title: group4, Phenobarbital CAR/PXR KO 4014

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1283


title: group3, control CAR/PXR KO 3024

status: Public on Aug 24 2014

type: RNA

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

description:
group3, control CAR/PXR KO
NUID-0000-0136-1265

hyb_protocol: Processing of miRNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

scan_protocol: Processing of mi RNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix mi-croRNA chips were preprocessed and normalized according to the Affymetrix miRNA QCTool manual. Briefly, the back- ground control probes of the chips were grouped into bins of same dinucleotide Guanine-Cytosine (GC) content. The median signal of the background bin that matches with the GC con- tent of the probe was then subtracted from the probe signal. The background corrected probes (for all probes on the chip in- cluding those of other species) were quantile normalized across chips, log2 transformed and summarized into probe sets with the median polish method as in standard RMA (Bolstad et al., 2003). We floored all normalized signal values to 1.0.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse liver

growth_protocol: C57BL/6 male wild-type, knock-out CARKO -PXRKO and humanized CARh - PXRh mice were obtained from TaconicArtemis (Germany). For the 13-week time course study, 9–11 week-old mice (age selected to avoid the confounding effect of liver maturation observed in younger animals) were allowed to acclimatize for 5 days prior to being randomly divided into two treatment groups (n = 5 per time point).

extract_protocol: Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was stored at −80◦C. miRNA was quantified using the Rediplate Ribogreen RNA quantitation kit (Life Technologies).

treatment_protocol: Phenobarbital (PB; free acid, >99.0%, Sigma, St Louis, MO, no. 04710, 0.05% (wt/vol) in drinking water) was administered to one group through ad libitum access to drinking water, as previously reported (see methods in PMID: 24690595). Mice were reated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.checked daily for activity and behavior and sacrificed on the indicated dates. Liver (incl. left, caudal and median parts) were sampled. To ensure sample homo- geneity for different molecular profiling methods, frozen liver samples were reduced to powder with CovarisCryoprep (Co- varis Inc., Woburn, MA) system and aliquoted on dry ice. For the 4-week dose response study, mice (n = 4 per group) were treated with PB starting at 8 weeks of age. PB was adminis- tered via the drinking water (PB solution prepared freshly every fourth day) at concentrations of 0.005, 0.01, 0.02, and 0.05% (wt/vol). Mice were kept on a 12 h dark/light cycle and had ac- cessed to food and water ad libitum. All animals were sacrificed between 9 and 11 a.m. to avoid circadian influences.

tag: tissue

value: liver

tag: genotype

value: CAR/PXR knock-out

tag: age

value: 9 to 11 weeks

tag: treatment

value: control

tag: time point

value: 91 days

tag: donorid


title: group4, Phenobarbital CAR/PXR KO 4004

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1273

label_protocol: Processing of miRNA 2.0 experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

value: Phenobarbital

value: 1 days


title: group4, Phenobarbital CAR/PXR KO 4009

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1278

value: 7 days


title: group4, Phenobarbital CAR/PXR KO 4013

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1282

value: 14 days


title: group3, control CAR/PXR KO 3028

description:
group3, control CAR/PXR KO
NUID-0000-0136-1267

value: 119 days


title: group4, Phenobarbital CAR/PXR KO 4006

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1275


title: group4, Phenobarbital CAR/PXR KO 4003

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1272


title: group3, control CAR/PXR KO 3029

description:
group3, control CAR/PXR KO
NUID-0000-0136-1268


title: group4, Phenobarbital CAR/PXR KO 4007

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1276


title: group3, control CAR/PXR KO 3030

description:
group3, control CAR/PXR KO
NUID-0000-0136-1269


title: group4, Phenobarbital CAR/PXR KO 4005

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1274


title: group3, control CAR/PXR KO 3025

description:
group3, control CAR/PXR KO
NUID-0000-0136-1266


title: group4, Phenobarbital CAR/PXR KO 4008

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1277


title: group3, control CAR/PXR KO 3023

description:
group3, control CAR/PXR KO
NUID-0000-0136-1264


title: group3, control CAR/PXR KO 3018

description:
group3, control CAR/PXR KO
NUID-0000-0136-1259

value: 28 days


title: group3, control CAR/PXR KO 3016

description:
group3, control CAR/PXR KO
NUID-0000-0136-1257


title: group3, control CAR/PXR KO 3017

description:
group3, control CAR/PXR KO
NUID-0000-0136-1258


title: group4, Phenobarbital CAR/PXR KO 4016

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1287


title: group4, Phenobarbital CAR/PXR KO 4001

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1270


title: group4, Phenobarbital CAR/PXR KO 4010

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1279


title: group4, Phenobarbital CAR/PXR KO 4002

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-1271


title: group3, control CAR/PXR KO 3020

description:
group3, control CAR/PXR KO
NUID-0000-0136-1261


title: group3, control CAR/PXR KO 3015

description:
group3, control CAR/PXR KO
NUID-0000-0136-1256


title: group3, control CAR/PXR KO 3022

description:
group3, control CAR/PXR KO
NUID-0000-0136-1263


title: group3, control CAR/PXR KO 3019

description:
group3, control CAR/PXR KO
NUID-0000-0136-1260


title: group3, control CAR/PXR KO 3026

description:
group3, control CAR/PXR KO
NUID-0000-0136-1254


title: group3, control CAR/PXR KO 3021

description:
group3, control CAR/PXR KO
NUID-0000-0136-1262


title: group3, control CAR/PXR KO 3014

description:
group3, control CAR/PXR KO
NUID-0000-0136-1253


title: group3, control CAR/PXR KO 3027

description:
group3, control CAR/PXR KO
NUID-0000-0136-1255


title: group3, control CAR/PXR KO 3010

description:
group3, control CAR/PXR KO
NUID-0000-0136-1249


title: group3, control CAR/PXR KO 3013

description:
group3, control CAR/PXR KO
NUID-0000-0136-1252


title: group3, control CAR/PXR KO 3007

description:
group3, control CAR/PXR KO
NUID-0000-0136-1246


title: group3, control CAR/PXR KO 3011

description:
group3, control CAR/PXR KO
NUID-0000-0136-1250


title: group2, Phenobarbital wild-type 2030

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1239

value: wild type


title: group3, control CAR/PXR KO 3012

description:
group3, control CAR/PXR KO
NUID-0000-0136-1251


title: group3, control CAR/PXR KO 3008

description:
group3, control CAR/PXR KO
NUID-0000-0136-1247


title: group3, control CAR/PXR KO 3009

description:
group3, control CAR/PXR KO
NUID-0000-0136-1248


title: group3, control CAR/PXR KO 3002

description:
group3, control CAR/PXR KO
NUID-0000-0136-1241


title: group2, Phenobarbital wild-type 2028

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1237


title: group3, control CAR/PXR KO 3006

description:
group3, control CAR/PXR KO
NUID-0000-0136-1245


title: group3, control CAR/PXR KO 3003

description:
group3, control CAR/PXR KO
NUID-0000-0136-1242


title: group2, Phenobarbital wild-type 2024

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1235


title: group3, control CAR/PXR KO 3001

description:
group3, control CAR/PXR KO
NUID-0000-0136-1240


title: group2, Phenobarbital wild-type 2023

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1234


title: group3, control CAR/PXR KO 3004

description:
group3, control CAR/PXR KO
NUID-0000-0136-1243


title: group2, Phenobarbital wild-type 2022

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1233


title: group2, Phenobarbital wild-type 2029

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1238


title: group2, Phenobarbital wild-type 2026

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0344

hyb_protocol: Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).

data_processing: Affymetrix CEL files were normalized using the Robust Multichip Average (RMA) from R/Bioconductor (reported expressino values are log base 2 transformed).  Quality metrics from arrays prior and after normalization using Bioconductor’s array QualityMetrics package (Kauffmann et al., 2009) were within acceptable limits except for 11 chips which were removed from subsequent analyses (not included).

extract_protocol: Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instruc- tions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was stored at −80◦C. miRNA was quantified using the Rediplate Ribogreen RNA quantitation kit (Life Technologies).


title: group2, Phenobarbital wild-type 2021

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0352

scan_protocol: Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).


title: group2, Phenobarbital wild-type 2014

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0343

label_protocol: Processing of GeneChip experiments was conducted as recommended by the manufacturer of the GeneChip system (Affymetrix, Santa Clara, CA).


title: group2, Phenobarbital wild-type 2015

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0346


title: group3, control CAR/PXR KO 3005

description:
group3, control CAR/PXR KO
NUID-0000-0136-1244


title: group2, Phenobarbital wild-type 2025

description:
group2, Phenobarbital wild-type
NUID-0000-0136-1236


title: group2, Phenobarbital wild-type 2027

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0345


title: group2, Phenobarbital wild-type 2016

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0347


title: group2, Phenobarbital wild-type 2018

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0349


title: group2, Phenobarbital wild-type 2017

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0348


title: group2, Phenobarbital wild-type 2019

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0350


title: group2, Phenobarbital wild-type 2013

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0342


title: group2, Phenobarbital wild-type 2020

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0351


title: group2, Phenobarbital wild-type 2009

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0338


title: group2, Phenobarbital wild-type 2012

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0341


title: group2, Phenobarbital wild-type 2006

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0335


title: group1, control wild-type 1023

description:
group1, control wild-type
NUID-0000-0136-0324


title: group2, Phenobarbital wild-type 2011

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0340


title: group2, Phenobarbital wild-type 2007

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0336


title: group1, control wild-type 1029

description:
group1, control wild-type
NUID-0000-0136-0328


title: group2, Phenobarbital wild-type 2002

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0331


title: group2, Phenobarbital wild-type 2005

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0334


title: group2, Phenobarbital wild-type 2008

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0337


title: group2, Phenobarbital wild-type 2003

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0332


title: group1, control wild-type 1028

description:
group1, control wild-type
NUID-0000-0136-0327


title: group1, control wild-type 1025

description:
group1, control wild-type
NUID-0000-0136-0326


title: group1, control wild-type 1021

description:
group1, control wild-type
NUID-0000-0136-0322


title: group1, control wild-type 1018

description:
group1, control wild-type
NUID-0000-0136-0319


title: group1, control wild-type 1022

description:
group1, control wild-type
NUID-0000-0136-0323


title: group1, control wild-type 1011

description:
group1, control wild-type
NUID-0000-0136-0310


title: group1, control wild-type 1013

description:
group1, control wild-type
NUID-0000-0136-0312


title: group1, control wild-type 1030

description:
group1, control wild-type
NUID-0000-0136-0329


title: group1, control wild-type 1014

description:
group1, control wild-type
NUID-0000-0136-0313


title: group1, control wild-type 1017

description:
group1, control wild-type
NUID-0000-0136-0318


title: group2, Phenobarbital wild-type 2001

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0330


title: group2, Phenobarbital wild-type 2004

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0333


title: group1, control wild-type 1016

description:
group1, control wild-type
NUID-0000-0136-0317


title: group1, control wild-type 1019

description:
group1, control wild-type
NUID-0000-0136-0320


title: group1, control wild-type 1027

description:
group1, control wild-type
NUID-0000-0136-0315


title: group1, control wild-type 1010

description:
group1, control wild-type
NUID-0000-0136-0309


title: group1, control wild-type 1020

description:
group1, control wild-type
NUID-0000-0136-0321


title: group1, control wild-type 1008

description:
group1, control wild-type
NUID-0000-0136-0307


title: group1, control wild-type 1026

description:
group1, control wild-type
NUID-0000-0136-0314


title: group1, control wild-type 1006

description:
group1, control wild-type
NUID-0000-0136-0305


title: group1, control wild-type 1012

description:
group1, control wild-type
NUID-0000-0136-0311


title: group1, control wild-type 1004

description:
group1, control wild-type
NUID-0000-0136-0303


title: group5, control CAR/PXR  h 5007

description:
group5, control CAR/PXR  h
NUID-0000-0136-0296

value: human CAR/PXR


title: group5, control CAR/PXR  h 5009

description:
group5, control CAR/PXR  h
NUID-0000-0136-0298


title: group1, control wild-type 1005

description:
group1, control wild-type
NUID-0000-0136-0304


title: group1, control wild-type 1002

description:
group1, control wild-type
NUID-0000-0136-0301


title: group1, control wild-type 1007

description:
group1, control wild-type
NUID-0000-0136-0306


title: group5, control CAR/PXR  h 5008

description:
group5, control CAR/PXR  h
NUID-0000-0136-0297


title: group1, control wild-type 1003

description:
group1, control wild-type
NUID-0000-0136-0302


title: group1, control wild-type 1001

description:
group1, control wild-type
NUID-0000-0136-0300


title: group5, control CAR/PXR  h 5006

description:
group5, control CAR/PXR  h
NUID-0000-0136-0295


title: group5, control CAR/PXR  h 5027

description:
group5, control CAR/PXR  h
NUID-0000-0136-0287


title: group5, control CAR/PXR  h 5003

description:
group5, control CAR/PXR  h
NUID-0000-0136-0292


title: group5, control CAR/PXR  h 5022

description:
group5, control CAR/PXR  h
NUID-0000-0136-0282


title: group5, control CAR/PXR  h 5028

description:
group5, control CAR/PXR  h
NUID-0000-0136-0288


title: group5, control CAR/PXR  h 5025

description:
group5, control CAR/PXR  h
NUID-0000-0136-0285


title: group5, control CAR/PXR  h 5029

description:
group5, control CAR/PXR  h
NUID-0000-0136-0289


title: group5, control CAR/PXR  h 5002

description:
group5, control CAR/PXR  h
NUID-0000-0136-0291


title: group5, control CAR/PXR  h 5019

description:
group5, control CAR/PXR  h
NUID-0000-0136-0280


title: group5, control CAR/PXR  h 5005

description:
group5, control CAR/PXR  h
NUID-0000-0136-0294


title: group5, control CAR/PXR  h 5023

description:
group5, control CAR/PXR  h
NUID-0000-0136-0283


title: group5, control CAR/PXR  h 5026

description:
group5, control CAR/PXR  h
NUID-0000-0136-0286


title: group5, control CAR/PXR  h 5030

description:
group5, control CAR/PXR  h
NUID-0000-0136-0290


title: group5, control CAR/PXR  h 5010

description:
group5, control CAR/PXR  h
NUID-0000-0136-0299


title: group5, control CAR/PXR  h 5016

description:
group5, control CAR/PXR  h
NUID-0000-0136-0277


title: group5, control CAR/PXR  h 5015

description:
group5, control CAR/PXR  h
NUID-0000-0136-0276


title: group5, control CAR/PXR  h 5004

description:
group5, control CAR/PXR  h
NUID-0000-0136-0293


title: group5, control CAR/PXR  h 5017

description:
group5, control CAR/PXR  h
NUID-0000-0136-0278


title: group5, control CAR/PXR  h 5021

description:
group5, control CAR/PXR  h
NUID-0000-0136-0281


title: group5, control CAR/PXR  h 5001

description:
group5, control CAR/PXR  h
NUID-0000-0136-0271


title: group5, control CAR/PXR  h 5014

description:
group5, control CAR/PXR  h
NUID-0000-0136-0275


title: group6, Phenobarbital CAR/PXR h 6027

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0267


title: group5, control CAR/PXR  h 5024

description:
group5, control CAR/PXR  h
NUID-0000-0136-0284


title: group6, Phenobarbital CAR/PXR h 6030

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0137-0710


title: group6, Phenobarbital CAR/PXR h 6029

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0269


title: group5, control CAR/PXR  h 5011

description:
group5, control CAR/PXR  h
NUID-0000-0136-0272


title: group5, control CAR/PXR  h 5013

description:
group5, control CAR/PXR  h
NUID-0000-0136-0274


title: group6, Phenobarbital CAR/PXR h 6026

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0266


title: group5, control CAR/PXR  h 5018

description:
group5, control CAR/PXR  h
NUID-0000-0136-0279


title: group6, Phenobarbital CAR/PXR h 6021

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0261


title: group6, Phenobarbital CAR/PXR h 6025

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0265


title: group6, Phenobarbital CAR/PXR h 6020

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0260


title: group6, Phenobarbital CAR/PXR h 6019

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0259


title: group6, Phenobarbital CAR/PXR h 6022

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0262


title: group5, control CAR/PXR  h 5012

description:
group5, control CAR/PXR  h
NUID-0000-0136-0273


title: group6, Phenobarbital CAR/PXR h 6023

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0263


title: group6, Phenobarbital CAR/PXR h 6017

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0257


title: group6, Phenobarbital CAR/PXR h 6014

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0254


title: group6, Phenobarbital CAR/PXR h 6004

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0244


title: group6, Phenobarbital CAR/PXR h 6001

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0241


title: group6, Phenobarbital CAR/PXR h 6007

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0247


title: group6, Phenobarbital CAR/PXR h 6018

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0258


title: group6, Phenobarbital CAR/PXR h 6003

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0243


title: group4, Phenobarbital CAR/PXR KO 4030

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0240


title: group6, Phenobarbital CAR/PXR h 6012

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0252


title: group6, Phenobarbital CAR/PXR h 6015

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0255


title: group4, Phenobarbital CAR/PXR KO 4025

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0238


title: group6, Phenobarbital CAR/PXR h 6008

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0248


title: group4, Phenobarbital CAR/PXR KO 4022

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0235


title: group6, Phenobarbital CAR/PXR h 6016

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0256


title: group4, Phenobarbital CAR/PXR KO 4023

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0236


title: group6, Phenobarbital CAR/PXR h 6005

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0245


title: group6, Phenobarbital CAR/PXR h 6006

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0246


title: group6, Phenobarbital CAR/PXR h 6013

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0253


title: group6, Phenobarbital CAR/PXR h 6010

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0250


title: group4, Phenobarbital CAR/PXR KO 4021

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0234


title: group6, Phenobarbital CAR/PXR h 6002

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0242


title: group6, Phenobarbital CAR/PXR h 6011

description:
group6, Phenobarbital CAR/PXR h
NUID-0000-0136-0251


title: group4, Phenobarbital CAR/PXR KO 4024

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0137-0709


title: group4, Phenobarbital CAR/PXR KO 4028

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0239


title: group4, Phenobarbital CAR/PXR KO 4015

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0228


title: group4, Phenobarbital CAR/PXR KO 4018

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0231


title: group4, Phenobarbital CAR/PXR KO 4027

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0227


title: group4, Phenobarbital CAR/PXR KO 4026

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0226


title: group4, Phenobarbital CAR/PXR KO 4010

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0221


title: group4, Phenobarbital CAR/PXR KO 4017

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0230


title: group4, Phenobarbital CAR/PXR KO 4019

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0232


title: group4, Phenobarbital CAR/PXR KO 4016

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0229


title: group4, Phenobarbital CAR/PXR KO 4013

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0224


title: group4, Phenobarbital CAR/PXR KO 4020

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0233


title: group4, Phenobarbital CAR/PXR KO 4011

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0222


title: group4, Phenobarbital CAR/PXR KO 4007

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0218


title: group4, Phenobarbital CAR/PXR KO 4008

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0219


title: group4, Phenobarbital CAR/PXR KO 4004

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0215


title: group3, control CAR/PXR KO 3029

description:
group3, control CAR/PXR KO
NUID-0000-0136-0210


title: group4, Phenobarbital CAR/PXR KO 4014

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0225


title: group3, control CAR/PXR KO 3023

description:
group3, control CAR/PXR KO
NUID-0000-0136-0206


title: group4, Phenobarbital CAR/PXR KO 4005

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0216


title: group3, control CAR/PXR KO 3021

description:
group3, control CAR/PXR KO
NUID-0000-0136-0204


title: group4, Phenobarbital CAR/PXR KO 4003

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0214


title: group3, control CAR/PXR KO 3030

description:
group3, control CAR/PXR KO
NUID-0000-0136-0211


title: group3, control CAR/PXR KO 3028

description:
group3, control CAR/PXR KO
NUID-0000-0136-0209


title: group4, Phenobarbital CAR/PXR KO 4009

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0220


title: group4, Phenobarbital CAR/PXR KO 4012

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0223


title: group3, control CAR/PXR KO 3020

description:
group3, control CAR/PXR KO
NUID-0000-0136-0203


title: group4, Phenobarbital CAR/PXR KO 4001

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0212


title: group4, Phenobarbital CAR/PXR KO 4002

description:
group4, Phenobarbital CAR/PXR KO
NUID-0000-0136-0213


title: group3, control CAR/PXR KO 3024

description:
group3, control CAR/PXR KO
NUID-0000-0136-0207


title: group3, control CAR/PXR KO 3025

description:
group3, control CAR/PXR KO
NUID-0000-0136-0208


title: group3, control CAR/PXR KO 3022

description:
group3, control CAR/PXR KO
NUID-0000-0136-0205


title: group3, control CAR/PXR KO 3018

description:
group3, control CAR/PXR KO
NUID-0000-0136-0201


title: group3, control CAR/PXR KO 3017

description:
group3, control CAR/PXR KO
NUID-0000-0136-0200


title: group3, control CAR/PXR KO 3019

description:
group3, control CAR/PXR KO
NUID-0000-0136-0202


title: group3, control CAR/PXR KO 3016

description:
group3, control CAR/PXR KO
NUID-0000-0136-0199


title: group3, control CAR/PXR KO 3010

description:
group3, control CAR/PXR KO
NUID-0000-0136-0191


title: group3, control CAR/PXR KO 3009

description:
group3, control CAR/PXR KO
NUID-0000-0136-0190


title: group3, control CAR/PXR KO 3013

description:
group3, control CAR/PXR KO
NUID-0000-0136-0194


title: group3, control CAR/PXR KO 3002

description:
group3, control CAR/PXR KO
NUID-0000-0136-0183


title: group3, control CAR/PXR KO 3004

description:
group3, control CAR/PXR KO
NUID-0000-0136-0185


title: group3, control CAR/PXR KO 3007

description:
group3, control CAR/PXR KO
NUID-0000-0136-0188


title: group3, control CAR/PXR KO 3026

description:
group3, control CAR/PXR KO
NUID-0000-0136-0196


title: group2, Phenobarbital wild-type 2029

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0180


title: group3, control CAR/PXR KO 3014

description:
group3, control CAR/PXR KO
NUID-0000-0136-0195


title: group3, control CAR/PXR KO 3005

description:
group3, control CAR/PXR KO
NUID-0000-0136-0186


title: group3, control CAR/PXR KO 3011

description:
group3, control CAR/PXR KO
NUID-0000-0136-0192


title: group3, control CAR/PXR KO 3001

description:
group3, control CAR/PXR KO
NUID-0000-0136-0182


title: group2, Phenobarbital wild-type 2024

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0177


title: group3, control CAR/PXR KO 3003

description:
group3, control CAR/PXR KO
NUID-0000-0136-0184


title: group3, control CAR/PXR KO 3012

description:
group3, control CAR/PXR KO
NUID-0000-0136-0193


title: group3, control CAR/PXR KO 3027

description:
group3, control CAR/PXR KO
NUID-0000-0136-0197


title: group2, Phenobarbital wild-type 2022

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0175


title: group2, Phenobarbital wild-type 2030

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0181


title: group2, Phenobarbital wild-type 2023

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0176


title: group2, Phenobarbital wild-type 2028

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0179


title: seq-SDQ3861_LET418_N2_L3_ChIP_Rep2

status: Public on Aug 28 2013

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: ChIP DNA; Antibody information listed below: official name: LET-418 SDQ3861;target name: LET-418;host: Rabbit;antigen: RAAEREEKKKGALEAARAAKKAKLEKGEEAENNDYCEECKQDGELLLCDTCPRAYHTVCIDENMEEPP EGDWSCAHCIEHGPEVVKEEPAKQNDEFCKIC;clonal: Polyclonal;purified: Affinity;company: SDI;catalog: SDQ3861;short description: An Affinity purified Rabbit Polyclonal antibody to LET-418 obtained from SDI (LET-418 SDQ3861)

library_source: genomic

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is wiggles are ce6, peak calls are ce10   ChIP-Seq_MACS_Peak-calling_over_reps:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is wiggles are ce6, peak calls are ce10

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worms are frozen, ground, crosslinked for 20 minutes in EGS, and for an additional 10 minutes in EGS plus formaldehyde. Later, washed pellets are resuspended in FA buffer and subjected to sonication in Bioruptor (20-30 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
DNA was incubated with an enzyme mix (Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends. The DNA fragments were ligated with appropriate adaptor (Illumina) and then amplified by PCR. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: strain

tag: developmental stage

value: L3 Larva

tag: sex type

value: mixed Male and Hermaphrodite population


title: RNA from S. cerevisiae

status: Public on Jul 03 2013

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

country: USA

institute: Harvard Medical School

description:
For this Sample, the rawest possible data file is not available.  It is not possible to obtain the rawest form of the data, as Helicos is now out of business.  Helicos supplied the sequence output as an aligned txt file, JGY2000_fc1.ch01.filtered.txt.gz (linked below as a supplementary file).  It is the most unmanipulated form of the data and contains the raw reads.
Note: GSM1154250 raw data file is identical to GSM1262423 raw data file.

library_source: transcriptomic

data_processing:
alignment to genome (Helicos Helisphere)
separation of unambiguous data by yeast species
counting of sequence tags by coordinate on each strand
classification of coordinates by associated ORF on appropriate strand
Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Saccharomyces cerevisiae: SGD genome build 61 (2008/06/05), version S288C_reference_genome_R61-1-1_20080605.tgz; http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/.
Genome_build: D. hansenii: ASM644v1
Genome_build: K. lactis: ASM251v1
Supplementary_files_format_and_content: Tab-delimited text files of tag counts at each coordinate in the 400 nt downstream of each ORF.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were cultured  to mid-log phase in rich medium (YPD for S. cerevisiae).

extract_protocol:
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified

tag: direct rna sequence from

value: Saccharomyces cerevisiae


title: OE-HRA1 #1_2HS

status: Public on Jul 30 2014

city: Riverside

first: Seung Cho

last: Lee

state: CA

address: 2150 Batchelor Hall

department: Botany & Plant Sciences

institute: University of California Riverside

hyb_protocol: Hybridization of 12 μg of biotin-labeled cRNA to each Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy MAS5.0 package .

organism: Arabidopsis thaliana

source_name: 7-d-old seedlings_OE-HRA1#1_2HS

label_protocol: biotin

growth_protocol: Arabidopsis seeds were sterilized, stratified for 3 days at 4 °C and grown on solid MS media [0.43 % (w/v) Murashigi Skoog (MS) salts (Sigma)], 0.4 % (w/v) Phytagel (Sigma), 1 % (w/v) sucrose, pH 5.7) in a vertical orientation in a growth chamber (Model # CU36L5, Percival Scientific, Perry, IA) under a long day cycle (16 h light at ~80 μmol photons m-2 s-1 and 8 h darkness) at 23°C for 7 days before treatments.

extract_protocol: Total RNA was extracted from frozen pulverized plant tissues using QIAGEN RNeasy Plant Mini kit according to the manufacture's protocol. RNase-Free DNase treatment was conducted during the column purification process.

treatment_protocol: Plates with 7-d-old seedlings were transferred to Lucite chambers where they were deprived of air by displacement for argon gas (99.9%) for 2 hours. The hypoxic stress (2HS) treatment was applied under dim light (5 to 7 μmol photons m-2 s-1) at the end of light cycle. For non-stress (2NS) treatment, MS plates were placed for 2 hours in the Lucite chambers that were open to ambient air.

tag: ecotype

tag: genotype/variation

value: HRA1 overexpression

value: 2 h hypoxia stress (2HS)

value: 7-day-old seedlings


title: MDA_FFPE77

status: Public on Feb 10 2014

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

hyb_protocol: Standard Illumina whole genome DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization in the Linear Models for Microarray Data (LIMMA) package in the R language environment was used to normalize the data

label: whole genome DASL

organism: Homo sapiens

source_name: Bladder tumor

label_protocol: Standard Illuminal whole genome DASL method

extract_protocol: Total RNA from FFPE was extracted by High Pure miRNA Isolation Kit (Roche). Quality control was performed by NanoDrop ND-1000.

tag: cstage

tag: histology tur

value: urothelial

tag: pstage

tag: cystectomy histology

value: no tumor identified

tag: nac

value: yes-MVAC/A

tag: age (at diagnosis)

tag: race

value: Caucasian

tag: gender

value: M

tag: os censor

value: censored

tag: dss censor

tag: survival (mo)


title: MDA_FFPE81

value: F

value: uncensored


title: seq-OD0039_SMC4_N2_Mxemb_ChIP_Rep1

description: ChIP DNA; Antibody information listed below: official name: SMC-4 OD00039;target name: SMC-4;host: Rabbit;antigen: CGSTPKRSPMKPLTPSSKKKEKAIVDDDDDME;clonal: Polyclonal;purified: Affinity;company: Other;catalog: OD00039;short description: An Affinity purified Rabbit Polyclonal antibody to SMC-4 obtained from Other (SMC-4 OD00039)

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce10   ChIP-Seq_MACS_Peak-calling_over_reps:JL:1 protocol. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters:tagSize = 25mfold = 10,30genomeSize = 90000000bandwidth = 300pvalue = 1e-5  Processed data are obtained using following parameters: genome version is ce10

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C.

extract_protocol:
Worm_embryo_extraction_vSE3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131) + phosphatase inhibitors (Calbiochem Cat# 524624), and dounced 30 times. Using samples were sonicated in Bioruptor using settings: high 30 sec on 30 sec off 15 minutes. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4ºC, and taking the supernatant for ChIP. For a detailed protocol see http://www.modencode.org/.
Worm_chromatin_immunoprecipitation_v3. 2mg extract was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit and concentrated using by Speed vac.
DNA for Library Prep is incubated with an End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends. It is then purified and incubated with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3? ends (a single A-overhang for more efficient and directed ligation of the adaptors). After a second purification, the DNA fragments is ligated with single-end ?Homebrew? adaptors which contain an index sequence within (Corbin Jones? lab). After ligation, the samples are purified TWICE using SPRI beads, allowing for a size selection step getting rid of excess adaptors. Samples are then amplified by PCR with single end primers. Depending on the original fragmentation of the DNA, samples can either be purified by SPRI or by separation and purification from an agarose gel.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: strain

value: Mixed Embryo

tag: genotype


title: group2, Phenobarbital wild-type 2025

description:
group2, Phenobarbital wild-type
NUID-0000-0136-0178

tag: tissue

value: liver

value: wild type

tag: age

value: 9 to 11 weeks

tag: treatment

value: Phenobarbital

tag: time point

value: 91 days

tag: donorid


title: MDA_FFPE73

tag: cstage

tag: histology tur


title: Control r4

status: Public on Feb 04 2014

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Gene expression data from WBC from mice.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized using RMA. Analyzed using BRB array tools.

source_name: Control r8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

extract_protocol: Extraction of total RNA was performed with QIAGEN RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Used the Cecal Ligation and Puncture model

value: control

tag: cell type

value: WBC

value: 20-24 months


title: MDA_FFPE69

value: urothelial

tag: pstage

tag: cystectomy histology

tag: nac


title: MDA_FFPE68

tag: age (at diagnosis)

tag: race

tag: gender


title: MDA_FFPE71

value: no tumor identified

tag: os censor

tag: dss censor

tag: survival (mo)


title: Control r2

source_name: Control r6


title: MDA_FFPE78

value: yes-MVAC/A


title: MDA_FFPE82

value: Caucasian


title: MDA_FFPE75


title: MDA_FFPE74

value: urothelial with focal micropapillary

value: M


title: MDA_FFPE72

value: censored


title: Control r1

source_name: Control r5


title: MDA_FFPE76

value: urothelial focal glandular

value: uncensored


title: Control r3

source_name: Control r7


title: OE-HRA1 #2_2NS

source_name: 7-d-old seedlings_OE-HRA1#2_2NS

tag: ecotype

tag: genotype/variation

value: HRA1 overexpression

value: 2 h non-stress (2NS)

tag: tissue

value: 7-day-old seedlings


title: MDA_FFPE83


title: MDA_FFPE70

value: urothelial- focal micropapillary

value: urothelial with micropap and squam diff

value: F


title: Kidney_PB_19_rep2

status: Public on Dec 16 2011

type: genomic

description:
18538402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

hyb_protocol: Pooling and hybridization the samples to the arrays using a NimbleGen Hybridization Kit and NimbleGen Hybridization System 4 or 12. 5. Washing the arrays using the NimbleGen Wash Buffer Kit and the NimbleGen Microarray Dryer

scan_protocol: Scaning the array using the 2-μm, high-resolution NimbleGen MS 200 Microarray Scanner

data_processing: Image analysis with NimbleScan software, followed by M-value calculation (log2(cy5/cy3) of channels), loess smoothing M-values, averaging probes in promotors, median centering all scaling chips (see Lempiäinen et al., PLoS One. 2011 Mar 24), summarized per promotor (therefore probes of the same SEQ_ID entry have the same value per sample)

label_protocol: Labeling of the immunoprecipitated (IP) and Input DNA samples with Cy5 and Cy3 respectively, using the NimbleGen Dual-Color DNA Labeling Kit.

extract_protocol: Genomic DNA from liver and kidney tissue samples was prepared by overnight Proteinase K (pK) treatment in lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM EDTA pH 8.0, 100 mM NaCl, 0.5% SDS), phenol-chloroform extraction, ethanol precipitation and RNaseA digestion. Genomic DNA was sonicated (Bioruptor, Diagenode) to produce random fragments ranging in size from 300 to 1,000 bp and 6 µg of fragmented DNA was used for a MeDIP assay: DNA was denatured for 10 min at 95°C and immunoprecipitated for 2 hrs at 4°C with 10 µl of monoclonal antibody against 5-methylcytidine (Eurogentec) in a final volume of 500 µl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100). The mixture was incubated with 60 µl magnetic beads (Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen) for 2 hrs at 4°C and washed three times with 700 µl of IP buffer. Beads were subsequently treated with pK for 3 hrs at 50°C and the methylated DNA recovered by phenol-chloroform extraction followed by ethanol precipitation. For microarray analysis the genomic input DNA and MeDIP enriched DNA was amplified using WGA2: GenomePlex Complete Whole Genome kit (Sigma) and 3 µg of DNA was sent to Roche Nimblegen (Madison, USA) for Cy3 and Cy5 labeling and hybridization on mouse promoter tiling arrays.

tag: strain

value: B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀)

value: male

value: kidney

tag: treatment

value: Phenobarbital

tag: duration

value: 4 weeks

tag: medip antibody

value: anti-5-Methylcytosine antibody

tag: medip antibody vendor

value: Eurogentec

tag: medip antibody cat#

source_name: Kidney_PB_19_Input DNA


title: Kidney_PB_20_rep2

description:
18566602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_20_Input DNA


title: Kidney_PB_19_rep1

description:
18538002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_20_rep1

description:
18538502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_17_rep2

description:
18459302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_17_Input DNA


title: Kidney_PB_18_rep2

description:
18515702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_18_Input DNA


title: Kidney_PB_18_rep1

description:
18511902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_15_rep1

description:
18454402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_15_Input DNA


title: Kidney_PB_17_rep1

description:
18458902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_12_rep2

description:
18453802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_12_Input DNA


title: Kidney_PB_16_rep1

description:
18457502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_16_Input DNA


title: MDA_FFPE79

tag: cstage

tag: histology tur

value: urothelial

tag: pstage

tag: cystectomy histology

value: yes-MVAC/A

value: Caucasian


title: Kidney_PB_14_rep2

description:
18454302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

tag: gender

source_name: Kidney_PB_14_Input DNA


title: Kidney_PB_16_rep2

description:
18458702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_15_rep2

description:
18457402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_10_rep2

description:
18453402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

value: Control

source_name: Kidney_Control_10_Input DNA


title: Kidney_PB_11_rep2

description:
18453602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_11_Input DNA


title: Kidney_Control_10_rep1

description:
18448402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_14_rep1

description:
18454002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_6_rep2

description:
18444502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_6_Input DNA


title: Kidney_Control_8_rep2

description:
18448002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_8_Input DNA


title: Kidney_PB_13_rep2

description:
18454102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_PB_13_Input DNA


title: Kidney_PB_13_rep1

description:
18453902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_7_rep2

description:
18444902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_7_Input DNA


title: Kidney_Control_9_rep2

description:
18448302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_9_Input DNA


title: Kidney_Control_8_rep1

description:
18447702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_11_rep1

description:
18453502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_5_rep2

description:
18444302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_5_Input DNA


title: Kidney_Control_9_rep1

description:
18448102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_PB_12_rep1

description:
18453702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_2_rep1

description:
18432002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_2_Input DNA


title: Kidney_Control_7_rep1

description:
18444802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_4_rep2

description:
18441702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_4_Input DNA


title: Kidney_Control_3_rep1

description:
18438802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_3_Input DNA


title: Liver_PB_20_rep2

description:
18786602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

value: liver

source_name: Liver_PB_20_Input DNA


title: Kidney_Control_1_rep2

description:
18429902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_1_Input DNA


title: Kidney_Control_3_rep2

description:
18438902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_4_rep1

description:
18440802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_20_rep1

description:
18786502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_15_rep2

description:
18446702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_15_Input DNA


title: Liver_PB_18_rep2

description:
18786002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_18_Input DNA


title: Liver_PB_14_rep2

description:
18444702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_14_Input DNA


title: Liver_PB_19_rep2

description:
18786202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_19_Input DNA


title: Liver_PB_16_rep2

description:
18454602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_16_Input DNA


title: Liver_PB_15_rep1

description:
18445002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_17_rep1

description:
18457702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_17_Input DNA


title: Liver_PB_13_rep1

description:
18442002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_13_Input DNA


title: Liver_PB_19_rep1

description:
18786102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_5_rep1

description:
18441902
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_18_rep1

description:
18785802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Kidney_Control_2_rep2

description:
18438002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_16_rep1

description:
18448202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_12_rep2

description:
18441802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_12_Input DNA


title: Liver_PB_14_rep1

description:
18444202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_13_rep2

description:
18442102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_Control_10_rep2

description:
18429502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_10_Input DNA


title: Liver_PB_17_rep2

description:
18785502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_11_rep1

description:
18429602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_PB_11_Input DNA


title: Liver_PB_11_rep2

description:
18441502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_PB_12_rep1

description:
18441602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_Control_7_rep2

description:
18418002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_7_Input DNA


title: Liver_Control_10_rep1

description:
18428402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Liver_treated_17

status: Public on Dec 14 2011

hyb_protocol: The arrays were washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix).

data_processing: The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files. Affymetrix chips were normalized with the MAS5 method (scaled to a trimmed mean of 150 per chip, Affymetrix, I. (2002) Statistical Algorithms Description Document http://www.affymetrix.com/support/technical/whitepapers.affx). For gene expression analysis, we excluded all probe sets with an average MAS5 signal of less than 50 in both groups (liver control and treated) to avoid large fold changes in genes that are not expressed under both of the experimental conditions. The cut-off of 50 is empirical, and we found that it performs better than the suggested present/absent calls of MAS5. This reduces the number of probe sets from 45,037 to 18,981 probes.

source_name: 4 wk_Phenobarbital treatment_liver

label_protocol: Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3′ IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented.

growth_protocol: 29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10) and phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28).

extract_protocol: Frozen liver and kidney samples were homogenized in TRIzol reagent (Invitrogen) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.

treatment_protocol: Liver and kidney tissues were removed, split into several sections, frozen in liquid nitrogen and stored at −80°C.

value: B6C3F1/Crl (C57BL/6 male  x C3H/He female)

value: Liver

tag: donor id


title: PB_Liver_treated_16


title: PB_Liver_treated_19


title: Liver_Control_9_rep2

description:
18428302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_9_Input DNA


title: PB_Liver_treated_20


title: PB_Liver_treated_18


title: Liver_Control_6_rep1

description:
18416102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_6_Input DNA


title: Liver_Control_7_rep1

description:
18416402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_Control_9_rep1

description:
18426402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Liver_treated_11


title: PB_Liver_treated_12


title: Liver_Control_5_rep1

description:
18412602
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_5_Input DNA


title: PB_Liver_treated_14


title: Liver_Control_3_rep1

description:
18413202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_3_Input DNA


title: PB_Kidney_treated_19

source_name: 4 wk_Phenobarbital treatment_kidney

value: Kidney


title: Kidney_Control_6_rep1

description:
18444402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_6_Input DNA


title: PB_Kidney_treated_13


title: Liver_Control_2_rep2

description:
18412302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_2_Input DNA


title: Kidney_Control_1_rep1

description:
18429802
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Kidney_Control_1_Input DNA


title: Liver_Control_2_rep1

description:
18412202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_Control_8_rep2

description:
18419102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_8_Input DNA


title: Liver_Control_4_rep1

description:
18412402
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_4_Input DNA


title: Liver_Control_1_rep2

description:
18411202
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)

source_name: Liver_Control_1_Input DNA


title: Liver_Control_4_rep2

description:
18412502
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Liver_Control_7

source_name: 4 wk_ control treatment_liver


title: PB_Kidney_treated_20


title: PB_Liver_Control_8


title: PB_Kidney_treated_17


title: PB_Liver_Control_5


title: PB_Liver_Control_4


title: Liver_Control_6_rep2

description:
18416302
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: Liver_Control_1_rep1

description:
18409102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Kidney_treated_11


title: PB_Liver_treated_15


title: PB_Kidney_treated_16


title: Liver_Control_3_rep2

description:
18416002
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Kidney_treated_12


title: PB_Liver_Control_1


title: PB_Kidney_treated_14


title: PB_Kidney_treated_15


title: PB_Liver_Control_2


title: PB_Liver_Control_6


title: PB_Liver_Control_9


title: Liver_Control_5_rep2

description:
18412702
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Liver_treated_13


title: PB_Kidney_treated_18


title: Liver_Control_8_rep1

description:
18418102
The two sources labeled cy5 and cy3 are from the same sample (two replicates for each sample)


title: PB_Liver_Control_10


title: PB_Kidney_Control_3

source_name: 4 wk_ control treatment_kidney


title: PB_Kidney_Control_9


title: PB_Kidney_Control_6


title: PB_Kidney_Control_7


title: PB_Kidney_Control_4


title: PB_Kidney_Control_2


title: PB_Kidney_Control_1


title: PB_Kidney_Control_10


title: T47D_RU486__6h_rep2

status: Public on Jul 23 2011

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

institute: ETH Zurich

description: replicate 2

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The raw expression data were normalized using the Robust Spline Normalization (RSN) algorithm implemented in the lumi package in R Bioconductor

source_name: T47D cell, RU486, 6 hr

label_protocol: According to Illumina protocol

growth_protocol: T47D cells were cultured in RPMI 1640 with 10 % FBS. Human uterine leiomyoma smooth muscle cells were cultured in DEME/F12 with 10% FBS.

extract_protocol: Total RNA from T47D and leiomyoma cells was extracted using Tri-reagent (Sigma-Aldrich). Complementary DNA was prepared with Superscript III first-Strand Synthesis System (Invitrogen)

treatment_protocol: T47D cells were hormone starved 2 days in RPMI 1640 with 5% charcol stripped FBS before treated with vehicle (ethanol) or RU486 (10-6 M). Uterine leiomyoma smooth muscle cells were hormone starved for 1 day in DMEM/F12 containing 1% charcol stripped FBS before treated with vehicle (ethanol) or RU486 (10-6 M).

value: breast

tag: Sex

value: female

tag: source

value: pleural efusion of an infiltrating ductal carcinoma of the breast

tag: cell line


title: Leiomyoma_RU486_6h_rep1

description: replicate 1

source_name: Leiomyoma smooth muscle cell, RU486, 6 hr

value: uterine

value: uterine leiomyoma


title: PB_Kidney_Control_8

value: male


title: Notch1 wildtype, replicate 2

status: Public on Aug 09 2011

description: flox/flox, uterus

hyb_protocol: Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide  arrays.

data_processing: The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.

source_name: Uterus

label_protocol: Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.

growth_protocol: The RNA was pooled from the uteri of three mice per genotype and treatment.

extract_protocol: Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions

treatment_protocol: Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.

tag: age

value: 6 weeks

value: Female

tag: genotype

value: Notch1 f/f (floxed, wild type)

value: Uterus


title: Notch1 knockout, replicate 2

description: PRCre/+, uterus

scan_protocol: Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide  arrays.

tag: strain

value: Notch1 d/d (knockout)

tag: tissue


title: Leiomyoma_RU486_6h_rep3

description: replicate 3


title: Leiomyoma_RU486_6h_rep2

description: replicate 2


title: T47D_RU486_6h_rep3

description: replicate 3


title: PB_Kidney_Control_5

tag: treatment

tag: duration

value: 4 weeks


title: Leiomyoma_ethanol_6h_rep2

description: replicate 2

source_name: Leiomyoma smooth muscle cell, ethanol, 6 hr


title: Leiomyoma_ethanol_6h_rep1

description: replicate 1


title: T47D_ethanol_6h_rep3

description: replicate 3

source_name: T47D cell, ethanol, 6 hr


title: Notch1 wildtype, replicate 3

description: flox/flox, uterus


title: Leiomyoma_ethanol_6h_rep3

description: replicate 3


title: PB_Liver_Control_3

value: Control


title: Notch1 knockout, replicate 3

description: PRCre/+, uterus


title: Notch1 wildtype, replicate 1

description: flox/flox, uterus


title: Notch1 knockout, replicate 1

description: PRCre/+, uterus


title: T47D_ethanol_6h_rep2

description: replicate 2


title: T47D_RU486_6h_rep1

description: replicate 1


title: T47D_ethanol_6h_rep1

description: replicate 1