Use whereNotIn to check if there is id or not in a specific column

But, here i have one column 'deleted_by_org' which store data as in format [1,2,5].

You mean the deleted_by_org column literally has [1,2,5] as the value? I sure hope not...

That is just an example, it might also have [1] or can be even null. Actually, I am trying to store organization id, such as if an organization delete a record, this should not be visible to any member of that organization but should be visible to member of other organization. So, if organization 1 deletes it, delete_by_org will be filled with [1]. Again, if is deleted by org by 2 the previous data will be updated as [1,2]

Those really should be stored in a separate one to many table, where each "delete" is stored as a separate row. You're violating some sql relational database standards, and will make your queries a LOT more complex to work around it.

https://stackoverflow.com/questions/5033047/mysql-query-finding-values-in-a-comma-separated-string

http://makitweb.com/search-value-within-comma-separated-values-mysql/

You will need to write queries using raw statements if you want to continue to do it the way you are. Eloquent only handles stuff that are standard.

Ok, how can I handle it with eloquent if i created another one to many table

In the docs it shows this example. So it won't get users whose id is 1 or 2 or 3.

$users = DB::table('users')
    ->whereNotIn('id', [1, 2, 3])
    ->get();

https://laravel.com/docs/5.6/queries#where-clauses

It's the same for Eloquent. User::whereNotIn('id', [1, 2, 3])->get()

Yeah, that is quite straight forward. But, with another table, i think there should be some relation.

base_record_id | deleted_by_org
12          | 1
12          | 2 
13          | 3
13          | 1

Now, how can I check this, as actually I am retrieving data on base voter table

I don't know your model names, etc., but something like

$ids = [1,2,3];

MainModel::with(['relationship' => function($query) use ($ids) {
    $query->whereNotIn('id', $ids);
}]);

I don't know enough about your app with the information provided to know how to get $ids for you that you want to limit by.

I don't know, but it looks like quite opposite scenario. I feels like I require instead lie where $ids does not contain $id

Something like

->where delete_by_org doesnot contain $id

Is there anything in laravel to solve this

You could use the BelongsToMany relationship like this:

MainModel::whereDoesntHave(['relationship' => function($query) use($ids) {
    $query->whereIn('id', $ids);
}]);