Data Set Group2: UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2

Data Set: UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 GN Accession: GN843 GEO Series: No Geo series yet Title: Multiomic Profiling of the Liver Across Diets and Age in a Diverse Mouse Population Organism: Mouse (Mus musculus, mm10) Group: BXD-Longevity Tissue: Liver mRNA Dataset Status: Private Platforms: SOLID-BasicGencode-Ensembl82-2015-10-02.bed Normalization: RNA-seq

Contact Information Robert Williams University of Tennessee Health Science Center 71 S Manassas St, Room 405 TSRB Memphis, TN 38163 USA Tel. 901 448-7050 rwilliams@uthsc.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

RNA-Seq Log2

Summary:

We profiled the liver transcriptome, proteome, and metabolome from 347 individuals from 58 isogenic strains of the BXD mouse population across age (7 to 24 months) and diet (low or high fat) to link molecular variations to metabolic traits. Several hundred genes are affected by diet and/or age at the transcript and protein levels. Orthologs of two aging-associated genes, St7 and Ctsd, were knocked down in C. elegans, reducing longevity in wildtype and mutant long-lived strains. The multiomics data were analyzed as segregating gene networks according to each independent variable, providing causal insight into segregating edges. Candidate hits were cross-examined in an independent Diversity Outbred mouse liver dataset segregating for similar diets, with ~80-90% of diet-related candidate genes found in common across datasets. Together, we have developed a large multiomics resource for multivariate analysis of complex traits and demonstrate a methodology for moving from observational associations to causal connections.

About the cases used to generate this set of data:

About the cases used to generate this set of data: All animal care was handled according to the NIH's Guidelines for the Care and Use of Laboratory Animals and was also approved by the Animal Care and Use Committee of the University of Tennessee Health Science Center (UTHSC). 2157 mice from 89 strains of the BXD family (including parents and both F1s) were followed in the colony. 159 animals were males and 1998 animals were females. Animals were maintained in the UTHSC vivarium in Specific Pathogen-Free (SPF) housing throughout the longevity experiment. The housing environment was a 12-hour day/night cycle in 20–24°C temperature with housing cages of 145 in2 with up to 10 animals per cage. Diets were either Harlan Teklad 2018 (CD; 24% calories from protein, 18% from fat, 58% from carbohydrates) or Harlan Teklad 06414 (HFD; 18.3% calories from protein, 60.3% from fat, 21.4% from carbohydrates). Water was Memphis city municipal tap water. Food and water were ad libitum. All animals were followed from their point of entry into the colony (typically around 5 months of age) until death. Animals were checked daily for morbidity and were weighed approximately every 2-3 months throughout their lives. 662 animals were sacrificed at specific ages for tissue collection across cohort (i.e. diet, strain, sex, and age). These 662 animals were selected for tissue harvest with the following aims: 2 animals per strain, diet, and age, for a target of 4 age points, i.e. up to a target maximum of 16 sacrificed animals per strain (2 replicates * 2 diets * 4 ages). Transcriptomics were acquired for 291 individuals, which had targeted data generation for 1 animal of each of the 309 cohorts (i.e of the 662 individuals, just over half had a biological replicate which was age, diet, strain, and sex-matched). The target ages were 7, 12, 18, and 24 months of age. Roughly every 3 months for the duration of the experiment, ~40 animals were selected for sacrifice, with approximately 15 animals sacrificed per day over the course of 3 or 4 continuous days. Animals were removed from the aging colony the night prior to sacrifice, but retained access to food and water. CaseID Strain Diet Sex Age EarTag current GN-SampleID 062013.09 C57BL/6J HF F 544 514 H0514 091914.09 C57BL/6J CD F 537 1103 H1103 012615.26 C57BL/6J CD M 361 1590 H1590 102414.06 C57BL/6J HF F 182 1681 H1681 062013.12 D2B6F1 CD F 545 646 H0646 062013.13 D2B6F1 HF F 540 642 H0642 101713.20 D2B6F1 HF F 214 1150 H1150 101713.18 D2B6F1 CD F 210 1154 H1154 083016.07 DBA/2J CD F 764 1818 H1818 091914.05 DBA/2J HF F 549 1142 H1142 091914.07 DBA/2J HF M 544 1140 H1140 101713.10 DBA/2J CD F 212 1147 H1147 101713.11 DBA/2J HF F 212 1144 H1144 121214.29 B6D2F1 CD F 640 1227 H1227 012615.07 B6D2F1 CD F 552 1569 H1569 102616.04 B6D2F1 HF F 547 2288 H2288 102616.05 B6D2F1 HF F 547 2290 H2290 101713.13 B6D2F1 CD F 216 1223 H1223 101713.15 B6D2F1 HF F 216 1302 H1302 082214.11 BXD9 CD F 548 1006 H1006 082214.09 BXD9 HF F 548 1009 H1009 102616.12 BXD9 CD F 245 2577 H2577 083016.08 BXD24 HF F 688 2259 H2259 012615.19 BXD24 CD F 205 1792 H1792 012615.08 BXD29 CD F 724 1044 H1044 111314.10 BXD29 HF F 630 1037 H1037 061913.04 BXD29 HF F 577 669 H0669 111314.11 BXD29 CD F 574 1040 H1040 061913.01 BXD29 CD F 572 742 H0742 121515.05 BXD29 HF F 182 2349 H2349 101014.02 BXD32 HF F 539 1137 H1137 083016.01 BXD32 CD F 386 2494 H2494 042015.22 BXD32 CD F 200 2034 H2034 042015.20 BXD32 HF F 200 2030 H2030 101513.05 BXD34 CD F 554 765 H0765 101014.05 BXD34 HF F 537 1052 H1052 101513.02 BXD34 CD F 201 1054 H1054 101513.04 BXD34 HF F 197 1056 H1056 010614.06 BXD39 CD F 730 673 H0673 102414.02 BXD39 CD F 550 1322 H1322 121214.22 BXD39 HF F 350 1474 H1474 121214.21 BXD39 HF F 350 1473 H1473 061913.06 BXD40 CD F 578 680 H0680 121214.13 BXD40 HF F 358 1593 H1593 111314.05 BXD40 HF F 291 1488 H1488 102414.08 BXD40 CD F 180 1691 H1691 102414.12 BXD44 HF F 715 1687 H1687 012615.15 BXD44 CD F 379 1505 H1505 012615.12 BXD44 HF F 379 1501 H1501 042015.07 BXD44 CD F 240 1822 H1822 042015.10 BXD44 HF F 240 1825 H1825 121515.12 BXD45 CD F 507 1826 H1826 121515.15 BXD45 HF F 503 1940 H1940 012615.11 BXD45 CD F 384 1762 H1762 042915.13 BXD48 HF F 595 1377 H1377 121515.18 BXD48 CD F 518 1835 H1835 042015.24 BXD48 HF F 189 2046 H2046 042015.27 BXD48 CD F 188 2054 H2054 062013.06 BXD48a HF F 543 699 H0699 051112.05 BXD48a CD F 233 209 H0209 051112.04 BXD48a HF F 233 210 H0210 010614.07 BXD53 HF F 713 833 H0833 062013.16 BXD53 CD F 571 848 H0848 021213.14 BXD60 CD F 530 171 H0171 050912.08 BXD60 CD F 235 235 H0235 121515.23 BXD61 CD F 524 1841 H1841 121515.25 BXD61 HF F 524 1843 H1843 111414.02 BXD61 CD F 188 1770 H1770 111414.03 BXD61 HF F 188 1922 H1922 111414.04 BXD61 HF F 188 1722 H1722 082214.10 BXD62 HF F 548 1315 H1315 042915.19 BXD62 HF F 488 1434 H1434 121214.20 BXD62 CD F 353 1436 H1436 042015.05 BXD62 CD F 253 1847 H1847 102616.17 BXD63 HF F 752 2091 H2091 083016.03 BXD63 CD F 751 1872 H1872 121214.24 BXD63 CD F 344 1414 H1414 121214.26 BXD63 HF F 344 1416 H1416 090412.08 BXD63 CD F 218 818 H0818 111414.09 BXD63 HF F 186 1715 H1715 121615.09 BXD65 CD F 541 1787 H1787 121615.06 BXD65 HF F 541 1784 H1784 051012.01 BXD65 HF F 230 458 H0458 042015.13 BXD65 CD F 222 2098 H2098 121615.12 BXD65b CD F 527 1793 H1793 121615.11 BXD65b HF F 527 1790 H1790 111414.05 BXD65b CD F 187 1766 H1766 102414.18 BXD65b HF F 174 1713 H1713 121214.04 BXD66 HF F 367 1560 H1560 121214.19 BXD66 CD F 354 1558 H1558 042415.08 BXD66 CD F 184 2128 H2128 042415.05 BXD66 HF F 184 2124 H2124 082214.02 BXD68 CD F 545 1080 H1080 082214.08 BXD68 HF F 545 1290 H1290 101613.05 BXD68 CD F 201 1068 H1068 101613.08 BXD68 HF F 201 1071 H1071 061913.13 BXD69 CD F 558 591 H0591 121214.23 BXD69 HF F 528 1328 H1328 101613.09 BXD69 HF F 210 1087 H1087 042415.23 BXD69 CD F 157 2142 H2142 121615.14 BXD70 HF F 578 1728 H1728 121214.16 BXD70 CD F 357 1512 H1512 050115.06 BXD70 CD F 261 1855 H1855 051012.08 BXD70 HF F 239 188 H0188 121615.17 BXD73 CD F 539 1906 H1906 121214.10 BXD73 CD F 361 1451 H1451 121214.11 BXD73 HF F 361 1447 H1447 042015.18 BXD73 HF F 206 2071 H2071 050115.15 BXD73b CD F 497 1466 H1466 050115.12 BXD73b HF F 474 1545 H1545 051112.12 BXD73b CD F 238 184 H0184 051112.14 BXD73b HF F 237 183 H0183 121615.19 BXD77 HF F 511 1866 H1866 050115.17 BXD77 CD F 460 1398 H1398 061913.18 BXD79 HF F 571 583 H0583 050115.19 BXD79 CD F 468 1555 H1555 090412.10 BXD79 CD F 217 825 H0825 061913.19 BXD87 CD F 581 296 H0296 121615.21 BXD87 HF F 512 1945 H1945 051012.14 BXD87 HF F 241 243 H0243 090612.10 BXD87 CD F 200 550 H0550 101014.04 BXD89 HF F 539 1321 H1321 051112.01 BXD89 HF F 243 176 H0176 090612.14 BXD89 CD F 193 555 H0555 062013.03 BXD90 HF F 570 736 H0736 062013.02 BXD90 CD F 549 756 H0756 101613.19 BXD90 HF F 218 1093 H1093 102414.03 BXD90 CD F 188 1702 H1702 062013.17 BXD91 CD F 562 883 H0883 062013.19 BXD91 HF F 562 881 H0881 102414.20 BXD95 HF F 550 1273 H1273 101014.10 BXD95 CD F 536 1742 H1742 101613.21 BXD95 HF F 213 1275 H1275 012615.17 BXD98 CD F 384 1769 H1769 012615.16 BXD98 CD F 384 1524 H1524 111414.14 BXD99 CD F 535 1354 H1354 050914.05 BXD99 HF F 182 1355 H1355 111314.15 BXD100 CD F 567 1190 H1190 050914.04 BXD100 HF F 537 1187 H1187 051112.07 BXD100 CD F 223 247 H0247 051112.08 BXD100 CD F 223 248 H0248 042415.12 BXD100 HF F 176 2085 H2085 102616.20 BXD101 CD F 756 2114 H2114 042715.19 BXD101 HF F 493 1422 H1422 111414.20 BXD101 CD F 349 1425 H1425 051112.09 BXD101 CD F 223 468 H0468 042915.01 BXD102 CD F 501 1499 H1499 121214.07 BXD102 HF F 366 1498 H1498 053014.01 BXD102 CD F 183 1363 H1363 052814.04 BXD102 HF F 183 1361 H1361

About the tissue used to generate this set of data:

Tissue collection started at approximately 9 am with the anesthetic Avertin used via intraperitoneal injection of 0.2 mL per 10 g of body weight. Animals were perfused with ice-cold phosphate-buffered saline. The liver was the first organ harvested. The gall bladder was removed, the liver weighed, and then immediately frozen in liquid nitrogen in 20 mL scintillator vials. Roughly 20 mg of pre-pulverized liver tissue was mixed with 1 mL of TRIzol reagent at 4°C for RNA extraction. The sample was then further homogenized in TRIzol with a metallic bead for 2x30s at 25 Hz. The homogenate was transferred to a new tube (without the bead) and 200 µL of chloroform was added and mixed. Samples were centrifuged at 12,000g for 15 minutes at 4°C. ~400 µL of the clear top phase was taken and added to a tube with 400 µL isopropanol, followed by vortexing and the same centrifugation. The RNA pellet was observed and the liquid was discarded. The RNA pellet was resuspended in ethanol by pipetting, then the samples were centrifuged again. The ethanol was removed and the sample was air dried and quantified by Nanodrop. Next, samples were cleaned up using the RNEasy MinElute kits (Qiagen) as per manufacturing instructions.

About the array platform:

RNA-seq and RNA integrity (RIN) checks were performed by an Agilent 2100 Bioanalyzer, and samples with RIN ≥ 6 were retained for RNA-seq, which was run on a NovoGene HiSeq 3000 with 150 bp end paired reads after polyA+ enrichment at the University of Tennessee Health Science Center transcriptomics platform. Samples were measured with an average of 24±2.7 million reads (mean±standard deviation).

About data values and data processing:

Raw fastq files were aligned to the reference mouse genome using STAR version 2.6.0c, using the UCSC genome assembly version GRCm38 (mm10). An average of 86.4±2.6% of reads were mapped per sample. Reads were counted using RSeQC version 2.6.4. Read counts were normalized to RPKM values using gene lengths from ENSEMBL82 v2015-10-02. All RNA-seq data were then scaled by adding 1 to the normalized counts and then taking the log2.

Notes:

Experiment Type:

RNA sequencing

Contributor:

Citation:

Data source acknowledgment:

Study Id:

269

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)