title: E3_4_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. 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: D4_14_m10 [COPRO-Seq]

status: Public on May 20 2011

type: SRA

city: Saint Louis

first: Jeremiah

middle: J

last: Faith

state: MO

address: Campus Box 8510

country: USA

institute: Washington University in St. Louis

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. Sample was taken after mouse was on the diet for 14 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

library_source: genomic

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.

molecule: genomic DNA

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: D3_7_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D3_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: E2_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. 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: E3_2_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. Sample was taken after mouse was on the diet for 2 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: D2_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. 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: D2_2_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. Sample was taken after mouse was on the diet for 2 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: E1_14_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. Sample was taken after mouse was on the diet for 14 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: D3_4_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. 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: D3_7_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. 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: E2_4_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D2_2_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. Sample was taken after mouse was on the diet for 2 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: D2_4_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: D3_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. 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: E1_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. 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: D2_14_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. Sample was taken after mouse was on the diet for 14 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: E2_1_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. 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: D3_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. 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: D3_14_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. Sample was taken after mouse was on the diet for 14 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: E1_2_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. Sample was taken after mouse was on the diet for 2 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: D2_4_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: E2_14_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. Sample was taken after mouse was on the diet for 14 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: D3_4_m13 [COPRO-Seq]

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria

value: Mouse was fed Harlan Teklad Diet TD.09053

value: Sample was taken after mouse was on the diet for 4 days.


title: D3_4_m4 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09058


title: D4_4_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. 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: D3_1_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: D4_2_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. Sample was taken after mouse was on the diet for 2 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: D3_14_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057. Sample was taken after mouse was on the diet for 14 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: D3_1_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. 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: E3_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: E3_7_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: D4_7_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. 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: D2_7_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. 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: E2_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. 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: D4_14_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. Sample was taken after mouse was on the diet for 14 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: E3_14_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. Sample was taken after mouse was on the diet for 14 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: D2_14_m12 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09057

value: Sample was taken after mouse was on the diet for 14 days.


title: D4_1_m13 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: E3_1_m5 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09054

value: Sample was taken after mouse was on the diet for 1 days.


title: D2_2_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. Sample was taken after mouse was on the diet for 2 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: D3_14_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. Sample was taken after mouse was on the diet for 14 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: D3_14_m2 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09055


title: E1_14_m7 [COPRO-Seq]


title: D4_4_m13 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: E1_7_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. 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: D3_1_m11 [COPRO-Seq]


title: D4_2_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. Sample was taken after mouse was on the diet for 2 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: E3_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. 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: D4_14_m13 [COPRO-Seq]


title: E1_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. 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: E3_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. 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: E2_14_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052. Sample was taken after mouse was on the diet for 14 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: D4_14_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. Sample was taken after mouse was on the diet for 14 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: E1_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D3_1_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. 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: E1_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: D2_7_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. 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: D4_2_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. Sample was taken after mouse was on the diet for 2 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: E1_2_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. Sample was taken after mouse was on the diet for 2 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: E3_4_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. 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: D2_14_m13 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. Sample was taken after mouse was on the diet for 14 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: D3_7_m13 [COPRO-Seq]

value: Sample was taken after mouse was on the diet for 7 days.


title: D3_7_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: E3_4_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D2_1_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. 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: E3_7_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. 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: E3_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. 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: E2_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. 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: D4_4_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: E3_2_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. Sample was taken after mouse was on the diet for 2 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: D4_2_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052. Sample was taken after mouse was on the diet for 2 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: E2_2_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. Sample was taken after mouse was on the diet for 2 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: E3_7_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D3_7_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052. 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: D4_7_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: D3_2_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. Sample was taken after mouse was on the diet for 2 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: E1_4_m2 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09620


title: E3_2_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. Sample was taken after mouse was on the diet for 2 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: E1_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. 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: D2_7_m3 [COPRO-Seq]


title: E2_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. 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: D2_1_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: E2_4_m6 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09624


title: E1_14_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. Sample was taken after mouse was on the diet for 14 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: D2_14_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052. Sample was taken after mouse was on the diet for 14 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: D3_14_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. Sample was taken after mouse was on the diet for 14 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: D2_4_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. 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: D2_4_m13 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D2_2_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. Sample was taken after mouse was on the diet for 2 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: D3_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. 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: E1_1_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. 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: E2_7_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: D3_2_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. Sample was taken after mouse was on the diet for 2 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: D4_2_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. Sample was taken after mouse was on the diet for 2 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: D4_1_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. 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: D3_1_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057. 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: E2_1_m1 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09623


title: D3_2_m4 [COPRO-Seq]

value: Sample was taken after mouse was on the diet for 2 days.


title: D4_14_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. Sample was taken after mouse was on the diet for 14 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: D4_14_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. Sample was taken after mouse was on the diet for 14 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: D4_2_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. Sample was taken after mouse was on the diet for 2 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: E1_2_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. Sample was taken after mouse was on the diet for 2 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: E2_1_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: E2_4_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. 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: D2_4_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: D2_1_m13 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D2_1_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: POLYA_DP_RNAseq

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Poly-adenylated RNA isolation.

library_source: transcriptomic

data_processing:
RNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. Tags were then processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment positive strand: RNA_polyA_mm9_bins_50_elongation_0_strand_+_.wig
Piled alignment negative strand: RNA_polyA_mm9_bins_50_elongation_0_strand_-_.wig

molecule: polyA RNA

organism: Mus musculus

source_name: Primary T-cells

extract_protocol:
For strand-specific sequencing of RNA, total RNA was extracted using TRIzol (Invitrogen, USA) and DNA was digested. Poly(A) RNA was purified from 8Âµg of total RNA using the Illumina poly(A) purification kit. Poly(A) purification was verified using RNA Pico chips on a 2100 Bioanalyzer. The RNA sample was fragmented to ~150bp using RNase H (Ambion, USA) at 37C for 10 minutes. The size distribution of fragmented RNA was again validated using RNA Pico chips on a 2100 Bioanalyzer. Library preparation using the Illumina small RNA kit was essentially carried out as per manufacturer's instructions. In brief, 5â adapters were ligated and the reaction was separated on a 10% polyacrylamide gel for 2 hours. All RNA above 30bp was recovered by gel cutting, eluted using 300mM NaCl at room temperature under rotation and purified using the RNeasy kit (Qiagen, Germany) with the addition of 1.5 volumes of Ethanol to ensure recovery of all RNAs. These steps were repeated after the ligation of 3â adapters. The library was reverse-transcribed, PCR amplified, size selected (corresponding to ~20-100 bp without adapters) from an agarose gel and sequenced according to the manufacturer's small RNA kit instructions, except that 36bp tags were sequenced instead of 75bp.
CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.

tag: strain

tag: tissue

value: thymus

tag: cell type

value: T cells

tag: developmental stage

value: CD4+/CD8+ double-positive (DP)


title: D4_2_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. Sample was taken after mouse was on the diet for 2 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: TFIIE_ChIPSeq

description: Chromatin IP against TFIIE.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TFIIE_176_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TFIIE_176_merged__no_artefacts_Scaled_BGSub.area.gff

extract_protocol:
EDTA-free protease inhibitors (Roche, France) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1ug/ml pepstatin. Phosphatase inhibitors (Roche, France) were added to a final concentration of 1x for Pol II phospho-serine ChIPs. Aliquots of 5x10^7 cells were lysed after resuspension in 2.5ml LB1 (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) for 20 minutes on a rotating wheel at 4C. Chromatin was collected by centrifugation for 5 minutes at 4C and 1.350g in a tabletop centrifuge, and washed in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8) on a rotating wheel for 10 minutes at 4C. Chromatin was collected, resuspended in 1.5ml of LB3 (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 4000 (Misonix Inc, USA) sonicator for 10 cycles (30 seconds on, 30 seconds off, amplitude 40) with the tubes submerged in ice-cold sonication solution (500mM NaCl, 20% Ethanol). After the addition of Triton X-100 to a final concentration of 1%, particulates were collected through centrifugation at 20.000g and 4C for 20 minutes. For batch processing, supernatants were combined, mixed thoroughly and subsequently aliquoted and snap-frozen in liquid nitrogen. Extracts were kept at -80C until use and 50ul aliquots were taken to serve as input controls.  All experiments were performed using Dynabeads (Invitrogen, USA) coated with Protein-G, with the exception of sheep alpha-rabbit coated beads (M-280) for the ETS1 ChIP. For biological replicates, all steps were repeated using a biologically independent sample. Beads were washed 3x with 1ml and subsequently resuspended in 250ul of blocking solution (0.5% BSA in 1x DPBS). After the addition of the antibody, the beads were incubated at 4C overnight on a rotating wheel. Unbound antibodies were removed through three further washes with 1ml of blocking solution. Beads were resuspended in 100ul of blocking solution, extracts were added and the mix was incubated overnight at 4C on a rotating wheel.  EDTA-free protease inhibitors (Roche) were added to all washing buffers to a final concentration of 1x together with 0.2mM PMSF and 1ug/ml pepstatin. Phosphatase inhibitors (Roche) were added to a final concentration of 1x in the case of Pol II phospho-serine ChIPs. Beads were washed 8 times in RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 10 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE+ (10mM Tris pH8, 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65C for 15 and 10 minutes in 110ul and 100ul of elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) respectively. The two eluates were combined and incubated at 65C overnight (13-15 hours) for crosslink reversal. DNA was purified as described for the input.

CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.

tag: antibody (clone)

value: TFIIE (C-21)

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog number

tag: antibody lot number


title: E1_4_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. 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: D3_4_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09052. 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: TFIIH_ChIPSeq

description: Chromatin IP against TFIIH.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TFIIH_171__merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TFIIH_171_merged__no_artefacts_Scaled_BGSub.area.gff

value: TFIIH (S-19)


title: D3_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. 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: D3_7_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057. 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: TFIIA_ChIPSeq

description: Chromatin IP against TFIIA.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TFIIA_171_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TFIIA_171_merged__no_artefacts_Scaled_BGSub.area.gff

value: TFIIA (FL-109)


title: TFIIF_ChIPSeq

description: Chromatin IP against TFIIF.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TFIIF_171__merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TFIIF_171_merged__no_artefacts_Scaled_BGSub.area.gff

value: TFIIF (C-18)


title: E2_4_m2 [COPRO-Seq]

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria

value: Mouse was fed Harlan Teklad Diet TD.09052

value: Sample was taken after mouse was on the diet for 4 days.


title: TOTAL_DP_RNAseq

description: Total RNA isolation.

data_processing:
RNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. Tags were then processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment positive strand: RNA_total_mm9_bins_50_elongation_0_strand_+_.wig
Piled alignment negative strand: RNA_total_mm9_bins_50_elongation_0_strand_-_.wig

molecule: total RNA

extract_protocol:
For strand-specific sequencing of RNA, total RNA was extracted using TRIzol (Invitrogen, USA) and DNA was digested. For total RNA samples, ribosomal RNA from 8Âµg of total RNA was depleted using the eukaryotic Ribominus kit (Invitrogen, USA) according to manufacturer's instructions. Ribosomal RNA depletion was verified using RNA Pico chips on a 2100 Bioanalyzer. The RNA samples was fragmented to ~150bp using RNase H (Ambion, USA) at 37C for 10 minutes. The size distribution of fragmented RNA was again validated using RNA Pico chips on a 2100 Bioanalyzer. Library preparation using the Illumina small RNA kit was essentially carried out as per manufacturer's instructions. In brief, 5â adapters were ligated and the reaction was separated on a 10% polyacrylamide gel for 2 hours. All RNA above 30bp was recovered by gel cutting, eluted using 300mM NaCl at room temperature under rotation and purified using the RNeasy kit (Qiagen, Germany) with the addition of 1.5 volumes of Ethanol to ensure recovery of all RNAs. These steps were repeated after the ligation of 3â adapters. The library was reverse-transcribed, PCR amplified, size selected (corresponding to ~20-100 bp without adapters) from an agarose gel and sequenced according to the manufacturer's small RNA kit instructions, except that 36bp tags were sequenced instead of 75bp.
CD4+/CD8+ double-positive mouse T cells were obtained as follows. Thymuses were extracted from wild-type Bl6 mice (5-6 weeks) and kept on ice in RPMI 1640 medium (Invitrogen, USA) with 10% FCS for a maximum of one hour. Single cell suspensions were obtained by filtering through a 70Âµm nylon mesh (BD Biosciences, USA). For ChIP-seq experiments, cells were washed twice with cold 1x DPBS (Invitrogen, USA), resuspended in room temperature 1x DPBS and crosslinked with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 50mM Hepes pH 7.8) for a final formaldehyde concentration of 1% for 10 minutes at room temperature. The reaction was quenched with the addition of 250mM glycine and an incubation at room temperature for 5 minutes. Cells were washed twice with cold DPBS and counted using a Vi-CELL cell counter (Beckman Coulter, France). For RNA-seq experiments, the crosslinking and quenching steps were omitted.
Cells were sorted using the AutoMACS (Miltenyi, France) system. After labeling with alpha-CD8 antibodies coupled to PE, cells were incubated with alpha-PE multisort magnetic beads according to manufacturer's instructions. Sorting was performed using a single positive selection. Cells were released and incubated with anti-CD4 magnetic beads according to manufacturer's instructions. After a subsequent single positive selection, sorting efficiency was verified through flow cytometry analysis.


title: E3_14_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. Sample was taken after mouse was on the diet for 14 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: Taf1_ChIPSeq

description: Chromatin IP against Taf1.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: Taf1_155_rep1__no_artefacts_Scaled_BGSub.wig
Peak (GFF): Taf1_155_rep1_no_artefacts_Scaled_BGSub.area.gff


title: E1_4_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. 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: D4_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. 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: TFIIB_ChIPSeq

description: Chromatin IP against TFIIB.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: TFIIB_145_rep1__no_artefacts_Scaled_BGSub.wig
Peak (GFF): TFIIB_145_rep1__no_artefacts_Scaled_BGSub.area.gff

value: TFIIB (C-18)


title: D3_14_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. Sample was taken after mouse was on the diet for 14 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: E2_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625. 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: E1_4_m7 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09053


title: E1_14_m8 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09621

value: Sample was taken after mouse was on the diet for 14 days.


title: D3_14_m3 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. Sample was taken after mouse was on the diet for 14 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: D2_1_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057. 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: ETS1_ChIPSeq

description: Chromatin IP against ETS1.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: Ets1_156_166_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): Ets1_156_166_merged__no_artefacts_Scaled_BGSub.area.gff


title: E3_4_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. 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: PolII_N20_ChIPSeq

description: Chromatin IP against Total PolII.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: N20_136_151_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): N20_136_151_merged__no_artefacts_Scaled_BGSub_peak.area.gff

value: total (N-20)


title: E2_14_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620. Sample was taken after mouse was on the diet for 14 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: D3_14_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056. Sample was taken after mouse was on the diet for 14 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: D2_14_m4 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. Sample was taken after mouse was on the diet for 14 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: D3_2_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053. Sample was taken after mouse was on the diet for 2 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: D2_14_m10 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049. Sample was taken after mouse was on the diet for 14 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: E1_7_m3 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09625

value: Sample was taken after mouse was on the diet for 7 days.


title: D4_14_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09057. Sample was taken after mouse was on the diet for 14 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: D4_4_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. 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: D2_2_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. Sample was taken after mouse was on the diet for 2 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: E2_14_m1 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623. Sample was taken after mouse was on the diet for 14 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: D3_7_m2 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055. 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: E2_2_m6 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624. Sample was taken after mouse was on the diet for 2 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: E1_2_m6 [COPRO-Seq]

value: Sample was taken after mouse was on the diet for 2 days.


title: E1_1_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: D4_2_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. Sample was taken after mouse was on the diet for 2 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: E3_7_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09622. 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: D4_4_m9 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058. 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: D4_4_m12 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050. 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: E1_2_m1 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09624


title: D3_1_m7 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059. 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: E1_7_m8 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621. 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: D2_4_m11 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09051. 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: D2_7_m5 [COPRO-Seq]

description:
Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09054. 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: CBP_ChIPSeq

description: Chromatin IP against CBP.

data_processing:
DNA Samples were sequenced on an Illumina Genome Analyzer and aligned against the mouse 2007 (mm9, NCBI Build 37) genome using the integrated Eland software. The Eland output files provide tag sequences, scores and coordinates. For experiments with multiple sequencing lanes (technical replicates), these files were directly merged and then processed as described. As pre-filtering steps, only uniquely mapped tags were used for further processing and all duplicate tags (those with identical sequences/coordinates) were filtered out to remove possible sequencing and/or alignment artefacts. Remaining tags were processed using a custom R pipeline, employing the ShortRead library.

Peak detection was carried out for each experiment using the final wiggle track in the CoCAS pipeline. Each 10bp track was converted to a General Feature Format (GFF) file in PERL and loaded into the peak detection module. Peak detection was performed using the neighborhood effect method.

Piled alignment: CBP_136_merged__no_artefacts_Scaled_BGSub.wig
Peak (GFF): CBP_136_rep2__no_artefacts_Scaled_BGSub.area.gff

value: thymus

value: T cells

value: CD4+/CD8+ double-positive (DP)

value: CBP

value: Abcam