain - Cortex | Right cerebral frontal pole cortex (sampled at donor collection site and preserved in PAXgene fixative). | 205 | Brain_Cortex.3aTWAS.gz |
| Brain - Frontal Cortex (BA9) | Right cerebral frontal pole cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 175 | Brain_Frontal_Cortex_BA9.3aTWAS.gz |
| Brain - Hippocampus | Hippocampus (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 165 | Brain_Hippocampus.3aTWAS.gz |
| Brain - Hypothalamus | Hypothalamus (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 170 | Brain_Hypothalamus.3aTWAS.gz |
| Brain - Nucleus accumbens (basal ganglia) | Nucleus accumbens basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 202 | Brain_Nucleus_accumbens_basal_ganglia.3aTWAS.gz |
| Brain - Putamen (basal ganglia) | Putamen basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 170 | Brain_Putamen_basal_ganglia.3aTWAS.gz |
| Brain - Spinal cord (cervical c-1) | Spinal cord (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 126 | Brain_Spinal_cord_cervical_c-1.3aTWAS.gz |
| Brain - Substantia nigra | Substantia nigra (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 114 | Brain_Spinal_cord_cervical_c-1.3aTWAS.gz |
| Breast - Mammary Tissue | Central breast subareolar region of the right breast, 1-2 cm under the skin surface of nipple region. | 396 | Breast_Mammary_Tissue.3aTWAS.gz |
| Cells - Cultured fibroblasts | Cultured primary fibroblasts. | 483 | Cells_EBV-transformed_lymphocytes.3aTWAS.gz |
| Cells - EBV-transformed lymphocytes | Transformed lymphocytes. | 147 | Cells_Cultured_fibroblasts.3aTWAS.gz |
| Colon - Sigmoid | Sigmoid colon, Obtain muscularis only; discard mucosa. | 318 | Colon_Sigmoid.3aTWAS.gz |
| Colon - Transverse | Transverse, Full thickness: mucosa and muscularis | 368 | Colon_Transverse.3aTWAS.gz |
| Esophagus - Gastroesophageal Junction | Muscularis propria in the lowest portion of the esophagus just proximal to the stomach. | 330 | Esophagus_Gastroesophageal_Junction.3aTWAS.gz |
| Esophagus - Mucosa | Squamous region (distal/lower third), at least 4 cm above gastroesophageal junction. | 497 | Esophagus_Mucosa.3aTWAS.gz |
| Esophagus - Muscularis | Squamous region (distal/lower third), at least 4 cm above gastroesophageal junction. | 465 | Esophagus_Muscularis.3aTWAS.gz |
| Heart - Atrial Appendage | Right atrial appendage, tip (if fatty or discolored, take more proximally) | 372 | Heart_Atrial_Appendage.3aTWAS.gz |
| Heart - Left Ventricle | Anterior left ventricle, 1 cm above apex and 1 cm from left anterior descending coronary artery. | 386 | Heart_Left_Ventricle.3aTWAS.gz |
| Kidney - Cortex | Left kidney cortex. | 73 | Liver.3aTWAS.gz |
| Liver | Central right lobe, 1 cm below capsule. | 208 | Liver.3aTWAS.gz |
| Lung | Inferior segment of left upper lobe, 1 cm below the pleural surface. | 515 | Lung.3aTWAS.gz |
| Minor Salivary Gland | Inner surface of lower lip. | 144 | Muscle_Skeletal.3aTWAS.gz |
| Muscle - Skeletal | The gastrocnemius muscle, 2 cm below the patella. | 706 | Muscle_Skeletal.3aTWAS.gz |
| Nerve - Tibial | Left tibial. Peripheral tibial nerve from gastrocnemius region | 532 | Nerve_Tibial.3aTWAS.gz |
| Ovary | Most normal regions of the left ovary (and right if necessary to obt ain sufficient aliquots). | 167 | Ovary.3aTWAS.gz |
| Pancreas | Mid-portion (not tail). | 305 | Pancreas.3aTWAS.gz |
| Pituitary | Entire pituitary gland. | 237 | Pituitary.3aTWAS.gz |
| Prostate | Non-nodular region of representative region. | 221 | Prostate.3aTWAS.gz |
| Skin - Not Sun Exposed (Suprapubic) | Extension of the abdominal incision to the suprapubic area avoiding pubic hair. | 517 | Skin_Not_Sun_Exposed.gz |
| Skin - Sun Exposed (Lower leg) | Left or right leg 2 cm below patella on medial side. | 605 | Skin_Sun_Exposed.3aTWAS.gz |
| Small Intestine - Terminal Ileum | Thickened mucosa corresponding to lymphoid nodules (Peyer Patches) just proximal to the ileocecal valve in the most distal part of the small intestine. | 174 | Small_Intestine_Terminal_Ileum.3aTWAS.gz |
| Spleen | Central region, 5 mm below capsule. | 227 | Spleen.3aTWAS.gz |
| Stomach | Body (Gently rinse mucosa with normal saline before aliquot preparation) | 324 | Stomach.3aTWAS.gz |
| Testis | Left testis (and right testis if necessary to obtain sufficient tissue for aliquots). | 322 | Testis.3aTWAS.gz |
| Thyroid | Most grossly non-nodular normal regions from either side (whichever side is observed to be more normal). | 574 | Thyroid.3aTWAS.gz |
| Uterus | Corpus. Bivalve uterus along endocervical canal to fundus. | 129 | Uterus.3aTWAS.gz |
| Vagina | Anterior. | 141 | Vagina.3aTWAS.gz |
| Whole Blood | Femoral vein; subclavian vein and heart are other possible sites. | 670 | Whole_Blood.3aTWAS.gz |
| Tissue | Main Sampling Site | Sample Size | 3′aTWAS Moldes File Name |
|---|---|---|---|
| DLPFC | The dorsolateral prefrontal cortex tissue | 579 | ROSMAP.DLPFC.3aTWAS.gz |
| Tissue | Main Sampling Site | Sample Size | 3′aTWAS Moldes File Name |
|---|---|---|---|
| DLPFC | The dorsolateral prefrontal cortex tissue | 1520 | PsychENCODE.DLPFC.3aTWAS.gz |
3. Download 3′aTWAS results in 11 brain disorders
Contact
If you have any further questions or comments, please don't hesitate to contact us.
Albert R. La Spada (Lab website):
alaspada@hs.uci.edu
Departments of Neurology, School of Medicine, University of California Irvine, California, USAWei Li (Lab website):
wei.li@uci.edu
Department of Biological Chemistry, School of Medicine, University of California Irvine, California, USA