Tang CY, Wu M, Zhao D, Edwards D, McVicar A, Luo Y, Zhu G, Wang Y, Zhou HD, Chen W, Li YP. Runx1 is a central regulator of osteogenesis for bone homeostasis by orchestrating BMP and WNT signaling pathways. PLoS Genet. 2021 Jan 21;17(1):e1009233. doi: 10.1371/journal.pgen.1009233. Erratum in: PLoS Genet. 2022 Oct 31;18(10):e1010480. PMID: 33476325; PMCID: PMC7819607.
Libraries were analyzed using Illumina next-generation sequencing, and relative quantification was provided by Admera Health. Read counts were subjected to paired differential expression analysis using the R package DESeq2.51
Bosco DB, Zheng J, Xu Z, Peng J, Eyo UB, Tang K, Yan C, Huang J, Feng L, Wu G, Richardson JR, Wang H, Wu LJ. RNAseq analysis of hippocampal microglia after kainic acid-induced seizures. Mol Brain. 2018 Jun 20;11(1):34. doi: 10.1186/s13041-018-0376-5. PMID: 29925434; PMCID: PMC6011524.
Bradley CP, Chen C, Oetjen KA, Yan C, Panjwani R, Hauffe S, Calvo KR, Yuan C, Patel PA, Montgomery ND, Foster MC, Battiwalla M, Barrett AJ, Gibbons RJ, Ito S. Persistence of skewed X-chromosome inactivation in pre-B acute lymphoblastic leukemia of a female ATRX mutation carrier. Blood Adv. 2019 Sep 10;3(17):2627-2631. doi: 10.1182/bloodadvances.2019000013. PMID: 31501157; PMCID: PMC6737413.
Allen SD , Liu YG , Kim T , Bobbala S , Yi S , Zhang X , Choi J , Scott EA . Celastrol-loaded PEG-b-PPS nanocarriers as an anti-inflammatory treatment for atherosclerosis. Biomater Sci. 2019 Jan 29;7(2):657-668. doi: 10.1039/c8bm01224e. PMID: 30601470; PMCID: PMC6368678.
Chiari Y, Howard L, Moreno N, Relyea S, Dunnigan J, Boyer MC, Kardos M, Glaberman S, Luikart G. Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation. Mol Ecol Resour. 2023 May;23(4):803-817. doi: 10.1111/1755-0998.13757. Epub 2023 Feb 23. PMID: 36704853.
HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma.
Courtney KD, Ma Y, Diaz de Leon A, Christie A, Xie Z, Woolford L, Singla N, Joyce A, Hill H, Madhuranthakam AJ, Yuan Q, Xi Y, Zhang Y, Chang J, Fatunde O, Arriaga Y, Frankel AE, Kalva S, Zhang S, McKenzie T, Reig Torras O, Figlin RA, Rini BI, McKay RM, Kapur P, Wang T, Pedrosa I, Brugarolas J. HIF-2 Complex Dissociation, Target Inhibition, and Acquired Resistance with PT2385, a First-in-Class HIF-2 Inhibitor, in Patients with Clear Cell Renal Cell Carcinoma. Clin Cancer Res. 2020 Feb 15;26(4):793-803. doi: 10.1158/1078-0432.CCR-19-1459. Epub 2019 Nov 14. PMID: 31727677; PMCID: PMC7024660.
High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer.
Echeverria GV, Powell E, Seth S, Ge Z, Carugo A, Bristow C, Peoples M, Robinson F, Qiu H, Shao J, Jeter-Jones SL, Zhang X, Ramamoorthy V, Cai S, Wu W, Draetta G, Moulder SL, Symmans WF, Chang JT, Heffernan TP, Piwnica-Worms H. High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer. Nat Commun. 2018 Nov 29;9(1):5079. doi: 10.1038/s41467-018-07406-4. PMID: 30498242; PMCID: PMC6265294.
A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans.
Grozdanov PN, Masoumzadeh E, Kalscheuer VM, Bienvenu T, Billuart P, Delrue MA, Latham MP, MacDonald CC. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Nucleic Acids Res. 2020 Sep 25;48(17):9804-9821. doi: 10.1093/nar/gkaa689. PMID: 32816001; PMCID: PMC7515730.
Ho CH, Silva AA, Tomita B, Weng HY, Ho IC. Differential impacts of TNFα inhibitors on the transcriptome of Th cells. Arthritis Res Ther. 2021 Jul 23;23(1):199. doi: 10.1186/s13075-021-02558-z. PMID: 34301319; PMCID: PMC8299604.
Kang Y, Ji Z, Li H, Tsao H. Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping. J Invest Dermatol. 2023 May;143(5):842-853.e6. doi: 10.1016/j.jid.2022.03.039. Epub 2022 Dec 16. PMID: 36529262.
Kemski MM, Rappleye CA, Dabrowski K, Bruno RS, Wick M. Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens). Sci Rep. 2020 Mar 4;10(1):3998. doi: 10.1038/s41598-020-59691-z. PMID: 32132548; PMCID: PMC7055240.
SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice.
Lee KS, Wong TY, Russ BP, Horspool AM, Miller OA, Rader NA, Givi JP, Winters MT, Wong ZYA, Cyphert HA, Denvir J, Stoilov P, Barbier M, Roan NR, Amin MS, Martinez I, Bevere JR, Damron FH. SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice. PLoS One. 2022 Aug 29;17(8):e0273430. doi: 10.1371/journal.pone.0273430. PMID: 36037222; PMCID: PMC9423646.
Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury.
Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal AG, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology. 2020 May;158(6):1698-1712.e14. doi: 10.1053/j.gastro.2020.01.026. Epub 2020 Jan 20. PMID: 31972235; PMCID: PMC8902703.
Liu TW, Gammon ST, Yang P, Ma W, Wang J, Piwnica-Worms D. Inhibition of myeloperoxidase enhances immune checkpoint therapy for melanoma. J Immunother Cancer. 2023 Feb;11(2):e005837. doi: 10.1136/jitc-2022-005837. PMID: 36805920; PMCID: PMC9944647.
Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines.
Maier TR, Masonbrink RE, Vijayapalani P, Gardner M, Howland AD, Mitchum MG, Baum TJ. Esophageal Gland RNA-Seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode Heterodera glycines. Mol Plant Microbe Interact. 2021 Sep;34(9):1084-1087. doi: 10.1094/MPMI-03-21-0051-A. Epub 2021 Sep 29. PMID: 33900122.
Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair.
Myles IA, Castillo CR, Barbian KD, Kanakabandi K, Virtaneva K, Fitzmeyer E, Paneru M, Otaizo-Carrasquero F, Myers TG, Markowitz TE, Moore IN, Liu X, Ferrer M, Sakamachi Y, Garantziotis S, Swamydas M, Lionakis MS, Anderson ED, Earland NJ, Ganesan S, Sun AA, Bergerson JRE, Silverman RA, Petersen M, Martens CA, Datta SK. Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair. Sci Transl Med. 2020 Sep 9;12(560):eaaz8631. doi: 10.1126/scitranslmed.aaz8631. PMID: 32908007; PMCID: PMC8571514.jm
Namous H, Braz CU, Wang Y, Khatib H. The Activation of Protamine 1 Using Epigenome Editing Decreases the Proliferation of Tumorigenic Cell. sFront Genome Ed. 2022 Jun 16;4:844904. doi: 10.3389/fgeed.2022.844904. PMID: 35783678; PMCID: PMC9244402.
Variations in Fibrinogen-like 1 (FGL1) Gene Locus as a Genetic Marker Related to Fat Deposition Based on Pig Model and Liver RNA-Seq Data.
Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M. Variations in Fibrinogen-like 1 (FGL1) Gene Locus as a Genetic Marker Related to Fat Deposition Based on Pig Model and Liver RNA-Seq Data. Genes (Basel). 2022 Aug 9;13(8):1419. doi: 10.3390/genes13081419. PMID: 36011329; PMCID: PMC9407393.
Read JA, Rouce RH, Mo F, Mamonkin M, King KY. Apoptosis of Hematopoietic Stem Cells Contributes to Bone Marrow Suppression Following Chimeric Antigen Receptor T Cell Therapy. Transplant Cell Ther. 2023 Mar;29(3):165.e1-165.e7. doi: 10.1016/j.jtct.2022.12.020. Epub 2022 Dec 31. PMID: 36592718; PMCID: PMC9991966.
Rodriguez-Casariego JA, Cunning R, Baker AC, Eirin-Lopez JM. Symbiont shuffling induces differential DNA methylation responses to thermal stress in the coral Montastraea cavernosa. Mol Ecol. 2022 Jan;31(2):588-602. doi: 10.1111/mec.16246. Epub 2021 Nov 5. PMID: 34689363.
Rosani U, Shapiro M, Venier P, Allam B. A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. Viruses. 2019 Mar 1;11(3):205. doi: 10.3390/v11030205. PMID: 30832203; PMCID: PMC6466128.
Sania RE, Cardoso JCR, Louro B, Marquet N, Canário AVM. A new subfamily of ionotropic glutamate receptors unique to the echinoderms with putative sensory role. Mol Ecol. 2021 Dec;30(24):6642-6658. doi: 10.1111/mec.16206. Epub 2021 Oct 14. PMID: 34601781.
Singla N, Xie Z, Zhang Z, Gao M, Yousuf Q, Onabolu O, McKenzie T, Tcheuyap VT, Ma Y, Choi J, McKay R, Christie A, Torras OR, Bowman IA, Margulis V, Pedrosa I, Przybycin C, Wang T, Kapur P, Rini B, Brugarolas J. Pancreatic tropism of metastatic renal cell carcinoma. JCI Insight. 2020 Apr 9;5(7):e134564. doi: 10.1172/jci.insight.134564. PMID: 32271170; PMCID: PMC7205259.
Vieira P, Shao J, Vijayapalani P, Maier TR, Pellegrin C, Eves-van den Akker S, Baum TJ, Nemchinov LG. A new esophageal gland transcriptome reveals signatures of large scale de novo effector birth in the root lesion nematode Pratylenchus penetrans. BMC Genomics. 2020 Oct 23;21(1):738. doi: 10.1186/s12864-020-07146-0. PMID: 33096989; PMCID: PMC7585316.
Perlegos AE, Shields EJ, Shen H, Liu KF, Bonini NM. Mettl3-dependent m6A modification attenuates the brain stress response in Drosophila. Nat Commun. 2022 Sep 14;13(1):5387. doi: 10.1038/s41467-022-33085-3. PMID: 36104353; PMCID: PMC9474545.
Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet. 2023 Mar 2;19(3):e1010468. doi: 10.1371/journal.pgen.1010468. PMID: 36862752; PMCID: PMC10013926.
Wang H, Xu Z, Xia Z, Rallo M, Duffy A, Matise MP. Inactivation of Hedgehog signal transduction in adult astrocytes results in region-specific blood-brain barrier defects. Proc Natl Acad Sci U S A. 2021 Aug 24;118(34):e2017779118. doi: 10.1073/pnas.2017779118. PMID: 34417306; PMCID: PMC8403837.
Fluorescently labeled Gli1+ cells, sorted from spinal cord or cortex were sent to Admera Health LLC to perform RNAseq.
Moopanar K, Nyide ANG, Senzani S, Mvubu NE. Clinical strains of Mycobacterium tuberculosis exhibit differential lipid metabolism-associated transcriptome changes in in vitro cholesterol and infection models. Pathog Dis. 2023 Jan 17;81:ftac046. doi: 10.1093/femspd/ftac046. PMID: 36509392; PMCID: PMC9936260.
Mineo M, Lyons SM, Zdioruk M, von Spreckelsen N, Ferrer-Luna R, Ito H, Alayo QA, Kharel P, Giantini Larsen A, Fan WY, Auduong S, Grauwet K, Passaro C, Khalsa JK, Shah K, Reardon DA, Ligon KL, Beroukhim R, Nakashima H, Ivanov P, Anderson PJ, Lawler SE, Chiocca EA. Tumor Interferon Signaling Is Regulated by a lncRNA INCR1 Transcribed from the PD-L1 Locus. Mol Cell. 2020 Jun 18;78(6):1207-1223.e8. doi: 10.1016/j.molcel.2020.05.015. Epub 2020 Jun 5. PMID: 32504554; PMCID: PMC7377926.
RNA sequencing on BT333 patient derived cell lines was performed by Admera Health.
Zhu G, Chen W, Tang CY, McVicar A, Edwards D, Wang J, McConnell M, Yang S, Li Y, Chang Z, and Li Y. 2022. Knockout and Double Knockout of Cathepsin K and Mmp9 reveals a novel function of Cathepsin K as a regulator of osteoclast gene expression and bone homeostasis. Int J Biol Sci, 18(14): 5522-5538.
RNA-sequencing and analysis was performed as previously described [37]. Total RNA was isolated using TRIzol reagent (Invitrogen Corp., Carlsbad, CA) from the osteoclasts that were cultured for 14 days in osteogenic differentiation medium following the manufacturer's protocol and was submitted to Admera Health (South Plainsfield, NJ) who assessed sample quality with the Agilent Bioanalyzer and prepared the library using the NEBnext Ultra RNA - Poly-A kit. Libraries were analyzed using Illumina next generation sequencing and relative quantification was provided by Admera Health.
Namous H, Braz CU, Wang Y, Khatib H. The Activation of Protamine 1 Using Epigenome Editing Decreases the Proliferation of Tumorigenic Cells. Front Genome Ed. 2022 Jun 16;4:844904. doi: 10.3389/fgeed.2022.844904. PMID: 35783678; PMCID: PMC9244402.
RNA-Seq was performed at Admera Health Biopharma (South Plainfield, NJ, United States).
McCall JL, Varney ME, Rice E, Dziadowicz SA, Hall C, Blethen KE, Hu G, Barnett JB, Martinez I. Prenatal Cadmium Exposure Alters Proliferation in Mouse CD4+ T Cells via LncRNA Snhg7. Front Immunol. 2022 Jan 11;12:720635. doi: 10.3389/fimmu.2021.720635. PMID: 35087510; PMCID: PMC8786704.
RNA sequencing was conducted by Admera Health (South Plainfield, NJ) on the Hi-seq 2x150 platform.
