Datasets List
19 datasets

Publication name and date Genotypes Phenotypes Omics Data Sample size Dataset access Phenotype IDS Publication link Authors

Gunturkun et al., Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders. Front Psychiatry. 2022 Feb 14;13:790566. doi: 10.3389/fpsyt.2022.790566. PMID: 35237186; PMCID: PMC8882588.

2022
3,513,494 Version R8
Locomotion
Novel Object
Interaction
+1
None
1246
More details ontology for behavior phenotypes Hakan Gunturkun, Mustafa Chen, Hao Wang, Tengfei Chitre, Apurva St. Pierre, Celine Bimschleger, Hannah Cheng, Riyan Polesskaya, Oksana Solberg-Woods, Leah Palmer, Abraham Garcia Martinez, Angel Holl, Katie Gao, Jianjun

U01: Genetic Basis of Opioid Dependence Vulnerablility (U01DA045300)

9/30/2018
4,609,405, version R9
self- administration
drug-seeking
RNA-Seq
Goal: 1000 Current: 655
More details https://reporter.nih.gov/search/uklKYfh_tkGvcRicTWjt9w/project-details/10223254 Peter Kalivas W CHUNG, DONGJUN HARDIMAN, GERARD THOMAS SOLBERG WOODS,LEAH CICCOCIOPPO, ROBERTO

U01: Genomic analysis of avoidance learning in addiction (U01DA044468)

4/15/2018
4,609,405, version R9
Avoidance-Learning
RNA-Seq
Goal: 1200 Current: 1239
More details https://reporter.nih.gov/search/QH2CQwXvTEiz41loh28b6A/project-details/10098021 Thomas Jhou

U01: Genetics of Compulsive Cocaine Intake in Rats (U01DA043799)

4/1/2017
4,609,405, version R9
Addiction Index
Aggression Behavior
Defensive Behavior
+2
None
Goal: 1000 Current: 882
More details https://reporter.nih.gov/search/UmvTCDBpc0qYTmrAE7ML_w/project-details/9873956 Olivier George Abraham Palmer

U01: Genetics of Compulsive Oxycodone Intake in HS Rats (U01DA044451)

8/13/2019
4,609,405, version R9
Oxycodone infusions
Reward intake
Tail immersion
+1
None
Goal: 1000 Current: 619
More details measure,trait_covariate,description 0,box,covariate,self administration box 1,cohort,covariate,batch 2,lga_12_age,covariate,age of animal on day 12 of long access session 3,pr_01_age,covariate,age of animal on day 1 of progressive ratio at breakpoint 4,pr_02_age,covariate,age of animal on day 2 of progressive ratio at breakpoint 5,room,covariate,experimental room 6,sex,covariate,sex of animal 7,sha_01_age,covariate,age of animal on day 1 of short access session 8,sha_04_age,covariate,age of animal on day 4 of short access session 9,weight_surgery,covariate,weight at surgery date 10,death_comment,metadata, 11,labanimalid,metadata,unique lab assigned id to animal 12,rfid,metadata,unique rfid assigned to animal 13,add_ind_olivier,trait,index calculated by Giordano's team 14,add_ind_sexcohort,trait,index calculated by Palmer team 15,add_ind_no_sex,trait,index calculated by Palmer team with no seperate Zscore of male and female 16,add_ind_no_sexcohort,trait,index calculated by Palmer team with no seperate Zscore of male and female or cohort 17,sha_mean_01_02,trait,average of the number of oxycodone infusions during the first three sessions of short access self administration (2 hours) 18,sha_mean_03_04,trait,average of the number of oxycodone infusions during the last three sessions of short access self administration (2 hours) 19,sha_mean_inactive_01_02,trait,average of the number of inactive during the first three sessions of short access self administration (2 hours) 20,sha_mean_inactive_03_04,trait,average of the number of inactive during the last three sessions of short access self administration (2 hours) 21,sha_mean_to_01_02,trait,average of the number of TO response during the first three sessions of short access self administration (2 hours) 22,sha_mean_to_03_04,trait,average of the number of TO response during the last three sessions of short access self administration (2 hours) 23,sha_iti_coefficient_of_variation_03_04,trait,standard deviation of ITI/mean of ITI within SHA (days 03-04) 24,sha_iti_coefficient_of_variation_01_02,trait,standard deviation of ITI/mean of ITI within SHA (days 01-02) 25,sha_iti_median_03_04,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) 26,sha_loading_phase_intake_01_02,trait,number of rewards during the first ten minutes of SHA (days 01-02) 27,sha_loading_phase_intake_03_04,trait,number of rewards during the first ten minutes of SHA (days 03-04) 28,sha_titration_phase_01_02,trait,intake during the last 60 min in SHA (days 01-02) 29,sha_titration_phase_03_04,trait,intake during the last 60 min in SHA (days 03-04) 30,lga_mean_delta_esc,trait,average of the escalation values during the last three sessions of long access self administration (12 hours) 31,lga_mean_01_02,trait,average of the number of oxycodone infusions during the first 2 sessions of long access self administration (12 hours) 32,lga_mean_inactive_01_02,trait,average of the inactive during the first 2 sessions of long access self administration (12 hours) 33,lga_mean_active_01_02,trait,average of the active during the first 2 sessions of long access self administration (12 hours) 34,lga_mean_to_01_02,trait,average of the TO escalation values during the first 2 sessions of long access self administration (12 hours) 35,lga_iti_coefficient_of_variation_01_02,trait,standard deviation of ITI/mean of ITI wtihin LGA (days 01-02) 36,lga_iti_median_01_02,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) first 2 sessions of LgA 37,lga_loading_phase_intake_01_02,trait,number of rewards during the first ten minutes of LGA (days 01-02) 38,lga_titration_phase_01_02,trait,intake during the last 6 * 60 min in LGA (days 01-02) (hour 5-11) 39,lga_mean_12_14,trait,average of the number of oxycodone infusions during the last three sessions of long access self administration (12 hours) 40,lga_mean_inactive_12_14,trait,average of the inactive during the last three sessions of long access self administration (12 hours) 41,lga_mean_active_12_14,trait,average of the active during the last three sessions of long access self administration (12 hours) 42,lga_mean_to_12_14,trait,average of the TO escalation values during the last three sessions of long access self administration (12 hours) 43,lga_iti_coefficient_of_variation_12_14,trait,standard deviation of ITI/mean of ITI wtihin LGA (days 12-14) 44,lga_iti_median_12_14,trait,Median of ITI (ITI being the time in sec between reward events using the timestamp data) 45,lga_loading_phase_intake_12_14,trait,number of rewards during the first ten minutes of LGA (days 12-14) 46,lga_titration_phase_12_14,trait,intake during the last 6 * 60 min in LGA (days 12-14) (hour 5-11) 47,tail_immersion_analgesia,trait,change in latency (tail imm 2 - tail imm BSL) note: positive number is more analgesia 48,tail_immersion_tolerance,trait,change in latency (tail imm 2 - tail imm 3) note: positive number is more tolerance 49,tail_immersion_baseline,trait,baseline latency (tail imm BSL) 50,tail_immersion_oxypresa,trait,tail imm 2 51,tail_immersion_oxypostsa,trait,tail imm 3 52,von_frey_force_bsl,trait,threshold force at baseline 53,von_frey_force_difference,trait,change in average force achieved (BSL - Withdrawal) 54,von_frey_force_percent,trait,percent change in average force achieved (BSL-Withdrawal) / BSL*100 55,von_frey_force_withdrawal,trait,threshold force in withdrawal 56,von_frey_time_bsl,trait,threshold time at baseline 57,von_frey_time_difference,trait,change in average time achieved (BSL - Withdrawal) 58,von_frey_time_percent,trait,percent change in average time achieved (BSL-Withdrawal) / BSL*100 59,von_frey_time_withdrawal,trait,threshold time in withdrawal 60,pr_01_sha,trait,number of oxycodone infusions received during day 1 (post-ShA) 61,pr_01_inactive,trait,number of inactive lever presses during day 1 (post-ShA) of progressive ratio session 62,pr_01_active,trait,number of active lever presses during day 1 (post-ShA) of progressive ratio session 63,pr_01_sha_breakpoint,trait,last completed number of oxycodone active lever presses during day 1 (post-ShA) of progressive ratio at breakpoint 64,pr_02_lga,trait,number of oxycodone infusions received during day 2 (post-LgA) 65,pr_02_inactive,trait,number of inactive lever presses during day 2 (post-LgA) of progressive ratio session 66,pr_02_active,trait,number of active lever presses during day 2 (post-LgA) of progressive ratio session 67,pr_02_lga_breakpoint,trait,last completed number of oxycodone active lever presses during day 2 (post-ShA) of progressive ratio at breakpoint 68,treatments_pr_vehicle,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (vehicle) 69,treatments_pr_buprenorphine,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (buprenorphine) 70,treatments_pr_methadone,trait,percent of vehicle for each pharmacological treatment ( (treatment PR - PR02) / PR02 x 100% ) (methadone) 71,treatments_pr_naltrexone,trait,percent of vehicle for each pharmacological treatment ( (ttreatment PR - PR02) / PR02 x 100% ) (naltrexone) 72,pr_saline_active,trait,number of active lever presses during saline treatment 73,pr_saline_breakpoint,trait,breakpoint (last completed ratio) during saline treatment 74,pr_saline_inactive,trait,number of inactive lever presses during saline treatment 75,pr_saline_rewards,trait,number of oxycodone infusions received during saline treatment 76,pr_buprenorphine_active,trait,number of active lever presses during buprenorphine treatment 77,pr_buprenorphine_breakpoint,trait,breakpoint (last completed ratio) during buprenorphine treatment 78,pr_buprenorphine_inactive,trait,number of inactive lever presses during buprenorphine treatment 79,pr_buprenorphine_rewards,trait,number of oxycodone infusions received during buprenorphine treatment 80,pr_methadone_active,trait,number of active lever presses during methadone treatment 81,pr_methadone_breakpoint,trait,breakpoint (last completed ratio) during methadone treatment 82,pr_methadone_inactive,trait,number of inactive lever presses during methadone treatment 83,pr_methadone_rewards,trait,number of oxycodone infusions received during methadone treatment 84,pr_naltrexone_active,trait,number of active lever presses during naltrexone treatment 85,pr_naltrexone_breakpoint,trait,breakpoint (last completed ratio) during naltrexone treatment 86,pr_naltrexone_inactive,trait,number of inactive lever presses during naltrexone treatment 87,pr_naltrexone_rewards,trait,number of oxycodone infusions received during naltrexone treatment 88,sha_iti_mode_03_04,trait,most frequent ITI for last 2 days 89,sha_iti_numburst_03_04,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for last 2 days 90,sha_iti_maxburst_03_04,trait,maximum number of rewards contain in a single burst in one session for last 2 days 91,sha_iti_meannumrewards_03_04,trait,average number of rewards in a burst over all bursts in the session for last 2 days 92,sha_iti_pctrewards_03_04,trait,percantage of rewards that fall in a burst of total rewards for the session for last 2 days 93,sha_iti_mode_01_02,trait,most frequent ITI for first 2 days 94,sha_iti_numburst_01_02,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for first 2 days 95,sha_iti_maxburst_01_02,trait,maximum number of rewards contain in a single burst in one session for first 2 days 96,sha_iti_meannumrewards_01_02,trait,average number of rewards in a burst over all bursts in the session for first 2 days 97,sha_iti_pctrewards_01_02,trait,percantage of rewards that fall in a burst of total rewards for the session for first 2 days 98,lga_iti_mode_12_14,trait,most frequent ITI for last 3 days 99,lga_iti_numburst_12_14,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for last 3 days 100,lga_iti_maxburst_12_14,trait,maximum number of rewards contain in a single burst in one session for last 3 days 101,lga_iti_meannumrewards_12_14,trait,average number of rewards in a burst over all bursts in the session for last 3 days 102,lga_iti_pctrewards_12_14,trait,percantage of rewards that fall in a burst of total rewards for the session for last 3 days 103,lga_iti_mode_01_02,trait,most frequent ITI for first 2 days 104,lga_iti_numburst_01_02,trait,number of bursts (= grouped rewards that are seperated by max 120 sec) in a session for first 2 days 105,lga_iti_maxburst_01_02,trait,maximum number of rewards contain in a single burst in one session for first 2 days 106,lga_iti_meannumrewards_01_02,trait,average number of rewards in a burst over all bursts in the session for first 2 days 107,lga_iti_pctrewards_01_02,trait,percantage of rewards that fall in a burst of total rewards for the session for first 2 days https://reporter.nih.gov/search/f6C7xo1EpESCW4neFmUNOg/project-details/10356094 Olivier George Abraham Palmer

R01: Identification of Genes Regulating Bone Matrix Composition and Quality

9/15/2016
None
Bone density
None
Goal = 4800
More details Douglas Adams

U01:Characterization of Tandem Repeat and Structural Variants Contributing to Addictive Behaviors in Mice and Rats

Not available
4,609,405, version R9 None
None
More details Abraham Palmer Melissa Gymrek Jonathan Sebat

U01: Decoding the grammar of transcriptional enhancers regulating different stages of opioid use disorder

9/30/2020
4,609,405, version R9
RNA-Seq
ATAC-seq
RNA-Seq
None
More details Francesca Telese

Genetic basis for unilateral renal agenesis in heterogenous stock rats

TBD
Version R8
Unilateral renal agenesis
None
5585
More details Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Wenyan Han Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro

Structural equation modeling for understanding the genetic architecture of cocaine contextual conditioning and cocaine conditioned cue preference in heterogeneous stock rats undercover candidate genes for behavioral variation caused by cocaine exposure

TBD
Version R8
Cocaine contextual conditioning
cocaine conditioned cue preference
3050
More details Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Wenyan Han Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro

Genetic architecture for cecum metabolomics of heterogeneous stock rats undercover candidate genes for metabolome abundance and presence

TBD
Version R8
Cocaine Contextual Conditioning
Cocaine Conditioned cue Preference
Metabolomics
1000
More details Joel D. Leal-Gutiérrez Apurva S. Chitre Oksana Polesskaya Riyan Cheng Alexander F. Gileta Keita Ishiwari Christopher P. King Alexander Lamparelli Tengfei Wang Hao Chen Shelly B. Flagel Paul Meyer Terry E. Robinson Leah C. Solberg Woods Abraham A. Palmer Denghui Chen Wenyan Han Michael Garrett Jerry Richards Cassandra L. Versaggi Connor Martin Celine L. St. Pierre, Jordan A. Tripi Aidan Horvath Alesa Hughson Milad Mortazavi Hannah Bimschleger, Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Bonnie Lin Daniel Munro

Chitre AS et al. Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity (Silver Spring). 2020 Oct;28(10):1964-1973. doi: 10.1002/oby.22927. Epub 2020 AUG 29. PMID: 32860487; PMCID: PMC7511439.

2022
3,400,759 SNPs Version 2018
Body length with no tail
body length with tail
body weight
+5
None
3173
UCSD library parametrial-fat-weight-g_UBERON_UBERON:0010413 parametrial-fat-weight-g_MGI_MP:0005375 Body length with no tail CMO_0002804 (ontobee/PATO) Body length with tail CMO_0000078 (ontobee/PATO) Body weight CMO_0000079 (ontobee/PATO) Body Mass Index NoTail CMO_0002781 (ontobee/PATO) Retroperitoneal fat pad UBERON:0010411 Epididymal fat pad UBERON:0010412 https://pubmed.ncbi.nlm.nih.gov/32860487/ Apurva S Chitre Oksana Polesskaya Riyan Cheng Hannah Bimschleger Hao Chen Shelly B Flagel Paul Meyer Terry E Robinson Abraham A Palmer Leah C Solberg Woods Alexander F Gileta Keita Ishiwari Christopher P King Alexander Lamparelli Angel Garcia Martinez Tony George Katie Holl Jianjun Gao Cassandra L Versaggi Celine L St Pierre Jordan A Tripi Tengfei Wang Wenyan Han Jerry Richards Alesa Hughson

P50 Project 1: Neurogenetic Substrates of Cocaine Addiction

2019-2024
4,609,405, version R9
Intermittent access to cocaine
RNA-Seq
Goal: 1600 Current: 1911
More details None https://ratgenes.org/research-projects/rp1new/ Paul Meyer Chris King

P50 Project 2: Socially-acquired nicotine self-administration

4,609,405, Version R9
Open Field
Novel Object Interaction Test
Nicotine self-administration
+1
None
Goal: 4800 Current: 2600
More details trait,InterLex ID novel_object_age,ILX:0793285 novel_object_arena,ILX:0793286 novel_object_batchnumber,ILX:0793287 novel_object_cntrdurat,ILX:0793288 novel_object_cntrfreq,ILX:0793289 novel_object_cntrlate,ILX:0793290 novel_object_color,ILX:0793291 novel_object_dist2ctrmean,ILX:0793292 novel_object_dist2ctrtotal,ILX:0793293 novel_object_sex,ILX:0793294 novel_object_totaldistance,ILX:0793295 open_field_age,ILX:0793296 open_field_arena,ILX:0793297 open_field_batchnumber,ILX:0793298 open_field_cntrdurat,ILX:0793299 open_field_cntrfreq,ILX:0793300 open_field_cntrlate,ILX:0793301 open_field_color,ILX:0793302 open_field_dist2ctrmean,ILX:0793303 open_field_dist2ctrtotal,ILX:0793304 open_field_sex,ILX:0793305 open_field_totaldistance,ILX:0793306 rfid,ILX:0793307 social_interaction_age,ILX:0793308 social_interaction_arena,ILX:0793309 social_interaction_batchnumber,ILX:0793310 social_interaction_color,ILX:0793311 social_interaction_dist2objzonemean,ILX:0793312 social_interaction_dist2objzonetotal,ILX:0793313 social_interaction_dist2socmean,ILX:0793314 social_interaction_dist2soctotal,ILX:0793315 social_interaction_inobjzonedura,ILX:0793316 social_interaction_inobjzonefreq,ILX:0793317 social_interaction_inobjzonelate,ILX:0793318 social_interaction_insoczonedura,ILX:0793319 social_interaction_insoczonefreq,ILX:0793320 social_interaction_insoczonelate,ILX:0793321 social_interaction_sex,ILX:0793322 social_interaction_totaldistance,ILX:0793323 bmi_wo_tail,ILX:0793324 bmi_w_tail,ILX:0793325 body_weight_g,ILX:0793326 epididymis_fat_weight_g,ILX:0793327 glucose_reading_mg_dl,ILX:0793328 length_wo_tail_cm,ILX:0793329 length_w_tail_cm,ILX:0793330 parametrial_fat_weight_g,ILX:0793331 retroperitoneal_fat_weight_g,ILX:0793332 tail_length,ILX:0793333 Hao Chen

P50 Project 3: Association between behavioral regulation and cocaine cue preference

2014-2024
4,609,405, version R9
Locomotor Response
Delay Discounting
Light Reinforcement
+5
None
Goal: 1600 Current: 1066
More details https://ratgenes.org/research-projects/rp3/ David Dietz Keita Ishiwari Paul Meyer Suzanne Mitchell Jerry Richards

P50 Project 4, P50: Network-based analysis

2019-2024
4,609,405, version R9
N/A
None
various
More details https://ratgenes.org/research-projects-rp4-networks/ Trey Ideker

P50 Project 1, P50: Genetic Studies of Incentive Salience

2014-2019
4,609,405, Version R9
Cocaine Contextual Conditioning
Novelty seeking
Pavlovian Conditioned Approach
None
1600
More details https://ratgenes.org/research-projects/rp1/ Shelly Flagel Terry Robinson

U01: Single-cell resolution analysis of chromatin accessibility and gene expression (U01DA050239)

5/1/2020
4,609,405, version R9
RNA-Seq
ATAC-seq
H3K27Ac
+1
RNA-seq, ATAC-seq, H3K27Ac, PLAC-seq
Goal: 96 Current: 96
More details https://reporter.nih.gov/search/4O2ekcqX80yU0a3FTHylnw/project-details/10360680 Francesca Telese

U01: Genetic Features of Delay Discounting in an HS Rat Model (U01DA046077)

7/1/2018
4,609,405, version R9
Delay Discounting
impulsivity
5-choice serial reaction time task
RNA-Seq
Goal: 1560 Current: 901
More details https://reporter.nih.gov/search/a5pMHTPdZkyjaaOw8MpZZA/project-details/10146324 Suzanne Mitchell
  • Abraham Palmer, PHD

    Abraham
  • Paul Meyer

    Paul
  • Trey Ideker

    Trey
  • Oksana Polesskaya

    Oksana
  • Leah Solsberg-Woods

    Leah
  • Anita Bandrowski

    Anita
  • Hao Chen

    Hao
  • Maryann Martone

    Maryann
  • David Dietz

    David
  • Jeffrey Grethe

    Jeffrey