title: in vitro culture NM1200_InVitro_3_T3t2

description:
Bifidobacterium animalis subsp. lactis CNCM I-2494,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519,Lactococcus lactis subsp. cremoris CNCM I-1631,Streptococcus thermophilus CNCM I-1631
rRNA-depleted total RNA
RNA isolated from a fermented milk product (Danone, Activia) at the end of product fermentation (3 hours after initial inoculation of the milk), prior to cooling and packaging.  B. animalis subsp. lactis represents approximately 9% of the total CFUs in these samples.  Biological replicate #2 of 3.


title: human feces TSDA10.3_long

status: Public on Nov 01 2011

type: SRA

city: Saint Louis

first: Nathan

middle: P

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

country: USA

institute: Washington University School of Medicine

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 F5T2, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 76 nucleotides.

library_source: transcriptomic

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.

molecule: total RNA

organism: human gut metagenome

source_name: human feces

extract_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.

tag: sample type

value: feces of a human subject

tag: source


title: human feces TSDA2.1

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 "Pre4") 4 weeks prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: hen1 mutant polyA

status: Public on Nov 09 2011

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description:
VASAGFPHEN1minusMALE
Small RNA sequence data
Processed data file: VASAGFPHEN1minusMALE.processed.txt
barcode: first 4 bases

data_processing: 3' adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome (Zv8)

organism: Danio rerio

source_name: testis

extract_protocol: Small RNAs in the size range of 19-31 bases were excised from a denaturing gel. RNA was poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adaptor to the 5'-phosphate of the small RNAs. First-strand cDNA synthesis was performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. After amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.

tag: strain

value: TL

tag: genotype/variation

value: Hen1 mutant

tag: tissue

value: testis

tag: small rna library prep method

value: polyA tailing


title: human feces TSDA1.9

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 F1T1, timepoint "Post4") 4 weeks after their completion of a 7-week consumption regimen consisting of two daily servings of a fermented milk product (Danone, Activia).  Read length is 36 nucleotides.


title: human feces TSDA1.4

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 F1T1, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 36 nucleotides.


title: human feces TSDA1.4_long

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 F1T1, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 76 nucleotides.


title: 4X2_leaf_small_RNA_seq

status: Public on Nov 11 2011

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
imbalanced cross
small RNA sequencing

data_processing: Short reads (40-nt) were parsed to remove 3’ adaptors and mapped to Arabidopsis thaliana genome (TAIR9) using CASHX (http://asrp.cgrb.oregonstate.edu/db/download.html). To reduce ambiguity, only the perfectly matched reads were used for further analysis. The sequences from chloroplast and mitochondrial and structural non-coding RNAs including ribosomal RNAs, transfer RNAs, snoRNAs and snRNAs were excluded from the analysis.

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Diploids (2n = 2x = 10) and tetraploids (2n = 4x = 20) of Arabidopsis thaliana Col-0 ecotype was grown under 16h light at 22°C and 8h darkness at 20°C.

extract_protocol: Total RNA was extracted from seeds and leaves using Plant RNA reagent (Invitrogen) and subjected to electrophoresis in a 15% urea-polyacrylamide gel. The small RNA fraction (18-30-nt) was recovered from the gel. The small RNAs were ligated to 5’ and 3’ RNA oligo adapters (Supplementary Table x3) and reverse-transcribed to produce first strand cDNAs, which were amplified by PCR and sequenced by Illumina Genome Analyzer II (at UC Davis Genome Center).

treatment_protocol: Reciprocal interploidy crosses were made by pollinating diploid flowers with tetraploid pollens (2x4) or tetraploid flowers with diploid pollens (4x2) 24h after manual emasculation. Diploid and tetraploid flowers were manually self-pollinated to serve as balanced dosage controls. Seeds were dissected from the siliques at 3, 4, 5, 6, 7 days after pollination (DAP) to eliminate maternal tissue contamination. Small RNA library construction and gene expression assays were performed using the seeds dissected at 6DAP.

tag: ecotype

tag: cross

value: 4x X 2x

value: rosette leaves

tag: Stage

value: Before bolting


title: human feces TSDA1.3

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 F1T1, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: mouse_WT_RNA-seq

status: Public on Nov 03 2011

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

description: RNA-seq of mouse thyroid tissue from wild type littermates.

data_processing: Single reads split by barcode into individual files using PERL script. The reads with good quality were aligned to reference sequence (RefSeq) databases of human (UCSC hg18) or mouse (UCSC mm9) genomes, RefSeq exons, splicing junctions and contamination databases including ribosome and mitochondria sequences using the BWA alignment algorithm, and the alignment files in SAM format were generated. After filtering reads mapped to contamination databases, the reads that  have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of the corresponding transcript. The read count at exon, splice-junction, transcript and gene levels were summarized and normalized to relative abundance in Fragments Per Kilobase of exon model per Million (FPKM) in order to compare transcription level among samples.

organism: Mus musculus

source_name: pool of thyroid gland tissues, wild type

growth_protocol: Human thyroid primary cells were prepared from fresh, non-cancerous thyroid tissue adjacent to thyroid tumors that were removed at surgery. Tissue was minced and incubated in 200 U/ml of collagenase solution for 1 hour at 37°C. Cells were harvested and cultured in DMEM supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 µg/ml) (P0). Cells were passaged at 1:2 dilution and cultured until confluent.

extract_protocol: According to the Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA was hybridized to poly-dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first-strand synthesis with RTase, randomers second-strand synthesis. Then, end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.

treatment_protocol: Confluent human primary thyroid cultures were exposed to human IFNα (5,000 U/ml) for 0, 12 or 24 hours, followed by RNA isolation.

tag: genotype

value: wild type

tag: age

value: ~6 months

value: thyroid


title: human_T24_RNA-seq

description: RNA-seq of human thyroid primary cell with IFN-alpha treatment at 5000 u/ml for 24 hours.

organism: Homo sapiens

source_name: primary thyroid cell line, IFN-alpha, 24 hrs

tag: treatment

value: 24 hour IFN alpha treatment (5,000 U/ml)


title: human feces TSDA1.2

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 F1T1, timepoint "Pre2") 2 weeks prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: human feces TSDA1.3_long

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 F1T1, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 76 nucleotides.


title: wildtype polyA

description:
VASAGFPHEN1plusMALE
Small RNA sequence data
Processed data file: VASAGFPHEN1plusMALE.processed.txt
barcode: first 4 bases

value: Hen1 wildtype


title: human feces TSDA1.6

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 F1T1, timepoint "FMP4") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 4 weeks. Read length is 36 nucleotides.


title: human feces TSDA1.1

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 F1T1, timepoint "Pre4") 4 weeks prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: Mouse feces 10-C

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 6, 7, 20, 21, 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

library_source: genomic

data_processing: After parsing each sequencing lane's data by barcode, we excised the barcodes and mapped the reads to an appropriate set of reference genomes using Illumina's ELAND aligner.  The alignment results for each 30-nt (trimmed) sequencing read were evaluated to determine if the read mapped perfectly and uniquely (to only one position in only one reference genome) or if it mapped redundantly (to more than one position within and/or across genomes).  Reads which failed to map perfectly to one of the reference genomes were filtered out and mapped to the Illumina adapter sequences as well as the mouse reference genome to determine what fraction of non-mapping reads were from host-derived DNA or Illumina adapter dimers produced during library creation.  Redundantly mapping reads were also filtered out.  To account for the latter filtering step, the value representing the number of raw hits to each reference genome was normalized using a that genome's "informative genome size", which is (for a given k-mer size) the number of all possible k-mers in that genome that map uniquely (to that genome) when considering all genomes in the analysis.  The processed data files report the "raw counts", the "normalized counts" and the "normalized percentage" (proportion of all normalized counts attributable to a particular species) for each reference genome included in the analysis of each sample.

molecule: genomic DNA

organism: Bacteria

source_name: Mouse feces

growth_protocol: Fecal samples obtained from mice were frozen immediately in liquid nitrogen, stored at -80C, and maintained at this temperature prior to DNA extraction and library preparation.

extract_protocol: Libraries were prepared according a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, gDNA 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 II following the manufacturer's protocols.

tag: host organism

value: Mus musculus

tag: host strain

tag: time of gut bacteria

value: 42 days prior

tag: time when gavaged with fermented milk strains


title: Mouse feces 08-C


title: human feces TSDA5.3

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 F3T1, timepoint "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 36 nucleotides.


title: human feces TSDA10.4_long

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 F5T2, timepoint "FMP1") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 1 week. Read length is 76 nucleotides.


title: wildtype ligation

description:
WTTESTIS
Small RNA sequence data
Processed data file: WTTESTIS.processed.txt
barcode: none

extract_protocol: Small RNAs in the size range of 19-31 bases were excised from a denaturing gel. Adaptors were ligated to the 5' and 3' ends of the isolated RNA, and the product was converted to cDNA using a primer on the 3' adaptor. After 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.

value: adapter ligation


title: Mouse feces 09-C


title: Mouse feces 05-C

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 42 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 27 and 28 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 27 and 28 days prior


title: Mouse feces 06-C


title: Mouse feces 04-C


title: Mouse feces 07-C


title: Mouse feces 03-C


title: Mouse feces 01-C


title: Mouse feces 10-42


title: Mouse feces 07-42


title: Mouse feces 09-42


title: Mouse feces 06-42


title: Mouse feces 03-42


title: Mouse feces 04-42


title: Mouse feces 01-42


title: Mouse feces 10-38

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 38 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 2, 3, 16, 17, 23 and 24 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 38 days prior


title: Mouse feces 08-42


title: mouse_TG_RNA-seq

description: RNA-seq of thyroid tissue of IFN-alpha tansgenic mice.

source_name: pool of thyroid gland tissues, IFN-alpha transgenic

value: transgenic mice overexpressing IFN-alpha under control of bovine thyroglobulin promoter


title: Mouse feces 09-38


title: human feces TSDA2.3_long

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 "Pre1") 1 week prior to their first consumption of a fermented milk product (Danone, Activia). Read length is 76 nucleotides.

value: feces of a human subject


title: Mouse feces 05-42


title: Mouse feces 02-C


title: Mouse feces 07-38


title: hen1 mutant ligation

description:
HEN1TESTIS
Small RNA sequence data
Processed data file: HEN1TESTIS.processed.txt
barcode: none

value: TL

value: Hen1 mutant

value: testis


title: Mouse feces 08-38


title: Mouse feces 10-37

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 37 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1, 2, 15, 16, 22 and 23 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 37 days prior


title: human feces TSDA2.6

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 "FMP4") who had been consuming 2 servings of a fermented milk product (Danone, Activia) daily for 4 weeks. Read length is 36 nucleotides.


title: Mouse feces 09-37


title: Mouse feces 08-37


title: Mouse feces 09-35

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 13, 14, 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 35 days prior

value: 13, 14, 20 and 21 days prior


title: Mouse feces 10-35


title: Mouse feces 06-37


title: Mouse feces 07-37


title: Mouse feces 08-35


title: Mouse feces 07-35


title: Mouse feces 04-35

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 35 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 20 and 21 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 20 and 21 days prior


title: Mouse feces 06-35


title: Mouse feces 03-35


title: Mouse feces 06-38


title: human_T0_RNA-seq

description: RNA-seq of human thyroid primary cell.

source_name: primary thyroid cell line, untreated

value: thyroid


title: Soybean_degradome

status: Public on Nov 02 2011

city: Beijing

first: Hu

last: Zheng

address: No.12 South Street, Zhongguancun, Haidian District

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing: Individual sequence reads with the base quality scores were produced by Illumina/Solexa. A perl scripts was wrote to cut the first 17bp from each reads, and add CATG to the 5' end. All the tags were mapped onto the longest cDNA of each gene of  Glycine max of Phytozome(http://www.phytozome.net/index.php) using the program SOAP(Li et al. 2008).The locus sequence that with 20bp upstream and downstream was extracted from cDNA. Total small RNA sequences were used to query SAGE tag locus sequence for potential target site using Patscan with default parameters. Three mismatches, 0 insertions, and 0 deletions can be permitted. Only hits that with less than two mismatches in positions 1-9, no mismatches in positions 10 and 11, and less than three mismatches after position 11 in the mature miRNAs were considered good target sequences.

molecule: polyA RNA

organism: Glycine max

source_name: root, stem, leaf, and inflorescence

growth_protocol: The plant samples for RNA isolation were obtained from the different tissues of the soybean cultivars Williams 82. The soybeans were grown in greenhouse under natural daylight conditions. The root, stem and leaf were collected and quickly frozen in liquid nitrogen for RNA isolation from four-week-old seedlings. During the soybean flowering stage, the leaf and inflorescence tissues were collected and frozen in liquid nitrogen.

extract_protocol: Total RNA from different samples was extracted separately using the TRIzol reagent (Invitrogen), according to the manufacturer’s instructions. mRNAs were isolated using PolyATract mRNA isolation systems (Progema) from the pooled total RNAs. The mRNAs were directly ligated to a RNA oligonucleotide adaptor (5′-ACAGGUUCAGAGUUCUACAGUCCGACAUG-3′; Takara) using T4 RNA ligase (New England Biolabs) and were reverse transcribed using the primer (5′-GCTGTCAACGATACGCTACGTAACGGCATGACAGTG(T)24-3′) and Superscript III reverse transcriptase (Invitrogen). The cDNA were amplified for 10 cycles using Phusion DNA polymerase (Finnzymes) and purified using QIAquick PCR Purification Kit (Qiagen). These amplified products were digested with Mme I (New England Biolabs) and purified on the 10% Polyacrylamide gel. The desired band was recovered and used for deep sequencing.

tag: cultivar

value: Williams 82


title: Mouse feces 08-28

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 28 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 6, 7, 13 and 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 28 days prior

value: 6, 7, 13 and 14 days prior


title: Mouse feces 07-28

value: Mus musculus


title: Mouse feces 01-35


title: Mouse feces 06-28


title: Mouse feces 10-28


title: Mouse feces 04-28

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 28 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 13 and 14 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 13 and 14 days prior


title: Mouse feces 05-28


title: Mouse feces 02-35


title: Mouse feces 01-28


title: Mouse feces 03-28


title: Mouse feces 02-28


title: Mouse feces 10-24

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 24 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 2, 3, 9 and 10 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 24 days prior

value: 2, 3, 9 and 10 days prior


title: Mouse feces 09-24


title: Mouse feces 08-24


title: Mouse feces 07-24


title: Mouse feces 06-24


title: Mouse feces 08-23

description:
The Bacteria organisms are Bacteroides caccae ATCC 43185, Bacteroides ovatus ATCC 8483, Bacteroides thetaiotaomicron VPI-5482, Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Bacteroides sp. WH2,Bifidobacterium animalis subsp. lactis CNCM I-2494, Clostridium scindens ATCC 35704, Clostridium spiroforme DSM 1552, Collinsella aerofaciens ATCC 25986, Dorea longicatena DSM 13814, Eubacterium rectale ATCC 33656, Faecalibacterium prausnitzii M21/2, Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1632,Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, Lactococcus lactis subsp. cremoris CNCM I-1631, Parabacteroides distasonis ATCC 8503, Ruminococcus obeum ATCC 29174, Ruminococcus torques ATCC 27756, and Streptococcus thermophilus CNCM I-1630
DNA isolated from the fecal pellet of a mouse (C57Bl/6J) colonized with 15 species of gut bacteria (B. caccae, B. ovatus, B. thetaiotaomicron, B. uniformis, B. vulgatus, B. WH2, C. aerofaciens, C. scindens, C. spiroforme, D. longicatena, E. rectale, F. prausnitzii, P. distasonis, R. obeum, R. torques) 23 days prior which was also gavaged with 5 fermented milk strains (B. animalis subsp. lactis, L. lactis subsp. cremoris, two strains of L. delbrueckii subsp. bulgaricus, S. thermophilus) 1, 2, 8 and 9 days prior. Mouse was fed B&K rat and mouse autoclavable chow #7378000, Zeigler Bros., Inc.).

value: 23 days prior

value: 1, 2, 8 and 9 days prior


title: Mouse feces 09-23


title: Mouse feces 07-23


title: Mouse feces 06-23