title: Snyder_ALY-2_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180


title: Snyder_ALY-2_Input_L1 extraction1_seq1 aliquote 1

status: Public on May 24 2011

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

library_source: genomic

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

molecule: genomic DNA

organism: Caenorhabditis elegans

extract_protocol:
Worms are grown on peptone-enriched plates seeded with E. coli (HB101) and maintained according to standard protocol. Briefly, starved and synchronized L1s are first obtained, and then plated on peptone-enriched plates with HB101, which serves as a food source. Worms are grown at 20ºC to the desired developmental stage before harvesting. Since growth rates are frequently strain-specific, we use developmental milestones to determine developmental stages. Worms at the designed developmental stage are immediately crosslinked with 2% formaldehyde, quenched with 100 mM Tris buffer, washed with M9 buffer, and then stored at -80 as packed pellets.
The current ChIP Protocol is modified from Ercan et al., Nature Genetics 39: 403-408 (2007). Worm samples are lysed and solubilized by sonication in the presence of protease inhibitors and non-ionic detergents. The cellular debris is removed by centrifugation and the supernatant containing any formaldehyde crosslinked chromatin is saved for preparing input DNA and collecting immunocomplexes. 10% (or 50 ul) of the above supernatant from each sample is saved as input sample (control). Input sample (also known as whole cell extract) represents the total genomic DNA and is processed later (treated with RNAase A, proteinase K and reverse crosslink steps) along with the ChIPed samples to isolate genomic DNA (input DNA). The remaining supernatant is incubated with affinity-purified anti-GFP antibodies and Protein G-sepharose beads to collect the immunocomplexes containing a targeted transcription factor that is C-terminally tagged with GFP and its genomic binding fragments. Alternatively, the 8WG16 mouse monoclonal antibodies and Protein A-sepharose beads are used to collect the immunocomplexes containing RNA polymerase II. After extensive washing, any immunocomplexes are eluted and the protein-DNA crosslinks are reversed. The degree of sonication is assessed by running a small aliquot of DNA on a 2% agarose gel. Quantitative PCR is used to check if the ChIPed sample contains any of the targeted transcription factor's known genomic binding sites.
DNA fragments recovered following chromatin IP are size selected using gel electrophoresis.  The DNA is then prepared for deep sequencing using the protocols and reagents provided by Illumina.  This involves rendering the ends blunt, followed by the addition of single deoxy adenylate residues on each end.  The fragments are ligated to Illumina's propietary adapters and amplified.  After a final gel purification step the DNA is loaded into a flow cell for sequencing.

tag: strain

value: OP217(official name :OP217 genotype :unc119(ed3);wgIs217(aly-2:TY1 EGFP FLAG;unc119) outcross :3 transgene :aly-2 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ALY-2::EGFP fusion protein is expressed in the correct aly-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ALY-2 transcription factor. made_by :Mihail Sarov )

tag: developmental stage

value: fed L1

tag: genotype

tag: Sex

value: Hermaphrodite

tag: transgene


title: Snyder_DAF-12_GFP_L3_rep1 extraction3_seq3 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Anti-eGFP;target name: eGFP;host: Goat;antigen: Full-length EGFP;clonal: Polyclonal;purified: Affinity;company: Lab;catalog: Hyman Goat anti-GFP;reference: PMID: 18391959;short description: A Bacterially expressed full-length EGFP protein tagged with 6xHis was used to raise a goat antisera and the resulting antibodies were affinity-purified.;

data_processing: Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment.  The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA.  These calculations result in an enrichment ratio and a corresponding P-value.  Processed data are obtained using following parameters: genome version is WS180

value: OP222(official name :OP222 genotype :unc119(ed3);wgIs222(daf-12:TY1 EGFP FLAG;unc119) outcross :3 transgene :daf-12 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by :Mihail Sarov )


title: Snyder_DAF-12_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ALY-2_GFP_L3_rep2 extraction4_seq4 aliquote 1


title: Snyder_DAF-12_GFP_L3_rep2 extraction4_seq4 aliquote 1


title: Snyder_DAF-12_GFP_L4_rep2 extraction4_seq4 aliquote 1


title: Snyder_DAF-12_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_F45C12.2_GFP_L3_rep2 extraction4_seq4 aliquote 1

value: OP212(official name :OP212 genotype :unc119(ed3);wgIs212(F45C12.2:TY1 EGFP FLAG;unc119) outcross :3 transgene :F45C12.2 tags :Bombard tag :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by :Mihail Sarov )


title: Snyder_DAF-12_Input_L4 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_DAF-12_Input_L4 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_F45C12.2_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_F45C12.2_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_R02D3.7_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: OP218(official name :OP218 genotype :unc-119(ed3); wgIs218(R02D3.7:TY1 EGFP FLAG; unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The R02D3.7::EGFP fusion protein is expressed in the correct R02D3.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the RO2D3.7 transcription factor. made_by : )


title: Snyder_ZAG-1_GFP_L1_rep2 extraction4_seq4 aliquote 1

value: OP83(official name :OP83 genotype :unc119(ed3);wgIs83(zag-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The ZAG-1::EGFP fusion protein is expressed in the correct zag-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZAG-1 transcription factor. made_by :R Waterston )


title: Snyder_ZAG-1_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_GFP_L3_rep2 extraction4_seq4 aliquote 1


title: Snyder_ZAG-1_Input_L1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_Input_L1 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_F45C12.2_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_GFP_L1_rep1 extraction3_seq3 aliquote 1


title: Snyder_ZAG-1_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Embryonic fibroblast L139_MEF_88

status: Public on May 25 2011

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing: Barcodes were removed and reads were aligned using Bowtie.

molecule: total RNA

organism: Mus musculus

source_name: Embryonic fibroblast

growth_protocol: ES R1 cells were cultured as previously described (Moliner et al. 2008). MEFs were grown in DMEM with 10% FBS, 1x penicillin/streptomycin, 1x Glutamax and 0.05 mM 2-mercaptoethanol. All reagents were from Invitrogen.

extract_protocol: Custom protocol designed to capture the 5' end of transcripts, and maintain strand-information. See accompanying publication for details.

tag: cell type

value: Embryonic fibroblast

tag: source cell line

tag: well


title: Snyder_ALY-2_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_UNC-62_GFP_L1_rep1 extraction3_seq3 aliquote 1

value: OP600(official name :OP600 genotype :unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by :S Kim )


title: Snyder_ALY-2_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_UNC-62_Input_L1 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-6v2_GFP_L2_rep2 extraction4_seq4 aliquote 1

value: OP90(official name :OP90 genotype :unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG] outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-6::EGFP fusion protein is expressed in neurons surrounding pharynx at L2 stage.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-6 transcription factor. made_by :R. Waterston )


title: Snyder_NHR-6v2_GFP_L2_rep1 extraction3_seq3 aliquote 1

value: unc-119(ed3) III; wgIs90 [unc-119(+) nhr-6::TY1::EGFP::3xFLAG]


title: Snyder_NHR-6v2_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_DAF-12_GFP_L4_rep1 extraction3_seq3 aliquote 1


title: Snyder_EOR-1_GFP_L3_rep2 extraction4_seq4 aliquote 1

value: OP81(official name :OP81 genotype :unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross :0 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_C01B12.2_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: OP343(official name :OP343 genotype :unc119(ed3);wgIs343(C01B12.2:TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The C01B12.2::EGFP fusion protein has broad expression pattern at L2 stage.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DPL-1 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_UNC-62_Input_L1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_EOR-1_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;

value: unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG]


title: Snyder_EOR-1_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_C01B12.2_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_UNC-62_GFP_L2_rep2 extraction4_seq4 aliquote 1


title: Snyder_NHR-6v2_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_C01B12.2_GFP_L2_rep2 extraction4_seq4 aliquote 1


title: Snyder_UNC-62_GFP_L1_rep2 extraction4_seq4 aliquote 1


title: Snyder_UNC-62_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_UNC-62_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_UNC-62_GFP_L3_rep2 extraction4_seq4 aliquote 1


title: Snyder_FOS-1_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: OP304(official name :OP304 genotype :unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by :R Waterston )


title: Snyder_FOS-1_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_EOR-1_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_UNC-62_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_NHR-28_Input_L4 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP317(official name :OP317 genotype :unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by :R Waterston )


title: Snyder_UNC-62_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_C01B12.2_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_NHR-28_Input_L4 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-28_GFP_L4_rep2 extraction4_seq4 aliquote 1


title: Snyder_FOS-1_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_NHR-28_GFP_L4_rep1 extraction3_seq3 aliquote 1


title: Snyder_FOS-1_GFP_L2_rep2 extraction4_seq4 aliquote 1


title: Snyder_UNC-62_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_Input_L2 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_CES-1_GFP_L4_rep2 extraction4_seq4 aliquote 1

value: OP174(official name :OP174 genotype :unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by :S. Kim )


title: Snyder_CES-1_Input_L4 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119)


title: Snyder_ZAG-1_Input_L2 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZAG-1_GFP_L2_rep2 extraction4_seq4 aliquote 1


title: Snyder_CES-1_GFP_L4_rep1 extraction3_seq3 aliquote 1


title: Snyder_ZAG-1_GFP_L2_rep1 extraction3_seq3 aliquote 1


title: Snyder_CES-1_Input_L4 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZTF-7_Input_L4 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;

value: OP332(official name :ZTF-7 genotype :unc119(ed3);wgIs332(ztf-71::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-7::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-7 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_ZTF-7_GFP_L4_rep1 extraction3_seq3 aliquote 1

value: Hermaphrodite


title: Snyder_ZTF-7_GFP_L4_rep2 extraction4_seq4 aliquote 1


title: Snyder_ZTF-4_GFP_L3_rep2 extraction4_seq4 aliquote 1

value: OP322(official name :ZTF-4 genotype :unc119(ed3);wgIs322(ztf-4::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by :Bob Waterston's lab from UW )


title: Snyder_ZTF-7_Input_L4 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_ZTF-4_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Snyder_UNC-62_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_W03F9.2_Input_YA extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: OP215(official name :OP215 genotype :unc119(ed3);wgIs215(W03F9.2::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain.  The W03F9.2::EGFP fusion protein is mainly expressed in germline cells.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the W03F9.2 transcription factor. made_by :Tony Hyman's lab from MPI-CBG )

value: L4-Young Adult


title: Snyder_ZTF-4_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA-4_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: OP37(official name :OP37 genotype :unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] outcross :3 mutagen :Bombard tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by :R. Waterston and S. Kim )


title: Snyder_TLP-1_GFP_L1_rep2 extraction4_seq4 aliquote 1

value: OP321(official name :TLP-1 genotype :unc119(ed3);wgIs321(tlp-1::TY1 EGFP FLAG;unc119) outcross :0 mutagen :None tags :GFP::3xFlag description :This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The spatio-temporal expression pattern of TLP-1::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the TLP-1 transcription factor. made_by :Bob Waterston's lab from UW )

value: fed L1


title: Snyder_PHA-4_GFP_L3_rep2 extraction4_seq4 aliquote 1

value: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]


title: Snyder_W03F9.2_GFP_YA_rep1 extraction3_seq3 aliquote 1


title: Snyder_W03F9.2_GFP_YA_rep2 extraction4_seq4 aliquote 1


title: Snyder_W03F9.2_Input_YA extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_TLP-1_Input_L1 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_TLP-1_GFP_L1_rep1 extraction3_seq3 aliquote 1


title: Snyder_TLP-1_Input_L1 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA-4_Input_L3 extraction1_seq1 aliquote 1

description: channel ch1 is input DNA;


title: Snyder_PHA-4_GFP_L3_rep1 extraction3_seq3 aliquote 1


title: Th2_MAP

status: Public on May 23 2011

city: Edinburgh

first: Adrian

last: Bird

address: Mayfield Road

department: WTCCB

country: United Kingdom

institute: The University of Edinburgh

description:
MBD affinity purification
library strategy: MAP-Seq
library selection: MAP

data_processing:
Alignment (concat_*.wig files): Single-end sequence reads were mapped to the mouse genome (NCBIm37) using MAQ (http://maq.sourceforge.net/). Reads with a mapping score greater or equal to 30 where retained. Alignment was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.
Combining and normalisation: Replicate lanes were combined to give one sample for each cell type. Samples were then normalised to the average read number across all samples of a given purification type.

source_name: Th2 cells MAP-seq

extract_protocol:
Cells were purified by FACS or magnetic separation. Genomic DNA was extracted from these cells using phenol/chloroform and sheared to approximately 500 bp.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating immunoprecipitated DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was extracted using MiniElute PCR clean up columns (Qiagen) and PCR amplified with Illumina primers for 10-12 cycles. DNA was purified using QIAquick PCR Purification columns (Qiagen). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

treatment_protocol:
DNA was extracted using phenol/chloroform and sheared to approximately 500 bp using sonication. Methylated DNA was purified by two step MBD Affinity Purification as described in Skene et al., 2010.
MAP or ChIP as indicated

value: Male+female

value: Th2 cells

tag: mbd affinity column/chip antibody

value: MBD affinity column


title: DC_H3K4me3

description: Chromatin IP against H3K4me3

source_name: Dendritic cells H3K4me3 ChIP-seq

treatment_protocol:
Cells were crosslinked using 1% formaldehyde. Chromatin was sheared using sonication. Protein-DNA complexes were immunoprecipitated with an H3K4me3 antibody and the DNA was subsequently extracted.
MAP or ChIP as indicated

value: Dendritic cells

value: anti-H3K4me3 (07-473; Millipore)


title: Th1_H3K4me3

description: Chromatin IP against H3K4me3

source_name: Th1 cells H3K4me3 ChIP-seq

tag: sex

value: Th1 cells


title: DC_MAP

source_name: Dendritic cells MAP-seq


title: CD4_1_MAP

source_name: CD4 T cells MAP-seq

value: Male

value: CD4 T cells


title: CD4_2_MAP


title: DC_H3K27me3

description: Chromatin IP against H3K27me3

source_name: Dendritic cells H3K27me3 ChIP-seq

treatment_protocol: Cells were crosslinked using 1% formaldehyde. Chromatin was sheared using sonication. Protein-DNA complexes were immunoprecipitated with an H3K4me3 antibody and the DNA was subsequently extracted.

value: anti-H3K27me3 (07-499; Millipore)


title: Snyder_ZTF-4_Input_L3 extraction2_seq2 aliquote 1

description: channel ch1 is input DNA;

value: Hermaphrodite


title: Th1_H3K27me3

description: Chromatin IP against H3K27me3

source_name: Th1 cells H3K27me3 ChIP-seq


title: J1_DMNT_TKO_mRNA-seq

status: Public on May 21 2011

city: Vancouver

first: Eric

last: Chuah

state: BC

address: 570 West 7th Ave

institute: BC Genome Sciences Centre

description: Non-directional mRNA-seq

data_processing:
Alignment (RNA-seq): Sequence reads were aligned to the mouse reference genome (mm9) using MAQ v0.7.1 (Li et al., 2008), with Smith-Waterman alignment disabled and annotated exon-exon junctions compiled from Ensembl v54, RefSeq and UCSC gene annotation sources (downloaded from http://genome.ucsc.edu on March 17, 2009), as described (Morin et al., 2010; Shah et al., 2009). Sequence reads that could be uniquely assigned a position in the transcript resource (exon-exon junctions) were computationally repositioned to the genomic mm9 coordinates and a single merged bam file (Li et al., 2009) generated for downstream analyses.
Wigs (RNA-seq):The Samtools pileup utility (Li et al., 2009) and FindPeaks 3.1 (Fejes et al., 2008) was used to generate data tracks for visualization (wig and bigWig (Kent et al., 2010)) in the UCSC browser. Repbase (Jurka et al., 2005), a comprehensive database of repetitive elements, was used for alignment of reads to repetitive elements.

molecule: polyA RNA

source_name: Embyonic Stem Cell

growth_protocol: J1 and TT2 ES cells were passaged every 48-72 hours in DMEM supplemented with 15% FBS (HyClone), 20mM HEPES, 0.1mM nonessential amino acids, 0.1mM 2- mercaptoethanol, 100 units/ml penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (LIF) and 2mM glutamine on gelatinized plates.

extract_protocol:
RNA was extracted using TRIzol following the manufactures instructions and DNaseI treated (Invitrogen, Carlsbad, CA, USA). PolyA+ RNA was purified using the MACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) from 10ug of DNaseI-treated total RNA as per manufacturer?s instructions. mRNA-seq libraries were constructed from purified polyA RNA, as described in Morin et al. (Morin et al., 2008), from 10ug of DNAse1 treated total RNA and sequenced on an Illumina Genome AnalyzerIIx following the manufactures recommended protocol (Illumina Inc., Hayward, CA).
Sheared cDNA or IPed material was resolved on a 12% acrylamide gel and the 100-300bp size fraction was eluted from the gel slice overnight at 4oC in 300 ml of elution buffer (5:1, LoTE, 7.5M Ammonium Acetate).   DNA was recovered from the resulting gel slurry using a QIAquick PCR Purification Kit (Qiagen). Following column elution, the DNA ends were repaired using a 1:5 mixture of T4 and Klenow DNA polymerases (New England Biolabs), purified by phenol chloroform isoamyl alcohol (pH 8.0, 100ul, Fisher) extraction and EtOH precipitated. A single "A" base was added to the DNA fragments using Klenow exo- (3' and 5' exo minus) (New England Biolabs). Adapters (Illumina) were ligated to ends of the "A"-tailed DNA and adapter-modified DNA fragments enriched by PCR using Phusion polymerase (Finnzymes) and PCR primer 1.1 and 2.1 (Illumina) following the manufacturer's instructions (15 PCR cycles). The resulting PCR product was purified using a 8% PAGE (Nuvex; Invitrogen, Burlington, ON, Canada) to remove small products including adapter dimers, and the DNA quality assessed using an Agilent DNA 1000 series II assay and quantified by Qubit fluorometer (Invitrogen, Burlington, ON, Canada) and then diluted to 10nM. Cluster generation and 51 or 76 cycles of sequencing were performed on the Illumina cluster station and Illumina Genome AnalyzerIIx sequencing platform

value: Embyonic Stem Cell

tag: genotype/variation

value: DMNT1 TKO

tag: chip antibody


title: J1_WT_mRNA-seq

description: Non-directional mRNA-seq

value: WT


title: J1_DMNT_TKO_H3K9me3_NChIP-seq

description: Chromatin IP against H3K9me3

data_processing:
Alignment (ChIP-seq): Sequence reads were mapped to mm9 (NCBI 37) using MAQ (v 0.7.1) (Li et al., 2008) and default parameters.
Wigs (ChIP-seq):Reads having identical coordinates were collapsed into a single read and reads with mapQ >=7 passed to FindPeaks 3.1 (Fejes et al., 2008) (with a fixed directional read extension of 150bp) for segmentation and visualization

extract_protocol:
Chromatin was divided into aliquots of 2 x 106 cell equivalents per IP tube and the volume adjusted to 325 ul with IP buffer. Three aliquots were used for H3K9me3 immunoprecipitation and 1 aliquot was used for control IgG immunoprecipitation. Antibodies specific for H3K9me3 (5 ul; Active Motif, 39161), H3K27 (07-449, Millipore) or control IgG (20 ug; Sigma I8140) were added to each tube and rotated at 4 oC for 1 hour. The antibody-protein-DNA complex was precipitated by adding 20 ul of the blocked protein A/G beads and rotated at 4 0C overnight. The immunoprecipitated complex was washed twice with 400 ul of ChIP Wash buffer (20 mM Tris-HCl, pH 8.0, 0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 150 mM NaCl, 1X PIC), followed by a single wash with ChIP Final Wash Buffer (20 mM Tris-HCl (pH 8.0), 0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 500 mM NaCl, 1X PIC). The protein-DNA complex was eluted by incubating the beads in 200 ul of elution buffer (100 mM NaHCO3, 1% SDS) for 2 hours at 680C. Immunoprecipitated material was purified using the QIAquick PCR Purification Kit (Qiagen), according to the manufacturers protocol.
Sheared cDNA or IPed material was resolved on a 12% acrylamide gel and the 100-300bp size fraction was eluted from the gel slice overnight at 4oC in 300 ml of elution buffer (5:1, LoTE, 7.5M Ammonium Acetate).   DNA was recovered from the resulting gel slurry using a QIAquick PCR Purification Kit (Qiagen). Following column elution, the DNA ends were repaired using a 1:5 mixture of T4 and Klenow DNA polymerases (New England Biolabs), purified by phenol chloroform isoamyl alcohol (pH 8.0, 100ul, Fisher) extraction and EtOH precipitated. A single "A" base was added to the DNA fragments using Klenow exo- (3' and 5' exo minus) (New England Biolabs). Adapters (Illumina) were ligated to ends of the "A"-tailed DNA and adapter-modified DNA fragments enriched by PCR using Phusion polymerase (Finnzymes) and PCR primer 1.1 and 2.1 (Illumina) following the manufacturer's instructions (15 PCR cycles). The resulting PCR product was purified using a 8% PAGE (Nuvex; Invitrogen, Burlington, ON, Canada) to remove small products including adapter dimers, and the DNA quality assessed using an Agilent DNA 1000 series II assay and quantified by Qubit fluorometer (Invitrogen, Burlington, ON, Canada) and then diluted to 10nM. Cluster generation and 51 or 76 cycles of sequencing were performed on the Illumina cluster station and Illumina Genome AnalyzerIIx sequencing platform

treatment_protocol:
none
To generate chromatin, 1 x 107 infected ES cells for each cell line were harvested and washed in PBS. Cells were resuspended in 250 ul of douncing buffer (10 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 1X Protease inhibitory cocktail (PIC) and homogenized through a 25 G5/8 needle syringe for 20 repetitions. 1.875 ul of 20 U/ul of MNase (Worthington Biochemicals) was added and incubated at 37 0C for 7 min. The reaction was quenched by 0.5 M EDTA and incubated on ice for 5 min. 1ml of hypotonic buffer (0.2 mM EDTA, pH 8.0, 0.1 mM benzamidine, 0.1 mM phenylmethylsulfonyl fluoride, 1.5 mM dithiothreitol, 1X PIC) was added and incubated for 1 hour on ice. Cellular debris was pelleted and the supernatant was recovered.

value: H3K9me3 (Active Motif, #39161, lot #170)


title: J1_WT_H3K9me3_NChIP-seq

description: Chromatin IP against H3K9me3

value: H3K9me3 (Active Motif, cat #39161, lot #170)


title: TT2_WT_H3K9me3_NChIP-seq

description: Chromatin IP against H3K9me3

value: TT2 (C57BL/6/CBA F1)


title: TT2_SETDB1_KO_mRNA-seq

description: Non-directional mRNA-seq

treatment_protocol: Induction of the SETDB1 knock- out was conducted as described (Matsui et al., 2010)

value: SETDB1 KO


title: Th1_MAP

source_name: Th1 cells MAP-seq

value: Male+female


title: TT2_SETDB1_KO_H3K9me3_NChIP-seq

description: Chromatin IP against H3K9me3

treatment_protocol:
Induction of the SETDB1 knock- out was conducted as described (Matsui et al., 2010)
To generate chromatin, 1 x 107 infected ES cells for each cell line were harvested and washed in PBS. Cells were resuspended in 250 ul of douncing buffer (10 mM Tris-HCl, pH 7.5, 4 mM MgCl2, 1 mM CaCl2, 1X Protease inhibitory cocktail (PIC) and homogenized through a 25 G5/8 needle syringe for 20 repetitions. 1.875 ul of 20 U/ul of MNase (Worthington Biochemicals) was added and incubated at 37 0C for 7 min. The reaction was quenched by 0.5 M EDTA and incubated on ice for 5 min. 1ml of hypotonic buffer (0.2 mM EDTA, pH 8.0, 0.1 mM benzamidine, 0.1 mM phenylmethylsulfonyl fluoride, 1.5 mM dithiothreitol, 1X PIC) was added and incubated for 1 hour on ice. Cellular debris was pelleted and the supernatant was recovered.


title: Bcell_MAP

source_name: B cells MAP-seq

value: B cells


title: Endoderm input DNA pool

city: Stanford

first: Si Wan

last: Kim

state: CA

address: 300 Pasteur Drive M313

department: Genetics

country: USA

institute: Stanford University

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genomes (hg18; March, 2006) using the Illumina Genome Analyzer Pipeline.
Peaks: Transcription factor ChIP-Seq reads were processed to call peaks using CisGenome (Ji et al., 2008, Nat Biotechnol 26, 1293-1300). The setting for peak-calling and sliding window size was 300 bp and the threshold number of reads required for peak to be called was 11 reads. The false discovery rate allowed was 0.01. Histone H3K4me3 and H3K27me3 peaks were called using QuEST 2.4 (Valouev et al., 2008, Nat Methods 5, 829-834). We used the âhistoneâ bandwidth setting with ârelaxedâ peak-calling parameters.

organism: Homo sapiens

source_name: endoderm precursor cells

growth_protocol:
First 9 samples: Undifferentiated H9 hESCs were maintained on mouse embryonic fibroblast (MEF) feeder layers or on Matrigel (1:20 dilution; BD Biosciences) in mouse embryonic fibroblast-conditioned medium (CM). CM was produced by conditioning of MEFs for at least 24 hours in Dulbecco's modified Eagle's medium/Ham's F-12 medium (DMEM/F12) supplemented with 20% knockout serum replacement (Gibco), 1 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol and 8 ng/ml recombinant human fibroblast growth factor-basic (bFGF; Peprotech). Cultures were routinely passed with 200 U/ml type IV collagenase (Gibco) in 1:4 ratio every 4â5 days.
Last 9: Derived endoderm was generated from hESCs as previously described (D'Amour et al., 2005, Nat Biotechnol 23, 1534-1541). Differentiation was performed in RPMI-1640 medium supplemented with glutamax, 100 ng/ml recombinant human Activin A (R&D Systems), penicillin/streptomycin, and defined fetal bovine serum (FBS; HyClone) at sequentially increasing concentrations (0, 0.2 to 2%). 2% FBS was maintained afterwards in cultures over the duration of differentiation.

extract_protocol: Lysates were clarified from sonicated nuclei and transcription factor-DNA or histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

tag: cell line

value: ESC-derived endoderm

tag: passages


title: Endoderm input DNA pool (for histone modifications)

description: input DNA


title: hESC input DNA pool (for histone modifications)

description: input DNA

source_name: human embryonic stem cells

value: embryonic stem cells


title: Endoderm FOXH1 ChIP-Seq pool

description: Chromatin IP against FOXH1

value: FOXH1, sheep polyclonal

tag: chip antibody manufacturer

value: R&D Systems

tag: chip antibody catalog #


title: Endoderm SMAD2/3 B ChIP-Seq rep1

description: Chromatin IP against SMAD2/3

value: SMAD2/3, goat polyclonal


title: Endoderm H3K27me3 ChIP-Seq pool

description: Chromatin IP against H3K27me3

value: H3K27me3, rabbit polyclonal

value: Upstate


title: Endoderm SMAD3 ChIP-Seq rep1

description: Chromatin IP against SMAD3

value: SMAD3, rabbit polyclonal

value: Abcam


title: Endoderm H3K4me3 ChIP-Seq pool

description: Chromatin IP against H3K4me3

value: H3K4me3, rabbit polyclonal


title: Endoderm SMAD2/3 A ChIP-Seq pool

description: Chromatin IP against SMAD2/3

value: SMAD2/3, rabbit polyclonal

value: Santa Cruz


title: Neuronal_polII_ChIP_Dudek

city: RTP

first: Ramendra

middle: N

last: Saha

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Neurobiology

institute: NIEHS, NIH

description:
Chromatin IP against Rpb1 (Pol II)
Instrument model: Illumina Genome Analyzer IIx

data_processing: FASTQ files will aligned to the prebuilt Bowtie R. norvegicus, UCSC rn4 index using bowtie 0.12.3. Files were in agreement and combined. Hits were centered by moving hit locations 75 nt in a strand specific manner and binned in 25nt bins for visualization as .bedGraph

organism: Rattus norvegicus

source_name: Dissociated primary neurons

growth_protocol: Rat neurons were derived from

extract_protocol: Lysates were clarified from sonicated nuclei and Pol II-DNA complexes were isolated with antibody. Immunoprecipitated DNA fragments were used to prepare ChIP-Seq libraries. These libraries were constructed using the standard protocol from Illumina with NEBNext DNA Sample Prep Reagent Set 1 and 2 (New England Biolabs; E600L; E6020L) and single-end adapters from Illumina (Genomic DNA Sample Prep Oligo Only Kit; FC-102-1003) with two modifications to the protocol.  Platinum® Pfx DNA Polymerase (Invitrogen; 11708-039) was used for library amplification and Agencourt AmPure Reagent (Beckman Coulter Genomics; A29152) was used to clean up the amplification reaction.  Libraries were quantitated by qPCR (Power SYBR® Green PCR Master Mix; 4368702; Life Technologies, Inc.) Flow cells were prepared with Illumina’s Standard Cluster Generation Kit V 2 (FC-103-2001) on an Illumina Cluster Station and run on a Genome AnalyzerIIx within one week using 36-Cycle Sequencing Kits V4 at National Intramural sequencing center (NISC), NIH.

treatment_protocol: None. Resting neurons were used

value: Sprague Dawley

tag: tissue

value: Neurons obtained from dissociated pre-natal cortices

value: anti-Rpb1 (M01)

tag: antibody manufacturer

value: Abgent


title: hESC H3K27me3 ChIP-Seq pool

description: Chromatin IP against H3K27me3


title: hESC H3K4me3 ChIP-Seq pool

description: Chromatin IP against H3K4me3


title: hESC FOXH1 ChIP-Seq pool

description: Chromatin IP against FOXH1


title: hESC input DNA pool

description: input DNA


title: hESC SMAD2/3 A ChIP-Seq pool

description: Chromatin IP against SMAD2/3


title: hESC SMAD3 ChIP-Seq rep1

description: Chromatin IP against SMAD3


title: hESC SMAD2/3 B ChIP-Seq rep1

description: Chromatin IP against SMAD2/3


title: E11_1_m4 [COPRO-Seq]

status: Public on May 20 2011

city: Saint Louis

first: Jeremiah

middle: J

last: Faith

state: MO

address: Campus Box 8510

institute: Washington University in St. Louis

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,OAT:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1

data_processing: After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were discarded.

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

source_name: mouse feces

growth_protocol: Fecal samples obtained from mice were span frozen in liquid nitrogen and stored at -80¬∞C and maintained at this temperature prior to processing.

extract_protocol:
Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were suspended in a solution containing 500 ul of acid-washed glass beads (Sigma-Aldrich), 500 ul of extraction buffer A (200 mM Tris [pH 8], 200 mM NaCl, 20 mM EDTA), 200 ul of 20% SDS, and 500 ul of a mixture of phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate and resuspended in 100 ul TE. The resuspension was further purified with a Qiagen PCR column and eluted into 30 ul of EB buffer.
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, gDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode).  Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.library strategy

tag: sample source

tag: diet

tag: time


title: E11_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_1_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:666.7,RICE:222.2,BEEF:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_1_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,APPLE:222.2,BEEF:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,CHICK:222.2,BEEF:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: hESC SMAD4 ChIP-Seq rep1

description: Chromatin IP against SMAD4

value: SMAD4, goat polyclonal


title: Endoderm SMAD4 ChIP-Seq rep1

description: Chromatin IP against SMAD4

value: ESC-derived endoderm


title: TT2_WT_mRNA-seq

description: Non-directional mRNA-seq

value: Embyonic Stem Cell

tag: strain

value: TT2 (C57BL/6/CBA F1)

value: WT


title: E11_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => BEEF:666.7,PEACH:222.2,SWEET_POTATO:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => RICE:666.7,APPLE:222.2,SWEET_POTATO:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => BEEF:666.7,PEACH:222.2,SWEET_POTATO:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_4_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:666.7,RICE:222.2,BEEF:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_4_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,OAT:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_6_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,PEACH:222.2,CHICK:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_6_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,CHICK:222.2,BEEF:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => RICE:666.7,APPLE:222.2,SWEET_POTATO:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,OAT:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,CHICK:222.2,BEEF:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_6_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,OAT:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,APPLE:222.2,BEEF:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,PEACH:222.2,CHICK:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_6_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:666.7,RICE:222.2,BEEF:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => RICE:666.7,APPLE:222.2,SWEET_POTATO:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E11_7_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => BEEF:666.7,PEACH:222.2,SWEET_POTATO:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,OAT:222.2,PEACH:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,PEACH:222.2,BEEF:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => BEEF:666.7,RICE:222.2,PEA:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => BEEF:666.7,RICE:222.2,PEA:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,APPLE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,BEEF:222.2,CHICK:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,APPLE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,BEEF:222.2,CHICK:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,OAT:222.2,SWEET_POTATO:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_6_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,OAT:222.2,PEACH:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_6_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,OAT:222.2,CHICK:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_6_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,PEACH:222.2,BEEF:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,OAT:222.2,CHICK:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,OAT:222.2,SWEET_POTATO:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,OAT:222.2,CHICK:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,CHICK:222.2,OAT:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,APPLE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,OAT:222.2,CHICK:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,BEEF:222.2,CHICK:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,SWEET_POTATO:222.2,RICE:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,OAT:222.2,SWEET_POTATO:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => APPLE:666.7,PEACH:222.2,CHICK:55.6,RICE:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,APPLE:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,APPLE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,OAT:222.2,PEACH:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,APPLE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E13_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,OAT:222.2,PEACH:55.6,PEA:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,SWEET_POTATO:222.2,RICE:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,APPLE:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,PEACH:222.2,RICE:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,RICE:222.2,PEACH:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,APPLE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,CHICK:222.2,OAT:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,RICE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,RICE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,APPLE:55.6,CHICK:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,RICE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:666.7,PEACH:222.2,RICE:55.6,OAT:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_6_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,RICE:222.2,PEACH:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 6 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,APPLE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,RICE:222.2,SWEET_POTATO:55.6,PEACH:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_1_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:421.1,APPLE:421.1,BEEF:105.3,RICE:52.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:421.1,RICE:421.1,CHICK:105.3:APPLE:52.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEA:666.7,CHICK:222.2,OAT:55.6,SWEET_POTATO:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => SWEET_POTATO:666.7,RICE:222.2,PEACH:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 7 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => CHICK:421.1,BEEF:421.1,PEA:105.3,APPLE:52.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:421.1,BEEF:421.1,OAT:105.3,RICE:52.6. Sample was taken after mouse was on the diet for 1 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:421.1,RICE:421.1,CHICK:105.3:APPLE:52.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E17_4_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => OAT:421.1,APPLE:421.1,BEEF:105.3,RICE:52.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1


title: E15_4_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed a meal of human pureed food in the following concentrations (g/kg) => PEACH:666.7,PEA:222.2,RICE:55.6,BEEF:55.6. Sample was taken after mouse was on the diet for 4 days.
library strategy: COPRO-Seq
Eubacterium rectale ATCC 33656
Bacteroides caccae ATCC 43185
Bacteroides ovatus ATCC 8483
Bacteroides thetaiotaomicron VPI-5482
Clostridium symbiosum
Collinsella aerofaciens ATCC 25986
Blautia hydrogenotrophica DSM 10507
Bryantella formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Desulfovibrio piger GOR1