title: E2_4_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 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_m4 [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.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

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: E2_2_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 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_14_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 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_4_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 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_m5 [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 14 days.


title: D4_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: D3_1_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 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_14_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 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_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 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_1_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 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_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 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_4_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 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_1_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 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_14_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 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_2_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 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_2_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 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_14_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 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_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 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_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 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_m3 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09052

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


title: D2_7_m8 [COPRO-Seq]


title: E2_1_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 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_m7 [COPRO-Seq]

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


title: D4_1_m10 [COPRO-Seq]

value: Mouse was fed Harlan Teklad Diet TD.09049


title: E1_14_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 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_2_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 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_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 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_4_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 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_14_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 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_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 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_m3 [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: D4_2_m5 [COPRO-Seq]

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


title: D2_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: E2_2_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 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_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: D3_4_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 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_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 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_2_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 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_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: D3_2_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 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_14_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 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_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 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_14_m6 [COPRO-Seq]


title: D3_2_m13 [COPRO-Seq]


title: D3_2_m12 [COPRO-Seq]


title: E3_14_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 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_14_m8

description:
run325.1_lane2
rRNA depleted total RNA
The following Organisms are included in these Samples: 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: transcriptomic

molecule: total RNA

growth_protocol: Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were treated with RNAProtect (Qiagen) and suspended in a solution containing 500 μl of acid-washed glass beads (Sigma-Aldrich), 500 μl of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 μl of 20% SDS, and 500 μl of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000 × g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5).

extract_protocol:
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand.
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, cDNA 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.

treatment_protocol: rRNA depletion: Genomic DNA was removed with TURBO DNAse (Ambion), and then total RNA was run over two MEGAClear columns (Ambion) to deplete tRNAs and 5S rRNA. In between the two column purifications, a second DNAse digestion was performed (Baseline-ZERO Epicenter).  16S and 23S rRNA were depleted using MICROBExpress (Ambion) and custom depletion oligos (Rey et.al. 2010; JBC).

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


title: E2_14_m4

description:
run324_lane2
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09620


title: E1_14_m2

description:
run321_lane5
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

description:
run322.1_lane8
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09623


title: E1_14_m8

description:
run324_lane1
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09621


title: E1_14_m4

description:
run321_lane7
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_m6

description:
run324_lane4
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09624


title: E1_14_m1

description:
run321_lane4
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_m3

description:
run321_lane6
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09625


title: E2_14_m3

description:
run324_lane3
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m11

description:
run320.1_lane5
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09059


title: D4_10_m10

description:
run299_lane6
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09049


title: D4_10_m12

description:
run320.1_lane6
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09050


title: D4_10_m9

description:
run299_lane5
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09058


title: D4_10_m8

description:
run299_lane4
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09055


title: D4_10_m6

description:
run216_lane3
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m4

description:
run216_lane2
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09056


title: D4_10_m7

description:
run216_lane4
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

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


title: D4_10_m5

description:
run299_lane3
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

value: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053


title: D4_10_m13

description:
run320.1_lane7
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_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 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_2_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 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_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 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_10_m13

description:
run319.1_lane8
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m12

description:
run319.1_lane7
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

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


title: D4_10_m2

description:
run236.1_lane6
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

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


title: D3_10_m11

description:
run319.1_lane6
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m10

description:
run299_lane2
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m1

description:
run236.1_lane5
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

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


title: D3_10_m8

description:
run298_lane8
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m7

description:
run236.1_lane4
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m6

description:
run236.1_lane3
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m5

description:
run298_lane7
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

extract_protocol:
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand.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, cDNA 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.


title: D3_10_m2

description:
run235.4_lane8
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

extract_protocol:
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand.
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA 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.


title: D3_10_m1

description:
run235.4_lane7
rRNA depleted total RNA
The following Organisms are included in these Samples: 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

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.
Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand.
Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA 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.


title: D3_10_m4

description:
run236.1_lane2
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m9

description:
run299_lane1
rRNA depleted total RNA
The following Organisms are included in these Samples: 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: Lsh-/-  H3K4me3

status: Public on May 19 2011

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

description: Sequence tag

data_processing:
The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer 2Ã following manufacturer protocols.
Sequenced tags were mapped to the mouse genome (Mm8) (tag number per 200-bp window) using the Illumina Analysis Pipeline
Peaks represent frequency of readout

organism: Mus musculus

source_name: Lsh-/-  H3K4me3 sequence

growth_protocol: Lsh-/- and Lsh+/+ mouse embryonic fibroblasts (MEF) were grown in DMEM (Invitrogen/GIBCO) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and antibiotics (Invitrogen/GIBCO).

extract_protocol: DNA purified from precipitated chromatin from WT (Lsh+/+) or Lshâ/â MEFs with anti-H3K4me3 antibody. The ChIP DNA ends were repaired using PNK and Klenow enzymes (ER0720; Epicenter Biotechnology), followed by treatment with Taq polymerase I to generate a protruding 3â² A base used for adaptor ligation. Following ligation of a pair of Illumina adaptors to the repaired ends, the ChIP DNAs were amplified using the adaptor primers for 20 cycles and fragments of 200 to 400 bp were isolated from a 2% agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer 2Ã following manufacturer protocols.

treatment_protocol: Lshâ/â and WT mouse embryonic fibroblast (MEF) cell lines (20,000,000 cells) were treated with MNase to generate mostly mononucleosomes, and chromatin was precipitated with anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam).

tag: cell type

value: Mouse embryonic fibroblast

tag: antibody

tag: genotype/variation

value: Lsh-/-


title: D3_10_m3

description:
run236.1_lane1
rRNA depleted total RNA
The following Organisms are included in these Samples: 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_10_m3

description:
run216_lane1
rRNA depleted total RNA
The following Organisms are included in these Samples: 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: Lsh+/+  H3K4me3

description: Sequence tag

source_name: Lsh+/+  H3K4me3 sequence

value: anti-histone 3 lysine 4 trimethylation (anti-H3K4me3) (Abcam)

value: Lsh+/+


title: SAGA_RC_ChIP-seq

city: Dallas

first: Ling

last: Cai

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center at Dallas

description: Chromatin IP against SAGA

data_processing:
Alignment: Sequence reads were obtained and mapped to the saccharomyces cerevisiae (build sacCer1, Oct, 2003) genomes using the bowtie.
Peaks: Peak detection was performed with CisGenome

organism: Saccharomyces cerevisiae

source_name: YMC RC phase

growth_protocol: Yeast cells from SPT7-FLAG strain were cultured in fermentor under low glucose continuous growth condition described in Tu., et al 2005.

extract_protocol:
ChIP protocol: About 50 OD cycling cells collected from the appropriate time point were rapidly fixed in 1% formaldehyde for 15 min in 50 ml total volume and then quenched using 3 ml 2.5 M glycine for 10 min. The fixed cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine-HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input.
For ChIP with histone antibodies, 50 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. For SAGA ChIP, 500 µl WCE and 2 µg Flag M2 antibody was used. After incubation overnight, 20 µl magnetic beads resuspended in ChIP lysis buffer was added and incubated for 1.5 h. Beads were washed twice with ChIP lysis buffer, once with DOC buffer (10 mM Tris-Cl pH 8.0, 0.25 M LiCl, 0.5% DOC, 1 mM EDTA) and once with TE. 60 µl of TES buffer (50 mM Tris-Cl pH 8.0,10 mM EDTA, 1% SDS) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. 150 µl TES was added to the input sample. Reverse crosslinking was performed for the ChIP and input sample by incubating for 6 hours at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K was added to the samples after reverse crosslinking and samples were incubated for 2 hours at 37°C. DNA was then purified with a QIAquick PCR purification kit.
Chromatin was sheared with Bioruptor and precleared before immunoprecipitation with histone or Flag antibody, ChIP-seq library construction was following protocol from http://bioinfo.mbb.yale.edu/array/Solexa_LibraryPrep_20080229ge.pdf

treatment_protocol: OX and RC phase cells were collected and crosslinked for 15min at room temperature with 1% formaldehyde and quenched with 150mM glycine before flash frozen

tag: strain

value: CEN.PK a SPT7-FLAG::Nat

tag: chip antibody


title: Input_OX_ChIP-seq

description: Input DNA

source_name: YMC OX phase cells


title: ESC CTCF-GFP IgG

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description: input DNA (IgG control)

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse m37 genome assembly (mm9; July 2007) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: ESC

growth_protocol: Maintained on Gelatine-coated dishes in DMEM (GLUTAMAX high-glucose, Gibco) media supplemented with 15% FBS (Gibco), 0.055mM b-mercaptoethanol (Gibco), 1x MEM non-essential amino acids (Invitrogen), 5000u/ml penicillin-streptomycin (Invitrogen) and 50uM LIF

extract_protocol: 20ng of the immunoprecipitated DNA was used to generate the ChIP-seq library according to the manufacture’s protocol (Illumina) and sequenced with the Genome Analyzer II (Illumina).

treatment_protocol: 30mio. cells were crosslinked with formaldehyde at 1% final concentration, lysates were sonicated to average fragment size of 500bp, IP was performed with 5ug antibody

value: R1/E ESC

value: Goat IgG isotype control

tag: chip antibody manufacturer

value: Jackson Immunoresearch

tag: chip antibody lot#

tag: chip antibody catalog#


title: ESC CTCF-GFP ChIP

description: Chromatin IP against GFP

value: goat-anti-eGFP, raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP

value: generated by the Antibody and Protein purification facility of MPI-CBG


title: SAGA_OX_ChIP-seq

description: Chromatin IP against SAGA


title: ESC Rad21-GFP IgG

description: input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse m37 genome assembly (mm9; July 2007) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

tag: differentiation day

tag: antibody manufacturer

tag: antibody lot number

tag: antibody catalog number


title: ESC Rad21-GFP ChIP

description: Chromatin IP against GFP


title: EB Rad21-GFP IgG

description: input DNA

source_name: EB

value: R1/E-derived EB


title: Input_RC_ChIP-seq

description: Input DNA


title: H3_RC_ChIP-seq

description: Chromatin IP against H3


title: H3_OX_ChIP-seq

description: Chromatin IP against H3


title: H3K9ac_RC_ChIP-seq

description: Chromatin IP against H3K9ac

value: H3K9ac [06-942 (Millipore)]


title: EB Rad21-GFP ChIP

description: Chromatin IP against GFP


title: H3K9ac_OX_ChIP-seq

description: Chromatin IP against H3K9ac


title: ChIP Sequencing Mock

status: Public on May 16 2011

city: Cambridge

first: Vikram

last: Vijayan

state: MA

address: 52 Oxford Street, Room 440

institute: Harvard University

description: ChIP Sequencing

data_processing: Sequence tags were aligned to the S. elongatus genome with Bowtie. GenBank CP000100, CP000101, and S89470 were used to align reads to the chromosome and endogenous plasmids. Uniquely mappable reads with a maximum of 3 mismatches were mapped to the genome. Reads were then extended 150 base-pairs to cover the average length of insert DNA between sequencing adaptors as determined by the Agilent Bioanalyzer. WIG files for ChIP and ChIP input were normalized such that the genome average is 100 reads/nucleotide. WIG files for Mock and Mock input were normalized such that the genome average is 200 reads/nucleotide.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: AMC 408

growth_protocol: A continuous culture apparatus kept cells in constant light and growth conditions and provided real-time bioluminescence readings. S. elongatus (stain AMC 408): psbAI::luxCDE fusion in NS1 (spectinomycin and streptomycin) and purF::luxAB fusion in NSII (chloramphenicol) was grown in a 6-L cylindrical spinner flask at a volume of 4.5 L. Cells were grown in BG-11 medium with the following modifications: 0.0010 g/L FeNH4 citrate was used instead of 0.0012 g/L FeNH4 citrate and citric acid was supplemented at 0.00066 g/L. Cells were initially inoculated in the presence of antibiotics (5 ug/mL spectinomycin and 5 ug/mL chloramphenicol), and subsequently diluted with modified BG-11 lacking antibiotics. Cells were exposed to surface flux of approximately 25 umol photons m-2 s-1 cool white florescent light, bubbled with 500 mL/min 1% CO2 in air, maintained at 30 C, and stirred at 1 rotation per second. Constant optical density (OD750 0.15) and volume are achieved via a two state controller. OD does not fluctuate greater than 8% during an experiment. Cells are exposed to two twelve hour light-dark cycles for entrainment before release into continuous light.

extract_protocol:
Cells were mechanically lysed by beat beating with 0.1 mm glass beads in cold lysis buffer A (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate) with protease inhibitors (Roche).  Chromatin was fragmented by sonication of the lysate to a median of ~300 base-pairs and the protein concentration of the supernatant was measured by BCA (Pierce) using BSA as standard. 750 ug of lysate was incubated with 30 ug of antibody - RNA polymerase beta subunit antibody WP023 (Neoclone) or mouse whole IgG mock (Jackson ImmunoResearch) - and incubated overnight at 4 C. We verified that the monoclonal RNA polymerase beta subunit antibody WP023 reacts with S. elongatus RNA polymerase beta by Western blot analysis of whole cell extract, where it produces a single band of the expected size. Lysate was supplemented with Protein G Sepharose Fast-Flow beads (Invitrogen) and incubated for an additional 2 hours at 4 C. After incubation, Sepharose beads were washed in cold buffer at room temperature: 2 x 5 minutes lysis buffer A; 1 x 5 minutes lysis buffer B (50 mM HEPES, pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate); 1 x 5 minutes wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.1% Na-Deoxycholate); 1 x 5 minutes TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Protein-DNA was eluted from beads by incubation of samples at 65 C for 1 hour in elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS). Crosslinks were reversed in supernatant by incubation of samples at 65 C overnight in elution buffer. Western blot of supernatant of mock versus IP shows 45% efficicency pull-down of the beta subunit and 25% co-IP of beta' subunit in the IP using Neoclone antibodies WP023 and WP001, respectively. Proteins were digested with 0.2 mg/ml proteinase K for 2 hours at 37 C.  Nucleic acid was then purified with phenol/chloroform extraction and precipitated with ethanol and LiCl. Nucleic acid was re-suspended in TE buffer and RNA was digested in 20 ug/mL RNase and subsequently phenol/chloroform purified. For input control 5% of the volume of cell lysate was removed after sonication and used to prepare the input DNA. ChIP DNA concentration was estimated with the Pico-green DNA detection kit (Invitrogen).
ChIP sequencing libraries were prepared for samples ZT 32 (subjective dusk) and ZT 44 (subjective dawn) as these timepoints showed maximal/minimal gene expression for canonical circadian mRNAs kaiC and purF by microarray. Mock ChIP sequencing libraries were prepared for an equal mix of lysate from ZT 32 through ZT 52 (collected at 4 hour intervals). Sequencing libraries were prepared from 10 ng DNA following the Illumina ChIP protocol (Revision A) and libraries with size between 200 to 300 base-pairs were selected for amplification. Libraries were assayed with the Agilent Bioanalyzer and 8 pM of template was used for cluster generation. Libraries were sequenced using Illumina primers on an Illumina Genome analyzer II.

treatment_protocol: 250 mL cells from continuous culture (OD750 0.15) were crosslinked with 1% formaldehyde for 15 minutes and then quenched with 125 mM glycine for 5 minutes at room temperature. Cells were collected by centrifugation and washed twice with cold PBS buffer, pH 7.4. The cell pellet was snap frozen in liquid nitrogen and stored in -80C. Samples were collected 32 to 52 hours after release into continuous light in 4 hour intervals.

tag: circadian time

value: equal mix of circadian times

value: mouse whole IgG (Jackson ImmunoResearch)


title: ChIP Sequencing ZT 44 Input

description: ChIP Sequencing

value: circadian time 20 hours

value: WP023 (Neoclone)


title: ChIP Sequencing Mock Input

description: ChIP Sequencing


title: ChIP Sequencing ZT 44

description: ChIP Sequencing


title: ChIP Sequencing ZT 32 Input

description: ChIP Sequencing

value: circadian time 8 hours


title: RNA Sequencing Technical Replicate 1

description: Strand Specific RNA Sequencing

data_processing: Sequence tags were stripped of the terminal poly-(A) sequence and aligned to the S. elongatus genome with Bowtie. GenBank CP000100, CP000101, and S89470 were used to align reads to the chromosome and endogenous plasmids. Uniquely mappable reads with a maximum of 3 mismatches were mapped to the genome and extended by the length of the individual read.

extract_protocol: Eight ug of RNA was fragmented for 40 minutes at 95 C in fresh 2 mM EDTA, 100 mM NaCO2, pH 9.2. Fragmentation reactions were immediately precipitated in 300 mM NaOAc, pH 5.2, glycogen, and isopropanol. Fragmented RNA was resuspended in RNA loading buffer (Fisher), briefly denatured, and loaded in a 15% TBE-Urea polyacrylamide gel (BioRad) for size selection. Gels were stained with Sybr Gold (Invitrogen) and a 25-30 nucleotide band was excised using a synthesized 28 nucleotide RNA and denatured 10 base-pair DNA ladder (Invitrogen) as standards. The gel slice was physically disrupted and RNA was recovered in 300 mM NaOAc, 1 mM EDTA, 0.1 units/ul SUPERase-In (Ambion) overnight at room temperature. Solution was transferred to a Spin-X cellulose acetate filter (Corning) to remove gel debris and precipitated with glycogen and isopropanol. Size selected fragmented RNA was denatured briefly and dephosphorylated in a 30 ul reaction with 1 X T4 polynucleotide kinase buffer without ATP (NEB), 20 units SUPERase-In, and 15 units T4 polynucleotide kinase (NEB) at 37 C for 1 hour. The reaction was precipitated, resuspended, briefly denatured, and poly-(A) tailed in a 25 ul reaction with 1 X poly-(A) polymerase buffer (NEB), 5 units SUPERase-In, 1 mM ATP, and 1.25 units E. coli poly-(A) polymerase (NEB) at 37 C for 10 minutes. Reactions were quenched with 80 ul of 5 mM EDTA and precipitated.  Reverse transcription was carried out from the introduced poly-(A) tail anchor of denatured RNA using primer oNTI255 with the SuperScript III reverse-transcriptase system (Invitrogen) supplemented with 2 units/ul of SUPERase-In at 48 C for 30 minutes. RNA was subsequently hydrolyzed in 0.1 M NaOH at 98 C for 15 minutes and loaded in a 10% TBE-Urea polyacrylamide gel (BioRad) and the extended first-strand product was excised and recovered as above in 300 mM NaCl, 10 mM Tris, pH 7.9, 1 mM EDTA. First-strand cDNA was circularized in a 20 ul reaction with 1 X CircLigase buffer (Epientre), 50 uM ATP, 2.5 mM MnCl2, and 1 ul CircLigase (Epientre) for 1 hour at 60 C, and then heat-inactivated 10 minutes at 80 C.  One ul of circularized cDNA template was amplified using Phusion Hot Start High-Fidelity enzyme (NEB) and primers oNTI230 and oNTI231 to create DNA with Illumina cluster generation sequences on each end along with the Illumina small RNA sequencing primer binding site. PCR was carried out with an initial 30 second denaturation at 98 C, followed by 8 cycles of 10 second denaturation at 98 C, 10 second annealing at 60 C, and 5 second extension at 72 C. PCR product was loaded in a non-denaturing 10 % TBE polyacrylamide gel (BioRad) and a 113 to 125 nucleotide band was excised using 10 base-pair ladder as standard. DNA was recovered as previously described. Libraries were quantified using an Agilent Bioanalyzer and 4 to 6 pM of template was used for cluster generation and sequenced on Illumina Genome analyzer II with the Illumina small RNA sequencing primer.

treatment_protocol: 120 mL cells from continuous culture were collected by vacuum filtration, snap frozen in liquid nitrogen, and stored in -80C for no more than one week prior to RNA extraction. RNA was extracted from frozen cells in two steps. First, cells were lysed in 65 C phenol/SDS (sodium dodecyl sulfate) by vortexing and total RNA was purified by phenol/chloroform extraction. Second, total RNA was subjected to DNase I treatment followed by a second phenol/chloroform extraction. Total RNA was analyzed on agarose gel and Agilent Bioanalyzer to assess integrity. Total RNA was prepared for timepoints collected at 4 hour intervals from 76 to 96 hours after release into continuous light and mixed in equal proportions. Mixed total RNA was supplemented with RNase Out to a final concentration of 2 units/ul and depleted of 23S and 16S ribosomal subunits using the MICROBExpress Bacterial mRNA Enrichment Kit according to manufacturer's instructions.

value: equal proportion of each circadian time


title: RNA Sequencing Technical Replicate 2

description: Strand Specific RNA Sequencing


title: RNA Sequencing Technical Replicate 3

description: Strand Specific RNA Sequencing


title: LNCAP-GroSeq-dht-siCTRL

status: Public on May 15 2011

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: strand-specific RNA-Seq of nuclear run-on RNA (nascent RNA) from LNCaP cells treated with control siRNA and DHT for 1h

data_processing:
Alignment: Reads were truncated to 25 bp (ChIP-Seq) or 32 bp (RNA, GRO-Seq) and aligned to the human hg18 genome (NCBI Build 36) using Bowtie.  Only reads that mapped to a single, unique position were used for downstream analysis.
Data analysis was performed using HOMER, a software suite for high-throughput sequencing analysis and created in part to support this study (http://biowhat.ucsd.edu/homer/).  Each sequencing experiment was normalized to a total of 10 million uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.  UCSC Genome Browser bedGraph files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.  GRO-Seq bedGraph files are strand specific and contain pileups assuming a RNA fragment size of ~75 bp.  Focal peaks (~200 bp) were found for transcription factors/co-factors, and broad, variable lengthed regions of enrichment were found for histone modifications using the default settings in HOMER.  GRO-Seq data was initially pooled across all samples to identify contigous regions of nascent RNA enrichment to identify transcription units without prior knowledge of genes.

organism: Homo sapiens

source_name: Prostate cancer cell line (LNCaP)

extract_protocol: For GRO-Seq, ~20 million cell nuclei from DHT- or vehicle-treated, mock or FOXA1 siRNA-transfected LNCaP cells were extracted and harvested, and RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.

treatment_protocol: LNCaP cells were cultured in RPMI 1640 supplemented with 10% FBS.  Control (1027280) and the specific siRNA against  FOXA1 (M-010319) were purchased from Qiagen or Dharmacon. One day prior to transfection, LNCaP cells were seeded in RPMI 1640 medium. Six hours after transfection with Lipofectamine 2000 (Invitrogen), cells were washed twice with PBS and then maintained in hormone-deprived phenol-free RPMI 1640 media.  Cells were then cultured for 96 hours following transfection and then treated with DHT or vehicle for 1 hrs.

tag: cell line

value: LNCaP

tag: sirna transfection

tag: agent

value: DHT

tag: transgenes


title: LNCAP-GroSeq-dht-siFoxA1

description: strand-specific RNA-Seq of nuclear run-on RNA (nascent RNA) from LNCaP cells treated with siRNA against FoxA1 and DHT for 1h


title: LNCaP-MED12-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against MED12 in ThioMac treated with Kdo2 for 1h

extract_protocol: Chromatin immunoprecipitation was performed using ~10 million cell crosslinked with 1% formaldehyde at room temperature for 15 min. After sonication, the soluble chromatin was incubated with 1-5ug of antibody. Specific immunocomplexes were precipitated with Protein A or G beads (Sigma-Aldrich). Complexes were washed and the DNA was extracted and purified by QIAquick Spin columns (Qiagen). For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Solexa GAII system according to manufacturer's instruction (Illumina).

tag: chip antibody vendor

value: Bethyl


title: LNCaP-MED12-dht-siCTRL-ChIP-Seq


title: LNCaP-p300-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against p300 in ThioMac treated with Kdo2 for 1h

value: Santa Cruz


title: LNCaP-input-dht-ChIP-Seq

description: Mock chromatin IP in LNCaP cells treated with DHT for 1h


title: LNCaP-p300-dht-siCTRL-ChIP-Seq


title: LNCaP-H4K5ac-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H4K5ac in LNCaP cells treated with control siRNA and with DHT for 1h

value: Upstate


title: LNCaP-H2A.Z-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H2A.Z in LNCaP cells treated with control siRNA and with DHT for 1h

value: Abcam


title: LNCaP-H4K5ac-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against H4K5ac in LNCaP cells treated with siRNA against FoxA1 and with DHT for 1h


title: LNCaP-H3K27ac-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H3K27ac in LNCaP cells treated with control siRNA and with DHT for 1h


title: LNCaP-H3K27ac-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against H3K27ac in LNCaP cells treated with siRNA against FoxA1 and with DHT for 1h


title: LNCaP-H3K36me3-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H3K36me3 in LNCaP cells treated with control siRNA and with DHT for 1h


title: LNCaP-H2A.Z-dht-siFoxA1-ChIP-Seq

description: Chromatin IP against H2A.Z in LNCaP cells treated with siRNA against FoxA1 and with DHT for 1h


title: LNCaP-H3K4me2-dht-siFoxA1-Mnase-ChIP-Seq

description: Chromatin IP against H3K4me2 mononucleosomes in LNCaP cells treated with siRNA against FoxA1 and with DHT for 4 hrs

extract_protocol:
After formaldehyde fixation, the LNCaP cells were resuspended in digestion buffer with 50U MNase and incubated at 37 degree for 8 min, and then the reaction was stopped by adding EDTA. The digested cells should generate mainly mononucleosomes with minor fraction of dinucleosomes. The samples were then sonicated and subjected to same library preparation protocol as the otherÂ  ChIP-seq samples.
Chromatin immunoprecipitation was performed using ~10 million cell crosslinked with 1% formaldehyde at room temperature for 15 min. After sonication, the soluble chromatin was incubated with 1-5ug of antibody. Specific immunocomplexes were precipitated with Protein A or G beads (Sigma-Aldrich). Complexes were washed and the DNA was extracted and purified by QIAquick Spin columns (Qiagen). For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Solexa GAII system according to manufacturer's instruction (Illumina).

treatment_protocol: LNCaP cells were cultured in RPMI 1640 supplemented with 10% FBS.  Control (1027280) and the specific siRNA against  FOXA1 (M-010319) were purchased from Qiagen or Dharmacon. One day prior to transfection, LNCaP cells were seeded in RPMI 1640 medium. Six hours after transfection with Lipofectamine 2000 (Invitrogen), cells were washed twice with PBS and then maintained in hormone-deprived phenol-free RPMI 1640 media.  Cells were then cultured for 96 hours following transfection and then treated with DHT or vehicle for 4 hrs.

tag: mnase digestion

value: yes


title: ChIP Sequening ZT 32

description: ChIP Sequencing


title: LNCaP-H3K4me3-dht-siCTRL-ChIP-Seq

description: Chromatin IP against H3K4me3 in LNCaP cells treated with control siRNA and with DHT for 1h


title: mRNA-Seq_siRNA_GFP

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing: The raw reads were processed on the CLIPZ server (Khorshid et al., Nucleic Acids Research 2011, 39:D245)

molecule: polyA RNA

growth_protocol: HEK293 cells were routinely grown in DMEM supplemented with 10% FCS in the presence of antibiotics.

extract_protocol: RNA-Seq

treatment_protocol: When mentioned, 4-Thiouridine was added to cells grown in monolayer at 1mM final concentration 12-14 hours prior to harvest.  If stated, Crosslinking of 4-thiouridine treated samples were done at 365 nm UV before harvesting. For other samples, the cells were either harvested directly or harvested after crosslinking at 254 nm UV.

tag: modified nucleotide

tag: crosslinking

value: anti-GFP


title: mRNA-Seq_NO4SU_254XL_repB


title: LNCaP-H3K4me2-dht-siCTRL-Mnase-ChIP-Seq

description: Chromatin IP against H3K4me2 mononucleosomes in LNCaP cells treated with control siRNA and with DHT for 4 hrs

tag: chip antibody


title: mRNA-Seq_NO4SU_NOXL_repA


title: mRNA-Seq_NO4SU_NOXL_repB


title: mRNA-Seq_NO4SU_254XL_repA


title: LNCAP-GroSeq-vehicle-siCTRL

description: strand-specific RNA-Seq of nuclear run-on RNA (nascent RNA) from LNCaP cells treated with control siRNA and vehicle for 1h

value: vehicle


title: mRNA-Seq_4SU_NOXL_repB


title: LNCaP-H3K4me2-vehicle-siCTRL-Mnase-ChIP-Seq

description: Chromatin IP against H3K4me2 mononucleosomes in LNCaP cells treated with control siRNA and with vehicle for 4 hrs


title: LNCaP-H3K4me2-vehicle-siFoxA1-Mnase-ChIP-Seq

description: Chromatin IP against H3K4me2 mononucleosomes in LNCaP cells treated with siRNA against FoxA1 and with vehicle for 4 hrs


title: mRNA-Seq_siRNA_HuR

value: anti-HuR


title: mRNA-Seq_4SU_365XL_repA


title: rpaR mutant plus pC-HSL (1)

city: Seattle

first: Somsak

last: Phattarasukol

state: WA

address: 1705 NE Pacific St., HSC K-327

department: Microbiology

institute: University of Washington

description:
YO7
rpaR mutant with pC-HSL signal addition
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq

data_processing: Alignment: Sequence reads were mapped to Rhodopseudomonas palustris CGA009 genome (build GI:39748133) using the Burrows-Wheeler Alignment (BWA) tool. All reads mapping to a unique location with two or fewer mismatches were selected for determining gene expression.

organism: Rhodopseudomonas palustris

source_name: bacterial cells

growth_protocol: cells were grown photoheterotrophically in photosynthetic medium plus 10 mM succinate at 30C; at OD660 = 0.1 cells were treated as indicated and growth continued until an OD660 = 0.5 was reached; cells were pelleted, flash frozen, and stored at -80C until processed for RNA extraction

extract_protocol: Total RNA was purified from frozen cell pellets using a miRNeasy Mini Kit following the manufacture’s instruction. RNA was treated with TURBO DNase and purified with a RNeasy MinElute Cleanup Kit. The construction of cDNA library was performed as described previously (Armour et. al., 2009). Briefly, first strand cDNA synthesis was carried out using first-strand NSR (Not-So-random) primer mix and SuperScript III enzyme. RNA template was then removed by RNase H. Second strand synthesis was carried out with exo- Klenow fragment and second-strand NSR primer mix. After PCR amplification, double-stranded DNA was purified using a QIAquick PCR Purification Kit.

treatment_protocol: pellet was frozen at -80C

tag: strain

tag: genotype/variation

value: rpaR mutant

value: 10 uM p-coumaroyl-homoserine lactone


title: wild-type minus pC-HSL (2)

description:
YO2
wild-type untreated
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq

value: wild-type


title: mRNA-Seq_4SU_365XL_repB


title: RNA_Ago2_PAR-CLIP_completeT1_repB

molecule: cytoplasmic RNA

extract_protocol: CLIP, PAR-CLIP

treatment_protocol: For samples subjected to PAR-CLIP, 4-Thiouridine was added to cells grown in monolayer at 1mM final concentration 12-14 hours prior to crosslinking at 365 nm UV. For samples subjected to CLIP, the cells were directly crosslinked at 254 nm UV.

tag: clip variant

value: PAR-CLIP

tag: enzymatic digestion

value: complete T1 digestion

tag: protein


title: RNA_Ago2_PAR-CLIP_completeT1_repA


title: RNA_Ago2_CLIP_completeT1_repB

value: CLIP


title: RNA_HuR_PAR-CLIP_mildT1_repB

value: mild T1 digestion

value: HuR


title: RNA_HuR_PAR-CLIP_mildMNase_repA

value: mild MNase digestion


title: RNA_HuR_PAR-CLIP_mildMNase_repB


title: rpaR mutant minus pC-HSL (1)

description:
YO5
rpaR mutant untreated
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq


title: rpaR mutant minus pC-HSL (2)

description:
YO6
rpaR mutant untreated
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq


title: wild-type plus pC-HSL (1)

description:
YO3
wild-type with pC-HSL signal addition
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq


title: wild-type minus pC-HSL (1)

description:
YO1
wild-type untreated
Barcode: CTTA
library strategy: Not-so-random (NSR) RNA-seq


title: RNA_HuR_CLIP_completeT1_repB


title: RNA_Ago2_CLIP_completeT1_repA


title: RNA_HuR_CLIP_completeT1_repA


title: mRNA-Seq_4SU_NOXL_repA


title: WT_col_ovules

city: Montpellier

first: Daniel

last: Grimanelli

address: 911 Av Agropolis

country: France

institute: IRD

data_processing: Trimming of adapter sequences performed using the bioconductor ShortRead package.

organism: Arabidopsis thaliana

source_name: mature ovules

growth_protocol: Ovules collected from mature carpels grown in screen-house conditions, temperature 20 (night) -22 (days) with 16 hours of light/day.

extract_protocol: RNAs isolated using TRIZOL.  Illumina libraries were constructed for the wild type and mutant samples following Illumina/Solexa's standard protocols for small RNA isolation

tag: ecotype

tag: cell type

value: Ovules


title: RNA_HuR_PAR-CLIP_completeT1_repA


title: PSD_cocaine_smallRNA

status: Public on May 13 2011

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing: Sequences were extracted from image files using Firecrest and Bustard. The 3' adaptor sequences were trimmed from the reads, and reads 18-30 nt in length were aligned to all annotated mouse microRNAs from miRBase (www.mirbase.org; version 16) with Bowtie (bowtie-bio.sourceforge.net; version 0.12.7); only perfectly aligning reads were considered for miRNA expression level analysis. A custom Perl script was used to calculate the number of reads aligning to each specific miRNA gene.

source_name: Striatal postsynaptic density

growth_protocol: All mice were allowed to acclimate to the colony for at least one week before handling or injections. Mice were kept in the University of Connecticut Health Center animal facility on a 12 h light/dark cycle (lights on 7:00 am to 7:00 pm) and handled in accordance with University of Connecticut Health Center Institutional Animal Care and Use Committee guidelines. To reduce stress from handling during the injections, animals in all groups were handled for 1min/animal/day for 2-3 days prior to the start of injections. During injections, animals were brought into the behavior room to acclimate to the new environment for 45-60 minutes each day before the beginning of experiments.

extract_protocol: TRIzol; PSD sample buffers contained RNASecure

treatment_protocol: Mice were given a saline or cocaine injection and had their locomotor activity monitored for the subsequent 45 minutes. In the experiments in which RNA from NAc lysates was used for miRNA-Seq library preparation, animals were given injections of 20 mg/kg cocaine or saline (10 ml/kg) intraperitoneally each for 7 days. For all other experiments, animals received a lower dose of cocaine (10 mg/kg) on the first and last (7th) day, with the standard 20 mg/kg cocaine dose on days 2-6.

tag: tissue

value: Brain

tag: treatment

value: Cocaine

tag: read length


title: Hybrid BAD

first: Avraham

last: Levy

address: Hertzl St

department: Plant Sciences Dept

institute: The Weizmann Institute of Science

description:
small RNA
sequence tags
whole plant_2 months old three plants

data_processing: Sequences were trimmed by a perl script to remove: adaptor by identifying 7 bases from the adaptor (allowing one mismatch) and a polymer of seven poly(A), as well as any downstream sequence from the adaptor or poly(A).  Sequences that contained more than 3 N's or shorter than 18 bases were discarded. The output is a list of tags i.e. a list of the unique processed sequences and their  frequency.

organism: Triticum aestivum

source_name: whole plant

growth_protocol: Seeds were germinated on wet 3MM papers in petri dishes. All seeds were imbibed for 24 hr at room temperature under regular light. Seeds of Aegilops tauschii then underwent 3-6 weeks of vernalization, at 4oC in the dark. After germination, plantlets were placed in 5-liter pots and  grown in a greenhouse. All plants were grown during the winter, at 20oC and under short-daylight conditions.

extract_protocol: Total RNA was extracted from 2 g of whole 2-month-old plant tiller tissue, using 25 ml TRI reagent  (Molecular Research Center, Cincinnati, OH), according to the manufacturer's protocol, with the exception of isopropanol precipitations and ethanol washes, which were performed overnight, at -20oC.   ere at the vegetative phase. 195  Small RNA library preparation: RNA quality of all samples was verified using a bio-analyzer. Cloning of small RNAs was performed by Illumina (San Diego, CA), using the DGE small- RNA sample preparation kit protocol v1.0 (Illumina, Hayward, 199 CA). In brief, small RNAs (18-32 nt long) were size selected, purified, and ligated with adaptors. Four cDNA libraries of size-selected RNA from the four pools of plants were prepared by reverse-transcription PCR, followed by PCR.

tag: plant

value: Hybrid BAD

value: whole plant


title: Polyploid BBAADD

description:
small RNA
sequence tags
whole plant_2 months old_six plants

value: Polyploid BBAADD


title: Parent BBAA

organism: Triticum turgidum subsp. durum

tag: cultivar

value: Langdon TTR16

value: Parent BBAA


title: PSD_saline_smallRNA

data_processing: Sequences were extracted from image files using Firecrest and Bustard. The 3'adaptor sequences were trimmed from the reads, and reads 18-30 nt in length were aligned to all annotated mouse microRNAs from miRBase (www.mirbase.org; version 16) with Bowtie (bowtie-bio.sourceforge.net; version 0.12.7); only perfectly aligning reads were considered for miRNA expression level analysis. A custom Perl script was used to calculate the number of reads aligning to each specific miRNA gene.

value: Saline


title: RNA_HuR_PAR-CLIP_completeT1_repB

tag: cell line


title: Parent DD

organism: Aegilops tauschii

value: Parent DD


title: NAc_cocaine_smallRNA

source_name: Nucleus accumbens


title: DCs_0h_RNASeq

status: Public on May 12 2011

first: Brian

last: Haas

address: 7 Cambridge Center

institute: Broad Institute

description: RNA Sequencing

data_processing: reads were aligned to the mouse reference genome (mm9) using the TopHat aligner

source_name: Dendritic cells

growth_protocol: 6-8 week old female C57BL/6J mice were obtained from the Jackson Laboratories. Bone marrow dendritic cells (BMDCs) were collected from femora and tibiae and plated on non-tissue culture treated plastic dishes in RPMI medium (Gibco, Invitrogen), supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, MEM non-essential amino acids, HEPES, sodium pyruvate, B-mercaptoethanol, and GM-CSF (15 ng/uL; Peprotech). At day 5, floating CD11c+ cells were sorted on the autoMACS separator with the CD11c (N418) MicroBeads kit (Myltenyi Biotec). CD11c+ cells where re-plated at a concentration of 106 cells/ml and RNA was collected 16 hours post sorting.

extract_protocol:
Total RNA was extracted with QIAzol reagent following the miRNeasy kit's procedure (Qiagen), and sample quality was tested on a 2100 Bioanalyzer (Agilent).
We prepared the polyA+ RNA-Seq libraries using the "dUTP second strand (strand specific)" protocol as described in Levin et. A. Nature Methods, 2010, with the following modification: we fragmented RNA by incubation in 1x RNA fragmentation buffer (Affymetrix) at 80 degrees for 4 min. Libraries were analyzed on Illumina GAII system,generating ~90 million paired-end reads per sample. Average insert size (distance between two paired reads): 300 bases.

tag: age

value: 6-8 week old

tag: gender

value: female

value: Dendritic cells

tag: time after stimulation

value: 0 hours


title: Digital Genomic Footprinting assay of IMR90 Cell Line; DGF.DS13219

first: Northwest

last: REMC

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS13219
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7461
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM723024_UW.IMR90.Digital_Genomic_Footprinting.DGF.DS13219.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS13219.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of IMR90 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the IMR90 Cell Line, Library DGF.DS13219 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.7628
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 259,183,172
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4729
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.5004
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4993
POISSON_PERCENTILE: 20

**********************************************************************

ANALYSIS FILE NAME: GSM723024_UW.IMR90.Digital_Genomic_Footprinting.DGF.DS13219.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS13219.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from the IMR90 Cell Line, Library DGF.DS13219 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.7633
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: IMR90 DGF 19
BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line Digital Genomic Footprinting Library DGF.DS13219 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 259,183,172
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.4729
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.5004
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4993
POISSON_PERCENTILE: 20

**********************************************************************

source_name: IMR90 Cell Line.; DGF.DS13219

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: IMR90 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

value: Female

tag: batch

value: Digital Genomic Footprinting

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Digital Genomic Footprinting assay of Fetal Lung; DGF.DS14724

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS14724
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7409
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM723025_UW.Fetal_Lung.Digital_Genomic_Footprinting.H-23266.DGF.DS14724.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS14724.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Lung, Donor H-23266, Library DGF.DS14724 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.7631
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 288,539,741
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6616
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.6416
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9961
IROC_PERCENTILE: 20
POISSON_SCORE: 0.6651
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM723025_UW.Fetal_Lung.Digital_Genomic_Footprinting.H-23266.DGF.DS14724.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS14724.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Lung, Donor H-23266, Library DGF.DS14724 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.7636
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FL DGF 66 24
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Digital Genomic Footprinting Donor H-23266 Library DGF.DS14724 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 288,539,741
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6616
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.6416
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9961
IROC_PERCENTILE: 20
POISSON_SCORE: 0.6651
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Fetal Lung primary tissue, day 85; DGF.DS14724

value: Fetal Lung

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: day 85