title: STEMI patient, blood collected on discharge (Patient 28)

description:
Sample name: Patient 28_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: discharge (after 4-6 days of MI)


title: STEMI patient, blood collected on admission (Patient 26)

status: Public on Oct 23 2014

type: RNA

city: Warsaw

first: Beata

last: Burzynska

address: Pawinskiego 5A

department: Genetics

country: Poland

institute: Institute of Biochemistry and Biophysics

description:
Sample name: Patient 26_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

hyb_protocol: Following fragmentation, 5.5 ug ssDNA were hybridized for 16 hr at 45˚C on GeneChip® Human Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 GeneArray Scanner.

data_processing: The data were analyzed with the Partek Genomics Suite software (Partek Inc, St. Louis, MO, USA) using RMA (robust multiarray average) background correction, quantile normalization, median polish method for probesets summarization, and log values of probes signals using base 2.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Biotin-labeled ssDNA were prepared from 100 ng total RNA by using the Ambion® WT Expression Kit followed by Affymetrix® GeneChip® WT Terminal Labeling Kit according to the manufacturer's instruction.

extract_protocol: Total RNA from peripheral blood mononuclear cells (PBMCs) samples was isolated using MagNA Pure Compact System (Roche Diagnostics GmbH, Germany) according to the manufacturer's recommendations. The amount of RNA was quantified by UV absorption (Nanodrop, LabTech International, UK) and its quality was determined using an Agilent 2100 Bioanalizer© and RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). For all RNA samples the RNA integrity number value was above eight.

tag: individual

value: Patient 26

tag: cardiovascular disease state

value: STEMI

tag: collection of blood samples

value: admission (on the 1st day of MI)

tag: cell type

value: PBMC


title: STEMI patient, blood collected on admission (Patient 27)

description:
Sample name: Patient 27_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 27


title: STEMI patient, blood collected on discharge (Patient 27)

description:
Sample name: Patient 27_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected 6 months after MI (Patient 26)

description:
Sample name: Patient 26_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: follow-up (6 months after MI)


title: STEMI patient, blood collected on discharge (Patient 26)

description:
Sample name: Patient 26_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on admission (Patient 25)

description:
Sample name: Patient 25_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 25


title: STEMI patient, blood collected 6 months after MI (Patient 24)

description:
Sample name: Patient 24_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 24


title: STEMI patient, blood collected on discharge (Patient 24)

description:
Sample name: Patient 24_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 22)

description:
Sample name: Patient 22_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 22


title: STEMI patient, blood collected 6 months after MI (Patient 25)

description:
Sample name: Patient 25_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on discharge (Patient 25)

description:
Sample name: Patient 25_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected 6 months after MI (Patient 22)

description:
Sample name: Patient 22_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected 6 months after MI (Patient 23)

description:
Sample name: Patient 23_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 23


title: STEMI patient, blood collected on admission (Patient 23)

description:
Sample name: Patient 23_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 21)

description:
Sample name: Patient 21_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 21


title: STEMI patient, blood collected on admission (Patient 22)

description:
Sample name: Patient 22_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 19)

description:
Sample name: Patient 19_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 19


title: STEMI patient, blood collected on admission (Patient 24)

description:
Sample name: Patient 24_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on admission (Patient 19)

description:
Sample name: Patient 19_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on discharge (Patient 23)

description:
Sample name: Patient 23_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected 6 months after MI (Patient 18)

description:
Sample name: Patient 18_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 18


title: STEMI patient, blood collected on discharge (Patient 20)

description:
Sample name: Patient 20_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 20


title: STEMI patient, blood collected on admission (Patient 21)

description:
Sample name: Patient 21_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 20)

description:
Sample name: Patient 20_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on admission (Patient 17)

description:
Sample name: Patient 17_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 17


title: STEMI patient, blood collected on discharge (Patient 19)

description:
Sample name: Patient 19_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 17)

description:
Sample name: Patient 17_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 18)

description:
Sample name: Patient 18_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 21)

description:
Sample name: Patient 21_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on admission (Patient 18)

description:
Sample name: Patient 18_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on discharge (Patient 16)

description:
Sample name: Patient 16_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 16


title: STEMI patient, blood collected on admission (Patient 16)

description:
Sample name: Patient 16_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 17)

description:
Sample name: Patient 17_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on admission (Patient 20)

description:
Sample name: Patient 20_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on admission (Patient 14)

description:
Sample name: Patient 14_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 14


title: STEMI patient, blood collected on admission (Patient 15)

description:
Sample name: Patient 15_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 15


title: STEMI patient, blood collected on discharge (Patient 15)

description:
Sample name: Patient 15_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: STEMI

value: discharge (after 4-6 days of MI)


title: STEMI patient, blood collected on discharge (Patient 14)

description:
Sample name: Patient 14_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: PBMC


title: STEMI patient, blood collected 6 months after MI (Patient 15)

description:
Sample name: Patient 15_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on discharge (Patient 13)

description:
Sample name: Patient 13_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 13


title: STEMI patient, blood collected 6 months after MI (Patient 16)

description:
Sample name: Patient 16_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: follow-up (6 months after MI)


title: STEMI patient, blood collected on admission (Patient 12)

description:
Sample name: Patient 12_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 12

value: admission (on the 1st day of MI)


title: STEMI patient, blood collected on admission (Patient 13)

description:
Sample name: Patient 13_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 13)

description:
Sample name: Patient 13_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected 6 months after MI (Patient 12)

description:
Sample name: Patient 12_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on discharge (Patient 12)

description:
Sample name: Patient 12_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 10)

description:
Sample name: Patient 10_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 10


title: STEMI patient, blood collected 6 months after MI (Patient 14)

description:
Sample name: Patient 14_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on admission (Patient 9)

description:
Sample name: Patient 9_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 9


title: STEMI patient, blood collected 6 months after MI (Patient 10)

description:
Sample name: Patient 10_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on discharge (Patient 9)

description:
Sample name: Patient 9_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on admission (Patient 10)

description:
Sample name: Patient 10_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on admission (Patient 11)

description:
Sample name: Patient 11_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 11


title: STEMI patient, blood collected 6 months after MI (Patient 9)

description:
Sample name: Patient 9_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on discharge (Patient 8)

description:
Sample name: Patient 8_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 8


title: STEMI patient, blood collected on discharge (Patient 11)

description:
Sample name: Patient 11_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on admission (Patient 8)

description:
Sample name: Patient 8_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 5)

description:
Sample name: Patient 5_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 5


title: STEMI patient, blood collected 6 months after MI (Patient 8)

description:
Sample name: Patient 8_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on admission (Patient 6)

description:
Sample name: Patient 6_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: Patient 6


title: STEMI patient, blood collected 6 months after MI (Patient 4)

description:
Sample name: Patient 4_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 4


title: STEMI patient, blood collected on discharge (Patient 7)

description:
Sample name: Patient 7_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 7


title: STEMI patient, blood collected on discharge (Patient 5)

description:
Sample name: Patient 5_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected 6 months after MI (Patient 6)

description:
Sample name: Patient 6_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected 6 months after MI (Patient 7)

description:
Sample name: Patient 7_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up


title: STEMI patient, blood collected on admission (Patient 5)

description:
Sample name: Patient 5_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on discharge (Patient 4)

description:
Sample name: Patient 4_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on discharge (Patient 6)

description:
Sample name: Patient 6_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: STEMI patient, blood collected on admission (Patient 7)

description:
Sample name: Patient 7_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected 6 months after MI (Patient 3)

description:
Sample name: Patient 3_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 3


title: STEMI patient, blood collected on admission (Patient 3)

description:
Sample name: Patient 3_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: STEMI patient, blood collected on discharge (Patient 3)

description:
Sample name: Patient 3_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: Control patient with stable CAD (Control 9)

description:
Sample name: Control 9
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 9

value: CAD

value: admission


title: STEMI patient, blood collected 6 months after MI (Patient 2)

description:
Sample name: Patient 2_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 2

value: STEMI

value: PBMC


title: Control patient with stable CAD (Control 11)

description:
Sample name: Control 11
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 11


title: STEMI patient, blood collected on admission (Patient 4)

description:
Sample name: Patient 4_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission

value: admission (on the 1st day of MI)


title: Control patient with stable CAD (Control 8)

description:
Sample name: Control 8
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 8


title: Control patient with stable CAD (Control 10)

description:
Sample name: Control 10
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 10


title: Control patient with stable CAD (Control 14)

description:
Sample name: Control 14
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 14


title: Control patient with stable CAD (Control 4)

description:
Sample name: Control 4
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 4


title: STEMI patient, blood collected on discharge (Patient 1)

description:
Sample name: Patient 1_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge

value: Patient 1

value: discharge (after 4-6 days of MI)


title: STEMI patient, blood collected on admission (Patient 2)

description:
Sample name: Patient 2_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: Control patient with stable CAD (Control 5)

description:
Sample name: Control 5
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 5


title: Control patient with stable CAD (Control 7)

description:
Sample name: Control 7
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 7


title: STEMI patient, blood collected 6 months after MI (Patient 1)

description:
Sample name: Patient 1_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: follow-up (6 months after MI)


title: STEMI patient, blood collected on admission (Patient 1)

description:
Sample name: Patient 1_admission
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on admission


title: Control patient with stable CAD (Control 13)

description:
Sample name: Control 13
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 13


title: STEMI patient, blood collected on discharge (Patient 2)

description:
Sample name: Patient 2_discharge
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI on discharge


title: Control patient with stable CAD (Control 12)

description:
Sample name: Control 12
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 12

value: CAD


title: Control patient with stable CAD (Control 2)

description:
Sample name: Control 2
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 2

value: admission


title: Control patient with stable CAD (Control 6)

description:
Sample name: Control 6
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 6

value: PBMC


title: Dental pulp cells control sample triplicate 1

city: La Jolla

first: Alysson

middle: Renato

last: Muotri

state: CA

address: Scenic Road - Sanford Consortium, Room 3005

department: Dept. Cellular & Molecular Medicine

country: USA

institute: University of California San Diego

description: gene expression data from dental pulp cells

hyb_protocol: GeneChip Affymetrix Human Gene 1.0 ST Array

scan_protocol: GeneChips were scanned using the Scanner 3000 7G System

data_processing: The data were analyzed using R/Bioconductor affy package

source_name: dental pulp cells obtained from milk teeth

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol

growth_protocol: Dental pulp cells were grown in DMEM/F12 media supplemented with 1% non-essential aminoacids and 15% fetal bovine serum. iPSC cells were grown in mTeSR media (Stem cell Technologies). Embryonic cells were grown in human embryonic stem cells media (DMEM/F12 media supplemented with 20% knockout serum replacement; 50uM b-mercaptoethanol, 1% non-essential aminoacids; 10ng/ml FGF)

extract_protocol: total RNA was extracted using Tryzol based extraction method

treatment_protocol: no treatment protocol was used

value: dental pulp cells


title: Dental pulp cells idipopathic autistic patient triplicate 3


title: Control patient with stable CAD (Control 1)

description:
Sample name: Control 1
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 1


title: Control patient with stable CAD (Control 3)

description:
Sample name: Control 3
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with stable CAD

value: Control 3


title: Dental pulp cells TRPc6-mut patient triplicate 2


title: iPSC TRPC6-mut patient clone3 triplicate 3

description: gene expression data from induced pluripotent stem cells generated from dental pulp cells

source_name: induced pluripotent stem cells obtained from dental pulp cells

value: induced pluripotent stem cells


title: iPSC TRPC6-mut patient clone6 triplicate 2


title: iPSC TRPC6-mut patient clone4 triplicate 2


title: Dental pulp cells TRPc6-mut patient triplicate 3


title: Dental pulp cells control sample triplicate 2


title: iPSC TRPC6-mut patient clone3 triplicate 2


title: Dental pulp cells idipopathic autistic patient triplicate 1


title: iPSC TRPC6-mut patient clone6 triplicate 1


title: iPSC TRPC6-mut patient clone4 triplicate 1


title: embryonic stem cell triplicate 3

description: gene expression data from human embryonic stem cells (lineage H1)

source_name: H1 embryonic stem cell lineage

value: embryonic stem cells


title: embryonic stem cell triplicate 2


title: iPSC idiopathic autistic patient triplicate 3


title: Dental pulp cells idipopathic autistic patient triplicate 2


title: iPSC control triplicate 2


title: Dental pulp cells TRPc6-mut patient triplicate 1


title: iPSC idiopathic autistic patient triplicate 2


title: iPSC idiopathic autistic patient triplicate 1


title: Dental pulp cells control sample triplicate 3


title: iPSC TRPC6-mut patient clone3 triplicate 1


title: iPSC control triplicate 1


title: iPSC TRPC6-mut patient clone4 triplicate 3


title: dental pulp cell from TRPC6-mut patient triplicate 3

description: gene expression data from DPC in passage #6

growth_protocol: Cells were grown in DMEM/F12 media supplemented with 1% non-essential aminoacids, 15% fetal bovine serum and 1% penicilin/streptomicin

extract_protocol: RNA was extracted using Tryzol based extraction protocol

treatment_protocol: no treatment was used

tag: tissue

tag: genotype

value: TRPC6 mutant

tag: passages


title: STEMI patient, blood collected 6 months after MI (Patient 11)

description:
Sample name: Patient 11_6 months
Gene expression data from peripheral blood mononuclear cells (PBMCs) of patient with STEMI 6 months follow-up

value: Patient 11

value: STEMI


title: dental pulp cell from TRPC6-mut patient triplicate 2


title: iPSC control triplicate 3


title: dental pulp cell from control 6

value: control


title: dental pulp cell from TRPC6-mut patient triplicate 1


title: dental pulp cell from control 3


title: dental pulp cell from control 1


title: dental pulp cell from control 2

description: gene expression data from DPC in passage #7


title: M-/-.3ABY721 I CONST

city: New York

first: E. Richard

last: Stanley

state: New York

address: 1300 Morris Park Ave

department: Dev and Molecular Biology

institute: Albert Einstein College of Medicine

description: GeneChip Mouse Gene 1.0 ST Array

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized by the Genomics Core at Einstein, according to manufacturer’s instructions, for 16 hr at 45C on GeneChip Mouse Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned by the Genomics Core at Einstein using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: R/Bioconductor

organism: Mus musculus

source_name: M-/-.3ABY721 cells constitutively grown in CSF-1

label_protocol: Biotinylated cRNA were prepared by the Genomics core at Einstein according to the standard Affymetrix protocol from 100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: M-/-.WT, M-/-.Y721F, M-/-.3ABY721, M-/-.3AB cell lines were cultured in alpha modified Eagle’s medium (α-MEM) containing 10% newborn calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin. Unless otherwise specified 120 ng/mL human recombinant CSF-1 was added to the cultures.

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

treatment_protocol: Cells were either starved overnight for CSF-1 and subsequently stimulated with CSF-1 for 0min, 20 min, 60 min and 180 min, or constitutively grown in CSF-1.

tag: treatment

value: CSF-1 grown

tag: cell line

value: M-/-.3ABY721 cells


title: M-/-.3AB I UR

description: GeneChip Mouse Gene 1.0 ST Array

source_name: CSF-1 starved, M-/-.3AB cells

value: CSF-1 starved

value: M-/-.3AB cells


title: M-/-.3ABY721 I UR

description: GeneChip Mouse Gene 1.0 ST Array

source_name: CSF-1 starved, M-/-.3ABY721 cells


title: M-/-.Y721F I CONST

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.Y721F cells constitutively grown in CSF-1

value: M-/-.Y721F cells


title: M-/-.3ABY721 II UR

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F II CONST

description: GeneChip Mouse Gene 1.0 ST Array


title: embryonic stem cell triplicate 1


title: M-/-.WT I UR

description: GeneChip Mouse Gene 1.0 ST Array

source_name: CSF-1 starved, M-/-.WT cells

value: M-/-.WT cells


title: M-/-.3AB I CONST

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.3AB cells constitutively grown in CSF-1


title: M-/-.WT I CONST

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.WT cells constitutively grown in CSF-1


title: M-/-.3AB II UR

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F II 180 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.Y721F CSF-1 starved cells stimulated with CSF-1 for180 min

value: CSF-1 treated

tag: time

value: 180 min


title: M-/-.3ABY721 II CONST

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.WT II UR

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.3AB II CONST

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.WT II CONST

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F II UR

description: GeneChip Mouse Gene 1.0 ST Array

source_name: CSF-1 starved, M-/-.Y721F cells


title: M-/-.Y721F I UR

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F II 0min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F I 0min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F I180 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.Y721F CSF-1 starved cells stimulated with CSF-1 for 180 min


title: M-/-.Y721F II 20 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.Y721F CSF-1 starved cells stimulated with CSF-1 for 20 min

value: 20 min


title: M-/-.WT II 60 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.WT CSF-1 starved cells stimulated with CSF-1 for 60 min

value: 60 min


title: M-/-.WT II 20 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.WT CSF-1 starved cells stimulated with CSF-1 for 20 min


title: M-/-.Y721F II 60 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.Y721F CSF-1 starved cells stimulated with CSF-1 for 60 min


title: M-/-.WT II 0min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F I 20 min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.Y721F I 60 min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.WT I 180 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.WT CSF-1 starved cells stimulated with CSF-1 for180 min


title: M-/-.WT II 180 min

description: GeneChip Mouse Gene 1.0 ST Array

source_name: M-/-.WT CSF-1 starved cells stimulated with CSF-1 for 180 min


title: M-/-.WT I 60 min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.WT I 0min

description: GeneChip Mouse Gene 1.0 ST Array


title: M-/-.WT I 20 min

description: GeneChip Mouse Gene 1.0 ST Array


title: Neural stem cells 1

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

country: Australia

institute: Telethon Kids Institute

description: CD133 positive cells isolated from neurospheres by FACS

hyb_protocol: Biotinylated cRNA (15 μg) was hybridized to  HG-U133A arrays, which were washed, stained,  and scanned using a GeneArray Scanner (Agilent  Technologies) according to the Affymetrix protocol

scan_protocol: Not provided

data_processing: Array images were reduced to intensity values  for each probe (cel files) using Affymetrix  Microarray Suite (MAS) 5.0 and these cel files  were analyzed using the statistical software package  R, which is available from www.r-project.org.  The software, Methods for Affymetrix Oligonucleotide  Arrays, a suite of functions for R,  is available from the bioconductor website (www.  bioconductor.org). We obtained expression measures  after robust multiarray analysis (RMA).

label: Biotin

source_name: Neural stem cells

label_protocol: Biotinylated cRNA target for hybridization  was prepared from 10 μg of total RNA,  respectively, according to Affymetrix  protocols.

growth_protocol: Human neurospheres were derived from embryonic stem cell (hESC) lines hES3, hES4 (ES Cell International, Singapore, http://www.escellinternational.com) and MEL1 (StemCore, Melbourne, VIC, Australia, http://www.stemcore.com.au), derived from three different individuals. hESCs were co-cultured for 14 days on a layer of mitomycin-C-treated mouse embryo fibroblasts in the presence of the BMP2-antagonist, Noggin (500ng/ml). Cell clumps were mechanically excised from Noggin-treated colonies and transferred to 96-well ultra-low adherence plates. Neurospheres were cultured up to 12 weeks in neural basal medium (NBM)  supplemented with N2, B27, Penicillin/Streptomycin, L-Glutamine, Interferrin-Transferrin-Selenium, EGF (20ng/ml) and bFGF (20ng/ml). Growth factors were added fresh every 2-3 days during media change. Neurospheres were quartered and replated for propagation.

extract_protocol: Tumour and foetal brain tissue were disrupted using an immersion processor and cells were washed in PBS and pelleted before resuspension in TRIzol. After 5 min of incubation at RT, 0.2 ml of chloroform was added to each 1 ml TRIzol. The phases were mixed and centrifuged (13000 rpm) for 15 min at 4ºC. The upper phase was collected and adjusted to 35% ethanol by adding 100% pure ethanol. The solution was applied to an RNeasy column (Qiagen) and RNA was purified according to the manufacturer’s instructions. The RNA was eluted using 50 μl diethyl pyrocarbonate (DEPC)-treated water and precipitated by the addition of 0.1 volume NaOAc, 2.5 volume of 100% ethanol and 1μl glycogen. After 1 hr at -20ºC, the samples were centrifuged (13000 rpm) for 20 min at 4ºC. The RNA pellet was washed twice with 80% ethanol and air-dried prior to resuspension in 10μl DEPC-treated water. RNA integrity was measured with an Agilent 2100 Bioanalyser.

tag: age

tag: Sex

tag: diagnosis note

tag: location


title: Neural stem cells 2


title: IMP3

city: Taipei

first: Yi-Shuan

last: Sheen

address: 7 Chun-Shan South Road

department: Dermatology

country: Taiwan

institute: Natioanl Taiwan University Hospital

description: biological replicate 1 of 2

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Human Whole Genome Oligo 4×44K microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: IMP3 transfected MeWo melanoma cells

label_protocol: One μg of total RNA was amplified by a Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes.

growth_protocol: MeWo melanoma cells were obtained from the American Type Culture Collection and cultured in Dulbecco's Modified Eagle’s medium (Gibco-BRL, Gaithersburg, MD, USA)

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

treatment_protocol: The IMP-3 expression plasmid (pCMV-IMP3) was kindly provided by Dr. Yung-Ming Jeng. pCMV-IMP3 was transfected into MeWo cells using the Lipofetamine 2000 reagent (Invitrogen, Carlsbad, CA, USA). Vec plasmid was used as a control. Stable clones of the above cell lines were selected using puromycin.

value: MeWo melanoma cells

tag: plasmid

source_name: Vec

value: Vec


title: Normal foetal germinal matrix 2

source_name: Normal foetal germinal matrix

value: 16 weeks

value: M


title: Neural progenitor cells 3

description: CD133 negative cells isolated from neurospheres by FACS

source_name: Neural progenitor cells


title: Normal foetal brain

description: Pooled RNA from 50 individuals

source_name: Normal foetal brain

value: 22-33 weeks


title: Neural progenitor cells 1


title: Medulloblastoma 32A

source_name: Medulloblastoma

value: F

value: desmoplastic

value: posterior fossa


title: MeWo- IMP3

description: biological replicate 2 of 2

source_name: MeWo-Vec


title: Neural progenitor cells 2


title: Donor_8_VSL3andLPS

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

country: Netherlands

institute: TNO

description: monocyte derived DC

data_processing:
For each experimental condition, cDNA from 6 individual donors was analyzed. Gene expression was normalized to internal controls (housekeeping genes) to determine the fold change in gene expression between test and control samples by ΔΔCt (SuperArray Bioscience).
Fold change are compared to unstimulated cells

label: SYBR Green

source_name: Donor 8

label_protocol: 500 ng RNA was used for single stranded cDNA synthesis using a High Capacity RNA-to-cDNA kit (Applied Biosystems, Carlsbad, CA USA) and incubated for 60 min at 37 oC and 5 minutes at 95 oC. cDNA was used for PCR-array analysis by using the RT2-Profiler PCR Array (human cytokine & chemokine array) from SuperArray Bioscience (Frederick, MD, USA). The PCR array combines the quantitative performance of SYBR Green-based real-time PCR with the multiple gene profiling capabilities of microarray. 96-well plates containing gene-specific primer sets for 84 chemokines and cytokines, 5 housekeeping genes, and 2 negative controls were used.

growth_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated from buffy coats of healthy donors (Sanquin, Leiden, the Netherlands) by Histopaque (Sigma Diagnostics St.Louis, MO, USA) density gradient centrifugation. Human monocytes were purified from PBMC by positive selection using anti-CD14-conjugated magnetic microbeads (StemCell Technologies, Grenoble, France). The recovered cells were 95 % to 99 % CD14+ as determined by flow cytometry. Monocytes were cultured at 2 × 106/ml in RPMI1640 supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, 10 μM ultraglutamin and 5% (v/v) FBS (Lonza, Verviers, Belgium). In order to stimulate their differentiation into DC, cells were cultured in the presence of GM-CSF (50 ng/ml) and IL-4 (40 ng/ml). After 5 days of culture, immature DC were washed and seeded at 106/well in 24-well plates.

extract_protocol: Total RNA was isolated from 106 cells using a RNAEasy Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Stimuli – all in culture medium – were added to these DC and after 48 hours of culture supernatants were harvested for cytokine and chemokine profiling. For RNA profiling, RNA was isolated after 4 hours of culture. VSL#3, a mixture containing 8 different lactic acid bacteria, was purchased from Ferring Pharmaceuticals (Berkshire, UK). Freshly reconstituted bacteria from lyophilized stocks were added to DC cultures at a bacteria – DC ratio of 10 to 1.  Ultrapure LPS E. coli K12 (final concentration 1 μg/ml) was purchased from Invivogen (San Diego, California, USA).

value: human DC


title: Donor_8_VSL3

description: monocyte derived DC


title: Normal foetal germinal matrix 1


title: Donor_9_LPS

description: monocyte derived DC

source_name: Donor 9


title: Donor_9_VSL3andLPS

description: monocyte derived DC


title: Donor_9_VSL3

description: monocyte derived DC


title: Donor_8_LPS

description: monocyte derived DC


title: Neural stem cells 3


title: Medulloblastoma 37

value: cerebellum


title: Medulloblastoma 31

value: classic


title: Donor_9_Unstimulated

description: monocyte derived DC


title: Medulloblastoma 30


title: Medulloblastoma 28


title: Medulloblastoma 29

value: large cell


title: Medulloblastoma 26


title: Donor_2_LPS

description: monocyte derived DC

source_name: Donor 2


title: Donor_7_VSL3andLPS

description: monocyte derived DC

source_name: Donor 7


title: Donor_2_VSL3

description: monocyte derived DC


title: Medulloblastoma 19

value: focal desmoplasia

value: post fossa


title: Donor_8_Unstimulated

description: monocyte derived DC


title: Medulloblastoma 21


title: Donor_2_VSL3andLPS

description: monocyte derived DC


title: Donor_4_VSL3

description: monocyte derived DC

source_name: Donor 4


title: Donor_4_LPS

description: monocyte derived DC


title: Donor_4_Unstimulated

description: monocyte derived DC


title: Donor_2_Unstimulated

description: monocyte derived DC


title: Donor_4_VSL3andLPS

description: monocyte derived DC


title: Donor_7_LPS

description: monocyte derived DC


title: Donor_7_Unstimulated

description: monocyte derived DC


title: Donor_7_VSL3

description: monocyte derived DC


title: Medulloblastoma 17

value: IV ventricle


title: Medulloblastoma 15

value: vermis


title: Medulloblastoma 18


title: Donor_6_Unstimulated

description: monocyte derived DC

source_name: Donor 6


title: Donor_6_VSL3

description: monocyte derived DC


title: NDLiCD8

city: Beijing

first: yujun

last: zhang

address: No 11 xizhimen Nan street

country: China

institute: Peking University People's hospital

hyb_protocol: each sample was hybridized on the Agilent mouse miRNA microarray,Release 18.0,8x60K(Agilent)

scan_protocol: Scanning was performed with the Agilent microarray scanner

data_processing: Agilent feature extraction(v10.7) is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.

source_name: CD8+T lymphacyte of Liver

label_protocol: each sample was labeled using the miRNA complete labeling and Hyb kit

growth_protocol: The mice was fed with high fat diet or normal fat diet for 12 weeks

extract_protocol: Total RNA was harvested from two pairs of CD4+T lymphocytes of liver and mescentic lymphatic nodes in NAFLD mice and normal mice and purified using mirVana miRNA Isolation kit.

treatment_protocol: liver cells and mescentic cells were isolated and stained with fluorochrome-conjugated antibodies against CD4 and CD8,After washing,CD+4 T cells CD8+ T cells were sorted using FACSAria II flow cytometer

tag: strain

value: 7 weeks

tag: gender

value: male


title: dental pulp cell from control 5

source_name: dental pulp cells obtained from milk teeth

value: dental pulp cells

value: control


title: HFLiCD8


title: NDMLCD8

source_name: CD8+T lymphacyte of Mesenteric Lymph nodes


title: Medulloblastoma 11

value: M


title: HFMLCD8


title: Donor_6_VSL3andLPS

description: monocyte derived DC


title: Medulloblastoma 10


title: NDLiCD4

source_name: CD4+T lymphacyte of Liver


title: HFLiCD4


title: Medulloblastoma 14


title: Donor_6_LPS

description: monocyte derived DC


title: Test_sample_933

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

description: Test

data_processing:
Normalization of results was done using RQ Manager (Applied Biosystems). A common threshold was established across all array cards for each miRNA, expression levels were normalized to MammU6 and average delta-Ct was used in downstream analyses
RQ Manager (Applied Biosystems) was used to compute normalized signals.

label: FAM

source_name: Prostate cancer cells

label_protocol: The miRNA was reverse transcribed using Megaplextm pool A and B (Applied Biosystems) followed by pre amplification. The cDNA pool was applied to the multiplex array cards and the experiment was run on the ABI 7900 HT platform using cycling conditions as provided by the manufacturer

extract_protocol: Total RNA was extracted using RNeasy® Micro kit from Qiagen (Germany) folloed by mikroRNA extraction using the RNeasy micro kit .

treatment_protocol: Laser Micro dissection of prostate biopsies was performed using the PALM laser microbeam system

tag: recurrence

value: yes

tag: gleason grade

tag: t-stage

tag: margin status

value: Positive

tag: preoperative psa


title: Test_sample_904

description: Test


title: NDMLCD4

source_name: CD4+T lymphacyte of Mesenteric Lymph nodes


title: Test_sample_948

description: Test


title: Test_sample_866

description: Test


title: Test_sample_832

description: Test

value: Negative


title: HFMLCD4


title: Mixed rumen culture received peppermint oil (0.5 g/L) Replicate 1

type: genomic

city: Columbus

first: Amlan

middle: Kumar

last: Patra

state: OHIO

address: 2029 Fyffe Road

department: Animal Science

institute: The Ohio State University

description:
Sample name: PEO-rep1
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.

hyb_protocol: Microarray hybridization was performed using Agilent Technologies’ Hybridization gasket slides.The hybridization solution and 150 ng labeled cRNA was incubated at 65oC for 5 min and then placed on ice for 5 min. The assembled cassette was placed in a HB-1000 hybridization oven (UVP, LLC) preset at 45oC to allow hybridization for 18 hours with rotation set at 10 rpm.

scan_protocol: Scanned on a GenePix 4000B Scanner (Axon Instruments, Union City, CA). The Cy5 fluorescence signal at each probe spot was measured using the GenePix®Pro 6.0 program (Axon Instruments).

data_processing: The local median background signal intensity was subtracted from the median hybridization signal intensity of each separate probe spot. After background subtraction, normalization was performed based on the signal intensity of internal control probes targeting the bovine mitochondrial rRNA gene region.

molecule: genomic DNA

organism: bovine gut metagenome

source_name: In vitro rumen mixed culture

label_protocol: The cRNA was labeled with Cy5 at 37oC for 1 hour using a Label IT®uArrayCy3/Cy5 Labeling kit (Mirus, Madison, WI, USA). The labeled cRNA was again purified to remove the free Cy5 dye using a MEGAclear kit.

extract_protocol: Metagenomic DNA was extracted from 0.5 ml of each in vitro rumen mixed culture sample using the repeated bead beating (on a Mini-Beadbeater™, BioSpec Products, Bartlesville, OK, USA) and column purification (using QIAamp DNA Stool Mini Kit, Qiagen, Valencia, CA, USA) method. nearly full-length 16S rRNA genes were amplified from each metagenomic DNA sample using the universal primer set 27F (5’-AGA GTT TGA TCM TGG CTC AG-3’) and T7/1492R (5’-TCT AAT ACG ACT CAC TAT AGG GGG YTA CCT TGT TAC GAC TT-3’). The amplicons were purified using a PCR purification Kit (Qiagen, Valencia, CA, USA) and then used in preparation of complementary RNA (cRNA) using a MEGAScript T7 in vitro transcription kit (Ambion, Austin, TX, USA). The cRNA was purified using a MEGAclear kit (Ambion, Austin, TX, USA).

tag: host

value: Bos indicus

tag: bacteria

value: Cultured and uncultured bacteria from B. indicus rumen

tag: agent

value: peppermint oil

tag: incubation

value: Rumen mixed culture was incubated in vitro for 24 h


title: Mixed rumen culture received peppermint oil (0.5 g/L) Replicate 3

description:
Sample name: PEO-rep3
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Mixed rumen culture received peppermint oil (0.5 g/L) Replicate 2

description:
Sample name: PEO-rep2
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: dental pulp cell from control 4

description: gene expression data from DPC in passage #5

tag: tissue

tag: genotype

tag: passages


title: Medulloblastoma 8

tag: age

tag: Sex

tag: diagnosis note

value: classic

value: cerebellum


title: Medulloblastoma 7

tag: location


title: Medulloblastoma 6


title: Medulloblastoma 2

value: F

value: astrocytic elements


title: Mixed rumen culture received origanum oil (0.5 g/L) Replicate 3

description:
Sample name: ORO-rep3
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.

value: origanum oil


title: Test_sample_751

description: Test


title: Test_sample_750

description: Test


title: Test_sample_717

description: Test


title: Mixed rumen culture received origanum oil (0.5 g/L) Replicate 2

description:
Sample name: ORO-rep2
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Test_sample_711

description: Test


title: Test_sample_539

description: Test


title: Test_sample_646

description: Test


title: Mixed rumen culture received origanum oil (0.5 g/L) Replicate 1

description:
Sample name: ORO-rep1
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Mixed rumen culture received garlic oil (0.5 g/L) Replicate 3

description:
Sample name: GAO-rep3
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.

value: garlic oil


title: Mixed rumen culture received garlic oil (0.5 g/L) Replicate 1

description:
Sample name: GAO-rep1
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Test_sample_486

description: Test


title: Test_sample_265

description: Test


title: Test_sample_247

description: Test


title: Test_sample_244

description: Test


title: Test_sample_828

description: Test


title: Test_sample_188

description: Test


title: Test_sample_187

description: Test


title: Test_sample_173

description: Test


title: Control without any essential oils Replicate 3

description:
Sample name: CON-rep3
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.

value: control (no essential oils)


title: Control without any essential oils Replicate 1

description:
Sample name: CON-rep1
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Control_sample_930

description: control

source_name: normal prostate glandular epithelium

value: no


title: Test_sample_171

description: Test


title: Test_sample_168

description: Test


title: Control_sample_913

description: control


title: Mixed rumen culture received garlic oil (0.5 g/L) Replicate 2

description:
Sample name: GAO-rep2
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Control without any essential oils Replicate 2

description:
Sample name: CON-rep2
Metagenomic DNA was extracted, amplified using the universal primer set 27F and T7/1492R. The amplicons were purified and used in preparation of complementary RNA (cRNA). The cRNA was purified, and labeledwith Cy5.


title: Control_sample_888

description: control


title: Control_sample_836

description: control


title: Test_sample_251

description: Test


title: Control_sample_825

description: control


title: Control_sample_746

description: control


title: Control_sample_713

description: control


title: 1 mM MNU, Mouse 2

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

institute: RIVM

description:
Quality control: approved
98_D05

hyb_protocol: According to the protocol provided with the Affymetrix 3' IVT Express Labeling Kit (#901229).

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix).

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

source_name: Primary mouse hepatocytes, mouse #2, MNU

label_protocol: Biotin-labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3' IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Primary mouse hepatocytes were isolated from 8- to 10-week-old male C57BL/6 mice by a modified two-step collagenase perfusion technique. Cells were cultured in a sandwich configuration in 6-wells at 1.3 x 10^6 cells per well.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer's protocol.

treatment_protocol: Hepatocytes were exposed for 24 hours to the 16 non-genotoxic carcinogens. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 24 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

tag: strain

tag: gender

value: male

value: 8-10 weeks

tag: cell type

value: primary mouse hepatocytes

tag: mouse identifier

tag: chemical

value: N-Nitroso-N-Methylurea (MNU)

tag: abbreviation

value: MNU

tag: concentration

value: 1 mM MNU


title: 30 μM HCE, Mouse 2

description:
Quality control: approved
96_H05

source_name: Primary mouse hepatocytes, mouse #2, HCE

value: Heptachlor epoxide (HCE)

value: HCE

value: 30 μM HCE


title: Control_sample_296

description: control

tag: recurrence

tag: gleason grade

tag: t-stage

tag: margin status

value: Negative

tag: preoperative psa


title: PBS, Mouse 2

description:
Quality control: approved
97_C07

source_name: Primary mouse hepatocytes, mouse #2, PBS

value: PBS control

value: PBS


title: 1 μM CSPT, Mouse 2

description:
Quality control: approved
99_B07

source_name: Primary mouse hepatocytes, mouse #2, CSPT

value: Cisplatin (CsPt)

value: CSPT

value: 1 μM CSPT


title: 0.3 μM MMC, Mouse 2

description:
Quality control: approved
95_G07

source_name: Primary mouse hepatocytes, mouse #2, MMC

value: Mitomycine C (MMC)

value: MMC

value: 0.3 μM MMC


title: 100 μM WY, Mouse 2

description:
Quality control: approved
94_B05

source_name: Primary mouse hepatocytes, mouse #2, WY

value: male

value: 8-10 weeks

value: WY

value: 100 μM WY


title: Control_sample_279

description: control

value: no


title: Control_sample_266

description: control


title: 30 μM ARO, Mouse 2

description:
Quality control: approved
91_E07

source_name: Primary mouse hepatocytes, mouse #2, ARO

value: primary mouse hepatocytes

value: Aroclor 1254

value: ARO

value: 30 μM ARO


title: 1 mM DIDP, Mouse 2

description:
Quality control: approved
93_C05

source_name: Primary mouse hepatocytes, mouse #2, DIDP

value: Diisodecyl phthalate (DIDP)

value: DIDP

value: 1 mM DIDP


title: Control_sample_255

description: control

value: Negative


title: 30 μM FK509, Mouse 2

description:
Quality control: approved
92_D07

source_name: Primary mouse hepatocytes, mouse #2, FK506

value: Tacrolimus (FK-506)


title: Control_sample_254

description: control


title: 1 mM PB, Mouse 2

description:
Quality control: approved
84_A07

source_name: Primary mouse hepatocytes, mouse #2, PB

value: Phenobarbital (Pb)

value: PB

value: 1 mM PB


title: DMSO, Mouse 2

description:
Quality control: approved
82_A05

source_name: Primary mouse hepatocytes, mouse #2, DMSO

value: male

value: DMSO control

value: DMSO

value: 0.5% DMSO


title: Control_sample_172

description: control

value: no


title: 1 mM DM, Mouse 2

description:
Quality control: approved
79_C05

source_name: Primary mouse hepatocytes, mouse #2, DM

value: 8-10 weeks

value: primary mouse hepatocytes

value: D-mannitol

value: DM

value: 1 mM DM


title: H82_THZ1_25nM_1

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: Batches of microarray experiments were normalized within themselves to ERCC spike-in probes as described in (Loven et al. 2012).  Briefly, probes were combined into probesets using expresso with mas5 normalization.  Probeset expression profiles were normalized using loess from the affy R package to equilibrate ERCC spike-in probes across microarrays in a given batch.  Where possible, log2 values of biological replicates were averaged.  Fold-changes were taken by subtracting average log2 DMSO signal from average log2 treatment signal.  Expressed genes were those with log2(expression) > log2(100) in the corresponding DMSO sample.

source_name: NCI-H82 cells

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228).  Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: NCI-H69, GLC16 and NCI-H82 cells were grown in RPMI medium supplemented with 10% FBS and 1% penn/strep.  All cells were cultured at 37 degrees C in a humidified chamber in the presence of 5% CO2, unless otherwise noted.

extract_protocol: Total RNA and sample preparation was performed as previously described (Loven et al. 2012).  Briefly, biological duplicates (equivalent to 5 million cells per replicate for NCI-H69, GLC16 and NCI-H82 cells) were subsequently collected and homogenized in 1 ml of TRIzol Reagent (Life Technologies, 15596-026),           followed by 0.2 chloroform to allow for phase-seperation by centrifugation. RNA was precipitated using isopropanol and further washed with 80 % ethanol and resuspended in nuclease-free water. Hereafter, DNAse treatment was performed with subsequent clean-up using RNAeasy mini kit (Qiagen). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740), treated with DNA-freeTM DNase I (Ambion, AM1906) and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: NCI-H69, GLC16 and NCI-H82 were plated at the appropriate densities (500,000 cells/ mL per 100-mm plate) and incubated in media containing THZ1 or DMSO at the indicated concentrations/dilutions and specified duration of time.  At the end of the experiment cells were collected by centrifugation and cell numbers were determined by manually counting with hemocytometer using tryphan blue to distinguish between live and dead cells

tag: treatment

value: Cells were plated in fresh media T day 0 and 25 nM THZ1 was added to cells day 1 for 6 hours


title: 1 nM OA, Mouse 2

description:
Quality control: approved
83_F05

source_name: Primary mouse hepatocytes, mouse #2, OA

tag: age

value: Okadaic Acid (OA)

value: OA

value: 1 nM OA


title: 1 μM CSA, Mouse 2

description:
Quality control: approved
86_H07

source_name: Primary mouse hepatocytes, mouse #2, CsA

value: Cyclosporin A (CsA)

value: CsA

value: 1 μM CSA


title: 10 nM TCDD, Mouse 2

description:
Quality control: approved
85_F07

source_name: Primary mouse hepatocytes, mouse #2, TCDD

value: male

value: TCDD

value: 10 nM TCDD


title: 300 μM CT, Mouse 2

description:
Quality control: approved
81_G05

source_name: Primary mouse hepatocytes, mouse #2, CT

value: Carbon Tetrachloride (CT)

value: CT

value: 300 μM CT


title: H82_THZ1_100nM_2

value: Cells were plated in fresh media T day 0 and 100 nM THZ1 was added to cells day 1 for 6 hours


title: 1 mM CF, Mouse 2

description:
Quality control: approved
78_E05

source_name: Primary mouse hepatocytes, mouse #2, CF

value: 8-10 weeks

value: primary mouse hepatocytes

value: Clofibrate

value: CF

value: 1 mM CF


title: Control_sample_230

description: control

source_name: normal prostate glandular epithelium

value: no

value: Negative


title: H82_THZ1_25nM_2

value: Cells were plated in fresh media T day 0 and 25 nM THZ1 was added to cells day 1 for 6 hours


title: 10 μM LAC, Mouse 2

description:
Quality control: approved
80_B05

source_name: Primary mouse hepatocytes, mouse #2, LAC

value: Lead Acetate (LAc)

value: LAC

value: 10 μM LAC


title: H82_THZ1_100nM_1


title: C20_N_FF

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

hyb_protocol: Ligated bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software

label: Cy3 and Cy5

source_name: colon tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from FFPE and FF tissue (tumor and surrounding healthy tissue) using Puregene Core kit A (Qiagen, Maryland, USA).

tag: disease state

value: Normal

tag: tissue

value: FF


title: C20_N_FFPE

value: FFPE


title: 300 μM DEM, Mouse 2

description:
Quality control: approved
77_G07

source_name: Primary mouse hepatocytes, mouse #2, DEM

value: male

value: Diethyl maleate (Dem)

value: DEM

value: 300 μM DEM


title: C16_N_FF


title: 30 μM ETP, Mouse 2

description:
Quality control: approved
76_A05

source_name: Primary mouse hepatocytes, mouse #2, ETP

value: 8-10 weeks

value: primary mouse hepatocytes

value: Etoposide

value: ETP

value: 30 μM ETP


title: H69_THZ1_100nM_1

source_name: NCI-H69 cells

value: Cells were plated in fresh media T day 0 and 100 nM THZ1 was added to cells day 1 for 6 hours


title: C19_N_FF


title: H82_DMSO_2

value: day 0 and DMSO (1/1000 dilution) was added to cells day 1 for 6 hours


title: H69_THZ1_100nM_2


title: 10 μM BPA, Mouse 2

description:
Quality control: approved
73_D05

source_name: Primary mouse hepatocytes, mouse #2, BPA

value: Bisphenol A (BPA)

value: BPA

value: 10 μM BPA


title: 10 μM TCPOBOP, Mouse 2

description:
Quality control: approved
74_G05

source_name: Primary mouse hepatocytes, mouse #2, TCPOBOP

value: TCPOBOP

value: 10 μM TCPOBOP


title: H82_DMSO_1


title: 1 nM CA, Mouse 2

description:
Quality control: approved
71_F05

source_name: Primary mouse hepatocytes, mouse #2, CA

value: Calyculin A (CA)

value: CA

value: 1 nM CA


title: C19_N_FFPE

value: Normal

value: FFPE


title: C16_N_FFPE


title: H69_THZ1_25nM_2

value: Cells were plated in fresh media T day 0 and 25 nM THZ1 was added to cells day 1 for 6 hours


title: H69_THZ1_25nM_1


title: 0.3 μM TBTO, Mouse 2

description:
Quality control: approved
67_D07

source_name: Primary mouse hepatocytes, mouse #2, TBTO

value: male

value: 8-10 weeks

value: primary mouse hepatocytes

value: Tributyltinoxide (TBTO)

value: TBTO

value: 0.3 μM TBTO


title: C12_N_FF

value: FF


title: C12_N_FFPE


title: C10_N_FF


title: 3 μM MEN, Mouse 2

description:
Quality control: approved
70_C07

source_name: Primary mouse hepatocytes, mouse #2, MEN

value: Menadion

value: MEN

value: 3 μM MEN


title: H69_DMSO_2

value: day 0 and DMSO (1/1000 dilution) was added to cells day 1 for 6 hours


title: C9_N_FF


title: C9_N_FFPE


title: C10_N_FFPE


title: 1 mM TCE, Mouse 2

description:
Quality control: approved
69_H05

source_name: Primary mouse hepatocytes, mouse #2, TCE

value: Methyl chloroform (1,1,1-TCE)

value: TCE

value: 1 mM TCE


title: 3 μM SAR, Mouse 2

description:
Quality control: approved
68_F07

source_name: Primary mouse hepatocytes, mouse #2, SAR

value: Sodium Arsenite (SAr)

value: SAR

value: 3 μM SAR


title: GLC16_THZ1_100nM_1

source_name: GLC16 cells

value: Cells were plated in fresh media T day 0 and 100 nM THZ1 was added to cells day 1 for 6 hours


title: C8_N_FFPE

value: Normal

value: FFPE


title: H69_DMSO_1


title: 30 μM FK508, Mouse 1

description:
Quality control: approved
64_B05

source_name: Primary mouse hepatocytes, mouse #1, FK506

value: male

value: 8-10 weeks

value: primary mouse hepatocytes

value: Tacrolimus (FK-506)


title: 100 μM HCH, Mouse 2

description:
Quality control: approved
66_H07

source_name: Primary mouse hepatocytes, mouse #2, HCH

value: beta-Hexachlorocyclohexane (HCH)

value: HCH

value: 100 μM HCH


title: GLC16_DMSO_2

value: day 0 and DMSO (1/1000 dilution) was added to cells day 1 for 6 hours


title: C8_N_FF

value: FF


title: 1 μM CSPT, Mouse 1

description:
Quality control: approved
63_D05

source_name: Primary mouse hepatocytes, mouse #1, CSPT

value: Cisplatin (CsPt)

value: CSPT

value: 1 μM CSPT


title: GLC16_THZ1_100nM_2


title: C7_N_FF


title: GLC16_THZ1_25nM_1

value: Cells were plated in fresh media T day 0 and 25 nM THZ1 was added to cells day 1 for 6 hours


title: C6_N_FFPE


title: 1 nM OA, Mouse 1

description:
Quality control: approved
58_E07

source_name: Primary mouse hepatocytes, mouse #1, OA

value: Okadaic Acid (OA)

value: OA

value: 1 nM OA


title: GLC16_DMSO_1


title: GLC16_THZ1_25nM_2


title: 0.3 μM TBTO, Mouse 1

description:
Quality control: approved
61_F05

source_name: Primary mouse hepatocytes, mouse #1, TBTO

value: Tributyltinoxide (TBTO)

value: TBTO

value: 0.3 μM TBTO


title: 1 mM CF, Mouse 1

description:
Quality control: approved
60_G07

source_name: Primary mouse hepatocytes, mouse #1, CF

value: male

value: 8-10 weeks

value: primary mouse hepatocytes

value: Clofibrate

value: CF

value: 1 mM CF


title: C4_N_FF

source_name: colon tissue

value: Normal

value: FF


title: 1 mM TCE, Mouse 1

description:
Quality control: approved
54_C05

source_name: Primary mouse hepatocytes, mouse #1, TCE

value: Methyl chloroform (1,1,1-TCE)

value: TCE

value: 1 mM TCE


title: C4_N_FFPE

value: FFPE


title: C7_N_FFPE


title: C6_N_FF


title: 100 μM HCH, Mouse 1

description:
Quality control: approved
57_G05

source_name: Primary mouse hepatocytes, mouse #1, HCH

value: beta-Hexachlorocyclohexane (HCH)

value: HCH

value: 100 μM HCH


title: PBS, Mouse 1

description:
Quality control: approved
55_A07

source_name: Primary mouse hepatocytes, mouse #1, PBS

value: PBS control

value: PBS


title: C2_N_FF


title: 30 μM HCE, Mouse 1

description:
Quality control: approved
56_E05

source_name: Primary mouse hepatocytes, mouse #1, HCE

value: male

value: Heptachlor epoxide (HCE)

value: HCE

value: 30 μM HCE


title: C2_N_FFPE


title: RBP_PfDHFR-TS_eluted_vs_total_RNA_rep4

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

description: Ribonomic experimental replicate 4 of 4

hyb_protocol: Purified Cy3- and Cy5-labelled cDNA were mixed in a Short Oligo Hybridization Solution (Corning Inc.), and hybridized to P. falciparum spotted 70-mer oligo microarrays for 16-18 hr at 45°C. Arrays were washed at room temperature in a solution of 2x SSC (Sodium Saline Citrate) containing 0.2% SDS, and then in 0.1x SSC.

scan_protocol: Scanned on an GenePix 4000B scanner and images analyzed using GenePix Pro 6.1.0.4

data_processing: Microarray feature signals of irregular shape were flagged (i.e. marked as not available for analysis) manually in the GenePix Pro software. The .gpr files were pre-processed using the Aroma package implemented in R 2.13.0 to flag features with low signal:noise (SNR <2) and calculate raw log2(Cy5/Cy3) values. The raw log2(Cy5/Cy3) values were collated for replicate arrays of each RBP experiment and data were filtered to remove features with ≥50% flags across all replicates. The filtered data from the experiments with PfAda protein were assigned as Mock data for normalization. Filtered RBP data were normalized with the Mock data using the ADNorm algorithm (Salzman et al., 2013)  implemented in R 2.13.0.

organism: Plasmodium falciparum

source_name: Mixed-stage Plasmodium falciparum

label_protocol: 10 µg of total RNA or ≤2 μg of RNA eluted from Ni2+ sepharose bead-bound 6xHis-tagged protein were annealed with 5 µg of oligo (dT)21 and reverse transcribed to produce aminoallyl-dUTP(Ambion)-containing cDNA using SuperscriptIII reverse transcriptase (Invitrogen). The cDNA from the total RNA preparations was then labelled with monoreactive Cy5 (GE Healthcare) and cDNA from Ni2+ sepharose eluted RNA labelled with Cy3 (GE Healthcare) .

growth_protocol: Parasites were cultured in vitro using the standard method of Trager and Jensen (1976). The parasite culture was composed of human erythrocytes type O Rh+ in RPMI 1640 supplemented with 25 mM HEPES pH 7.4, 0.2% NaHCO3 0.2% glucose, 0.025 mg/ml hypoxanthine, 40 µg/ml gentamicin and 8% (v/v) pooled human serum. The culture was maintained in a 3% CO2 incubator at 37°C.

treatment_protocol: Mixed asexual stage parasites (about 10% trophozoite, 0.5% ring) were harvested and liberated from host cells by 0.1% saponin lysis.

tag: sample type

value: total RNA reference

source_name: RNA eluted from RBP PfDHFR-TS bound beads

tag: eluate

value: Ni2+ sepharose eluted RNA


title: 10 nM TCDD, Mouse 1

description:
Quality control: approved
53_F07

source_name: Primary mouse hepatocytes, mouse #1, TCDD

tag: strain

tag: gender

value: 8-10 weeks

value: primary mouse hepatocytes

value: TCDD

value: 10 nM TCDD


title: RBP_PfDHFR-TS_eluted_vs_total_RNA_rep3

description: Ribonomic experimental replicate 3 of 4

value: RNA eluted from RBP PfDHFR-TS bound beads


title: RBP_PfDHFR-TS_eluted_vs_total_RNA_rep1

description: Ribonomic experimental replicate 1 of 4


title: RBP_PfDHFR-TS_eluted_vs_total_RNA_rep2

description: Ribonomic experimental replicate 2 of 4


title: 30 μM ARO, Mouse 1

description:
Quality control: approved
52_H05

source_name: Primary mouse hepatocytes, mouse #1, ARO

tag: cell type

tag: mouse identifier

value: Aroclor 1254

value: ARO

value: 30 μM ARO


title: C1_N_FF

value: Normal

value: FF


title: C1_N_FFPE

value: FFPE


title: RBP_PfCELF2_eluted_vs_total_RNA_rep5

description: Ribonomic experimental replicate 5 of 6

source_name: RNA eluted from RBP PfCELF2 bound beads

value: RNA eluted from RBP PfCELF2 bound beads


title: 3 μM SAR, Mouse 1

description:
Quality control: approved
50_B07

source_name: Primary mouse hepatocytes, mouse #1, SAR

value: male

tag: chemical

value: Sodium Arsenite (SAr)

tag: abbreviation

value: SAR

value: 3 μM SAR


title: 30 μM ETP, Mouse 1

description:
Quality control: approved
51_A05

source_name: Primary mouse hepatocytes, mouse #1, ETP

value: Etoposide

value: ETP

tag: concentration

value: 30 μM ETP


title: RBP_PfCELF2_eluted_vs_total_RNA_rep4

description: Ribonomic experimental replicate 4 of 6

value: total RNA reference

value: Ni2+ sepharose eluted RNA


title: C19_T_FFPE

value: colorectal cancer


title: RBP_PfCELF2_eluted_vs_total_RNA_rep6

description: Ribonomic experimental replicate 6 of 6


title: RBP_PfCELF2_eluted_vs_total_RNA_rep2

description: Ribonomic experimental replicate 2 of 6


title: C20_T_FF


title: DMSO, Mouse 1

description:
Quality control: approved
49_D07

source_name: Primary mouse hepatocytes, mouse #1, DMSO

value: 8-10 weeks

value: primary mouse hepatocytes

value: DMSO control

value: DMSO

value: 0.5% DMSO


title: 10 μM TCPOBOP, Mouse 1

description:
Quality control: approved
48_E05

source_name: Primary mouse hepatocytes, mouse #1, TCPOBOP

value: TCPOBOP

value: 10 μM TCPOBOP


title: C16_T_FF

value: FF


title: 0.3 μM MMC, Mouse 1

description:
Quality control: approved
44_F07

source_name: Primary mouse hepatocytes, mouse #1, MMC

value: male

value: Mitomycine C (MMC)

value: MMC

value: 0.3 μM MMC


title: 1 mM DM, Mouse 1

description:
Quality control: approved
45_A07

source_name: Primary mouse hepatocytes, mouse #1, DM

value: D-mannitol

value: DM

value: 1 mM DM


title: C16_T_FFPE

value: FFPE


title: 300 μM DEM, Mouse 1

description:
Quality control: approved
43_C05

source_name: Primary mouse hepatocytes, mouse #1, DEM

value: Diethyl maleate (Dem)

value: DEM

value: 300 μM DEM


title: 3 μM MEN, Mouse 1

description:
Quality control: approved
42_B07

source_name: Primary mouse hepatocytes, mouse #1, MEN

value: 8-10 weeks

value: primary mouse hepatocytes

value: Menadion

value: MEN

value: 3 μM MEN


title: RBP_PfCELF2_eluted_vs_total_RNA_rep1

description: Ribonomic experimental replicate 1 of 6

value: total RNA reference

value: RNA eluted from RBP PfCELF2 bound beads

value: Ni2+ sepharose eluted RNA


title: RBP_PfCELF1_eluted_vs_total_RNA_rep7

description: Ribonomic experimental replicate 7 of 7

source_name: RNA eluted from RBP PfCELF1 bound beads

value: RNA eluted from RBP PfCELF1 bound beads


title: C20_T_FFPE

source_name: colon tissue

value: colorectal cancer


title: C19_T_FF

value: FF


title: C12_T_FF


title: C10_T_FFPE


title: 1 mM MNU, Mouse 1

description:
Quality control: approved
40_E07

source_name: Primary mouse hepatocytes, mouse #1, MNU

value: male

value: N-Nitroso-N-Methylurea (MNU)

value: MNU

value: 1 mM MNU


title: RBP_PfCELF2_eluted_vs_total_RNA_rep3

description: Ribonomic experimental replicate 3 of 6


title: RBP_PfCELF1_eluted_vs_total_RNA_rep5

description: Ribonomic experimental replicate 5 of 7


title: RBP_PfCELF1_eluted_vs_total_RNA_rep6

description: Ribonomic experimental replicate 6 of 7


title: 1 mM DIDP, Mouse 1

description:
Quality control: approved
38_G07

source_name: Primary mouse hepatocytes, mouse #1, DIDP

value: Diisodecyl phthalate (DIDP)

value: DIDP

value: 1 mM DIDP


title: C12_T_FFPE

value: FFPE


title: C9_T_FF


title: RBP_PfCELF1_eluted_vs_total_RNA_rep4

description: Ribonomic experimental replicate 4 of 7

source_name: Mixed-stage Plasmodium falciparum


title: 100 μM WY, Mouse 1

description:
Quality control: approved
39_G05

source_name: Primary mouse hepatocytes, mouse #1, WY

value: 8-10 weeks

value: primary mouse hepatocytes

value: WY

value: 100 μM WY


title: C9_T_FFPE


title: 10 μM LAC, Mouse 1

description:
Quality control: approved
37_H05

source_name: Primary mouse hepatocytes, mouse #1, LAC

value: Lead Acetate (LAc)

value: LAC

value: 10 μM LAC


title: C8_T_FFPE

value: colorectal cancer


title: 1 nM CA, Mouse 1

description:
Quality control: approved
41_A05

source_name: Primary mouse hepatocytes, mouse #1, CA

value: Calyculin A (CA)

value: CA

value: 1 nM CA


title: RBP_PfCELF1_eluted_vs_total_RNA_rep1

description: Ribonomic experimental replicate 1 of 7

value: total RNA reference

value: RNA eluted from RBP PfCELF1 bound beads

value: Ni2+ sepharose eluted RNA


title: 1 mM PB, Mouse 1

description:
Quality control: approved
36_D05

source_name: Primary mouse hepatocytes, mouse #1, PB

value: male

value: Phenobarbital (Pb)

value: PB

value: 1 mM PB


title: C10_T_FF

value: FF


title: Mock_PfAda_eluted_vs_total_RNA_rep5

description: Ribonomic experimental replicate 5 of 5

source_name: RNA eluted from mock Ada bound beads

value: RNA eluted from mock Ada bound beads


title: 300 μM CT, Mouse 1

description:
Quality control: approved
35_F05

source_name: Primary mouse hepatocytes, mouse #1, CT

value: 8-10 weeks

value: primary mouse hepatocytes

value: Carbon Tetrachloride (CT)

value: CT

value: 300 μM CT


title: 1 mM MNU, Mouse 4

description:
Quality control: approved
169_D07

source_name: Primary mouse hepatocytes, mouse #4, MNU

value: N-Nitroso-N-Methylurea (MNU)

value: MNU

value: 1 mM MNU


title: C8_T_FF

value: colorectal cancer


title: RBP_PfCELF1_eluted_vs_total_RNA_rep2

description: Ribonomic experimental replicate 2 of 7

value: total RNA reference

value: RNA eluted from RBP PfCELF1 bound beads


title: RBP_PfCELF1_eluted_vs_total_RNA_rep3

description: Ribonomic experimental replicate 3 of 7

value: Ni2+ sepharose eluted RNA


title: Mock_PfAda_eluted_vs_total_RNA_rep3

description: Ribonomic experimental replicate 3 of 5


title: C7_T_FF


title: Mock_PfAda_eluted_vs_total_RNA_rep4

description: Ribonomic experimental replicate 4 of 5


title: 10 μM BPA, Mouse 1

description:
Quality control: approved
33_C07

source_name: Primary mouse hepatocytes, mouse #1, BPA

value: male

value: Bisphenol A (BPA)

value: BPA

value: 10 μM BPA


title: C7_T_FFPE

value: FFPE


title: Mock_PfAda_eluted_vs_total_RNA_rep1

description: Ribonomic experimental replicate 1 of 5

value: RNA eluted from mock Ada bound beads


title: C6_T_FF

value: FF


title: C6_T_FFPE


title: 30 μM HCE, Mouse 4

description:
Quality control: approved
166_E07

source_name: Primary mouse hepatocytes, mouse #4, HCE

value: 8-10 weeks

value: primary mouse hepatocytes

value: Heptachlor epoxide (HCE)

value: HCE

value: 30 μM HCE


title: 10 nM TCDD, Mouse 4

description:
Quality control: approved
168_G07

source_name: Primary mouse hepatocytes, mouse #4, TCDD

value: TCDD

value: 10 nM TCDD


title: 1 mM CF, Mouse 4

description:
Quality control: approved
167_A07

source_name: Primary mouse hepatocytes, mouse #4, CF

value: Clofibrate

value: CF

value: 1 mM CF


title: 30 μM FK507, Mouse 4

description:
Quality control: approved
164_A05

source_name: Primary mouse hepatocytes, mouse #4, FK506

value: male

value: Tacrolimus (FK-506)


title: C2_T_FFPE

value: colorectal cancer


title: C4_T_FF


title: 1 μM CSA, Mouse 4

description:
Quality control: approved
160_F05

source_name: Primary mouse hepatocytes, mouse #4, CsA

value: Cyclosporin A (CsA)

value: CsA

value: 1 μM CSA


title: C4_T_FFPE

source_name: colon tissue

value: FFPE


title: Mock_PfAda_eluted_vs_total_RNA_rep2

description: Ribonomic experimental replicate 2 of 5

value: total RNA reference

value: RNA eluted from mock Ada bound beads

value: Ni2+ sepharose eluted RNA


title: 1 μM CSA, Mouse 4, rep2

description:
Quality control: approved
161_C07

value: 8-10 weeks

value: primary mouse hepatocytes


title: 1 mM PB, Mouse 4

description:
Quality control: approved
159_B05

source_name: Primary mouse hepatocytes, mouse #4, PB

value: Phenobarbital (Pb)

value: PB

value: 1 mM PB


title: C1_T_FFPE


title: control.6hr.5

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: 750 ng of the labeled cRNA was fragmented and hybridized to arrays as described in manufacturer’s hybridization kit

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent’s Feature Extraction software 11.0 was used to analyze acquired array images

source_name: RNA purified from cultured neurons

label_protocol: Briefly, total RNA sample was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. The labeled cRNA was purified using RNeasy mini kit (Qiagen, San Diego, CA). cRNA yield and Cy-dye incorporation was determined using ND-1000 spectrophotometer (Thermo Scientific)

growth_protocol: DIV 21 dissociated mouse hippocampal neurons in 6 well plates were treated by Vehicle, 100 μM AP5, 100 nM NVP-AAM077 or 1 μM Ro25-4891 for 6 hours in a cell culture incubator

extract_protocol: Total RNA was isolated using RNeasy plus kit (Qiagen)

value: neurons

value: vehicle control for 6 hrs

source_name: universal mouse reference (Stratagene, La Jolla, CA)

value: reference


title: C1_T_FF

value: FF


title: control.6hr.3


title: control.6hr.2


title: 0.3 μM MMC, Mouse 4

description:
Quality control: approved
158_H05

source_name: Primary mouse hepatocytes, mouse #4, MMC

value: male

value: Mitomycine C (MMC)

value: MMC

value: 0.3 μM MMC


title: control.6hr.4


title: C2_T_FF

value: colorectal cancer


title: 30 μM ARO, Mouse 4

description:
Quality control: approved
157_D07

source_name: Primary mouse hepatocytes, mouse #4, ARO

value: Aroclor 1254

value: ARO

value: 30 μM ARO


title: control.6hr.1


title: Ro25.6hr.5

value: 1 uM Ro25-4891 for 6 hrs


title: Ro25.6hr.4


title: 100 μM HCH, Mouse 4

description:
Quality control: approved
153_B07

source_name: Primary mouse hepatocytes, mouse #4, HCH

value: 8-10 weeks

value: primary mouse hepatocytes

value: beta-Hexachlorocyclohexane (HCH)

value: HCH

value: 100 μM HCH


title: PBS, Mouse 4

description:
Quality control: approved
154_A05

source_name: Primary mouse hepatocytes, mouse #4, PBS

value: PBS control

value: PBS


title: Ro25.6hr.2

value: neurons

value: reference


title: Ro25.6hr.1


title: 100 μM WY, Mouse 4

description:
Quality control: approved
152_D05

source_name: Primary mouse hepatocytes, mouse #4, WY

value: male

value: WY

value: 100 μM WY


title: 10 μM TCPOBOP, Mouse 4

description:
Quality control: approved
151_F07

source_name: Primary mouse hepatocytes, mouse #4, TCPOBOP

value: TCPOBOP

value: 10 μM TCPOBOP


title: NVP.6hr.3

value: 100 nM NVP-AAM077 for 6 hrs


title: NVP.6hr.4


title: NVP.6hr.2


title: 10 μM BPA, Mouse 4

description:
Quality control: approved
156_C07

source_name: Primary mouse hepatocytes, mouse #4, BPA

value: Bisphenol A (BPA)

value: BPA

value: 10 μM BPA


title: Ro25.6hr.3

value: 1 uM Ro25-4891 for 6 hrs


title: 300 μM CT, Mouse 4

description:
Quality control: approved
149_E05

source_name: Primary mouse hepatocytes, mouse #4, CT

value: 8-10 weeks

value: primary mouse hepatocytes

value: Carbon Tetrachloride (CT)

value: CT

value: 300 μM CT


title: 0.3 μM TBTO, Mouse 4

description:
Quality control: approved
150_G05

source_name: Primary mouse hepatocytes, mouse #4, TBTO

value: Tributyltinoxide (TBTO)

value: TBTO

value: 0.3 μM TBTO


title: 30 μM ETP, Mouse 4

description:
Quality control: approved
148_G07

source_name: Primary mouse hepatocytes, mouse #4, ETP

value: male

value: Etoposide

value: ETP

value: 30 μM ETP


title: 1 mM DM, Mouse 4

description:
Quality control: approved
146_C05

source_name: Primary mouse hepatocytes, mouse #4, DM

value: D-mannitol

value: DM

value: 1 mM DM


title: 3 μM MEN, Mouse 4

description:
Quality control: approved
147_A07

source_name: Primary mouse hepatocytes, mouse #4, MEN

value: Menadion

value: MEN

value: 3 μM MEN


title: NVP.6hr.1

value: neurons

value: 100 nM NVP-AAM077 for 6 hrs

value: reference


title: AP5.6hr.5

value: 100 uM AP5 for 6 hrs


title: AP5.6hr.1


title: AP5.6hr.3


title: PBS, Mouse 3

description:
Quality control: approved
132_G05

source_name: Primary mouse hepatocytes, mouse #3, PBS

value: 8-10 weeks

value: primary mouse hepatocytes

value: PBS control

value: PBS


title: 10 μM LAC, Mouse 3

description:
Quality control: approved
133_E05

source_name: Primary mouse hepatocytes, mouse #3, LAC

value: male

value: Lead Acetate (LAc)

value: LAC

value: 10 μM LAC


title: AP5.6hr.4


title: 30 μM FK506, Mouse 3

description:
Quality control: approved
134_F05

source_name: Primary mouse hepatocytes, mouse #3, FK506

value: Tacrolimus (FK-506)


title: 1 μM CSPT, Mouse 4

description:
Quality control: approved
145_H07

source_name: Primary mouse hepatocytes, mouse #4, CSPT

value: Cisplatin (CsPt)

value: CSPT

value: 1 μM CSPT


title: AP5.6hr.2

source_name: RNA purified from cultured neurons

source_name: universal mouse reference (Stratagene, La Jolla, CA)


title: Nuclei whole embryo, biological rep 3

city: Tübingen

first: Daniel

last: Slane

state: Baden-Württemberg

address: Spemannstrasse 35

department: Cell Biology

country: Germany

institute: Max Planck Institute for Developmental Biology

description:
nEMB #3
Gene expression data from nuclei.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using "affy" package (v1.32.1).

organism: Arabidopsis thaliana

source_name: Arabidopsis embryos 2-16 cell stage, whole embryo, nuclei

label_protocol: Biotinylated cRNA was prepared according to the ENZO BioArray™ Single-round RNA amplification and biotin labeling system.

growth_protocol: Long day 16 hours light/8 hours dark.

extract_protocol: Nuclear extraction with CelLyticTM PN kit (Sigma). RNA extraction with buffer containing proteinase K.

treatment_protocol: Ovules including embryos from 2-16 cell stage were dissected from siliques and fixed with 0.1% PFA (paraformaldeyhde).

tag: ecotype

value: whole embryo

tag: developmental stage

value: embryo (2-16 cell stage)


title: Nuclei suspensor, biological rep 3

description:
nSUS #3
Gene expression data from nuclei.

source_name: Arabidopsis embryos 2-16 cell stage, suspensor, nuclei

value: suspensor


title: 300 μM DEM, Mouse 3

description:
Quality control: approved
131_E07

source_name: Primary mouse hepatocytes, mouse #3, DEM

value: Diethyl maleate (Dem)

value: DEM

value: 300 μM DEM


title: 300 μM CT, Mouse 3

description:
Quality control: approved
127_A05

source_name: Primary mouse hepatocytes, mouse #3, CT

value: 8-10 weeks

value: primary mouse hepatocytes

value: Carbon Tetrachloride (CT)

value: CT

value: 300 μM CT


title: Nuclei suspensor, biological rep 2

description:
nSUS #2
Gene expression data from nuclei.


title: Nuclei whole embryo, biological rep 2

description:
nEMB #2
Gene expression data from nuclei.


title: 1 nM CA, Mouse 3

description:
Quality control: approved
129_C05

source_name: Primary mouse hepatocytes, mouse #3, CA

value: male

value: Calyculin A (CA)

value: CA

value: 1 nM CA


title: Nuclei whole embryo, biological rep 1

description:
nEMB #1
Gene expression data from nuclei.


title: 3 μM SAR, Mouse 3

description:
Quality control: approved
128_F07

source_name: Primary mouse hepatocytes, mouse #3, SAR

value: Sodium Arsenite (SAr)

value: SAR

value: 3 μM SAR


title: Lame 239 Area4

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol.

data_processing: Data were normalized with Lowess intra-array and quantile inter-array normalizations using the FlexArray software (Génome Québec, http://www.gqinnovationcenter.com/services/bioinformatics/flexarray)

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: To initiate a new follicular wave, all follicles larger than 5 mm in diameter were punctured on days 8–11 post-oestrus. Administration of follicle-stimulating hormone (Folltropin-V, Bioniche Animal Health, Belleville, ON, Canada) was begun 36 h after follicular removal. Follicle-stimulating hormone was injected twice a day in doses of 40 mg for a total of 240 mg (six injections). Forty-eight hours after the final injection, the ultrasound-based pick-up procedure was performed using an 18G needle and COOK aspiration device (COOK Medical, Bloomington, IN, USA). Cumulus-oocyte complexes (COC) thus recovered were submitted to in vitro maturation. Cumulus-oocyte complexes were twice washed thoroughly in HEPES-buffered Tyrode's medium containing 10 % bovine serum, 200 μM pyruvate and 50 μg/mL gentamycin to ensure total removal of follicular liquid. Healthy COCs were then placed in maturation medium (groups of 10 per 50 μL droplet) under filtered mineral oil (9 mL) for 24 h at 38.5 °C in a humidified 5 % CO2, 20 % O2 atmosphere. The maturation medium contained TCM199 (Gibco 11150-059, Invitrogen, Burlington, ON, Canada), 10 % foetal calf serum (Sterile Foetal Bovine Serum for Cell Culture, Medicorp, Montreal, QC, Canada), 200 μM pyruvate, 50 μg/mL gentamycin and 0.1 μg/mL folliclestimulating hormone (Gonal-f, Serono Canada Inc., Mississauga, ON, Canada). Washed and matured COCs were placed in groups of five per droplet (50 μL) of modified Tyrode’s lactate medium (containing 0.6 % bovine serum albumin Sigma fraction V and 200 μM gentamycin) under filtered mineral oil. Two μL of a solution containing 1 mM hypotaurine, 2 mM penicillamine and 250 mM epinephrine were then added to each droplet. In vitro fertilization with frozen semen (pooled ejaculate) of the Jersey or Holstein breed (provided by L’Alliance Boviteq) was performed without delay. The semen was thawed at 37 °C in a water bath, laid on a discontinuous Percoll gradient (2 mL of 45 % Percoll over 2 mL of 90 % Percoll) and centrifuged at 700 x g for 30 min at room temperature. The supernatant was discarded and the pellet was re-suspended in modified Tyrode’s lactate medium such that 50,000 spermatozoa (based on count using a haemocytometer) were used to fertilize each group of five COC.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: Presumptive zygotes were stripped of cumulus cells and spermatozoa by gentle pipetting in pre-incubated synthetic oviduct fluid then allocated randomly to two groups for culture in synthetic oviduct fluid (SOF) either with 0.5 mM L-carnitine (the “treated” or “ + LC ” group) or without (the “control” or “ – LC” group). The SOF media was a standard culture medium containing amino acids and 0.4 % fatty-acid-free bovine serum albumin (ICP-Bio, Auckland, New Zealand). Ten zygotes were placed in a single droplet (10 μL) under filtered mineral oil (#8410, Sigma). The culture dishes were incubated at 38.5 °C in a humidified atmosphere containing 6.5 % CO2, 5 % O2 and 88.5 % N2. Ten embryos were transferred to each fresh droplets (10 μL) at 72 h and 120 h (20 μL) after fertilization to prevent ammonia intoxication (from amino acid metabolism) and nutrient depletion. Embryos remained under these conditions until Day 6, when morulas and early blastocysts were categorized according to IETS system for comparison purposes. Samples were produced using seven independent in vitro production runs. The COCs from different donor cows were pooled within respective breed and randomly allocated to treatment or control groups. Morula stage embryos were used for lipid quantification and mitochondrial activity measurement while blastocysts were used for mitochondrial DNA and RNA analyses.

tag: breed (cattle)

value: holstein


title: 2L mDNA

city: Duarte

first: Marc

last: Jung

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 49

hyb_protocol: According to standard NimbleGen Protocol

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Samples were quantile-normalized and arrays were normalized by Nimblegen's recommended method, tukey-biweight.

source_name: MIRA DNA_primary skin fibroblast_late

growth_protocol: Primary Skin Fibroblast cells were grown with culture medium (DMEM supplemented with 6% fetal bovine serum) for 2 -3 passages.

extract_protocol: Primary Embryonic Fibroblast cells were grown in a 150 mm dish containing 25 ml of culture medium (DMEM supplemented with 6% fetal bovine serum (FBS) to about 5x107 cells).  Fresh formaldehyde was added directly into media to a final concentration of 1% and incubated at RT for exactly 2 minutes on an orbiting platform. Cross-linking reaction was stopped by adding 2.6 ml of 1.25 M glycine solution. Media was removed and cells were washed twice with 20 ml ice-cold PBS without Ca and Mg. Cells were pelleted by centrifugation for 3 minutes at 250g at 4°C. For sonification, cells were resuspended from each 150 mm dish in 350 µl ChIP Lysis Buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl, pH 8.1) containing protease inhibitors (complete protease inhibitor cocktail tablets, Roche applied science, Cat.# 1697498). Sonication was carried out in 1.7 ml Eppendorf tubes using Branson Sonifer with a micro tip. Sonication condition were 10 times at 15sec on, 45sec off, at output 25%. Sheared chromatin was centrifuged at 14,000 rpm for 15 minutes at 4C.  For Methylated-CpG island recovery assay (MIRA), the methylated faction of sonicated genomic DNA from human skin fibroblast cells was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify MIRA-enriched DNA.

tag: donor age (yrs)

value: primary skin fibroblast

tag: time point

value: late timepoint (L)

tag: chip antibody

value: MIRA

source_name: Input DNA from primary skin fibroblast, early timepoint

value: early timepoint (E)

value: none, input DNA


title: 7L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 51

label_protocol: According to standard NimbleGen Protocol


title: 1 mM DIDP, Mouse 3

description:
Quality control: approved
124_A07

source_name: Primary mouse hepatocytes, mouse #3, DIDP

tag: age

value: 8-10 weeks

value: primary mouse hepatocytes

value: Diisodecyl phthalate (DIDP)

value: DIDP

value: 1 mM DIDP


title: 14L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 54

source_name: Input DNA from primary skin fibroblast, late timepoint


title: 9L mDNA

description:
MIRA-chip primary skin fibroblasts, late timepoint mDNA
Sample 52


title: Lame 239 Area2


title: Nuclei suspensor, biological rep 1

description:
nSUS #1
Gene expression data from nuclei.

tag: tissue

value: suspensor

value: embryo (2-16 cell stage)