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Structural segregation of the gut microbiota between colorectal cancer (CRC) patients and healthy volnuteers

Identifiers: SRA: SRP005150
: Human CRC Microbiome Project
Study Type: 
Metagenomics
Abstract: 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.
Description: 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
Center Project: Human CRC Microbiome Project
External Link: /pubmed:21850056

Related SRA data

Experiments:
1 ( 1 samples )
Runs:
1 (64.9Mbp; 39.5Mb)