#!/usr/bin/perl --
use strict; use warnings; use Data::Dump;

open my($DF), '<', \q{
brain0001
lung0001
brain00002
kidney0003
brain00003
};

my %dfs;
while( <$DF> ){
    chomp;
    /^(brain|lung|kidney)/
        and push @{$dfs{$1}}, $_;
}
close $DF;

dd \%dfs;
__END__
{
  brain  => ["brain0001", "brain00002", "brain00003"],
  kidney => ["kidney0003"],
  lung   => ["lung0001"],
}