eamag/protocols-with-steps huggingface dataset:
TITLE: Quantitative RT-PCR using the TaqMan® Gene Expression Assays on  StepOnePlus™ Real-Time PCR System
AUTHORS: Lisa-Maria Rosenthal, Giang Tong, Katharina Schmitt

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Quantitative RT-PCR using the TaqMan® Gene Expression Assays on</span><span> </span></div><div class = "text-block"><span style = "font-weight:bold;">StepOnePlus™ Real-Time PCR System</span><span></span></div></div>

[STEPS]
?. 
?. Primers  ABCD1Primers2GeneGene Assay IDGeneGene Assay ID3RBM3Hs00943160_g1CIRPHs00989762_g14IL-6Hs00174131_m1MCP-1 (Ccl2)Hs00234140_m15iNOSHs01075529_m1GAPDHHs02786624_g1P
ABCD1Primers2GeneGene Assay IDGeneGene Assay ID3RBM3Hs00943160_g1CIRPHs00989762_g14IL-6Hs00174131_m1MCP-1 (Ccl2)Hs00234140_m15iNOSHs01075529_m1GAPDHHs02786624_g1
?. AB1ComponentVolume (µL)2Gene Assay Primers0.53TaqMan Gene Expression PCR Master Mix5.04cDNA0.55Nuclease-free H2O4.06Total per reaction10.0
AB1ComponentVolume (µL)2Gene Assay Primers0.53TaqMan Gene Expression PCR Master Mix5.04cDNA0.55Nuclease-free H2O4.06Total per reaction10.0
?. ABCDE1StepTimes and Temperatures22. PCR StepInitial StepsPCR (40 Cycles)3AmpErase ® UNG ActivationAmpliTaq Gold®&nbsp;DNA Polymerase ActivationMeltAnneal/ Extend4HOLDHOLDCYCLE52 min @ 50 °C10 min @ 95 °C15 sec @ 95 °C1 min @ 60 °C
ABCDE1StepTimes and Temperatures22. PCR StepInitial StepsPCR (40 Cycles)3AmpErase ® UNG ActivationAmpliTaq Gold®&nbsp;DNA Polymerase ActivationMeltAnneal/ Extend4HOLDHOLDCYCLE52 min @ 50 °C10 min @ 95 °C15 sec @ 95 °C1 min @ 60 °C
TITLE: DNA Extraction with ZymoBIOMICS MiniPrep Kit
AUTHORS: Carlos Goller

[DESCRIPTION]
DNA extraction of bacterial DNA Using ZymoBIOMICS‱ DNA Miniprep Kit (D4300) using lysis tubes with DNA/RNA Shield. 

[STEPS]
SECTION: D
1. Add  to a ZR BashingBead‱ Lysis Tubes (0.1 & 0.5 mm). Add750 µL ZymoBIOMICS‱ Lysis Solution to the tube and cap tightly.   Note: For samples stored and lysed in   Lysis Tubes, do not add ZymoBIOMICS‱ Lysis Solution and proceed to Step 2.


 


SECTION: D
2. Obtain DNA/RNA Shield Lysis Tubes with samples/swab heads from instructors.  Secure in a bead beater fitted with a 2 ml tube holder assembly and process using optimized beat-beating conditions (speed and time) for different devices. We will use a Vortex Genie with 2ml Bashing Bead tubes for 40 min. 

SECTION: D
3. Centrifuge the ZR BashingBead‱ Lysis Tubes (0.1 & 0.5 mm) in a microcentrifuge at ≥ 10000 rpm, 1 min, 20 °C.

SECTION: D
4. Transfer up to 400 µL supernatant to the Zymo-Spin‱ III-F Filter in a Collection Tube and centrifuge at 8.000 x g, 1 min. Discard the Zymo-Spin‱ III-F Filter.

SECTION: D
5. Add 1200 µL of ZymoBIOMICS‱ DNA Binding Buffer to the filtrate in the Collection Tube from Step 4. Mix well.

SECTION: D
6. Transfer 800 µL of the mixture from Step 5 to a Zymo-Spin‱ IICR Column in a Collection Tube and centrifuge at 10.000 x g, 1 min.

SECTION: D
7. Discard the flow through from the Collection Tube and repeat Step 6.
SECTION: D
8. Add 400 µL ZymoBIOMICS‱ DNA Wash Buffer 1 to the ZymoSpin‱ IICR Column in a new Collection Tube and centrifuge at 10.000 x g, 1 min. Discard the flow-through.

SECTION: D
9. Add 700 µL ZymoBIOMICS‱ DNA Wash Buffer 2 to the ZymoSpin‱ IICR Column in a Collection Tube and centrifuge at 10.000 x g, 1 min. Discard the flow-through.

SECTION: D
10. Add 200 µL ZymoBIOMICS‱ DNA Wash Buffer 2 to the ZymoSpin‱ IICR Column in a Collection Tube and centrifuge at 10.000 x g, 1 min.

SECTION: D
11. Transfer the Zymo-Spin‱ IICR Column to a clean 1.5 ml microcentrifuge tube and add 100 µl (50 µl minimum) ZymoBIOMICS‱ DNase/RNase Free Water directly to the column matrix and incubate for 1 min. Centrifuge at 10.000 x g, 1 min to elute the DNA5, 6.

SECTION: D
12. Place a Zymo-Spin‱ III-HRC Filter in a new Collection Tube and add 600 µL ZymoBIOMICS‱ HRC Prep Solution. Centrifuge at 8.000 x g, 3 min.

SECTION: D
13. Transfer the eluted DNA (Step 11) to a prepared Zymo-Spin‱ III-HRC Filter in a clean 1.5 ml microcentrifuge tube and centrifuge at exactly 16.000 x g, 3 min.  The filtered DNA is now suitable for PCR and other downstream applications.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><strong>Objective</strong> To correlate the value of lactate in fetal scalp blood at delivery and the outcomes of the offspring at four years of age.</p>
<p><strong>Methods:</strong> Cases where scalp blood lactate was taken within sixty minutes before delivery were identified from the randomized trial "Determination of pH or lactate in fetal scalp blood in management of intrapartum fetal distress”. Data were divided according to the generally accepted cutoffs for normality, pre-acidemia, acidemia and concentrations above mean +2 SD during the second stage. The outcome measures included gross-/fine motor function, vision, hearing, speaking and cognitive disorders, signs of central motor damage and referral to specialized pediatric services.</p>
<p><strong>Results:</strong> 307 cases were available for final analyse. With normal scalp lactate concentration, the number of children with a diagnosed disorder was lower compared to the pre-acidemic/acidemic groups, although the findings were only significant for fine motor dysfunction (p = 0.036). Elevated lactate values were significantly associated with increased risk for a poorer capacity of attention and understanding of instructions (OR 1.37, 95% CI 1.07-1.74), and for fine motor dysfunction (OR 1.22, 95% CI 1.00-1.49) at the age of four.</p>
<p><strong>Conclusion</strong>: Higher levels of lactate in fetal scalp blood are associated with increased risk of an aberrant developmental outcome at four years of age in some areas. If scalp lactate is normal, it seems safe to allow labor to continue.</p>

[STEPS]
TITLE: Sensor Guided Needle Entry Procedures: A Scoping Review of Advancements to the Veress Needle &amp; selected Needle Entry Techniquesnique Advancements
AUTHORS: Chimwemwe Miti, Richard Scott, Hermes Gadelha-Bloomfield

[DESCRIPTION]
Primary entry during minimally invasive abdominal surgery remains the one step associated with controversy and complications. 
This scoping review attempts to draw literature describing sensor augmented techniques for introducing the primary trocar or Veress needle into the abdomen in a bid to reduce associated challenges. Publications related to other relevant needle entry techniques into critical spaces where sensors are successfully utilised are also briefly reviewed. 
It is expected that an overview of related areas in which the technology is applicable and modifications to established techniques alongside the added improvements will be described.

[STEPS]
SECTION: Eligibility Criteria
1. Studies in English
SECTION: Eligibility Criteria
2. Publication period 1992- May 2024
SECTION: Eligibility Criteria
3. Articles with full text available
SECTION: Eligibility Criteria
4. Human subjects
5. 
6.
TITLE: A-Tailing with Taq Polymerase
AUTHORS: New  England   Biolabs

[DESCRIPTION]
This protocol can be used to add As to the blunt-ends of DNA fragments that have been amplified using a high-fidelity polymerase (such as Q5® High Fidelity DNA Polymerase).

[STEPS]
1. Clean-up the amplified DNA from the PCR components  
 

2. Set-up the reaction by adding the following components:  
 

3. Incubate the reaction at 72 °C for 20 min.
TITLE: LC-MS/MS Untargeted Metabolomics Data Acquisition
AUTHORS: Kevin Contrepois

[DESCRIPTION]
Scope:
To describe the procedure to acquire metabolomics data using our broad spectrum plateform.

Expected outcome/data:
Metabolite extracts are analyzed four times using HILIC and RPLC in positive and negative ionization modes.

[STEPS]
1. Untargeted metabolomics was performed using a combination of HILIC- and RPLC-MS methods.
2. Metabolic extracts were analyzed four times using HILIC and RPLC separation in both positive and negative ionization modes. 
3. Data were acquired on a Thermo Q Exactive HF mass spectrometer for HILIC (Thermo Fisher Scientific, Bremen, Germany) and a Thermo Q Exactive mass spectrometer for RPLC (Thermo Fisher Scientific, Bremen, Germany). 
4. Both instruments were equipped with a HESI-II probe and operated in full MS scan mode. 
5. MS/MS data were acquired on quality control samples (QC) consisting of an equimolar mixture of all samples in the study. 
SECTION: HILIC
6. HILIC experiments were performed using a ZIC-HILIC column 2.1 x 100 mm, 3.5 μm, 200Å (Merck Millipore, Darmstadt, Germany) and mobile phase solvents consisting of 10 mM ammonium acetate in 50/50 acetonitrile/water (A) and 10 mM ammonium acetate in 95/5 acetonitrile/water (B). 
SECTION: RPLC
7. RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50 mm, 1.7 μm, 100Å (Agilent Technologies, Palo Alto, CA) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B). 
8. Data quality was ensured by (i) injecting 6 and 12 pool samples to equilibrate the LC-MS system prior to running the sequence for RPLC and HILIC, respectively, (ii) injecting a pool sample every 10 injections to control for signal deviation with time, and (iii) checking mass accuracy, retention time and peak shape of internal standards in each sample.
TITLE: Sanger sequencing
AUTHORS: iGEM Dusseldorf

[STEPS]
?. Label 1.5 mL tubes with barcodes from sequencing company
?. . Add template (400 to 500 ng), primer and water (10 uL total volume, details below)  AB1uL per Reaction2Template400-500ng310 uM Primer2.54Waterfill up with water5Total Volume10.0
AB1uL per Reaction2Template400-500ng310 uM Primer2.54Waterfill up with water5Total Volume10.0
?. Place tubes inside a small plastic bag and drop off in sequecing company collection Box
?. Results are usually ready to download from the sequecing companys website
TITLE: BASIC PROTOCOL 1: Species Prescreening
AUTHORS: miriam.goldman  , chunyu.zhao  

[DESCRIPTION]
Reference-based metagenotyping depends crucially on the choice and customization of reference database. Therefore, a typical MIDAS2 workflow starts with a species prescreening step for each metagenome, which enables customization of the reference database to match the species in the sample. This protocol describes the species selection step: estimating species coverage per sample, merging the single-sample profiling results, and generating a list of species confidently detected in at least one sample. MIDAS2 estimates species coverage per sample by aligning reads to a database of sequences of 15 universal, single-copy genes (SCGs) and using the median (or mean) coverage of each species’ SCGs.

[STEPS]
1. Install MIDAS2 (See Support Protocol 1)

2. Create a work folder containing the FASTQ files (here example input files are downloaded from Zenodo)
 

3. Initialize a local copy of a MIDAS Reference Database (MIDASDB). Here the SCG data from the UHGG MIDASDB is downloaded:



 




4. Run the single-sample species analysis to identify confidently detectable (i.e., relatively abundant) species in each sample, looping through samples. The output file is created automatically under the directories midas2_output/SRR172902/species and midas2_output/SRR172903/species
 





5. Prepare the sample manifest file for the purpose of merging metagenotyping results across samples in the SNV and CNV modules. Generate the desired sample manifest file for SRR172902 and SRR172903.
 



6. Merge species profiling results for the samples listed in the list_of_samples.tsv. The --min_cov flag defines the minimum median_marker_coverage for estimating species prevalence. The output files are created automatically under the directory midas2_output/merge/species.
TITLE: FFPE Blocking and Sectioning - UMN TMCs
AUTHORS: Colleen Forster, HT(ASCP)QIHC, David A Bernlohr, Laura J Niedernhofer

[DESCRIPTION]
FFPE Blocking and Sectioning protocol from BLS Histology at the University of Minnesota. 

  


[STEPS]
SECTION: FFPE Blocking
1. Specimen Preparation: 

The tissues for processing should be well fixed, rinsed in running tap and placed into 80%
alcohol. The suggested fixation is perfusion with 4% paraformaldehyde, fresh tissue dropped
into 4% paraformaldehyde or 10% formalin for 24-48 hours or alcohol fixed tissues.
To improve fixation, fix small pieces of tissue so solution can penetrate better.
SECTION: FFPE Slide Sectioning
14. Remove excess wax from the sides of the plastic cassettes by scraping or melting.
SECTION: FFPE Slide Sectioning
15. Orient the block in chuck holder
SECTION: FFPE Slide Sectioning
16. Begin carefully cutting into paraffin block until a full face of tissue is exposed
SECTION: FFPE Slide Sectioning
17. Place block onto ice/water and soak for 15 minutes or longer if necessary
SECTION: FFPE Slide Sectioning
18. Cut section at desired thickness ensuring proper orientation 
SECTION: FFPE Slide Sectioning
19. Carefully pick up section and place in a water bath
SECTION: FFPE Slide Sectioning
20. Place tissue section on required glass slide 
SECTION: FFPE Slide Sectioning
21. Air dry for minimum of 1 hour and then move to the 37 degree oven
SECTION: FFPE Slide Sectioning
22. Dry slides overnight.
SECTION: FFPE Blocking
2. Label cassettes using a pencil.
SECTION: FFPE Blocking
3. Block tissues according to researcher requests.
SECTION: FFPE Blocking
4. Place into labeled cassette, cover and place into container under running tap water.
SECTION: FFPE Blocking
5. Rinse well.
SECTION: FFPE Blocking
6. Drain tap water and replace with 80% alcohol
SECTION: FFPE Blocking
7. Bring to Rm2-155 Jackson Hall for processing.
 

SECTION: FFPE Blocking
8. Place cassettes in paraffin bath at embedding center
SECTION: FFPE Blocking
9. Cover with paraffin.
SECTION: FFPE Blocking
10. Move to cold plate for hardening.
SECTION: FFPE Blocking
11. Pop cooled block out of mold and trim edges.
SECTION: FFPE Blocking
12. Block is ready to cut.
SECTION: FFPE Blocking
13. When cutting the tissue, prepare sections according to the Histology Request sheet.
TITLE: 城市微生物相調查計畫—採集土壤教學
AUTHORS: Hsin-Mao  Wu

[DESCRIPTION]
吳昕懋

[STEPS]
SECTION: 採土與iNaturalist紀錄教學
1. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中   
   

SECTION: 採土與iNaturalist紀錄教學
2. 將塑膠袋中的土均勻混合，倒入採集罐之中，並且將鏟子清潔乾淨。  
 

 



SECTION: 採土與iNaturalist紀錄教學
3. 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊  

SECTION: 採土與iNaturalist紀錄教學
4. 最後拍兩張照片
 

   
        

 

SECTION: 採土與iNaturalist紀錄教學
5. 接著打開iNaturalist app
SECTION: 採土與iNaturalist紀錄教學
5.1. 如圖所示，點選右下角的加號  

SECTION: 採土與iNaturalist紀錄教學
5.2. 如下圖所示接著需選擇觀察類型，請點「選擇照片」   

SECTION: 採土與iNaturalist紀錄教學
5.3. 請點選左上角紅框處的相機圖示，上傳第二張照片；接著點選圖中央綠框處，定位採集地點 
  

 

SECTION: 採土與iNaturalist紀錄教學
5.4. 按下打勾處完成定位  

SECTION: 採土與iNaturalist紀錄教學
5.5. 最後點選圖中藍框處，將樣本加入「台灣土壤微生物相調查」專案中
SECTION: 採土與iNaturalist紀錄教學
6. 上傳完成後，若是搭載Android之裝置，可在app中的詮釋資料，找到iNaturalist ID (如下圖紅框處)  



SECTION: 採土與iNaturalist紀錄教學
6.1. 若是搭載iOS之裝置，請在app中的觀察紀錄右上角，點選分享按鈕後，開啟瀏覽器，並在網址列末端找到iNaturalist ID   
  

SECTION: 採土與iNaturalist紀錄教學
7. 在採集紀錄紙上填入ID，並將紀錄紙下半部，沿虛線撕下並放入採集罐中    

SECTION: 採土與iNaturalist紀錄教學
8. 記得將採集地點恢復原狀！   

SECTION: 採土與iNaturalist紀錄教學
9. 將採集罐保存於室溫，並將樣本放置回收處，詳細地址資訊附於採集工具包中。
待團隊評估樣品品質後，會再與您通知。
TITLE: Coronavirus Lateral Flow Assay (LFA) operation protocol v2
AUTHORS: peijun he

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Coronavirus Lateral Flow Assay (LFA) operation protocol</div></div>

[STEPS]
?. Place ELISA plate on lid so that angled towards you.
?. Vortex conjugate to mix (gold particles settle out) and pipette  into front of first well (A1).
1 µl
?. Pipette  into first well of next row (B1).
[PBS]
?. Add  of sample (follow the sample preparation protocol for sample preparation) to conjugateand mix by pipetting, keeping mixture at front of well.
40 µl
?. Place bottom end of LFA strip in conjugate/sample mixture.
?. Allow reagents to move up strip by capillary action for approximately
?. Transfer strip to PBS well for approximately   to wash away unbound gold conjugate and improve signal vs background.
?. Read results on strips. The upper band (control line) should be present in all samples, ensuringcorrect performance of the assay. The ‘test line’ will appear below the ‘control line’ if the sample isSARS-CoV-2 positive.
TITLE: Tween 60-esculin Agar (TE slant)
AUTHORS: Amy Gladfelter

[DESCRIPTION]
This media is used to determine ability of Malassezia species to hydrolyzeesculin and utilize Tween 60.

[GUIDELINES]
This media is used to determine ability of Malassezia species to hydrolyze esculin and utilize Tween 60.

[STEPS]
1. peptone 10 g

2. glucose 10 g

3. yeast extract 2 g

4. ferric ammonium citrate 0.5 g

5. esculin 1 g

6. agar 15 g

7. Tween 60 5 mL

8. dH2O 1 L

9. Sterilize by autoclaving.
TITLE: Libraries construction for HPV targeted NGS
AUTHORS: monia.ardhaoui 

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol allow the construction of libraries for targeted NGS. Customized primers were designed and indexes were used to permit a one run sequencing.</div></div>

[STEPS]
?. A first PCR with PGMY09/11primers was performed using 50μl mixture containing 3mM MgCl2, 10 μmol of each primer, 1.5 mM of dNTP (dATP, dCTP, TTP, dGTP), 5μl of the Taq DNA polymerase buffer, 1U of Taq DNA Polymerase, and 10 μl of DNA preparation was aliquoted. The PCR cycling parameters were composed of a 10 minutes initial denaturation at 94°C, followed by 30 amplification cycles of 30 s at 94°C, 1 min at 50°C and 1 min at 72°C, and a final extension step for 7 minutes at 72°C.
?. 2.5 µl from the PYGMY PCR were amplified by a second PCR using 25µl mixture. PCR mixture contained 12.5µL Kapa Mix(Kapa Taq Extra Hot Start Mix, TXHSRMK Roche), 10µl of each designed primers: (P5-GP5+:	TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG TTT GTT ACT GTG GTA GAT ACCAC/ P7-GP6+:	GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG GAA AAA TAA ACT GTA AAT CAT ATT). The PCR cycling parameters were composed of a 5 minutes of initial denaturation at 95°C, followed by 14 amplification cycles of 30 seconds at 94°C, 1 minutes at 55°C and 1 minutes at 72°C, and a final extension step for 5 minutes at 72°C.
?. The size of PCR products (~200 pub) was evaluated with the 2100 Bio analyzer system (Cat. no. G2940CA; Agilent Technologies, Santa Clara, CA, USA).
?. samples were purified using the Agent court® Apure® XP beads (Cat. no. A63881; Beckman Coulter Genomics, Danvers, MA, USA).
?. 96 different indexes (NextEra XT Index Kit) were added using a PCR reaction (40µl). PCR mixture contained 5µl of the previous  purified PCR product, 25 µl of Kapa Mix and 5µl of each index. The PCR cycling parameters were composed of a  3 minutes of initial denaturation at 95°C, followed by 8 amplification cycles of 30 seconds at 94°C, 1 minutes at 55°C and 30 seconds at 72°C, and a final extension step for 5 minutes at 72°C.
?. Libraries were purified
?. Librairies were quantified using Real Time PCR.
?. Librairies were pooled at equimolar ratios (4nM) to yield one sequencing sample.
?. In preparation for cluster generation and sequencing, pooled libraries are denatured with NaOH, diluted with hybridization buffer, and then heat denatured before MiSeq sequencing. The sequencing was performed using the Miseq V2 Kit.
TITLE: Stereotaxic Injections and Implants 
AUTHORS: Jonathan Tang

[DESCRIPTION]
Methods for Stereotaxic injections and implants from Tang et al 2023. 


[STEPS]
SECTION: VTA AAV Viral Steriotaxic Injections
1. Using a standard mouse surgical suite (see references for example), 750nl of rAAV.EF1a.DIO.hChR2(H134R).eYFP or rAAV.EF1a.DIO.eYFP (3-4 x 10^12 vg/ml,
AAV5, University of North Carolina Vector Core; 1-2 x 10^13 vg/ml, AAV1,
Addgene, 27056-AAV1 and 20298-AAV1) were injected into each hemisphere of the
VTA of 3–4-month-old DAT-Cre mice.

SECTION: Dual Optic Fiber Cannula Implant
2. For each mouse, a dual optic fiber cannula (200/240 μm diameter, 6 mm length, 0.7 mm center-to-center FLT, 0.22 NA; Doric, DFC_200/240-0.22_6mm_DF0.7_FLT) was placed 200 μm above
the injection site and fixed to the skull. 
SECTION: VTA AAV Viral Steriotaxic Injections
1.1. For viral injections, the coordinates are AP - 3.52 mm, ML - +/- 0.35 mm, DV – 4.3
mm. Injections were made at 0.2 Hz pulses. Each pulse injects 4.6 nl volume.
SECTION: VTA AAV Viral Steriotaxic Injections
1.2.  Injected needles were kept in place in the injection site for ~15 minutes before withdrawal. 
SECTION: Dual Optic Fiber Cannula Implant
3. Next, a 4-position receptacle connector (Harwin Inc., M52-5000445) was fixed anteriorly to the dual optic fiber cannula, with its posterior edge set at -0.6 mm.
SECTION: Dual Optic Fiber Cannula Implant
3.1.  Skull implants are then fixed with dental cement. 
SECTION: Dual Optic Fiber Cannula Implant
3.2. A 4-position connector (Harwin Inc., M52-040023V0445) with pins removed from one end was used to cap the receptacle connector.
SECTION: Photometry Experiments
4. The conditions used for VTA injections and implants were as above, and 3–5-month-oldDAT-Cre males were used.
SECTION: Photometry Experiments
4.1. Additionally, 1 μl and 500 nl of AAV9-hSyn-GRAB-rDA1m (2 x 10^13 vg/ml; RRID:Addgene_140556) were injected into the dorsal striatum (AP 0.5 mm, ML +2.1 (right), DV 2.3 (from brain surface)) and ventral striatum (AP 1.15mm, ML +1.65 (right),DV 4.2 (from Bregma)), respectively.
SECTION: Photometry Experiments
5. For photometry fiber implants, mono fiberoptic cannula were used (400/430 μm diameter, 4 mm length (dorsal striatum) and 6 mm length(ventral striatum), 0.37 NA, 1.25 diameter ferrule, flat; Doric, MFC_400/430-0.37_6mm_MF1.25_FLT (ventral striatum) and MFC_400/430-0.37_4mm_MF1.25_FLT
(dorsal striatum)). Implants were inserted at a 22 degrees angle.
TITLE: Fluorescence microscope (Zeiss)
AUTHORS: x.chu  

[DESCRIPTION]
How to operate the fluorescence microscope in the lab. Beware of safety hazards: This instrument uses led radiation. Do not stare at the operating lamp for a prolonged period of time in fluorescence mode.

[STEPS]
SECTION: Microscope layout
1.   

SECTION: Operating microscope
2. Turn on the white light intensity and shutter
SECTION: Operating microscope
3. Turn on the zoom controller
SECTION: Operating microscope
4. Turn on the LED, if using fluorescent mode
SECTION: Operating microscope
5. Turn on the software on the computer: Pylon viewer
SECTION: Operating microscope
6. Place sample in the microscope and adjust the eyepiece 
SECTION: Operating microscope
7. Focus the sample using the wheel on the left-hand side whilst observing through the eyepiece
SECTION: Operating microscope
8. Using the white light shutter on the right to block out the white light, only fluorescence from the sample reaches the eyepiece.
SECTION: Operating microscope
9. To capture an image, switch to computer mode using the switch on the upper right-hand side.
SECTION: Operating microscope
10. Press the camera symbol in the software to capture an image. Parameters such as acquisition time can be set in the software.
SECTION: Operating microscope
11. The best results are obtained when the plastic cover is on and the background light in the room is kept at a minimum.
SECTION: Operating microscope
12. Turn off the white light, LED, and zoom controller when finished using the microscope.
SECTION: Operating microscope
13. Enclose with plastic cover.
SECTION: Trouble-shooting
14. The software does not connect to the camera:
Make sure the USB cable is plugged in to a USB 3.0 port on the computer. Check that the camera is on. Make sure the correct driver is installed.
SECTION: Trouble-shooting
15. The zoom controller, white light or LED don't turn on:
Make sure that the microscope is plugged in.
SECTION: Trouble-shooting
16. Nothing can be seen through the eyepiece:
Make sure nothing is blocking the path between the sample and the objective lens. Make sure that the microscope is not switched to camera view.