TBX3 antibody

Catalog No. ABIN6265491

Product Details anti-TBX3 Antibody

Target: TBX3 (T-Box 3 (TBX3))

Reactivity: Human, Mouse, Rat

Host: Rabbit

Clonality: Polyclonal

Conjugate: This TBX3 antibody is un-conjugated

Application: Western Blotting (WB), ELISA, Immunocytochemistry (ICC), Immunofluorescence (IF), Cleavage Under Targets and Release Using Nuclease (CUT&RUN)

Specificity: TBX3 antibody detects endogenous levels of total TBX3

Cross-Reactivity: Human, Mouse (Murine), Rat (Rattus)

Purification: The antiserum was purified by peptide affinity chromatography using SulfoLink^TM Coupling Resin (Thermo Fisher Scientific).

Immunogen: A synthesized peptide derived from human TBX3

Isotype: IgG

Application Details

Application Notes: WB: 1:500~1:3000, IF/ICC 1:100-1:500

Restrictions: For Research Use only

Independent Validation (CUT&RUN)

Validation #104234 (Cleavage Under Targets and Release Using Nuclease)

by: Mattias Pernebrink and Claudio Cantù; Cantù Lab, Gene Regulation during Development and Disease, Linköping University

No.: #104234

Date: 03/01/2021

Antigen: TBX3

Lot Number: 10H2885

Method validated: Cleavage Under Targets and Release Using Nuclease

Positive Control: Recombinant anti-H3K27me3 CUT&RUN Positive Control antibody (antibodies-online, ABIN6923144)

Negative Control: Monoclonal anti-FLAG (Sigma-Aldrich, F3165)

Notes:

Passed. ABIN6265491 allows for TBX3 targeted digestion using CUT&RUN.

Validation Images

Bioanalyzer profiles comparing fragment size distributions between reads obtained from CUT&RUN using an anti-H3K27me3 CUT&RUN Positive Control antibody (ABIN6923144) and anti-TBX3 (ABIN6265491) after library preparation.

Alignment tracks from CUT&RUN targeting TBX3 in mouse front limbs. 1. Peaks called by MACS2 from CUT&RUN data using anti-TBX3 antibody ABIN6265491 in cells derived from mouse embryonal front limbs. 2. Alignment track for CUT&RUN reads obtained using anti-TBX3 antibody ABIN6265491 in mouse embryonal front limbs. 2. Overlayed alignment tracks from ChIP-seq of TBX3 in mouse embryonal front limbs (Zimmerli et. al., 2020). Reads are normalized to sequencing depth per million reads.

Full Methods

Primary Antibody: ABIN6265491

Full Protocol:

• Cell harvest
• • Harvest cells from day 10.5 mouse embryo front limbs, estimating 90,000 cells per antibody to be used at RT.
  • Centrifuge cell solution 3 min at 600 x g at RT.
  • Remove the liquid carefully.
  • Gently resuspend cells in 1 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, Roche Complete Protease Inhibitor EDTA-free) by pipetting and transfer cell solution to a 2 mL microcentrifuge tube.
  • Centrifuge cell solution 3 min at 600 x g at RT and discard the supernatant.
  • Repeat twice for a total of three washes.
  • Resuspend cell pellet in 1 mL Wash Buffer by gently pipetting.
• Concanavalin A beads preparation
• • Prepare one 1.5 mL microcentrifuge tube.
  • Gently resuspend the magnetic Concanavalin A Beads (antibodies-online, ABIN6923139).
  • Pipette 10 µL Con A Beads slurry for each sample into the 1.5 mL microcentrifuge tube.
  • Place the tube on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tube from the magnetic stand.
  • Pipette 1 mL Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl₂, 1 mM MnCl₂) into each tube and resuspend ConA beads by gentle pipetting.
  • Spin down the liquid from the lid with a quick pulse in a table-top centrifuge.
  • Place the tubes on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tube from the magnetic stand.
  • Repeat twice for a total of three washes.
  • Gently resuspend the ConA Beads in a volume of Binding Buffer corresponding to the original volume of bead slurry, i.e. 10 µL per sample.
• Cell immobilization – binding to Concanavalin A beads
• • Carefully vortex the cell suspension and add 10 µL of the Con A beads in Binding Buffer to the cell suspension for each sample.
  • Close tube tightly and rotate for 10 min at RT.
• Cell permeabilization and primary antibody binding
• • Divide cell suspension into separate 2 mL microcentrifuge tubes, one for each antibody (500,000 cells per sample).
  • Place the microcentrifuge tubes on a magnetic stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tubes from the magnetic stand.
  • Place each tube at a low angle on the vortex mixer set to a low speed and add 150 µL Digitonin Wash buffer (wash buffer with 0.025% (wt/vol) Digitonin) supplemented with 2 mM EDTA.
  • Gently vortex the microcentrifuge tubes until the beads are resuspended.
  • Add 1.5 µL antibody (Anti TBX3 (ABIN6265491), positive control, and negative control) to the respective tube, corresponding to a 1:100 dilution.
  • Rotate the microcentrifuge tubes ON at 4 °C.
  • Spin down the liquid and place the tubes on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tubes from the magnetic stand.
  • Resuspend with 1 mL Digitonin Wash Buffer and mix by inversion. If clumping occurs, gently remove the clumps with a 1 ml pipette tip.
  • Repeat once for a total of two washes.
• pA-MNase Binding
• • Place the tubes on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tubes from the magnetic stand.
  • Vortex the sample at low speed and add 150 μL pA-MNase solution at 700 ng/mL (1:200 dilution of a 140 µg/mL glycerol stock in Digitonin Wash Buffer) per sample, gently resuspending the beads by pipetting.
  • Rotate the microcentrifuge tubes for 1 h at 4 °C.
  • Spin down the liquid and place the tubes on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Remove the microcentrifuge tubes from the magnetic stand.
  • Resuspend with 1 mL Digitonin Wash Buffer and mix by inversion. If clumping occurs, gently remove the clumps with a 1 mL pipette tip.
  • Repeat once for a total of two washes.
• MNase digestion and release of pA-MNase-antibody-chromatin complexes
• • Spin down the liquid from the lid with a quick pulse in a table-top centrifuge.
  • Place the tubes on a magnet stand until the fluid is clear. Remove the liquid carefully.
  • Place each tube at a low angle on the vortex mixer set to a low speed and add 100 μL Digitonin Wash buffer per sample along the side of the tube.
  • Place tubes in a heat block, kept on ice, and allow to chill.
  • Add 2 μL 0.1 M CaCl2 to each sample.
  • Incubate tubes at 0 °C for 30 min.
  • Add 100 μL 2xSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% (wt/vol) Digitonin, 100 μg/mL RNAse A, 50 μg/mL Glycogen).
  • Incubate tubes at 37 °C for 30 min.
  • Place the tubes on a magnet stand until the fluid is clear.
  • Transfer the supernatant containing the pA-MNase-bound digested chromatin fragments to fresh 1.5 mL microcentrifuge tubes.
• DNA extraction
• • Add 2 µL 10% SDS to a final concentration of 0.1% and 2.5 µL Proteinase K (20 mg/mL) to each supernatant.
  • Gently vortex tubes at a low speed of approximately 1,100 rpm.
  • Incubate tubes at 50 °C for 1 h.
  • Add 200 µL PCI to tube.
  • Vortex tubes thoroughly at high speed until the liquid appears milky.
  • Centrifuge tubes in a tabletop centrifuge at 16,000 x g at RT for 5 min.
  • Carefully transfer to upper aqueous phase to a fresh 1.5 mL microcentrifuge tube containing 2 µL glycogen (diluted 1:10 to 2 mg/mL from the 20 mg/mL stock solution).
  • Add 20 µL 3 M NaOAc pH 5.2.
  • Add 400 µL 100% ethanol.
  • Place tubes for at -20 °C ON.
  • Centrifuge tubes in a tabletop centrifuge at 16,000 x g at 4 °C for 5min.
  • Remove the liquid carefully with a pipette.
  • Wash pellet with 1ml 70% ethanol.
  • Centrifuge tubes in a tabletop centrifuge at 16,000 x g at 4 °C for 1 min.
  • Remove the liquid carefully with a pipette.
  • Air-dry the pellet, then dissolve in 30 µL 1 mM Tris-HCl, 0.1 mM EDTA.
• Library preparation and sequencing
• • Libraries were prepared using KAPA HyperPrep Kit using KAPA Dual-Indexed adapters according to protocol.
  • Samples were sequenced on an Illumina NextSeq 500 sequencer, using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles), 36bp PE.
• Peak calling
• • Reads were mapped to the GRCm38 (mm10) mouse genome using Bowtie2 with options: --local --very-sensitive- local --no-unal --no-mixed --no-discordant.
  • Peaks were called using MACS2 with options -f BAMPE --keep-dup all –nomodel.

Experimental Notes:

Peaks generated using ABIN6265491 for CUT&RUN aligned well with TBX3 ChIP-seq tracks from the same tissue (Zimmerli et. al., 2020).

Handling

Format: Liquid

Concentration: 1 mg/mL

Buffer: Rabbit IgG in phosphate buffered saline ,  pH 7.4, 150  mM NaCl, 0.02 % sodium azide and 50 % glycerol.

Preservative: Sodium azide

Precaution of Use: This product contains Sodium azide: a POISONOUS AND HAZARDOUS SUBSTANCE which should be handled by trained staff only.

Storage: -20 °C

Storage Comment: Store at -20 °C.Stable for 12 months from date of receipt

Expiry Date: 12 months

Target Details for TBX3

Target: TBX3 (T-Box 3 (TBX3))

Alternative Name: TBX3 (TBX3 Products)

Synonyms: xtbx3 antibody, ums antibody, xhl antibody, tbx3-iso antibody, TBX3 antibody, TBX3-ISO antibody, UMS antibody, XHL antibody, D5Ertd189e antibody, T-box 3 antibody, T-box 3 S homeolog antibody, TBX3 antibody, tbx3.S antibody, tbx3 antibody, Tbx3 antibody

Background:

Description: Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation. Acts as a negative regulator of PML function in cellular senescence.

Gene: TBX3

Molecular Weight: 79kDa

Gene ID: 6926

UniProt: O15119, Q13207

Pathways: Hormone Transport, Stem Cell Maintenance, Regulation of Muscle Cell Differentiation, Skeletal Muscle Fiber Development