Team:Heidelberg/Notebook/Material

From 2010.igem.org

(Difference between revisions)

Latest revision as of 23:14, 27 October 2010

Materials

Kits

**table 1**: Used kits.
Kits	Supplier	Catalog Number
HiSpeed® Plasmid Maxi Kit (25)	QIAGEN	12663
CompactPrep Plasmid Maxi Kit (25)	QIAGEN	12763
RNeasy® Mini Kit (25)	QIAGEN	74106
QIAquick® Miniprep Kit (250)	QIAGEN	27106
QIAquick® Gel Extraction Kit (250)	QIAGEN	28706
QIAquick® Nucleotid Removal Kit (250)	QIAGEN	28306
QIAquick® PCR Purification Kit (250)	QIAGEN	28106
GeneMorph® II EZC Clone Domain Mutagenesis Kit	Stratagene	200552-5

Marker

**table 2**: Used DNA ladders for gel electrophoresis.
Name	Supplier	Range
GeneRuler™ High Range DNA Ladder	Fermentas	10,171-48,502 bp
GeneRuler™ 1 kb Plus DNA Ladder	Fermentas	75-20,000 bp

↑

Enzymes

**table 3**: Used NEB restriction enzymes.
Name	Number/ID	NEB buffer1	NEB buffer2	NEB buffer3	NEB buffer4	BSA
AflII	27	50%	100%	25%	100%	x
AgeI	1	100%	50%	10%	75%
ApaI	-	25%	50%	0%	100%	x
AseI	not	75%	100%	not
AvrII	-	100%	100%	50%	100%
BamHI	2	75%	100%	100%	100%	x
BamHI	-	75%	100%	100%	100%	x
BclI	-	50%	100%	100%	75%
BglI	-	50%	75%	100%	50%
BglII	13	10%	75%	100%	10%
BsrGI	-	25%	100%	10%	100%	x
DpnI	6	100%	100%	75%	100%
DpnI	-	100%	100%	75%	100%
EcoRI	-	100%	100%	100%	100%
EcoRV	-	50%	75%	100%	50%	x
FseI	-	100%	75%	0%	100%
HindIII	-	10 50%	100%	10%	50%
HindIII	-	50%	100%	10%	50%
KpnI	11	100%	75%	0%	50%	x
MfeI-HF™	-	75%	50%	10%	100%
NarI	26	100%	75%	75%	100%
NcoI	12	100%	100%	100%	100%
NdeI	-	75%	100%	75%	100%
NheI	-	100%	100%	10%	100%	x
NotI	14	0%	50%	100%	25%
NsiI	-	10%	75%	100%	25%
PciI	-	50%	75%	100%	50%	x
PstI	15	75%	75%	100%	50%
SacI	16	100%	50%	10%	100%
ScaI	18	not	not	100%	not
SfcI	19	75%	50%	10%	100%	x
SfcI	-	75%	50%	10%	100%	x
SpeI	-	75%	100%	25%	100%	x
SphI	-	100%	100%	50%	100%
SspI	-	50%	100%	50%	50%
XbaI	23	0%	100%	75%	100%	x
XbaI	56	0%	100%	75%	100%	x
XhoI	24	75%	100%	100%	100%	x
XmaI	25	25%	50%	0%	100%	x

NEBuffers are color-coded (NEBuffer 1-yellow, NEBuffer 2-blue, NEBuffer 3-red, NEBuffer 4-green) and supplied as 10X

Bacteria

**table 4**: Used *E. coli* strains.
Name	Purpose	Reference
DH5α	Amplification of Plasmids	Invitrogen
SCS110	Amplification of unmethylated Plasmids	Stratagene
Top10	Amplification of Plasmids	Invitrogen

Media and Antibiotics

LB (10 g tryptone, 5 g yeast extract, 10 g sodium chloride, ad 1 L ddH₂O)

**table 5**: Used antibiotics.
Antibiotic	Final Concentration	Solvent
Ampicillin	100 µg/ml	ddH₂O
Chloramphenicol	25 µg/ml	100% Ethanol
Kanamycin	50 µg/ml	ddH₂O

↑

Primers & Oligos

Please find our Primers & Oligos on an extra subpage.

Instruments

**table 6**: Used instruments.
Description	Name	Firm
Table Centrifuge	Microfuge® 18 Centrifuge	Beckman Coulter^TM
Table Centrifuge	MicrofugeR 22® Centrifuge	Beckman Coulter^TM
Centrifuge	Allegra X-12	Beckman Coulter^TM
Shaker	VORTEXGENIER 2	Scientific Industries, SI^TM
Heating plate (magnet stirrer)	MR Hei-Standard	Heidolph
Heatblock	QBD4	Grant
Heatblock (shakeing function)	Thermomixer comfort	Eppendorf
PCR-machine	MyCycler^TM thermo cycler	BioRad
UV-chamber	Transluminator	Vilber Lourmat
Scale (fine)	Pioneer^TM PA114C	OHAUS
Scale	Pioneer^TM PA4101C	OHAUS
Fridge	KTP 1750 Premium	Liebherr
Freezer	GP 1366 Premium	Liebherr
-86 Freezer	-86°C Ultralow Freezer	NUAIRE^TM
Hood	Tischabzug	Wesemann® Laboreinrichtung
Draw-off pump	Vacuhand control	Vacubrand
Incubator	HT Multitron Version 2	INFORS
Incubator (cell culture)	HERAcell 150	Thermo electron coorperation
Hood (cell culture)	HERAsafe	Thermo electron coorperation
Plate reader	Infinite M200	TECAN
FACS	Cytomics FC 500 MPL	Beckman Coulter^TM
Microscope	CKX41	Olympus
Computer		Sun Microsystems
UV/Visivle Spectrometer	Ultrospec 3300 pro	Amersham Biosciences
Photometer	NanoDrop® ND-1000 Spectrophotometer	peQLab Biotechnologie GmbH
Photometer	NanoVue^TM	General Electric
Ice Machine	MF22	SCOTSMAN®
Gel electrophoresis chamber	Mupid®-One	Advance
Pipetting robot	QIAcube^TM	QIAGEN
Wide field microscope	Nikon Eclipse 90i	Nikon
PCR machine	MyCycler thermal cycler	BIO-RAD
Real-time PCR machine	StepOnePlus^TM Real-time PCR System	Applied Biosystems^TM

Cell lines

**table 7:** Used Cell Lines.
Cell line	Tissue of origin	Transfection
HeLa P4	epithelial cervical cancer, human	easy
HEK 293T	embryonic kidney cells, human	easy
Flp-In™ T-REx™ 293	embryonic kidney cells, human	easy
Hep G2	hepatocellular carcinoma, human	medium
Hepa 1-6	liver hepatoma, mouse	medium
HuH7	hepatocarcinoma, mouse	medium
primary hepatocytes	liver, mouse	hard

Plasmids

**table 7:** Used Plasmids.
Name	Use	Sequence Information	Reference
pcDNA5	expression of shRNAs	CMV_shRNA_polyA	[http://tools.invitrogen.com/content/sfs/manuals/pcdna5frtto_man.pdf Invitrogen]
pcDNA6/TR	amplification of Tet Repressor	CMV_TetR_polyA	[http://tools.invitrogen.com/content/sfs/vectors/pcdna6tr_map.pdf Invitrogen]
PsiCheck2	cloning of tuning construct	HSV_hRluc/SV40_hFluc	[http://www.promega.com/catalog/catalogproducts.aspx?categoryname=productleaf_1602 Promega]
pBSU6	virus packaging (ssDNA)	ITR (AAV2)	Addgene
pTRUF3	virus packaging (dsDNA)	ITR (AAV2)
pBSH1	virus packaging (ssDNA)	ITR (AAV2)
pSB1A3	3A assembly cloning	Ampicillin Resistance	[http://partsregistry.org/Part:pSB1A3 Parts Registry]
pSB1K3	3A assembly cloning	Kanamycin Resistance	[http://partsregistry.org/Part:pSB1K3 Parts Registry]
pSB1C3	3A assembly cloning	Chloramphenicol Resistance	[http://partsregistry.org/Part:pSB1C3 Parts Registry]

Other

**table 8:** Other reagents.
Name	Suplier	Cat. No.
Matrix Reagent Reservoirs	Thermo Scientific	8094
cell culture flasks 75cm2	TPP	90076
Dual-Luciferase® Reporter Assay System	Promega	E1910
white 96-well plates, lumitrac200	Greiner	655075
Rapid DNA Ligation Kit 40	Roche	11635379001
Quick ligation kit	NEB	M2200 S
15 cm petri dishes	BD falcons
Master Mix Phusion, HF	Finnzymes
6x Loading Dye	Fermentas
Penicilin Streptomycin	Gibco
T4 DNA ligase	Fermentas
FuGENE 6	Roche
Proteinase K	Qiagen
poly-L-lysine	Sigma
Benzonase (5kU)	Clontech

↑

@@ Line 257: / Line 257: @@
 {| class="wikitable sortable" border="0" align="center" style="text-align: left"
 |-bgcolor=#009be1
-|+ align="top, left"| Used Cell Lines.
+|+ align="top, left"| '''table 7:''' Used Cell Lines.
 | Cell line||Tissue of origin||Transfection
 |-
@@ Line 280: / Line 280: @@
 {| class="wikitable sortable" border="0" align="center" style="text-align: left"
 |-bgcolor=#009be1
-|+ align="top, left"|'''table 7''': Used Plasmids.
+|+ align="top, left"|'''table 7:''' Used Plasmids.
 | Name||Use|| Sequence Information||Reference
 |-
@@ Line 301: / Line 301: @@
 |align="right"| pSB1C3 || 3A assembly cloning || Chloramphenicol Resistance || [http://partsregistry.org/Part:pSB1C3 Parts Registry]  ||
 |}
+===Other===
+{| class="wikitable sortable" border="0" align="center" style="text-align: left"
+|-bgcolor=#009be1
+|+ align="top, left"|'''table 8:''' Other reagents.
+| Name||Suplier|| Cat. No.
+|-
+| Matrix Reagent Reservoirs || Thermo Scientific || 8094
+|-
+| cell culture flasks 75cm2 || TPP || 90076
+|-
+| Dual-Luciferase® Reporter Assay System || Promega || E1910
+|-
+| white 96-well plates, lumitrac200 || Greiner || 655075
+|-
+| Rapid DNA Ligation Kit 40 || Roche || 11635379001
+|-
+| Quick ligation kit || NEB || M2200 S
+|-
+| 15 cm petri dishes || BD falcons||
+|-
+| Master Mix Phusion, HF || Finnzymes ||
+|-
+| 6x Loading Dye || Fermentas ||
+|-
+| Penicilin Streptomycin || Gibco  ||
+|-
+| T4 DNA ligase || Fermentas  ||
+|-
+| FuGENE 6 || Roche  ||
+|-
+| Proteinase K ||  Qiagen ||
+|-
+| poly-L-lysine || Sigma  ||
+|-
+| Benzonase (5kU)|| Clontech ||
+|-
+|}
 <html>
 <div class="backtop">

Team:Heidelberg/Notebook/Material

From 2010.igem.org

Latest revision as of 23:14, 27 October 2010

Contents

Materials

Kits

Marker

Enzymes

Bacteria

Media and Antibiotics

Primers & Oligos

Instruments

Cell lines

Plasmids

Other