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| Status |
Public on Nov 01, 2011 |
| Title |
human feces TSDA2.4 |
| Sample type |
SRA |
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| Source name |
human feces
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| Organism |
human gut metagenome |
| Characteristics |
sample type: feces of a human subject
source: the feces of a human subject (subject F1T2, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, cDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant Illumina adapter sequence (with or without a 4-nt barcode). Adaptered-DNA was then size-selected by agarose gel electrophoresis. Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (IIx) following the manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Akkermansia muciniphila ATCC BAA-835,Bacteroides caccae ATCC 43185,Bacteroides thetaiotaomicron VPI-5482,Bacteroides vulgatus ATCC 8482,Bifidobacterium longum NCC2705,Bifidobacterium longum DJO10A,Bifidobacterium adolescentis ATCC 15703,Bacteroides fragilis YCH46,Bacteroides fragilis NCTC 9343,Bacteroides ovatus ATCC 8483,Bacteroides uniformis ATCC 8492,Blautia hydrogenotrophica DSM 10507,Bryantella formatexigens DSM 14469,Clostridium scindens ATCC 35704,Clostridium spiroforme DSM 1552,Collinsella aerofaciens ATCC 25986,Dorea longicatena DSM 13814,Escherichia coli str. K-12 substr. MG1655,Eubacterium eligens ATCC 27750,Eubacterium rectale ATCC 33656,Faecalibacterium prausnitzii A2-165,Faecalibacterium prausnitzii M21/2,Helicobacter pylori HPAG1,Lactobacillus reuteri DSM 20016,Methanobrevibacter smithii ATCC 35061,Methanosphaera stadtmanae DSM 3091,Parabacteroides distasonis ATCC 8503,Lactococcus lactis subsp. lactis Il1403,Streptococcus thermophilus LMG 18311,Streptococcus thermophilus CNRZ1066,Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842,Lactobacillus casei ATCC 334,Lactococcus lactis subsp. cremoris SK11,Streptococcus thermophilus LMD-9,Lactococcus lactis subsp. cremoris MG1363,Escherichia fergusonii ATCC 35469,Bifidobacterium animalis subsp. lactis AD011,Ruminococcus obeum ATCC 29174,Ruminococcus torques ATCC 27756,Vibrio cholerae O1 biovar eltor str. N16961 chromosome I,Vibrio cholerae O1 biovar eltor str. N16961 chromosome II,Clostridium bolteae ATCC BAA-613,Clostridium sporogenes ATCC 15579,Bacteroides dorei DSM 17855,Bifidobacterium catenulatum DSM 16992,Clostridium asparagiforme DSM 15981,Bifidobacterium adolescentis L2-32,Alistipes putredinis DSM 17216,Ruminococcus lactaris ATCC 29176,Anaerococcus hydrogenalis DSM 7454,Bifidobacterium angulatum DSM 20098,Catenibacterium mitsuokai DSM 15897,Bacteroides capillosus ATCC 29799,Anaerotruncus colihominis DSM 17241,Coprococcus comes ATCC 27758,Bifidobacterium gallicum DSM 20093,Blautia hansenii DSM 20583,Ruminococcus gnavus ATCC 29149,Anaerofustis stercorihominis DSM 17244,Citrobacter youngae ATCC 29220,Collinsella intestinalis DSM 13280,Bifidobacterium breve DSM 20213,Anaerostipes caccae DSM 14662,Bacteroides coprocola DSM 17136,Butyrivibrio crossotus DSM 2876,Providencia alcalifaciens DSM 30120,Bacteroides cellulosilyticus DSM 14838,Eubacterium ventriosum ATCC 27560,Parabacteroides merdae ATCC 43184,Clostridium sp. L2-50,Eubacterium dolichum DSM 3991,Clostridium leptum DSM 753,Parvimonas micra ATCC 33270,Coprococcus eutactus ATCC 27759,Clostridium bartlettii DSM 16795,Clostridium ramosum DSM 1402,Bacteroides stercoris ATCC 43183,Clostridium sp. SS2/1,Providencia stuartii ATCC 25827,Streptococcus infantarius subsp. infantarius ATCC BAA-102,Bacteroides intestinalis DSM 17393,Bifidobacterium animalis subsp. lactis HN019,Providencia rustigianii DSM 4541,Bifidobacterium pseudocatenulatum DSM 20438,Dorea formicigenerans ATCC 27755,Bacteroides plebeius DSM 17135,Bacteroides eggerthii DSM 20697,Proteus penneri ATCC 35198,Mitsuokella multacida DSM 20544,Clostridium nexile DSM 1787,Bacteroides finegoldii DSM 17565,Collinsella stercoris DSM 13279,Desulfovibrio piger ATCC 29098,Parabacteroides johnsonii DSM 18315,Clostridium hylemonae DSM 15053,Roseburia intestinalis L1-82,Eubacterium biforme DSM 3989,Methanobrevibacter smithii DSM 2374,Methanobrevibacter smithii DSM 2375,Bacteroides fragilis 3_1_12,Bacteroides sp. D1,Prevotella copri DSM 18205,Holdemania filiformis DSM 12042,Providencia rettgeri DSM 1131,Fusobacterium sp. 4_1_13,Shigella sp. D9,Clostridium methylpentosum DSM 5476,Eubacterium hallii DSM 3353,Bacteroides sp. D2,Bacteroides sp. 1_1_6,Fusobacterium varium ATCC 27725,Actinomyces odontolyticus ATCC 17982,Victivallis vadensis ATCC BAA-548,Clostridium hiranonis DSM 13275,Subdoligranulum variabile DSM 15176,Clostridium sp. M62/1,Bacteroides coprophilus DSM 18228,Bacteroides WH2,Bifidobacterium dentium,Bacteroides thetaiotaomicron 3731,Bacteroides thetaiotaomicron 7330,Bacteroides xylanisolvens XB1A,Clostridium symbiosum,Desulfovibrio piger GOR1,Enterobacter cancerogenus,Eubacterium rectale DSM17629,M23A,Ruminococcus bromiiL263,Lactobacillus casei DN114001,Lactobacillus delbrueckii DN100107,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus DN001147,Streptococcus thermophilus CNCM I-1630,Bifidobacterium animalis subsp. lactis CNCM I-2494
rRNA-depleted total RNA
RNA isolated from the feces of a human subject (subject F1T2, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 36 nucleotides.
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| Data processing |
After parsing each sequencing lane's data by barcode (where appropriate), we excised the barcodes and mapped the reads to an appropriate set of reference genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32-nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32-nt barcoded samples; 33 was the minimum score used for 36-nt and 76-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36 nucleotides a large fraction of reads map to multiple locations (within a genome and/or across genomes). Reads that map non-uniquely were added to each gene in proportion to each gene's fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will result in 0.9 counts being tallied to gene A and 0.1 counts being tallied to gene B). We added a pseudocount (i.e. added a value of 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were ultimately normalized to reads/kb gene length/million mapped reads (RPKM) following gene count assignments.
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| Submission date |
Aug 25, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Nathan P McNulty |
| E-mail(s) |
nathan.p.mcnulty@gmail.com
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| Phone |
314-362-3963
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| Organization name |
Washington University School of Medicine
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| Department |
Center for Genome Sciences and Systems Biology
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| Lab |
Gordon
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| Street address |
4444 Forest Park Ave. (5th Floor)
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL14348 |
| Series (1) |
| GSE31670 |
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. (RNA-Seq) |
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| Relations |
| SRA |
SRX093101 |
| BioSample |
SAMN00714029 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM786097_TSDA2.4.counts.txt.gz |
661.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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