Mapping Transcription Factor Binding in Vascular Cells

Data from ENCODE^{26 (link)} were explored as described in eMethods. ChIP-seq experiments were performed on confluent HCASMC (Cell Applications 350-05a & Lonza CC-2583; cultured in SmGM-2 BulletKit media; Lonza) as described.^{27 (link)} TCF21 (Abcam ab49475), Jun (Santa Cruz Biotechnology sc-1694), JunD (Santa Cruz Biotechnology sc-74), and CEBP (Santa Cruz Biotechnology sc-150) transcription factor binding was interrogated and H3K27ac data were acquired using the same ChIP protocol with an anti-H3K27ac antibody (Abcam; ab4729). Reads were aligned to the human genome (GRCh37p13) using STAR.^{28 (link)}

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Saleheen D., Zhao W., Young R., Nelson C.P., Ho W., Ferguson J.F., Rasheed A., Ou K., Nurnberg S.T., Bauer R.C., Goel A., Do R., Stewart A.F., Hartiala J., Zhang W., Thorleifsson G., Strawbridge R.J., Sinisalo J., Kanoni S., Sedaghat S., Marouli E., Kristiansson K., Zhao J.H., Scott R., Gauguier D., Shah S.H., Smith A.V., van Zuydam N., Cox A.J., Willenborg C., Kessler T., Zeng L., Province M.A., Ganna A., Lind L., Pedersen N.L., White C.C., Joensuu A., Kleber M.E., Hall A.S., März W., Salomaa V., O’Donnell C., Ingelsson E., Feitosa M.F., Erdmann J., Bowden D.W., Palmer C.N., Gudnason V., De Faire U., Zalloua P., Wareham N., Thompson J.R., Kuulasmaa K., Dedoussis G., Perola M., Dehghan A., Chambers J.C., Kooner J., Allayee H., Deloukas P., McPherson R., Stefansson K., Schunkert H., Kathiresan S., Farrall M., Frossard P.M., Rader D.J., Samani N.J, & Reilly M.P. (2017). Loss of Cardio-Protective Effects at the ADAMTS7 Locus Due to Gene-Smoking Interactions. Circulation, 135(24), 2336-2353.

Publication 2017

CC-2583 SmGM-2 BulletKit media sc-1694 CEBP ab4729

Anti antibody Cebp Cell Chip Chip seq Cultured media Human genome Transcription factor

Corresponding Organization :

Other organizations : Center for Non-Communicable Diseases, University of Cambridge, University of Leicester, University of Pennsylvania

Top 5 similar protocols

Variable analysis

independent variables

TCF21 transcription factor binding
Jun transcription factor binding
JunD transcription factor binding
CEBP transcription factor binding

dependent variables

H3K27ac data

control variables

Confluent HCASMC (Cell Applications 350-05a & Lonza CC-2583) cell line
SmGM-2 BulletKit media (Lonza)

controls

Positive control: Anti-H3K27ac antibody (Abcam; ab4729)
Negative control: Not explicitly mentioned

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!