title: WT_ABA_rep3

status: Public on Jan 31 2016

type: RNA

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

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

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: whole plant

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

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: The signals of microarray probes were applied to 75 percentile normalization

molecule: total RNA

organism: Arabidopsis thaliana

source_name: WT with ABA

label_protocol: 100 ng of total RNA samples were used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Two of ONSEN inserted lines (13-7, 19-4),  parent line (nrpd1), and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on MS medium with and without 2μM ABA for 7 days

extract_protocol: Total RNA was extracted from 7 day-old seedlings using TRI Reagent (Sigma T9424), according to the supplier’s recommendations.

treatment_protocol: MS medium plates containg 2μM abscisic acid (ABA)

tag: ecotype

value: Columbia

tag: line

value: wild-type


title: 19-4_con_rep3

description: ONSEN inserted line

source_name: 19-4 without ABA


title: 13-7_ABA_rep2

description: ONSEN inserted line

source_name: 13-7 with ABA


title: nrpd1_con_rep2

source_name: nrpd1 without ABA


title: nrpd1_ABA_rep3

source_name: nrpd1 with ABA


title: 13-7_ABA_rep3

description: ONSEN inserted line


title: 13-7_con_rep2

description: ONSEN inserted line

source_name: 13-7 without ABA


title: nrpd1_con_rep3


title: 13-7_ABA_rep1

description: ONSEN inserted line


title: 19-4_ABA_rep2

description: ONSEN inserted line

source_name: 19-4 with ABA


title: 19-4_con_rep2

description: ONSEN inserted line


title: nrpd1_ABA_rep1


title: 19-4_ABA_rep1

description: ONSEN inserted line


title: WT_ABA_rep1

description: whole plant


title: nrpd1_ABA_rep2


title: 13-7_con_rep3

description: ONSEN inserted line


title: 19-4_ABA_rep3

description: ONSEN inserted line


title: 19-4_con_rep1

description: ONSEN inserted line


title: 13-7_con_rep1

description: ONSEN inserted line


title: WT_con_rep3

description: whole plant

source_name: WT without ABA


title: WT_con_rep2

description: whole plant


title: WT_ABA_rep2

description: whole plant


title: nrpd1_con_rep1


title: WT_con_rep1

description: whole plant


title: Infected with H37Ra and treated with T0901317, replicate 3

city: Montreal

first: David

last: Laperriere

state: QC

address: 2950, chemin de Polytechnique

department: IRIC - Institut de recherche en immunologie et en cancerologie

country: Canada

institute: Université de Montréal

description: Monocyte cell line terminally differentiated into macrophages by PMA treatment

hyb_protocol: cDNA was hybridized onto Affymetrix Human Gene 2.0 ST chips

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed using Flexarray v1.6

label: biotin

organism: Homo sapiens

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

growth_protocol: Cells were grown and infected in RPMI-1640 with 10% FBS

extract_protocol: Trizol-choloform extraction

treatment_protocol: Cells were differentiated with PMA

tag: cell line


title: Infected with H37Ra and treated with T0901317, replicate 2


title: mouse Ape1 3

city: Lexington

first: Tadahide

last: Izumi

state: KY

address: 1095 VA Dr

department: Toxicology

country: USA

institute: University of Kentucky

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: the set of nine RNA samples (3 preparations from 3 cell lines) were analyzed with Mouse GeneChip ST2.0 using GeneChip FLUIDICS station 450 at the Microarray Core of the University of Kentucky.

data_processing: Raw data were processed with the Exon Array Computational Tool (PARTEK). Specifically, the entire 41,345 genes (anova_011014.xlsx) based on false discovery rate (FDR) (P < 0.05) generated 7,115 genes and recorded in the file named ANOVA_FDR005.txt.

organism: Mus musculus

source_name: mouse embryonic fibroblast

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

growth_protocol: The cells wee cultured in DMEM supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 1% L-glutamine at 37˚C in a 5% CO2 incubator.

extract_protocol: Total RNA was isolated from the triplicated 60mm dishes with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The qualities of RNA samples were verified by Agilent 2100 Bioanalyzer (Agilent Technology) and then the set of nine RNA samples (3 preparations from 3 cell lines) were analyzed using GeneChip FLUIDICS station 450 and Affymetrix GeneChip Scanner 7G (Affymetrix) at the Microarray Core of the University of Kentucky. Transcriptional intensities of 41,344 genes were processed using PARTEK.

treatment_protocol: Cells were in the logarithmically growing phase, and grown to semi-confluency in 60mm dishes (Corning).

tag: strain

value: isogenic to C56BL/6

tag: tissue

value: Fibroblast

tag: Sex

value: male


title: Infected with H37Ra, replicate 1

source_name: Infected with H37Ra, replicate 1


title: Infected with H37Ra, replicate 2

source_name: Infected with H37Ra, replicate 2


title: Infected with H37Ra, replicate 3

source_name: Infected with H37Ra, replicate 3


title: mouse Ape1 2

scan_protocol: Affymetrix GeneChip Scanner 7G (Affymetrix) at the Microarray Core of the University of Kentucky.


title: human APE1 2


title: Infected with H37Ra and treated with T0901317, replicate 1


title: human APE1 1


title: mouse Ape1 1


title: human APE1 3


title: vector control 1


title: vector control 2


title: slide3-array1

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

description: Comparing D7.5 embryos from CAN vs. SUN (biological replicate set 1).

hyb_protocol: Hybridization mixture was prepared along with Spike-In control according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.

scan_protocol: Arrays were immediately scanned at 5 μm resolution after slides were washed and dried with an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) using the autoscan feature from the default setting. Images were analysed with GenePix Pro 6.0. software.

data_processing: FlexArray software was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Bos taurus

label_protocol: Antisense RNA (aRNA) labelling was done under ozone-free environmental chamber. Antisense RNA (aRNA) was used for labeling using ULS™ Fluorescent Labeling Kit (Kreatech, Inc., Durham, NC, USA) for Agilent arrays (with Cy3 and Cy5). Labelling was also done under ozone-free environmental chamber.

extract_protocol:
Embryos: Holstein embryos were non-surgically collected at 7.5 d post-insemination from the maternal cows related to each diet treatment group mentioned in the overall design. Soon after collection and morphological evaluation, similar stage embryos from each cow were pooled and snap-frozen in liquid nitrogen and then kept at -80 °C until RNA extraction. RNA was extracted from the same stage embryos (blastocyst).
RNA: Total RNA from Day 7.5 embryos was extracted and purified using the PicoPure RNA Isolation Kit (Life Science). After DNase digestion (Qiagen), quality and concentration of extracted RNA were analyzed by Bioanalyzer (Agilent).

treatment_protocol: Gene expression of embryos was evaluated in CAN (n=4) vs. FLX (n=4) & CAN (n=4) vs. SUN (n=4) (n=number of biological replicates in each group). In data analysis, canola was defined as control, FLX & SUN as treatment groups.

tag: breed

value: Holstein

tag: developmental stage

value: day 7.5 embryo

value: whole body

tag: treatment group

value: canola/maternal feeding

value: sunflower/maternal feeding


title: slide3-array2

description: Dye-swap replicate of biological replicate set 1.


title: vector control 3


title: slide3-array4

description: Dye-swap replicate of biological replicate set 2.


title: slide4-array4

description: Dye-swap replicate of biological replicate set 4.


title: slide4-array3

description: Comparing D7.5 embryos from CAN vs. SUN (biological replicate set 4).


title: slide1-array3

description: Comparing D7.5 embryos from CAN vs. FLX (biological replicate set 2).

value: flaxseed/maternal feeding


title: slide2-array1

description: Comparing D7.5 embryos from CAN vs. FLX (biological replicate set 3).


title: slide4-array1

description: Comparing D7.5 embryos from CAN vs. SUN (biological replicate set 3).


title: slide4-array2

description: Dye-swap replicate of biological replicate set 3.


title: slide2-array2


title: slide1-array4


title: slide3-array3

description: Comparing D7.5 embryos from CAN vs. SUN (biological replicate set 2).


title: slide2-array4


title: slide1-array2


title: slide2-array3

description: Comparing D7.5 embryos from CAN vs. FLX (biological replicate set 4).


title: slide1-array1

description: Comparing D7.5 embryos from CAN vs. FLX (biological replicate set 1).


title: Subject 1069 Visit 3

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Samples were hybridized on  HG-133-plus-PM plates

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish

source_name: Subject 1069 Visit 3

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject

tag: vaccine

value: ATIV

tag: cohort

value: C

tag: visit

tag: day

value: Male

tag: age

value: whole blood


title: Subject 1067 Visit 4

source_name: Subject 1067 Visit 4

value: TIV

value: B

value: Female


title: Subject 1069 Visit 4

source_name: Subject 1069 Visit 4


title: Subject 1063 Visit 3

source_name: Subject 1063 Visit 3

value: A


title: Subject 1069 Visit 1

source_name: Subject 1069 Visit 1


title: Subject 1067 Visit 1

source_name: Subject 1067 Visit 1


title: Subject 1067 Visit 3

source_name: Subject 1067 Visit 3


title: Subject 1063 Visit 4

source_name: Subject 1063 Visit 4


title: Subject 1063 Visit 1

source_name: Subject 1063 Visit 1


title: Subject 1058 Visit 4

source_name: Subject 1058 Visit 4


title: Subject 1007 Visit 4

source_name: Subject 1007 Visit 4


title: Subject 1058 Visit 3

source_name: Subject 1058 Visit 3


title: Subject 1057 Visit 1

source_name: Subject 1057 Visit 1


title: Subject 1057 Visit 3

source_name: Subject 1057 Visit 3


title: Subject 1057 Visit 4

source_name: Subject 1057 Visit 4


title: Subject 1056 Visit 1

source_name: Subject 1056 Visit 1


title: Subject 1055 Visit 3

source_name: Subject 1055 Visit 3


title: Subject 1056 Visit 4

source_name: Subject 1056 Visit 4


title: Subject 1056 Visit 3

source_name: Subject 1056 Visit 3


title: Subject 1053 Visit 1

source_name: Subject 1053 Visit 1


title: Subject 1054 Visit 1

source_name: Subject 1054 Visit 1


title: Subject 1053 Visit 3

source_name: Subject 1053 Visit 3


title: Subject 1048 Visit 4

source_name: Subject 1048 Visit 4


title: Subject 1055 Visit 4

source_name: Subject 1055 Visit 4


title: Subject 1048 Visit 1

source_name: Subject 1048 Visit 1


title: Subject 1007 Visit 1

source_name: Subject 1007 Visit 1


title: Subject 1007 Visit 3

source_name: Subject 1007 Visit 3


title: Subject 1054 Visit 3

source_name: Subject 1054 Visit 3


title: Subject 1055 Visit 1

source_name: Subject 1055 Visit 1


title: Subject 1053 Visit 4

source_name: Subject 1053 Visit 4


title: Subject 1044 Visit 3

source_name: Subject 1044 Visit 3


title: Subject 1048 Visit 3

source_name: Subject 1048 Visit 3


title: Subject 1004 Visit 4

source_name: Subject 1004 Visit 4


title: Subject 1058 Visit 1

source_name: Subject 1058 Visit 1


title: Subject 1046 Visit 3

source_name: Subject 1046 Visit 3


title: Subject 1046 Visit 4

source_name: Subject 1046 Visit 4


title: Subject 1044 Visit 1

source_name: Subject 1044 Visit 1


title: Subject 1054 Visit 4

source_name: Subject 1054 Visit 4


title: Subject 1046 Visit 1

source_name: Subject 1046 Visit 1


title: Subject 1043 Visit 4

source_name: Subject 1043 Visit 4


title: Subject 1044 Visit 4

source_name: Subject 1044 Visit 4


title: Subject 1042 Visit 4

source_name: Subject 1042 Visit 4


title: Subject 1043 Visit 1

source_name: Subject 1043 Visit 1


title: Subject 1043 Visit 3

source_name: Subject 1043 Visit 3


title: Subject 1042 Visit 3

source_name: Subject 1042 Visit 3


title: Subject 1042 Visit 1

source_name: Subject 1042 Visit 1


title: Subject 1040 Visit 4

source_name: Subject 1040 Visit 4


title: Subject 1040 Visit 1

source_name: Subject 1040 Visit 1


title: Subject 1035 Visit 3

source_name: Subject 1035 Visit 3


title: Subject 1039 Visit 4

source_name: Subject 1039 Visit 4


title: Subject 1039 Visit 1

source_name: Subject 1039 Visit 1


title: Subject 1037 Visit 3

source_name: Subject 1037 Visit 3


title: Subject 1033 Visit 1

source_name: Subject 1033 Visit 1


title: Subject 1032 Visit 3

source_name: Subject 1032 Visit 3


title: Subject 1033 Visit 4

source_name: Subject 1033 Visit 4


title: Subject 1039 Visit 3

source_name: Subject 1039 Visit 3


title: Subject 1032 Visit 4

source_name: Subject 1032 Visit 4


title: Subject 1032 Visit 1

source_name: Subject 1032 Visit 1


title: Subject 1035 Visit 4

source_name: Subject 1035 Visit 4


title: Subject 1030 Visit 4

source_name: Subject 1030 Visit 4


title: Subject 1033 Visit 3

source_name: Subject 1033 Visit 3


title: Subject 1030 Visit 1

source_name: Subject 1030 Visit 1


title: Subject 1002 Visit 4

source_name: Subject 1002 Visit 4


title: Subject 1027 Visit 3

source_name: Subject 1027 Visit 3


title: Subject 1002 Visit 3

source_name: Subject 1002 Visit 3


title: Subject 1037 Visit 4

source_name: Subject 1037 Visit 4


title: Subject 1031 Visit 3

source_name: Subject 1031 Visit 3


title: Subject 1035 Visit 1

source_name: Subject 1035 Visit 1


title: Subject 1031 Visit 4

source_name: Subject 1031 Visit 4


title: Subject 1027 Visit 4

source_name: Subject 1027 Visit 4


title: Subject 1028 Visit 3

source_name: Subject 1028 Visit 3


title: Subject 1028 Visit 4

source_name: Subject 1028 Visit 4


title: Subject 1030 Visit 3

source_name: Subject 1030 Visit 3


title: Subject 1031 Visit 1

source_name: Subject 1031 Visit 1


title: Subject 1024 Visit 4

source_name: Subject 1024 Visit 4


title: Subject 1023 Visit 1

source_name: Subject 1023 Visit 1


title: Subject 1132 Visit 1

source_name: Subject 1132 Visit 1


title: Subject 1132 Visit 3

source_name: Subject 1132 Visit 3


title: Subject 1138 Visit 3

source_name: Subject 1138 Visit 3


title: Subject 1138 Visit 1

source_name: Subject 1138 Visit 1


title: Subject 1108 Visit 3

source_name: Subject 1108 Visit 3


title: Subject 1023 Visit 4

source_name: Subject 1023 Visit 4


title: Subject 1023 Visit 3

source_name: Subject 1023 Visit 3


title: Subject 1120 Visit 4

source_name: Subject 1120 Visit 4


title: Subject 1108 Visit 1

source_name: Subject 1108 Visit 1


title: Subject 1078 Visit 1

source_name: Subject 1078 Visit 1


title: Subject 1006 Visit 4

source_name: Subject 1006 Visit 4


title: Subject 1090 Visit 1

source_name: Subject 1090 Visit 1


title: Subject 1105 Visit 1

source_name: Subject 1105 Visit 1


title: Subject 1051 Visit 4

source_name: Subject 1051 Visit 4


title: Subject 1120 Visit 1

source_name: Subject 1120 Visit 1


title: Subject 1006 Visit 1

source_name: Subject 1006 Visit 1


title: Subject 1119 Visit 4

source_name: Subject 1119 Visit 4


title: Subject 1105 Visit 3

source_name: Subject 1105 Visit 3


title: Subject 1090 Visit 3

source_name: Subject 1090 Visit 3


title: Subject 1022 Visit 4

source_name: Subject 1022 Visit 4


title: Subject 1078 Visit 3

source_name: Subject 1078 Visit 3


title: Subject 1119 Visit 1

source_name: Subject 1119 Visit 1


title: Subject 1051 Visit 1

source_name: Subject 1051 Visit 1


title: Subject 1144 Visit 4

source_name: Subject 1144 Visit 4


title: Subject 1139 Visit 1

source_name: Subject 1139 Visit 1


title: Subject 1143 Visit 1

source_name: Subject 1143 Visit 1


title: Subject 1144 Visit 1

source_name: Subject 1144 Visit 1


title: Subject 1137 Visit 1

source_name: Subject 1137 Visit 1


title: Subject 1022 Visit 3

source_name: Subject 1022 Visit 3


title: Subject 1143 Visit 4

source_name: Subject 1143 Visit 4


title: Subject 1040 Visit 3

source_name: Subject 1040 Visit 3


title: Subject 1139 Visit 4

source_name: Subject 1139 Visit 4


title: Subject 1143 Visit 3

source_name: Subject 1143 Visit 3


title: Subject 1026 Visit 1

source_name: Subject 1026 Visit 1


title: Subject 1144 Visit 3

source_name: Subject 1144 Visit 3


title: Subject 1019 Visit 1

source_name: Subject 1019 Visit 1


title: Subject 1139 Visit 3

source_name: Subject 1139 Visit 3


title: Subject 1022 Visit 1

source_name: Subject 1022 Visit 1


title: Subject 1024 Visit 1

source_name: Subject 1024 Visit 1


title: Subject 1137 Visit 3

source_name: Subject 1137 Visit 3


title: Subject 1137 Visit 4

source_name: Subject 1137 Visit 4


title: Subject 1036 Visit 4

source_name: Subject 1036 Visit 4


title: Subject 1036 Visit 1

source_name: Subject 1036 Visit 1


title: Subject 1026 Visit 3

source_name: Subject 1026 Visit 3


title: Subject 1002 Visit 1

source_name: Subject 1002 Visit 1


title: Subject 1036 Visit 3

source_name: Subject 1036 Visit 3


title: Subject 1026 Visit 4

source_name: Subject 1026 Visit 4


title: Subject 1024 Visit 3

source_name: Subject 1024 Visit 3


title: Subject 1016 Visit 3

source_name: Subject 1016 Visit 3


title: Subject 1019 Visit 3

source_name: Subject 1019 Visit 3


title: Subject 1019 Visit 4

source_name: Subject 1019 Visit 4


title: Subject 1130 Visit 4

source_name: Subject 1130 Visit 4


title: Subject 1016 Visit 4

source_name: Subject 1016 Visit 4


title: Subject 1027 Visit 1

source_name: Subject 1027 Visit 1


title: Subject 1136 Visit 3

source_name: Subject 1136 Visit 3


title: Subject 1136 Visit 4

source_name: Subject 1136 Visit 4


title: Subject 1136 Visit 1

source_name: Subject 1136 Visit 1


title: Subject 1131 Visit 1

source_name: Subject 1131 Visit 1


title: Subject 1010 Visit 4

source_name: Subject 1010 Visit 4


title: Subject 1130 Visit 1

source_name: Subject 1130 Visit 1


title: Subject 1016 Visit 1

source_name: Subject 1016 Visit 1


title: Subject 1131 Visit 4

source_name: Subject 1131 Visit 4


title: Subject 1129 Visit 3

source_name: Subject 1129 Visit 3


title: Subject 1128 Visit 4

source_name: Subject 1128 Visit 4


title: Subject 1129 Visit 1

source_name: Subject 1129 Visit 1


title: Subject 1128 Visit 3

source_name: Subject 1128 Visit 3


title: Subject 1129 Visit 4

source_name: Subject 1129 Visit 4


title: Subject 1127 Visit 3

source_name: Subject 1127 Visit 3


title: Subject 1127 Visit 4

source_name: Subject 1127 Visit 4


title: Subject 1131 Visit 3

source_name: Subject 1131 Visit 3


title: Subject 1124 Visit 1

source_name: Subject 1124 Visit 1


title: Subject 1128 Visit 1

source_name: Subject 1128 Visit 1


title: Subject 1124 Visit 4

source_name: Subject 1124 Visit 4


title: Subject 1123 Visit 4

source_name: Subject 1123 Visit 4


title: Subject 1123 Visit 3

source_name: Subject 1123 Visit 3


title: Subject 1127 Visit 1

source_name: Subject 1127 Visit 1


title: Subject 1010 Visit 3

source_name: Subject 1010 Visit 3


title: Subject 1123 Visit 1

source_name: Subject 1123 Visit 1


title: Subject 1124 Visit 3

source_name: Subject 1124 Visit 3


title: Subject 1122 Visit 1

source_name: Subject 1122 Visit 1


title: Subject 1010 Visit 1

source_name: Subject 1010 Visit 1


title: Subject 1117 Visit 4

source_name: Subject 1117 Visit 4


title: Subject 1117 Visit 3

source_name: Subject 1117 Visit 3


title: Subject 1122 Visit 4

source_name: Subject 1122 Visit 4


title: Subject 1115 Visit 1

source_name: Subject 1115 Visit 1


title: Subject 1122 Visit 3

source_name: Subject 1122 Visit 3


title: Subject 1117 Visit 1

source_name: Subject 1117 Visit 1


title: Subject 1130 Visit 3

source_name: Subject 1130 Visit 3


title: Subject 1116 Visit 1

source_name: Subject 1116 Visit 1


title: Subject 1116 Visit 3

source_name: Subject 1116 Visit 3


title: Subject 1009 Visit 4

source_name: Subject 1009 Visit 4


title: Subject 1113 Visit 4

source_name: Subject 1113 Visit 4


title: Subject 1113 Visit 3

source_name: Subject 1113 Visit 3


title: Subject 1115 Visit 3

source_name: Subject 1115 Visit 3


title: Subject 1116 Visit 4

source_name: Subject 1116 Visit 4


title: Subject 1115 Visit 4

source_name: Subject 1115 Visit 4


title: Subject 1109 Visit 4

source_name: Subject 1109 Visit 4


title: wild type WT44

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization using the IlluminaGenomeStudio software

source_name: bone marrow stromal cells

label_protocol: Standard Illumina protocol

extract_protocol: RNA was isolated with TRIzol reagent

tag: genotype

value: wild type

tag: cell type

value: bone marrow stromal cells

value: Mixed CD1/C57BL6 background


title: HDAC3 conditional knock-out KO46

description: replicate 2

value: HDAC3 conditional knock-out


title: Subject 1111 Visit 3

source_name: Subject 1111 Visit 3


title: HDAC3 conditional knock-out KO47

description: replicate 2


title: Subject 1113 Visit 1

source_name: Subject 1113 Visit 1


title: Subject 1111 Visit 4

source_name: Subject 1111 Visit 4


title: Subject 1111 Visit 1

source_name: Subject 1111 Visit 1


title: HDAC3 conditional knock-out KO23

description: replicate 2


title: Subject 1009 Visit 3

source_name: Subject 1009 Visit 3


title: wild type WT22

description: replicate 1


title: wild type WT21

description: replicate 1


title: HDAC3 conditional knock-out KO16

description: replicate 2


title: Subject 1109 Visit 1

source_name: Subject 1109 Visit 1


title: Subject 1107 Visit 3

source_name: Subject 1107 Visit 3


title: Subject 1103 Visit 1

source_name: Subject 1103 Visit 1


title: HDAC3 conditional knock-out KO24

description: replicate 2


title: HDAC3 conditional knock-out KO32

description: replicate 2


title: Subject 1103 Visit 4

source_name: Subject 1103 Visit 4


title: Subject 1107 Visit 1

source_name: Subject 1107 Visit 1


title: Subject 1109 Visit 3

source_name: Subject 1109 Visit 3


title: Subject 1107 Visit 4

source_name: Subject 1107 Visit 4


title: wild type WT13

description: replicate 1


title: Subject 1102 Visit 4

source_name: Subject 1102 Visit 4


title: HDAC3 conditional knock-out KO15

description: replicate 2


title: wild type WT14

description: replicate 1


title: Subject 1103 Visit 3

source_name: Subject 1103 Visit 3


title: Subject 1102 Visit 3

source_name: Subject 1102 Visit 3


title: wild type WT30

description: replicate 1


title: wild type WT42

description: replicate 1


title: Subject 1102 Visit 1

source_name: Subject 1102 Visit 1


title: wild type WT5

description: replicate 1

source_name: bone marrow stromal cells


title: HDAC3 conditional knock-out KO7

description: replicate 2


title: mDA_SNC_Pitx3-KO_2

first: Panojot

last: Bifsha

address: 3175 Chemin de la Côte Ste-Catherine

department: Pediatrics

institute: CHU Sainte-Justine

description: Gene expression data of FAC-sorted GFP+ neurons dissociated from SNc of newborn Pitx3 KO mice

hyb_protocol: According to manufacturer protocol (Affymetrix Gene1.0ST expression arrays)

data_processing: Gene expression summary values were computed after normalization and background correction with RMA Express. Fold-change expression values and statistics were determined using the Local Pooled Error (LPE) algorithm embedded in FlexArray program (Genome Quebec).

label_protocol: Total RNA was linearly amplified using WT-Ovation Pico RNA Amplification kit (Nu-  Gen) and further processed accoding to Affymetrix recommendations

growth_protocol: SNc and VTA were microdissected from ventral midbrain of newborn mice.

extract_protocol: Total RNA was purified using the RNeasy Micro kit (Qiagen) according to the manufacturer recommendations

treatment_protocol: Microdissected SNc and VTA were dissociated into individual neurons using the Papain dissociation kit (Worthington). Propidium iodide-negative/EGFP+ neurons were directly sorted into RNAlater (Ambion) using the MOFLO instrument (Beckman Coulter).

tag: mouse strain

tag: mouse age


title: Subject 1101 Visit 4

source_name: Subject 1101 Visit 4


title: Subject 1101 Visit 1

source_name: Subject 1101 Visit 1


title: Subject 1101 Visit 3

source_name: Subject 1101 Visit 3


title: Subject 1100 Visit 4

source_name: Subject 1100 Visit 4


title: mDA_SNC_Pitx3-KO_1

scan_protocol: According to manufacturer protocol (Affymetrix Gene1.0ST expression arrays)

value: FAC-sorted GFP+ neurons dissociated from SNc of newborn Pitx3 KO mice


title: purified natural  β cells from pancreatic tissue

type: genomic

city: Jerusalem

first: Deborah

last: Nejman

address: Ein Kerem

country: Israel

institute: Hebrew University

hyb_protocol: The labeled Input and Bound DNAs were combined and hybridized for 60 h at 67°C in 15% deionized formamide to a CpG island microarray using the Agilent aCGH hybridization buffer and protocol.

scan_protocol: Arrays were washed according to the Agilent aCGH protocol, immediately scanned on an Agilent microarray scanner and processed using Agilent Feature extraction software version 9.5.

data_processing: Probe log ratio Cy5/Cy3 signals were Loess normalized and transformed into Z-scores according to their Tm.

molecule: genomic DNA

label_protocol: The Input and Bound DNAs were labeled using the Agilent Technologies Genomic Labeling kit Plus according to the manufacturer’s instructions. Briefly, 300ng of each sample was labeled with Cyanine-3 or Cyanine-5 dUTP and purified using microcon YM 30 columns.

extract_protocol: mouse (40µg) DNA was sonicated to an average fragment size of 300–1000 bp, precipitated with  400 mM NaCl, 2 volumes of ethanol and 1 µl glycogen. 1.5 µg were set aside as the Input fraction. DNA was denatured and anti-5-methylcytidine  monoclonal antibody (10 µl for 5 µg) was added and incubated on a rotator at 4°C overnight. 40 µl Dynabeads (Sheep anti-Mouse IgG) were prewashed  with 0.1% BSA/PBS and added to the DNA. The DNA was then washed 3 times and Ab-bound DNA resuspended and extracted with proteinase K,  phenol-chloroform and ethanol precipitation.

tag: sample type

value: input

value: bound

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #


title: mDA_SNC_WT_2

description: Gene expression data of FAC-sorted GFP+ neurons dissociated from SNc of newborn WT mice


title: mDA_VTA_WT_2

description: Gene expression data of FAC-sorted GFP+ neurons dissociated from VTA of newborn WT mice


title: mDA_VTA_Pitx3-KO_2

description: Gene expression data of FAC-sorted GFP+ neurons dissociated from VTA of newborn Pitx3 KO mice


title: Subject 1100 Visit 3

source_name: Subject 1100 Visit 3

tag: Sex

tag: tissue


title: aTC cell line

tag: cell line

value: aTC cell line


title: mDA_SNC_WT_1

value: FAC-sorted GFP+ neurons dissociated from SNc of newborn WT mice


title: mDA_VTA_WT_1

value: FAC-sorted GFP+ neurons dissociated from VTA of newborn WT mice


title: Endoderm Replicate 2 differentiated from EB5

value: Endoderm differentiated from EB5


title: Subject 1098 Visit 3

source_name: Subject 1098 Visit 3

tag: subject

value: ATIV

value: Male

value: whole blood


title: Mesoderm differentiated from EB5

value: Mesoderm differentiated from EB5


title: Subject 1100 Visit 1

source_name: Subject 1100 Visit 1

tag: vaccine

value: TIV

value: A


title: Retinoic Acid treated mouse embryonic stem cells TT2


title: mDA_VTA_Pitx3-KO_1

value: FAC-sorted GFP+ neurons dissociated from VTA of newborn Pitx3 KO mice


title: Subject 1098 Visit 4

source_name: Subject 1098 Visit 4

tag: cohort

value: B


title: Subject 1094 Visit 4

source_name: Subject 1094 Visit 4

tag: visit


title: Min6 cell line

value: Min6 cell line


title: day 4 differentiated oligodendrocytes + PD169 (rep 3)

first: Guillermina

last: Almazan

state: Quebec

address: 3655 Prom. Sir William Osler

department: Pharmacology and Therapeutics

institute: McGill University

data_processing: FlexArray Software (GenomeQuebec)

organism: Rattus norvegicus

label_protocol: Cy3 - according to Illumina manufacturer instructions CATALOG # BD-901-1002

growth_protocol: Oligodendrocytes were isolated according to the protocol of McCarthy & De Vellis (PMID: 6248568)

extract_protocol: Extracted using the Qiagen Rneasy RNA extraction kit

treatment_protocol: Oligodendrocyte progenitors were treated for 24 or 48 hrs with PD169316

value: Sprague-Dawley neonatal rat isolated oligodendrocytes

tag: strain

value: Sprague-Dawley

value: oligodendrocytes

tag: differentiation state

value: day 4 differentiated oligodendrocyte

tag: treatment


title: teratoma Replicate 1 generated from J1

tag: cell type

value: teratoma generated from J1

value: input

value: bound

value: Diagenode


title: day 4 differentiated oligodendrocytes + PD169 (rep 2)

hyb_protocol: according to Illumina manufacturer instructions


title: Endoderm Replicate 1 differentiated from EB5

value: Endoderm differentiated from EB5


title: Subject 1008 Visit 4

source_name: Subject 1008 Visit 4

value: ATIV

tag: day

value: Female

tag: age


title: teratoma Replicate 2 generated from J1

tag: sample type


title: Subject 1098 Visit 1

source_name: Subject 1098 Visit 1

value: Male

value: whole blood


title: mouse embryonic stem cells TT2

tag: antibody


title: mouse embryoid bodies from es TT2

value: mouse embryoid bodies from es TT2

tag: antibody manufacturer


title: Subject 1094 Visit 3

source_name: Subject 1094 Visit 3


title: Subject 1093 Visit 4

source_name: Subject 1093 Visit 4

value: A


title: Subject 1093 Visit 3

source_name: Subject 1093 Visit 3


title: mouse embryonic stem cells J1

tag: antibody catalog #


title: Subject 1094 Visit 1

source_name: Subject 1094 Visit 1

value: B

tag: Sex


title: mouse embryonic stem cells EB5


title: day 4 differentiated oligodendrocytes + PD169 (rep 1)

scan_protocol: according to Illumina manufacturer instructions


title: day 2 differentiated oligodendrocytes + PD169 (rep 3)

value: day 2 differentiated oligodendrocyte


title: Subject 1091 Visit 4

source_name: Subject 1091 Visit 4

tag: tissue


title: Embryo 12.5 days

value: Embryo 12.5 days

tag: gender


title: Embryo 11.5 days

value: Embryo 11.5 days


title: day 0 differentiated oligodendrocytes (rep 1)

value: Sprague-Dawley neonatal rat isolated oligodendrocytes

value: Sprague-Dawley

value: oligodendrocytes

value: day 0 differentiated oligodendrocyte


title: day 2 differentiated oligodendrocytes + PD169 (rep 1)


title: day 2 differentiated oligodendrocytes (rep 3)


title: Subject 1093 Visit 1

source_name: Subject 1093 Visit 1

tag: subject


title: Embryo 10.5 days

value: Embryo 10.5 days

value: input

value: bound


title: day 0 differentiated oligodendrocytes (rep 3)


title: day 2 differentiated oligodendrocytes + PD169 (rep 2)


title: Subject 1091 Visit 1

source_name: Subject 1091 Visit 1

tag: vaccine

value: ATIV


title: muscle Replicate 2

value: muscle

value: 3 months

value: Diagenode


title: day 2 differentiated oligodendrocytes (rep 2)


title: spleen Replicate 2

value: spleen

value: Male


title: Embryo 9.5 days

value: Embryo 9.5 days


title: spleen Replicate 1

value: Female


title: Embryo 8.5 days

value: Embryo 8.5 days


title: day 0 differentiated oligodendrocytes (rep 2)


title: day 2 differentiated oligodendrocytes (rep 1)

value: day 2 differentiated oligodendrocyte


title: Subject 1008 Visit 3

source_name: Subject 1008 Visit 3

tag: cohort

value: A

value: whole blood


title: Subject 1091 Visit 3

source_name: Subject 1091 Visit 3

value: B

tag: visit


title: Subject 1089 Visit 4

source_name: Subject 1089 Visit 4

value: TIV


title: Subject 1089 Visit 3

source_name: Subject 1089 Visit 3


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipE

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Colorectal carcinoma cells with overexpressed TP53

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

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

value: colorectal carcinoma cells

value: induced expression of TP53


title: lung Replicate 2

value: lung

value: input

value: bound


title: day 1 differentiated oligodendrocytes + PD169 (rep 2)

value: Sprague-Dawley neonatal rat isolated oligodendrocytes

tag: strain

value: Sprague-Dawley

value: oligodendrocytes

value: day 1 differentiated oligodendrocyte


title: Subject 1085 Visit 4

source_name: Subject 1085 Visit 4

value: C

value: Male


title: day 1 differentiated oligodendrocytes (rep 2)

tag: differentiation state


title: Subject 1082 Visit 4

source_name: Subject 1082 Visit 4

value: Female


title: day 1 differentiated oligodendrocytes (rep 1)


title: liver Replicate 2

value: liver

value: 3 months

value: Diagenode


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipE

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with our novel permutation approach TileShuffle.

source_name: Colorectal carcinoma cells with defunct TP53

tag: treatment

value: with defunct TP53


title: muscle Replicate 1

value: muscle


title: Subject 1082 Visit 3

source_name: Subject 1082 Visit 3

value: TIV

value: whole blood


title: lung Replicate 1

value: lung


title: Subject 1089 Visit 1

source_name: Subject 1089 Visit 1

value: A


title: day 1 differentiated oligodendrocytes + PD169 (rep 3)

tag: cell type


title: day 1 differentiated oligodendrocytes (rep 3)


title: SpT WT B

city: bonn

first: Neha

last: Sharma

address: sigmund freud str-25

institute: Institute of Pathology

description: 3 biological replicated pooled

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

source_name: murine placenta

label_protocol: standard Illumina protocol

extract_protocol: The placenta was snap frozen in liquid nitrogen. 10 micrometer sections were cut and the junctional zone of control and mutant placenta was extracted using laser microdissection. RNA was isolated using Rneasy Micro Kit (Qiagen).Quality control was performed with Agilent Bioanalyser.

value: junctional zone of placenta

tag: developmental stage


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipE

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with our permutation approach (TileShuffle).

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: cell line

tag: tumor

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: Subject 1008 Visit 1

source_name: Subject 1008 Visit 1

value: ATIV

tag: day

tag: age


title: brain Replicate 1

value: brain

tag: sample type

value: input

value: bound

tag: antibody

tag: antibody manufacturer

tag: antibody catalog #


title: Subject 1082 Visit 1

source_name: Subject 1082 Visit 1

tag: subject

value: C

tag: Sex

value: Female

tag: tissue


title: kidney Replicate 1

value: kidney

tag: gender

value: 3 months


title: kidney Replicate 2

value: Male

value: Diagenode


title: Subject 1081 Visit 1

source_name: Subject 1081 Visit 1

tag: vaccine

tag: cohort

tag: visit


title: Subject 1085 Visit 1

source_name: Subject 1085 Visit 1

value: TIV


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipL

tag: cell type

value: colorectal carcinoma cells

tag: treatment

value: induced expression of TP53


title: liver Replicate 1

value: liver


title: day 1 differentiated oligodendrocytes + PD169 (rep 1)

value: Sprague-Dawley neonatal rat isolated oligodendrocytes

tag: strain

value: Sprague-Dawley

value: oligodendrocytes

tag: differentiation state

value: day 1 differentiated oligodendrocyte


title: Subject 1081 Visit 4

source_name: Subject 1081 Visit 4

value: ATIV

value: A

tag: day

value: whole blood


title: pancreas Replicate 2

value: pancreas

tag: age

value: input

value: bound


title: Subject 1081 Visit 3

source_name: Subject 1081 Visit 3


title: SpT KO A

description: 3 biological replicates pooled

value: junctional zone of placenta

tag: developmental stage


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipL

value: with defunct TP53


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipH


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipL

tag: cell line

tag: tumor

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: brain Replicate 2

value: brain

value: Male

value: 3 months

tag: sample type

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipH

value: colorectal carcinoma cells


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipL

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with our permutation approach (TileShuffle).

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipH

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: colorectal carcinoma cells with defunct TP53 using TAS ChipL

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with TAS.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). We set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150.


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipH


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipH

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with TAS.

value: induced expression of TP53


title: colorectal carcinoma cells with defunct TP53 using TAS ChipH


title: INA6 cells using TAS (IL-6 withdrawal) ChipH

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with Tiling Array Software (TAS).


title: colon Replicate 2

tag: tissue

value: colon

tag: gender


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipL

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 1e-5 which yielded the best results from the set of tested parameter values.


title: INA6 cells using TAS (IL-6 withdrawal) ChipL


title: INA6 cells using TAS (IL-6 restimulation) ChipL

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with Tiling Array Software (TAS).


title: Subject 1079 Visit 3

source_name: Subject 1079 Visit 3

tag: subject

tag: vaccine

value: ATIV

tag: cohort

value: C

tag: Sex

value: Female


title: Subject 1079 Visit 4

source_name: Subject 1079 Visit 4

tag: visit

value: whole blood


title: INA6 cells using TAS (IL-6 restimulation) ChipH

tag: treatment


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipH

source_name: Colorectal carcinoma cells with overexpressed TP53

tag: cell type


title: colorectal carcinoma cells with defunct TP53 using MAT ChipL

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.

value: defunct TP53


title: INA6 cells using MAT (IL-6 withdrawal) ChipL

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with MAT.


title: Subject 1079 Visit 1

source_name: Subject 1079 Visit 1

tag: day

tag: age


title: Subject 1076 Visit 4

source_name: Subject 1076 Visit 4

value: TIV


title: colorectal carcinoma cells with defunct TP53 using MAT ChipH

source_name: Colorectal carcinoma cells with defunct TP53


title: Subject 1076 Visit 1

source_name: Subject 1076 Visit 1


title: colon Replicate 1

value: input

value: bound


title: Subject 1076 Visit 3

source_name: Subject 1076 Visit 3


title: Subject 1074 Visit 3

source_name: Subject 1074 Visit 3

value: B


title: INA6 cells using MAT (IL-6 restimulation) ChipL

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.

tag: cell line

value: multiple myeloma


title: Subject 1074 Visit 4

source_name: Subject 1074 Visit 4

value: Male


title: INA6 cells using MAT (IL-6 withdrawal) ChipH

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: tumor

value: IL-6 has been withdrawn for 13 hours


title: Subject 1074 Visit 1

source_name: Subject 1074 Visit 1


title: INA6 cells using MAT (IL-6 restimulation) ChipH


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipG


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipG

value: with defunct TP53


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipG


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipJ

value: colorectal carcinoma cells


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipJ


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipG

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipJ


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipG

value: induced expression of TP53


title: colorectal carcinoma cells with defunct TP53 using TAS ChipG


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipJ


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipJ


title: INA6 cells using TAS (IL-6 withdrawal) ChipG


title: INA6 cells using TAS (IL-6 restimulation) ChipG


title: colorectal carcinoma cells with defunct TP53 using TAS ChipJ


title: INA6 cells using TAS (IL-6 withdrawal) ChipJ


title: T_232245

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

department: Pathology

institute: University of North Carolina

hyb_protocol: Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100)  as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapsed by averaging. Samples from  different batches  were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with no covariates included.  Normalized data provided is the filtered, batch combined,  non-median centered data used to draw conclusions in the study.

source_name: TRP allograft tumor_radiation

label_protocol: Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent.  1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes.  Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes.  Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.

extract_protocol: Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions

treatment_protocol: Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.

tag: strain background

tag: mouse id

tag: survival (days)

value: radiation

value: high-grade astrocytoma allografts

source_name: Stratagene whole mouse reference RNA

tag: sample type

value: reference


title: T_230946

tag: tissue


title: T_231705


title: T_231671


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipG


title: INA6 cells using TAS (IL-6 restimulation) ChipJ


title: T_231439


title: T_230958


title: colorectal carcinoma cells with defunct TP53 using MAT ChipG


title: T_230936


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipJ


title: INA6 cells using MAT (IL-6 withdrawal) ChipG


title: T_230168


title: T_230235


title: T_229688


title: INA6 cells using MAT (IL-6 restimulation) ChipG


title: colorectal carcinoma cells with defunct TP53 using MAT ChipJ


title: INA6 cells using MAT (IL-6 withdrawal) ChipJ


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipN


title: T_229687


title: T_226111


title: T_226085


title: T_226082


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipN


title: T_222565


title: T_220715


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipI


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipN


title: T_219668


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipI


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipN


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipI


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipN


title: INA6 cells using TAS (IL-6 withdrawal) ChipN


title: colorectal carcinoma cells with defunct TP53 using TAS ChipN


title: INA6 cells using MAT (IL-6 restimulation) ChipJ


title: colorectal carcinoma cells with defunct TP53 using TAS ChipI


title: INA6 cells using TAS (IL-6 restimulation) ChipN


title: INA6 cells using TAS (IL-6 restimulation) ChipI


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipI


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipN


title: T_242907

source_name: TRP allograft tumor_untreated

value: untreated


title: T_243531


title: INA6 cells using TAS (IL-6 withdrawal) ChipI


title: T_243533


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipI


title: INA6 cells using MAT (IL-6 withdrawal) ChipN


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipI


title: colorectal carcinoma cells with defunct TP53 using MAT ChipI


title: INA6 cells using MAT (IL-6 restimulation) ChipN


title: T_241254


title: INA6 cells using MAT (IL-6 withdrawal) ChipI


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipE


title: INA6 cells using MAT (IL-6 restimulation) ChipI


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipE


title: colorectal carcinoma cells with defunct TP53 using MAT ChipN


title: T_242903


title: T_241253


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipK


title: T_240933


title: INA6 cells using TAS (IL-6 withdrawal) ChipE


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipK


title: T_240417


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipK


title: T_240649


title: T_240418


title: INA6 cells using TAS (IL-6 restimulation) ChipE


title: T_237482


title: T_234751


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipE


title: pancreas Replicate 1

value: pancreas

tag: gender

value: 3 months

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipK


title: T_240385


title: colorectal carcinoma cells with defunct TP53 using MAT ChipE

value: defunct TP53


title: T_230446


title: T_233445


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipL


title: INA6 cells using MAT (IL-6 restimulation) ChipE


title: INA6 cells using TAS (IL-6 withdrawal) ChipK


title: T_226785


title: colorectal carcinoma cells with defunct TP53 using TAS ChipE


title: INA6 cells using TAS (IL-6 restimulation) ChipK


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipK


title: colorectal carcinoma cells with defunct TP53 using MAT ChipK


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipK


title: INA6 cells using MAT (IL-6 withdrawal) ChipK


title: colorectal carcinoma cells with defunct TP53 using TAS ChipK


title: INA6 cells using MAT (IL-6 restimulation) ChipK


title: INA6 cells using MAT (IL-6 withdrawal) ChipE


title: T_221965


title: Overfed_ovary-pool1

city: Little Rock

first: Aline

last: Andres

state: Arkansas

address: 15 Children's Way

institute: Arkansas Children's Nutrition Center

description:
ovarian gene expression
Groups of female rats were fed liquid diets at either 155 kcal/kg¾  (lean) or 220 kcal/kg¾(overfed) via total enteral nutrition for 28 days. Rats were mated with lean male counterparts. On dpc 4.5 all rats were scarifice and ovaries  were collected and flash frozen in liquid nitrogen.
Ovary tissuses were collected on dpc 4.5 from rats at sacrifice and flash frozen in liquid nitrogen

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip Rat Genome 230 2.0  (N = 3/group) for 16 h at 45ºC in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using GCOS and utilized for analysis using GeneSpring  v 11.5.1

source_name: days post coitum 4.5-rat ovary

label_protocol: First- and second- strand cDNA synthesis (from 0.5 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Total RNA from ovarian tissue was isolated from the lean and overfed TEN fed rats using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion

tag: diet

value: TEN fed- 220 kcal

value: female

value: ovary


title: Lean_ovary_pool3

value: TEN fed- 155kcal


title: T_226253


title: Overfed_ovary_pool2


title: Lean_ovary_pool1


title: NRASQ61R  (day4)

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

institute: DKFZ

description: Biological replicate 1 of 2. NRASQ61R infected melanocytes, harvested after 4 days.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Technologies, Inc.) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were sequentially washed.

scan_protocol: Microarray slides were scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Bioconductor's limma package was employed for preprocessing and normalization. Thus,Â background was corrected using the normexp method andÂ data were normalized using the loess and quantiles methodÂ for within-array and inter-array normalization, respectively.

source_name: NRASQ61R  (day4)

label_protocol: 500 ng of total RNA were primed with the T7 promoter primer at 65Â°C for 10 min, then reversed transcribed at 40Â°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ÂºC (all reagents were obtained from Agilent Technologies, Inc.).

growth_protocol: melanocytes were cultured in melanocyte specific medium

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's instructions

value: melanocyte

tag: time

value: day 4

value: skin

source_name: Universal Human Reference RNA

value: Universal Human Reference RNA


title: NRASA18T  (day4)

description: Biological replicate 1 of 2. NRASA18T infected melanocytes, harvested after 4 days.

source_name: NRASA18T  (day4)

tag: treatment


title: T_222844


title: 5K jurkat control  5557641015_K

city: Groningen

first: vincent

last: bloks

country: Netherlands

institute: UMCG

data_processing: Quantile Normalized and corrected for intra-experimental variation (Combat) generating robust gene-expression profiles (pubmed: 20181233).

label: Biotin

source_name: 5K jurkat control

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit ( Applied Biosystems)

growth_protocol: Dld-1 cells ( human intestinal epithelial) and Jurkat ( human T-lymfocytes) were cultured in T75 flask

extract_protocol: Total RNA was extracted with TriReagent (Sigma, St. Louis, MO, USA). The quality and concentration of the RNA were determined using the Experion automated electrophoresis system (Bio-Rad Laboratories, Inc), The RQI values returned ranged between 9.3-9.6

treatment_protocol: in the precence =smoke or absence=control of cigarette smoke extract ( CSE 20%) for 2 to 6 hours

value: jurkat

value: control

tag: dose

value: 0% CSE


title: Overfed_ovary_pool3


title: T_217870

value: high-grade astrocytoma allografts

value: reference


title: 5L dld control  5557641015_L

source_name: 5L dld control


title: BRAFV600E (day4)

description: Biological replicate 1 of 2. BRAFV600E infected melanocytes, harvested after 4 days.

source_name: BRAFV600E (day4)

tag: cell type


title: NRASG12V  (day4)

description: Biological replicate 1 of 2. NRASG12V infected melanocytes, harvested after 4 days.

source_name: NRASG12V  (day4)


title: HRASG12V  (day4)

description: Biological replicate 1 of 2. HRASG12V infected melanocytes, harvested after 4 days.

source_name: HRASG12V  (day4)


title: Lean_ovary_pool2


title: BRAFV600E (day2)

description: Biological replicate 1 of 2. BRAFV600E infected melanocytes, harvested after 2 days.

source_name: BRAFV600E (day2)

value: day 2


title: Empty vector day4

description: Biological replicate 1 of 2. empty vector infected melanocytes, harvested after 4 days.

source_name: Empty vector day4

value: Empty vector


title: HRASG12V  (day2)

description: Biological replicate 1 of 2. HRASG12V infected melanocytes, harvested after 2 days.

source_name: HRASG12V  (day2)


title: NRASWT    (day4)

description: Biological replicate 1 of 2. NRASWT infected melanocytes, harvested after 4 days.

source_name: NRASWT    (day4)

value: NRASWT


title: 5I jurkat smoke  5557641015_I

source_name: 5I jurkat smoke

value: smoke

value: 20% CSE


title: 5J dld smoke  5557641015_J

source_name: 5J dld smoke


title: 5H jurkat control  5557641015_H

source_name: 5H jurkat control


title: NRASA18T  (day2)

description: Biological replicate 1 of 2. NRASA18T infected melanocytes, harvested after 2 days.

source_name: NRASA18T  (day2)


title: Non infected day4

description: Biological replicate 1 of 2. Control melanocytes, untreated, harvested after several passages.

source_name: Non infected day4

value: Non infected


title: 5G dld control  5557641015_G

source_name: 5G dld control


title: nAg treatment nAg vs cont

city: Beijing

first: Zhe

last: Wang

address: 18 Shuangqing Road

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

description: compare gene expression profiles of control cells

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio). For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5).

data_processing:
A space- and intensity-dependent normalization based on a LOWESS program was employed. Significance Analysis of Microarrays (SAM, version 3.02) were employed to determine the differentially expressed genes.
Changes of gene expression at either 2-fold greater or less than 0.5-fold were defined as significant differently expressed genes.

source_name: E14.5 fetal liver cell-nAg

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. The amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Male and female BALB/c mice (6 wks old) were housed under sterile conditions.

extract_protocol: Fetal liver cells were removed from embryos, and total RNA was extracted with Trizol Reagent according to the manufacturer's instructions (Invitrogen) and isopropanol precipitation.

treatment_protocol: Mice were injected intraperitoneally with nAg at 22 μg/kg (in 200 μl) or PBS 3 times a wk for 30 d. Male and female mice were mated immediately after the final injection. Pregnant mice were anaesthetized and embryos were dissected from uteri and weighed on day 14.5 of pregnancy (E14.5).

value: fetal liver cell

tag: age

tag: strain

value: BALB/c

value: nAg

source_name: E14.5 fetal liver cell-Cont


title: 5C jurkat smoke  5557641015_C

source_name: 5C jurkat smoke

tag: cell line


title: 5E jurkat control  5557641015_E

source_name: 5E jurkat control


title: NRASQ61R  (day2)

description: Biological replicate 1 of 2. NRASQ61R infected melanocytes, harvested after 2 days.

source_name: NRASQ61R  (day2)

value: melanocyte

source_name: Universal Human Reference RNA


title: 5F jurkat control  5557641015_F

source_name: 5F jurkat control


title: MR1-1 ESCs rat alleles

first: Xiaolong

last: Cui

address: No.1 Beichen West Road

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Genomic DNA from same number of cells were used for both channels.

hyb_protocol: Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit (Cat#5188‐5380, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 65℃, 20rpm for 24 hours. Array wash was performed using Agilent Oligo aCGH Wash Buffer 1 and 2 set (Cat#5188‐5226, Agilent technologies, Santa Clara, CA, US) in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) follow the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US),scan resolution= 3μm, PMT 100% to generate tiff image.

data_processing: Raw data was acquired and normalized(algorithm: LOWESS) using Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).Calculate Z‐score for each CNV region using DNA Analytics 4.0.81 software (Agilent technologies, Santa Clara, CA, US), window size is set to 1M and Z‐score threshold is set to 4.0.

source_name: allodiploid embryonic stem cells

label_protocol: Experimental sample and control sample were labeled with Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US) and Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) respectively, using Agilent Genomic DNA Labeling Kit PLUS (Cat#5188‐5309, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions. Labeled DNA fragments were purified using Amicon Ultra‐0.5, Ultracel‐30 Membrane,30 kDa(Cat#UFC5030BK, Millipore, Billerica, MA, US). Measured the absorbance at A260nm (DNA),A550nm (Cyanine 3),and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.

growth_protocol: N2B27 + 2i + LIF

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), Use Nano Drop (Cat#ND‐1000, ThermoFisher, Waltham, MA, US) and 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

treatment_protocol: FACS sorting G0/G1 stage cells

source_name: embryonic stem cells

value: normal rat ESCs


title: RM1-1 ESCs rat alleles


title: NRASG12V  (day2)

description: Biological replicate 1 of 2. NRASG12V infected melanocytes, harvested after 2 days.

source_name: NRASG12V  (day2)

value: skin

value: Universal Human Reference RNA


title: 5D dld control  5557641015_D

source_name: 5D dld control

value: control


title: 5B dld control  5557641015_B

source_name: 5B dld control

value: 0% CSE


title: homo3

city: Fukuoka

first: Hirosuke

last: Inoue

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Pediatrics

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression in Nod1 -/- fetal artery 6hr after administration of FK565 to Nod1 -/- pregnant mouse

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Nod1 -/- mice, aortic artery, E18.5, FK565

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Mice were housed in a specific pathogen-free environment.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Pregnant mice were subcutaneously injected with 500 μg FK565 at E18.5. Six hours later, aortic arteries of the fetuses were separated.

tag: protocol

tag: genotype/variation (fetus)

value: fetal aortic artery


title: NRASWT    (day2)

description: Biological replicate 1 of 2. NRASWT infected melanocytes, harvested after 2 days.

source_name: NRASWT    (day2)


title: 5A dld control  5557641015_A

source_name: 5A dld control


title: 4K jurkat control  5557641014_K

source_name: 4K jurkat control

value: jurkat


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with our novel permutation approach TileShuffle.

source_name: Colorectal carcinoma cells with defunct TP53

value: colorectal carcinoma cells

value: with defunct TP53


title: Non infected day2

source_name: Non infected day2

value: day 2


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.

source_name: Colorectal carcinoma cells with overexpressed TP53

value: induced expression of TP53


title: homo2

value: administration of FK565 to Nod1 -/- pregnant mouse


title: homo1


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with our permutation approach (TileShuffle).

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: tumor

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: hetero1

description: Gene expression in Nod1 +/- fetal artery 6hr after administration of FK565 to Nod1 -/- pregnant mouse

source_name: Nod1 +/- mice, aortic artery, E18.5, FK565


title: 4L dld smoke  5557641014_L

source_name: 4L dld smoke

value: smoke

value: 20% CSE


title: 4J dld control  5557641014_J

source_name: 4J dld control


title: 4I dld control  5557641014_I

source_name: 4I dld control


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with TAS.


title: Empty vector day2

description: Biological replicate 1 of 2. empty vector infected melanocytes, harvested after 2 days.

source_name: Empty vector day2

value: melanocyte

value: Empty vector

source_name: Universal Human Reference RNA

tag: sample type


title: 4H jurkat control  5557641014_H

source_name: 4H jurkat control


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with our permutation approach (TileShuffle).

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: 4G dld control  5557641014_G

source_name: 4G dld control


title: hetero3

tag: tissue


title: colorectal carcinoma cells with defunct TP53 using TAS ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with TAS.


title: 4D jurkat smoke  5557641014_D

source_name: 4D jurkat smoke


title: 4E dld smoke  5557641014_E

source_name: 4E dld smoke


title: INA6 cells using TAS (IL-6 restimulation) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with Tiling Array Software (TAS).


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with MAT.


title: hetero2


title: INA6 cells using TAS (IL-6 withdrawal) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with Tiling Array Software (TAS).


title: colorectal carcinoma cells with defunct TP53 using MAT ChipA

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.

value: defunct TP53


title: 4C jurkat control  5557641014_C

source_name: 4C jurkat control


title: INA6 cells using MAT (IL-6 restimulation) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.


title: 4F dld smoke  5557641014_F

source_name: 4F dld smoke


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipC


title: Pro-T.1 mono

city: Boston

first: Guray

last: Kuzu

address: 185 Cambridge Street

institute: Massachusetts General Hospital

hyb_protocol: 34 µg of test sample and 34 µg of reference sample were combined and resuspended in 12.3 µl of water. Hybridization buffer was added and hybridization permormed frollowing the CGX NimbleGen protocol.

scan_protocol: Arrays were scanned on an GenePix 4000B Microarray Scanner following manufacturer's protocol instructions.

data_processing: Arrays were processed using Nimblegen's standard protocol for data extraction.

source_name: mononucleosomal DNA from p53-/- Rag1-/- pro-T cells

label_protocol: 0.5 µg of either mononucleosomal DNA or bare genomic DNA were labeled using the NimbleGen Dual-Color DNA labeling Kit (REF 06370250001) and following manufacturer's protocol for CGX arrays.

growth_protocol: p53-/- Rag1-/- pro-T cell line was grown in RPMI + 10% FBS + P/S + B-Me

extract_protocol: Cells were grown exponentially until they reached confluence. Cells were crosslinked with formaldheyde for 10' at RT and reaction was stopped with 0.125 M of glycine for 5’ at RT. Cells were then washed twice with cold PBS and nuclei were excracted using a sucrose buffer [0.3 M sucrose, 2 mM MgOAc2, 1% Triton X-100, 10 mM HEPES (pH 7.8)]. MNase digestion was performed at 37°C for 5' in MNase digestion buffer [25mM KCl, 4 mM MgCl2, 1 mM CaCl2, 12.5% glycerol and 50 mM TrisHCl (pH 7.4)] and reaction was terminated using an equal amount of MNase stop buffer [2% SDS, 0.2 M NaCl, 20 mM EGTA, 20 mM EDTA and 50 mM TrisHCl (pH 8)]. Samples were RNased for 1hr at 37ºC and decrosslinked O/N at 65ºC together with proteinase K. Digests were extracted with phenol:chloroform, and DNA recovered by isopropanol precipitation. DNA was loaded on a prestained 2% TAE agarose gel and mononucleosomal DNA exctracted.

tag: genotype/variation

value: pro-T cell line

tag: fraction

value: mononucleosomal DNA

source_name: MNased digested bare genomic DNA from p53-/- Rag1-/- pro-T cells

value: MNased digested bare genomic DNA


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipC

source_name: Colorectal carcinoma cells with defunct TP53


title: 4A jurkat control  5557641014_A

source_name: 4A jurkat control

value: control

value: 0% CSE


title: INA6 cells using MAT (IL-6 withdrawal) ChipA

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with MAT.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours


title: 3I jurkat smoke  5557641013_I

source_name: 3I jurkat smoke

value: jurkat


title: MEFs.2 mono

source_name: mononucleosomal DNA from Rag2-/- MEFs

growth_protocol: RAG2-/- MEFs were grown in DMEM + 10%FBS + P/S

value: embryonic fibroblasts

source_name: MNased digested bare genomic DNA from Rag2-/- MEFs


title: Pro-T.2 mono


title: 3J jurkat smoke  5557641013_J

source_name: 3J jurkat smoke


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipC

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipC


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipC

source_name: Colorectal carcinoma cells with overexpressed TP53

value: colorectal carcinoma cells

value: induced expression of TP53


title: Pro-B.2 mono

source_name: mononucleosomal DNA from Rag2-/-  pro-B Abelson-transformed cell line

growth_protocol: Rag2-/- pro-B Abelson-transformed cell line was grown in RPMI + 10% FBS + P/S + B-Me

value: pro-B Abelson-transformed cell line

source_name: MNased digested bare genomic DNA from Rag2-/-  pro-B Abelson-transformed cell line


title: 3K jurkat control  5557641013_K

source_name: 3K jurkat control


title: colorectal carcinoma cells with defunct TP53 using TAS ChipC

value: with defunct TP53


title: 3L jurkat control  5557641013_L

source_name: 3L jurkat control


title: INA6 cells using TAS (IL-6 withdrawal) ChipC

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: INA6 cells using TAS (IL-6 restimulation) ChipC

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: Pro-B.1 mono


title: 3H dld control  5557641013_H

source_name: 3H dld control


title: MEFs.1 mono


title: T47D_CD28pos_rep3

city: Aurora

first: Aaron

last: Knox

state: Colorado

department: School of Medicine, Division of Endocrinology

institute: UCDenver

description: For CD28 staining, medium was aspirated and cells were dissociated by 5 min incubation at 37C with TrypLE (Life technologies), inactivated with 5% culture medium, pelleted and blocked with PBS containing 10% normal human serum + 0.5% BSA. Cells were washed, counted and incubated at RT with 1.5 g/million FITC-conjugated anti-human CD28 antibody (Invitrogen).

hyb_protocol: Hybridization was performed at MOgene LC (www.mogene.com).

scan_protocol: Initial analyses were performed at MOgene LC (www.mogene.com).

data_processing: The data were filtered and any probes with a detection P value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization using Partek® Genomics Suite™ 6.6.

source_name: T47D, CD28 positive cells

label_protocol: Labeling was performed at MOgene LC (www.mogene.com).

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies) containing 5% Charcoal stripped fetal bovine serum (FBS, Japan Serum) in the presence of 1nM β-Estradiol + 10nM Progesterone for 5 days. .

extract_protocol: RNA was extracted (PicoPure; Arcturus) following the manufacturer's recommendations. RNA was quantified using a Nanodrop ND1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: parental cell line


title: 3G dld smoke  5557641013_G

source_name: 3G dld smoke

value: smoke

value: 20% CSE


title: T47D_CD28pos_rep1


title: 3E dld smoke  5557641013_E

source_name: 3E dld smoke


title: colorectal carcinoma cells with defunct TP53 using MAT ChipC

source_name: Colorectal carcinoma cells with defunct TP53

value: defunct TP53


title: 3D dld control  5557641013_D

source_name: 3D dld control


title: INA6 cells using MAT (IL-6 withdrawal) ChipC

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours


title: INA6 cells using MAT (IL-6 restimulation) ChipC


title: T47D_CD28neg_rep1

source_name: T47D, CD28 negative cells


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipB


title: 3C jurkat control  5557641013_C

source_name: 3C jurkat control


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipC


title: 3B dld control  5557641013_B

source_name: 3B dld control


title: T47D_CD28neg_rep3


title: T47D_CK5pos_rep3

description: For CK5-staining, single cell suspensions were permeabilized and fixed with RNAlater (Ambion Inc.), and incubated with 2 µg anti-CK5 mAb (Novocastra Cat# NCL-L-CK5) labeled with Zenon Alexa Fluor 488 (Invitrogen; Z-25002). Stained cells were centrifuged and resuspended in RNAse-free NST buffer containing DAPI and FACS sorted (Beckman Coulter XDP-100 MoFlo) based on CK5+ vs. CK5– expression.

source_name: T47D, CK5 positive cells


title: T47D_CD28neg_rep2


title: T47D_CK5pos_rep2


title: 3A jurkat control  5557641013_A

source_name: 3A jurkat control


title: OSFWD2

city: Kharagpur

first: Jyotirmoy

last: Chatterjee

state: West Bengal

address: Near Vikramshila complex

department: School of Medical Science and Technology

country: India

institute: Indian Institute of Technology Kharagpur

description:
6303248059_I
Biological replicate 2

hyb_protocol: One microgram of the biotinylated sample was then hybridized at 58 °C overnight with an Illumina (San Diego, CA, USA) HumanHT-12 V3.0 expression beadchip.

data_processing: Intensity values from  mRNA microarray data were quality checked, log2-transformed and normalized using the Robust Spline Normalization method in GenomeStudio™ Software v2011.1 (Illumina).

source_name: Oral buccal mucosa

label_protocol: RNA was then converted into biotinlated cRNA using the Illumina RNA TotalPrep amplification kit (Ambion/Life Technologies). For preparation of biotinlated cRNA, first 0.5ug of RNA was reverse transcribed to single stranded cDNA using Oligo(dT) primer and  later converted into dsDNA. Purified ds cDNA was transcribed into multiple copies of biotinylated cRNA using biotin labelled NTPs.

extract_protocol: Total RNA from tissues was isolated using TRIzol (Invitrogen/Life Technologies) reagent. The extracted RNA was further purified using a Qiagen RNeasy Qiagen, Hilden, Germany) Mini kit in accordance with the manufacturer's protocols. The integrity and purity of RNA was checked by Quib it (invitrogen ) and Bio-analyzer (Agilent, Santa Clara, CA, USA). RNA sample with RIN number above 7

tag: disease state

value: Oral submucous fibrosis with dysplasia

value: Oral buccal mucosa


title: OSCC2

description:
6303248059_J
Biological replicate 2

value: OSF associated squamous cell carcinoma


title: NOM2

description:
6303248059_G
Biological replicate 2

value: Normal Oral mucosa


title: T47D_CK5neg_rep2

source_name: T47D, CK5 negative cells


title: OSFWT2

description:
6303248059_H
Biological replicate 2

value: Oral submucous fibrosis without dysplasia


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipB


title: OSCC


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipB


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipB

source_name: Colorectal carcinoma cells with overexpressed TP53


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipB


title: colorectal carcinoma cells with defunct TP53 using TAS ChipB


title: UM-UC3_HDAC1_HDAC2_siRNA_rep3

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: gene expression data from HDAC1 and HDAC2 siRNA (each 10 nM) transfected UM-UC-3 cells

hyb_protocol: After fragmentation labelled aRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples

source_name: Urothelial carcinoma UM-UC-3 cells transfected with 10 nM HDAC1 and 10 nM HDAC2 siRNA for 72 h

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturers´ protocol (3´ IVT Express Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labelling of aRNA

growth_protocol: Cells were grown in DMEM supplemented with 10 % FCS.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer´s instruction.

treatment_protocol: Cells were transfected with 10 nM irrelevant (Silencer® Select Negative Control #2; #4390846) or HDAC1/HDAC2 siRNA (each 10 nM; Silencer® Select validated siRNA; #4390824, HDAc1: s73, HDAC2:s6493) for 72 h using Lipofectamine RNAi MAX (Life Technologies, Darmstadt, Germany).

tag: tumor type

value: urothelial cancer


title: UM-UC3_HDAC1_HDAC2_siRNA_rep2


title: T47D_CK5neg_rep3


title: OSFWD


title: UM-UC3_HDAC1_HDAC2_siRNA_rep1


title: INA6 cells using TAS (IL-6 withdrawal) ChipB


title: UM-UC3_irrelevant_siRNA_rep2

description: gene expression data from irrelevant siRNA (10 nM) transfected UM-UC-3 cells

source_name: Urothelial carcinoma UM-UC-3 cells transfected with 10 nM irrelevant siRNA for 72 h


title: OSFWT


title: Sclera, EY1424B, P1

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Gene expression data from Infant eye, Sclera, P1

hyb_protocol: Biotinylated cRNA was hybridized with a probe array for 16h at 45C, and the hybridized biotinylated cRNA was stained with streptavidin-PE.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Palo Alto).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) with GeneSpring version 13.0 (Agilent Technologies).

source_name: Sclera, P1

label_protocol: Biotin-labelled.

growth_protocol: The scleral pieces were minced and then cultured in a growth medium (GM): Dulbecco’s modified Eagle’s medium (DMEM)/Nutrient mixture F12 (1:1) with high glucose supplemented with 10% fetal bovine serum, insulin-transferrin-selenium, and MEM-NEAA (Gibco). The scleral cells began growing out almost 1 week after the start of cultivation.

extract_protocol: Total RNA was extracted from a total of 5 × 106 cultured human scleral cells using the RNeasy Plus Mini-Kit® (Qiagen).

value: Infant eye, 1Y9M, Sclera, P1

value: sclera

value: 1 M


title: INA6 cells using TAS (IL-6 restimulation) ChipB

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: Sclera, EY1424F, P1


title: Sclera, EY1422B, P1

value: Infant eye, 4M, Sclera, P1

value: 4 M


title: NOM


title: Sclera, EY1422F, P1


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipB

value: colorectal carcinoma cells

value: induced expression of TP53


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with our novel permutation approach TileShuffle.

value: with defunct TP53


title: colorectal carcinoma cells with defunct TP53 using MAT ChipB


title: INA6 cells using MAT (IL-6 withdrawal) ChipB

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.


title: UM-UC3_irrelevant_siRNA_rep1


title: T47D_CK5pos_rep1


title: T47D_CK5neg_rep1


title: VM-CUB1_HDAC1_HDAC2_siRNA_rep3

description: gene expression data from HDAC1 and HDAC2 siRNA (each 10 nM) transfected VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells transfected with 10 nM HDAC1 and 10 nM HDAC2 siRNA for 72 h


title: 4B dld control  5557641014_B

source_name: 4B dld control

value: control

value: 0% CSE


title: VM-CUB1_HDAC1_HDAC2_siRNA_rep1


title: Sclera, EY1406B, P1

value: Infant eye, 10M, Sclera, P1


title: VM-CUB1_HDAC1_HDAC2_siRNA_rep2


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with our permutation approach (TileShuffle).


title: INA6 cells using MAT (IL-6 restimulation) ChipB

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: Sclera, EY1406F, P1


title: 3F jurkat smoke  5557641013_F

source_name: 3F jurkat smoke

value: jurkat

value: smoke

value: 20% CSE


title: VM-CUB1_irrelevant_siRNA_rep2

description: gene expression data from irrelevant siRNA (10 nM) transfected VM-CUB1 cells

source_name: Urothelial carcinoma VM-CUB1 cells transfected with 10 nM irrelevant siRNA for 72 h

value: urothelial cancer


title: VM-CUB1_irrelevant_siRNA_rep1


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with our permutation approach (TileShuffle).


title: Sclera, EY1406M, P1

value: sclera


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with TAS.


title: colorectal carcinoma cells with defunct TP53 using TAS ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with TAS.

source_name: Colorectal carcinoma cells with defunct TP53


title: INA6 cells using TAS (IL-6 withdrawal) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with Tiling Array Software (TAS).

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours


title: INA6 cells using TAS (IL-6 restimulation) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with Tiling Array Software (TAS).


title: colorectal carcinoma cells with overexpressed TP53 using MAT ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with MAT.


title: colorectal carcinoma cells with defunct TP53 using MAT ChipD

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.

value: defunct TP53


title: T47D_CD28pos_rep2

description: For CD28 staining, medium was aspirated and cells were dissociated by 5 min incubation at 37C with TrypLE (Life technologies), inactivated with 5% culture medium, pelleted and blocked with PBS containing 10% normal human serum + 0.5% BSA. Cells were washed, counted and incubated at RT with 1.5 g/million FITC-conjugated anti-human CD28 antibody (Invitrogen).

source_name: T47D, CD28 positive cells


title: INA6 cells using MAT (IL-6 restimulation) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.


title: INA6 cells using MAT (IL-6 withdrawal) ChipD

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with MAT.


title: UM-UC-3_DMSO_24h_rep3

description: gene expression data from DMSO treated UM-UC-3 cells

hyb_protocol: After fragmentation labeled aRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability . Input data pre-processing was concluded by baseline transformation to the median of all samples

source_name: Urothelial carcinoma UM-UC-3 cells treated with 0.1% DMSO for 24 h

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturer´s protocol (3´ IVT Plus Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labeling of aRNA

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instruction.

treatment_protocol: Cells were treated with 0.1 % DMSO, 3 nM Romidepsin, 0.5 µM Givinostat, or 2.5 M SAHA for 24 h.


title: UM-UC-3_SAHA_24h_rep1

description: gene expression data from SAHA treated UM-UC-3 cells

source_name: Urothelial carcinoma UM-UC-3 cells treated with 2.5 µM SAHA for 24 h


title: UM-UC-3_Givinostat_24h_rep3

description: gene expression data from Givinostat treated UM-UC-3 cells

source_name: Urothelial carcinoma UM-UC-3 cells treated with 0.5 µM Givinostat for 24 h


title: UM-UC-3_DMSO_24h_rep2


title: UM-UC-3_SAHA_24h_rep3


title: UM-UC-3_DMSO_24h_rep1


title: MR1-1 ESCs mouse alleles

description: Genomic DNA from same number of cells were used for both channels.

source_name: allodiploid embryonic stem cells

source_name: embryonic stem cells

value: normal mouse ESCs


title: UM-UC-3_Givinostat_24h_rep2


title: UM-UC-3_Givinostat_24h_rep1


title: colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipM

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Colorectal carcinoma cells with overexpressed TP53


title: INA6 cells using TileShuffle (IL-6 withdrawal) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Expression data was processed with our permutation approach (TileShuffle).


title: colorectal carcinoma cells with defunct TP53 using TileShuffle ChipM

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with our novel permutation approach TileShuffle.


title: INA6 cells using TileShuffle (IL-6 restimulation) ChipM

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with our permutation approach (TileShuffle).


title: RM1-1 ESCs mouse alleles


title: UM-UC-3_SAHA_24h_rep2


title: colorectal carcinoma cells with overexpressed TP53 using TAS ChipM

description: Whole transcriptome expression analysis of colorectal carcinoma cells with overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with TAS.