fix broken 2008 broken URLs

RobertsLab · Dec 18, 2023 · 3b437a9 · 3b437a9
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diff --git a/posts/2008/2008-12-09-sdspagewestern-anti-hsp70-ab-test/index.qmd b/posts/2008/2008-12-09-sdspagewestern-anti-hsp70-ab-test/index.qmd
@@ -10,7 +10,6 @@ title: SDS/PAGE/Western - anti-HSP70 Ab test
 categories:
   - 2008
   - Miscellaneous
-tags:
   - anti-HSP70
   - antibody
   - Coomassie
@@ -25,9 +24,9 @@ tags:
   - skin
 ---
 
-Test of the new [anti-HSP70 Ab (ABR cat# MA3-006)(https://aquacul4.fish.washington.edu/Protocols:Information%20Sheets/Product%20Information%20Sheets/Antibodies/ABR%20-%20HSP70%20Ab.jpg). Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled to result in 10ug protein of control and 10ug protein of VE in a volume of 10uL each. The two samples were mixed with an equal volume of 2x sample reducing buffer. O. rubescans samples were taken from Rachel's -20C box. 15uL of each sample was mixed with 2x sample reducing buffer. All samples were boiled for 5mins and spot spun. Samples were loaded onto Pierce 4-20% Tris-Glycine SDS/PAGE gels. 10uL of SeeBlue ladder was loaded. Gel was run @ 150V for 45mins.
+Test of the new [anti-HSP70 Ab (ABR cat# MA3-006)](https://github.com/RobertsLab/resources/blob/master/protocols/Commercial_Protocols/Invitrogen_Antibody-HSP70-MA3-006.pdf). Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled to result in 10ug protein of control and 10ug protein of VE in a volume of 10uL each. The two samples were mixed with an equal volume of 2x sample reducing buffer. O. rubescans samples were taken from Rachel's -20C box. 15uL of each sample was mixed with 2x sample reducing buffer. All samples were boiled for 5mins and spot spun. Samples were loaded onto Pierce 4-20% Tris-Glycine SDS/PAGE gels. 10uL of SeeBlue ladder was loaded. Gel was run @ 150V for 45mins.
 
-Gel was transferred to nitrocellulose membrane (equilibrated in tris-glycine transfer buffer for 5mins) @15V for 20mins. Membrane washed briefly in 1x TBS-T, then blocked for 1hr. in 15mL of blocking solution. Primary Ab was added at a 1:5000 dilution per the [HSP70 data sheet](https://aquacul4.fish.washington.edu/Protocols:Information%20Sheets/Product%20Information%20Sheets/Antibodies/ABR%20-%20HSP70%20Ab.jpg) and incubated O/N @ 4C. Gel was stained for 1hr in Coomassie stain and then destained w/ 10% acetic acid O/N.
+Gel was transferred to nitrocellulose membrane (equilibrated in tris-glycine transfer buffer for 5mins) @15V for 20mins. Membrane washed briefly in 1x TBS-T, then blocked for 1hr. in 15mL of blocking solution. Primary Ab was added at a 1:5000 dilution per the [HSP70 data sheet](https://github.com/RobertsLab/resources/blob/master/protocols/Commercial_Protocols/Invitrogen_Antibody-HSP70-MA3-006.pdf) and incubated O/N @ 4C. Gel was stained for 1hr in Coomassie stain and then destained w/ 10% acetic acid O/N.
 
 ![](https://eagle.fish.washington.edu/Arabidopsis/SDS-PAGE/20081210.JPG)
 

diff --git a/posts/2008/2008-12-16-sdspagewestern-anti-hsp70-ab-re-test/index.qmd b/posts/2008/2008-12-16-sdspagewestern-anti-hsp70-ab-re-test/index.qmd
@@ -10,7 +10,6 @@ title: SDS/PAGE/Western - anti-HSP70 Ab Re-test
 categories:
   - 2008
   - Miscellaneous
-tags:
   - anti-HSP70
   - antibody
   - chemiluminescent
@@ -24,7 +23,7 @@ tags:
   - SeeBlue Plus
 ---
 
-Another attempt to determine appropriate amounts of anti-HSP70 Ab [(ABR cat# MA3-006)(https://aquacul4.fish.washington.edu/Protocols:Information%20Sheets/Product%20Information%20Sheets/Antibodies/ABR%20-%20HSP70%20Ab.jpg)and/or protein needed for better detection of HSP70 in Gigas protein samples. Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled. The two samples were mixed with an equal volume of 2x sample reducing buffer. 100uL of hemolymph were extracted from Gigas muscles and mixed with an equal volume of 2x sample reducing buffer. Samples were boiled for 5mins. and loaded onto a Pierce 4-20% tris-hepes gel. Also loaded 10uL of SeeBlue ladder. Ran gel @ 150V for 45mins. Samples were transferred to nitrocellulose 20V for 30mins. Well locations were marked on the membrane with a pencil. Gel was stained with Coomassie stain for 30 mins and then destained with 10% acetic acid until bands were clearly visible.
+Another attempt to determine appropriate amounts of anti-HSP70 Ab [(ABR cat# MA3-006)](https://github.com/RobertsLab/resources/blob/master/protocols/Commercial_Protocols/Invitrogen_Antibody-HSP70-MA3-006.pdf)and/or protein needed for better detection of HSP70 in Gigas protein samples. Gigas gill protein extracts from 20080617 (both control and Vibrio exposure samples) were each pooled. The two samples were mixed with an equal volume of 2x sample reducing buffer. 100uL of hemolymph were extracted from Gigas muscles and mixed with an equal volume of 2x sample reducing buffer. Samples were boiled for 5mins. and loaded onto a Pierce 4-20% tris-hepes gel. Also loaded 10uL of SeeBlue ladder. Ran gel @ 150V for 45mins. Samples were transferred to nitrocellulose 20V for 30mins. Well locations were marked on the membrane with a pencil. Gel was stained with Coomassie stain for 30 mins and then destained with 10% acetic acid until bands were clearly visible.
 
 ![external image 20081216.JPG](https://eagle.fish.washington.edu/Arabidopsis/SDS-PAGE/20081216.JPG)
 
@@ -46,4 +45,4 @@ Membrane was cut in two (between lanes 7 & 8) for probing with two different pri
 
 Results:
 
-No image of any sort! Not even the pencil marks were visible. Just a blank screen. I'm starting to suspect that something is wrong with the imaging system or something. This is basically a repeat of the Western on [20081210](https://genefish.wikispaces.com/Sam%27s+Notebook#sjw20081210) which worked. Now I'm not sure what to do at all. This blows.
+No image of any sort! Not even the pencil marks were visible. Just a blank screen. I'm starting to suspect that something is wrong with the imaging system or something. This is basically a repeat of the Western on [20081210](https://robertslab.github.io/sams-notebook/posts/2008/2008-12-10-sdspagewestern-anti-hsp70-ab-test-continued-from-yesterday/) which worked. Now I'm not sure what to do at all. This blows.
diff --git a/posts/2008/2008-12-16-vibrio-challenge/index.qmd b/posts/2008/2008-12-16-vibrio-challenge/index.qmd
@@ -10,7 +10,6 @@ title: Vibrio challenge
 categories:
   - 2008
   - Miscellaneous
-tags:
   - bacterial challenge
   - bacterial culture
   - Vibrio exposure

diff --git a/posts/2008/2008-12-22-rna-isolation-v-tubiashii-from-challenge-see-20081216/index.qmd b/posts/2008/2008-12-22-rna-isolation-v-tubiashii-from-challenge-see-20081216/index.qmd
@@ -10,7 +10,6 @@ title: RNA Isolation - V. tubiashii from challenge (see 20081216)
 categories:
   - 2008
   - Miscellaneous
-tags:
   - MICROBExpress Kit
   - NanoDrop1000
   - RNA isolation
@@ -19,7 +18,7 @@ tags:
   - Vibrio tubiashii
 ---
 
-Added 10mL TriReagent to 2 x 50mL pellets (5.63 x 10^11 total bacteria; see calcs on [20081219](https://genefish.wikispaces.com/Sam%27s+Notebook#sjw20081219)) from the control samples collected on [20081219](http://genefish.wikispaces.com/Sam%27s+Notebook#sjw20081219). Added 10mL TriReagent to 1 x 50mL pellet (1.835 x 10^12 total bacteria; see calcs on [20081219](http://genefish.wikispaces.com/Sam%27s+Notebook#sjw20081219)) from the V.tubi + oyster samples collected on [20081219](http://genefish.wikispaces.com/Sam%27s+Notebook#sjw20081219). Scaled rest of RNA protocol to match. Resuspended pellets in 100uL 0.1%DEPC-H2O. Samples were NanoDropped.
+Added 10mL TriReagent to 2 x 50mL pellets (5.63 x 10^11 total bacteria; see calcs on [20081219](https://robertslab.github.io/sams-notebook/posts/2008/2008-12-19-vibrio-challenge-continued-from-yesterday/) from the control samples collected on [20081219](https://robertslab.github.io/sams-notebook/posts/2008/2008-12-19-vibrio-challenge-continued-from-yesterday/). Added 10mL TriReagent to 1 x 50mL pellet (1.835 x 10^12 total bacteria; see calcs on [20081219](https://robertslab.github.io/sams-notebook/posts/2008/2008-12-19-vibrio-challenge-continued-from-yesterday/) from the V.tubi + oyster samples collected on [20081219](https://robertslab.github.io/sams-notebook/posts/2008/2008-12-19-vibrio-challenge-continued-from-yesterday/). Scaled rest of RNA protocol to match. Resuspended pellets in 100uL 0.1%DEPC-H2O. Samples were NanoDropped.
 
 ![external image 20081222%20RNA%20SJW.PNG](https://eagle.fish.washington.edu/Arabidopsis/RNA%20Spec%20Readings/20081222%20RNA%20SJW.PNG)
 

diff --git a/posts/2008/2008-12-24-rrna-removal-v-tubiashii-total-rna-from-yesterday/index.qmd b/posts/2008/2008-12-24-rrna-removal-v-tubiashii-total-rna-from-yesterday/index.qmd
@@ -20,7 +20,7 @@ tags:
   - Vibrio tubiashii
 ---
 
-rRNA removal was continued from O/N precipitation. Processed the samples according to the [Ambion MICROBExpress Kit protocol](https://aquacul4.fish.washington.edu/Protocols:Information%20Sheets/Commercial%20Protocols:Manuals/Ambion%20-%20MICROBexpress%20bacterial%20mRNA%20kit.pdf) and resuspended final pellets in 25uL of The RNA Storage Solution. Samples were spec'd on the NanoDrop.
+rRNA removal was continued from O/N precipitation. Processed the samples according to the [Ambion MICROBExpress Kit protocol](https://github.com/RobertsLab/resources/blob/master/protocols/Commercial_Protocols/Ambion_MICROBexpress_bacterial_mRNA_kit.pdf) and resuspended final pellets in 25uL of The RNA Storage Solution. Samples were spec'd on the NanoDrop.
 
 ![external image 20081224%20RNA%20SJW.PNG](https://eagle.fish.washington.edu/Arabidopsis/RNA%20Spec%20Readings/20081224%20RNA%20SJW.PNG)
 

diff --git a/...-12-31-sdspage-western-blot-test-of-new-western-breeze-kit-hsp70-ab-for-fish441/index.qmd b/...-12-31-sdspage-western-blot-test-of-new-western-breeze-kit-hsp70-ab-for-fish441/index.qmd
@@ -10,7 +10,6 @@ title: SDS/PAGE, Western Blot - Test of new Western Breeze Kit & HSP70 Ab for FI
 categories:
   - 2008
   - Miscellaneous
-tags:
   - anti-HSP70
   - anti-myc
   - antibody

diff --git a/posts/2023/2023-12-01-Daily-Bits---December-2023/index.qmd b/posts/2023/2023-12-01-Daily-Bits---December-2023/index.qmd
@@ -11,6 +11,10 @@ categories:
   - Daily Bits
 ---
 
+## 20231218
+
+- Tested out some broken URL GitHub action modifications to deal with my notebook.
+
 ## 20231215
 
 ### [Coral E5](https://github.com/urol-e5/deep-dive) (GitHub repo)