Structural segregation of the gut microbiota between colorectal cancer (CRC) patients and healthy volnuteers
This dataset is generated by relatively relaxed criteria (as described below) than those used in the related paper, so as to allow for a complete picture of the data and more data to be preserved for other types of analyses. The primers used for amplification of the 16S rRNA gene V3 region are: the forward primer 5’-NNNNNNNNCCTACGGGAGGCAGCAG-3’ and the reverse primer 5’-NNNNNNNNATTACCGCGGCTGCT-3’. The NNNNNNNN are the sample-unique 8- base barcode. So each read has been labeled with a 8 nucleotide tag adjacent to the primer, however, the first 2 nucleotides are for protection and only the last 6 nucleotides ( 3rd to 8th position of the tag from 5’ to 3’ end ) are used as barcode. All reads from a whole sequencing run are assigned to their corresponding samples as follows:  1)    Search the primer with BLAST (Word size=4, e value=0.1) at the sequencing end;  2)    Locate the barcode according to the position of the primer;  3)    If the barcode is complete, assign the read to the corresponding sample based on the barcode list of the samples of this experiment;  4)    If the barcode is not complete, go to the other end to search the primer with BLAST (Word size=4, e value=0.1);  5)    Repeat step 2 and 3;  6)    If the barcode is not complete, discard the sequence;  7)    Repeat this process until all the reads have been checked.    Both barcodes and primers are included in the texts of the FASTA file. Barcodes are listed below(C for colorectal cancer patients and H for healthy volunteers):     Sample name barcode  C01 AGAGACAT  C03 AGAGATGT  C05 AGATGTAG  C07 AGCGATCT  C09 AGCTCTAG  C11 AGTACGAG  C13 AGTGACGT  C15 AGTGCTCG  C17 ACAGCTAT  C19 ACATGCAG  C21 ACTGTGAT  C23 ACGCATAT  C25 CAGCTAGT  C27 ACTATCAG  C29 ACTCAGAT  C31 ATAGTACG  C33 ATACATAT  C35 ATACGTGT  C37 ATACTGTG  C39 ATGACTAT  C41 ATGATGAT  C43 ATGCGATG  C45 ATGTACAG  C47 ATCGTACT  C49 ACGAGATG  C51 ACGTATCG  C53 ATCTCAGT  C55 ACTGTGTG  C57 CAGTGACT  C59 CAGTGCGT  C61 CACACTCT  C63 CACTAGAG  C65 CATACGAT  C67 CATGACAT  C69 CATGATCG  C71 CATGCATG  C73 CGAGAGAT  C75 CGAGTGAG  C77 CGAGTCAT  C79 CGACTAGT  C81 CGATATCG  C83 CGATCAGT  C85 CGATCGAT  C87 AGCTAGTG  C89 CGTACTCT  C93 CTAGTCAG  H01 CTACGAGT  H02 CTGATAGT  H03 CTGATCAT  H04 CTGTGAGT  H05 CTCAGCAT  H06 TAGACAGT  H07 TAGACATG  H08 TAGACGAT  H09 TACGACTG  H10 TACTGTAT  H11 TATAGCAT  H12 TATAGTAG  H13 TATAGTGT  H14 TATATCTG  H15 TATGAGCG  H16 TATCATGT  H18 TATCGACG  H19 TATCTATG  H20 TGAGAGCG  H21 ACTCAGTG  H22 ACTCATCT  H23 ACTCTACG  H24 ATAGAGTG  H25 TGACAGAG  H26 TGCACTAG  H27 ATAGACGT  H30 TGTGCACG  H32 ATAGCTGT  H33 TCGAGACT  H34 TCTATGTG  H35 AGAGCGAG  H36 ATAGACTG  H37 ACTCTCAG  H38 ACTCGTCT  H39 ACTCATAT  H40 ACGTGCAT  H41 ACGTATAT  H42 ACGAGCGT  H43 ACATCTAT  H44 ACACGACT  H45 ACAGTGCG  H46 ACAGCTAG  H47 AGTGTGAG  H48 AGTGCTAG  H49 AGTGCACT  H50 AGTATCAT  H51 AGCGTGTG  H52 AGCGCTCT  H53 AGATCACT  H54 AGCGAGAT  H55 AGTACATG  H56 AGTATGAT  H57 AGTGACAG  H58 AGTGATAT  H59 AGTGTACG  H60 AGTCAGCT
In this study we explored diversity of V3 region of 16S rRNA genes obtained via barcoded 454 pyrosequencing to demonstrate an overall structural imbalance of the gut microbiota of colorectal cancer patients.