title: ethanol and salt stress rep. 4

status: Public on May 31 2017

type: RNA

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description:
ethanol
salt stress

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 3.2.3 program.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: ethanol and salt stress

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: The seeds of Arabidopsis thaliana (ecotype Columbia-0) were sterilized and sown in half-strength Murashige and Skoog (MS) liquid medium (1% sucrose, 0.1% agar) and the plants were grown at 22°C under 16-h-light/8-h-dark for 4 days.

extract_protocol: RNA was extracted from four biological replicates with the Plant RNA Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions

treatment_protocol: 5-day-old seedlings that were treated with or without 100 mM NaCl for 2 h after 24 h treatment with 0.3 % ethanol

tag: ecotype

tag: tissue

value: whole plant


title: salt stress rep. 1

description:
water control
salt stress

source_name: salt stress


title: ethanol rep. 2

description:
ethanol
non-stress

source_name: ethanol


title: salt stress rep. 4

description:
water control
salt stress


title: EC-Mef2cCdh5EKO-rep2

city: Albany

first: John

middle: J

last: Schwarz

state: NY

address: 47 New Scotland Ave.

department: Department of Molecular and Cellular Physiology

country: USA

institute: Albany Medical College

description: SST-RMA expression value derived from Expression Console software

hyb_protocol: labeled samples (5.5ug) were hybridized to Mouse Transcriptome1.0 Array (Affymetrix) using standard protocol

scan_protocol: The arrays were scanned on a GCS3000 7G scanner using standard Affymetrix protocols

data_processing: The CEL files were converted to CHP files using Expression Consolev 1.4. Further statistical analysis was done using Affymetrix Transcriptome Console v3.0

label: Biotin

organism: Mus musculus

source_name: Cdh5-CreERT2+; Mef2c f/f mice injected with tamoxicen to delete Mef2c in endothelium

label_protocol: 5ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Pico protocol (Affymetrix)

growth_protocol: Mice were housed in specific-pathogen free facility.

extract_protocol: Total RNA was isolated from TRIzol reagent (ThermoFisher) that flushed through the lumen of individaul mouse thoracic aortas according to manufacturer’s protocol with LPA (Sigma-Aldrich) precipitation.

treatment_protocol: Endothelial-specific, inducible-deletion of Mef2c was mediated by Cdh5-CreERT2 through 5 daily tamoxifen (dissolved in sunflower seed oil with 10% ethanol) injections (Mef2cCdh5EKO) in 10 weeks old mice. Littermates who received vehicle injection (sunflower seed oil with 10% ethanol) served as controls. Thoracic aortas from these mice were harvest 14 days after the first injection.

value: Thoracic aortic endothelium

tag: Sex

value: Female


title: ethanol and salt stress rep. 1

description:
ethanol
salt stress


title: ethanol and salt stress rep. 2

description:
ethanol
salt stress


title: ethanol rep. 1

description:
ethanol
non-stress


title: EC-Mef2cCdh5EKO-rep4


title: ethanol rep. 4

description:
ethanol
non-stress


title: ethanol and salt stress rep. 3

description:
ethanol
salt stress


title: water control rep. 2

description:
water control
non-stress

source_name: water control


title: salt stress rep. 3

description:
water control
salt stress


title: ethanol rep. 3

description:
ethanol
non-stress


title: EC-Mef2cCdh5EKO-rep1


title: EC-Control-rep1

source_name: Cdh5-CreERT2+; Mef2c f/f mice injected with vehicle control


title: EC-Control-rep4


title: EC-Mef2cCdh5EKO-rep3


title: salt stress rep. 2

description:
water control
salt stress


title: EC-Control-rep2


title: water control rep. 4

description:
water control
non-stress


title: water control rep. 3

description:
water control
non-stress


title: EC-Control-rep3


title: water control rep. 1

description:
water control
non-stress


title: F1_WAT_calorierestricted_biologicalrep4

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

description: Gene expression data from mice consuming calorie restricted diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Affymetrix Expression Console using the gene-level RMA-Sketch algorithm.

label: biotin

source_name: WAT, Calorie Restricted diet, replicate 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Male mice were purchased from Jackson Laboratory at six weeks of age and were individually housed and fed 84 kcal/week of a diet based on the AIN93M formulation for two weeks

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

treatment_protocol: Starting at 8 weeks of age, mice were maintained on the control diet or were fed a calorie restricted diet (Bio-Serv; Frenchtown, NJ, USA; Catalog# F05314)

value: white adipose

tag: strain

tag: gender

value: male


title: F1_WAT_calorierestricted_biologicalrep7

source_name: WAT, Calorie Restricted diet, replicate 7


title: F1_WAT_control_biologicalrep7

description: Gene expression data from mice consuming control diet

source_name: WAT, Control diet, replicate 7


title: F1_WAT_control_biologicalrep5

source_name: WAT, Control diet, replicate 5


title: DBA_WAT_calorierestricted_biologicalrep8

source_name: WAT, Calorie Restricted diet, replicate 8


title: F1_WAT_control_biologicalrep6

source_name: WAT, Control diet, replicate 6


title: F1_WAT_calorierestricted_biologicalrep2

source_name: WAT, Calorie Restricted diet, replicate 2


title: F1_WAT_calorierestricted_biologicalrep5

source_name: WAT, Calorie Restricted diet, replicate 5


title: F1_WAT_calorierestricted_biologicalrep3

source_name: WAT, Calorie Restricted diet, replicate 3


title: F1_WAT_control_biologicalrep8

source_name: WAT, Control diet, replicate 8


title: F1_WAT_control_biologicalrep3

source_name: WAT, Control diet, replicate 3


title: F1_WAT_calorierestricted_biologicalrep6

source_name: WAT, Calorie Restricted diet, replicate 6


title: DBA_WAT_calorierestricted_biologicalrep6


title: F1_WAT_control_biologicalrep1

source_name: WAT, Control diet, replicate 1


title: DBA_WAT_calorierestricted_biologicalrep4


title: DBA_WAT_calorierestricted_biologicalrep3


title: DBA_WAT_calorierestricted_biologicalrep5


title: F1_WAT_control_biologicalrep2

source_name: WAT, Control diet, replicate 2


title: F1_WAT_calorierestricted_biologicalrep1

source_name: WAT, Calorie Restricted diet, replicate 1


title: DBA_WAT_calorierestricted_biologicalrep7


title: F1_WAT_calorierestricted_biologicalrep8


title: DBA_WAT_calorierestricted_biologicalrep2


title: DBA_WAT_control_biologicalrep3


title: DBA_WAT_control_biologicalrep8


title: DBA_WAT_control_biologicalrep5


title: DBA_WAT_control_biologicalrep7


title: DBA_WAT_control_biologicalrep2


title: CBA_WAT_calorierestricted_biologicalrep8

value: CBA/J


title: DBA_WAT_control_biologicalrep6


title: F1_WAT_control_biologicalrep4

source_name: WAT, Control diet, replicate 4


title: DBA_WAT_control_biologicalrep1


title: CBA_WAT_calorierestricted_biologicalrep3


title: DBA_WAT_control_biologicalrep4


title: DBA_WAT_calorierestricted_biologicalrep1


title: CBA_WAT_calorierestricted_biologicalrep5


title: CBA_WAT_calorierestricted_biologicalrep1


title: CBA_WAT_calorierestricted_biologicalrep6


title: CBA_WAT_control_biologicalrep4


title: CBA_WAT_control_biologicalrep8


title: CBA_WAT_calorierestricted_biologicalrep7


title: CBA_WAT_control_biologicalrep7


title: CBA_WAT_calorierestricted_biologicalrep2


title: CBA_WAT_control_biologicalrep5


title: CBA_WAT_control_biologicalrep3


title: CBA_WAT_calorierestricted_biologicalrep4


title: C3H_WAT_calorierestricted_biologicalrep8


title: CBA_WAT_control_biologicalrep2


title: C3H_WAT_calorierestricted_biologicalrep5


title: C3H_WAT_control_biologicalrep8


title: CBA_WAT_control_biologicalrep1


title: C3H_WAT_calorierestricted_biologicalrep3


title: C3H_WAT_calorierestricted_biologicalrep4


title: C3H_WAT_calorierestricted_biologicalrep7


title: C3H_WAT_calorierestricted_biologicalrep1


title: C3H_WAT_calorierestricted_biologicalrep2


title: C3H_WAT_calorierestricted_biologicalrep6


title: C3H_WAT_control_biologicalrep2


title: C3H_WAT_control_biologicalrep7


title: C3H_WAT_control_biologicalrep5


title: CBA_WAT_control_biologicalrep6


title: B6_WAT_calorierestricted_biologicalrep8


title: C3H_WAT_control_biologicalrep1


title: C3H_WAT_control_biologicalrep3


title: B6_WAT_calorierestricted_biologicalrep5


title: C3H_WAT_control_biologicalrep4


title: B6_WAT_calorierestricted_biologicalrep6


title: B6_WAT_calorierestricted_biologicalrep4


title: B6_WAT_calorierestricted_biologicalrep7


title: C3H_WAT_control_biologicalrep6


title: B6_WAT_calorierestricted_biologicalrep2


title: B6_WAT_control_biologicalrep6


title: B6_WAT_calorierestricted_biologicalrep3


title: B6_WAT_control_biologicalrep7


title: B6_WAT_control_biologicalrep8


title: B6_WAT_control_biologicalrep3


title: B6_WAT_calorierestricted_biologicalrep1


title: B6_WAT_control_biologicalrep4


title: B6_WAT_control_biologicalrep5


title: BALB_WAT_control_biologicalrep8

value: Balbc/J


title: BALB_WAT_control_biologicalrep5


title: 129_WAT_calorierestricted_biologicalrep8


title: BALB_WAT_control_biologicalrep7


title: BALB_WAT_control_biologicalrep2


title: BALB_WAT_calorierestricted_biologicalrep7


title: BALB_WAT_calorierestricted_biologicalrep5


title: 129_WAT_calorierestricted_biologicalrep6


title: BALB_WAT_calorierestricted_biologicalrep1


title: B6_WAT_control_biologicalrep2


title: BALB_WAT_control_biologicalrep4


title: 129_WAT_calorierestricted_biologicalrep7


title: B6_WAT_control_biologicalrep1


title: BALB_WAT_calorierestricted_biologicalrep4


title: BALB_WAT_control_biologicalrep3


title: BALB_WAT_calorierestricted_biologicalrep8


title: BALB_WAT_calorierestricted_biologicalrep3


title: BALB_WAT_calorierestricted_biologicalrep6


title: BALB_WAT_control_biologicalrep6


title: 129_WAT_calorierestricted_biologicalrep5


title: BALB_WAT_control_biologicalrep1


title: 129_WAT_calorierestricted_biologicalrep2


title: 129_WAT_control_biologicalrep7


title: 129_WAT_calorierestricted_biologicalrep4


title: 129_WAT_calorierestricted_biologicalrep3


title: 129_WAT_control_biologicalrep8


title: BALB_WAT_calorierestricted_biologicalrep2


title: 129_WAT_calorierestricted_biologicalrep1


title: F1_HEART_control_biologicalrep6

source_name: HEART, Control diet, replicate 6

value: heart


title: 129_WAT_control_biologicalrep4


title: 129_WAT_control_biologicalrep2


title: F1_HEART_calorierestricted_biologicalrep7

source_name: HEART, Calorie Restricted diet, replicate 7


title: 129_WAT_control_biologicalrep1


title: F1_HEART_control_biologicalrep8

source_name: HEART, Control diet, replicate 8


title: F1_HEART_calorierestricted_biologicalrep5

source_name: HEART, Calorie Restricted diet, replicate 5


title: 129_WAT_control_biologicalrep6


title: F1_HEART_calorierestricted_biologicalrep4

source_name: HEART, Calorie Restricted diet, replicate 4


title: F1_HEART_calorierestricted_biologicalrep2

source_name: HEART, Calorie Restricted diet, replicate 2


title: F1_HEART_calorierestricted_biologicalrep8

source_name: HEART, Calorie Restricted diet, replicate 8


title: 129_WAT_control_biologicalrep5

source_name: WAT, Control diet, replicate 5


title: F1_HEART_control_biologicalrep7

source_name: HEART, Control diet, replicate 7


title: F1_HEART_calorierestricted_biologicalrep3

source_name: HEART, Calorie Restricted diet, replicate 3


title: F1_HEART_control_biologicalrep2

source_name: HEART, Control diet, replicate 2


title: 129_WAT_control_biologicalrep3

source_name: WAT, Control diet, replicate 3


title: F1_HEART_calorierestricted_biologicalrep1

source_name: HEART, Calorie Restricted diet, replicate 1


title: F1_HEART_control_biologicalrep5

source_name: HEART, Control diet, replicate 5


title: F1_HEART_calorierestricted_biologicalrep6

source_name: HEART, Calorie Restricted diet, replicate 6


title: F1_HEART_control_biologicalrep4

source_name: HEART, Control diet, replicate 4


title: F1_HEART_control_biologicalrep1

source_name: HEART, Control diet, replicate 1


title: F1_HEART_control_biologicalrep3

source_name: HEART, Control diet, replicate 3


title: DBA_HEART_calorierestricted_biologicalrep6


title: DBA_HEART_calorierestricted_biologicalrep7

source_name: HEART, Calorie Restricted diet, replicate 7


title: DBA_HEART_calorierestricted_biologicalrep5


title: DBA_HEART_calorierestricted_biologicalrep1


title: DBA_HEART_calorierestricted_biologicalrep3


title: DBA_HEART_calorierestricted_biologicalrep2


title: DBA_HEART_control_biologicalrep5


title: CBA_HEART_calorierestricted_biologicalrep8


title: DBA_HEART_control_biologicalrep3


title: DBA_HEART_control_biologicalrep8

source_name: HEART, Control diet, replicate 8


title: DBA_HEART_control_biologicalrep6

source_name: HEART, Control diet, replicate 6


title: DBA_HEART_control_biologicalrep1


title: CBA_HEART_calorierestricted_biologicalrep3


title: CBA_HEART_calorierestricted_biologicalrep4

source_name: HEART, Calorie Restricted diet, replicate 4


title: DBA_HEART_calorierestricted_biologicalrep4


title: CBA_HEART_calorierestricted_biologicalrep6


title: DBA_HEART_control_biologicalrep4


title: CBA_HEART_control_biologicalrep6


title: CBA_HEART_calorierestricted_biologicalrep7


title: CBA_HEART_control_biologicalrep1


title: DBA_HEART_control_biologicalrep7


title: DBA_HEART_calorierestricted_biologicalrep8


title: CBA_HEART_control_biologicalrep7


title: DBA_HEART_control_biologicalrep2


title: CBA_HEART_calorierestricted_biologicalrep5

source_name: HEART, Calorie Restricted diet, replicate 5


title: CBA_HEART_control_biologicalrep8


title: CBA_HEART_control_biologicalrep5


title: CBA_HEART_control_biologicalrep3


title: CBA_HEART_calorierestricted_biologicalrep2

source_name: HEART, Calorie Restricted diet, replicate 2


title: C3H_HEART_calorierestricted_biologicalrep8

source_name: HEART, Calorie Restricted diet, replicate 8


title: CBA_HEART_control_biologicalrep2


title: CBA_HEART_calorierestricted_biologicalrep1


title: C3H_HEART_calorierestricted_biologicalrep7


title: C3H_HEART_calorierestricted_biologicalrep2


title: C3H_HEART_calorierestricted_biologicalrep3


title: C3H_HEART_control_biologicalrep6


title: CBA_HEART_control_biologicalrep4


title: C3H_HEART_calorierestricted_biologicalrep5


title: C3H_HEART_control_biologicalrep1


title: C3H_HEART_control_biologicalrep7

source_name: HEART, Control diet, replicate 7


title: C3H_HEART_calorierestricted_biologicalrep4


title: C3H_HEART_control_biologicalrep3


title: C3H_HEART_control_biologicalrep8


title: C3H_HEART_control_biologicalrep2


title: C3H_HEART_control_biologicalrep5


title: C3H_HEART_calorierestricted_biologicalrep1


title: B6_HEART_calorierestricted_biologicalrep8


title: C3H_HEART_calorierestricted_biologicalrep6


title: B6_HEART_calorierestricted_biologicalrep3

source_name: HEART, Calorie Restricted diet, replicate 3


title: B6_HEART_calorierestricted_biologicalrep7


title: C3H_HEART_control_biologicalrep4


title: B6_HEART_calorierestricted_biologicalrep5


title: B6_HEART_calorierestricted_biologicalrep2


title: B6_HEART_calorierestricted_biologicalrep4


title: B6_HEART_control_biologicalrep8


title: B6_HEART_control_biologicalrep7


title: B6_HEART_control_biologicalrep6


title: B6_HEART_control_biologicalrep5


title: B6_HEART_calorierestricted_biologicalrep6


title: BALB_HEART_calorierestricted_biologicalrep5


title: B6_HEART_control_biologicalrep3


title: B6_HEART_control_biologicalrep1


title: B6_HEART_calorierestricted_biologicalrep1


title: BALB_HEART_calorierestricted_biologicalrep6


title: B6_HEART_control_biologicalrep4


title: B6_HEART_control_biologicalrep2

source_name: HEART, Control diet, replicate 2


title: BALB_HEART_calorierestricted_biologicalrep8


title: BALB_HEART_calorierestricted_biologicalrep7


title: BALB_HEART_calorierestricted_biologicalrep4


title: BALB_HEART_calorierestricted_biologicalrep2


title: BALB_HEART_control_biologicalrep7


title: BALB_HEART_control_biologicalrep8


title: BALB_HEART_calorierestricted_biologicalrep1


title: BALB_HEART_control_biologicalrep3


title: BALB_HEART_control_biologicalrep4


title: BALB_HEART_calorierestricted_biologicalrep3


title: BALB_HEART_control_biologicalrep6


title: BALB_HEART_control_biologicalrep5


title: BALB_HEART_control_biologicalrep2


title: BALB_HEART_control_biologicalrep1


title: 129_HEART_calorierestricted_biologicalrep5


title: 129_HEART_calorierestricted_biologicalrep8


title: 129_HEART_calorierestricted_biologicalrep4


title: 129_HEART_calorierestricted_biologicalrep3


title: 129_HEART_control_biologicalrep7


title: 129_HEART_calorierestricted_biologicalrep7


title: 129_HEART_control_biologicalrep5


title: 129_HEART_control_biologicalrep2


title: 129_HEART_control_biologicalrep1


title: F1_GASTROC_calorierestricted_biologicalrep5

source_name: GASTROC, Calorie Restricted diet, replicate 5

value: gastrocnemius muscle


title: F1_GASTROC_calorierestricted_biologicalrep4

source_name: GASTROC, Calorie Restricted diet, replicate 4


title: 129_HEART_control_biologicalrep4


title: F1_GASTROC_calorierestricted_biologicalrep3

source_name: GASTROC, Calorie Restricted diet, replicate 3


title: 129_HEART_calorierestricted_biologicalrep2


title: F1_GASTROC_calorierestricted_biologicalrep8

source_name: GASTROC, Calorie Restricted diet, replicate 8


title: 129_HEART_control_biologicalrep6


title: 129_HEART_control_biologicalrep3


title: 129_HEART_calorierestricted_biologicalrep1

source_name: HEART, Calorie Restricted diet, replicate 1


title: F1_GASTROC_calorierestricted_biologicalrep7

source_name: GASTROC, Calorie Restricted diet, replicate 7


title: 129_HEART_control_biologicalrep8


title: F1_GASTROC_control_biologicalrep8

source_name: GASTROC, Control diet, replicate 8


title: 129_HEART_calorierestricted_biologicalrep6

source_name: HEART, Calorie Restricted diet, replicate 6


title: F1_GASTROC_control_biologicalrep7

source_name: GASTROC, Control diet, replicate 7


title: F1_GASTROC_calorierestricted_biologicalrep1

source_name: GASTROC, Calorie Restricted diet, replicate 1


title: F1_GASTROC_calorierestricted_biologicalrep2

source_name: GASTROC, Calorie Restricted diet, replicate 2


title: F1_GASTROC_control_biologicalrep6

source_name: GASTROC, Control diet, replicate 6


title: F1_GASTROC_control_biologicalrep5

source_name: GASTROC, Control diet, replicate 5


title: F1_GASTROC_control_biologicalrep4

source_name: GASTROC, Control diet, replicate 4


title: F1_GASTROC_calorierestricted_biologicalrep6

source_name: GASTROC, Calorie Restricted diet, replicate 6


title: F1_GASTROC_control_biologicalrep2

source_name: GASTROC, Control diet, replicate 2


title: DBA_GASTROC_calorierestricted_biologicalrep6


title: F1_GASTROC_control_biologicalrep1

source_name: GASTROC, Control diet, replicate 1


title: DBA_GASTROC_calorierestricted_biologicalrep8


title: DBA_GASTROC_calorierestricted_biologicalrep5

source_name: GASTROC, Calorie Restricted diet, replicate 5


title: DBA_GASTROC_calorierestricted_biologicalrep3


title: CBA_GASTROC_calorierestricted_biologicalrep7


title: DBA_GASTROC_calorierestricted_biologicalrep4

source_name: GASTROC, Calorie Restricted diet, replicate 4


title: F1_GASTROC_control_biologicalrep3

source_name: GASTROC, Control diet, replicate 3


title: DBA_GASTROC_control_biologicalrep2


title: DBA_GASTROC_control_biologicalrep5


title: DBA_GASTROC_control_biologicalrep4


title: CBA_GASTROC_control_biologicalrep7


title: DBA_GASTROC_calorierestricted_biologicalrep1


title: CBA_GASTROC_calorierestricted_biologicalrep4


title: DBA_GASTROC_calorierestricted_biologicalrep7


title: CBA_GASTROC_calorierestricted_biologicalrep5


title: DBA_GASTROC_calorierestricted_biologicalrep2


title: DBA_GASTROC_control_biologicalrep7


title: CBA_GASTROC_control_biologicalrep6


title: CBA_GASTROC_calorierestricted_biologicalrep3

source_name: GASTROC, Calorie Restricted diet, replicate 3


title: DBA_GASTROC_control_biologicalrep1


title: CBA_GASTROC_calorierestricted_biologicalrep6


title: DBA_GASTROC_control_biologicalrep3


title: CBA_GASTROC_calorierestricted_biologicalrep8

source_name: GASTROC, Calorie Restricted diet, replicate 8


title: DBA_GASTROC_control_biologicalrep8


title: DBA_GASTROC_control_biologicalrep6


title: CBA_GASTROC_calorierestricted_biologicalrep2


title: CBA_GASTROC_control_biologicalrep8


title: C3H_GASTROC_calorierestricted_biologicalrep8


title: C3H_GASTROC_calorierestricted_biologicalrep7

source_name: GASTROC, Calorie Restricted diet, replicate 7


title: B6_GASTROC_calorierestricted_biologicalrep4


title: C3H_GASTROC_calorierestricted_biologicalrep5


title: CBA_GASTROC_calorierestricted_biologicalrep1


title: C3H_GASTROC_control_biologicalrep7


title: CBA_GASTROC_control_biologicalrep5


title: CBA_GASTROC_control_biologicalrep3


title: C3H_GASTROC_calorierestricted_biologicalrep3


title: CBA_GASTROC_control_biologicalrep4


title: C3H_GASTROC_calorierestricted_biologicalrep1


title: CBA_GASTROC_control_biologicalrep2


title: C3H_GASTROC_control_biologicalrep6


title: B6_GASTROC_calorierestricted_biologicalrep8


title: B6_GASTROC_calorierestricted_biologicalrep3


title: CBA_GASTROC_control_biologicalrep1


title: C3H_GASTROC_control_biologicalrep2


title: C3H_GASTROC_calorierestricted_biologicalrep4


title: B6_GASTROC_calorierestricted_biologicalrep6


title: C3H_GASTROC_control_biologicalrep4


title: C3H_GASTROC_calorierestricted_biologicalrep2


title: B6_GASTROC_calorierestricted_biologicalrep5


title: C3H_GASTROC_control_biologicalrep5


title: C3H_GASTROC_control_biologicalrep1


title: C3H_GASTROC_calorierestricted_biologicalrep6


title: C3H_GASTROC_control_biologicalrep3


title: C3H_GASTROC_control_biologicalrep8

source_name: GASTROC, Control diet, replicate 8


title: B6_GASTROC_calorierestricted_biologicalrep7


title: B6_GASTROC_calorierestricted_biologicalrep2


title: WEE1 siRNA rep4

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

description:
SAMPLE8
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was subtracted and quantile normalization was applied.

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: DMEM/F - 12 (+ 10% fetal bovine serum)

extract_protocol: Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: 15 nM siRNA for 48h

tag: cell line

value: HepG2 Liver Cancer Cell Line

tag: treatment

value: WEE1 siRNA


title: B6_GASTROC_control_biologicalrep1


title: genomic DNA from cord blood 379

type: genomic

city: Berkeley

first: Nina

last: Holland

state: CA

address: 733 University Hall

institute: University of California, Berkeley

description: normal cord blood sample

hyb_protocol: DNA was whole genome amplified, enzymatically fragmented, purified, and hybridised to the Illumina Infinium HumanMethylation450 BeadChips according to the Illumina methylation protocol

scan_protocol: 450K BeadChips were handled by robotics and analyzed using the Illumina Hi-Scan system

data_processing:
Probe signal intensities were extracted by Illumina GenomeStudio software (version XXV2011.1, Methylation Module 1.9) methylation module and background subtracted. The All Sample Mean Normalization (ASMN) algorithm was used to adjust for color channel bias, batch effects, and difference in Infinium chemistry [Yousefi et al. 2013]. This was followed by Beta Mixture Quantile (BMIQ) normalization for differences between type I and type II probes [Teschendorff et al. 2013]. Samples were retained only if 95% of sites assayed had detection P-values > 0.01. Sites with annotated probe SNPs (n=65) and with common SNPs (minor allele frequency >5%) within 50bp of the target identified in the MXL (Mexican ancestry in Los Angeles, California) HapMap population (n=49,748), and cross-reactive probes identified by Chen et al. [Chen et al. 2013] (n=25,248). Probes where 95% of samples had detection P-values >0.01 were also dropped (n= 460).
Normalized (ASMN and BMIQ) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cord blood 379

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from the banked non-heparinized umbilical cord blood clot samples using QIAamp DNA Blood Maxi Kits according to the manufacturer’s protocol

tag: cohort

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)

value: cord blood


title: BALB_GASTROC_calorierestricted_biologicalrep5


title: genomic DNA from cord blood 380

description: normal cord blood sample

source_name: cord blood 380


title: genomic DNA from cord blood 378

description: normal cord blood sample

source_name: cord blood 378


title: WEE1 siRNA rep1

description:
SAMPLE5
replicate 1


title: B6_GASTROC_control_biologicalrep6


title: Negative Control siRNA rep4

description:
SAMPLE4
replicate 4

value: control


title: BALB_GASTROC_calorierestricted_biologicalrep4


title: B6_GASTROC_control_biologicalrep7

source_name: GASTROC, Control diet, replicate 7


title: B6_GASTROC_control_biologicalrep8


title: WEE1 siRNA rep2

description:
SAMPLE6
replicate 2


title: B6_GASTROC_control_biologicalrep4


title: B6_GASTROC_control_biologicalrep5


title: BALB_GASTROC_calorierestricted_biologicalrep8


title: BALB_GASTROC_calorierestricted_biologicalrep6


title: B6_GASTROC_calorierestricted_biologicalrep1

source_name: GASTROC, Calorie Restricted diet, replicate 1


title: B6_GASTROC_control_biologicalrep2


title: BALB_GASTROC_calorierestricted_biologicalrep3


title: BALB_GASTROC_calorierestricted_biologicalrep2

source_name: GASTROC, Calorie Restricted diet, replicate 2


title: BALB_GASTROC_control_biologicalrep8


title: BALB_GASTROC_calorierestricted_biologicalrep1


title: BALB_GASTROC_control_biologicalrep7


title: genomic DNA from cord blood 377

description: normal cord blood sample

source_name: cord blood 377


title: WEE1 siRNA rep3

description:
SAMPLE7
replicate 3


title: genomic DNA from cord blood 376

description: normal cord blood sample

source_name: cord blood 376


title: Negative Control siRNA rep3

description:
SAMPLE3
replicate 3


title: B6_GASTROC_control_biologicalrep3


title: genomic DNA from cord blood 374

description: normal cord blood sample

source_name: cord blood 374


title: genomic DNA from cord blood 372

description: normal cord blood sample

source_name: cord blood 372


title: genomic DNA from cord blood 375

description: normal cord blood sample

source_name: cord blood 375


title: genomic DNA from cord blood 371

description: normal cord blood sample

source_name: cord blood 371


title: BALB_GASTROC_calorierestricted_biologicalrep7


title: genomic DNA from cord blood 373

description: normal cord blood sample

source_name: cord blood 373


title: genomic DNA from cord blood 369

description: normal cord blood sample

source_name: cord blood 369


title: Negative Control siRNA rep1

description:
SAMPLE1
replicate 1


title: Negative Control siRNA rep2

description:
SAMPLE2
replicate 2


title: genomic DNA from cord blood 368

description: normal cord blood sample

source_name: cord blood 368


title: genomic DNA from cord blood 367

description: normal cord blood sample

source_name: cord blood 367


title: BALB_GASTROC_control_biologicalrep6

source_name: GASTROC, Control diet, replicate 6


title: genomic DNA from cord blood 366

description: normal cord blood sample

source_name: cord blood 366


title: genomic DNA from cord blood 365

description: normal cord blood sample

source_name: cord blood 365


title: BALB_GASTROC_control_biologicalrep4

source_name: GASTROC, Control diet, replicate 4


title: 129_GASTROC_calorierestricted_biologicalrep4

source_name: GASTROC, Calorie Restricted diet, replicate 4


title: genomic DNA from cord blood 370

description: normal cord blood sample

source_name: cord blood 370


title: 129_GASTROC_calorierestricted_biologicalrep5

source_name: GASTROC, Calorie Restricted diet, replicate 5


title: BALB_GASTROC_control_biologicalrep3

source_name: GASTROC, Control diet, replicate 3


title: genomic DNA from cord blood 364

description: normal cord blood sample

source_name: cord blood 364


title: 129_GASTROC_calorierestricted_biologicalrep7

source_name: GASTROC, Calorie Restricted diet, replicate 7


title: BALB_GASTROC_control_biologicalrep2

source_name: GASTROC, Control diet, replicate 2


title: 129_GASTROC_calorierestricted_biologicalrep6

source_name: GASTROC, Calorie Restricted diet, replicate 6


title: genomic DNA from cord blood 361

description: normal cord blood sample

source_name: cord blood 361


title: genomic DNA from cord blood 363

description: normal cord blood sample

source_name: cord blood 363


title: genomic DNA from cord blood 362

description: normal cord blood sample

source_name: cord blood 362


title: BALB_GASTROC_control_biologicalrep1

source_name: GASTROC, Control diet, replicate 1


title: 129_GASTROC_calorierestricted_biologicalrep2

source_name: GASTROC, Calorie Restricted diet, replicate 2


title: 129_GASTROC_calorierestricted_biologicalrep3

source_name: GASTROC, Calorie Restricted diet, replicate 3


title: 129_GASTROC_calorierestricted_biologicalrep8

source_name: GASTROC, Calorie Restricted diet, replicate 8


title: genomic DNA from cord blood 360

description: normal cord blood sample

source_name: cord blood 360


title: genomic DNA from cord blood 358

description: normal cord blood sample

source_name: cord blood 358


title: genomic DNA from cord blood 359

description: normal cord blood sample

source_name: cord blood 359


title: genomic DNA from cord blood 357

description: normal cord blood sample

source_name: cord blood 357


title: 129_GASTROC_control_biologicalrep8

source_name: GASTROC, Control diet, replicate 8


title: 129_GASTROC_calorierestricted_biologicalrep1

source_name: GASTROC, Calorie Restricted diet, replicate 1


title: genomic DNA from cord blood 356

description: normal cord blood sample

source_name: cord blood 356


title: 129_GASTROC_control_biologicalrep4

source_name: GASTROC, Control diet, replicate 4


title: 129_GASTROC_control_biologicalrep3

source_name: GASTROC, Control diet, replicate 3


title: 129_GASTROC_control_biologicalrep7

source_name: GASTROC, Control diet, replicate 7


title: 129_GASTROC_control_biologicalrep5

source_name: GASTROC, Control diet, replicate 5


title: genomic DNA from cord blood 351

description: normal cord blood sample

source_name: cord blood 351


title: 129_GASTROC_control_biologicalrep6

source_name: GASTROC, Control diet, replicate 6


title: 129_GASTROC_control_biologicalrep1

source_name: GASTROC, Control diet, replicate 1


title: BALB_GASTROC_control_biologicalrep5


title: 129_GASTROC_control_biologicalrep2

source_name: GASTROC, Control diet, replicate 2


title: genomic DNA from cord blood 355

description: normal cord blood sample

source_name: cord blood 355


title: genomic DNA from cord blood 352

description: normal cord blood sample

source_name: cord blood 352


title: genomic DNA from cord blood 347

description: normal cord blood sample

source_name: cord blood 347


title: genomic DNA from cord blood 349

description: normal cord blood sample

source_name: cord blood 349


title: genomic DNA from cord blood 354

description: normal cord blood sample

source_name: cord blood 354


title: genomic DNA from cord blood 353

description: normal cord blood sample

source_name: cord blood 353


title: genomic DNA from cord blood 348

description: normal cord blood sample

source_name: cord blood 348


title: genomic DNA from cord blood 350

description: normal cord blood sample

source_name: cord blood 350


title: genomic DNA from cord blood 344

description: normal cord blood sample

source_name: cord blood 344


title: genomic DNA from cord blood 346

description: normal cord blood sample

source_name: cord blood 346


title: genomic DNA from cord blood 342

description: normal cord blood sample

source_name: cord blood 342


title: F1_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6

value: cerebral cortex


title: genomic DNA from cord blood 345

description: normal cord blood sample

source_name: cord blood 345


title: genomic DNA from cord blood 343

description: normal cord blood sample

source_name: cord blood 343


title: F1_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: F1_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: F1_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: F1_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: F1_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: F1_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: F1_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: genomic DNA from cord blood 341

description: normal cord blood sample

source_name: cord blood 341


title: genomic DNA from cord blood 338

description: normal cord blood sample

source_name: cord blood 338


title: genomic DNA from cord blood 340

description: normal cord blood sample

source_name: cord blood 340


title: genomic DNA from cord blood 339

description: normal cord blood sample

source_name: cord blood 339


title: F1_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: genomic DNA from cord blood 337

description: normal cord blood sample

source_name: cord blood 337


title: genomic DNA from cord blood 336

description: normal cord blood sample

source_name: cord blood 336


title: DBA_CORTEX_calorierestricted_biologicalrep7


title: F1_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: genomic DNA from cord blood 331

description: normal cord blood sample

source_name: cord blood 331


title: genomic DNA from cord blood 334

description: normal cord blood sample

source_name: cord blood 334


title: genomic DNA from cord blood 332

description: normal cord blood sample

source_name: cord blood 332


title: genomic DNA from cord blood 333

description: normal cord blood sample

source_name: cord blood 333


title: F1_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: genomic DNA from cord blood 335

description: normal cord blood sample

source_name: cord blood 335


title: F1_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: DBA_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: F1_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: F1_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: F1_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: DBA_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: genomic DNA from cord blood 330

description: normal cord blood sample

source_name: cord blood 330


title: genomic DNA from cord blood 328

description: normal cord blood sample

source_name: cord blood 328


title: genomic DNA from cord blood 326

description: normal cord blood sample

source_name: cord blood 326


title: DBA_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: DBA_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: DBA_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: genomic DNA from cord blood 327

description: normal cord blood sample

source_name: cord blood 327


title: DBA_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: DBA_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: genomic DNA from cord blood 329

description: normal cord blood sample

source_name: cord blood 329


title: genomic DNA from cord blood 324

description: normal cord blood sample

source_name: cord blood 324


title: genomic DNA from cord blood 322

description: normal cord blood sample

source_name: cord blood 322


title: genomic DNA from cord blood 325

description: normal cord blood sample

source_name: cord blood 325


title: DBA_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: DBA_CORTEX_control_biologicalrep7


title: DBA_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: genomic DNA from cord blood 320

description: normal cord blood sample

source_name: cord blood 320


title: genomic DNA from cord blood 323

description: normal cord blood sample

source_name: cord blood 323


title: DBA_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: genomic DNA from cord blood 319

description: normal cord blood sample

source_name: cord blood 319


title: genomic DNA from cord blood 321

description: normal cord blood sample

source_name: cord blood 321


title: DBA_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: genomic DNA from cord blood 318

description: normal cord blood sample

source_name: cord blood 318


title: genomic DNA from cord blood 317

description: normal cord blood sample

source_name: cord blood 317


title: genomic DNA from cord blood 316

description: normal cord blood sample

source_name: cord blood 316


title: F1_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: genomic DNA from cord blood 315

description: normal cord blood sample

source_name: cord blood 315


title: DBA_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: DBA_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: CBA_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: CBA_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: genomic DNA from cord blood 314

description: normal cord blood sample

source_name: cord blood 314


title: CBA_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: CBA_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: CBA_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: genomic DNA from cord blood 311

description: normal cord blood sample

source_name: cord blood 311


title: genomic DNA from cord blood 313

description: normal cord blood sample

source_name: cord blood 313


title: genomic DNA from cord blood 310

description: normal cord blood sample

source_name: cord blood 310


title: genomic DNA from cord blood 309

description: normal cord blood sample

source_name: cord blood 309


title: genomic DNA from cord blood 312

description: normal cord blood sample

source_name: cord blood 312


title: DBA_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: CBA_CORTEX_calorierestricted_biologicalrep3


title: CBA_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: genomic DNA from cord blood 308

description: normal cord blood sample

source_name: cord blood 308


title: genomic DNA from cord blood 307

description: normal cord blood sample

source_name: cord blood 307


title: CBA_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: genomic DNA from cord blood 306

description: normal cord blood sample

source_name: cord blood 306


title: CBA_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: CBA_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: genomic DNA from cord blood 303

description: normal cord blood sample

source_name: cord blood 303


title: genomic DNA from cord blood 305

description: normal cord blood sample

source_name: cord blood 305


title: genomic DNA from cord blood 302

description: normal cord blood sample

source_name: cord blood 302


title: CBA_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: genomic DNA from cord blood 299

description: normal cord blood sample

source_name: cord blood 299


title: CBA_CORTEX_control_biologicalrep3


title: genomic DNA from cord blood 297

description: normal cord blood sample

source_name: cord blood 297


title: CBA_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: genomic DNA from cord blood 298

description: normal cord blood sample

source_name: cord blood 298


title: genomic DNA from cord blood 296

description: normal cord blood sample

source_name: cord blood 296


title: genomic DNA from cord blood 300

description: normal cord blood sample

source_name: cord blood 300


title: CBA_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: genomic DNA from cord blood 304

description: normal cord blood sample

source_name: cord blood 304


title: genomic DNA from cord blood 301

description: normal cord blood sample

source_name: cord blood 301


title: C3H_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: C3H_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: C3H_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: CBA_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: C3H_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: CBA_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: C3H_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: C3H_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: C3H_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: genomic DNA from cord blood 295

description: normal cord blood sample

source_name: cord blood 295


title: genomic DNA from cord blood 294

description: normal cord blood sample

source_name: cord blood 294


title: genomic DNA from cord blood 293

description: normal cord blood sample

source_name: cord blood 293


title: C3H_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: C3H_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: C3H_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: genomic DNA from cord blood 292

description: normal cord blood sample

source_name: cord blood 292


title: C3H_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: genomic DNA from cord blood 291

description: normal cord blood sample

source_name: cord blood 291


title: genomic DNA from cord blood 290

description: normal cord blood sample

source_name: cord blood 290


title: C3H_CORTEX_control_biologicalrep5


title: genomic DNA from cord blood 288

description: normal cord blood sample

source_name: cord blood 288


title: genomic DNA from cord blood 287

description: normal cord blood sample

source_name: cord blood 287


title: C3H_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: genomic DNA from cord blood 289

description: normal cord blood sample

source_name: cord blood 289


title: genomic DNA from cord blood 285

description: normal cord blood sample

source_name: cord blood 285


title: C3H_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: genomic DNA from cord blood 284

description: normal cord blood sample

source_name: cord blood 284


title: genomic DNA from cord blood 286

description: normal cord blood sample

source_name: cord blood 286


title: genomic DNA from cord blood 283

description: normal cord blood sample

source_name: cord blood 283


title: genomic DNA from cord blood 282

description: normal cord blood sample

source_name: cord blood 282


title: C3H_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: C3H_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: genomic DNA from cord blood 281

description: normal cord blood sample

source_name: cord blood 281


title: genomic DNA from cord blood 280

description: normal cord blood sample

source_name: cord blood 280


title: B6_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: B6_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: B6_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: B6_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: B6_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: B6_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: B6_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: B6_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: genomic DNA from cord blood 279

description: normal cord blood sample

source_name: cord blood 279


title: genomic DNA from cord blood 278

description: normal cord blood sample

source_name: cord blood 278


title: genomic DNA from cord blood 276

description: normal cord blood sample

source_name: cord blood 276


title: B6_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: genomic DNA from cord blood 277

description: normal cord blood sample

source_name: cord blood 277


title: genomic DNA from cord blood 275

description: normal cord blood sample

source_name: cord blood 275


title: genomic DNA from cord blood 273

description: normal cord blood sample

source_name: cord blood 273


title: genomic DNA from cord blood 272

description: normal cord blood sample

source_name: cord blood 272


title: B6_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: genomic DNA from cord blood 274

description: normal cord blood sample

source_name: cord blood 274


title: genomic DNA from cord blood 270

description: normal cord blood sample

source_name: cord blood 270


title: genomic DNA from cord blood 271

description: normal cord blood sample

source_name: cord blood 271


title: B6_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: B6_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: B6_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: genomic DNA from cord blood 268

description: normal cord blood sample

source_name: cord blood 268


title: genomic DNA from cord blood 269

description: normal cord blood sample

source_name: cord blood 269


title: B6_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: BALB_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: genomic DNA from cord blood 267

description: normal cord blood sample

source_name: cord blood 267


title: B6_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: BALB_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: BALB_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: genomic DNA from cord blood 264

description: normal cord blood sample

source_name: cord blood 264


title: genomic DNA from cord blood 265

description: normal cord blood sample

source_name: cord blood 265


title: BALB_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: B6_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: genomic DNA from cord blood 263

description: normal cord blood sample

source_name: cord blood 263


title: genomic DNA from cord blood 261

description: normal cord blood sample

source_name: cord blood 261


title: BALB_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: genomic DNA from cord blood 259

description: normal cord blood sample

source_name: cord blood 259


title: genomic DNA from cord blood 260

description: normal cord blood sample

source_name: cord blood 260


title: genomic DNA from cord blood 266

description: normal cord blood sample

source_name: cord blood 266


title: genomic DNA from cord blood 257

description: normal cord blood sample

source_name: cord blood 257


title: genomic DNA from cord blood 258

description: normal cord blood sample

source_name: cord blood 258


title: genomic DNA from cord blood 255

description: normal cord blood sample

source_name: cord blood 255


title: genomic DNA from cord blood 262

description: normal cord blood sample

source_name: cord blood 262


title: genomic DNA from cord blood 256

description: normal cord blood sample

source_name: cord blood 256


title: BALB_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: BALB_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: BALB_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: genomic DNA from cord blood 254

description: normal cord blood sample

source_name: cord blood 254


title: BALB_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: BALB_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: BALB_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: genomic DNA from cord blood 253

description: normal cord blood sample

source_name: cord blood 253


title: BALB_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: BALB_CORTEX_calorierestricted_biologicalrep2

source_name: CORTEX, Calorie Restricted diet, replicate 2


title: BALB_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: 129_CORTEX_calorierestricted_biologicalrep8

source_name: CORTEX, Calorie Restricted diet, replicate 8


title: genomic DNA from cord blood 251

description: normal cord blood sample

source_name: cord blood 251


title: 129_CORTEX_calorierestricted_biologicalrep4

source_name: CORTEX, Calorie Restricted diet, replicate 4


title: BALB_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: genomic DNA from cord blood 250

description: normal cord blood sample

source_name: cord blood 250


title: 129_CORTEX_calorierestricted_biologicalrep2


title: 129_CORTEX_calorierestricted_biologicalrep5

source_name: CORTEX, Calorie Restricted diet, replicate 5


title: 129_CORTEX_calorierestricted_biologicalrep7

source_name: CORTEX, Calorie Restricted diet, replicate 7


title: genomic DNA from cord blood 248

description: normal cord blood sample

source_name: cord blood 248


title: genomic DNA from cord blood 247

description: normal cord blood sample

source_name: cord blood 247


title: 129_CORTEX_control_biologicalrep8

source_name: CORTEX, Control diet, replicate 8


title: genomic DNA from cord blood 244

description: normal cord blood sample

source_name: cord blood 244


title: 129_CORTEX_calorierestricted_biologicalrep3

source_name: CORTEX, Calorie Restricted diet, replicate 3


title: 129_CORTEX_calorierestricted_biologicalrep1

source_name: CORTEX, Calorie Restricted diet, replicate 1


title: 129_CORTEX_control_biologicalrep7

source_name: CORTEX, Control diet, replicate 7


title: 129_CORTEX_calorierestricted_biologicalrep6

source_name: CORTEX, Calorie Restricted diet, replicate 6


title: genomic DNA from cord blood 249

description: normal cord blood sample

source_name: cord blood 249


title: genomic DNA from cord blood 245

description: normal cord blood sample

source_name: cord blood 245


title: genomic DNA from cord blood 252

description: normal cord blood sample

source_name: cord blood 252


title: genomic DNA from cord blood 243

description: normal cord blood sample

source_name: cord blood 243


title: genomic DNA from cord blood 246

description: normal cord blood sample

source_name: cord blood 246


title: 129_CORTEX_control_biologicalrep2

source_name: CORTEX, Control diet, replicate 2


title: genomic DNA from cord blood 240

description: normal cord blood sample

source_name: cord blood 240


title: BALB_CORTEX_control_biologicalrep8


title: 129_CORTEX_control_biologicalrep5

source_name: CORTEX, Control diet, replicate 5


title: 129_CORTEX_control_biologicalrep6

source_name: CORTEX, Control diet, replicate 6


title: 129_CORTEX_control_biologicalrep4

source_name: CORTEX, Control diet, replicate 4


title: genomic DNA from cord blood 242

description: normal cord blood sample

source_name: cord blood 242


title: 129_CORTEX_control_biologicalrep3

source_name: CORTEX, Control diet, replicate 3


title: genomic DNA from cord blood 235

description: normal cord blood sample

source_name: cord blood 235


title: genomic DNA from cord blood 236

description: normal cord blood sample

source_name: cord blood 236


title: genomic DNA from cord blood 241

description: normal cord blood sample

source_name: cord blood 241


title: genomic DNA from cord blood 239

description: normal cord blood sample

source_name: cord blood 239


title: genomic DNA from cord blood 230

description: normal cord blood sample

source_name: cord blood 230


title: genomic DNA from cord blood 237

description: normal cord blood sample

source_name: cord blood 237


title: genomic DNA from cord blood 238

description: normal cord blood sample

source_name: cord blood 238


title: genomic DNA from cord blood 234

description: normal cord blood sample

source_name: cord blood 234


title: genomic DNA from cord blood 232

description: normal cord blood sample

source_name: cord blood 232


title: genomic DNA from cord blood 233

description: normal cord blood sample

source_name: cord blood 233


title: genomic DNA from cord blood 229

description: normal cord blood sample

source_name: cord blood 229


title: don 31

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

description: gene expression

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned by Agilent G2565BA scanner and images were processed by Feature Extraction software v.9.5.3.1 (Agilent Technologies)

data_processing: Tab-delimited text files containing FE results were acquired and analyzed with Rv3.2.1 software using the limma package of Bioconductor. Data were preliminarily corrected for background and normalized in order to have similar distributions across the set of arrays. Ranking of genes by their evidence for differential expression was made using the paired moderated t-statistics based on empirical Bayes moderation of the standard errors

source_name: BM from healthy donor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com).  Dye incorporation and cRNA yield were checked with Nanodrop (Thermo Scientific).

growth_protocol: BM of healthy donors and BM of localized NB were directly subjected to RNA extraction

extract_protocol: Total RNA extraction was performed by the RNeasy Mini kit (qiagen) according to the manufacturer's instructions, including an Rnase-free DNAse digestion. Total RNA was quantified and the quality assessed by RNA 6000 Nano chip on the 2100 Bioanalyzer (Agilent technologies). only samples with RNA integrity number greater than 6 were included in the study.

treatment_protocol: To isolate resident BM cells, the BM samples from patients with localized and metastatic NB were subjected to immunomagnetic separation,after lysis of erythrocytes, cells were incubated for 30 minutes at 4°C with the anti-GD2 mAb in the presence of human Fc blocking reagent. After washing, the cell pellet was incubated for 15 minutes at 4°C with goat anti-mouse IgG2a microbeads (Miltenyi). Cells were then washed twice, suspended in 500 L of sterile ice-cold PBS and loaded onto a MS column (Miltenyi).The GD2 negative fractions were then subjected to RNA extraction.

tag: age (years)

value: M

tag: inss stage

value: Not Applicable

tag: mycn status

tag: date of sampling/diagnosis

tag: patient's id


title: don 18

description: gene expression


title: don 34

description: gene expression

value: F


title: don 30

description: gene expression


title: 129_CORTEX_control_biologicalrep1

source_name: CORTEX, Control diet, replicate 1


title: don 27

description: gene expression


title: don 19

description: gene expression


title: don 32

description: gene expression


title: genomic DNA from cord blood 231

description: normal cord blood sample

source_name: cord blood 231


title: genomic DNA from cord blood 227

description: normal cord blood sample

source_name: cord blood 227


title: genomic DNA from cord blood 226

description: normal cord blood sample

source_name: cord blood 226


title: genomic DNA from cord blood 224

description: normal cord blood sample

source_name: cord blood 224


title: genomic DNA from cord blood 228

description: normal cord blood sample

source_name: cord blood 228


title: genomic DNA from cord blood 223

description: normal cord blood sample

source_name: cord blood 223


title: genomic DNA from cord blood 225

description: normal cord blood sample

source_name: cord blood 225


title: don 33

description: gene expression


title: genomic DNA from cord blood 222

description: normal cord blood sample

source_name: cord blood 222


title: genomic DNA from cord blood 220

description: normal cord blood sample

source_name: cord blood 220


title: genomic DNA from cord blood 216

description: normal cord blood sample

source_name: cord blood 216


title: genomic DNA from cord blood 221

description: normal cord blood sample

source_name: cord blood 221


title: genomic DNA from cord blood 218

description: normal cord blood sample

source_name: cord blood 218


title: genomic DNA from cord blood 219

description: normal cord blood sample

source_name: cord blood 219


title: genomic DNA from cord blood 214

description: normal cord blood sample

source_name: cord blood 214


title: genomic DNA from cord blood 217

description: normal cord blood sample

source_name: cord blood 217


title: genomic DNA from cord blood 215

description: normal cord blood sample

source_name: cord blood 215


title: genomic DNA from cord blood 213

description: normal cord blood sample

source_name: cord blood 213


title: genomic DNA from cord blood 212

description: normal cord blood sample

source_name: cord blood 212


title: Farage_IL4+CHOP, biological rep2

city: SEOUL

first: Heejei

last: Yoon

state: SEOUL

address: 50 ILWON-DONG

department: SAMSUNG BIOMEDICAL RESEARCH INSTITUTE

country: South Korea

institute: SAMSUNG MEDICAL CENTER

description:
IL4 (50 ng/ml) and CHOP (1 μg/ml)-treated cells for 2 days
CHOP+IL4_2

hyb_protocol: End-labeled cDNA was hybridized for 16 hours at 45° and 60 rpm according to the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix)

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix) and scanned using a Genechip Array scanner 3000 7G (Affymetrix)

data_processing:
Affymetrix Command Console Software version 1.1 was used to process the raw images into CEL files. Gene expression estimates were normalized using the robust multiarray averaging (RMA) method.
HuGene-2_0-st.pgf
HuGene-2_0-st-v1.na33.hg19.transcript.csv

source_name: Farage, IL4+CHOP

label_protocol: One hundred nanograms of high quality total RNA was converted to double-stranded cDNA. Subsequent amplification of cRNA, labeling of probes, and scanning signals were performed according to the company’s protocol.

growth_protocol: Farage cells were cultured in an RPMI-1640 media supplemented with 10% heat-inactivated fetal bovine serum and antibiotics (100 μg/mL penicillin and streptomycin).

extract_protocol: Total RNA was extracted from the harvested cells using the RNeasy kit (QIAGEN, Germany).

treatment_protocol: 1) Farage cells were treated with 1 μg/ml CHOP for 2 days and 3 days. 2) Farage cells were incubated with 1 μg/ml CHOP plus 50 ng/ml IL4 or 50 ng/ml IL4 alone for 2 days

tag: cancer type

value: DLBCL

value: B cell lymphoma

tag: ebv status

value: EBV+

tag: cell type

value: Farage cells

value: IL4 and CHOP

tag: time

value: 2 days


title: don 29

description: gene expression

source_name: BM from healthy donor


title: don 21

description: gene expression


title: 3921a

description: gene expression

source_name: BM from localized NB

value: NOT DONE


title: 3289

description: gene expression

value: SINGLE COPY


title: 3278

description: gene expression


title: 464

description: gene expression


title: 3355

description: gene expression


title: don 22

description: gene expression


title: 994

description: gene expression


title: 3774

description: gene expression


title: Farage_IL4+CHOP, biological rep1

description:
IL4 (50 ng/ml) and CHOP (1 μg/ml)-treated cells for 2 days
CHOP+IL4_1


title: 3923a

description: gene expression

value: AMPLIFIED


title: 617

description: gene expression


title: don 17

description: gene expression


title: 3911a

description: gene expression

value: GAIN


title: 2056

description: gene expression


title: 3362

description: gene expression


title: Farage_IL4, biological rep2

description:
IL4 (50 ng/ml)-treated cells for 2 days
IL4_2

source_name: Farage, IL4


title: don 24

description: gene expression


title: 1803

description: gene expression


title: genomic DNA from cord blood 211

description: normal cord blood sample

source_name: cord blood 211

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: 770

description: gene expression


title: 693

description: gene expression


title: 3400

description: gene expression


title: 1472

description: gene expression


title: 3418

description: gene expression


title: Farage_IL4, biological rep1

description:
IL4 (50 ng/ml)-treated cells for 2 days
IL4_1


title: 1556

description: gene expression


title: genomic DNA from cord blood 210

description: normal cord blood sample

source_name: cord blood 210

value: cord blood


title: Farage_No drug, biological rep2

description:
No drug treated cells for 3 days
NoDrug_2

source_name: Farage, No drug

value: No drug treated

value: 3 days


title: 1135

description: gene expression

value: M


title: genomic DNA from cord blood 208

description: normal cord blood sample

source_name: cord blood 208


title: genomic DNA from cord blood 207

description: normal cord blood sample

source_name: cord blood 207


title: genomic DNA from cord blood 209

description: normal cord blood sample

source_name: cord blood 209


title: genomic DNA from cord blood 206

description: normal cord blood sample

source_name: cord blood 206


title: genomic DNA from cord blood 204

description: normal cord blood sample

source_name: cord blood 204


title: genomic DNA from cord blood 203

description: normal cord blood sample

source_name: cord blood 203


title: genomic DNA from cord blood 202

description: normal cord blood sample

source_name: cord blood 202


title: genomic DNA from cord blood 201

description: normal cord blood sample

source_name: cord blood 201


title: 3798a

description: gene expression

source_name: GD2 negative cells from localized NB


title: genomic DNA from cord blood 205

description: normal cord blood sample

source_name: cord blood 205


title: 3787

description: gene expression


title: Farage_No drug, biological rep1

description:
No drug treated cells for 2 days
NoDrug_1


title: Farage_CHOP, biological rep2

description:
CHOP (1 μg/ml)-treated cells for 3 days
CHOP_2

source_name: Farage, CHOP

value: CHOP


title: 3872

description: gene expression


title: 3723

description: gene expression

value: F


title: Farage_SLAMF1_low, biological rep2

description:
Bottom 10% most dimly labeled cells
SLAM_low_2

source_name: Farage, SLAMF1_low

value: DLBCL

tag: slam status

value: low


title: 3834

description: gene expression


title: 3746

description: gene expression


title: Farage_CHOP, biological rep1

description:
CHOP (1 μg/ml)-treated cells for 2 days
CHOP_1

tag: tissue

value: B cell lymphoma

value: EBV+


title: 3726

description: gene expression

tag: Sex


title: 3736

description: gene expression


title: Farage_SLAMF1_low, biological rep3

description:
Bottom 10% most dimly labeled cells
SLAM_low_3

value: Farage cells


title: Farage_SLAMF1_high, biological rep3

description:
Top 10% most brightly labeled cells
SLAM_high_3

source_name: Farage, SLAMF1_high

value: high


title: Farage_SLAMF1_high, biological rep2

description:
Top 10% most brightly labeled cells
SLAM_high_2


title: Farage_SLAMF1_high, biological rep1

description:
Top 10% most brightly labeled cells
SLAM_high_1


title: genomic DNA from cord blood 200

description: normal cord blood sample

source_name: cord blood 200


title: genomic DNA from cord blood 199

description: normal cord blood sample

source_name: cord blood 199


title: Farage_SLAMF1_low, biological rep1

description:
Bottom 10% most dimly labeled cells
SLAM_low_1


title: 3760a

description: gene expression


title: Chicken miR Embryo Leg sampleC10_17

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: microRNA expression of broiler M. gastrocnemius treat by varience incubation temperature

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on  GeneChip® miRNA-3_0-st-v3 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Gallus gallus

source_name: Musculus  gastrocnemius

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: stage/age of sampling

value: Embryo

tag: incubation temperature in treatment interval

value: Control 37.8 C

tag: time interval of varied incubation temperature


title: genomic DNA from cord blood 198

description: normal cord blood sample

source_name: cord blood 198


title: 3571

description: gene expression

value: SINGLE COPY


title: 3510

description: gene expression


title: genomic DNA from cord blood 197

description: normal cord blood sample

source_name: cord blood 197


title: genomic DNA from cord blood 196

description: normal cord blood sample

source_name: cord blood 196


title: genomic DNA from cord blood 195

description: normal cord blood sample

source_name: cord blood 195


title: genomic DNA from cord blood 194

description: normal cord blood sample

source_name: cord blood 194


title: 3501

description: gene expression

value: AMPLIFIED


title: Chicken miR Embryo Leg sampleC10_18


title: genomic DNA from cord blood 193

description: normal cord blood sample

source_name: cord blood 193

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: genomic DNA from cord blood 192

description: normal cord blood sample

source_name: cord blood 192

value: cord blood


title: Chicken miR Embryo Leg sampleC10_63


title: genomic DNA from cord blood 191

description: normal cord blood sample

source_name: cord blood 191


title: genomic DNA from cord blood 190

description: normal cord blood sample

source_name: cord blood 190


title: 3482

description: gene expression

source_name: GD2 negative cells from localized NB


title: genomic DNA from cord blood 189

description: normal cord blood sample

source_name: cord blood 189


title: Chicken miR Embryo Leg sampleC10_64


title: 5GD2-

description: gene expression

source_name: GD2 negative cells from metastatic NB


title: Chicken miR Embryo Leg sampleC13_39


title: 6GD2-

description: gene expression


title: 3917GD2-

description: gene expression


title: 3487

description: gene expression


title: 7GD2-

description: gene expression


title: genomic DNA from cord blood 188

description: normal cord blood sample

source_name: cord blood 188


title: genomic DNA from cord blood 187

description: normal cord blood sample

source_name: cord blood 187


title: Chicken miR Embryo Leg sampleC13_40


title: Chicken miR Embryo Leg sampleC13_87


title: Chicken miR Embryo Leg sampleC13_88


title: genomic DNA from cord blood 186

description: normal cord blood sample

source_name: cord blood 186


title: Chicken miR Embryo Leg sampleH10_12

value: High 38.8 C


title: 15GD2-

description: gene expression


title: 17GD2-

description: gene expression


title: 19GD2-

description: gene expression


title: 20GD2-

description: gene expression


title: Chicken miR Embryo Leg sampleH10_13


title: genomic DNA from cord blood 185

description: normal cord blood sample

source_name: cord blood 185


title: 14GD2-

description: gene expression

value: GAIN


title: Chicken miR Embryo Leg sampleH10_4

source_name: Musculus  gastrocnemius


title: Chicken miR Embryo Leg sampleH10_14


title: genomic DNA from cord blood 184

description: normal cord blood sample

source_name: cord blood 184


title: Chicken miR Embryo Leg sampleH10_9


title: Chicken miR Embryo Leg sampleH13_26


title: Chicken miR Embryo Leg sampleH10_6


title: Chicken miR Embryo Leg sampleH13_25


title: genomic DNA from cord blood 183

description: normal cord blood sample

source_name: cord blood 183


title: genomic DNA from cord blood 181

description: normal cord blood sample

source_name: cord blood 181


title: genomic DNA from cord blood 180

description: normal cord blood sample

source_name: cord blood 180


title: 13GD2-

description: gene expression


title: genomic DNA from cord blood 182

description: normal cord blood sample

source_name: cord blood 182


title: genomic DNA from cord blood 178

description: normal cord blood sample

source_name: cord blood 178


title: Chicken miR Embryo Leg sampleH13_27


title: genomic DNA from cord blood 179

description: normal cord blood sample

source_name: cord blood 179


title: Chicken miR Embryo Leg sampleH13_28


title: genomic DNA from cord blood 177

description: normal cord blood sample

source_name: cord blood 177


title: HCT116 PINCR KO treated with 5-FU rep 2

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

data_processing: The data were normalised using quantile normalization within lumi package in R

source_name: HCT116 PINCR KO treated with 5-FU

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

growth_protocol: HCT116 cells were cultured in DMEM with 10% FBS, at 37oC, 5%CO2

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HCT116 cells were genetic knockout for long noncoding RNA PINCR. PINCR WT and PINCR KO cells were kept untreated or treated with 100µM 5-FU for 24 hr.

tag: cell line

value: colorectal cancer cells

tag: genotype/variation

value: PINCR knockout

tag: treated with

value: 100µM 5-FU for 24 hr


title: Chicken miR Embryo Leg sampleH13_30


title: Chicken miR Embryo Leg sampleL10_55

value: Low 36.8 C


title: HCT116 PINCR KO treated with 5-FU rep 3


title: HCT116 PINCR KO treated with 5-FU rep 1


title: Chicken miR Embryo Leg sampleH13_29


title: HCT116 PINCR KO Control rep 3

source_name: HCT116 PINCR KO Control

value: none (untreated control)


title: Chicken miR Embryo Leg sampleL10_56


title: Chicken miR Embryo Leg sampleL10_57


title: HCT116 PINCR WT treated with 5-FU rep 2

source_name: HCT116 PINCR WT treated with 5-FU

value: WT


title: Chicken miR Embryo Leg sampleL10_59


title: HCT116 PINCR KO Control rep 1


title: HCT116 PINCR KO Control rep 2


title: genomic DNA from cord blood 176

description: normal cord blood sample

source_name: cord blood 176

tag: cohort


title: genomic DNA from cord blood 175

description: normal cord blood sample

source_name: cord blood 175


title: HCT116 PINCR WT treated with 5-FU rep 3


title: genomic DNA from cord blood 173

description: normal cord blood sample

source_name: cord blood 173


title: Chicken miR Embryo Leg sampleL10_60


title: genomic DNA from cord blood 174

description: normal cord blood sample

source_name: cord blood 174


title: HCT116 PINCR WT treated with 5-FU rep 1


title: HCT116 PINCR WT Control rep 3

source_name: HCT116 PINCR WT Control


title: genomic DNA from cord blood 172

description: normal cord blood sample

source_name: cord blood 172


title: genomic DNA from cord blood 171

description: normal cord blood sample

source_name: cord blood 171


title: genomic DNA from cord blood 170

description: normal cord blood sample

source_name: cord blood 170


title: genomic DNA from cord blood 168

description: normal cord blood sample

source_name: cord blood 168


title: genomic DNA from cord blood 169

description: normal cord blood sample

source_name: cord blood 169


title: Chicken miR Embryo Leg sampleL13_72

source_name: Musculus  gastrocnemius


title: Chicken miR Embryo Leg sampleL10_61


title: genomic DNA from cord blood 167

description: normal cord blood sample

source_name: cord blood 167


title: HCT116 PINCR WT Control rep 2


title: Chicken miR Embryo Leg sampleL13_74


title: genomic DNA from cord blood 166

description: normal cord blood sample

source_name: cord blood 166


title: Chicken miR Embryo Leg sampleL13_76


title: Chicken miR Embryo Leg sampleL13_73


title: T-101

city: seoul

first: minhee

last: park

address: shinchondong

institute: student

description: sample name: 12-67931T

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in MATLAB

source_name: colorectal carcinoma-101

extract_protocol: RNA was extracted with Trizol reagent, followed by  Dnase digestion and clean-up procedures. Quality control was performed with Agilent Bioanalyser.

value: colorectal carcinoma

tag: patient diagnosis

tag: disease stage

value: stageIII

tag: gender

value: male


title: Chicken miR Embryo Leg sampleL13_75

value: Embryo


title: T-99

description: sample name: 12-67316T

source_name: colorectal carcinoma-99


title: T-98

description: sample name: 12-66732T

source_name: colorectal carcinoma-98

value: female


title: HCT116 PINCR WT Control rep 1


title: T-100

description: sample name: 12-67924T

source_name: colorectal carcinoma-100


title: genomic DNA from cord blood 165

description: normal cord blood sample

source_name: cord blood 165


title: Chicken miR Embryo Leg sampleL13_77


title: T-96

description: sample name: 12-58382T

source_name: colorectal carcinoma-96


title: Chicken miR Mature Leg sampleC10_29

value: Mature

value: Control 37.8 C


title: Chicken miR Mature Leg sampleC10_30


title: T-95

description: sample name: 12-57995T

source_name: colorectal carcinoma-95


title: Chicken miR Mature Leg sampleC10_77


title: genomic DNA from cord blood 163

description: normal cord blood sample

source_name: cord blood 163

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: genomic DNA from cord blood 162

description: normal cord blood sample

source_name: cord blood 162

value: cord blood


title: T-97

description: sample name: 12-64221T

source_name: colorectal carcinoma-97


title: genomic DNA from cord blood 164

description: normal cord blood sample

source_name: cord blood 164


title: genomic DNA from cord blood 161

description: normal cord blood sample

source_name: cord blood 161


title: Chicken miR Mature Leg sampleC13_68


title: Chicken miR Mature Leg sampleC13_70


title: Chicken miR Mature Leg sampleC10_90


title: T-94

description: sample name: 12-53807T

source_name: colorectal carcinoma-94


title: Chicken miR Mature Leg sampleC13_81


title: genomic DNA from cord blood 160

description: normal cord blood sample

source_name: cord blood 160


title: genomic DNA from cord blood 159

description: normal cord blood sample

source_name: cord blood 159


title: T-93

description: sample name: 12-49610T

source_name: colorectal carcinoma-93


title: genomic DNA from cord blood 158

description: normal cord blood sample

source_name: cord blood 158


title: genomic DNA from cord blood 157

description: normal cord blood sample

source_name: cord blood 157


title: T-92

description: sample name: 12-48575T

source_name: colorectal carcinoma-92


title: genomic DNA from cord blood 156

description: normal cord blood sample

source_name: cord blood 156


title: T-90

description: sample name: 12-44663T

source_name: colorectal carcinoma-90


title: genomic DNA from cord blood 155

description: normal cord blood sample

source_name: cord blood 155


title: T-89

description: sample name: 12-38739T

source_name: colorectal carcinoma-89


title: Chicken miR Mature Leg sampleC13_83

source_name: Musculus  gastrocnemius


title: Chicken miR Mature Leg sampleH10_13

value: High 38.8 C


title: T-87

description: sample name: 12-35756T

source_name: colorectal carcinoma-87


title: Chicken miR Mature Leg sampleH10_66


title: T-88

description: sample name: 12-37897T

source_name: colorectal carcinoma-88


title: Chicken miR Mature Leg sampleH10_3


title: Chicken miR Mature Leg sampleH10_15


title: genomic DNA from cord blood 154

description: normal cord blood sample

source_name: cord blood 154


title: genomic DNA from cord blood 153

description: normal cord blood sample

source_name: cord blood 153


title: Chicken miR Mature Leg sampleH10_67


title: T-84

description: sample name: 12-34296T

source_name: colorectal carcinoma-84


title: Chicken miR Mature Leg sampleH10_72


title: T-86

description: sample name: 12-34710T

source_name: colorectal carcinoma-86


title: genomic DNA from cord blood 152

description: normal cord blood sample

source_name: cord blood 152


title: T-83

description: sample name: 12-33016T

source_name: colorectal carcinoma-83


title: T-85

description: sample name: 12-34460T

source_name: colorectal carcinoma-85


title: T-82

description: sample name: 12-31540T

source_name: colorectal carcinoma-82


title: genomic DNA from cord blood 151

description: normal cord blood sample

source_name: cord blood 151


title: genomic DNA from cord blood 150

description: normal cord blood sample

source_name: cord blood 150


title: genomic DNA from cord blood 149

description: normal cord blood sample

source_name: cord blood 149


title: Chicken miR Mature Leg sampleH13_31


title: genomic DNA from cord blood 148

description: normal cord blood sample

source_name: cord blood 148


title: Chicken miR Mature Leg sampleH13_34


title: T-81

description: sample name: 12-30931T

source_name: colorectal carcinoma-81


title: Chicken miR Mature Leg sampleH10_74


title: genomic DNA from cord blood 146

description: normal cord blood sample

source_name: cord blood 146


title: Chicken miR Mature Leg sampleH13_39

source_name: Musculus  gastrocnemius


title: T-79

description: sample name: 12-19589T

source_name: colorectal carcinoma-79


title: T-78

description: sample name: 12-18063T

source_name: colorectal carcinoma-78


title: Chicken miR Mature Leg sampleH13_50


title: T-76

description: sample name: 12-07444T

source_name: colorectal carcinoma-76


title: genomic DNA from cord blood 145

description: normal cord blood sample

source_name: cord blood 145


title: Chicken miR Mature Leg sampleH13_58


title: Chicken miR Mature Leg sampleH13_53


title: T-75

description: sample name: 11-67862T

source_name: colorectal carcinoma-75


title: T-77

description: sample name: 12-12728T

source_name: colorectal carcinoma-77


title: Chicken miR Mature Leg sampleH13_43


title: genomic DNA from cord blood 144

description: normal cord blood sample

source_name: cord blood 144


title: genomic DNA from cord blood 143

description: normal cord blood sample

source_name: cord blood 143


title: genomic DNA from cord blood 147

description: normal cord blood sample

source_name: cord blood 147


title: genomic DNA from cord blood 142

description: normal cord blood sample

source_name: cord blood 142


title: Chicken miR Mature Leg sampleL10_116


title: Chicken miR Mature Leg sampleH13_60


title: T-73

description: sample name: 11-67303T

source_name: colorectal carcinoma-73


title: T-91

description: sample name: 12-48031T

source_name: colorectal carcinoma-91


title: Chicken miR Mature Leg sampleL10_145


title: T-72

description: sample name: 11-67012T

source_name: colorectal carcinoma-72


title: T-71

description: sample name: 11-67008T

source_name: colorectal carcinoma-71


title: T-74

description: sample name: 11-67607T

source_name: colorectal carcinoma-74


title: genomic DNA from cord blood 141

description: normal cord blood sample

source_name: cord blood 141


title: Chicken miR Mature Leg sampleL10_153

source_name: Musculus  gastrocnemius


title: T-70

description: sample name: 11-65728T

source_name: colorectal carcinoma-70


title: genomic DNA from cord blood 139

description: normal cord blood sample

source_name: cord blood 139


title: genomic DNA from cord blood 140

description: normal cord blood sample

source_name: cord blood 140


title: genomic DNA from cord blood 138

description: normal cord blood sample

source_name: cord blood 138


title: genomic DNA from cord blood 137

description: normal cord blood sample

source_name: cord blood 137


title: genomic DNA from cord blood 135

description: normal cord blood sample

source_name: cord blood 135


title: genomic DNA from cord blood 136

description: normal cord blood sample

source_name: cord blood 136


title: T-68

description: sample name: 11-54207T

source_name: colorectal carcinoma-68


title: Chicken miR Mature Leg sampleL10_170


title: Chicken miR Mature Leg sampleL10_64


title: genomic DNA from cord blood 134

description: normal cord blood sample

source_name: cord blood 134


title: Chicken miR Mature Leg sampleL10_155


title: Chicken miR Mature Leg sampleL10_51


title: Chicken miR Mature Leg sampleL13_122


title: Chicken miR Mature Leg sampleL10_76


title: T-67

description: sample name: 11-54129T

source_name: colorectal carcinoma-67


title: T-69

description: sample name: 11-59287T

source_name: colorectal carcinoma-69


title: T-66

description: sample name: 11-52318T

source_name: colorectal carcinoma-66


title: Chicken miR Mature Leg sampleH10_11


title: T-65

description: sample name: 11-44446T

source_name: colorectal carcinoma-65


title: T-64

description: sample name: 11-42848T

source_name: colorectal carcinoma-64


title: genomic DNA from cord blood 131

description: normal cord blood sample

source_name: cord blood 131


title: genomic DNA from cord blood 130

description: normal cord blood sample

source_name: cord blood 130


title: genomic DNA from cord blood 133

description: normal cord blood sample

source_name: cord blood 133


title: Chicken miR Mature Leg sampleL13_161

source_name: Musculus  gastrocnemius


title: genomic DNA from cord blood 129

description: normal cord blood sample

source_name: cord blood 129


title: Chicken miR Mature Leg sampleL13_163


title: genomic DNA from cord blood 132

description: normal cord blood sample

source_name: cord blood 132


title: T-61

description: sample name: 11-27404T

source_name: colorectal carcinoma-61


title: T-60

description: sample name: 11-24177T

source_name: colorectal carcinoma-60


title: T-62

description: sample name: 11-34678T

source_name: colorectal carcinoma-62


title: T-63

description: sample name: 11-40633T

source_name: colorectal carcinoma-63


title: Chicken miR Mature Leg sampleL13_178


title: Chicken miR Mature Leg sampleL13_179


title: Chicken miR Mature Leg sampleL13_6


title: Chicken miR Mature Leg sampleL13_180


title: T-57

description: sample name: 11-13680T

source_name: colorectal carcinoma-57


title: T-59

description: sample name: 11-20764T

source_name: colorectal carcinoma-59


title: genomic DNA from cord blood 126

description: normal cord blood sample

source_name: cord blood 126


title: genomic DNA from cord blood 125

description: normal cord blood sample

source_name: cord blood 125


title: genomic DNA from cord blood 127

description: normal cord blood sample

source_name: cord blood 127


title: genomic DNA from cord blood 124

description: normal cord blood sample

source_name: cord blood 124


title: genomic DNA from cord blood 128

description: normal cord blood sample

source_name: cord blood 128


title: Chicken miR Embryo Breast sample C10_17

description: microRNA expression of broiler M. longissimus dorsi treat by varience incubation temperature

source_name: Musculus  pectoralis


title: genomic DNA from cord blood 123

description: normal cord blood sample

source_name: cord blood 123


title: T-58

description: sample name: 11-17727T

source_name: colorectal carcinoma-58


title: T-56

description: sample name: 11-13591T

source_name: colorectal carcinoma-56


title: genomic DNA from cord blood 122

description: normal cord blood sample

source_name: cord blood 122


title: Chicken miR Embryo Breast sample C10_18


title: Chicken miR Embryo Breast sample C10_63


title: genomic DNA from cord blood 121

description: normal cord blood sample

source_name: cord blood 121


title: Chicken miR Mature Leg sampleL13_91

source_name: Musculus  gastrocnemius


title: Chicken miR Embryo Breast sample C13_39


title: T-55

description: sample name: 11-12086T

source_name: colorectal carcinoma-55


title: T-53

description: sample name: 11-06114T

source_name: colorectal carcinoma-53


title: Chicken miR Embryo Breast sample C10_64


title: T-54

description: sample name: 11-10575T

source_name: colorectal carcinoma-54


title: genomic DNA from cord blood 120

description: normal cord blood sample

source_name: cord blood 120


title: T-50

description: sample name: 08-50942T

source_name: colorectal carcinoma-50


title: T-80

description: sample name: 12-26249T

source_name: colorectal carcinoma-80


title: T-51

description: sample name: 09-08167T

source_name: colorectal carcinoma-51


title: Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 20

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Continuous anaerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: Wild type strain MG1655

tag: agent

value: control

value: 0 min

tag: culture conditions

value: anaerobic

value: 20 min


title: T-52

description: sample name: 11-02218T

source_name: colorectal carcinoma-52


title: genomic DNA from cord blood 119

description: normal cord blood sample

source_name: cord blood 119


title: T-49

description: sample name: 08-45632T

source_name: colorectal carcinoma-49


title: Chicken miR Embryo Breast sample H10_11

source_name: Musculus  pectoralis


title: Chicken miR Embryo Breast sample C13_87


title: Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 10

tag: time

value: 10 min


title: Chicken miR Embryo Breast sample C13_88


title: Chicken miR Embryo Breast sample C13_40


title: T-48

description: sample name: 08-45631T

source_name: colorectal carcinoma-48


title: T-47

description: sample name: 08-45024T

source_name: colorectal carcinoma-47


title: genomic DNA from cord blood 118

description: normal cord blood sample

source_name: cord blood 118


title: genomic DNA from cord blood 115

description: normal cord blood sample

source_name: cord blood 115


title: Chicken miR Embryo Breast sample H10_13


title: Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 2.5

value: 2.5 min


title: Chicken miR Embryo Breast sample H10_4


title: Chicken miR Embryo Breast sample H10_12


title: genomic DNA from cord blood 116

description: normal cord blood sample

source_name: cord blood 116


title: genomic DNA from cord blood 117

description: normal cord blood sample

source_name: cord blood 117


title: Chicken miR Embryo Breast sample H10_6


title: Chicken miR Embryo Breast sample H13_25


title: Slide 58_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 5

value: 5 min


title: genomic DNA from cord blood 112

description: normal cord blood sample

source_name: cord blood 112


title: genomic DNA from cord blood 113

description: normal cord blood sample

source_name: cord blood 113


title: genomic DNA from cord blood 114

description: normal cord blood sample

source_name: cord blood 114


title: genomic DNA from cord blood 110

description: normal cord blood sample

source_name: cord blood 110


title: genomic DNA from cord blood 111

description: normal cord blood sample

source_name: cord blood 111


title: genomic DNA from cord blood 109

description: normal cord blood sample

source_name: cord blood 109


title: genomic DNA from cord blood 108

description: normal cord blood sample

source_name: cord blood 108


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 80

source_name: Continuous anaerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: 80 min


title: Chicken miR Embryo Breast sample H13_26


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 20 Cy5 0


title: Chicken miR Embryo Breast sample H10_9


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 40 Cy5 0

value: 40 min


title: T-45

description: sample name: 08-43732T

source_name: colorectal carcinoma-45

value: colorectal carcinoma

value: stageIII

value: male


title: Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 40 Cy5 0


title: T-43

description: sample name: 08-40745T

source_name: colorectal carcinoma-43

value: female


title: T-38

description: sample name: 08-29075T

source_name: colorectal carcinoma-38


title: Chicken miR Embryo Breast sample H13_29

source_name: Musculus  pectoralis

value: Embryo


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 80 Cy5 0


title: Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 80 Cy5 0


title: T-40

description: sample name: 08-31789T

source_name: colorectal carcinoma-40


title: T-37

description: sample name: 08-23789T

source_name: colorectal carcinoma-37


title: Chicken miR Embryo Breast sample H13_30


title: Chicken miR Embryo Breast sample L10_55

value: Low 36.8 C


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 5 Cy5 0


title: T-46

description: sample name: 08-44735T

source_name: colorectal carcinoma-46


title: Chicken miR Embryo Breast sample H13_28

value: High 38.8 C


title: Chicken miR Embryo Breast sample H13_27


title: T-44

description: sample name: 08-41815T

source_name: colorectal carcinoma-44


title: T-42

description: sample name: 08-39721T

source_name: colorectal carcinoma-42


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 40

value: Wild type strain MG1655


title: T-36

description: sample name: 08-23629T

source_name: colorectal carcinoma-36


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 2.5 Cy5 0

value: control


title: genomic DNA from cord blood 107

description: normal cord blood sample

source_name: cord blood 107

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)

value: cord blood


title: T-39

description: sample name: 08-29740T

source_name: colorectal carcinoma-39


title: Chicken miR Embryo Breast sample L10_56


title: Slide 59_Anaerobic culture_CORM-401_biol rep 2_Cy3 10 Cy5 0

value: anaerobic

value: 0 min


title: T-41

description: sample name: 08-35263T

source_name: colorectal carcinoma-41


title: genomic DNA from cord blood 104

description: normal cord blood sample

source_name: cord blood 104


title: genomic DNA from cord blood 105

description: normal cord blood sample

source_name: cord blood 105


title: genomic DNA from cord blood 103

description: normal cord blood sample

source_name: cord blood 103


title: Chicken miR Embryo Breast sample L10_57


title: genomic DNA from cord blood 102

description: normal cord blood sample

source_name: cord blood 102


title: Chicken miR Embryo Breast sample L10_59