title: HF/HS_14_BACWH2

description:
17164.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_CLOSCI

status: Public on Aug 20 2013

type: RNA

city: Saint Louis

first: Nathan

middle: P

last: McNulty

state: MO

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

department: Center for Genome Sciences and Systems Biology

country: USA

institute: Washington University School of Medicine

description:
17160.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

hyb_protocol: Following fragmentation and labeling, cDNA (0.9-5.1 ug) was hybridized for 16 h at 45 C on custom GeneChip SynComm1 (Synthetic Human Gut Community GeneChip, v1.0, GEO platform GPL9803). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

data_processing: A custom mask file was first created for each of the 12 species analyzed, after which species-specific Expression Console custom configuration files were prepared (MAS5 probe set summarization; scaling by all select sets specified by probe masking file) and used to execute an advanced analysis. Raw values were then exported as pivot tables, filtered for those probe sets corresponding to the species being analyzed, and passed as input data to the Cyber-T web server. In each treatment group, genes for which at least 5 of 7 samples resulted in a 'present' call for the probe set were scored as having reliably detectable gene expression.

label: biotin

molecule: total RNA

organism: [Clostridium] scindens ATCC 35704

source_name: Defined bacterial assemblage of 12 species from a gnotobiotic mouse

label_protocol: cDNA was prepared from gDNA-free RNA using random hexamer priming and Invitrogen's SuperScript II enzyme. RNA template was degraded by NaOH treatment, and cDNA was subsequently fragmented by DNase I digestion. Finally, fragmented cDNA was biotinylated using the BioArray Terminal Labeling Kit with biotin-ddUTP (Enzo, 42630). Successful biotinylation of targets was verified using a shift assay with NeutrAvidin (Pierce, 31000).

growth_protocol: Bacteria from frozen culture stocks were introduced as an artificial community into 10-12 week-old male gnotobiotic C57BL/6J mice. Cells were therefore maintained over the course of the experiment within mice until sampling occurred.

extract_protocol: Samples previously stored at -80 C were incubated in Qiagen RNAprotect Bacteria Reagent per the manufacturer's instructions, after which they were mechanically disrupted using acid-washed glass beads in a Mini-BeadBeater-8 in the presence of acid phenol:chloroform:IAA (125:24:1). Following ethanol precipitation, RNA was further purified using the Qiagen RNeasy Mini Kit and subjected to two rounds of DNase treatment. All samples were shown to be free of contaminating gDNA by PCR before RT and labeling were performed.

treatment_protocol: Immediately after collection, samples were subjected to flash-freezing in liquid nitrogen and were stored at -80 C until total community RNA could be extracted.

tag: mouse

tag: diet group

value: HF/HS


title: HF/HS_11_BACWH2

description:
17161.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides sp. WH2


title: HF/HS_12_BACWH2

description:
17162.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACWH2

description:
17156.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

value: LF/HPP


title: LF/HPP_7_BACWH2

description:
17157.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_BACWH2

description:
17160.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACWH2

description:
17159.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_CLOSPI

description:
17158.CLOSPI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Thomasclavelia spiroformis DSM 1552


title: HF/HS_10_DORLON

description:
17160.DORLON
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Dorea longicatena DSM 13814


title: LF/HPP_2_BACWH2

description:
17152.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_BACWH2

description:
17153.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_BACWH2

description:
17151.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_BACVUL

description:
17161.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Phocaeicola vulgatus ATCC 8482


title: HF/HS_10_BACVUL

description:
17160.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_BACWH2

description:
17158.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_BACVUL

description:
17164.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_BACVUL

description:
17162.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_BACVUL

description:
17163.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_BACVUL

description:
17158.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_BACUNI

description:
17164.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides uniformis ATCC 8492


title: LF/HPP_5_BACWH2

description:
17155.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_BACVUL

description:
17152.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACVUL

description:
17154.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_CLOSCI

description:
17154.CLOSCI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACUNI

description:
17159.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACVUL

description:
17159.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_BACVUL

description:
17151.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACVUL

description:
17156.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_BACUNI

description:
17162.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_BACVUL

description:
17155.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_BACVUL

description:
17153.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACWH2

description:
17154.BACWH2
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_BACUNI

description:
17163.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_BACVUL

description:
17157.BACVUL
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_BACUNI

description:
17160.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_BACUNI

description:
17161.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_BACUNI

description:
17157.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_BACUNI

description:
17155.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACUNI

description:
17154.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_BACUNI

description:
17152.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_BACTHE

description:
17152.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides thetaiotaomicron VPI-5482


title: HF/HS_8_BACUNI

description:
17158.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_BACUNI

description:
17153.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACTHE

description:
17154.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_BACTHE

description:
17164.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACUNI

description:
17156.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_BACTHE

description:
17163.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_BACTHE

description:
17162.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_BACTHE

description:
17161.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACOVA

description:
17159.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides ovatus ATCC 8483


title: HF/HS_10_BACTHE

description:
17160.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACTHE

description:
17156.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_BACTHE

description:
17153.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_BACTHE

description:
17151.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_BACTHE

description:
17155.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_11_BACOVA

description:
17161.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_BACTHE

description:
17157.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_BACUNI

description:
17151.BACUNI
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_BACTHE

description:
17158.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_BACOVA

description:
17164.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_BACOVA

description:
17160.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_BACOVA

description:
17158.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_13_BACOVA

description:
17163.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACTHE

description:
17159.BACTHE
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_12_BACOVA

description:
17162.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACOVA

description:
17156.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_BACOVA

description:
17155.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_7_BACOVA

description:
17157.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACCAC

description:
17154.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.

organism: Bacteroides caccae ATCC 43185


title: LF/HPP_3_BACOVA

description:
17153.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_6_BACCAC

description:
17156.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_14_BACCAC

description:
17164.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_3_BACCAC

description:
17153.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_5_BACCAC

description:
17155.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_2_BACOVA

description:
17152.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_8_BACCAC

description:
17158.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_4_BACOVA

description:
17154.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: Mock rep3

city: Cardiff

first: Derek

last: Blake

address: Hadyn Ellis Building, Maindy Road

department: MRC Centre for Neuropsychiatric Genetics and Genomics

country: United Kingdom

institute: Cardiff University

description:
Mock_3
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.

hyb_protocol: Toray Oligo Chip kit (Toray Industries Inc., Kamakura, Japan).

scan_protocol: Arrays were scanned at 3 different gain levels with a 3D-Gene™ Scanner 3000 and the resulting data was analysed using the Toray Extraction and 3D-Gene™ Scanner 3000 software (Toray Industries Inc).

data_processing: Hybridized probe spots with signal intensity greater than the mean intensity of plus 2 standard deviations of the background signal were considered to be valid (Flag: OK). The background average was subtracted from the signal intensity and multiplied by the normalisation factor (25 divided by the medium signal intensity of all the subtracted background data) to generate the normalised data.

organism: Homo sapiens

source_name: SH-SY5Y cell line, mock

label_protocol: Amersham Cy5 Mono-Reactive Dye (GE Healthcare).

growth_protocol: Cells cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% foetal calf serum without antibiotics.

extract_protocol: RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: SH-SY5Y cells were transfected with 10nM of siRNA (Eurofinns) or mock transfected (RNAi MAX, Invitrogen). 48hrs after the first transfection, SH-SY5Y cells were re-transfected with the same conditions and left for a further 24hrs before extracting total RNA from the cells.

tag: cell line

tag: cell type

value: neuroblastoma cell line

tag: transfection reagent

value: present

tag: sirna

tag: targeted gene


title: HF/HS_11_BACCAC

description:
17161.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: LF/HPP_1_BACCAC

description:
17151.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: TCF4 KD2 rep2

description:
KD2_2
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.

source_name: SH-SY5Y cell line, TCF4 KD2


title: HF/HS_13_BACCAC

description:
17163.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: TCF4 KD1 rep2

description:
KD1_2
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.

source_name: SH-SY5Y cell line, TCF4 KD1


title: GAPDH KD rep3

description:
GAPDHKD_3
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.

source_name: SH-SY5Y cell line, GAPDH KD

value: GAPDH


title: TCF4 KD2 rep3

description:
KD2_3
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: TCF4 KD2 rep1

description:
KD2_1
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: LF/HPP_1_BACOVA

description:
17151.BACOVA
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: Mock rep1

description:
Mock_1
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: HF/HS_12_BACCAC

description:
17162.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_9_BACCAC

description:
17159.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: HF/HS_10_BACCAC

description:
17160.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: Mock rep2

description:
Mock_2
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: TCF4 KD1 rep1

description:
KD1_1
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: LF/HPP_7_BACCAC

description:
17157.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: GAPDH KD rep2

description:
GAPDHKD_2
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: TCF4 KD1 rep3

description:
KD1_3
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: LF/HPP_2_BACCAC

description:
17152.BACCAC
Cecal contents collected from a gnotobiotic mouse 42 days after being colonized with a defined assemblage of 12 human gut bacterial species. Each mouse was fed two different diets in an oscillatory fashion, with diet switches occurring at day 14 and day 28. The 'diet group'  field indicates the diet the animal was consuming at the time of sacrifice.


title: GAPDH KD rep1

description:
GAPDHKD_1
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.


title: neonatal rat beta cells: endocrine cells from postnatal day 2-3 pancreas of male and female rats, bio rep 3

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

description: neonatal rat beta cells: endocrine cells, FACS-sorted for their high side scatter (HSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, and containing approximately 65-70% insulin+ cells, biological replicate 3, pool of 30 animals

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity and correction for mismatch hybridization using the perfect match-mismatch correction option.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Pancreatic beta cells were FACS-purified from neonatal (postnatal day 2-3)and  10-weeks old Wistar rat pancreas, and immediately snap frozen in liquid nitrogen, prior to total RNA extraction in batch, from all biological replicates.

extract_protocol: RNEasy extraction of total RNA was performed according to the manufacturer's instructions. RNA integrity verified on Bioanalyzer with minimal RIN cutoff = 8.

treatment_protocol: None, freshly isolated beta cells snap frozen in liquid nitrogen immediately after isolation

value: neonatal rat beta cells

tag: gender

value: male and female

tag: strain

value: Wistar

tag: age


title: non-endocrine neonatal islet cells from postnatal day 2-3 pancreas of male and female rats, bio rep 3

description: non-endocrine neonatal islet cells: cells co-isolated with the endocrine cells, and FACS-sorted for their low side scatter (LSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, biological replicate 3, pool of 30 animals

value: non-endocrine neonatal islet cells


title: pancreatic beta cells from 10 week-old male rats, bio rep 4

description: pancreatic beta cells FACS-purified from 10 week-old male Wister rats, biological replicate 4

value: pancreatic beta cells

value: male

value: 10 wk


title: neonatal rat beta cells: endocrine cells from postnatal day 2-3 pancreas of male and female rats, bio rep 2

description: neonatal rat beta cells: endocrine cells, FACS-sorted for their high side scatter (HSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, and containing approximately 65-70% insulin+ cells, biological replicate 2, pool of 30 animals


title: HFF-RH-JSR-2

city: Cambridge

first: Ninghan

last: Yang

state: Massachusetts

address: 77 Massachusetts Ave, 68-270

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm. Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data was analyzed with Robust Multi-array Average (RMA) using default Affymetrix settings in Expression Console version 1.1. The log2 transformed values obtained were then set to minimum of 6.5 or higher.

label: Biotin

source_name: HFF + RH-JSR, 24 hours

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: Human foreskin fibroblasts were grown in 6 well plates at 37C, 5% CO2 confluency. Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Parasite strains were syringe lysed, washed once with PBS, and added to HFF monolayers for 24 hours.

tag: tissue

value: Human foreskin fibroblast

tag: treatment

value: infected with RH-JSR for 24 hours


title: non-endocrine neonatal islet cells from postnatal day 2-3 pancreas of male and female rats, bio rep 1

description: non-endocrine neonatal islet cells: cells co-isolated with the endocrine cells, and FACS-sorted for their low side scatter (LSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, biological replicate 1, pool of 30 animals


title: Lovo_cells_neg_rep1

city: Shanghai

first: Jie

last: Xu

address: Shandong Rd 145

department: Shanghai Renji Hospital

country: China

institute: Shanghai Institute for Digestive Diseases

hyb_protocol: An hybridization cocktail was prepared with 15 μg of cRNA (0.5 μg/μl) and hybridized to HG U133 Plus 2.0 microarrays for 16 h at 45°C in an Affymetrix Hybridization Chamber 640. Each cRNA sample was spiked with standard prokaryotic hybridization controls for quality monitoring.

scan_protocol: Hybridized microarrays were stained with streptavidin phycoerythrin and washed with a solution containing biotinylated anti-streptavidin antibodies using the Affymetrix Fluidics Station 450. Finally, the stained and washed microarrays were scanned with the Affymetrix Scanner 3000.

data_processing: The Affymetrix software package was used to transform raw microarray image files to digitized format. As for the Discovery set above, gene expression levels for the validation data set were calculated using MAS 5.0 (Affymetrix) for quality control purposes and with the RMA normalization algorithm for expression data.

source_name: Lovo cells transfected with pcDNA3.1 vector, replication 1

label_protocol: Biotin-labeled cRNA was prepared using 5 μg (1.0 μg/μl) total RNA (∼1 μg mRNA) with the “One-Cycle cDNA” kit [incorporating a T7-oligo (dT) primer] and the GeneChip IVT labeling kit. In vitro transcribed cRNA was fragmented (20 μg) and analyzed for quality control purposes by spectrophotometry and gel electrophoresis prior to hybridization.

growth_protocol: Lovo cells were maintained at 37 °C in an atmosphere of 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, penicillin and streptomycin (Invitrogen) in 25-ml culture flasks.

extract_protocol: Forth-eight hours after treatment, total RNA from each sample was isolated and quantified.Integrity and concentration of RNA was assessed after RNA extraction and prior to sample processing.

treatment_protocol: Lovo cells were transfected ArhGAP30 or control pcDNA3.1 vector.

value: Lovo


title: Lovo_cells_ArhGAP30_rep1

source_name: Lovo cells overexpressing ArhGAP30, replication 1


title: pancreatic beta cells from 10 week-old male rats, bio rep 5

description: pancreatic beta cells FACS-purified from 10 week-old male Wister rats, biological replicate 5


title: pancreatic beta cells from 10 week-old male rats, bio rep 2

description: pancreatic beta cells FACS-purified from 10 week-old male Wister rats, biological replicate 2


title: HFF-RH-JSR-1


title: Lovo_cells_neg_rep3

source_name: Lovo cells transfected with pcDNA3.1 vector, replication 3


title: HFF-RH-JSR-3


title: Lovo_cells_ArhGAP30_rep2

source_name: Lovo cells overexpressing ArhGAP30, replication 2


title: HFF-RH-ERP-3

source_name: HFF + RH-ERP, 24 hours

value: infected with RH-ERP for 24 hours


title: non-endocrine neonatal islet cells from postnatal day 2-3 pancreas of male and female rats, bio rep 2

description: non-endocrine neonatal islet cells: cells co-isolated with the endocrine cells, and FACS-sorted for their low side scatter (LSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, biological replicate 2, pool of 30 animals


title: HFF-GT1-3

source_name: HFF + GT1, 24 hours

value: infected with GT1 for 24 hours


title: HFF-GT1-2


title: neonatal rat beta cells: endocrine cells from postnatal day 2-3 pancreas of male and female rats, bio rep 1

description: neonatal rat beta cells: endocrine cells, FACS-sorted for their high side scatter (HSSC), from postnatal day 2-3 pancreas of male and female Wistar rats, and containing approximately 65-70% insulin+ cells, biological replicate 1, pool of 30 animals


title: Lovo_cells_neg_rep2

source_name: Lovo cells transfected with pcDNA3.1 vector, replication 2


title: pancreatic beta cells from 10 week-old male rats, bio rep 3

description: pancreatic beta cells FACS-purified from 10 week-old male Wister rats, biological replicate 3


title: pancreatic beta cells from 10 week-old male rats, bio rep 1

description: pancreatic beta cells FACS-purified from 10 week-old male Wister rats, biological replicate 1


title: Lovo_cells_ArhGAP30_rep3

source_name: Lovo cells overexpressing ArhGAP30, replication 3


title: F191G C

city: Baltimore

first: Russell

last: Williams

state: MD

address: 1550 Orleans St

department: Radiation Oncology

institute: Johns Hopkins University

description: total RNA from MyCaP culture

hyb_protocol: Affymetrix Mouse Exon 1.0 arrays, according to manufacturer's instructions, washed with Fluidics 450

scan_protocol: Affymetrix M10 scanner, using software Affymetrix Genechip Command Console v2.0.0.1029

data_processing: All analysis performed in R. Data normalized using RMA from the limma package, and further normalization for Twist1-expression was carried out. For R script used for analysis, see supplemental data (Gajula et al., 2013)

organism: Mus musculus

source_name: MycCap prostate cancer cells

label_protocol: Affymetrix WT Labeling kit, according to manufacturer's instructions

growth_protocol: after transfection and selection, cells were grown to confluence and harvested

extract_protocol: Trizol RNA purification

tag: batch

value: B

tag: knock-in

value: MycCap prostate cancer cells


title: HFF-RH-ERP-1


title: VEC C

description: total RNA from MyCaP culture

value: VEC


title: DQD C

description: total RNA from MyCaP culture

value: Twist-DQD


title: HFF-RH-ERP-2


title: WT C

description: total RNA from MyCaP culture

value: Twist-WT


title: AQA C

description: total RNA from MyCaP culture

value: Twist-AQA


title: SW480 cells with hiNOS overexpression

city: Pittsburgh

first: David

last: Geller

state: Pennsylvania

address: 200 Lothrop St. BST W1507

department: Surgery

institute: University of Pittsburgh

description: Changes in expression of Wnt signaling pathway gene with overexpression of hiNOS in the SW480iNOS-1 cell line

hyb_protocol: 1ug of cRNA was used for hybridization with the Genearray. Incubation was performed for 12hrs at 60C shaking at 500rpm.

scan_protocol: Arrays were visualized by autoradiography, and hybridization signals were scanned and analyzed for density in GEArray Expression Analysis Suite 2.0. The arrays were exposed at different time points starting for 1 min and maximum of 10 min to have the largest possible dynamic range for the individual signals and images acquire using x-ray film. X-ray film were scanned and save as TIFF file format.

data_processing:
The raw data were re-scaled to account for the differences in individual hybridization intensities and ratios of iNOS vs. empty vector control  were calculated after values were normalizing for each gene.
The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, and B-actin.

label: Biotin UTP

growth_protocol: Cells were sorted with GFP and grown for several weeks. GFP expression cells used for RNA extraction using Trizol (Invitrogen).

extract_protocol: Total RNA was isolated by Trizol (Invitrogen) .  1ug of total RNA was reverse-transcribed using oligo-dT primers (Superarray) and reverse transcriptase (Superarray) to perform cDNA. Then cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Roche Molecular Biochemicals) and RNA polymerase according to the instructions for the Gene

treatment_protocol: SW480 stable cells were used for RNA extraction

tag: genotype/variation

value: hiNOS overexpression and GFP


title: SW480 empty vector control (GFP)

description: SW480GFP-1 cells display basal levels of Wnt signaling pathway genes

label_protocol: cRNA synthesis was performed using the total cDNA reaction in the presence of 10 mM of Biotinylated-UTP (Roche Molecular Biochemicals) and RNA polymerase according to the instructions for the Gene

value: only GFP


title: Donor4_neg_mono

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, washing and scanning were performed according to the manufacturer's instructions.

scan_protocol: BeadArrays were  scanned using an Illumina BeadArray Reader. Scanner settings were set at a default for DirectHyb.

data_processing: Raw data were extracted using Illumina Genometudio Gene Expression Module v1.1. The data were transformed using variance stabilizing transformation (vst) and normalised using robust spline normalization with Bioconductor package lumi in R. Gene filtering was applied to retain only genes with IQR>0.7 (measure of the spread of the middle 50% of the intensity scores for each gene > 0.7 on a log base 2 scale).

label_protocol: Total RNA (50-100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies Inc., Austin, TX) and one round of amplification.  The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini (>1 million cells) or micro (≤1 million cells) kit in accordance with the prescribed protocol provided with the kits. Quality control was performed with Agilent 2100 Bioanalyzer.

tag: isolation method

value: Negative selection

value: primary monocytes


title: Donor2_neg_CD8

value: primary CD8+ T cells


title: WT B

description: total RNA from MyCaP culture

value: A


title: VEC A

description: total RNA from MyCaP culture


title: Donor5_pos_CD4

value: Positive selection

value: primary CD4+ T cells


title: AQA B

description: total RNA from MyCaP culture


title: DQD B

description: total RNA from MyCaP culture


title: Donor3_neg_B

value: primary B cells


title: DQD A

description: total RNA from MyCaP culture


title: Donor1_FACS_CD8

value: FACS


title: AQA A

description: total RNA from MyCaP culture


title: F191G B

description: total RNA from MyCaP culture


title: Donor3_pos_mono


title: WT A

description: total RNA from MyCaP culture


title: F191G A

description: total RNA from MyCaP culture


title: Fetus liver Group1-Control (Cy3) x Treatment FR (Cy5)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description:
Dye-swap (Cy3/Cy5) of 6 wks ME vs IE rat hippocampi Pool 1
Mouse Fetus Liver N=3

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 9.5.3.1

source_name: Liver Group 1 Control (normal diet)

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: C57BL/6J mice were purchased from Japan SLC Co. Ltd. (Hamamatsu, Japan).  The animals were housed at the Animal Institution in Showa University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Control (normal diet), Treatment (food restriction diet)

source_name: Liver Group 1 Treatment (food restriction diet)


title: Donor1_neg_CD4


title: Fetus liver Group2-Control (Cy5) x Treatment FR (Cy3)

description:
Dye-swap (Cy5/Cy3) of 6 wks ME vs IE rat hippocampi Pool 2
Mouse Fetus Liver N=3

source_name: Liver Group 2 Treatment (food restriction diet)

source_name: Liver Group 2 Control (normal diet)


title: Fetus liver Group2-Control (Cy3) x Treatment FR (Cy5)


title: Donor4_pos_CD8


title: Donor2_FACS_CD4


title: Donor1_neg_mono


title: Donor5_pos_B


title: Donor5_FACS_CD8


title: Donor3_pos_B


title: Fetus liver Pool 1-Control (Cy5) x Treatment FR (Cy3)

description:
Dye-swap (Cy5/Cy3) of 6 wks ME vs IE rat hippocampi Pool 2
Mouse Fetus Liver N=6

source_name: Liver Pool 1 Treatment (food restriction diet)

source_name: Liver Pool 1 Control (normal diet)


title: Donor2_FACS_B


title: VEC B

description: total RNA from MyCaP culture


title: Fetus liver Group1-Control (Cy5) x Treatment FR (Cy3)


title: Donor5_neg_CD4


title: Mother liver Pool 1-Control (Cy3) x Treatment FR (Cy5)

description:
Dye-swap (Cy3/Cy5) of 6 wks ME vs IE rat hippocampi Pool 1
Mouse Mother Liver N=6

source_name: Liver Pool1 Control (normal diet)

source_name: Liver pool 1 Treatment (food restriction diet)


title: Mother liver Pool 1-Control (Cy5) x Treatment FR (Cy3)

description:
Dye-swap (Cy5/Cy3) of 6 wks ME vs IE rat hippocampi Pool 2
Mouse Mother Liver N=6


title: Fetus liver Pool 1-Control (Cy3) x Treatment FR (Cy5)

description:
Dye-swap (Cy3/Cy5) of 6 wks ME vs IE rat hippocampi Pool 1
Mouse Fetus Liver N=6


title: 10mg/kg/day treatment, biological rep3

city: Beijing

first: Bin

last: Wan

address: 18 shuangqing road, Haidian District

institute: Research centre for eco-environmental sciences, CAS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome Array 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings with background correction on the PM values, quantile normalization across all the chips in the experiment, and Log2 transformation.

source_name: Mouse spleen with PFOS treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 6-8 week old female balb/c mice were cultured in pathogen free condition according to animal care requriments in Peking university

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Spleens were removed from mice, rinsed with PBS and placed on ice in the Trizol solution (GibcoBRL).

value: Balb/c

value: female

value: 6-8 week

tag: exposed to

value: 10mg/kg body weight PFOS per day for 3 wks

value: spleen


title: Donor2_pos_mono


title: Donor1_pos_CD8


title: Donor2_neg_B


title: Donor4_neg_B


title: Donor3_FACS_CD4


title: control, biological rep3

source_name: Mouse spleen without treatment


title: Donor4_pos_CD4


title: Donor5_FACS_CD4


title: Donor2_FACS_mono


title: Donor5_pos_CD8


title: Donor3_neg_mono


title: Donor4_neg_CD8


title: Donor1_FACS_B


title: control, biological rep2


title: 10mg/kg/day treatment, biological rep1


title: control, biological rep1


title: 10mg/kg/day treatment, biological rep2


title: Donor3_FACS_CD8


title: Donor4_FACS_CD8


title: Donor5_neg_mono


title: Donor3_pos_CD4


title: Donor3_neg_CD8


title: Donor2_neg_CD4


title: Donor1_pos_mono


title: Donor3_pos_CD8


title: Donor1_FACS_CD4


title: Donor5_pos_mono


title: Donor2_FACS_CD8


title: Donor2_pos_CD4


title: Donor4_FACS_CD4


title: Donor5_neg_B


title: Donor2_pos_CD8


title: Donor3_FACS_B


title: Bound fraction Sleep dep animal, biological rep 11

city: Madison

first: Michele

last: Bellesi

state: WI

address: 6001 Research Park Blvd

institute: University Wisconsin-Madison

description: Expression data from the bound fraction of sleep deprived mice

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays (n=36, one chip per mouse) following Affymetrix standard protocol

scan_protocol: Samples were scanned using the GC3000 7G scanner (Affymetrix)

data_processing: For both IP and UB replicates, GeneChip Cel files were imported into Bioconductor, data were converted to log2 scale, and transcripts called “absent” in all chips were not used for analysis. Data were normalized within each behavioral state group using Robust Multi-array Average (RMA, (Irizarry et al., 2003)).

source_name: Bound fraction Sleep deprived animal

label_protocol: Five µg of amplified material was then fragmented, biotin labeled with the Encore Biotin Module (Nugen, #4200)

extract_protocol: RNA, which represents the mRNA immunoprecipitated from the targeted cell type (B fraction), was purified following the Nanoprep protocol including on column DNase digestion. The RNA from the supernatant (unbound fraction; UB) was isolated using the RNeasy Mini kit (Qiagen).

treatment_protocol:
sleeping mice were killed during the light phase (at ~3-5 pm), at the end of a long period of sleep (> 45 min, interrupted by periods of wake of < 4 min), and after spending at least 75% of the previous 6–7 h asleep.
awake mice were killed during the dark period (at ~3-5 am) at the end of a long period of wake (> 1 h, interrupted by periods of sleep of < 5 min), and after spending at least 70% of the previous 6–7 h awake.
sleep deprived mice were spontaneously awake during most of the dark phase and then maintained awake during the light period for 4h by exposure to novel objects.

value: brain

value: Cnp – eGFP-L10a


title: Donor4_pos_B


title: Bound fraction Waking animal, biological rep 6

description: Expression data from the bound fraction of waking mice

source_name: Bound fraction Waking animal


title: Bound fraction Sleep dep animal, biological rep 9


title: Donor4_pos_mono


title: Donor4_neg_CD4


title: Bound fraction Sleep dep animal, biological rep 10


title: Ozone lifetime Takanari Seed 4

description: Dye-swap (Cy3/Cy5) of Ozone lifetime Pooled Takanari Seed 4

hyb_protocol: Agilent: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent Microarray scanner G2565BA

data_processing: Agilent Feature Extraction software (version 9.5.3.1)

organism: Oryza sativa

label_protocol: Manual: Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown in controlled greenhouse, small open top chamber (sOTC)

extract_protocol: Modified CTAB protocol plus QIAGEN, Rneasy Mini

treatment_protocol: control: filtered air, non-filtered air, O3, 37.2 ppb

tag: cultivar

value: Takanari

tag: developmental stage

value: mature plant

source_name: Control_filtered air


title: Bound fraction Waking animal, biological rep 4


title: Bound fraction Waking animal, biological rep 5


title: Bound fraction Sleep dep animal, biological rep 8


title: Bound fraction Sleep dep animal, biological rep 7


title: Ozone lifetime Takanari Seed 3

description: Dye-swap (Cy3/Cy5) of Ozone lifetime Pooled Takanari Seed 3


title: Donor3_neg_CD4

value: Negative selection


title: Donor2_pos_B


title: Bound fraction Waking animal, biological rep 3


title: Bound fraction Sleep dep animal, biological rep 6


title: Ozone lifetime Koshihikari Seed 2

description: Dye-swap (Cy3/Cy5) of Ozone lifetime Pooled Koshihikari Seed 2

value: Koshihikari


title: Bound fraction Waking animal, biological rep 1


title: Donor5_neg_CD8

value: primary CD8+ T cells


title: Bound fraction Sleep animal, biological rep 6

description: Expression data from the bound fraction of sleeping mice

source_name: Bound fraction Sleep animal


title: Nonolypotic TI, APCmin/+ (12wks), biological rep3

city: Buffalo

first: Allen

middle: Yicheng

last: Chung

state: NY

address: 3435 Main Street

department: Microbiology and Immunology

institute: University at Buffalo

description: Intestinal gene expression data from APCmin/+ nonpolypotic terminal ileum

hyb_protocol: Hydridization, washing and staining were completed using the Affymetrix Genechip Hybridization, Wash and Stain Kit. Following fragmentation, 12.5 ug aliquots of cRNA were hybridized for 16 hr at 45C on Affymetrix MOuse Genome 430A 2.0 Arrays. GeneChips were washed and stained using Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Array Scanner 3000. Affymetrix AGCC Software and Expression Console were used for image acquisition.

data_processing: The raw data were first preprocessed with RMA method using Afffymetrix Expression Console. Data were further normalized by scaling the individual log-tranformed signal intensities so that each sample has comparable lower quartile, median and upper quartile values. Then probe-set-level signals are collaped to gene-level signals by averaging the intensities of the probe sets corresponding to the same gene symbol. The data transformation are performed using an in-house script written in MATLAB.

source_name: TI from 12 week old APCmin/+ Nonpolypotic sections

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Genechip 3' IVT protocol from 100 ng of total RNA (MAQC Consortium et. al., 2006).

growth_protocol: Ex vivo derived whole intestinal sections from terminal ileum

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini Kit, as per the manufacturer's instructions. On-column DNase digestion with Qiagen DNase was applied for 25 minutes during extraction.

treatment_protocol: Intestinal segments were washed with ice cold PBS and minced with a scapel prior to RNA extraction

value: terminal ileum

value: 12 week-old

tag: genotype

value: APCmin/+

tag: polyposis

value: Nonpolypotic


title: Bound fraction Sleep animal, biological rep 5


title: Ozone lifetime Koshihikari Seed 1

description: Dye-swap (Cy3/Cy5) of Ozone lifetime Pooled Koshihikari Seed 1


title: Nonolypotic TI, APCmin/+ (12wks), biological rep4


title: Bound fraction Waking animal, biological rep 2


title: Polypotic TI, APCmin/+ (12wks), biological rep4

description: Intestinal gene expression data from APCmin/+ polypotic terminal ileum

source_name: TI from 12 week old APCmin/+ polypotic sections

value: Polypotic


title: Nonpolyptic TI, Wildtype Littermate(12wks), biological rep2

description: Intestinal gene expression data from wildtype B6 terminal ileum

source_name: TI from 12 week old littermate wildtpe B6 nonpolypitc sections

value: WT B6


title: Bound fraction Sleep animal, biological rep 4


title: Donor1_pos_CD4

value: Positive selection

tag: cell type

value: primary CD4+ T cells


title: Bound fraction Sleep animal, biological rep 2


title: Bound fraction Sleep animal, biological rep 3


title: Bound fraction Sleep animal, biological rep 1


title: Nonolypotic TI, APCmin/+ (12wks), biological rep2


title: Polypotic TI, APCmin/+ (12wks), biological rep2


title: Polypotic TI, APCmin/+ (12wks), biological rep3


title: Nonolypotic TI, APCmin/+ (12wks), biological rep1


title: Polypotic TI, APCmin/+ (12wks), biological rep1


title: WT HFSCs, biological rep2

city: Boulder

first: Zhaojie

last: Zhang

state: CO

address: 2300 Arapahoe Ave

institute: University of Colorado at Boulder

hyb_protocol: standard Affymetrix protocol for Mouse 430 2.0 array

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor with RMA as the background adjustment and normalization method.

source_name: WT HFSCs

label_protocol: standard Affymetrix protocol from 0.5 ug total RNA

growth_protocol: Mice were housed in the Mouse Facility under standard conditions.

extract_protocol: Cells sortd with FACS were put into Trizol and RNA extraction was performed according to the Trizol manufacturer's instructions.

treatment_protocol: We use two pairs of biological duplicates to perform the microarray analysis from the epidermal samples harvested from K14-rtTA/TRE-miR-203/K14-H2BGFP (DP) and TRE-miR-203/K14-H2BGFP (SP) littermates at P4, 24h after the Dox injection.

tag: strain background

value: WT

value: skin

value: hair follicle stem cells (HFSCs)


title: miR-205 KO HFSCs, biological rep1

source_name: miR-205 KO HFSCs

value: miR-205 KO


title: miR-205 KO HFSCs, biological rep2


title: Nonpolyptic TI, Wildtype Littermate(12wks), biological rep1

description: Intestinal gene expression data from wildtype B6 nonpolypotic terminal ileum


title: WT HFSCs, biological rep1


title: HCT116 (p53-/-) p53-R273C

status: Public on Aug 19 2013

city: Singapore

first: Bei

last: Wang

address: 8A Biomedical Grove, #03-06, Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) in 45ºC hybridization oven at 60rpm for 18 hours.

scan_protocol: After washing and staining of hybridized arrays with an Affymetrix Fluidics Station, arrays were scanned on Gene Array Scanner 2500 (Affymetrix) to capture the raw probe signal intensities in CEL files.

data_processing:
Background subtraction, quantile normalization, and summarizing probe sets from Affymetrix expression microarrays raw CEL files were done with Affymetrix Power Tools (APT) software.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-stv2.  na30.hg19.probeset.csv

label: TdT

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-R273C vector (24h)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the Ambion® WT Expression Kit and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HCT116 (p53-/-) cell lines were grown in DMEM supplemented with 10% fetal bovine serum and cultured at 37ºC incubator.

extract_protocol: RNA was isolated from transfected cells post 24 hours of transfection with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: HCT116 (p53-/-) cell lines were transiently transfected with pcDNA3.1 control plasmid, pCMV-p53WT, or pCMV-p53-mutants (R175H, C176F, G245D, R273C, R280T, and R282W) with Lipofectamine 2000 (Life Technologies) according to standard protocol.

tag: cell line

value: colorectal cancer cells


title: HCT116 (p53-/-) p53-G245D

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-G245D vector (24h)


title: HCT116 (p53-/-) p53-C176F

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-C176Fvector (24h)


title: Wild-TypeControl_1

type: genomic

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.

molecule: genomic DNA

source_name: Bone marrow CD41+ cells (MspI gDNA)

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: Bone marrow CD41+ cells

source_name: Bone marrow CD41+ cells (HpaII gDNA)


title: HCT116 (p53-/-) p53-R282W

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-R282W vector (24h)


title: HCT116 (p53-/-) p53-R280T

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-R280T vector (24h)


title: Wild-TypeControl_2


title: Spleen, C57BL/6J  mouse, males 5 wks

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Microbiology

country: Poland

institute: Gdansk University of Technology

description: Genomic DNA methylation profile in the spleen tissue of the C57BL/6J mouse

hyb_protocol: The combined test and input DNA samples were suspended in hybridization buffer (Roche, cat. no. 05583683001) cohybridized onto Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Arrays for 20 hr at 42°C, following washing with Nimblegen Wash Kit (Roche cat. no. 05584507001).

scan_protocol: The image was acquisited with MS200 Scanner (Roche, NimbleGen) at 2 µm resolution by using high-sensitivity and autogain settings.

data_processing: The data from scanned images were extracted and processed with DEVA v. 1.0.2 (Roche, Nimblegen) using default parameters. Data processing included obtaining log2 ratios, P-scores and peak identification. Log2 ratios represent the ratios of the immunoprecipitated DNA signal to the input DNA signal. The mean log2 ratios were calculated using a Tukey biweight mean. P-scores were calculated from log2 ratios by performing sliding-window (750 bp) Kolmogorov-Smirnov (KS) test around each probe applied to determine -log10 p-value from the windowed KS test around that probe. The methylation peaks were obtained by merging consecutive probes with P scores over the assumed cut-off (default 2.0) with maximum 500 bp spacing and minimum of two probes per peak.

source_name: MeDIP enriched genomic DNA

label_protocol: DNA labeling and hybridization was performed according to NimbleGen’s protocol with our modifications. The immunoprecipitated CpG methylated DNA (test) and the untreated, sonicated DNA (input control) were labeled by using the random priming with the Nimblegen Dual-Color DNA Labeling kit (Roche-Nimblegen, cat. No. 06370250001) with fluorescent dyes Cy3 and Cy5, respectively.

extract_protocol: Tissue samples (hearts, livers, spleens) from 5-week-old males of MRL/MpJ (stock #000486) and C57BL6/J (stock #000664) murine strains were purchased from the Jackson Laboratory. Genomic DNA was isolated using DNeasy Blood&Tissue Kit (QIAGEN).

value: spleen

source_name: input DNA


title: Ts1Rhr_3


title: Caco-2 Without Bacteria Replicate 6

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 6 of 6.

hyb_protocol: The labelled samples were hybridized onto Agilent Technologies 44k whole human genome oligonucleotide arrays (G4112A) according to the manufacturer’s instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies).

scan_protocol: The microarray slides were scanned using a DNA Microarray Scanner G2565CA (Agilent Technologies) according to the manufacturer’s instructions.

data_processing: Microarray data was processed using limma package in R 2.15.1.  Loess within array normalisation and Aquantile between array normalisation was applied, without background correction.

source_name: Caco-2 cell line co-cultured in an apical anaerobic environment with bacterial treatment.

label_protocol: The RNA samples were amplified and labeled with either cyanine-3 or cyanine-5 labeled CTP dye using the Agilent Quick-Amp Labeling Kit (5190-0424) as per the manufacturer's instructions (Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Technologies).

growth_protocol: Caco-2 cells were cultured in Transwell inserts in Medium 199 (M199) containing 10% (v/v) fetal bovine serum, 1% (v/v) nonessential amino acids (NEAA; 100x solution) and 1% Penicillin-Streptomycin (10,000 U penicillin G sodium salt and 10,000 mg streptomycin sulphate in 0.85% (v/v) saline) at 37°C in 5% CO₂.

extract_protocol: RNAprotect Cell Reagent (Qiagen) was added at a volume of approximately nine times the volume of the apical media to lyse the Caco-2 cells and stabilize the RNA. Total RNA was extracted from the Caco-2 cells using an RNeasy mini plus kit (Qiagen) as per the manufacturer’s protocol.

treatment_protocol: After 14 days the inserts were transfered to a custom built co-culture chamber placed inside an anaerobic workstation, thus exposing the Caco-2 cells to an anaerobic environement (10% CO₂, 10% H₂ in N₂) on the apical side, while maintaining an aerobic basal side (apical anaerobic conditions). The Caco-2 cells were co-cultured with  Faecalibacterium prausnitzii DSM17677, Lactobacilus rhamnosus HN001, UV-killed F. prausnitzii, or no bacteria in the apical side for four hours. Bacteria were added at a multiplicity of infection of 100.

tag: culture environement

value: 37°C; 10% H₂ 10% CO₂ in N₂

tag: treatment (bacteria)

value: No bacteria

source_name: Caco-2 cells, untreated, cultured under conventional cell culture conditions.

tag: culture conditions

value: 37°C; 5% CO₂


title: Heart, C57BL/6J  mouse, males 5 wks

description: Genomic DNA methylation profile in the heart tissue of the C57BL/6J mouse

tag: strain

tag: tissue

value: heart


title: Heart, MRL/MpJ mouse, males 5 wks

description: Genomic DNA methylation profile in the heart tissue of the MRL/MpJ mouse

value: MRL/MpJ


title: Liver, MRL/MpJ mouse males 5 wks

description: Genomic DNA methylation profile in the liver tissue of the MRL/MpJ mouse

value: liver


title: Caco-2 With  F. prausnitzii Replicate 5

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 5 of 6.

value: F. prausnitzii


title: Caco-2 With  UV killed F. prausnistzii Replicate 3

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 3 of 6.

value: UV killed F. prausnitzii


title: Ts1Rhr_2


title: Liver, C57BL/6J  mouse, males 5 wks

description: Genomic DNA methylation profile in the liver tissue of the C57BL/6J mouse


title: Spleen, MRL/MpJ mouse males 5 wks

description: Genomic DNA methylation profile in the spleen tissue of the MRL/MpJ mouse


title: Ts1Rhr_1


title: non-DS_AMKL_8

source_name: Non-Down syndrome AMKL blasts (MspI gDNA)

value: Non-Down syndrome AMKL blasts

source_name: Non-Down syndrome AMKL blasts (HpaII gDNA)


title: HCT116 (p53-/-) p53-R175H

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53-R175H vector (24h)


title: Caco-2 With  L. rhamnosus Replicate 2

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 2 of 6.

value: L. rhamnosus


title: DS-AMKL_7

source_name: Down syndrome AMKL blasts (MspI gDNA)

value: Down syndrome AMKL blasts

source_name: Down syndrome AMKL blasts (HpaII gDNA)


title: HCT116 (p53-/-) p53-Wildtype

source_name: HCT116 (p53-/-) cell line transiently transfected with pCMV-p53WT vector (24h)


title: Wild-TypeControl_3


title: Control_Fetal_liver_4

description: FL-MNC-H

source_name: Human fetal liver mononuclear cells from normal controls (MspI gDNA)

source_name: Human fetal liver mononuclear cells from normal controls (HpaII gDNA)


title: DS-TMD_6

source_name: Down syndrome TMD blasts (MspI gDNA)

value: Down syndrome TMD blasts

source_name: Down syndrome TMD blasts (HpaII gDNA)


title: non-DS_AMKL_7


title: DS-TMD_5


title: Control_Fetal_liver_3

description: FL-MNC-G

value: Human fetal liver mononuclear cells from normal controls


title: Control_Fetal_liver_2

description: FL-MNC-F


title: HCT116 (p53-/-) pcDNA3.1

source_name: HCT116 (p53-/-) cell line transiently transfected with pcDNA3.1 control vector (24h)


title: Caco-2 With  UV killed F. prausnistzii Replicate 2

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 2 of 6.


title: Caco-2 With  UV killed F. prausnistzii Replicate 4

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 4 of 6.


title: Caco-2 With  F. prausnitzii Replicate 2

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 2 of 6.


title: non-DS_AMKL_3


title: Caco-2 With  L. rhamnosus Replicate 5

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 5 of 6.


title: Caco-2 With  F. prausnitzii Replicate 1

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 1 of 6.


title: non-DS_AMKL_5


title: non-DS_AMKL_6


title: DS-TMD_4


title: DS-TMD_1


title: non-DS_AMKL_2


title: DS-TMD_2


title: Control_Fetal_liver_1

description: FL-MNC-E


title: Caco-2 Without Bacteria Replicate 1

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 1 of 6.


title: Caco-2 Without Bacteria Replicate 4

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 4 of 6.


title: DS-TMD_3


title: non-DS_AMKL_1


title: Caco-2 With  L. rhamnosus Replicate 4

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 4 of 6.


title: DS-AMKL_2


title: DS-AMKL_4


title: DS-AMKL_1


title: Normal_CD34+_8

source_name: Normal bone marrow CD34+ cells (MspI gDNA)

value: Normal bone marrow CD34+ cells

source_name: Normal bone marrow CD34+ cells (HpaII gDNA)


title: DS-AMKL_3


title: DS-AMKL_5


title: Caco-2 With  F. prausnitzii Replicate 3

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 3 of 6.


title: Caco-2 Without Bacteria Replicate 3

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 3 of 6.


title: Normal_CD34+_7


title: DS-AMKL_6


title: Normal_CD34+_5


title: Normal_CD34+_4


title: Normal_CD34+_6


title: Caco-2 With  L. rhamnosus Replicate 6

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 6 of 6.


title: Caco-2 With  UV killed F. prausnistzii Replicate 5

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 5 of 6.


title: Normal_CD34+_3


title: Normal_CD34+_2


title: Normal_CD34+_1


title: H1125_WM (dataset 4)

city: Oslo

middle: George

last: Murrell

address: Sognsvannsveien 20

department: Institute for Surgical Research

country: Norway

institute: Oslo University Hospital

description: SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R.

source_name: white matter, stem cells, adherent

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: Adherent cells.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: male

tag: age

value: brain white matter

value: stem cells

tag: growth type

value: adherent

tag: passage


title: H0991_GM (dataset 4)

description: SAMPLE 11

source_name: grey matter, stem cells, adherent

value: female

value: brain grey matter


title: Caco-2 With  F. prausnitzii Replicate 6

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 6 of 6.

source_name: Caco-2 cell line co-cultured in an apical anaerobic environment with bacterial treatment.

value: 37°C; 10% H₂ 10% CO₂ in N₂

value: 37°C; 5% CO₂


title: H0980_WM (dataset 4)

description: SAMPLE 7


title: H0938_HPC (dataset 4)

description: SAMPLE 5

source_name: hippocampus, stem cells, adherent

value: hippocampus


title: T21_Fetal_liver_4

description: FL-MNC-D

source_name: Human fetal liver mononuclear cells from Down syndrome (MspI gDNA)

source_name: Human fetal liver mononuclear cells from Down syndrome (HpaII gDNA)


title: non-DS_AMKL_4

source_name: Non-Down syndrome AMKL blasts (MspI gDNA)

source_name: Non-Down syndrome AMKL blasts (HpaII gDNA)


title: T21_Fetal_liver_1

description: FL-MNC-A

value: Human fetal liver mononuclear cells from Down syndrome


title: Caco-2 Without Bacteria Replicate 2

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 2 of 6.

value: No bacteria

source_name: Caco-2 cells, untreated, cultured under conventional cell culture conditions.


title: H0980_HPC (dataset 4)

description: SAMPLE 4


title: Caco-2 With  UV killed F. prausnistzii Replicate 6

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 6 of 6.

value: UV killed F. prausnitzii


title: Caco-2 Without Bacteria Replicate 5

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours without bacteria. Biological replicate 5 of 6.


title: H0938_WM (dataset 4)

description: SAMPLE 8


title: H0980_GM (dataset 4)

description: SAMPLE 10


title: H0995_HPC (dataset 4)

description: SAMPLE 6


title: H1125_GM (dataset 4)

description: SAMPLE 12


title: Caco-2 With  L. rhamnosus Replicate 1

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 1 of 6.

value: L. rhamnosus


title: T21_Fetal_liver_3

description: FL-MNC-C


title: H0938_SVZ (dataset 4)

description: SAMPLE 2

source_name: subventricular zone, stem cells, adherent

value: subventricular zone


title: Caco-2 With  L. rhamnosus Replicate 3

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with L. rhamnosus. Biological replicate 3 of 6.


title: H0980_SVZ (dataset 4)

description: SAMPLE 1


title: T1028 sphere (dataset 3)

description: SAMPLE 12

source_name: glioblastoma, stem cells, neurospheres

growth_protocol: Adherent cells or as neurospheres.

value: glioblastoma

value: neurospheres


title: Caco-2 With  UV killed F. prausnistzii Replicate 1

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with UV killed F. prausnistzii. Biological replicate 1 of 6.


title: Caco-2 With  F. prausnitzii Replicate 4

description: Caco-2 cells co-cultured in an apical anaerobic environment for four hours with F. prausnitzii. Biological replicate 4 of 6.

value: F. prausnitzii


title: T21_Fetal_liver_2

description: FL-MNC-B


title: H1125_SVZ (dataset 4)

description: SAMPLE 3

value: male


title: T1008 sphere (dataset 3)

description: SAMPLE 10


title: T1028 adh (dataset 3)

description: SAMPLE 6

source_name: glioblastoma, stem cells, adherent


title: H0991 SVZ sphere (dataset 3)

description: SAMPLE 8

source_name: subventricular zone, stem cells, neurospheres


title: H0991 WM Tiss (dataset 2)

description: SAMPLE 4

source_name: White matter, tissue

growth_protocol: Tissue: none; stem cells: adherent; differentiated cells: putative differentiation (1% FBS on Collagen IV).

value: brain white matter

value: tissue


title: H0995 SVZ sphere (dataset 3)

description: SAMPLE 9

value: stem cells


title: H0980 SVZ sphere (dataset 3)

description: SAMPLE 7

value: female


title: T1023 sphere (dataset 3)

description: SAMPLE 11


title: H0991 GM p2 (dataset 2)

description: SAMPLE 2

source_name: Grey matter, stem cells, adherent

value: brain grey matter

value: adherent


title: H0991 GM Tiss (dataset 2)

description: SAMPLE 1

source_name: Grey matter, tissue


title: H0980 WM adh (dataset 3)

description: SAMPLE 3


title: H0995_SVZ (dataset 1)

description: SAMPLE 3


title: H0991 WM p1 (dataset 2)

description: SAMPLE 5

source_name: White matter, stem cells, adherent


title: H0991 GM Diff (dataset 2)

description: SAMPLE 3

source_name: Grey matter, differentiated

value: differentiated cells


title: T1023 adh (dataset 3)

description: SAMPLE 5


title: H0991 WM Diff (dataset 2)

description: SAMPLE 6

source_name: White matter, differentiated


title: H0980 GM adh (dataset 3)

description: SAMPLE 2

source_name: grey matter, stem cells, adherent


title: T1008 adh (dataset 3)

description: SAMPLE 4


title: H0980_SVZ (dataset 1)

description: SAMPLE 2


title: H0980_HPC (dataset 1)

description: SAMPLE 5

source_name: hippocampus, stem cells, adherent

value: hippocampus


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 12

status: Public on Aug 18 2013

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 8

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction and dye-normalization were used.

source_name: Peripheral blood cells from Microscopic polyangiitis patient 12

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The RNAs of MPA patients’ and normal volunteers’ PBMCs were prepared by a standard method. Briefly, heparinized venous blood (10 mL) was mixed with an equal volume of 2% dextran/saline solution and incubated at room temperature for 30 min to precipitate the red blood cells. The PBMCs in the supernatant were then purified by density-gradient centrifugation on Percoll (density=1.064 g/mL). Total RNA was extracted from the PBMC pellets by adding guanidine-thiocyanate solution and the samples were used for acid guanidinium-phenol-chloroform extraction followed by ethanol precipitation and DNase I treatments for microarray analysis.

value: Male

tag: disease status

value: Microscopic polyangiitis (MPA)

tag: duration of disease

value: 1 month

tag: clinical manifestation

value: Fever, arthritis, body weight loss,interstitial pneumonia, peripheral nerve disturbance,dementia

tag: renal biopsy

value: Done

tag: histological findings of renal specimen

value: Diffuse mesangial proliferative GN with crescent formation

tag: angiography

value: ND

tag: interstitial pneumonia

value: present

tag: disaese activity (bvas 2003) (persistent/worse)

tag: associated diseses

value: Hypertension, prostata hypertrophy

tag: wbc ( /mm3)

tag: crp (mg/dl)

tag: creatinine (mg/dl)

tag: mpo-anca (u/ml)

tag: pr3-anca (u/ml)

value: negative

tag: treatment

value: IVCY, PSL50mg/d➝PSL20mg/d

source_name: Peripheral mononuclear blood cells from 17 healthy controls

value: 11 females and 6 males

value: healthy controls without any identified diseases


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 10

source_name: Peripheral blood cells from Microscopic polyangiitis patient 10

tag: age

tag: gender

value: Female

value: 4 months after treatment

value: Subsided all symptom except peripheral neuropathy

value: absent

value: Diabetes miiitus

value: PSL10mg/d, CY 75mg/d


title: EngTissue_EC.hMSC_cloneHS-27a_rep2

city: Seattle

first: Kareen

middle: L

last: Kreutziger

state: WA

address: 850 Republican Street

department: Pathology

institute: University of Washington

hyb_protocol: The standard Illumina hybridization protocol was used for the HumanHT12 beadchip.

scan_protocol: The standard Illumina scanning protocol was used for the HumanHT12 beadchip.

data_processing: Raw data was exported from Illumina's Genome Studio (non-normalized data matrix).  The data were processed by subtracting background using Genome Studio, then exported for quantile normalization using the function normalize.quantiles() in the preprocessCore library in R (normalized data matrix).

source_name: Engineered Tissue, scaffold-free tissue patches, cultured 8 days, 2:1 ratio mixture of human umbilical vein endothelial cells (HUVEC) and human MSC clone HS-27a

label_protocol: Amplified and biotinylated cRNA was generated using the Illumina TotalPrep RNA Amplification Kit (Ambion) as per manufacturer's protocols.  Cy3 was used to label biotinylated cRNA.

growth_protocol: Human MSC cells were cultured in 2D in tissue culture polystyrene plates prior to harvest.  Human engineered tissues (EC:MSC) were cultured in rotating suspension culture (3D) for 8 days prior to harvest.

extract_protocol: Total RNA was extracted using Buffer RLT with beta-mercaptoethanol, followed by homogenization with the QIAshredder spin column and treatment with DNase I for DNA digestion as per the manufacturer's protocol for the RNeasy Mini Kit (Qiagen).  Quality control was assessed by Agilent Bioanalyzer.

treatment_protocol: All cell lysis samples were collected in Buffer RLT (Qiagen) and frozen at -80 degrees C prior to further processing.

tag: cell composition

value: 2:1 ratio for EC:MSC upon formation of patches

tag: engineered tissue culture duration (days)


title: H1004_HPC (dataset 1)

description: SAMPLE 4

value: male

tag: tissue

value: hippocampus

tag: cell type

value: stem cells

tag: growth type

value: adherent

tag: passage