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REACTIVITY SENSITIVITY MW (kDa) Isotype
H M R Hm Mk B Dg Endogenous Rabbit 
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Flow Cytometry

Flow cytometric analysis of Jurkat cells using CDK9 (C12F7) Rabbit mAb (PE Conjugate) (blue) compared to concentration-matched Rabbit (DA1E) mAb IgG XP® Isotype Control (PE Conjugate) #5742 (red).

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Flow Cytometry, Methanol Permeabilization Protocol for Direct Conjugates

A. Solutions and Reagents

NOTE: Prepare solutions with reverse osmosis deionized (RODI) or equivalent grade water.

  1. 20X Phosphate Buffered Saline (PBS): (#9808) To prepare 1 L 1X PBS: add 50 ml 20X PBS to 950 ml dH2O, mix.
  2. 16% Formaldehyde (methanol free).
  3. 100% methanol.
  4. Incubation Buffer: Dissolve 0.5 g Bovine Serum Albumin (BSA) (#9998) in 100 ml 1X PBS. Store at 4°C.

B. Fixation

NOTE: If using whole blood, lyse red blood cells and wash by centrifugation prior to fixation.

  1. Collect cells by centrifugation and aspirate supernatant.
  2. Resuspend cells in 0.5-1 ml 1X PBS. Add formaldehyde to obtain a final concentration of 4%.
  3. Fix for 15 min at room temperature.
  4. Wash by centrifugation with excess 1X PBS. Discard supernatant in appropriate waste container. Resuspend cells in 0.5-1 ml 1X PBS.

C. Permeabilization

  1. Permeabilize cells by adding ice-cold 100% methanol slowly to pre-chilled cells, while gently vortexing, to a final concentration of 90% methanol.
  2. Incubate 30 min on ice.
  3. Proceed with immunostaining (Section D) or store cells at -20°C in 90% methanol.

D. Immunostaining

  1. Aliquot desired number of cells into tubes or wells.
  2. Wash cells by centrifugation in excess 1X PBS to remove methanol. Discard supernatant in appropriate waste container. Repeat if necessary.
  3. Resuspend cells in 100 µl of diluted antibody conjugate (prepared in incubation buffer at the recommended dilution).
  4. Incubate for 1 hr at room temperature. Protect from light.
  5. Wash by centrifugation in incubation buffer. Discard supernatant. Repeat.
  6. Resuspend cells in 1X PBS and analyze on flow cytometer; alternatively, for DNA staining, proceed to optional DNA stain (Section E).

E. Optional DNA Dye

  1. Resuspend cells in 0.5 ml of DNA dye (e.g. Propidium Iodide (PI)/RNase Staining Solution #4087).
  2. Incubate for at least 5 min at room temperature.
  3. Analyze cells in DNA staining solution on flow cytometer.

posted July 2009

revised June 2017

Protocol Id: 407

Product Usage Information

Application Dilutions
Flow Cytometry 1:50

Storage: Supplied in PBS (pH 7.2), less than 0.1% sodium azide and 2 mg/ml BSA. Store at 4°C. Do not aliquot the antibody. Protect from light. Do not freeze.

Specificity / Sensitivity

CDK9 (C12F7) Rabbit mAb (PE Conjugate) detects endogenous levels of total CDK9 protein, both 42 kDa and 55 kDa isoforms.


Species Reactivity: Human, Mouse, Rat, Hamster, Monkey, Bovine, Dog

Source / Purification

Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues near the carboxy terminus of human CDK9.

Product Description

This Cell Signaling Technology antibody is conjugated to phycoerythrin (PE) and tested in-house for direct flow cytometry analysis in human cells. This antibody is expected to exhibit the same species cross-reactivity as the unconjugated CDK9 (C12F7) Rabbit mAb #2316.


P-TEFb is a general transcription factor that regulates transcription elongation through phosphorylation of the C-terminal tail domain (CTD) of RNA polymerase II (RNAP II). The P-TEFb complex is composed of a catalytic subunit, CDK9, and its regulatory cyclin partner, which can be cyclin T1, T2a, T2b or K (reviewed in 1,2). P-TEFb is recruited by the HIV Tat protein to allow transcriptional elongation, and subsequent replication of the viral genome. Inhibition of P-TEFb function therefore has potential for HIV therapy. CDK9 exists as two isoforms, an abundant 42 kDa isoform, and a less abundant 55 kDa isoform, which contains an amino-terminal extension (3). The two forms likely have distinct purposes based on differential expression during lymphocyte activation (4,5) and on their localization within the nucleus (5).

Cyclin dependent kinases (CDKs) are activated in part by cyclin binding and by phosphorylation of a conserved threonine in the T-loop domain. Phosphorylation of CDK9 at the T-loop Thr186 by an unidentified nuclear kinase may be important in P-TEFb activation (6) and regulation of HIV transcription (7). Acetylation of CDK9 at Lys44 affects its ability to phosphorylate the RNAPII CTD (8).


1.  Rice, A.P. and Herrmann, C.H. (2003) Curr HIV Res 1, 395-404.

2.  De Falco, G. and Giordano, A. Cancer Biol Ther 1, 342-7.

3.  Shore, S.M. et al. (2003) Gene 307, 175-82.

4.  Shore, S.M. et al. (2005) Gene 350, 51-8.

5.  Liu, H. and Herrmann, C.H. (2005) J Cell Physiol 203, 251-60.

6.  Chen, R. et al. (2004) J Biol Chem 279, 4153-60.

7.  Ammosova, T. et al. (2005) Retrovirology 2, 47.

8.  Fu J et al. (2007) Mol Cell Biol 27, 4641–51

9.  De Falco, G. and Giordano, A. Cancer Biol Ther 1, 342-7.


Entrez-Gene Id 1025
Swiss-Prot Acc. P50750


For Research Use Only. Not For Use In Diagnostic Procedures.
Cell Signaling Technology is a trademark of Cell Signaling Technology, Inc.
XP is a registered trademark of Cell Signaling Technology, Inc.

32038
CDK9 (C12F7) Rabbit mAb (PE Conjugate)