A book about a Pipeline
===

###### tags: `book`

- [Front page](/rmughCTHTKu0SptwN2f3Ww)

### Meeting sessions
- [2nd March - First meeting "ScriptZ"](https://docs.google.com/presentation/d/1I4A-WMCDErGUSDyB2bR64aE8hz4Bpiv6L6sNFNCgqQU/edit?usp=sharing)
- [1st April](https://docs.google.com/presentation/d/1U2jTcgUKNph5TXAXz2vrPMatzesuBOxczPomrF4jhD8/edit?usp=sharing)

### Harmony
- [Deleting](/sCpxX0qXSgOFNC1o6R6Ezw)
- [Relocating datasets](/LaZ8pRe1RdGqyP9O3yc-xA)
- [Making a new script](/CkhSTtWZTcC8xbVJH3yBMg)
 
**Manuals**
- [PE Basic & advanced blocks](https://docs.google.com/presentation/d/1Ow12rJRYc643RQ6J_jf-qhq59UyeMaQSa3DrFnl9pLE/edit?usp=sharing)
- [PE Harmony4.6 & columbus](https://docs.google.com/presentation/d/1TurgrulNjJJStv9fqxND6qZgssCIvCFn6ckcGJFkop4/edit?usp=sharing)
- [PE Manuals](/qQyQzRqhQ7uNOa5pyreY_A)

### Dataset stitch
- [Moving datasets (PE tools)](/a5YwsUrrTjeV7GupAD47yw)
- [Stitching datasets (Acapella studio)](https://hackmd.io/RpIAQe7_SYWNpxBlIF5WGw)

- [RNAish Stitch & Import (Python)](/ENUlOM3xSMmX_soiUliyFw)

### Planning RNAscope
- [Experiment sheet example](https://docs.google.com/spreadsheets/d/1ZDZ5s9Hkg-AWRIC_Ef2Vf4RlSbn9ueigTm9TWy4LMvw/edit?usp=sharing)

### Master lists
- [Project Masterlist](https://docs.google.com/spreadsheets/d/1bbr8Diem7mwdGfsB4U5dd606IxCqjXhbXctkjWvgNe0/edit?usp=sharing)
- [Probes Masterlist](https://docs.google.com/spreadsheets/d/16pKuT3l-q5y_8JzyNqrK7Q6MfsLqR4YgH5ZMOPyfP_o/edit?usp=sharing)
- [Probe Orders/wishlist](https://docs.google.com/spreadsheets/d/1txFNGUWPjJEZW9utYYJS9lv9I1wH8IzvWBc6zKuafEw/edit?usp=sharing)
- [Antibodies Masterlist LVL3 + LVL8](https://docs.google.com/spreadsheets/d/1o0aabMR6CFHilzv00JuuAB6mWLw1xRi0L9L2PhbUSMk/edit?usp=sharing)
- [Slide Storage](https://docs.google.com/spreadsheets/d/1R-oM-OnQ0QTJKfI4kOKhKXA1cBeRn15pr7X_qz2fUGA/edit?usp=sharing)
 
- [ACD Probe catalogue](https://docs.google.com/spreadsheets/d/1QbKXW0HDZ7bVJfskS_vkqS061LMVI2WLzoiHWBDJlog/edit?usp=sharing)
- [ACD Validated antibodies](https://docs.google.com/spreadsheets/d/10mtW1cJ8QktE1H-PyvrT6NIBtFS7dnREtf1wvIncL2c/edit?usp=sharing)

### Files
- [Experiment sheet example](https://docs.google.com/spreadsheets/d/1ZDZ5s9Hkg-AWRIC_Ef2Vf4RlSbn9ueigTm9TWy4LMvw/edit?usp=sharing)
 
- [Tissue_Omer_Mm-Ukbrains1](https://docs.google.com/spreadsheets/d/17KyBZCc6Wo_LP0Lunhy0LdpDAnE9RzpnMUBB-bGSppo/edit?usp=sharing)
- [Tissue_Omer_Mm-Ukbrains2](https://docs.google.com/spreadsheets/d/1T14AtaCQs2VOPgiN0i3oq2jTuZquwLyENxY9LnuI300/edit?usp=sharing)
- [Tissue_Omer_Hs](https://docs.google.com/spreadsheets/d/1ZtEvgsxj5vSE2kccxb1WDz9IOSW3WASCB2uFrt11QyY/edit?usp=sharing)
- [Tissue_Hs_MS_Schirmer et al](https://docs.google.com/spreadsheets/d/1wwfNFkZCe2obHFlvLdmlmYR1wk3fREDUFiN1sY2X1PM/edit?usp=sharing)

### Running the Pipline
- [BOND maintenace](/_GZVr3QQRDaQQJiN77H76g)
- [Operetta maintenace](/pmr4ftTpQpKvmywAqF3ZZQ)
...

### Accessory notes
- [Optics 101](/k4JLioi0StK3zzNKE_ffzQ)
- [Pipedream - Game](https://classicreload.com/win3x-pipe-dream-1991.html)
- [Journal Club 2021](/3UTdFl91Q-KB3sbqYkb4QQ)
- [Microsoft teams](https://hackmd.io/zDGD9-5SSGiz7ncPc-RGIw?view)
Accounts and passwords (n/a) <!--](https://hackmd.io/_sevQXfsTQKPC3kxoR4nNA)-->
- [Remote desktop from JCBC](https://hackmd.io/z1v8k9wiQn28V17HkFkQMQ)
- [Remote desktop using Zerotier]
- [Alternative fixing solution](https://www.researchgate.net/post/How_do_you_detect_GFP_reporter_fluorescence_after_fixation)

### Staffans Notes

- [Analysis 01MM](/CvvDYeVmSE6tWTToiVg73Q)

- [Analysis 01MK](/3zkONK-zTJyANR-0ULinKA)

- [Analysis 01MG & 01MH](/bbzLeDp-TGqHattZ0QCmjw)

- [Analysis 01ML](/BYpOvWAgTt-0pcGlTMj9Qg)

- [Analysis 00CY-2](/OAOw2dWDSUe-Vvzc5vS23w)

# __Change_log__

> __2021-03-03__
> [name=MrDr.Staffan]
:::

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###### tags: `book` `SOP` `RNAscope` -->