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==scTHS-seq combinatorial indexing R2, human brain nuclei T5JC GTEX FC9/mouse fetal tissue E15.5 forebrain nuclei (scT7_r0XX_i5) and Tn5059== *Performing THS-seq on human brain nuclei sample T5JC GTEX FC9/mouse fetal tissue E15.5 forebrain nuclei. will use ~3,000 nuclei per reaction since lose nuclei because they are sticky, and less are viable. *Patient T5JC GTEX FC9 Sample, 01.26.2016 **NEB Buffer **NeuN+ DAPI+ **FACS Astrios (TSRI); sorted 250K unstained nuclei for euchromatin/heterochromatin project and 300K DAPI+ unstained nuclei for Drop-Seq optimization. Sorted 189K DAPI+NeuN positive singlets 3K into 1% FAF-BSA buffer and 77K DAPI+NeuN negative . Nuclei were spun down, filtered and resuspended in 10% DMSO, aliquoted and frozen -80C. *Ran THS-seq on GM12878 cells and mouse F123 ES cells, and barcode combinations map only to human and mouse, with a expected 11% collision rate. [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:LabNotes/Project1/2015-12-16 THS-seq_combinatorial_indexing_R1.2C_pooled_96K_cells_mouse.28F123_ES_cells.29.2Fhuman.28GM12878.29_.28scT7_r0XX_i5.29_and_Tn5059] ===Experiment/Protocol information=== {| {{table}} | align="center" style="background:#f0f0f0;"|'''for 5X transposome''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' |- | Additional Control|||||||||| |- | Reagent||Stock Conc (uM)||Final rxn conc (uM)||Vol (uL)|||| |- | Glycerol 75%||75%||0.3||14.4||3.6||1.8 |- | Annealed Transposon||50||5||3.6||0.9||0.45 |- | EZTn5||5||2.5||18||4.5||2.25 |- | Total|| || ||36||9||4.5 |- | Total % Glycerol||43.75|||||||| |- | |||||||||| |- | |||||||||| |- | incubate at RT, 30m|||||||||| |- | store -20C|||||||||| |- | |} 1. info *resuspend 1 tablet roche protease inhibitor in 1.5 mL N-H2O. Next day add 8.5 mL, then take 920 uL and add to 80 uL 50X LB Repeater combitips 100 uL combitip at 1 uL = 2.5 uL 100 uL combitip at 7 uL = 8.5 uL 200 uL combitip at 10 uL = 12.0 uL 200 uL combitip at 12 uL = 14.0 uL 500 uL combitip at 15 uL = 20.0 uL 1000 uL combitip at 150 uL = 157.0 uL *Lysis buffer is: 10ml 10X lysis buffer (LB, 100mM Tris.Hcl pH 7.5, 100mM NaCl, 30mM MgCl2, 1% NP40, Crawford et al. PNAS 2003) in nuclease free H2O. *FACS buffer: 2X (PBS, 4 mM EDTA, 2% BSA) *2. Samples samples before FACS sorting 1-96. scT7_r0XX_i5, 5X tn5059, ~2,000 nuclei per rxn, buffer D6, samples 1-96 after FACS sorting 1-92. 25 nuclei, 1% BSA FACS buffer, gHCl after sort, pooled 1-96 samples 93. 25 nuclei positive IVT control 12E 94. 25 nuclei positive IVT control 12F 95. NTC control 12G 96. NTC control 12H ===IVT Protocol=== *If need to make more transposome, do first 2 steps. If not goto step 3. '''Generation of transposomes''' 1. annealing of ME sequence to T7 transposon sequence a. Make 100 uM stock solution of tranposon and ME only bottom end. b. Incubate 10 uL of each oligo (100uM) with at 95C for 2 minutes, then cool to 14C at 0.1 C/s. c. Oligo's now at 50 uM in 20 uL. 2. Transposome complex generation, run controls!!! *add the below components into one tube and incubate for 30 minutes at RT a. Add 3.6 uL of 75% sterile glycerol to tube b. Add 0.9 uL of annealed transposon (50 uM) to the 75% sterile glycerol and mix well c. Add 4.5 uL of transposase to well. *store at -20, is good for a year 3. Prepare samples, lyse cells with lysis buffer CELL WASHING - (wash cells with PBS) a. count cells, spin down all cells at 250Xg for 5 minutes '''SPIN DOWN NUCLEI 500X G''' b. wash with 1X PBS, centrifuge 250Xg for 5 minutes c. Count cells again to be sure of cells/uL number CELL LYSIS AND MIXING a. dilute Lysis Buffer (LB) to 4X add protease inhibitors, or as needed (from 10X stock) '''80 uL 50X LB, 920 uL protease inhbiitors''' '''KEEP NUCLEI/CELLS ON ICE''' b. count cells in mouse and human cells and dilute to ~700 cells/uL each. Mix human and mouse cells in equal volumes when at same concentration. add 3 uL cells to each well in 96 well plate. c. add 1 uL 4X LB + protease inhibitors to each well, mix briefly d. transposition ready 3.5. start coating pooling tubes in 2056 uL 1X FACS buffer. coat for 1 hour 4. transposition reaction. Add all components and incubate at 37C FOR 30 MINUTES '''Added in 3 uL cells, then 1 uL 4X LB''' 4.0 uL lysed cells/pure genomic DNA 1.2 uL 5X Custom Tagmentation buffer USED BUFFER D6 1.2 uL T7 transposomes (5X tn5-059, indexed Tsome as listed) ___________ 6.4 uL total solution Incubate at 37C FOR 30 minutes 5. Stop reaction by adding (4.0 uL) 50 mM EDTA. (20 mM final EDTA) Incubate for 15 mins at 37C. 6. Nuclei pooling and recovery '''POOL ALL 96 SAMPLES''' a. Add 1 volume (10 uL) 2X FACS buffer to each well, so is 1X final FACS buffer. b. pool all samples into 1 tube and spin down at 500 x g for 5 minutes. resuspend in 400 uL 1X FACS buffer c. Add PI stain to each tube, 20 uL. (5 uL per 100 uL cells). d. take to FACS core for sorting. 25 nuclei per well, with some 500 nuclei (+) and NTC (-) controls -add 10 uL PBS to each well of sorting plate before hand -core checklist -put samples on ice to and from core. '''add guanidine HCl when get back to lab''' 7. Add 11 uL 8M guanidine HCl for a total of 22 uL. **For SPRI beads add 1.8X (39 uL) beads per well and follow beads purification protocol **remove 57 uL of flow through (leaves extra so don't remove beads). Remove excess during wash steps. **ELUTE IN 8 + 2 uL taq5X, '''VORTEX''' plate to resuspend. leave beads in solution. 8. Fill in reaction *Add 2 uL of 5X taq polymerase, mix thoroughly. Run at 72C for 3 minutes. 9. HiScribe T7 (NEB) T7 Protocol, IVT '''added hiscribe mastermix directly into tubes after taq5x incubation''' HiScribe (NEB) T7 protocol, IVT a. Thaw 10X Transcription Buffer and ribonucleotide solutions. Store the ribonucleotides (A, C, G, U) on ice, but keep 10X transcription buffer at room temp b. Assemble reaction mixture at room temperature, ADD IN ORDER AND MIX THOROUGHLY!!!! (10) uL DNA template (list 1 ug) 2 uL 10X Transcription Buffer 2 uL 100 mM ATP 2 uL 100 mM CTP 2 uL 100 mM GTP 2 uL 100 mM UTP 2 uL T7 Enzyme Mix _______________________ 22 uL total c. Incubate reactions at 37C overnight for ~16-19 hours. 10. Clean with RNA Clean & Concentrator 5, put solution and all beads on columns. *using beads could be an option? *elute samples in 9.0 uL of N-H2O *quanitate/view on TBU gel, only 1 sample? '''AFTER IVT RNA HAS ALREADY BEEN GENERATED AND CLEANED WITH ZYMO''' 11. single strand synthesis MMLV RT (Clontech) *Followed protocol for [http://genome-tech.ucsd.edu/LabNotes/index.php/Brandon:Protocols/SMART_MMLV_RT SMART MMLV Reverse Transcriptase] a. Add 2.5 uL 20 uM (100 ng total) RANDOM HEXAMERS to RNA sample. Bring to final volume of 11.5 uL with Nuclease free H2O b. heat the mixture to 70C for 3 minutes. Immediately cool on ice. c. Add the following to the reaction. 4 uL 5X first strand buffer 2 uL dNTP mix 2 uL 100 mM DTT .5 uL SMART MMLV RT and mix (ADD LAST!!!!!) ___________________________ 20 uL total d. Incuvate first at Room Temperature for 10 minutes. Then incubate at 42C for 60 minutes. e. Terminate the reaction by heating at 70C for 10 minutes 12. RNase H digestion *Use .5 Units for 20 uL reaction. Stock is at 5 Units/ul, thus dilute 10X and use 1 uL per reaction. a. Add 1 uL of 10X diluted Rnase H to the reaction. b. Incubate for 20 minutes at 37C. 13. Second strand synthesis: Adding sss_scnXTv2 primer and polymerases. Can incubate at higher temps (usually at 16C since RNA is nicked) since sss_scnXTv2 has a high Tm. a. Add 2.5 uL of 20 uM sss_scnXTv2 to each reaction. b. Incubate solutions for 2 minutes at 65C. Cool immediately on ice. c. Add 5.875 uL taq5X to reactions, Incubate at 72C for 8 minutes. 14. Clean DNA with AMPURE beads depending. *'''USED AMPURE DNA BEADS AT 1:1.8X RATIO''' *add 54 uL beads per reaction *'''ADDED 7 uL N-H20 TO BEADS, VORTEX TO RESUSPEND''' *'''LEFT BEADS IN SOLUTION, DID NOT REMOVE BEADS FROM ADDED N-H20''' 15. Fragmenting and 3' End tagging with [1X] custom nXTv2_i7 Tn5059 transposome '''RAN TAGMENTATION ON BEADS''' 2 uL custom tagmentation buffer '''USED BUFFER D6, 16% FINAL DMF''' X uL cDNA sample X uL Nuclase free H2O 2 uL prepared 1X T7 transposomes (MAKE SURE TO ADD LAST) ___________ 11 uL total solution Incubate at 55C for 6 minutes, cool briefly on ice after 16. Add 4 uL N-H2O, then added 15 uL 8M guanidine HCl 17. Purified on DNA clean and concentrator, 5 volumes DNA binding buffer, elute in 14 uL N-H2O *150 uL DNA binding buffer 18. PCR addition of barcodes '''USING NEXTERA XT V2 modified i5 (scT7_S5XX) AND i7 (N7XX) SEQUENCES!!!!!''' KAPA SYBR FAST qPCR mix until saturation, X35 cycles 18 uL 2X kapa sybr fast 2 uL scT7_S5XX index primer, 2 uL F. 2 uL nXTv2_i7XX index primer, 2 uL R, (i7XX_long or i7XX_orig) '''USE_ORIG''' 14 uL DNA template _____________ 36 uL KAPA SYBR cycles: 72C 3m, 95C 30s, (95C for 10s, 63C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C forever *terminate before curves saturate (usually cycle 6-8) 19. Run each sample on 6% PAGE gel, normalize concentrations. Pool samples, then Gel Size selection. *gel size select from 220-1000 bp, follow gel size selection protocol ===Results=== *FACS results [[File:Humanbrain fetalmouse nuclei crop.jpg|600px]] *TBU after IVT, single cell combinatorial indexing. whole reactions used (10 uL) [[File:ZhangLab 2 2016-01-27 20hr 23min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-01-27 20hr 24min-invert-labeled.jpg|600px]] *PCR curves [[File:2016-02-02 scTHS-seq bc mouse fetal and brain nuclei.bmp|600px]] *plate layout for i5/i7 barcodes {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''N701''' | align="center" style="background:#f0f0f0;"|'''N702''' | align="center" style="background:#f0f0f0;"|'''N703''' | align="center" style="background:#f0f0f0;"|'''N704''' | align="center" style="background:#f0f0f0;"|'''N705''' | align="center" style="background:#f0f0f0;"|'''N706''' | align="center" style="background:#f0f0f0;"|'''N707''' | align="center" style="background:#f0f0f0;"|'''N710''' | align="center" style="background:#f0f0f0;"|'''N711''' | align="center" style="background:#f0f0f0;"|'''N712''' | align="center" style="background:#f0f0f0;"|'''N714''' | align="center" style="background:#f0f0f0;"|'''N715''' |- | ||||1||2||3||4||5||6||7||8||9||10||11||12 |- | scT7_S502||A||A1, scT7_S502, N701||A2, scT7_S502, N702||A3, scT7_S502, N703||A4, scT7_S502, N704||A5, scT7_S502, N705||A6, scT7_S502, N706||A7, scT7_S502, N707||A8, scT7_S502, N710||A9, scT7_S502, N711||A10, scT7_S502, N712||A11, scT7_S502, N714||A12, scT7_S502, N715 |- | scT7_S503||B||B1, scT7_S503, N701||B2, scT7_S503, N702||B3, scT7_S503, N703||B4, scT7_S503, N704||B5, scT7_S503, N705||B6, scT7_S503, N706||B7, scT7_S503, N707||B8, scT7_S503, N710||B9, scT7_S503, N711||B10, scT7_S503, N712||B11, scT7_S503, N714||B12, scT7_S503, N715 |- | scT7_S505||C||C1, scT7_S505, N701||C2, scT7_S505, N702||C3, scT7_S505, N703||C4, scT7_S505, N704||C5, scT7_S505, N705||C6, scT7_S505, N706||C7, scT7_S505, N707||C8, scT7_S505, N710||C9, scT7_S505, N711||C10, scT7_S505, N712||C11, scT7_S505, N714||C12, scT7_S505, N715 |- | scT7_S506||D||D1, scT7_S506, N701||D2, scT7_S506, N702||D3, scT7_S506, N703||D4, scT7_S506, N704||D5, scT7_S506, N705||D6, scT7_S506, N706||D7, scT7_S506, N707||D8, scT7_S506, N710||D9, scT7_S506, N711||D10, scT7_S506, N712||D11, scT7_S506, N714||D12, scT7_S506, N715 |- | scT7_S507||E||E1, scT7_S507, N701||E2, scT7_S507, N702||E3, scT7_S507, N703||E4, scT7_S507, N704||E5, scT7_S507, N705||E6, scT7_S507, N706||E7, scT7_S507, N707||E8, scT7_S507, N710||E9, scT7_S507, N711||E10, scT7_S507, N712||E11, scT7_S507, N714||E12, scT7_S507, N715 |- | scT7_S508||F||F1, scT7_S508, N701||F2, scT7_S508, N702||F3, scT7_S508, N703||F4, scT7_S508, N704||F5, scT7_S508, N705||F6, scT7_S508, N706||F7, scT7_S508, N707||F8, scT7_S508, N710||F9, scT7_S508, N711||F10, scT7_S508, N712||F11, scT7_S508, N714||F12, scT7_S508, N715 |- | scT7_S510||G||G1, scT7_S510, N701||G2, scT7_S510, N702||G3, scT7_S510, N703||G4, scT7_S510, N704||G5, scT7_S510, N705||G6, scT7_S510, N706||G7, scT7_S510, N707||G8, scT7_S510, N710||G9, scT7_S510, N711||G10, scT7_S510, N712||G11, scT7_S510, N714||G12, scT7_S510, N715 |- | scT7_S511||H||H1, scT7_S511, N701||H2, scT7_S511, N702||H3, scT7_S511, N703||H4, scT7_S511, N704||H5, scT7_S511, N705||H6, scT7_S511, N706||H7, scT7_S511, N707||H8, scT7_S511, N710||H9, scT7_S511, N711||H10, scT7_S511, N712||H11, scT7_S511, N714||H12, scT7_S511, N715 |- | |} *gel quant {| {{table}} | align="center" style="background:#f0f0f0;"|'''2/3/2016''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' |- | sample||intensity||ng/ul|||||||| |- | ||5034.611755||5|||||||| |- | ||3223.284417||2.5||size select amt|||||| |- | 1A||2976.701668||2.159665671||6.945519484||||total||159.2922454 |- | 1B||2808.581288||1.927625365||7.781595049||||dye||31.85844908 |- | 1C||7263.07745||8.075735745||1.857415903||||||191.1506945 |- | 1D||9014.936439||10.49365733||1.429434898|||||| |- | 1E||8136.990243||9.281913079||1.616046161||||7 wells||27.30724207 |- | 1F||22956.08017||29.73527015||0.504451445|||||| |- | 1G||8181.891294||9.343885659||1.605327863|||||| |- | 1H||11042.49588||13.2921016||1.128489719|||||| |- | 2A||12637.28827||15.49323935||0.968164221|||||| |- | 2B||5936.802117||6.24520613||2.401842259|||||| |- | 2C||10597.96542||12.67855919||1.183099734|||||| |- | 2D||5832.807621||6.101672581||2.458342332|||||| |- | 2E||10450.49031||12.47501355||1.202403504|||||| |- | 2F||6522.883393||7.054117452||2.126417671|||||| |- | 2G||16852.24998||21.31074347||0.703870328|||||| |- | 2H||8777.822484||10.16639186||1.475449717|||||| |- | 3A||9678.826736||11.40996092||1.314640787|||||| |- | 3B||5126.122895||5.126303979||2.92608477|||||| |- | 3C||7218.85596||8.014701097||1.871560751|||||| |- | 3D||4350.954811||4.056414418||3.697847028|||||| |- | 3E||10193.6503||12.12052212||1.237570449|||||| |- | 3F||13529.7268||16.72498596||0.896861739|||||| |- | 3G||9784.772604||11.55618776||1.298005909|||||| |- | 3H||1488.3456||0.10543169||10|||||| |- | 4A||29704.25786||39.04912738||0.384131503|||||| |- | 4B||6892.974821||7.564918868||1.982836863|||||| |- | 4C||8365.481313||9.597277213||1.562943288|||||| |- | 4D||11175.08608||13.47510303||1.113164031|||||| |- | 4E||5168.700154||5.185069253||2.892921824|||||| |- | 4F||3762.178671||3.243783637||4.624229504|||||| |- | 4G||10134.39078||12.03873192||1.245978405|||||| |- | 4H||9100.105827||10.6112084||1.413599604|||||| |- | 5A||13386.08566||16.52673199||0.907620455|||||| |- | 5B||7934.771541||9.002810156||1.66614643|||||| |- | 5C||6291.424868||6.734657628||2.227284716|||||| |- | 5D||17084.71923||21.63159831||0.693430036|||||| |- | 5E||18771.14056||23.95920262||0.626064241|||||| |- | 5F||9525.370716||11.19816041||1.339505726|||||| |- | 5G||5541.402715||5.699474564||2.631821553|||||| |- | 5H||12586.35149||15.42293623||0.972577451|||||| |- | 6A||16161.97509||20.35802378||0.736810221|||||| |- | 6B||9149.775189||10.67976222||1.404525652|||||| |- | 6C||12311.76632||15.04395288||0.997078369|||||| |- | 6D||8342.36727||9.565375134||1.568155957|||||| |- | 6E||7652.580228||8.61332877||1.741486991|||||| |- | 6F||11647.9564||14.12776021||1.061739425|||||| |- | 6G||18686.92719||23.84297105||0.629116227|||||| |- | 6H||8069.824685||9.189210954||1.632349075|||||| |- | 7A||26949.38238||35.24683911||0.425570076|||||| |- | 7B||10242.30576||12.18767654||1.230751403|||||| |- | 7C||12507.36293||15.31391595||0.979501262|||||| |- | 7D||8876.831328||10.3030442||1.455880389|||||| |- | 7E||9935.320296||11.76397418||1.275079303|||||| |- | 7F||3874.584035||3.398925893||4.413158884|||||| |- | 7G||10647.41139||12.74680468||1.176765502|||||| |- | 7H||23019.73291||29.82312387||0.502965419|||||| |- | 8A||21079.31865||27.14495768||0.552588815|||||| |- | 8B||6438.083971||6.937077008||2.162294001|||||| |- | 8C||20296.29699||26.06422858||0.575501399|||||| |- | 8D||15494.79642||19.43718157||0.771716823|||||| |- | 8E||6482.500193||6.998380425||2.143353046|||||| |- | 8F||8868.812109||10.29197605||1.457446066|||||| |- | 8G||27307.32415||35.74087153||0.419687583|||||| |- | 8H||4546.166802||4.325846656||3.467529294|||||| |- | 9A||18730.5074||23.9031206||0.627533126|||||| |- | 9B||10668.17664||12.77546494||1.174125566|||||| |- | 9C||20844.30998||26.82059794||0.559271648|||||| |- | 9D||5969.194008||6.289913525||2.384770465|||||| |- | 9E||10539.65031||12.59807248||1.190658335|||||| |- | 9F||6179.253354||6.579838132||2.279691339|||||| |- | 9G||22914.50983||29.67789463||0.505426688|||||| |- | 9H||4428.09791||4.162887579||3.603268096|||||| |- | 10A||5798.132673||6.053814103||2.477776777|||||| |- | 10B||11280.10177||13.62004604||1.101317863|||||| |- | 10C||10455.08521||12.48135544||1.201792552|||||| |- | 10D||13476.13033||16.65101193||0.90084615|||||| |- | 10E||17736.73053||22.53150646||0.665734447|||||| |- | 10F||13524.29294||16.71748613||0.897264091|||||| |- | 10G||12936.8649||15.906716||0.942997914|||||| |- | 10H||17261.08051||21.87501274||0.685713886|||||| |- | 11A||17762.00592||22.56639165||0.664705294|||||| |- | 11B||12185.3122||14.86942048||1.008781749|||||| |- | 11C||9892.768167||11.70524359||1.281476962|||||| |- | 11D||9726.367319||11.47557659||1.307123863|||||| |- | 11E||4016.11012||3.594260665||4.173320023|||||| |- | 11F||2814.2753||1.93548426||7.749998442|||||| |- | 11G||14956.11682||18.6936942||0.802409617|||||| |- | 11H||16917.34939||21.4005939||0.700915127|||||| |- | 12A||25644.98537||33.44650603||0.448477338|||||| |- | 12B||24160.48722||31.39759675||0.477743571|||||| |- | 12C||18501.80035||23.58745837||0.63593117|||||| |- | 12D||10883.5706||13.07275239||1.147424777|||||| |- | |} *gel images [[File:ZhangLab 2 2016-02-03 11hr 53min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 11hr 56min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 11hr 58min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 11hr 59min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 15hr 21min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 15hr 23min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 15hr 24min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 15hr 26min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 15hr 27min-labeled.jpg|600px]] *gel size selection [[File:ZhangLab 2 2016-02-03 19hr 53min-labeled.jpg|600px]] [[File:ZhangLab 2 2016-02-03 19hr 54min-labeled.jpg|600px]] *after gel size selection of libraries [[File:ZhangLab 2 2016-02-04 11hr 53min-labeled.jpg|600px]]
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