2022_08_24updated

Resource updated
Jun-Lizst · Aug 24, 2022 · 2f81e6b · 2f81e6b
1 parent 61ee6f6
commit 2f81e6b
Show file tree

Hide file tree

Showing 89 changed files with 6,551 additions and 4,288 deletions.
diff --git a/content/page/research.md b/content/page/research.md
@@ -20,7 +20,7 @@ showActions:    false
 
 ## Brain vasculature system
 ![talkxssqwe](/img/576078_548648.png)
-Brain endothelial cells are major component ofbrain vasculature system and involved in many kinds of brain vasculaturedisease, like AVM, CCM, HHT.
+Our goal is to understand the principles underlying the formation of the brain vasculature system. Brain endothelial cells are one of the major components of brain vasculature system and involved in many kinds of brain vasculature disease, like AVM, CCM, HHT. 
 
 
 

diff --git a/content/resource/Imagingtools.md b/content/resource/Imagingtools.md
@@ -31,14 +31,16 @@ thumbnailImagePosition: left
 **Thorlabs**: https://www.thorlabs.com/index.cfm\
 **Ti:Sapphire Femtosecond Laser**: [From Thorlabs](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=8323)
 
+[AO (Adaptive optics) in 2PFM and for neurobiology](https://www.med.upenn.edu/ngg/assets/user-content/documents/ngg-documents/1-s2.0-s0959438817302453-main.pdf)
 
+---
 #### Commercial
 **Olympus**: [FVMPE-RS](https://www.olympus-lifescience.com.cn/en/laser-scanning/fvmpe-rs/)\
 **Leica**: [Leica-MP-4Tune]((https://www.leica-microsystems.com/products/confocal-microscopes/p/leica-tcs-sp8-mp/))\
 **Scientifica**: [Multiphoton Imaging System](https://www.scientifica.uk.com/products/multiphoton-imaging-system)
 
 
-**Ref labs**: [Ji Na lab, UCB](UCB:https://www.jilab.net/);
+**Ref labs**: [Ji Na lab, University of California, Berkeley](https://www.jilab.net/)\
 [Janelia farm](https://www.janelia.org/)
 
 ---
@@ -54,9 +56,10 @@ In this talk, two-photon microscopy-which uses strong pulsed infrared lasers to
 
 #### Lab DIY
 Thorlabs: \
-Liang Gao lab, Westlake University: Tiling Light-Sheet Microscope(TLSM)\
+**Tiling Light-Sheet Microscope(TLSM)**: Liang Gao lab, Westlake University\
 Open-top Light-Sheet Microscopy:\
-Axial-Sweeping technology: Fiolka Reto lab; UTSW
+**Axial-Sweeping technology**: Fiolka Reto lab, 
+- Dean, Kevin M., et al. "Deconvolution-free subcellular imaging with axially swept light sheet microscopy." Biophysical journal 108.12 (2015): 2807-2815. ([Link](https://www.cell.com/biophysj/fulltext/S0006-3495(15)00498-1)) ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ESykLKp0h4BFnzsJWAcaWFsBtPWYHDmxnvw4WFWgxvRpSQ?e=ujhNPB))
 
 #### Commercial
 Lavision BioTec Inc:
@@ -66,13 +69,13 @@ ZEISS: [ZEISS Lattice Lightsheet 7](https://zeiss.ly/yt-lattice-lightsheet-7)
 
 
 
-AO (Adaptive optics):
+[AO (Adaptive optics) in LSFM](https://opg.optica.org/ol/fulltext.cfm?uri=ol-44-10-2514&id=412284)
 
 
-**Ref labs**: Keffer lab, Janelia farm\
-Eric bezig lab; UCB\
-Fiolka Reto lab; UTSW\
-Liang Gao; Westlake University
+**Ref labs**: [Philipp Keller lab, Janelia farm](https://www.janelia.org/lab/keller-lab)\
+[Eric betzig lab, University of California, Berkeley](http://mcb.berkeley.edu/faculty/CDB/betzige)\
+[Reto Fiolka lab, UTSW](https://www.utsouthwestern.edu/labs/fiolka/)\
+[Liang Gao Lab, Westlake University](https://sls.westlake.edu.cn/en/Faculty/201912/t20191202_2417.shtml)
 
 ---
 
@@ -100,10 +103,10 @@ During 20 years of friendship, Betzig and Hess collaborated to create the first
 
 ---
 
-**Ref labs**: Xiaowei Zhuang, Harvard\
-Eric betzig lab; UCB\
-Liangyi Chen, PKU\
-Dong Li, IBP
+**Ref labs**: [Xiaowei Zhuang Lab, Harvard University](http://zhuang.harvard.edu/index.html)\
+[Eric betzig lab, University of California, Berkeley](http://mcb.berkeley.edu/faculty/CDB/betzige)\
+[Liangyi Chen, PKU](http://www.cls.edu.cn/english/PrincipalInvestigator/pi/index5506.shtml)\
+[Dong Li, IBP](http://english.ibp.cas.cn/faculty/index_18316.html?json=http://www.ibp.cas.cn/sourcedb_ibp_cas/cn/ibpexport/EN_xsszmL/202005/t20200519_5583002.json)
 
 
 

diff --git a/content/resource/clearingmethod.md b/content/resource/clearingmethod.md
@@ -29,14 +29,17 @@ This webinar will explain tissue clearing, how it functions, and the three main
 ---
 
 ### PEGASOS (Using in our lab, recommended):
+1. Jing, Dian, et al. "Tissue clearing of both hard and soft tissue organs with the PEGASOS method." Cell research 28.8 (2018): 803-818. ([Link](https://www.nature.com/articles/s41422-018-0049-z))
+([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EcRC9PmbyA9BrlgLKSaS3bIB9E8yuXrCHZV1DNa0FvrtzA?e=cCFpYf))
 
-
-PEGASOSv2
+2. **PEGASOSv2**
 
 
 ### CUBIC 
+1. Matsumoto, Katsuhiko, et al. "Advanced CUBIC tissue clearing for whole-organ cell profiling." Nature protocols 14.12 (2019): 3506-3537. ([Link](https://doi.org/10.1038/s41596-019-0240-9)) ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EWJ98QI4jH9EilElkpcsP_YBHCZWy2BbVRPylE8RaoM48w?e=1hmNwM))
 
 
-### 
-
-**Ref labs**: Ali Erturk lab;
+### **Ref labs**
+1. Ali Erturk lab,
+2. Hiroki R Ueda lab, RIKEN
+3. Hu Zhao lab, CIBR
diff --git a/content/resource/genomicsNGS.md b/content/resource/genomicsNGS.md
@@ -13,7 +13,7 @@ keywords:
 comments:       false
 showMeta:       false
 showActions:    false
-thumbnailImage: /img/pmx090121colgenetics-001-1630015763.jpg
+thumbnailImage: /img/genomics_NGSx1.png
 thumbnailImagePosition: left
 #thumbnailImage: //example.com/image.jpg
 ---

diff --git a/content/resource/molecularbiology.md b/content/resource/molecularbiology.md
@@ -0,0 +1,106 @@
+---
+title: "Molecular biology tools"
+date: 2022-08-21T20:27:51+08:00
+categories:
+- category
+- subcategory
+tags:
+- CRISPR
+- FP
+- Linux
+keywords:
+- tech
+comments:       false
+showMeta:       false
+showActions:    false
+thumbnailImage: /img/pmx090121colgenetics-001-1630015763.jpg
+thumbnailImagePosition: left
+#thumbnailImage: //example.com/image.jpg
+---
+
+
+
+## Fluorescence Proteins
+
+-iRFP: miRFPnano670
+
+- RFPs: mRuby3, mCherry
+
+
+- GFPs: mGreenLantern, EGFP
+
+
+- BFPs: TagBFP2, TagBFP
+
+
+---
+### Reference
+1. [FPbase](https://www.fpbase.org/): FPbase is a moderated, user-editable fluorescent protein database designed by microscopists.
+
+
+## Tissue/Cell type specific AAVs
+
+
+
+
+
+
+
+
+
+## Tissue/Cell type specific promoter
+
+
+
+
+
+
+
+
+## Genetically encoded indicators
+Calcium: GCaMP series (GCaMP8, GCaMP7, GCaMP6)\
+Potassium:
+Dopaine:
+Histamine:
+eCB:
+
+
+## CRISPR systems
+
+- DNA target Cas9 based:
+Knock out: SpCas9, SaCas9
+DNA base editor: dCas9-xxx
+Transcriptional activator:
+
+
+- RNA target Cas13
+RNA knockdown: Cas13d(RfxCas13d or CasRx, Cas13d from Ruminococcus flavefaciens XPD3002)
+
+- DNA base editor
+
+
+## Optogenetics tools
+
+Neuronal activity activation: [ChR2]()
+
+Neuronal activity scilence: 
+
+
+
+
+## Open Source & Commercial Softwares
+1. [Pymol](https://pymol.org/2/); [PyMOL Wiki](https://pymolwiki.org/index.php/Main_Page)
+2. [SnapGene](https://www.snapgene.com/)
+3. [Benchling](https://www.benchling.com/)
+4. [NEB cloner](https://nebcloner.neb.com/#!/)
+
+## Vendor company
+1. [New England Biolabs(NEB)](https://international.neb.com/): NEB is a leader in the discovery and development of molecular biology reagents.
+
+
+
+## Ref Labs
+1. [Feng Zhang lab, MIT](https://zlab.bio/)
+2. [Karl Deisseroth lab, Stanford](https://web.stanford.edu/group/dlab/about_pi.html)
+3. [Yulong Li lab, PKU](http://www.yulonglilab.org/)
+4. [David Liu lab, Harvard](https://www.liugroup.us/)
diff --git a/content/resource/programing.md b/content/resource/programing.md
@@ -26,7 +26,7 @@ gallery:
 
 tags:
 - image gallery
-thumbnailImage: //d1u9biwaxjngwg.cloudfront.net/image-gallery-showcase/city-140.jpg
+thumbnailImage: /img/programmingx1.jpg
 thumbnailImagePosition: left
 #thumbnailImage: //example.com/image.jpg
 ---

diff --git a/public/2018/09/25/index.en-us/index.html b/public/2018/09/25/index.en-us/index.html
@@ -136,7 +136,7 @@
 
   <body>
     <div id="blog">
-      <header id="header" data-behavior="4">
+      <header id="header" data-behavior="1">
   <i id="btn-open-sidebar" class="fa fa-lg fa-bars"></i>
   <div class="header-title">
     <a class="header-title-link" href="https://leoj.xyz/" aria-label="Go to homepage">Jun-Liszt Li</a>
@@ -156,7 +156,7 @@
 
 </header>
 
-      <nav id="sidebar" data-behavior="4">
+      <nav id="sidebar" data-behavior="1">
   <div class="sidebar-container">
 
       <div class="sidebar-profile">
@@ -336,7 +336,7 @@ <h5 class="sidebar-profile-bio">Hello, My name is Jun-Liszt Li. my science inter
 
 
 
-      <div id="main" data-behavior="4"
+      <div id="main" data-behavior="1"
         class="
                hasCoverMetaIn
                ">
@@ -665,7 +665,7 @@ <h2 id="related-websites">Related Websites：</h2>
 </footer>
 
       </div>
-      <div id="bottom-bar" class="post-bottom-bar" data-behavior="4">
+      <div id="bottom-bar" class="post-bottom-bar" data-behavior="1">
 
 <div class="post-actions-wrap">
   <nav >
@@ -731,7 +731,7 @@ <h2 id="related-websites">Related Websites：</h2>
 
       </div>
 
-<div id="share-options-bar" class="share-options-bar" data-behavior="4">
+<div id="share-options-bar" class="share-options-bar" data-behavior="1">
   <i id="btn-close-shareoptions" class="fa fa-times"></i>
   <ul class="share-options">
 

diff --git a/public/2019/05/01/r-plot-2d-density/index.html b/public/2019/05/01/r-plot-2d-density/index.html
@@ -136,7 +136,7 @@
 
   <body>
     <div id="blog">
-      <header id="header" data-behavior="4">
+      <header id="header" data-behavior="1">
   <i id="btn-open-sidebar" class="fa fa-lg fa-bars"></i>
   <div class="header-title">
     <a class="header-title-link" href="https://leoj.xyz/" aria-label="Go to homepage">Jun-Liszt Li</a>
@@ -156,7 +156,7 @@
 
 </header>
 
-      <nav id="sidebar" data-behavior="4">
+      <nav id="sidebar" data-behavior="1">
   <div class="sidebar-container">
 
       <div class="sidebar-profile">
@@ -336,7 +336,7 @@ <h5 class="sidebar-profile-bio">Hello, My name is Jun-Liszt Li. my science inter
 
 
 
-      <div id="main" data-behavior="4"
+      <div id="main" data-behavior="1"
         class="
                hasCoverMetaIn
                ">
@@ -598,7 +598,7 @@ <h1>Reference<br />
 </footer>
 
       </div>
-      <div id="bottom-bar" class="post-bottom-bar" data-behavior="4">
+      <div id="bottom-bar" class="post-bottom-bar" data-behavior="1">
 
 <div class="post-actions-wrap">
   <nav >
@@ -664,7 +664,7 @@ <h1>Reference<br />
 
       </div>
 
-<div id="share-options-bar" class="share-options-bar" data-behavior="4">
+<div id="share-options-bar" class="share-options-bar" data-behavior="1">
   <i id="btn-close-shareoptions" class="fa fa-times"></i>
   <ul class="share-options">
 

diff --git a/public/2019/06/14/the-origin-and-function-of-brain-oscillation/index.html b/public/2019/06/14/the-origin-and-function-of-brain-oscillation/index.html
@@ -138,7 +138,7 @@
 
   <body>
     <div id="blog">
-      <header id="header" data-behavior="4">
+      <header id="header" data-behavior="1">
   <i id="btn-open-sidebar" class="fa fa-lg fa-bars"></i>
   <div class="header-title">
     <a class="header-title-link" href="https://leoj.xyz/" aria-label="Go to homepage">Jun-Liszt Li</a>
@@ -158,7 +158,7 @@
 
 </header>
 
-      <nav id="sidebar" data-behavior="4">
+      <nav id="sidebar" data-behavior="1">
   <div class="sidebar-container">
 
       <div class="sidebar-profile">
@@ -338,7 +338,7 @@ <h5 class="sidebar-profile-bio">Hello, My name is Jun-Liszt Li. my science inter
 
 
 
-      <div id="main" data-behavior="4"
+      <div id="main" data-behavior="1"
         class="
                hasCoverMetaIn
                ">
@@ -679,7 +679,7 @@ <h1 id="references">References</h1>
 </footer>
 
       </div>
-      <div id="bottom-bar" class="post-bottom-bar" data-behavior="4">
+      <div id="bottom-bar" class="post-bottom-bar" data-behavior="1">
 
 <div class="post-actions-wrap">
   <nav >
@@ -745,7 +745,7 @@ <h1 id="references">References</h1>
 
       </div>
 
-<div id="share-options-bar" class="share-options-bar" data-behavior="4">
+<div id="share-options-bar" class="share-options-bar" data-behavior="1">
   <i id="btn-close-shareoptions" class="fa fa-times"></i>
   <ul class="share-options">