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Sc 899

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Sc-899 is a laboratory equipment product offered by Santa Cruz Biotechnology. It is a device designed for scientific research and analysis purposes. The core function of Sc-899 is to facilitate specific laboratory procedures, but a detailed description cannot be provided while maintaining an unbiased and factual approach without extrapolation.

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Lab products found in correlation

Ab4729, by Abcam (5 mentions) Ab5095, by Abcam (5 mentions) Ab1791, by Abcam (4 mentions) Ab5131, by Abcam (3 mentions) Adaptor ligation, by Illumina (2 mentions) Sc 484, by Santa Cruz Biotechnology (2 mentions) Ab8898, by Abcam (2 mentions) Ab9050, by Abcam (2 mentions) Ab28379, by Abcam (1 mentions) Nextseq 500 system, by Illumina (1 mentions) Truseq chip library preparation kit, by Illumina (1 mentions) Nb100 110, by Novus Biologicals (1 mentions) Cay10006421, by Cayman Chemical (1 mentions) Normal rabbit igg, by Merck Group (1 mentions) Ab77231, by Abcam (1 mentions) Adi spa 901, by Enzo Life Sciences (1 mentions) Sc 5286, by Santa Cruz Biotechnology (1 mentions) Mms 126r, by Fortrea (1 mentions) Ab56919, by Abcam (1 mentions) Sc 225, by Santa Cruz Biotechnology (1 mentions)

Close spelling variants of this product

RNA Pol II sc-899 (5 citations) RNAPII (N-20; sc-899; (3 citations) N20 (sc-899; (3 citations) Anti-RNA Polymerase II (sc-899; (2 citations)

25 protocols using sc 899

1

Chromatin Immunoprecipitation and Analysis

Cited 1 time
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Chromatin immunoprecipitation (ChIP) was carried out as previously described (16 (link)). For immunoprecipitation, antibodies against H3K27Ac (ab4729, Abcam), SMAD3 (ab28379, Abcam) or RNAPII (sc899, Santa Cruz) were used in this paper. Quantitative analysis of the precipitated and input DNA through real-time PCR was described above. The primer sets for ChIP-qPCR are listed in Supplementary Table S1. Results are pooled from at least three individual samples. For ChIP-seq, the precipitated DNA was followed library generation (TruSeq ChIP Library Preparation Kit, Illumina) and sequencing (NextSeq500 system, Illumina) performed by DNA Link, Inc. The generated reads were aligned to the human reference genome (hg19) using MACS2 (30 (link)). BAM files for ChIP-seq data of RNAPII in multiple cell lines were downloaded from ENCODE (https://www.encodeproject.org/).
Liu Y.T., Xu L., Bennett L., Hooks J.C., Liu J., Zhou Q., Liem P., Zheng Y, & Skapek S.X. (2019). Identification of de novo enhancers activated by TGFβ to drive expression of CDKN2A and B in HeLa cells. Molecular cancer research : MCR, 17(9), 1854-1866.
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2

ChIP-qPCR Assay for Transcription Factors

Cited 2 times
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ChIP experiments were performed as previously described using antibodies directed against HIF-1α (Cay10006421, rabbit polyclonal, Cayman Chemicals), HIF-1β (NB100–110, rabbit polyclonal, Novus Biologicals), RNApol 2 (SC-899, rabbit polyclonal, Santa Cruz), or H3K27ac (ab4729, rabbit polyclonal, Abcam) (11 (link), 25 (link)). Nonimmunized rabbit serum or purified normal rabbit IgG (12–370, Merck Millipore) were used as negative controls as appropriate. ChIP-qPCR was conducted as described earlier using primers provided in Table S2 (34 (link)).
Protze J., Naas S., Krüger R., Stöhr C., Kraus A., Grampp S., Wiesener M., Schiffer M., Hartmann A., Wullich B, & Schödel J. (2022). The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression. The Journal of Biological Chemistry, 298(3), 101699.
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3

Antibody-based Immunoblotting and ChIP-seq

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Antibodies used for immunoblotting were anti-SUMO2/3 (M114-3, MBL), anti-UBC9 (sc10759, Santa Cruz Biotechnology), anti-PIAS1 (ab77231, Abcam), anti-tubulin (sc5286, Santa Cruz Biotechnology), anti-laminB1 (sc6216, Santa Cruz Biotechnology), anti-Pol2 (sc-899, Santa Cruz Biotechnology), anti-histone H3 (ab1791, Abcam), and anti-HSF1 (ADI-SPA-901; ENZO Life Sciences). Antibodies used for ChIP-seq were anti-SUMO2/3 (M114-3, MBL), anti-PIAS1 (ab77231, Abcam), and anti-Pol2 (MMS-126R, Covance).
Niskanen E.A., Malinen M., Sutinen P., Toropainen S., Paakinaho V., Vihervaara A., Joutsen J., Kaikkonen M.U., Sistonen L, & Palvimo J.J. (2015). Global SUMOylation on active chromatin is an acute heat stress response restricting transcription. Genome Biology, 16(1), 153.
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4

ChIP-exo Analysis of Pol II Binding

Cited 3 times
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ES cells were grown and transfected with shRNA vectors as described above. Two independent transfection experiments were performed for each shRNA vector. Following a 10 min fixation with 1% formaldehyde in ES cell culture medium, chromatin was prepared from 5 to 10 million cells and sonicated as described32 (link). ChIP-exo experiments were carried out essentially as described33 (link). This included an immunoprecipitation step using antibodies against Pol II (sc-899, Santa Cruz Biotechnology) attached to magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads. After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR-amplified and gel-purified. Sequencing was performed using NextSeq500. Uniquely aligned sequence tags were mapped to the mouse genome (mm9) using BWA-MEM (version 0.7.9a-r786)34 (link). The uniquely aligned sequence tags were used for the downstream analysis.
de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., Dargham D.B., Jounier S., Humbertclaude H., Ribierre F., Baulard C., Farrell N.P., Park B., Keime C., Carrière L., Berlivet S., Gut M., Gut I., Werner M., Deleuze J.F., Olaso R., Aude J.C., Chantalat S., Pugh B.F, & Gérard M. (2016). Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature, 530(7588), 113-116.
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5

ChIP-exo Analysis of Pol II Binding

Cited 3 times
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ES cells were grown and transfected with shRNA vectors as described above. Two independent transfection experiments were performed for each shRNA vector. Following a 10 min fixation with 1% formaldehyde in ES cell culture medium, chromatin was prepared from 5 to 10 million cells and sonicated as described32 (link). ChIP-exo experiments were carried out essentially as described33 (link). This included an immunoprecipitation step using antibodies against Pol II (sc-899, Santa Cruz Biotechnology) attached to magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and lambda and recJ exonuclease digestion on the beads. After elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina adaptor was then ligated, and the products PCR-amplified and gel-purified. Sequencing was performed using NextSeq500. Uniquely aligned sequence tags were mapped to the mouse genome (mm9) using BWA-MEM (version 0.7.9a-r786)34 (link). The uniquely aligned sequence tags were used for the downstream analysis.
de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., Dargham D.B., Jounier S., Humbertclaude H., Ribierre F., Baulard C., Farrell N.P., Park B., Keime C., Carrière L., Berlivet S., Gut M., Gut I., Werner M., Deleuze J.F., Olaso R., Aude J.C., Chantalat S., Pugh B.F, & Gérard M. (2016). Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature, 530(7588), 113-116.
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6

Nuclear Protein Extraction and Western Blotting

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Nuclear extracts were prepared from hippocampal cells using a buffer that contains 420 mM NaCl, 25% glycerol, 0.2 mM EDTA, 1 mM DTT, 20 mM HEPES pH 7.9, 1.5 mM MgCl2, and protease inhibitors as reported previously (28 (link), 58 (link)). Proteins were detected by western blot using specific antibodies: monoclonal Ezh2 (AC22, Cell Signaling), polyclonal Ezh1 (ab13665, Abcam), monoclonal JBP1/PRMT5 (611539, BD Transduction Laboratories), monoclonal Wdr5 (ab56919, Abcam), polyclonal RNA Pol II (sc-899, Santa Cruz Biotechnology), polyclonal TFIIB (sc-225, Santa Cruz Biotechnology).
Aguilar R., Bustos F.J., Saez M., Rojas A., Allende M.L., van Wijnen A.J., van Zundert B, & Montecino M. (2016). Polycomb PRC2 complex mediates epigenetic silencing of a critical osteogenic master regulator in the hippocampus. Biochimica et biophysica acta, 1859(8), 1043-1055.
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7

Chromatin Immunoprecipitation: Antibody Panel

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GFP (ab290, 5 µl used; abcam, Cambridge, MA), BRD4 (10 µg; ref. 49 (link)), CDK9 (sc-8338, 10 µg; sc-484, 10 µg; both from Santa Cruz Biotechnology), H3 (ab1791, 5 µg; abcam), acetyl H3 (06–599, 5 µg; Millipore, Billerica, MA), H3 acetyl K27 (ab4729, 2 µg; abcam), acetyl H4 (06–866, 5 µg; Millipore), H4 acetyl K12 (ab1761, 5 µg; abcam), Pol II (pan) (sc-899, 5 µg; Santa Cruz Biotechnology), Ser2P Pol II (ab5095, 5 µg; abcam), Ser5P Pol 11 (ab5131, 5 µg; abcam), or normal rabbit IgG (12–370, 5 µg; Millipore).
Kanno T., Kanno Y., LeRoy G., Campos E., Sun H.W., Brooks S.R., Vahedi G., Heightman T.D., Garcia B.A., Reinberg D., Siebenlist U., O’Shea J.J, & Ozato K. (2014). BRD4 assists elongation of both coding and enhancer RNAs guided by histone acetylation. Nature structural & molecular biology, 21(12), 1047-1057.
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8

Immunoblotting of Protein Targets

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Membranes were incubated overnight with primary antibodies in 3% milk in PBST. The antibodies used for immunoblotting included rabbit anti-IKZF3 (ab139408, Abcam), rabbit anti-CDK8 (A302-501A, Bethyl Laboratories), and mouse anti-β-tubulin (T8328, Sigma-Aldrich) at a 1:2,000 dilution and rabbit anti-SHC (ab24787, Abcam), rabbit anti-SEPT9 (sc-899, Santa Cruz Biotechnology), and mouse anti-MAVS (sc-166583, Santa Cruz Biotechnology) at a 1:1,000 dilution. Membranes were then incubated with IRDye700-labeled donkey anti-mouse or anti-rabbit or IRDye800-labeled donkey anti-mouse (LI-COR Biosciences) at a 1:5,000 dilution. Blots were detected using an Odyssey® Infrared Imaging System (LI-COR Biosciences).
Verhoeven R.J., Tong S., Mok B.W., Liu J., He S., Zong J., Chen Y., Tsao S.W., Lung M.L, & Chen H. (2019). Epstein-Barr Virus BART Long Non-coding RNAs Function as Epigenetic Modulators in Nasopharyngeal Carcinoma. Frontiers in Oncology, 9, 1120.
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9

Comprehensive Antibody Characterization for Transcription Research

Cited 2 times
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The antibodies used were: rabbit anti-Rpb1 (sc-899; Santa Cruz Biotechnology), rabbit anti-Rpb1 (A304–405A & A304–405A, Bethyl Laboratories), rabbit anti-Rpb1 CTD pSer2 (ab5095, Abcam), rabbit anti-Spt5 (A300-868A, Bethyl Laboratories), mouse anti-Spt5 (sc-133217, Santa Cruz Biotechnology), rabbit anti-Spt5-pSer666 and -pThr806 (Twenty-first Century Century Biochemicals) previously described58 (link), rabbit anti-PP4R2 (A300–838A, Bethyl Laboratories), rabbit anti-PPP4C (A300–835A, Bethyl Laboratories), sheep anti-PP4R2-pThr173 (Division of Signal Transduction Therapy, University of Dundee Scotland)45 (link), rabbit phospho-PP1α (Thr320) antibody (2581S, Cell Signaling Technology), mouse anti-GFP (sc-9996, Santa Cruz Biotechnology), mouse anti-pan-PP1 (sc-7482, Santa Cruz Biotechnology), goat anti-PP1α (sc-6104, Santa Cruz Biotechnology), mouse anti-PP1β (sc-373782, Santa Cruz Biotechnology), rabbit anti-PP1γ (A300-906A, Bethyl Laboratories), goat anti-PP1γ (sc-6108, Santa Cruz Biotechnology), mouse anti-tubulin (T5168, Sigma-Aldrich), rabbit anti-GST (sc-459, Santa Cruz Biotechnology), mouse anti-FLAG® M2 (F3165, Sigma-Aldrich), and rabbit anti-FLAG (2368, Cell Signaling).
Parua P.K., Kalan S., Benjamin B., Sansó M, & Fisher R.P. (2020). Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. Nature Communications, 11, 4338.
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10

Antibody Generation for Epigenetic Regulation

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The antibodies to 5-methyl-cytosine (5mC) (Eurogentec, BI-MECY-0100), H3K9me3 (Abcam, ab8898), H3K27ac (Abcam, ab4729), ZFP57 (Abcam, ab45341), SETDB1 (Santa Cruz Biotechnology, sc-66884), and RNA Pol II (Santa Cruz Biotechnology, sc-899) are commercially available. Antibodies against AFF3 (Ab#1, antigen, a mixture of two peptides from amino acids 124–237 and amino acids 816–982 of human AFF3) were generated in our laboratory and have been described previously (Luo et al. 2012a (link)). A second antibody against AFF3 (Ab#2, antigen, human AFF3 amino acids 816–982) was also generated in our laboratory. Antigens were expressed as His tag fusion proteins in pET-16b, purified on NTA-agarose according to Qiagen's protocol, and sent to Pocono Rabbit Farm and Laboratory for immunization into rabbits.
Luo Z., Lin C., Woodfin A.R., Bartom E.T., Gao X., Smith E.R, & Shilatifard A. (2016). Regulation of the imprinted Dlk1-Dio3 locus by allele-specific enhancer activity. Genes & Development, 30(1), 92-101.
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