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Single Cell Transcriptomics – a simple walkthrough Adwait Sathe, PhD McDermott Center Bioinformatics Lab adwait.sathe@utsouthwestern.edu MCDERMOTT CENTER BIOINFORMATICS LAB 1 mailto:Adwait.sathe@utsouthwestern.edu RNASeq RNASeq 2 MCDERMOTT CENTER BIOINFORMATICS LAB https://www.10xgenomics.com/solutions/single-cell/ Single cell RNA Sequencing Workflow Dissociation of solid tissue Isolate single cells DROP-Seq, Smart-Seq etc. RNA cDNA Amplified RNA Amplified cDNA Sequencing

CANCER RESEARCH | MOLECULAR CELL BIOLOGY HIF2-Induced Long Noncoding RNA RAB11B-AS1 Promotes Hypoxia-Mediated Angiogenesis and Breast Cancer Metastasis Yanling Niu1, Lei Bao1, Yan Chen1, ChenliangWang1, Maowu Luo1, Bo Zhang1, Mi Zhou1, Jennifer E. Wang1, Yisheng V. Fang1, Ashwani Kumar2, Chao Xing2,3,4, Yingfei Wang1,5, and Weibo Luo1,6 ABSTRACT ◥ Hypoxia induces a vast array of long noncoding RNAs (lncRNA) in breast cancer cells, but their biological functions remain largely unknown. Here

Handbook for Postdoctoral Scholars at UT Southwestern Postdoctoral Affairs Office UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-9004 SGSPostdocOffice@UTSouthwestern.edu www.utsouthwestern.edu/Postdocs mailto:SGSPostdocOffice@UTSouthwestern.edu http://www.utsouthwestern.edu/Postdocs dbrekk Typewriter https://www.utsouthwestern.edu/edumedia/edufiles/graduate_school/postdoctoral_scholars/handbook.pdf 1 TABLE OF CONTENTS Welcome! 欢迎

#!/usr/bin/perl   open  (FILE,  "Input.fastq")  ||  die  "can't:  $!";     open  (OUTPUT1,">Output.fastq")  ||  die  "can't:  $!";   while(<FILE>)   {   $line  =  $_;   chomp($line);                  if($line=~/^@DJDP.*/)                  {                  $seq=<FILE>;                  chomp($seq);                  $seq1=$seq

Ultra-pH-Sensitive Nanoprobe Library with Broad pH Tunability and Fluorescence Emissions Xinpeng Ma,†,‡ Yiguang Wang,†,‡ Tian Zhao,† Yang Li,† Lee-Chun Su,† Zhaohui Wang,† Gang Huang,† Baran D. Sumer,§ and Jinming Gao*,†,∥ †Department of Pharmacology and §Department of Otolaryngology, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States ∥Department of Chemistry, University of Texas at Dallas, Richardson, Texas 75083, United

Articles https://doi.org/10.1038/s41551-020-00675-9 1Department of Pharmacology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA. 2Department of Pathology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA. 3Department of Otolaryngology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA. 4Howard Hughes

ARTICLES PUBLISHED ONLINE: 8 DECEMBER 2013 | DOI: 10.1038/NMAT3819 A nanoparticle-based strategy for the imaging of a broad range of tumours by nonlinear amplification of microenvironment signals Yiguang Wang1, Kejin Zhou1, Gang Huang1, Christopher Hensley2, Xiaonan Huang1, Xinpeng Ma1, Tian Zhao1, Baran D. Sumer3, Ralph J. DeBerardinis2 and Jinming Gao1* Stimuli-responsive nanomaterials are increasingly important in a variety of applications such as biosensing, molecular imaging, drug

\ PEGSITACIANINE FOR THE SURGICAL DETECTION OF HEAD AND NECK CANCER PURPOSE INCLUSION DESIGN To investigate whether Pegsitacianine a fluorescent nanoparticle can image head and neck cancer and unknown primary head and neck cancer during surgery or biopsy. 1. Adults ≥ 18 years of age 2. Patients with stage 1-4 Head and Neck Squamous Cell Carcinoma (HNSCC) undergoing surgical excision 1. Phase 2 Clinical trial of Pegsitacianine, which is

Ready; Catalysis Nonlinear Effects Outline Definitions Origins of nonlinear effects in enantioselective reactions ML2 model Reservoir model Transition-state model Kinetic aspects of nonlinear effects Asymmetric amplification Cool tricks Origin of biotic asymmetry? Key reviews Kagan, ACIEE, 1998, 2922 (a pretty complete review, source of many of my figures) Kagan, Advanced Syn. Cat., 2001, 227 (an overview) Blackmond, Accts, 2000, 402 (kinetic aspects) Soai

1 Kinetic Resolutions Material outline: For the Scientist in you: Definitions Theoretical treatment For the technician in you: Practical considerations Useful KR’s Oxidative KR of allylic alcohols An extreme example Acylation/deacylation Hydrogenation olefins ketones Dynamic kinetic resolution Epoxide ring opening A very extreme example Parallel kinetic resolution General References: Vedejs, ACIEE, 2005, 3974 Jacobsen, Adv. Syn