You could do this:

#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %dfs;
m[([a-z]+)(\d+)] and push @{ $dfs{ $1 } }, $2 while <DATA>;

pp \%dfs;

__DATA__
brain0001
lung0001
brain00002
kidney0003
brain00003
[download]

Outputs:

[14:52:38.81] C:\test>junk58
{
  brain  => ["0001", "00002", "00003"],
  kidney => ["0003"],
  lung   => ["0001"],
}
[download]

But maybe you don't want to load up anything you are not expecting? Maybe you want a warning for lines that don;t match your regex?