Journal: Neuron

Article Title: Somatosensory Cortex Plays an Essential Role in Forelimb Motor Adaptation in Mice

doi: 10.1016/j.neuron.2017.02.049

Figure Lengend Snippet: EXPERIMENTAL MODEL AND SUBJECT DETAILS

Article Snippet: A subset of mice (n = 2) in this study was first tested in a similar adaptation task (unpublished data) prior to participating in this study (but in no more than 8 sessions). table ft1 table-wrap mode="anchored" t5 REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Jax # 000664 Mouse: B6.Cg-Tg(Slc32a1COP4*H134R/EYFP)8Gfng/J The Jackson Laboratory Jax # 014548 Mouse: B6.SJL- Slc6a3 tm1.1(cre)Bkmn /J The Jackson Laboratory Jax # 006660 Mouse: B6.Cg-Tg(Thy1-YFP)HJrs/J The Jackson Laboratory Jax # 003782 Software and Algorithms MATLAB (versions used: 2012b 2014a) Mathworks http://www.mathworks.com Python Python https://www.python.org/ Prism 5 Graph Pad Software http://www.graphpad.com LabView 2013 National Instruments http://www.ni.com MClust software A. David Redish http://redishlab.neuroscience.umn.edu/MClust/MClust.html Other Isoflurane (for anesthesia) IsoSol Vedco N/A Ketoprofen (for analgesia) Patterson Veterinary Cat #07-803-7389 Buprenorphine Patterson Veterinary Cat #07-850-2280 Dexamethasone Patterson Veterinary Cat #07-808-8194 Joystick base Digi-Key Cat #679-2501-ND Solenoid magnet McMaster-Carr Cat #69905K25 FlexiForce System: ELF 2 System Tekscan Cat # {"type":"entrez-nucleotide","attrs":{"text":"A00675","term_id":"14589"}} A00675 Mouse platform grip: thin rubber McMaster-Carr Cat #8633K52 NI-DAQ card, PCI-e6251 National Instruments Cat # NI PCIe-6251 – 779512-01 Laser for optogenetics: Opto Engine 473 nm −100 mW Opto Engine Cat # MBL-III473/1~100 mW Fine tetrode wire (nichrome) Sandvik Kanthal Cat # PF000591 Digital Lynx 4SX Recording System Neuralynx N/A Open Ephys Acquisition Board and Intan headstage Open Ephys http://www.open-ephys.org/store/starter-kit NeuroNexus 8 shank probe (with tetrode configuration) NeuroNexus N/A Open in a separate window EXPERIMENTAL MODEL AND SUBJECT DETAILS

Techniques: Software, Optogenetics

Journal: Cell

Article Title: Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells.

doi: 10.1016/j.cell.2016.10.045

Figure Lengend Snippet: Figure 5. Interrogation of the Molecular Signature Associated with Distinct Functions of HSC Clones (A) To examine molecular differences associated with phenotypically distinct HSC clones, LT-HSC cells belonging to two selected clones (Cohort1.Y and Co- hort1.R) were harvested from a HUe recipient cohort, subjected to RNA-seq (transcriptome), WGBS (DNA methylation) assays, and flow cytometric measurement of multi-lineage reconstitution.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER QIAGEN Epitect Bisulfite kit QIAGEN Cat#:59104 Illumina Nextera DNA Preparation Kit Illumina Cat#:FC-121-1030 QIAGEN MinElute PCR purification Kit QIAGEN Cat#:28004 Deposited Data HUe RNA-Seq data GEO datasets http://www.ncbi.nlm.nih. gov/gds GEO: GSE60101 129P2 WGBS data GEO datasets http://www.ncbi.nlm.nih. gov/gds GEO: GSE56986 BALBcJ WGBS data GEO datasets http://www.ncbi.nlm.nih. gov/gds GEO: GSE60485 129P2 sequence structure annotation files http://www.sanger.ac.uk/science/ programmes/mouse-and-zebrafishgenetics 129P2 BALBcJ sequence structure annotation files http://www.sanger.ac.uk/science/ programmes/mouse-and-zebrafishgenetics BALBcJ Referenced RNA-Seq data of hematopoietic subtypes Lara-Astiaso et al., 2014 N/A Experimental Models: Organisms/Strains HUe mouse This paper N/A C57BL6/J Jackson Laboratories 000664 Mx1-Cre Jackson Laboratories 003556 Prx1-CreER This paper N/A Col(II)-CreER Jackson Laboratories 006774 Recombinant DNA HUe fluorescent cassette Livet et al., 2007 #6 – CMV-Brainbow-2.1 ‘‘R’’ [GYRC] pCAG promoter www.addgene.org Plasmid #13777 LoxP-STOP-LoxP-TOPO sequence www.addgene.org Plasmid #11584 LoxSL: ATAACTTCGTATA GTTCAACT TATACGAAGTTAT This paper N/A Sequence-Based Reagents Custom primers used for ATAC-Seq This paper Table S2 Software and Algorithms FlowJo software TreeStar Inc. N/A PAGODA package v1.99.3 Fan et al., 2016 http://pklab.med.harvard.edu/scde MASS R package N/A https://cran.r-project.org/ MClust R package N/A https://cran.r-project.org/ BSMap 2.7 N/A N/A BIC-seq2 Xi et al., 2016 http://www.math.pku.edu.cn/teachers/ xirb/downloads/software/BICseq2/ BICseq2.html bowtie2 Johns Hopkins University http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml tophat2 Johns Hopkins University https://ccb.jhu.edu/software/tophat/index. shtml DESeq Anders and Huber, 2010 https://www.bioconductor.org/ Homer package Heinz et al., 2010 http://homer.salk.edu/homer/ SPP package 1.13 Kharchenko et al., 2008 http://compbio.med.harvard.edu/ Supplements/ChIP-seq/ (Continued on next page) e2 Cell 167, 1310–1322.e1–e6, November 17, 2016

Techniques: Clone Assay, RNA Sequencing, DNA Methylation Assay