please reformat your posting:

• <p> between paragraphs
• <c> ... </c> around code and data
• [ ... ] around links

use strict;
use warnings;
my %result;                             # Hash of Arrays

my $headline = <DATA>;                         # ignore
while (my $line =<DATA>) {
  my ($gene,$sample) = split /\s+/, $line;
  push @{$result{$gene}},$sample;
}

for my $gene (sort keys %result) {
  print join "\t", $gene, @{$result{$gene}};
  print "\n";
}

__DATA__
Gene_name sample
gene_A    sample_1
gene_B    sample_1
gene_C    sample_1
gene_B    sample_2
gene_C    sample_2
gene_A    sample_3
[download]

-->

gene_A    sample_1    sample_3
gene_B    sample_1    sample_2
gene_C    sample_1    sample_2
[download]