Welcome to Brain TR-xQTLs atlas!
Here, we quantified the cis-effects of TR expansions on brain gene-regulatory cascade across distinct molecular phenotypes, based on 4,412 multi-omics samples from 1,597 donors, including 1,586 newly sequenced ones. Data underlying this project were generated from the NYGC ALS Consortium, Answer ALS Consortium, ROSMAP (available through Synapse) and GTEx v8 cohorts.
Reference
If you use data from this wetsite, please cite the following papers (Other related articles from our lab):
Multi-omics analysis reveals the impact of tandem repeat size variation on gene regulation in human brain
Ya Cui1,#,*, Frederick J. Arnold2,#, Leslie M. Thompson3,*, Albert R. La Spada2,*, and Wei Li1,* (Submmited, 2024).
Download TR-xQTL summary statistics
| Tissue | Main Sampling Site | Sample Size | TR-xQTL File Name |
|---|---|---|---|
| NYGCALS Frontal cortex | Frontal cortex | 467 | NYGCALS.Cortex_Frontal.TR-eQTL.txt.gz |
| NYGCALS Frontal cortex | Frontal cortex | 467 | NYGCALS.Cortex_Frontal.TR-sQTL.txt.gz |
| NYGCALS Frontal cortex | Frontal cortex | 467 | NYGCALS.Cortex_Frontal.TR-3aQTL.txt.gz |
| NYGCALS Temporal Cortex | Temporal Cortex | 107 | NYGCALS.Cortex_Temporal.TR-eQTL.txt.gz |
| NYGCALS Temporal Cortex | Temporal Cortex | 107 | NYGCALS.Cortex_Temporal.TR-sQTL.txt.gz |
| NYGCALS Temporal Cortex | Temporal Cortex | 107 | NYGCALS.Cortex_Temporal.TR-3aQTL.txt.gz |
| NYGCALS Motor Cortex | Motor Cortex | 395 | NYGCALS.Cortex_Motor.TR-eQTL.txt.gz |
| NYGCALS Motor Cortex | Motor Cortex | 395 | NYGCALS.Cortex_Motor.TR-sQTL.txt.gz |
| NYGCALS Motor Cortex | Motor Cortex | 395 | NYGCALS.Cortex_Motor.TR-3aQTL.txt.gz |
| NYGCALS Cerebellum | Cerebellum | 359 | NYGCALS.Cerebellum.TR-eQTL.txt.gz |
| NYGCALS Cerebellum | Cerebellum | 359 | NYGCALS.Cerebellum.TR-sQTL.txt.gz |
| NYGCALS Cerebellum | Cerebellum | 359 | NYGCALS.Cerebellum.TR-3aQTL.txt.gz |
| NYGCALS Cervical Spinal Cord | Cervical Spinal Cord | 403 | NYGCALS.Spinal_Cord_Cervical.TR-eQTL.txt.gz |
| NYGCALS Cervical Spinal Cord | Cervical Spinal Cord | 403 | NYGCALS.Spinal_Cord_Cervical.TR-sQTL.txt.gz |
| NYGCALS Cervical Spinal Cord | Cervical Spinal Cord | 403 | NYGCALS.Spinal_Cord_Cervical.TR-3aQTL.txt.gz |
| NYGCALS Lumbar Spinal Cord | Lumbar Spinal Cord | 379 | NYGCALS.Spinal_Cord_Lumbar.TR-eQTL.txt.gz |
| NYGCALS Lumbar Spinal Cord | Lumbar Spinal Cord | 379 | NYGCALS.Spinal_Cord_Lumbar.TR-sQTL.txt.gz |
| NYGCALS Lumbar Spinal Cord | Lumbar Spinal Cord | 379 | NYGCALS.Spinal_Cord_Lumbar.TR-3aQTL.txt.gz |
| ROSMAP DLPFC | The dorsolateral prefrontal cortex tissue | 579 | ROSMAP.DLPFC.TR-eQTL.txt.gz |
| ROSMAP DLPFC | The dorsolateral prefrontal cortex tissue | 579 | ROSMAP.DLPFC.TR-sQTL.txt.gz |
| ROSMAP DLPFC | The dorsolateral prefrontal cortex tissue | 579 | ROSMAP.DLPFC.TR-3aQTL.txt.gz |
| ROSMAP DLPFC | The dorsolateral prefrontal cortex tissue | 450 | ROSMAP.DLPFC.TR-hQTL.txt.gz |
| ROSMAP DLPFC | The dorsolateral prefrontal cortex tissue | 494 | ROSMAP.DLPFC.TR-mQTL.txt.gz |
| AnswerALS iPSC-MN | Induced pluripotent stem cells derived motor neurons | 348 | AnswerALS.iPSC-MN.TR-eQTL.txt.gz |
| AnswerALS iPSC-MN | Induced pluripotent stem cells derived motor neurons | 348 | AnswerALS.iPSC-MN.TR-sQTL.txt.gz |
| AnswerALS iPSC-MN | Induced pluripotent stem cells derived motor neurons | 348 | AnswerALS.iPSC-MN.TR-3aQTL.txt.gz |
| AnswerALS iPSC-MN | Induced pluripotent stem cells derived motor neurons | 253 | AnswerALS.iPSC-MN.TR-caQTL.txt.gz |
| AnswerALS iPSC-MN | Induced pluripotent stem cells derived motor neurons | 178 | AnswerALS.iPSC-MN.TR-pQTL.txt.gz |
| Tissue | Main Sampling Site | Sample Size | TR-xQTL File Name |
|---|---|---|---|
| Adipose - Subcutaneous | Subcutaneous tissue beneath the leg's skin sample. | 581 | Adipose_Subcutaneous.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Adrenal Gland | Left, followed by the right if necessary for sufficient aliquots. | 233 | Adrenal_Gland.TR-eQTL.txt.gz |
| Artery - Aorta | Ascending aorta or other thoracic regions (nonatherosclerotic). | 387 | Artery_Aorta.TR-eQTL.txt.gz |
| Artery - Coronary | Left and right, noncalcific regions only. | 213 | Artery_Coronary.TR-eQTL.txt.gz |
| Artery - Tibial | Left Tibial. Peripheral tibial artery from gastrocnemius region | 584 | Artery_Tibial.TR-eQTL.txt.gz |
| Brain - Amygdala | Amygdala (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 129 | Brain_Amygdala.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Brain - Caudate (basal ganglia) | Caudate (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 194 | Brain_Caudate_basal_ganglia.TR-eQTL.txt.gz |
| Brain - Cerebellar Hemisphere | Cerebellar hemisphere (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 175 | Brain_Cerebellar_Hemisphere.TR-eQTL.txt.gz |
| Brain - Cerebellum | Right cerebellum (sampled at donor collection site and preserved in PAXgene fixative). | 209 | Brain_Cerebellum.TR-eQTL.txt.gz |
| Brain - Cortex | Right cerebral frontal pole cortex (sampled at donor collection site and preserved in PAXgene fixative). | 205 | Brain_Cortex.TR-eQTL.txt.gz |
| Brain - Frontal Cortex (BA9) | Right cerebral frontal pole cortex (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 175 | Brain_Cortex_Frontal_BA9.TR-eQTL.txt.gz |
| Brain - Hippocampus | Hippocampus (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 165 | Brain_Hippocampus.TR-eQTL.txt.gz |
| Brain - Hypothalamus | Hypothalamus (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 170 | Brain_Hypothalamus.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Brain - Putamen (basal ganglia) | Putamen basal ganglia (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 170 | Brain_Putamen_basal_ganglia.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Brain - Substantia nigra | Substantia nigra (sampled at Miami Brain Bank and preserved as fresh frozen tissue). | 114 | Brain_Spinal_cord_cervical_c-1.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Cells - Cultured fibroblasts | Cultured primary fibroblasts. | 483 | Cells_EBV-transformed_lymphocytes.TR-eQTL.txt.gz |
| Cells - EBV-transformed lymphocytes | Transformed lymphocytes. | 147 | Cells_Cultured_fibroblasts.TR-eQTL.txt.gz |
| Colon - Sigmoid | Sigmoid colon, Obtain muscularis only; discard mucosa. | 318 | Colon_Sigmoid.TR-eQTL.txt.gz |
| Colon - Transverse | Transverse, Full thickness: mucosa and muscularis | 368 | Colon_Transverse.TR-eQTL.txt.gz |
| Esophagus - Gastroesophageal Junction | Muscularis propria in the lowest portion of the esophagus just proximal to the stomach. | 330 | Esophagus_Gastroesophageal_Junction.TR-eQTL.txt.gz |
| Esophagus - Mucosa | Squamous region (distal/lower third), at least 4 cm above gastroesophageal junction. | 497 | Esophagus_Mucosa.TR-eQTL.txt.gz |
| Esophagus - Muscularis | Squamous region (distal/lower third), at least 4 cm above gastroesophageal junction. | 465 | Esophagus_Muscularis.TR-eQTL.txt.gz |
| Heart - Atrial Appendage | Right atrial appendage, tip (if fatty or discolored, take more proximally) | 372 | Heart_Atrial_Appendage.TR-eQTL.txt.gz |
| Heart - Left Ventricle | Anterior left ventricle, 1 cm above apex and 1 cm from left anterior descending coronary artery. | 386 | Heart_Left_Ventricle.TR-eQTL.txt.gz |
| Kidney - Cortex | Left kidney cortex. | 73 | Liver.TR-eQTL.txt.gz |
| Liver | Central right lobe, 1 cm below capsule. | 208 | Liver.TR-eQTL.txt.gz |
| Lung | Inferior segment of left upper lobe, 1 cm below the pleural surface. | 515 | Lung.TR-eQTL.txt.gz |
| Minor Salivary Gland | Inner surface of lower lip. | 144 | Muscle_Skeletal.TR-eQTL.txt.gz |
| Muscle - Skeletal | The gastrocnemius muscle, 2 cm below the patella. | 706 | Muscle_Skeletal.TR-eQTL.txt.gz |
| Nerve - Tibial | Left tibial. Peripheral tibial nerve from gastrocnemius region | 532 | Nerve_Tibial.TR-eQTL.txt.gz |
| Ovary | Most normal regions of the left ovary (and right if necessary to obt ain sufficient aliquots). | 167 | Ovary.TR-eQTL.txt.gz |
| Pancreas | Mid-portion (not tail). | 305 | Pancreas.TR-eQTL.txt.gz |
| Pituitary | Entire pituitary gland. | 237 | Pituitary.TR-eQTL.txt.gz |
| Prostate | Non-nodular region of representative region. | 221 | Prostate.TR-eQTL.txt.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.TR-eQTL.txt.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.TR-eQTL.txt.gz |
| Spleen | Central region, 5 mm below capsule. | 227 | Spleen.TR-eQTL.txt.gz |
| Stomach | Body (Gently rinse mucosa with normal saline before aliquot preparation) | 324 | Stomach.TR-eQTL.txt.gz |
| Testis | Left testis (and right testis if necessary to obtain sufficient tissue for aliquots). | 322 | Testis.TR-eQTL.txt.gz |
| Thyroid | Most grossly non-nodular normal regions from either side (whichever side is observed to be more normal). | 574 | Thyroid.TR-eQTL.txt.gz |
| Uterus | Corpus. Bivalve uterus along endocervical canal to fundus. | 129 | Uterus.TR-eQTL.txt.gz |
| Vagina | Anterior. | 141 | Vagina.TR-eQTL.txt.gz |
| Whole Blood | Femoral vein; subclavian vein and heart are other possible sites. | 670 | Whole_Blood.TR-eQTL.txt.gz |
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Contact
If you have any further questions or comments, please don't hesitate to contact us.
Leslie M. Thompson (Lab website):
lmthomps@hs.uci.edu
Department of Psychiatry and Human Behavior, University of California Irvine, California, USAAlbert 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