Stock solutions

Stock solutions kdorfman Fri, 10/28/2011 - 15:35

ABA

ABA kdorfman Tue, 11/17/2015 - 19:28

(+)-cis,trans-abscisic acid

Plant Media 30631017-1 250 mg $68

soluble in EtOH, MeOH, DMSO 20 - 50 mg/mL

MW = 264.3

Store as powder in freezer.

Make 1 mL of 100mM solution:

0.1mol/1000mL x 164.3g/mol = 0.0264 g

Working concentration ~0.15 mM

In 30 mL MS agar, =

vi = 30mL x 0.15 mM/100 mM = 0.045 mL

ATP

ATP kdorfman Mon, 11/04/2013 - 17:02

10 mM ATP Stock
(from Maniotis)

60 mg ATP in 8 mL H2O
pH to 7.0 with 0.1 M NaOH
Bring volume to 10 mL with H2O

Aliquot and freeze.

Use at ~10 µM

Adenine

Adenine kdorfman Wed, 10/18/2017 - 22:41

Fisher AC147440250 25 gr.

1 mg/mL solution for yeast MV-Ade medium

heat (65C) and stir for one & a half hours

filter sterilize

Adenine hemi-sulfate

Adenine hemi-sulfate kdorfman Wed, 01/15/2020 - 21:39

10X Adenine hemi-sulfate (Sunrise ScienceProducts 1905-010)

2 g/L

Dissolve 2 g of Adenine per 1 L distilled water and filter sterilize. Store in the dark at 4 ˚C.

Antibiotics

Antibiotics kdorfman Wed, 12/28/2011 - 21:01

G418

Table of antibiotic stability in poured agar

Amphotericin

Amphotericin kdorfman Tue, 01/09/2018 - 18:29

Anti-Fungal

Stock solution: 10 mg/mL in DMSO (insoluble in ethanol)

Store at 4C short term, -20 long term (in 15 mL tube, wrapped in foil with tape label)

Keep in the dark.

Final concentration in medium = 10 ug/mL

Add 1 mL per L

Freezes in the refrigerator.

Protect from light.

Ampicillin

Ampicillin kdorfman Wed, 12/28/2011 - 21:02

50 mg/mL stock

(Final concentration in medium = 50 µg/mL)

Lasts up to 4 weeks in poured agar at 4C

0.5 g in 10 mL water

filter sterilize

1 mL aliquots (enough for 1 L medium)

0.4 mg/mL for QSB

Make 35 mL: 0.28 mL 50 mg/mL stock

35 mL sterile water

(filter sterilize if any doubt about sterility)

48 0.7 mL aliquots

Can also use carbenicillin

to make: mL amp solution
at this concentration: mg/mL
add: g dry ampicillin

Carbenicillin

Carbenicillin kdorfman Tue, 08/02/2016 - 15:05

(More stable than ampicillin)

Fisher 50841234b 25 mL Teknova C2130

100 mg/mL stock

effective concentration 50 - 100 µg/mL in medium

Freeze aliquots.

Cipro

Cipro kdorfman Wed, 12/28/2011 - 21:02

Ciprofloxacin 10 mg/mL stock

(final concentration in medium = 10 µg/mL)

100 mg in 10 mL dilute acid (add HCl drop by drop, mixing in between till it dissolves)

filter sterilize

1 mL aliquots

freeze

0.2 mg/mL for QSB

0.7 mL 10 mg/mL stock

35 mL water

filter sterilize

48 0.7 mL aliquots

To make mL 0.2 mg/mL cipro
you'll need: g cipro

freeze

Doxycycline

Doxycycline kdorfman Mon, 01/18/2016 - 13:27

Tetracycline category

solubility 50 mg/mL in water

disk has 30 ug

Erythromycin

Erythromycin kdorfman Fri, 01/20/2012 - 18:10

solubility

50 mg/mL in ethanol

lasts up to 4 weeks in poured agar at 4C

10 mg/mL stock

(10 µg/mL in medium)

0.25 g in 25 mL EtOH

1 mL aliquots

freeze

0.6 mg/mL for QSB

2.1 mL 10 mg/mL stock

33 mL EtOH1

48 0.7 mL aliquots

freeze

  1. Try 20 µL in 330 µL water to see if it dissolves. If so, then make aqueous solution, filter sterilize, and freeze. ↩︎

Kanamycin

Kanamycin kdorfman Wed, 12/28/2011 - 21:01

50 mg/mL stock (50 µg/mL in medium)

Concentration in poured agar drops to ~80% in 1 week, but stays stable for 3 more weeks at 4C

1.25 g in 25 mL H2O

filter sterilize

mL aliquots

freeze

1.2 mg/mL for QSB

0.84 mL 50 mg/mL stock

34.16 mL water

filter sterilize (if any doubt about sterility)

48 0.7 mL aliquots

To make mL 1.2 mg/mL kanamycin
you'll need: g kanamycin

freeze

Kan calcs

Kan calcs kdorfman Tue, 10/02/2012 - 16:23
if Kanamycin stock is: mg/mL
to make: mL medium
with a final Kan concentration of: mg/mL
Add: mL kanamycin stock

Streptomycin

Streptomycin kdorfman Tue, 10/17/2023 - 19:43

In refrigerator in 362A

Fisher Streptomycin sulfate 50g

BP910-50 (discontinued)

MW 1457.58

~50 mg/L for agar

Tetracycline

Tetracycline kdorfman Wed, 01/18/2012 - 20:28

Standard is 10 mg/mL stock

Stable for 2 weeks in poured agar at 4C; 75% after 4 weeks

15 mg/mL stock

0.275 g tetracycline in 25 mL EtOH

1 mL aliquots

freeze

1.2 mg/mL for QSB

2.8 mL 15 mg/mL stock in 32.2 mL EtOH1

48 0.7 mL aliquots

freeze

To make mL 1.2 mg/mL tetracylcine
you'll need: g tetracycline

  1. Try 28 µL in 322 µL water to see if it dissolves. If so, then make aqueous solution, filter sterilize, and freeze. ↩︎

Triclosan

Triclosan kdorfman Wed, 12/28/2011 - 21:02

Irgasan

Sigma 72779-5g-f

MW 289.54

Boric acid

Boric acid kdorfman Tue, 12/20/2011 - 15:09

Boric acid (H3BO3) 0.01 M (=10 mM)

1000x for M&S micronutrients

MW = 61.83

0.031 g/50 mL

MW of Boric acid:
Concentration: M
to make: mL
add: g boric acid

Calcium chloride

Calcium chloride kdorfman Tue, 12/20/2011 - 15:01

CaCl stocks in two concentrations:

MW (dihydrate) = 147

1 Molar

2.205 g/15 mL

7.35 g/50 mL

**Autoclave (or otherwise sterilize) for *C. elegans* medium**

0.5 Molar (=500 mM)

1.1 g/15 mL

3.675 g/50 mL

**Autoclave (or otherwise sterilize) for *C. elegans* medium**

MW:
Concentration: M
to make: mL
add: g CaCl2

Calcium nitrate

Calcium nitrate kdorfman Mon, 08/03/2015 - 18:47

Ca(NO3)2.4H2O

FW = 236.1

0.4M stock:

94.4g/L = 0.189g/50mL

MW of calcium nitrate:
Concentration: M
to make: mL
add: g calcium nitrate

Chelated Iron

Chelated Iron kdorfman Fri, 01/12/2024 - 21:28

FeSO4.7H2O 2.78 g/L
Disodium EDTA 3.73 g/L

Mix each component in 450 mL water

Heat EDTA to boiling

Add EDTA to the FeSO4 solution.

Boil for an hour, cool completely

Bring to final volume

Cholesterol

Cholesterol kdorfman Mon, 01/09/2012 - 17:47

5 mg/mL for C. elegans medium

Fisher AAA1147018 Alfa Aesar 50 g ~$35

in 95% ethanol

Stir for 3 hours

or vortex several minutes

Do not autoclave!

Cobalt Chloride

Cobalt Chloride kdorfman Tue, 12/20/2011 - 15:11

Cobalt Chloride (CoCl2) 105 µM (=~ 0.1 mM)

10,000X for M&S micronutrients

MW (hexahydrate) = 237.93

0.00125 g/50 mL

MW:
Concentration: M
to make: mL
add: g dry stuff

DNA standards

DNA standards kdorfman Wed, 12/22/2021 - 21:38

NEB MARKERS

NEB DNA standards (for general reference)

NEB 1Kb extend

NEB PCR Marker

NEB 100 bp quick load ladder

NEB 1 Kb ladder (we have quick load and regular)

FISHER MARKERS. (See attached pdfs below for pictures of ladders)

Thermofisher DNA ladders (for general reference)

Gene ruler ladders (for general reference)

Fisher Scientific molecular weight markers (for general reference)

GeneRuler 50 bp SM0373

GeneRuler 100 bp SM0243

Gene Ruler Mix SM0331

MassRuler Mix SM0403

MassRuler High MW SM0393

50bp GeneRuler
100bp GeneRuler
GeneRuler Mix
MassRuler Mix
MassRuler High Range

DTT

DTT kdorfman Fri, 05/31/2013 - 17:21

Dithiothreitol

Acros organics426380500 (store refrigerated in 362A) $98 at Fisher

154.25 MW

1M = 1.5425g in 10 mL H20

MW:
Concentration: M
to make: mL
add: g DTT

EDTA

EDTA kdorfman Tue, 12/20/2011 - 14:45

EDTA (disodium) 0.5 M pH 8.0

MW = 372.4

18.62 g/100 mL

9.31 g/50 mL

initial pH = ~6. Use NaOH pellets to bring to pH = 8. ~2 g NaOH/100 mL

MW:
Concentration: M
to make: mL
add: g EDTA

EGTA

EGTA kdorfman Fri, 08/09/2013 - 20:27

EGTA 0.5M

100 ml solution

19g EGTA (MW 380g/mol) ddH2O to 90ml adjust pH 7.5/8.0 with solid NaOH (>4g) adjust volume to 100ml

MW:
Concentration: M
to make: mL
start with: mL
add: g EDTA, adjust pH to 7.5 or 8 with NaOH pellets, then bring to final volume

Note: EGTA will not go into solution without NaOH. Once the pH has been raised sufficiently it dissolves quickly. For pH 7.5 the exact amount required is slightly above 4g. Add 3.5-4g immediately, then proceed carefully not to overshoot the desired pH.

from http://www.researchgate.net/post/How_can_I_dissolve_EGTA

Ferric citrate

Ferric citrate kdorfman Tue, 12/20/2011 - 15:14

Ferric citrate (C6H5FeO7) 89.4 mM

MW=244.95

1.095 g/50 mL

0.328 g/15 mL

Keep refrigerated

The 89.4 value is because Tobias Baskin's lab makes a 89.4 µM Fe-citrate medium, and it's easy to mix up a batch from the 1000x stock solution.

Maximum solubility is 1 g/100 mL hot H2O

MW of ferric citrate:
Concentration: M
to make: mL
add: g ferric citrate

Could in the future make a 10 mM batch with 0.1225 g in 50 mL, and for this lab: https://wahoo.nsm.umass.edu/content/reagents-61 , you would have easier calculations.

Ferrous sulfate

Ferrous sulfate kdorfman Tue, 12/20/2011 - 15:16

Ferrous sulfate (FeSO4) 10 mM

MW (heptahydrate) = 278.01

MS 10x = 28mg/L = 0.1 mM - 100 µM

MS 1x = 0.01 mM = 10 µM

make 1,000x for M&S medium = 0.01 M = 10 mM

MW of FeSO4:
Concentration: M
to make: mL
add: g FeSO4

Keep refrigerated

Turns yellow. Probably oxidation. Yellow comes off on a micropore filter.

Fluorescein

Fluorescein kdorfman Mon, 10/29/2018 - 17:44

MW = 332.31

Excitation wavelength: 460 nm Emission wavelength: 515 nm

Absorption maxima at 493.5 and 460 nm

A = Ecl

Molar extinction coefficient of fluorescein at 485nm = 50358/mol.cm

so Absorbance 10^-5M = 0.50358

(1/100 of a 1mM solution =10^-5M)

1 mM stock in 10mM NaOH

MW of Fluorescein:
Concentration: M
to make: mL
add: g Fluorescein

fluorescein_info_sheet.pdf

Histidine HCl

Histidine HCl kdorfman Wed, 01/15/2020 - 21:41

100X Histidine-hydrochloride

8.56 g/L

Dissolve 2.14 g Histidine in 250 mL distilled water and filter sterilize.

Store in the dark at 4 ˚C.

IPTG

IPTG kdorfman Tue, 12/11/2018 - 20:47

1 M IPTG Stock Solution (isopropyl Beta-D-thioglucopyranoside, MW 238.3 g/mol)

2.383 g IPTG in 10 mL ddH2O.

Filter sterilize with 0.22 um membrane cartridge.

or buy 25 mL 1M stock solution Teknova 13431 (Fisher)

Store at -20C

Leucine

Leucine kdorfman Wed, 01/15/2020 - 21:43

10X Leucine

1.8 g/L

Dissolve 0.18 g Leucine in 100 mL distilled water and filter sterilize.

Store in the dark at 4 ˚C.

LiOAc-SDS

LiOAc-SDS kdorfman Mon, 07/31/2023 - 21:51

LiOAc-SDS for DNA extraction from yeast

To make 100 mL of

Mix 20 mL LiOAc

with 5 mL SDS

and bring to final volume

To make mL LiOAc-SDS solution
with mM LiOAC
and % SDS
Mix mL 1M LiOAc
and mL 20 % SDS

and bring to final volume

Lithium Acetate

Lithium Acetate kdorfman Wed, 01/15/2020 - 21:26

Lithium acetate dihydrate
C2H7LiO4
Fisher AA1341730
MW = 102.014

MW of LiOAc:
Concentration: M
to make: mL (start with about 90% of final volume)
add: g LiOAc

adjust pH to 7.5 with dilute acetic acid for Laney's cell & Molec lab

filter sterilize

store at room temp

Lithium Chloride

Lithium Chloride kdorfman Mon, 03/12/2012 - 14:28

LiCl 6M

MW = 42.39

MW of LiCl:
Concentration: M
to make: mL
add: g LiCl

Gets hot!!

MES

MES kdorfman Sun, 09/11/2016 - 17:47

MW = 195.2

150 mM stock solution for LPGM

MW of MES:
Concentration: M
to make: mL
add: g MES

Magnesium chloride

Magnesium chloride kdorfman Tue, 12/20/2011 - 15:05

Magnesium chloride (MgCl2) 1M

MW (hexahydrate) = 203.31

10.166 g/50 mL

20.33 g/100 mL

MW of MgCl2:
Concentration: M
to make: mL
add: g MgCl2

For Marine Biology (424) anesthetic reagent

  • for Aiptasia, make 0.37M in 30 - 35 PSU seawater

  • for Nematostella, dilute again 1:1

Magnesium sulfate

Magnesium sulfate kdorfman Tue, 12/20/2011 - 15:06

Magnesium sulfate (MgSO4) 1M

MW (heptahydrate) = 246.48

MW of MgSO4:
Concentration: M
to make: mL
add: g MgSO4

Manganese chloride

Manganese chloride kdorfman Thu, 01/19/2012 - 07:30

MnCl2 4H2O

M.W.197.9

5 mM

0.0495g/50mL

MW of MnCl2:
Concentration: M
to make: mL
add: g MnCl2

Manganese sulfate

Manganese sulfate kdorfman Tue, 12/20/2011 - 18:03

MnSO4

MW (monohydrate) = 169

store dry in dessicator

MS 10X micronutrients: 16.9 mg/L = 0.1 mM

so 1X = 0.01mM = 10 µM

1000X MS = 10 mM

MW of MnSo4:
Concentration: M
to make: mL
add: g MnSO4

Mannitol

Mannitol kdorfman Tue, 08/12/2014 - 17:45

MW = 182.172

Concentration: %
to make: mL
add: g mannitol

Potassium acetate

Potassium acetate kdorfman Tue, 12/20/2011 - 15:15

Potassium acetate (C2H3O2K)

Fisher BP364-500 $46.30

MW = 98.14

49 g in 100 mL H2O

MW of KOAc:
Concentration: M
to make: mL
add: g KOAc

Cloudy. Heat? Stir overnight? Lower the pH?

Can buy 5M solution: RICCA R5866500-1A ~$90 for 1L from Fisher

Potassium chloride

Potassium chloride kdorfman Tue, 12/20/2011 - 15:04

Potassium chloride (KCl)

MW = 74.56

MW of KCl:
Concentration: M
to make: mL
add: g KCl

Potassium ferricyanide

Potassium ferricyanide kdorfman Tue, 12/20/2011 - 15:13

Potassium ferricyanide (K3Fe(CN)6) 50 mM (= 0.05 M)

red salt

MW = 329.26

0.8232 g/50 mL

MW of Potassium ferricyanide:
Concentration: M
to make: mL
add: g Potassium ferricyanide

Store frozen

Potassium ferrocyanide

Potassium ferrocyanide kdorfman Tue, 12/20/2011 - 15:12

Potassium ferrocyanide (K4Fe(CN)6) 50 mM (= 0.05M)

yellow salt

MW (trihydride) = 422.41

MW of Potassium ferrocyanide:
Concentration: M
to make: mL
add: g Potassium ferrocyanide

Store frozen

Potassium hydroxide

Potassium hydroxide kdorfman Thu, 01/19/2012 - 16:33

KOH

MW = 56.11

MW of KOH:
Concentration: M
to make: mL
add: g KOH

Use for adjusting PIPES pH

Potassium nitrate

Potassium nitrate kdorfman Tue, 12/20/2011 - 15:18

Potassium nitrate (KNO3)

MW of KNO3:
Concentration: M
to make: mL
add: g KNO3

Store in refrigerator

Potassium phosphate dibasic

Potassium phosphate dibasic kdorfman Sat, 01/14/2012 - 05:06

K2HPO4

MW = 174.18

MW of K2HPO4:
Concentration: M
to make: mL
add: g K2HPO4

Potassium phosphate monobasic

Potassium phosphate monobasic kdorfman Tue, 12/20/2011 - 14:58

Potassium phosphate monobasic (KH2PO4)

MW of KH2PO4:
Concentration: M
to make: mL
add: g KH2PO4

for C. elegans medium:

pH to 6.0 with solid KOH

(~1.7 g/100 mL)

Sterilize (can be autoclaved)

SDS

SDS kdorfman Tue, 12/20/2011 - 14:40

SDS 20%

Sodium dodecanesulfate (=Sodium lauryl sulfate, NOT laureth)

CH3(CH2)11OSO3Na

Concentration: %
to make: mL
add: g SDS

DO NOT AUTOCLAVE - it (like all detergents) can boil over

Sodium acetate

Sodium acetate kdorfman Tue, 12/20/2011 - 15:08

Sodium acetate (NaOAc) 3M

CH3COONa

MW (trihydrate) = 136.08

MW of NaOAc:
Concentration: M
to make: mL
add: g NaOAc

pH 5.2

Sodium azide

Sodium azide kdorfman Tue, 12/27/2011 - 18:08

For PBS-Tw-Azide

NaN3

MW = 65

10% w/vol

Concentration: %
to make: mL
add: g NaN3

Sodium bicarbonate

Sodium bicarbonate kdorfman Tue, 12/20/2011 - 14:54

Sodium bicarbonate (CHNaO3) 0.5 M (=500 mM)

MW = 84.01

MW of Sodium bicarbonate:
Concentration: M
to make: mL
add: g sodium bicarbonate

Write the date on it. Probably only stable for 2 weeks.

Sodium chloride

Sodium chloride kdorfman Tue, 12/20/2011 - 14:36

Sodium Chloride (NaCl) 5 M

MW = 58.44

Concentration: M
to make: mL
add: g NaCl

Sodium ferric EDTA

Sodium ferric EDTA kdorfman Mon, 08/03/2015 - 18:43

NaFe(III)EDTA

FW = 367.05

50 mM

MW of NaFe(III)EDTA:
Concentration: M
to make: mL
add: g NaFe(III)EDTA

Sodium hydroxide

Sodium hydroxide kdorfman Mon, 10/29/2018 - 17:55

NaOH

MW = ~40

10mM = 0.01M = 0.4g/L

MW of NaOH:
Concentration: M
to make: mL
add: g NaOH

if you have g of NaOH pellets
which has a MW of g/mol
and you want to make M NaOH
dissolve in mL water

Sodium phosphate dibasic

Sodium phosphate dibasic kdorfman Tue, 12/20/2011 - 15:00

Use 0.2M for colorimetric exercise

Aliquote ~400 uL for a pair of students to each do the exercise

MW of Na2HPO4:
Concentration: M
to make: mL
add: g dry stuff

Use hot water

Sodium phosphate monobasic

Sodium phosphate monobasic kdorfman Tue, 12/20/2011 - 14:52

Sodium phosphate monobasic (NaH2PO4)

MW (monohydrate) = 137.99

Use 0.2M for colorimetric exercise

Aliquot ~400 uL - enough for 2 students to each do one exercise.

MW of NaH2PO4:
Concentration: M
to make: mL
add: g dry stuff

Sodium sulfate

Sodium sulfate kdorfman Thu, 03/01/2012 - 14:17

Na2SO4.10H2O

MW = 322.2

MW of Na2SO4:
Concentration: M
to make: mL
add: g Na2SO4

Spermidine

Spermidine kdorfman Fri, 05/31/2013 - 18:21

Spermidine:

  • neutralizes and stabilizes the negative charge on the DNA phosphate backbone
  • displaces other ions from DNA
  • stimulates restriction enzyme reactions
  • increases specificity and reproducibility of Taq-mediated PCR

Used in Gene & Genome

1 M stock

1 g spermidine (entire contents of bottle) in 6.9 mL water

MW = 145.25

Filter sterilize (0.22 µm filter, 10 mL syringe)

Freeze 200 uL aliquots

20 mM student solutions

1 g spermidine (entire contents of bottle) in 6.9 mL water

MW = 145.25 Make 20 mM solution for students by adding 800 uL to the 200 uL of 1M in the tube, then aliquot 10 uL for each student.

To make µL 20mM Spermidine
add: µL 1M spermidine
to: µL water

TBSTw

TBSTw kdorfman Thu, 11/17/2022 - 17:24

Tris Buffered Saline with Tween

  • Tris 20 mM
  • NaCl 100 mM
  • Tween 0.1%
  • pH 7.4
To make mL TBSTw
add: mL 1M Tris
add: mL 5M NaCl
add: mL 10% Tween

Tris

Tris kdorfman Tue, 12/20/2011 - 14:42

Tris 1M

Tris base MW = 121.14

MW of Tris:
Concentration: M
to make: mL
add: g Tris

pH to 7.5 or 8.0, depending on the application

Tris-HCl

Tris-HCl kdorfman Tue, 06/21/2022 - 17:26

MW 157.6

Tris-HCl 1M

MW of Tris-HCl:
Concentration: M
to make: mL
add: g dry Tris-HCl

Triton X

Triton X kdorfman Tue, 12/20/2011 - 15:17

Triton X 10%

MW = 646.86

1 g = ~1 mL

Concentration: %
to make: mL
start with: mL Triton X

Tryptophan

Tryptophan kdorfman Wed, 01/15/2020 - 21:42

50X Tryptophan

7.5 g/L

Dissolve 1.875 g Tryptophan in 250 mL of distilled water (reserve some water to rinse the sides of the beaker). Leave it on the stir plate for a while. It's powdery and resistant to going into solution.

Filter sterilize.

Store in the dark at 4 ˚C.

Tween 10%

Tween 10% kdorfman Tue, 12/27/2011 - 18:01

Tween 10%

for PBS-Tween-Azide

1 g = ~1 mL [density = 1.095 g/mL at 25 °C (from Sigma website)]

Concentration: %
to make: mL
start with: mL Tween

Do not autoclave