In this example we will use MySQL database.
First, we will need to configure GlassFish JDBC resources. In GlassFish administration portal go to "Resources->JDBC->Connection Pools". Create new Connection Pool with name examplePool. Set Resource Type to java.sql.Driver; Database Vendor to MySql, com.mysql.jdbc.Driver.
Then go to "Resources->JDBC->JDBC Resources". Add new resource with JNDI Name jdbc/example. Set Pool Name to examplePool.

In the application under src/main/resource META-INF folder should be created. And inside META-INF folder persistence.xml file added with following content:

<?xml version="1.0" encoding="UTF-8"?>
    <persistence xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_1_0.xsd"
    version="1.0">
  <persistence-unit name="default" transaction-type="JTA">
    <jta-data-source><strong>${jtaDataSource}</strong></jta-data-source>
  </persistence-unit>
</persistence>

Where ${jtaDataSource} should be jdbc/example. Or you can enable filtering in Maven pom.xml file and specify jdbc/example there So afterwards it would be easier to change and maintain it:

<build>
  ...
  <resources>
    <resource>
      <directory>src/main/resources</directory>
      <filtering>true</filtering>
    </resource>
  </resources>
  ...
</build>
...
<properties>
  <jtaDataSource>jdbc/example</jtaDataSource>
</properties>

You are ready to go! Create Entity:

@Entity
@Table(name = "pencils")
public class Pencil {
  @Id
  private int id;

  @Column
  private String color;

  public int getId() {
    return id;
  }

  public String getColor() {
    return color;
  }
}

Inject javax.persistence.PersistenceContext:

@PersistenceContext
private EntityManager em;

And you can create queries:

Query q = em.createQuery("select p from Pencil p where p.color=:color");
q.setParameter("color", "blue");