title: GIST_25_KIT (copy number)

description: Copy number data from GIST with KIT mutation

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CHP files weregenerated from CEL files by Genotyping Console (Affymetrix) using the Birdseed algorithm. The sample tables contain the normalized expression values and Genotype Call produced by that algorithm.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash frozen tissue specimens from gastrointestinal stromal tumors using the Qiagen QiaAmp Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.


title: GIST_27_KIT (copy number)

status: Public on Aug 27 2010

type: genomic

city: Bologna

first: Maria

middle: Abbondanza

last: Pantaleo

state: BO

address: via Massarenti 9

department: Institute of Hematology and Medical Oncology "L.A.Seragnoli"

country: Italy

institute: Policlinico S. Orsola-Malpighi, University of Bologna

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: GIST tumor, KIT mutated

tag: tissue

value: gastrointestinal stromal tumor

tag: gender

value: M

tag: age


title: GIST_23_KIT (expression)

type: RNA

description: Gene expression data from GIST with KIT mutation

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Bioconductor affy package, using RMA algorithm for normalization and summarization.

label: biotin

molecule: total RNA

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

extract_protocol: Extraction of total RNA was performed with RNeasy spin columns on flash frozen tumor specimens, according to the manufacturer's instructions.

value: F


title: GIST_17_PDGFRA (copy number)

description: Copy number data from GIST with PDGFRA mutation

source_name: GIST tumor, PDGFRA mutated


title: GIST_23_KIT (copy number)


title: α5β1 integrin-mediated cell migration_110407

city: Porto

first: Rune

last: Matthiesen

address: Rua Dr. Roberto Frias s/n

country: Portugal

institute: IPATIMUP

description:
Treatment 2
07SE466MOE430A2.0_110407.CEL

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with the R package AFFYLMGUI default analysis settings.

organism: Mus musculus

source_name: MLP29 cells

label_protocol: Expression profiling was performed using the Affimetrix GeneChip ® technology, following the protocols recommended by the manufacturers.

growth_protocol: Mouse hepatic progenitor MLP29 and mouse HCC Hep16 cells were maintained in RPMI 1640 medium supplemented with 10% Fetal Bovine Serum (FBS) at 37ºC in a humidified 5% CO2 atmosphere. For experiments, after cell plating, the old medium was replaced with fresh medium containing low FBS (0.1%) and the cells were maintained under this serum starvation condition for at least 16 hours.

extract_protocol: RNA was isolated from cell plates subjected to the different treatments using the RNAeasy Mini kit (Qiagen) and treated with RNAase-free DNAase (Qiagen).

treatment_protocol: cells were treated with 10 μg/ml of a specific function-blocking anti-α5β1 integrin antibody (clone BMB5) purchased from Chemicon-Millipore (Temecula, CA, USA) or 20 ng/ml of HGF/SF1.

tag: cell line

value: hepatic progenitor MLP29 cell line

tag: agent


title: Family 4, father of 4.1 (92227)

city: Bergen

first: Torunn

last: Fiskerstrand

address: Jonas Lies vei

department: Center for medical genetics and molecular medicine

country: Norway

institute: Haukeland University Hospital

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
CHP files (generated by Affymetrix GTYPE using the BRLMM algorithm) were processed by the programs Progeny lab and  PLINK to identify possible areas of homozygosity in the affected in each family.
Primary data description: Genotype Call (SNP call): 11, 22, 33, 44, 12, 13 ,14 , 23, 24 and 00 (NoCall). The processed data are for each family (1-5 plus 7), and the genotype calls are sorted according to chromosome and position from pter. cM between markers and position in bp from pter are also given.
Sorted genotype calls data: see Series GSE23151 supplementary files.

source_name: Lymphocytes

label_protocol: Standard Affymetrix procedures

extract_protocol: Genomic DNA was extracted from lymphocytes obtained from peripheral blood using the M48 DNA purification system (Qiagen, Germany).

tag: sample name

tag: family

tag: individual

value: father of 4.1

value: peripheral blood

tag: cell type

value: lymphocyte


title: GIST_22_PDGFRA (expression)

description: Gene expression data from GIST with PDGFRA mutation


title: HGF/SF1 treated_110407

description:
Treatment 1
07SE423MOE430A2.0_110407.CEL


title: GIST_24_WT (copy number)

description: Copy number data from GIST wild type both for KIT and PDGFRA

source_name: GIST tumor, KIT and PDGFRA wild type


title: GIST_16_KIT (copy number)


title: GIST_22_PDGFRA (copy number)


title: Family 5, affected individual 5.1 (92321)

value: affected individual 5.1


title: GIST_15_PDGFRA (copy number)


title: GIST_21_WT (expression)

description: Gene expression data from GIST wild type both for KIT and PDGFRA


title: GIST_20_KIT (copy number)


title: GIST_18_KIT (copy number)


title: Control_110407

description:
Control
07SE422MOE430A2.0_110407.CEL

label: C

value: Control


title: HGF/SF1 treated_020807

description:
Treatment 1
07SE1068MOE430A2.0_020807.CEL


title: GIST_13_KIT (copy number)


title: α5β1 integrin-mediated cell migration_141106

description:
Treatment 2
06SE1361MOE430A2.0_141106.CEL

value: anti-α5β1 integrin antibody (clone BMB5)


title: GIST_28_KIT (copy number)


title: GIST_20_KIT (expression)


title: α5β1 integrin-mediated cell migration_020807

description:
Treatment 2
07SE1069MOE430A2.0_020807.CEL


title: GIST_21_WT (copy number)


title: GIST_18_KIT (expression)


title: HGF/SF1 treated_141106

description:
Treatment 1
06SE1360MOE430A2.0_141106.CEL


title: GIST_19_PDGFRA (copy number)


title: GIST_12_PDGFRA (copy number)


title: Control_020807

description:
Control
07SE1067MOE430A2.0_020807.CEL


title: Control_141106

description:
Control
06SE1359MOE430A2.0_141106.CEL


title: Family 4, mother of 4.1 (91923)

value: mother of 4.1


title: Toxoplasma gondii - CTK11/Cell Cycle - 11 hour release - 2

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

country: USA

institute: Washington University School of Medicine

description: Toxoplasma gondii CTK11 strain

hyb_protocol: Standard Affymetrix protocol with 5ug labeled cRNA.

data_processing: GeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per Chip and Per Gene: Median Polishing

organism: Toxoplasma gondii

source_name: Toxoplasma gondii CTK11 strain

label_protocol: Affymetrix One Cycle: 3ug starting RNA - Standard One Cycle protocol

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 11 hr

extract_protocol: Parasites were purified from host cells and RNA was extracted using the Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

tag: strain

value: CTK11 - RH with thymidine kinase

tag: developmental stage

value: tachyzoite


title: Toxoplasma gondii - CTK11/Cell Cycle - 12 hour release - 1

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 12 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - 12 hour release - 2

description: Toxoplasma gondii CTK11 strain


title: GIST_15_PDGFRA (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 11 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - 10 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 10 hr


title: GIST_11_KIT (copy number)


title: GIST_16_KIT (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 10 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - 9 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 9 hr


title: GIST_14_KIT (expression)


title: GIST_05_PDGFRA (copy number)


title: GIST_26_PDGFRA (copy number)


title: GIST_09_KIT (copy number)


title: GIST_13_KIT (expression)


title: Family 3, father of 3.1 (92146)

value: father of 3.1


title: Toxoplasma gondii - CTK11/Cell Cycle - 8 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 8 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - 8 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - 9 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: GIST_12_PDGFRA (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 7 hour release - 2

description: Toxoplasma gondii CTK11 strain

data_processing: GeneGeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per Chip and Per Gene: Median Polishing

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 7 hr


title: GIST_07_WT (copy number)


title: GIST_11_KIT (expression)


title: Family 4, affected individual 4.1 (70532)

value: affected individual 4.1


title: GIST_10_WT (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 6 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 6 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - 7 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: GIST_14_KIT (copy number)


title: GIST_04_KIT (copy number)


title: GIST_09_KIT (expression)


title: Family 2, healthy sister of 2.1 and 2.2 (90084)

value: healthy sister of 2.1 and 2.2


title: Family 2, healthy brother of 2.1 and 2.2 (83592)

value: healthy brother of 2.1 and 2.2


title: Family 3, affected individual 3.1 (51589)

value: affected individual 3.1


title: Family 3, mother of 3.1 (92047)

value: mother of 3.1


title: GIST_10_WT (copy number)

value: gastrointestinal stromal tumor

value: M


title: Toxoplasma gondii - CTK11/Cell Cycle - 5 hour release - 1

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 5 hr


title: GIST_08_KIT (copy number)


title: Family 2, affected individual 2.2 (83591)

value: affected individual 2.2

value: F


title: Family 2, healthy brother of 2.1 and 2.2 (83843)

value: peripheral blood

value: lymphocyte


title: GIST_02_KIT (copy number)


title: Toxoplasma gondii - CTK11/Cell Cycle - 4 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 4 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - 6 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - 4 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: GIST_08_KIT (expression)


title: GIST_07_WT (expression)


title: GIST_04_KIT (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 1 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 1 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - 5 hour release - 2

description: Toxoplasma gondii CTK11 strain


title: Family 1, healthy sister of 1.3 (30832)

value: healthy sister of 1.3


title: Toxoplasma gondii - CTK11/Cell Cycle - 2 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 2 hr


title: Toxoplasma gondii - CTK11/Cell Cycle - blocked - 1

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours


title: Toxoplasma gondii - CTK11/Cell Cycle - 3 hour release - 2

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts - blocked with 10 uM thymidine for 4 hours then released for 3 hr


title: GIST_05_PDGFRA (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - 2 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - blocked - 2

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - 1 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: GIST_02_KIT (expression)


title: Toxoplasma gondii - CTK11/Cell Cycle - asynchronous - 1

description: Toxoplasma gondii CTK11 strain

growth_protocol: growth condition: grown in human foreskin fibroblasts


title: Toxoplasma gondii - CTK11/Cell Cycle - 3 hour release - 1

description: Toxoplasma gondii CTK11 strain


title: Toxoplasma gondii - CTK11/Cell Cycle - asynchronous - 2

description: Toxoplasma gondii CTK11 strain


title: Mouse Spleen (dT)

status: Public on Aug 26 2010

city: Tsukuba

first: Yutaka

last: Watanabe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center (BRC)

country: Japan

institute: RIKEN Tsukuba Institute

description: Custom oligo (60mer) microarray was manufactured by Agilent Technologies.

hyb_protocol: The protocols supplied by Agilent Technologies were used.

data_processing: Numerical processed signal values (gProcessedSignal) of Agilent Feature Extraction File were obtained as representative expression levels for each probe within array. If a spot show signal lower than five, or if there is no significant differences between foreground and background signals, intensity value was adjusted to five (those probes are treated as “absent probes”). To perform normalization of signal intensity distribution between multiple arrays, whole mean signal of every hybridization experiment was adjusted to that of the data from SL10 by oligo-dT priming. Probes show lower than five and flagged as “saturated” were discarded for the inter-array-normalization step.

source_name: spleen

label_protocol: Total RNA was labeled using Low RNA Input Linear Amplification Kit (Agilent Technologies) according to manufacturer’s instruction.

extract_protocol: Total RNA was extracted by using Trizol (Invitrogen) according to the manufacturer’s instructions.

tag: Strain

value: C57BL/6J Jc1

tag: Age

value: 8-10 weeks old

tag: Gender

value: male and female

tag: Tissue

value: spleen


title: Mouse Stomach (dT)

scan_protocol: The protocols supplied by Agilent Technologies were used.

source_name: stomach

value: stomach


title: Family 1, healthy sister of 1.3 (30924)


title: Mouse Testis (dT)

source_name: testis

value: male

value: testis


title: Mouse Thymus (dT)

source_name: thymus

value: thymus


title: Family 2, affected individual 2.1 (61188)

value: affected individual 2.1


title: Mouse Placenta 10.5 (dT)

source_name: planceta 10.5 of days postcoitum (dpc) embryos

value: 10.5 of days postcoitum (dpc)

value: placenta


title: Zhiping_KD30_1126_MoGene-1_0-st-v1

city: Palo Alto

first: Zhiping

last: Pang

state: CA

address: 1050 Arastradero Road

department: Molecular and Cellular Physiology

institute: Stanford University School of Medicine

hyb_protocol: Starndard hyb protocol for the Affymetrix mouse gene ST_1.0 chip by the Protein and Nucleic Acid Facility at Stanford University

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Partex Genomic suite for background correction and quantile normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
Single channel data was analyzed as ratios of experimental/control. Raw data (CEL files) for the two control samples (ch2) are provided as supplementary files on the Series record.

source_name: Mouse cortical neurons

label_protocol: Standard label protocol for the Affymetrix mouse gene ST_1.0 chip by the Protein and Nucleic Acid Facility at Stanford University.

growth_protocol: Mouse cortical culture was made as described elsewhere. Briefly, the primary cortical neurons were isolated from P0 pups of Syt1 deficient or wild-type (WT) mice, dissociated by papain digestion and plated on Matrigel coated circle glass coverslips. The neurons were cultured in vitro for 13-16 days in MEM (Gibco) supplemented with B27 (Gibco), glucose, transferrin, fetal bovine serum and Ara-C (Sigma).

extract_protocol: Cultured cortical neurons (14-15 DIV) were lysed and total RNA was extracted and purified with RNAqueous-Micro kit (Ambion INC, TX) following the manufacturer's instructions.

treatment_protocol: Cortical neuronal culture was infected on 5 DIV with CaM 1-3 shRNA mediated by lentiviruses; shRNAs with shRNA-resistant wildtype CaM; and control lentiviruses

value: SV129 x C57BL/6 mixed

value: P0 pup

value: cortical neruons

tag: treatment group

value: infected with lentiviruses expressing the CaM shRNAs

tag: replicate date

value: control


title: Zhiping_KD30_1130_MoGene-1_0-st-v1


title: Mouse Placenta 13.5 (dT)

source_name: placenta 13.5 of days postcoitum (dpc)

value: 13.5 of days postcoitum (dpc)


title: Zhiping_rCaM_1130_MoGene-1_0-st-v1

value: infected with lentiviruses expressing the CaM shRNAs with a wild-type CaM rescue protein


title: Mouse Lung (dT)

source_name: lung

value: C57BL/6J Jc1

value: 8-10 weeks old

value: lung


title: SATO3_1 expression

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data was analysed using the Lumi bioconductor package. Samples were normalised using a variance stabilising transformation and a robust spline normalisation.

source_name: SATO3 Cells

label_protocol: RNA was labelled using Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

growth_protocol: Normally growing cells

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma)


title: SATO3_3 expression


title: Mouse Liver (dT)

source_name: liver

value: male and female

value: liver


title: Zhiping_rCaM_1126_MoGene-1_0-st-v1


title: Mouse Thymus (Random)

label_protocol: Total RNA was labeled using CyScribe First-Strand cDNA Labeling Kit (Amersham) according to manufacturer’s instruction.


title: Mouse Stomach (Random)

value: stomach


title: Mouse Heart (dT)

source_name: heart

value: heart


title: Family 1, mother of 1.3 (30825)

value: mother of 1.3

tag: tissue

value: peripheral blood

value: lymphocyte

value: F


title: Family 1, affected individual 1.3 (30906)

value: affected individual 1.3

tag: gender

value: M


title: Mouse Spleen (Random)

value: spleen


title: Mouse Kidney

source_name: kidney

value: kindney


title: Mouse Testis (Random)

value: male

value: testis


title: Family 1, father of 1.1 and 1.2 (30935)

value: father of 1.1 and 1.2

tag: age


title: Family 1, healthy brother of 1.1 and 1.2 (30937)

value: healthy brother of 1.1 and 1.2


title: Family 1, father of 1.3 (30824)

value: father of 1.3


title: SATO3_2 expression

tag: cell line


title: Family 1, healthy sister of 1.3 (31098)

value: healthy sister of 1.3


title: Family 1, mother of 1.1 and 1.2 (30936)

value: mother of 1.1 and 1.2


title: Family 1, affected individual 1.2 (31264)

value: affected individual 1.2


title: Mouse Placenta 10.5 (Random)

source_name: placenta of 10.5 days postcoitum (dpc) embryos

value: C57BL/6J Jc1

value: 10.5 days postcoitum

value: male and female

value: placenta


title: Mouse Kidney (Random)

label_protocol: Total RNA was labeled using CyScribe First-Strand cDNA Labeling Kit (Amersham) according to manufacturer’s instruction (random priming method).

extract_protocol: Total RNA was prepared using Trizol reagent according to manufacturer’s instruction (Invitrogen).

value: 8-10 weeks old

value: kidney


title: Mouse Intestine (dT)

source_name: small intestine

value: small intestine


title: Mouse Heart (Random)

value: heart


title: Mouse Intestine (Random)


title: Family 1, affected individual 1.1 (30907)

source_name: Lymphocytes

value: affected individual 1.1

value: peripheral blood

value: lymphocyte

value: F


title: Mouse Lung (Random)

value: lung


title: Mouse Placenta 13.5

data_processing: The values were obtained by following formula, log2(immunoprecipitated sample (rProcessedSignal)/input sample (gProcessedSignal)).

source_name: placenta 13.5 days postcoitum (dpc), immunoprecipitated

label_protocol: The immunoprecipitated sample was labeled with Cy-5 dCTP and washed by using BioPrime Array CGH Genomic Labeling Module (Invitrogen).

extract_protocol:
DNA was extracted by conventional methods. Briefly, freshly isolated tissues were minced in lysis buffer (50 mM Tris-HCl, 20 mM EDTA, 0.1 M NaCl, 1% SDS) and incubated in proteinase K (final concentration, 100 μg/ml in lysis buffer) at 55°C overnight, followed by phenol-chloroform extraction and ethanol precipitation.
The Genomic DNA was sonicated (Bioruptor, Cosmo Bio) to produce short random fragments. Sonicated DNA samples were size-fractionated by agarose gel electrophoresis and excision (200 to 1000 bp). To avoid DNA damage by UV light, gels were stained by using SYBR Safe Gel Stain (Invitrogen) and excised on a blue-light transilluminator (Safe Imager, Invitrogen). Excised DNA fragments were purified by using MinElute Gel Extraction Kit (Qiagen).
To form antibody-bead complexes we incubated 10 μg mouse anti-5-methylcytidine monoclonal antibody (Eurogentec) with 150 μl Dynabeads M-280 Sheep anti-Mouse IgG (Dynal Biotech) in 400 μl ice-cold 1xPBS-T (140 mM NaCl, 2.7 mM KCl, 10.1 mM Na2HPO4, 1.8 mM KH2PO4, 0.05 % Tween-20) on a rotator at 4°C overnight. We used 20 μg fragmented DNA for each methylated immunoprecipitation experiment. Fragmented DNA was denatured for 10 minutes at 95°C followed by chilling on ice for 3 minutes before immunoprecipitation. Fragmented, denatured DNA was incubated with antibody-bead complexes in 500 μl PBS-T on a rotator at 4°C overnight. The mixture was washed three times with ice-cold PBS-T. DNA-antibody-bead complexes were treated twice with 150 μl elution buffer (10 mM DTT, 1% SDS, 0.1 M NaHCO3) at 65°C with constant shaking for 15 minutes each followed by proteinase K treatment for 3 hours at 50°C. Immunoprecipitated DNA was purified by standard phenol-chloroform extraction followed by ethanol precipitation. DNA qualities and concentrations were assessed by using NanoDrop (Thermo Scientific).

value: 13.5 days postcoitum (dpc)

source_name: placenta 13.5 days postcoitum (dpc), input

label_protocol: The sonicated sample was labeled with Cy-3 dCTP and washed by using BioPrime Array CGH Genomic Labeling Module (Invitrogen).


title: CellLine-SL10-dT

growth_protocol:
Medium: DMEM+10%FBS+penicillin/streptomycin
Atmosphere: 5% CO2 at 37°C

tag: Mouse fibroblast cell line


title: Mouse Placenta 13.5 (Random)

source_name: placenta of 13.5 days postcoitum (dpc) embryos


title: Mouse Brain (Random)

source_name: whole brain

value: brain


title: Mouse Brain (dT)


title: Mouse Liver (Random)

value: liver


title: CAPUT vs CAUDA replicate 4

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

country: Canada

institute: INRS-Institut Armand-Frappier

description:
Replicate 4 of 4
A dye swap was applied to this sample before further analysis in GeneSpring Software 6.1.

hyb_protocol: 0.75 mg of cRNA were hybridized to the Agilent microarrays (Agilent Human 1A Microarray (V2) G411B) using the Agilent In Situ Hybridization Kit Plus) according to the protocol provided by the manufacturer.

scan_protocol: Following hybridization, microarrays were scanned with a ScanArray Express scanner (Perkin Elmer). Fluorescence ratios for array elements were extracted using the ScanArray Express Software (Perkin Elmer) and imported into the GeneSpring 6.1 software (Agilent Technologies) for further analysis.

data_processing: A dye swap was applied to the samples underlined in yellow (251209744988 (sample 1), 251209745020 (sample 3), 251209745023 (sample 5), 251209745156 (sample 8)) before further analysis.GeneSpring Software 6.1 (Agilent) was used for analysis following dye-sap and LOWESS normalization.

label: cyanine 5

source_name: CAPUT

label_protocol: Fluorescent cRNA were prepared from 500ng of total RNA using the Agilent Low RNA Input Linear Amplification Kit. As a last step of the extraction procedure, the cRNA was purified with the Rneasy Mini-Kit (Qiagen).

growth_protocol: Human epididymides were obtained from four patients (29–50 years of age) who were undergoing radical orchidectomy for localized testicular cancer (confined within the testicular tunica albuginea). Epididymides were subdivided into three separate segments (caput, corpus, and cauda epididymidis). All patients had active spermatogenesis. Tissues were received in cold culture medium that contained antibiotics (Dulbecco modified Eagle medium and Ham F-12 with penicillin-streptomycin) and were transported to the laboratory within 1 h of surgery. Tissues were frozen in liquid nitrogen for RNA preparation.

extract_protocol: Total cellular RNA was isolated using Absolutely RNA RT-PCR miniprep kit (Stratagene, La Jolla, CA)according to the manufacturer’s instructions. The quality of the total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: caput epididymis

label: cyanine 3

source_name: CORPUS

value: corpus epididymis


title: Mouse Thymus (Female)

source_name: thymus, immunoprecipitated

value: C57BL/6J Jc1

value: female

value: thymus

source_name: thymus, input

extract_protocol:
DNA was extracted by conventional methods. Briefly, freshly isolated tissues were minced in lysis buffer (50 mM Tris-HCl, 20 mM EDTA, 0.1 M NaCl, 1% SDS) and incubated in proteinase K (final concentration, 100 μg/ml in lysis buffer) at 55°C overnight, followed by phenol-chloroform extraction and ethanol precipitation.
The Genomic DNA was sonicated (Bioruptor, Cosmo Bio) to produce short random fragments. Sonicated DNA samples were size-fractionated by agarose gel electrophoresis and excision (200 to 1000 bp). To avoid DNA damage by UV light, gels were stained by using SYBR Safe Gel Stain (Invitrogen) and excised on a blue-light transilluminator (Safe Imager, Invitrogen). Excised DNA fragments were purified by using MinElute Gel Extraction Kit (Qiagen).


title: Mouse Placenta 10.5

source_name: placenta 10.5 days postcoitum (dpc), immunoprecipitated

value: 10.5 days postcoitum (dpc)

value: male and female

value: placenta

source_name: placenta 10.5 days postcoitum (dpc), input


title: Mouse Spleen (Female)

source_name: spleen, immunoprecipitated

value: 8-10 weeks old

value: spleen

source_name: spleen, input


title: SATO3 chromatin Open2

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: Standard Illumina

label: C-Bio and A-DNP

source_name: Tissue culture cells

label_protocol: Standard Illumina

growth_protocol: Normal cells

extract_protocol: Purification of DNA from Chromatin Fragments on Sucrose Gradient and Pulse Field Gel Fractionation

tag: sample type

value: open chromatin


title: CAPUT vs CORPUS replicate 3

description:
Replicate 3 of 4
A dye swap was applied to this sample before further analysis in GeneSpring Software 6.1.


title: CAPUT vs CORPUS replicate 4

description: Replicate 4 of 4

source_name: CAUDA

value: cauda epididymis


title: Mouse Lung (Female)

source_name: lung, immunoprecipitated

source_name: lung, input


title: Mouse Stomach (Female)

source_name: stomach, immunoprecipitated

value: stomach

source_name: stomach, input


title: Mouse Heart (Female)

source_name: heart, immunoprecipitated

value: heart

source_name: heart, input


title: CAPUT vs CAUDA replicate 2

description:
Replicate 2 of 4
A dye swap was applied to this sample before further analysis in GeneSpring Software 6.1.


title: CAPUT vs CAUDA replicate 3

description: Replicate 3 of 4


title: CAPUT vs CAUDA replicate 1

description: Replicate 1 of 4


title: CAPUT vs CORPUS replicate 2

description: Replicate 2 of 4


title: Mouse Intestine (Female)

source_name: small intestine, immunoprecipitated

value: small intestine

source_name: small intestine, input


title: Mouse Liver (Female)

source_name: liver, immunoprecipitated

source_name: liver, input


title: Mouse Brain (Female)

source_name: brain, immunoprecipitated

value: brain

source_name: brain, input


title: Mouse Thymus (Male)

source_name: thymus, immunoprecipitated

value: male

source_name: thymus, input


title: CAPUT vs CORPUS replicate 1

description:
Replicate 1 of 4
A dye swap was applied to this sample before further analysis in GeneSpring Software 6.1.

source_name: CAPUT

value: caput epididymis

source_name: CORPUS


title: Mouse Lung (Male)

value: lung


title: Mouse Testis

source_name: testis, immunoprecipitated

value: C57BL/6J Jc1

value: testis

source_name: testis, input


title: Mouse Liver (Male)

value: liver


title: Mouse Kidney (Female)

source_name: kidney, immunoprecipitated

value: female

value: kidney

source_name: kidney, input


title: Mouse Stomach (Male)

source_name: stomach, immunoprecipitated

source_name: stomach, input


title: Cebpa Cre-flox FL LSK EYFP-, replicate 2

city: Rotterdam

first: Albert

last: Wölfler

address: Dr. Molewaterplein 50

department: Hematology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with MAS 5.0 in R using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set 100.

source_name: fetal liver LSK EYFP- cells

label_protocol: Standard Affymetrix protocol.

extract_protocol: RNA was extracted with the RNeasy Micro Kit (Qiagen). After two steps of linear amplification with the RNA MessageAmp II aRNA Kit (Ambion, Applied Biosystems), aRNA was labelled and hybridized on the Mouse Genome 430 Affymetrix 2.0 Array according to Affymetrix standard protocols.

treatment_protocol: Bone marrow and fetal livers were harvested from 7- to 12-week-old mice and day E14.5 embryos, respectively. After lineage depletion, cells were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells and double-sorted by FACS. For the second round, cells were immediately sorted into RLT buffer (Qiagen).

tag: genotype

value: Cebpa Cre/fl R26 EYFP

value: embryo

value: fetal liver

value: LSK

tag: cebpa/eyfp induction


title: Cebpa Cre-wt FL LSK EYFP+, replicate 1

source_name: fetal liver LSK EYFP+ cells

value: Cebpa Cre/wt R26 EYFP

tag: cell type


title: SATO3 chromatin Input

source_name: Tissue culture cells

value: input


title: Mouse Kidney TD (Male)

tag: strain

value: 8-10 weeks old


title: 5nM-Testosterone-with100nM-VitD_rep3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: p14.2+T+D_252182710380_S01_miRNA-v1_10_Apr08_1_4.txt

hyb_protocol: labeled miRNA was hybridized onto Agilent Human miRNA microarrays v3 (G4771-A) rel 12.0 according to the manufacturer's instructions.

scan_protocol: The arrays were scanned on a Agilent G2565C scanner using the standard settings for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1 (Agilent) using default parameters (protocol miRNA-v1_10_Apr08 and Grid: 021827_D_20081121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent) according to the manufacturer's instructions

growth_protocol: LNCaP cells were grown in RPMI-1640 media with 10% fetal bovine serume supplemented with 100U penicillin and 0.1 mg/mL streptomycin in 37°C with 5%CO2 and 85% humidity.

extract_protocol: Total RNA was extracted using the miRNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Center for Functional Genomics at State University of New York at Albany (Rensselaer, NY, USA)

treatment_protocol: LNCaP cells were plated at 1x10^6 cells per 150 x 25mm dish with 25mL of growth media, and allowed to adhere for 48h prior to treatment. Each treatment was prepared at 6x concentration, so that 5mL of treatment soultion was added to the 25mL growth media.

value: LNCaP

tag: genotype/variation


title: Mouse Spleen (Male)

source_name: spleen, immunoprecipitated

value: spleen

source_name: spleen, input


title: Normal human epidermal melanocytes

city: Tokyo

first: Shigeki

middle: Ohta

last: Ohta

state: Tokyo

address: 35 Shinanomachi shinjyuku-ku

department: Institute for Advanced Medical Research

institute: Keio University

description: NHEM cells are commercial human primary cells provided from Kurabo (Osaka, Japan).

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of  55ul containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at room temperature with  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

Values below 0.01 were set to 0.01.
Each measurement was divided by the 50.0th percentile of all measurements in that sample.
Specific samples were normalized to one another: samples were normalized against the median of the control sample. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control sample.

source_name: Epidermal melanocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quick-Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cells by using Trizol (Invitrogen).  For purification of RNA, samples were subjected to the Purelink RNA Mini kit (Invitrogen) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Human 3F-iPS cells were established using retrovirus encoding Oct3/4, Sox2, KL4 following the method established by S. Yamanaka. After generation of embryonic body, iPS-derived cells were differentiated into melanocytes on fibronectin-coated dishes. Sample was extracted 8 weeks after differentiation.

value: normal foreskin-derived human epidermal melanocytes


title: Cebpa Cre-flox FL LSK EYFP+, replicate 1

tag: developmental stage


title: Cebpa Cre-wt FL LSK EYFP-, replicate 1


title: short-root mutant, biological rep3

city: Ghent

first: Stijn

last: Dhondt

address: Technolgiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB

description: shr-5, vegetative part of seedlings at stage 1.04

hyb_protocol: Standard affymetrix protocol

scan_protocol: Standard affymetrix protocol

data_processing: Expression data were processed using RMA (background correction, normalization and summarization) in BioConductor (Gentleman et al. 2004; Irizarry et al. 2003a; 2003b). An alternative CDF (tinesath1cdf) was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007; http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html)

organism: Arabidopsis thaliana

label_protocol: Standard affymetrix protocol

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer protocol

tag: ecotype

value: vegetative part

value: stage 1.04


title: short-root mutant, biological rep2


title: 5nM-Testosterone-with100nM-VitD_rep4

description: p14.2+T+D_252182710380_S01_miRNA-v1_10_Apr08_2_4.txt


title: Mouse Kidney (Male)

value: C57BL/6J Jc1

value: male


title: Human 3F-iPS-derived melanocytes

source_name: 3F-iPS-derived melanocytes

value: derived from WDT2

value: 3F-induced pluripotent stem (iPS) cell-derived melanocytes


title: Cebpa Cre-flox FL LSK EYFP-, replicate 1


title: Human 3F-iPS

source_name: 3F-iPS cells

value: 3F-induced pluripotent stem (iPS) cells


title: short-root mutant, biological rep1


title: Cebpa Cre-flox FL LSK EYFP+, replicate 2

value: Cebpa Cre/fl R26 EYFP


title: Mouse Brain (Male)

source_name: brain, immunoprecipitated

value: brain

source_name: brain, input


title: Cebpa Cre-wt bm LSK EYFP-, replicate 2

source_name: bone marrow LSK EYFP- cells

value: 7-12 weeks

value: bone marrow


title: Mouse Intestine (Male)

source_name: small intestine, immunoprecipitated

value: small intestine

source_name: small intestine, input


title: scarecrow mutant, biological rep3

description: scr-3, vegetative part of seedlings at stage 1.04


title: Cebpa Cre-wt bm LSK EYFP-, replicate 1

value: Cebpa Cre/wt R26 EYFP

value: LSK


title: No-Testosterone-withVitD_rep4

description: p14.2-T+D_252182710380_S01_miRNA-v1_10_Apr08_2_3.txt

source_name: No-Testosterone-withVitD

value: LNCaP


title: 5nM-Testosterone-with100nM-VitD_rep2

description: p14.1+T+D_252182710379_S01_miRNA-v1_10_Apr08_2_4.txt


title: 5nM-Testosterone-with100nM-VitD_rep1

description: p12+T+D_252182710379_S01_miRNA-v1_10_Apr08_1_4.txt


title: Cebpa Cre-wt bm LSK EYFP+, replicate 2

source_name: bone marrow LSK EYFP+ cells


title: Cebpa Cre-wt bm LSK EYFP+, replicate 3


title: No-Testosterone-withVitD_rep3

description: p14.2-T+D_252182710380_S01_miRNA-v1_10_Apr08_1_3.txt


title: Mouse Heart (Male)

source_name: heart, immunoprecipitated

value: 8-10 weeks old

value: heart

source_name: heart, input


title: No-Testosterone-withVitD_rep2

description: p14.1-T+D_252182710379_S01_miRNA-v1_10_Apr08_2_3.txt


title: scarecrow mutant, biological rep2

value: vegetative part


title: 5nM-Testosterone_rep3

description: p14.2+T_252182710380_S01_miRNA-v1_10_Apr08_1_2.txt


title: 5nM-Testosterone_rep2

description: p14.1+T_252182710379_S01_miRNA-v1_10_Apr08_2_2.txt


title: 5nM-Testosterone_rep4

description: p14.2+T_252182710380_S01_miRNA-v1_10_Apr08_2_2.txt


title: wild type, biological rep2

description: Wild type, vegetative part of seedlings at stage 1.04

source_name: Wild type

value: stage 1.04

value: WT


title: wild type, biological rep3


title: Cebpa Cre-wt bm LSK EYFP+, replicate 1


title: No-Testosterone-withVitD_rep1

description: p12-T+D_252182710379_S01_miRNA-v1_10_Apr08_1_3.txt


title: No-Testosterone_rep4

description: p14.2-T_252182710380_S01_miRNA-v1_10_Apr08_2_1.txt

source_name: No-Testosterone


title: 5nM-Testosterone_rep1

description: p12+T_252182710379_S01_miRNA-v1_10_Apr08_1_2.txt


title: wild type, biological rep1


title: scarecrow mutant, biological rep1


title: MouseDC-24hr-2

city: Winston-Salem

first: Elizabeth

last: Hiltbold-Schwartz

state: NC

address: Medical Center Boulevard

department: Microbiology & Immunology

institute: Wake Forest University Baptist Medical Center

description: Mouse bone marrow DC, Poly(I:C), 24hr, rep2

hyb_protocol: Affymetrix defined protocols for the GeneChip 3' IVT Express Kit were used.  User's manual for these protocols can be found at www.affymetrix.com.

source_name: bone marrow DC, poly I:C, 24hr

growth_protocol: Bone marrow was isolated from the femurs and tibias of 8-10 week old C57BL/6 mice.  Bone marrow cells were plated in GM-CSF-containing media for 6 days (10ng/ml).   Cells were fed with cytokine containing media on days 2 and 4.

extract_protocol: RNA was isolated and purified from all samples using the RNAqueous kit (Applied biolsystems) according to manufacturer instructions

treatment_protocol: Dendritic cells were harvested and plated in 60mm culture dishes at 3,000,000 DC/7 ml media and treated with Poly I:C at 2.5ug/ml for 0, 1, 3, 6, 12, or 24h.  At the indicated timepoints, media was aspirated and cells were treated with RNA later (Applied Biosystems) to preserve RNA until the end of the experiment.  RNA was isolated and purified using RNAqueous kit (aplied biosystems) according to manufacturer's instructions.

value: bone marrow from femurs and tibias

value: dendritic cells

value: 3-4 months


title: MouseDC-24hr-1

description: Mouse bone marrow DC, Poly(I:C), 24hr, rep1

scan_protocol: Affymetrix defined protocols for the GeneChip 3' IVT Express Kit were used.  User's manual for these protocols can be found at www.affymetrix.com.


title: MouseDC-12hr-1

description: Mouse bone marrow DC, Poly(I:C), 12hr, rep1

data_processing: Affymetrix defined protocols for the GeneChip 3' IVT Express Kit were used.  User's manual for these protocols can be found at www.affymetrix.com.

source_name: bone marrow DC, poly I:C, 12hr


title: MouseDC-12hr-2

description: Mouse bone marrow DC, Poly(I:C), 12hr, rep2

label_protocol: Affymetrix defined protocols for the GeneChip 3' IVT Express Kit were used.  User's manual for these protocols can be found at www.affymetrix.com.


title: MouseDC-6hr-1

description: Mouse bone marrow DC, Poly(I:C), 6hr, rep1

source_name: bone marrow DC, poly I:C, 6hr


title: No-Testosterone_rep2

description: p14.1-T_252182710379_S01_miRNA-v1_10_Apr08_2_1.txt


title: No-Testosterone_rep1

description: p12-T_252182710379_S01_miRNA-v1_10_Apr08_1_1.txt


title: MouseDC-6hr-2

description: Mouse bone marrow DC, Poly(I:C), 6hr, rep2


title: MouseDC-3hr-1

description: Mouse bone marrow DC, Poly(I:C), 3hr, rep1

source_name: bone marrow DC, poly I:C, 3hr


title: MouseDC-3hr-2

description: Mouse bone marrow DC, Poly(I:C), 3hr, rep2


title: No-Testosterone_rep3

description: p14.2-T_252182710380_S01_miRNA-v1_10_Apr08_1_1.txt


title: MouseDC-1hr-2

description: Mouse bone marrow DC, Poly(I:C), 1hr, rep2

source_name: bone marrow DC, poly I:C, 1hr


title: MouseDC-1hr-1

description: Mouse bone marrow DC, Poly(I:C), 1hr, rep1


title: SATO3 chromatin Open1

source_name: Tissue culture cells

value: open chromatin


title: fis1X2x fis1 mutant cross (Cy5-labelled)

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

hyb_protocol: For each experimental cross (interploidy or fis1X2x), one array was hybridised using a Cy3-labelled sample together with a Cy5-labelled 2xX2x control cross sample using Agilent standard operating protocols. Then the dyes were swapped and the hybridisation was repeated with additional arrays.

scan_protocol: Agilent standard operating protocol.

data_processing: Quantitation, background correction and normalisation was performed for each array separately and independently using Agilent Feature Extraction Software (Apr 2002). Probes with negative signal values were excluded, creating missing values. Values for multiply spotted probes were averaged.  For the fis1X2xCy3 and fis1X2xCy5 samples, probes with negative signal values and individual signal values for multiply spotted probes are included in the supplementary data files.

molecule: polyA RNA

source_name: Siliques

label_protocol: Cy3- and Cy5-labelling were carried out using Agilent standard operating protocols.

growth_protocol: Plants were grown at 18hr day cycles at 60% humidity. Male sterile lines were pollinated by the appropriate pollen depending on the cross and siliques harvested in liquid nitrogen at 5 days after pollination (DAP).

extract_protocol: mRNA was extracted from whole siliques using the hot borate method for total RNA extraction and the Oligotex mRNA Midi Kit (Qiagen) to isolate poly-A+ mRNA.

value: 5 days after pollination

tag: maternal ecotype

value: Ler

tag: paternal ecotype

tag: maternal genetic modification

value: fis1-3 (=mea-3/f644) homozygous mutant

tag: paternal genetic modification

value: A9-barnase transgene


title: MouseDC-0hr-1

description: Mouse bone marrow DC, Poly(I:C), 0hr, rep1

source_name: bone marrow DC, poly I:C, 0hr

tag: tissue


title: The effect of GFP-ERG overexpression in RWPE1 cells at 72hrs time point, array 1

city: Turku

first: Santosh

middle: Kumar

last: Gupta

address: 4th floor pharma city

department: University of Turku

country: Finland

institute: VTT medical biotechnology

description: RWPE1 cells were transfected with GFP-ERG construct at 72hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).

hyb_protocol: 1.5 µg each cRNA sample was hybridized to Illumina’s Bead Chip arrays at 58 °C overnight (19 h) according to Illumina 11225598_WGGEX_IntelliHyb_Seal_SystemManual_RevA.pdf.

scan_protocol: Chips were scanned with Illumina Bead Array Reader (Factor=1, PMT=521, Filter=100%)

data_processing: The numerical results were extracted with Bead Studio v3.2.6 without any normalization or background subtraction. Data were VST quantile normalized. Annotation: Illumina HumanRef-8 V2

source_name: GFP-ERG-transfected RWPE1 cells at 72hrs time point

label_protocol: cRNA was biotinylated during in vitro transcription reaction overnight (14h).

growth_protocol: RWPE1 cells were grown in KSFM growth media.

extract_protocol: Trizol method from Invitrogen.

tag: transfection

value: ERG

tag: time

value: 72 hours


title: 4xX2x interploidy cross (Cy5-labelled)


title: MouseDC-0hr-2

description: Mouse bone marrow DC, Poly(I:C), 0hr, rep2

tag: age


title: 2xX4x interploidy cross (Cy5-labelled)


title: The effect of GFP-ERG overexpression in RWPE1 cells at 48hrs time point, array 2

description: RWPE1 cells were transfected with GFP-ERG construct at 48hrs time point. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).

source_name: GFP-ERG-transfected RWPE1 cells at 48hrs time point

treatment_protocol: RWPE1 cells were transfected with GFP-ERG construct at 48hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).

tag: cell line

value: 48 hours


title: 2xX6x interploidy cross (Cy3-labelled)


title: fis1X2x fis1 mutant cross (Cy3-labelled)


title: The effect of GFP overexpression in RWPE1 cells at 48hrs time point, array 2

description: Human prostate epithelial cells. RWPE1 cells were transfected with GFP. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).

source_name: GFP-transfected RWPE1 cells at 48hrs time point

treatment_protocol: RWPE1 cells were transfected with GFP construct at 48hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).

value: control


title: The effect of GFP overexpression in RWPE1 cells at 48hrs time point, array 1


title: 6xX2x interploidy cross (Cy3-labelled)


title: The effect of GFP-ERG overexpression in RWPE1 cells at 48hrs time point, array 1

description: RWPE1 cells were transfected with GFP-ERG construct at 48hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).


title: 4xX2x interploidy cross (Cy3-labelled)


title: The effect of GFP-ERG overexpression in RWPE1 cells at 72hrs time point, array 2

treatment_protocol: RWPE1 cells were transfected with GFP-ERG construct at 72hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).


title: The effect of GFP overexpression in RWPE1 cells at 72hrs time point, array 2

description: Normal prostate epithelial cells. RWPE1 cells were transfected with GFP construct at 72hrs time point. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen) and used for Illumina array.

source_name: GFP-transfected RWPE1 cells at 72hrs time point

treatment_protocol: RWPE1 cells were transfected with GFP construct at 72hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).


title: The effect of GFP overexpression in RWPE1 cells at 72hrs time point, array 1

description: RWPE1 cells were transfected with GFP construct at 72hrs. Thereafter, the total cellular RNAs were isolated by Trizol (Invitrogen).


title: 2xX4x interploidy cross (Cy3-labelled)


title: HRPTEC cells 6hr after addition of 0.3mM HAMLET biological rep2

status: Public on Aug 25 2010

city: Singapore

first: Henry

last: Yang

address: 8A Biomedical Grove

department: Bioinformatics Group

country: Singapore

institute: SIgN

description: Biological replicate 2

hyb_protocol: 750ng of each cRNA sample was hybridized to HumanWG-6 v3 expression beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 1 as per manufacturer specifications.

data_processing:
The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006). Differentially expressed transcripts were identified based on the mean Log2 fold-change in expression values compared to the wild type ES cell controls with a cutoff at 1.5-fold change.
Background subtracted cross-correlation method normalised intensity values generated using MATLAB scripts
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: A498 cells were cultured in RPMI-1640 with non-essential amino acids (1:100), 1 mM sodium pyruvate, 50 µg/ml Gentamicin (Gibco), 5% fetal calf serum (FCS). Primary cultures of human renal tubular epithelial cells (HRTEC) were cultured in DMEM/F12 with 15% FCS. HAMLET was incubated with cells in serum-free RPMI-1640 at 37°C. FCS was added after 1 hour.

extract_protocol: Total RNA was extracted from 3 biological replicates of A498 or HPRTEC cells subjected to control and HAMLET @0.3 treatments using the RNeasy Mini kit (Qiagen) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: Cells were treated for 0min, 15min, 60min, 75min, 3hrs, 6hrs and 24 hrs with HAMLET at 0.3mM.

tag: treatment

value: HAMLET

value: HRPTEC


title: HRPTEC cells control 24hr biological rep1

description: Biological replicate 1

source_name: human renal tubular epithelial cells (HRTEC)


title: 2xX6x interploidy cross (Cy5-labelled)


title: HRPTEC cells 24hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells control 6hr biological rep3

description: Biological replicate 3


title: HRPTEC cells 24hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: HRPTEC cells control 24hr biological rep3

description: Biological replicate 3


title: HRPTEC cells 6hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells 3hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: HRPTEC cells control 3hr biological rep3

description: Biological replicate 3


title: HRPTEC cells 3hr after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells control 3hr biological rep2

description: Biological replicate 2


title: HRPTEC cells control 24hr biological rep2

description: Biological replicate 2


title: HRPTEC cells 24hr after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells 3hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells control 6hr biological rep2

description: Biological replicate 2


title: HRPTEC cells control 6hr biological rep1

description: Biological replicate 1


title: HRPTEC cells control 3hr biological rep1

description: Biological replicate 1


title: 6xX2x interploidy cross (Cy5-labelled)


title: HRPTEC cells control 75min biological rep1

description: Biological replicate 1


title: HRPTEC cells control 60min biological rep3

description: Biological replicate 3


title: HRPTEC cells control 75min biological rep3

description: Biological replicate 3


title: HRPTEC cells 75min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: HRPTEC cells 75min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells 75min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells 60min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells 60min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: HRPTEC cells control 75min biological rep2

description: Biological replicate 2


title: HRPTEC cells 60min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells control 60min biological rep2

description: Biological replicate 2


title: HRPTEC cells 15min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells control 60min biological rep1

description: Biological replicate 1


title: HRPTEC cells 15min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: NTac_liver_treated_150 mg/kg_96hr_4

city: Thousand Oaks

first: Sandra

last: Tran

address: One Amgen Center Drive

institute: Amgen

hyb_protocol: For each sample, 10 ug of biotinylated cRNA spiked with hybridization controls (bioB, bioC, bioD and cre) was hybridized to an Affymetrix Mouse 430_2 microarray for 16 h at 45ºC.

scan_protocol: Following hybridization, arrays were washed and stained in an Affymetrix GeneChip Fluidics Station and scanned with a GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA).  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

data_processing:
Log-ratios of gene expression data and associated platform p-values were generated in the Rosetta Resolver System (Rosetta Biosoftware, Seattle, WA, version 7.2) for all profiles relative to strain-matched vehicle-treated controls.
For each Affymetrix sequence (or probe set), log-ratio was defined to be the log10 of the intensity ratio of each animal (either treated with vehicle or CMP013) to the mean intensity of that sequence across the five profiles in the corresponding vehicle control group.

source_name: Liver from C57BL/6NTac mouse

label_protocol: Liver RNA from individual mice was profiled separately on the Affymetrix GeneChip® platform without technical replication.  Microarray profiling was performed by Cogenics (Morrisville, NC).  Briefly, 1 g of total RNA was reverse transcribed to double stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit and biotinylated cRNA was generated using the BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY).

extract_protocol: Total RNA was isolated from pieces of mouse liver according to the RNeasy extraction procedure (Qiagen, Valencia, CA).  Tissues were homogenized in QIAzol lysis buffer using the GenoGrinder 2000 homogenizer (SPEX SamplePrep, Metuchen, NJ).  Samples were processed on the Qiagen BioRobot Universal system according to the manufacturer’s instructions.  An on-column DNase digestion was performed to remove any residual genomic DNA contamination.  RNA concentration and yield were measured spectrophotometrically using the Nanodrop instrument.  Quality of the nucleic acid samples was evaluated with the RNA 6000 Nano chip kit (Agilent Technologies, Expert software).  Quality of samples was verified with distinct ribosomal 18S & 28S peaks, low baseline, and high RIN values (PXR+/+: 9.3-10; PXR-/-: 8.7-9.6).

value: Liver

value: PXR-/-

tag: treatment group

value: CMP013 150 mg/kg


title: NTac_liver_treated_150 mg/kg_96hr_3


title: HRPTEC cells control 15min biological rep1

description: Biological replicate 1


title: NTac_liver_treated_150 mg/kg_96hr_1


title: NTac_liver_treated_150 mg/kg_96hr_5


title: A498 cells 24hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3

source_name: A498 cells


title: NTac_liver_treated_150 mg/kg_96hr_2


title: HRPTEC cells control 0min biological rep1

description: Biological replicate 1


title: A498 cells 24hr after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells 15min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: NTac_liver_vehicle 0 mg/kg_96 hr_4

value: vehicle 0 mg/kg


title: A498 cells control 24hr biological rep3

description: Biological replicate 3


title: HRPTEC cells control 15min biological rep2

description: Biological replicate 2


title: NTac_liver_vehicle 0 mg/kg_96 hr_5


title: HRPTEC cells control 0min biological rep2

description: Biological replicate 2


title: A498 cells control 24hr biological rep1

description: Biological replicate 1


title: NTac_liver_vehicle 0 mg/kg_96 hr_3


title: A498 cells control 24hr biological rep2

description: Biological replicate 2


title: A498 cells 24hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells 6hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: NTac_liver_vehicle 0 mg/kg_96 hr_2


title: A498 cells 6hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: A498 cells 6hr after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: HRPTEC cells control 0min biological rep3

description: Biological replicate 3


title: A498 cells control 6hr biological rep2

description: Biological replicate 2


title: NTac_liver_vehicle 0 mg/kg_96 hr_1


title: WT_liver_treated_150 mg/kg_96hr_5

source_name: Liver from C57BL/6 mouse

value: PXR+/+


title: WT_liver_treated_150 mg/kg_96hr_4


title: A498 cells control 6hr biological rep1

description: Biological replicate 1


title: A498 cells 3hr after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: A498 cells control 3hr biological rep2

description: Biological replicate 2


title: A498 cells control 3hr biological rep3

description: Biological replicate 3


title: HRPTEC cells control 15min biological rep3

description: Biological replicate 3


title: A498 cells 3hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells control 3hr biological rep1

description: Biological replicate 1


title: A498 cells 75min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells 3hr after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: A498 cells control 75min biological rep3

description: Biological replicate 3


title: A498 cells 75min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: A498 cells control 75min biological rep1

description: Biological replicate 1


title: WT_liver_treated_150 mg/kg_96hr_2


title: A498 cells control 75min biological rep2

description: Biological replicate 2


title: WT_liver_vehicle 0 mg/kg_96 hr_5


title: WT_liver_treated_150 mg/kg_96hr_1


title: A498 cells 60min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells 60min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2


title: A498 cells 75min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: HRPTEC cells 6hr after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells 60min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: WT_liver_vehicle 0 mg/kg_96 hr_3


title: WT_liver_vehicle 0 mg/kg_96 hr_1


title: WT_liver_vehicle 0 mg/kg_96 hr_2


title: A498 cells control 6hr biological rep3

description: Biological replicate 3


title: A498 cells control 60min biological rep3

description: Biological replicate 3


title: A498 cells 15min after addition of 0.3mM HAMLET biological rep3

description: Biological replicate 3


title: WT_liver_treated_150 mg/kg_96hr_3


title: A498 cells control 0min biological rep2

description: Biological replicate 2


title: A498 cells control 60min biological rep1

description: Biological replicate 1


title: WT-_Bio replication 2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description:
WT-
2-11-08

hyb_protocol: Affymetrix standard hybridization protocol.

scan_protocol: Affymetrix standard scan protocol.

data_processing: RMA normalization using Partek.

source_name: WT, unstimulated

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

growth_protocol: NIDDK\NIH growth core lab protocol.

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

treatment_protocol: Control and Stat5a/b-null KSL cells were unstimulated or stimulated with a cocktail containing IL-3, IL-6, SCF, TPO and FL.

value: fetal liver-derived KSL cells

tag: genotype

value: WT

tag: stimulated

value: no


title: KO-_Bio replication 2

description:
KO-
2-11-08

source_name: KO, unstimulated

tag: cell type

value: Stat5a/b knockout


title: A498 cells control 15min biological rep3

description: Biological replicate 3


title: A498 cells control 0min biological rep3

description: Biological replicate 3


title: KO-_Bio replication 3

description:
KO-
6-21-07


title: A498 cells control 0min biological rep1

description: Biological replicate 1


title: A498 cells 15min after addition of 0.3mM HAMLET biological rep1

description: Biological replicate 1


title: A498 cells control 15min biological rep2

description: Biological replicate 2


title: WT_Col_replicate3_continuous light

city: Buenos Aires

first: Marcelo

middle: Javier

last: Yanovsky

state: Capital Federal

address: Av. San Martín 4453

department: Applied Biology

country: Argentina

institute: IFEVA

description: Gene expression data from plants grown always under continuous light

hyb_protocol: hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: scanning was performed according to the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

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

growth_protocol: WT and mutant plants were grown for three weeks under continuous light at 22 degrees centigrades.

extract_protocol: RNA was extracted from aerial tissue using Trizol according to the manufacturer's instructions.

value: Columbia

tag: genotype/variation

value: wild type

value: Aerial tissue


title: WT+_Bio replication 3

description:
WT+
6-21-07

source_name: WT, stimulated

value: yes


title: WT+_Bio replication 2

description:
WT+
2-11-08


title: WT_Col_replicate1_continuous light


title: prmt5-5_replicate2_continuous light

value: prmt5-5 mutant


title: WT_Col_replicate2_continuous light


title: prmt5-5_replicate3_continuous light


title: AP1 Domain at Flower Stage 4

city: Pasadena

first: Yuling

last: Jiao

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

description: AP1 domain translatome vs whole flower translatome

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.

data_processing: Data were processed in eCADS (Dabney and Storey (2007) Genome Biol. 8, R44).

source_name: AP1 domain cells at flower stage 4

label_protocol: First and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

extract_protocol: Polysome-associated RNA were isolated from immunopurified epitope-tagged polysomes as described in Zanetti et al. (2005) Plant Physiol 138: 624-635.

value: AP1 flower domain

tag: developmental stage

value: Early flower stage 4

tag: rna type

value: polysome-associated polyA+ RNA

source_name: Whole flower

value: whole flower


title: WT_liver_vehicle 0 mg/kg_96 hr_4

value: Liver

tag: strain


title: A498 cells control 15min biological rep1

description: Biological replicate 1

value: control


title: A498 cells control 60min biological rep2

description: Biological replicate 2


title: mut_skin_5dpn_rep1

city: Bar Harbor

first: Christopher

middle: S.

last: Potter

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

description: mutant

hyb_protocol: Ten micrograms of biotin-labeled and fragmented cRNA was hybridized onto MOE430v2.0 GeneChip arrays (Affymetrix) for 16 hrs at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix).  Finally, the arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: Average signal intensities for each probe set within arrays were calculated by the rma function provided within the Affymetrix package for R using a custom CDF file (Dai et al., 2005). The RMA method incorporates convolution background correction and summarization based on a multi-array model fit robustly using the median polish algorithm. Data was quantile-normalized to bring arrays onto a common scale.  For this experiment, one pair-wise comparison was used to statistically resolve gene expression differences between AP groups using the R/MAANOVA analysis package (Wu et al., 2003).  Specifically, differentially expressed genes were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/MAANOVA package (Cui et al., 2005; Wu et al., 2003).  Statistical significance levels of the pairwise comparison were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002).  Differentially expressed genes were declared at an FDR q-value threshold of 0.05.                                                                                References:    - Cui X, Hwang JT, Qiu J, Blades NJ, Churchill GA (2005) Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 6:59-75.                                               - Dai M, Wang P, Boyd A, Kostov G, Athey B, Jones E, et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Research 33.                                                       - Storey J (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society Series B:479-98.                                                                                - Wu H, Kerr M, Cui X, Churchill G (2003) MAANOVA: A software package for the analysis of spotted cDNA microarray experiments. In: The analysis of gene expression data, pp. 313-341 (Springer, New York, NY).

label_protocol: Following reverse transcription with an Oligo(dT)-T7 primer (Affymetrix, Santa Clara, CA), double stranded cDNA was synthesized with the GeneChip® Expression 3’-Amplification One-Cycle kit (Affymetrix, Santa Clara, CA).  In an in vitro transcription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified and labeled with biotinylated nucleotides (Affymetrix).

extract_protocol: Dissected skin was minced, and placed in RNAlater (Applied Biosystems, Austin, TX) overnight at 4°C. Tissue samples were kept at -80°C, until further processing within 48 hrs. Frozen samples were lysed in RLT Buffer from an RNeasy Mini Kit (Qiagen, Valencia, CA). Samples were frozen at -80°C for storage and then total RNA was isolated according to manufacturer’s protocol (Qiagen) including the optional DNase treatment step. Quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

value: Hoxc13 knockout Hoxc13tm1Mrc

tag: gender

value: male

tag: genetic background

value: skin


title: mut_skin_5dpn_rep2

description: mutant


title: wt_skin_5dpn_rep3

description: wild-type

value: WT


title: mut_skin_5dpn_rep3

description: mutant


title: HT29_NCP_day7_replicate1

city: Eiheiji

first: Yukie

last: Yoshii

address: 23-3, Matsuoka　Shimoaizuki

department: Biomedical Imaging Research Center

institute: University of Fukui

description: Gene expression of cells in NCP cluture on day 7

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HT-29 cells were maintained routinely as 2D monolayers in a humidified atmosphere of 5% CO2 in air at 37 °C in the growth medium recommended by suppliers. Exponentially growing cells were used in experiments, after trypsinization to detach them from the plates. Viable cells were counted using trypan blue dye-exclusion. For experiments, cells were seeded in 96-well plates at 1×10^4 cells/100 ul of NanoCulture Medium-M (Scivax) in either NCPs (Scivax), or in polystyrene plates for 2D monolayers, for 1 day or 7 days.

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HT-29 cells were seeded in 96-well plates at 1×10^4 cells/100 ul of NanoCulture Medium-M (Scivax) in either NanoCulture plates (NCPs) (Scivax), or in polystyrene plates for 2D monolayers, for 1 day or 7 days. Cells at each time point were collected and used for RNA extraction and DNA microarray analysis.

value: in vitro tumor cells

tag: growth condition

value: NCP 7 day


title: WT+_Bio replication 1

description:
WT+
1-3-08

value: fetal liver-derived KSL cells


title: KO+_Bio replication 2

description:
KO+
2-11-08

source_name: KO, stimulated

value: Stat5a/b knockout


title: KO+_Bio replication 1

description:
KO+
1-3-08


title: A498 cells 15min after addition of 0.3mM HAMLET biological rep2

description: Biological replicate 2

value: HAMLET


title: HT29_NCP_day7_replicate2


title: KO-_Bio replication 1

description:
KO-
1-3-08

value: no


title: WT-_Bio replication 1

description:
WT-
1-3-08


title: wt_skin_5dpn_rep1

description: wild-type

tag: tissue


title: KO+_Bio replication 3

description:
KO+
6-21-07

value: yes


title: HT29_2D_day7_replicate2

description: Gene expression of cells in 2D cluture on day 7

value: 2D monolayer 7 day


title: wt_skin_5dpn_rep2

description: wild-type


title: prmt5-5_replicate1_continuous light

tag: ecotype

value: Columbia

value: prmt5-5 mutant

value: Aerial tissue


title: WT-_Bio replication 3

description:
WT-
6-21-07


title: HT29_NCP_day1_replicate2

description: Gene expression of cells in NCP cluture on day 2

value: NCP 1 day


title: HT29_NCP_day1_replicate1

description: Gene expression of cells in NCP cluture on day 1


title: Leaf_Steptoe_rep1

city: Riga

first: Nils

last: Rostoks

address: 4 Kronvalda Blvd.

country: Latvia

institute: University of Latvia

description: Gene expression data from parental variety of fast neutron mutants (wt)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Barley1 Genome Array. GeneChips were washed and stained according to Affymetrix fluidics protocol EukGE-WS2v5_450.

scan_protocol: GeneChips were scanned using the scanner type M10

data_processing: Probeset summary data was obtained using Affymetrix Expression Console 1.1 and the MAS 5.0 processing algorithm

organism: Hordeum vulgare

source_name: Barley cultivar Steptoe leaf two weeks old

growth_protocol: Plants were grown in the greenhouse under natural light supplemented with artificial light (16 h light, 8 h dark)

extract_protocol: Total RNA was extracted using Trizol reagent and further purified using Qiagen RNeasy Mini kit

treatment_protocol: First leaf of a two weeks old plant was frozen in liquid nitrogen and stored at -80oC until total RNA extraction

value: leaf

tag: cultivar

value: Steptoe

value: wild type

value: 2 weeks


title: HT29_2D_day1_replicate1

description: Gene expression of cells in 2D cluture on day 1

value: 2D monolayer 1 day


title: Leaf_FN363_rep2

description: Gene expression data from fast neutron mutant allelic to nec3 mutant

source_name: Barley FN363 leaf two weeks old

value: FN363 fast neutron mutant

tag: age


title: Leaf_FN363_rep1


title: Leaf_Steptoe_rep2


title: Leaf_FN362_rep2

source_name: Barley FN362 leaf two weeks old

value: FN362 fast neutron mutant


title: PC 1 day AMPH Rat ID MT20

status: Public on Aug 24 2010

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

description: PC 1 day AMPH #20

hyb_protocol: 1.65 µg cRNA was fragmented and hybridized onto an Agilent 4x44K oligonucleotide microarray in a hybridization oven at 65°C for 17 hr using the Agilent Gene Expression Hybridization Kit (5188-5281).  The hybridized microarrays were disassembled at room temperature in Gene Expression Wash Buffer 1 (5188-5325), and then washed in Gene Expression Wash Buffer 1 at room temperature for 1 min.  This was followed by a wash for 1 min in Gene Expression Wash Buffer 2 (5188-5326) at an elevated temperature (≈31°C) and air dried.  To preserve the fluorescent signal intensity and prevent Cy3 degradation to environmental ozone, the entire procedure with the final drying step and scanning conducted was done inside a low-ozone biobubble (<1 ppb ozone).

scan_protocol: The arrays were scanned on an Axon 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA)

data_processing: Initially processing used GenePix Pro 6.0 software (Molecular Devices).  The resulting text files were uploaded into the ArrayTrack database (NCTR, Jefferson, AR) for analysis.  Briefly, the local background (determined from median "dark corners") was subtracted from the fluorescence values of each spot to obtain signal intensity values. We included in our analysis each probe for genes with less than 4 probes. For genes with 4 or more probes, we use the average signal intensity after discarding the minimum and maximum values. Gene expression data were normalized using quantile normalization (Bolstad et al., 2003).

organism: Rattus norvegicus

source_name: parietal cortex AMPH 1 day post

label_protocol: 500 ng of total RNA was used in the Agilent Quick Amp Labeling Kit according to the manufacturer's instructions.  The cRNA was fluorescently labeled by incorporation of cyanine (Cy)3-CTP.  After purification, using the RNeasy mini kit (Qiagen), cRNA yield and Cy3 incorporation efficiency (specific activity) into the cRNA were determined using a NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies).  All cRNAs had a yield >5 µg and a specific activity of 8–15 pmol/µg

growth_protocol: Animals used in these experiments were NCTR strain of Sprague-Dawley rat kept on a 12hour light cycle 6:00am to 6:00pm

extract_protocol: Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).

treatment_protocol: Tissues (meninges and associated vasculature, striatum and cortex) were extracted from 3 month old Sprague-Dawley rats (NCTR strain) at 3 hr or 1 day after saline, environmental hyperthermia or amphetamine exposure

value: parietal cortex (brain regions)

value: male

value: 3 months


title: PC 1 day AMPH Rat ID MT30

description: PC 1 day AMPH #30


title: PC 1 day AMPH Rat ID MT28

description: PC 1 day AMPH #28


title: PC 1 day AMPH Rat ID MT19

description: PC 1 day AMPH #19


title: Leaf_FN362_rep1


title: HT29_2D_day1_replicate2

value: in vitro tumor cells

tag: cell line


title: PC 1 day AMPH Rat ID MT16

description: PC 1 day AMPH #16


title: HT29_2D_day7_replicate1


title: PC 1 day AMPH Rat ID MT7

description: PC 1 day AMPH #7


title: PC 1 day EIH Rat ID MT21

description: PC 1 day EIH #21

source_name: parietal cortex EIH 1 day post


title: PC 1 day EIH Rat ID MT22

description: PC 1 day EIH #22


title: PC 1 day AMPH Rat ID MT10

description: PC 1 day AMPH #10


title: PC 3h AMPH Rat ID MT29

description: PC 3 hour AMPH #29

source_name: parietal cortex AMPH 3 day post


title: PC 3h AMPH Rat ID MT5

description: PC 3 hour AMPH #5

source_name: parietal cortex AMPH 3 hr post


title: PC 3h AMPH Rat ID MT26

description: PC 3 hour AMPH #26


title: PC 3h AMPH Rat ID MT17

description: PC 3 hour AMPH #17


title: PC 3h EIH Rat ID MT24

description: PC 3 hour EIH #24

source_name: parietal cortex EIH 3 hr post


title: PC 3h EIH Rat ID MT14

description: PC 3 hour EIH #14


title: Breast carcinoma mcrodissected tumor 3364

city: Oxford

last: Yau

address: 1 South Parks Road

department: Department of Statistics

institute: University of Oxford

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap610 Quod Genotyping BeadChips (Illumina).
Image data was analyzed using Beadstudio genotyping version 3.2.32 (Illumina).

source_name: Breast carcinoma

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

value: Female

value: Breast tumor, microdissected tumor

tag: disease state

value: carcinoma


title: PC 3h AMPH Rat ID MT18

description: PC 3 hour AMPH #18


title: PC 3h EIH Rat ID MT13

description: PC 3 hour EIH #13


title: Breast carcinoma tumor 3364

description: Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap610 Quod Genotyping BeadChips (Illumina).

value: Breast tumor


title: PC 3h Saline Control Rat ID MT3

description: PC 3 hour control #3

source_name: parietal cortex saline 3 hr post


title: PC 3h AMPH Rat ID MT27

description: PC 3 hour AMPH #27


title: PC 3h Saline Control Rat ID MT1

description: PC 3 hour control #1


title: Breast carcinoma tumor 601


title: PC 1 day AMPH Rat ID MT9

description: PC 1 day AMPH #9


title: Breast carcinoma microdissected tumor stroma 601

value: Breast tumor, microdissected stroma


title: PC 3h Saline Control Rat ID MT4

description: PC 3 hour control #4


title: Breast carcinoma microdissected tumor stroma114


title: Breast carcinoma mcrodissected tumor 601

description: GGenomic DNA extracted from breast tumors was genotyped using Infinium HumanHap610 Quod Genotyping BeadChips (Illumina).


title: STR 1 day AMPH Rat ID MT28

description: STR 1 day AMPH #28

source_name: striatum AMPH 1 day post

value: striatum (brain region)


title: Breast carcinoma tumor 114


title: STR 1 day AMPH Rat ID MT9

description: STR 1 day AMPH #9


title: STR 1 day AMPH Rat ID MT16

description: STR 1 day AMPH #16


title: PC 3h Saline Control Rat ID MT2

description: PC 3 hour control #2


title: PC 3h AMPH Rat ID MT6

description: PC 3 hour AMPH #6


title: STR 1 day AMPH Rat ID MT19

description: STR 1 day AMPH #19


title: STR 1 day AMPH Rat ID MT7

description: STR 1 day AMPH #7


title: STR 1 day EIH Rat ID MT22

description: STR 1 day EIH #22

source_name: striatum EIH 1 day post


title: STR 1 day EIH Rat ID MT11

description: STR 1 day EIH #11


title: STR 3h AMPH Rat ID MT27

description: STR 3 hour AMPH #27

source_name: striatum AMPH 3 hr post


title: Breast carcinoma microdissected tumor stroma 3364


title: PC 1 day EIH Rat ID MT25

description: PC 1 day EIH #25


title: Breast carcinoma microdissected tumor 114


title: STR 1 day EIH Rat ID MT25

description: STR 1 day EIH #25


title: STR 3h AMPH Rat ID MT29

description: STR 3 hour AMPH #29


title: STR 3h AMPH Rat ID MT18

description: STR 3 hour AMPH #18


title: STR 3h AMPH Rat ID MT26

description: STR 3 hour AMPH #26


title: STR 1 day EIH Rat ID MT23

description: STR 1 day EIH #23


title: PC 1 day EIH Rat ID MT11

description: PC 1 day EIH #11


title: STR 3h AMPH Rat ID MT6

description: STR 3 hour AMPH #6


title: PC 1 day EIH Rat ID MT23

description: PC 1 day EIH #23


title: STR 3h AMPH Rat ID MT5

description: STR 3 hour AMPH #5


title: STR 3h AMPH Rat ID MT17

description: STR 3 hour AMPH #17


title: STR 3h EIH Rat ID MT14

description: STR 3 hour EIH #14

source_name: striatum EIH 3 hr post


title: STR 1 day AMPH Rat ID MT30

description: STR 1 day AMPH #30


title: STR 3h Saline Control Rat ID MT4

description: STR 3 hour Control #4

source_name: striatum saline 3 hr post


title: STR 1 day AMPH Rat ID MT10

description: STR 1 day AMPH #10


title: MAV 1day AMPH Rat ID MT30

description: MAV 1 day AMPH #30

source_name: meninges & vasculature amphetamine 1 day post

value: meninges & vasculature


title: STR 3h EIH Rat ID MT24

description: STR 3 hour EIH #24


title: MAV 1day AMPH Rat ID MT16

description: MAV 1 day AMPH #16


title: MAV 1day AMPH Rat ID MT19

description: MAV 1 day AMPH #19


title: MAV 1day AMPH Rat ID MT28

description: MAV 1 day AMPH #28


title: MAV 1day AMPH Rat ID MT10

description: MAV 1 day AMPH #10


title: MAV 1day EIH Rat ID MT25

description: MAV 1 day EIH #25

source_name: meninges & vasculature EIH 1 day post


title: STR 3h EIH Rat ID MT13

description: STR 3 hour EIH #13


title: STR 3h Saline Control Rat ID MT3

description: STR 3 hour Control #3


title: STR 3h Saline Control Rat ID MT2

description: STR 3 hour Control #2


title: MAV 1day EIH Rat ID MT23

description: MAV 1 day EIH #23


title: STR 3h EIH Rat ID MT12

description: STR 3 hour EIH #12


title: MAV 1day AMPH Rat ID MT7

description: MAV 1 day AMPH #7


title: STR 1 day EIH Rat ID MT21

description: STR 1 day EIH #21


title: STR 3h Saline Control Rat ID MT1

description: STR 3 hour Control #1


title: MAV 1day AMPH Rat ID MT9

description: MAV 1 day AMPH #9


title: MAV 1day EIH Rat ID MT11

description: MAV 1 day EIH #11


title: MAV 1day EIH Rat ID MT21

description: MAV 1 day EIH #21


title: MAV 1day AMPH Rat ID MT20

description: MAV 1 day AMPH #20


title: MAV 3h AMPH Rat ID MT26

description: MAV 3 hour AMPH #26

source_name: meninges & vasculature amphetamine 3 hr post


title: MAV 3h AMPH Rat ID MT29

description: MAV 3 hour AMPH #29


title: MAV 1day EIH Rat ID MT22

description: MAV 1 day EIH #22


title: STR 1 day AMPH Rat ID MT20

description: STR 1 day AMPH #20


title: MAV 3h AMPH Rat ID MT18

description: MAV 3 hour AMPH #18


title: MAV 3h AMPH Rat ID MT27

description: MAV 3 hour AMPH #27


title: MAV 3h Saline Control Rat ID MT2

description: MAV 3 hour Control #2

source_name: meninges & vasculature saline 3 hr post


title: MAV 3h EIH Rat ID MT14

description: MAV 3 hour EIH #14

source_name: meninges & vasculature EIH 3 hr post


title: MAV 3h AMPH Rat ID MT5

description: MAV 3 hour AMPH #5


title: MAV 3h AMPH Rat ID MT17

description: MAV 3 hour AMPH #17


title: MAV 3h EIH Rat ID MT12

description: MAV 3 hour EIH #12


title: MAV 3h EIH Rat ID MT24

description: MAV 3 hour EIH #24


title: MAV 3h EIH Rat ID MT13

description: MAV 3 hour EIH #13


title: MAV 3h Saline Control Rat ID MT4

description: MAV 3 hour Control #4


title: MAV 3h Saline Control Rat ID MT1

description: MAV 3 hour Control #1


title: MAV 3h Saline Control Rat ID MT3

description: MAV 3 hour Control #3


title: 3. Day 13 dox (+)

city: South San Francisco

first: Robert

middle: A

last: Stull

address: 384 Oyster Point Blvd, Suite #8

department: Genomics

institute: VistaGen Therapeutics

description: Ainv18 mouse ES cells engineered to overexpress activated Notch4 upon doxycycline treatment

scan_protocol: see CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection, using Axon 4000B scanner

data_processing: median normalization, CodeLink Expression Analysis

source_name: engineered cells that express dox-inducible bicistronic Pdx1-IRES-Ngn3, 1 ug/ml doxycycline treatment

label_protocol: see CodeLink Gene Expression System: Manual Labelled cRNA target Preparation

growth_protocol: Ainv18 ES cells, and their engineered derivatives, were maintained on irradiated feeders in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal calf serum (FCS), 10% ES cell conditioned medium, penicillin, streptomycin, 1.5 x 10^-4 M monothioglycerol (MTG; Sigma) and LIF (1% conditioned medium). Prior to induction of differentiation, cells were passaged 2 times on gelatin-coated plates in Iscove Modified Dulbecco Medium (IMDM) containing the same supplements mentioned above to deplete the population of feeder cells.  bTC6 cells were cultured in DMEM supplemented with 15% FCS.

extract_protocol: Qiagen RNeasy Mini protocol for isolation of total RNA from animal cells, with on column Dnase treatment.

treatment_protocol:
After depletion of feeder cells, Ainv18 ES cells were dissociated into single cell suspensions and replated (2-4x10^4 cells/ml in 60 mm low attachment petri dishes) into serum-free differentiation medium that contains 75% IMDM / 25% Ham’s F12 medium supplemented with 0.5% N2 and 1% B27 (with vitamin A/retinoic acid, “RA”), 1% penicillin/streptomycin, 0.05% bovine serum albumin, 2 mM glutamine, 0.5 mM ascorbic acid and 4.5 x 10^-4 M MTG.
On day 2, EBs were dissociated and replated at a density of 2-6x10^4 cells/ml in new 60 mm petri dishes using differentiation medium supplemented with activin A (50 ng/ml).  On day 4, EBs were dissociated and reaggregated at high density (5x10^5 cells/ml) in 24-well low-cluster dishes (Nunc) in differentiation medium supplemented with BMP4 (50 ng/ml), bFGF (10 ng/ml), and activin A (50 ng/ml), with or without Dox (1 ug/ml).  On day 6, EBs were replated in 12-well low-cluster dishes to obtain non-adherent floating EBs in Protocol #2 medium, with N2 and/or B27(+RA), without either ascorbic acid or MTG, and with or without Dox (1 ug/ml).

tag: biological replicate

tag: tissue type

tag: treatment

value: doxycycline


title: MAV 3h AMPH Rat ID MT6

description: MAV 3 hour AMPH #6


title: 5. beta TC6

description: cell line material

hyb_protocol: see CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

source_name: beta TC6 insulinoma cell line

value: beta TC6 insulinoma cell line


title: 6. beta TC6

description: cell line material


title: 7. whole beta islet

description: whole islet tissue

source_name: whole islet tissue

value: whole islet tissue


title: CP724,714-treated_MCF10HER2/E7_45hour

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

description:
The MCF-10HER-2/E7 cell line is derived from the nontransformed breast epithelial cell line MCF-10A and is transduced to stably overexpress the HER-2 and E7 oncogenes.
Replicate 1 of 1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

source_name: MCF-10HER-2/E7 cell line, CP724,714, 45 hours

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit.

growth_protocol: MCF-10HER-2/E7 cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), and hydrocortisone (1 µg/mL).

extract_protocol: RNA was extracted every three hours from parallel cultures with the QIAGEN Rneasy Plus kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanylizer and the Agilent RNA 6000 Nano Kit.

treatment_protocol: Cells were treated with the addition of 1uM CP724,714 (Pfizer Inc, Groton, CT) to culture media for 45 hours total.

tag: cell type

value: nontransformed breast epithelial cells stably overexpressing HER-2 and E7

tag: treatment time

value: 45 hours


title: CP724,714-treated_MCF10HER2/E7_36hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 36 hours

value: 36 hours


title: 10. E15.5 pancreas

description: whole pancreas tissue

source_name: whole pancreas tissue

value: whole pancreas tissue


title: 9. E15.5 pancreas

description: whole pancreas tissue


title: 4. Day 13 dox (+)

value: Ainv18 mouse ES cells engineered to overexpress activated Notch4 upon doxycycline treatment


title: 1. Day 13 dox (-)

source_name: engineered cells that express dox-inducible bicistronic Pdx1-IRES-Ngn3, no doxycycline treatment


title: CP724,714-treated_MCF10HER2/E7_42hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 42 hours

value: 42 hours


title: 8. whole beta islet

description: whole islet tissue


title: CP724,714-treated_MCF10HER2/E7_39hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 39 hours

value: 39 hours


title: CP724,714-treated_MCF10HER2/E7_27hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 27 hours

value: 27 hours


title: CP724,714-treated_MCF10HER2/E7_30hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 30 hours

value: 30 hours


title: CP724,714-treated_MCF10HER2/E7_12hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 12 hours

value: 12 hours


title: CP724,714-treated_MCF10HER2/E7_6hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 6 hours

value: 6 hours


title: CP724,714-treated_MCF10HER2/E7_18hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 18 hours

value: 18 hours


title: CP724,714-treated_MCF10HER2/E7_3hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 3 hours

value: 3 hours


title: CP724,714-treated_MCF10HER2/E7_0hour

source_name: MCF-10HER-2/E7 cell line, untreated

value: 0 hours


title: CP724,714-treated_MCF10HER2/E7_33hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 33 hours

value: 33 hours


title: CP724,714-treated_MCF10HER2/E7_24hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 24 hours

value: 24 hours


title: CP724,714-treated_MCF10HER2/E7_21hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 21 hours

value: 21 hours


title: 2. Day 13 dox (-)


title: CP724,714-treated_MCF10HER2/E7_15hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 15 hours

value: nontransformed breast epithelial cells stably overexpressing HER-2 and E7

value: 15 hours


title: Gefitinib-treated_MCF10HER2_33hour

description:
The MCF-10HER-2 cell line is derived from the nontransformed breast epithelial cell line MCF-10A and is transduced to stably overexpress the HER-2 oncogene.
Replicate 1 of 1.

source_name: MCF-10HER-2 cell line, gefitinib, 33 hours

growth_protocol: MCF-10HER-2 cells were cultured in Ham's F-12 medium supplemented with 0.1% bovine serum albumin, fungizone (0.5 µg/mL), gentamicin (5 µg/mL), ethanolamine (5 mmol/L), HEPES (10 mmol/L), transferrin (5 µg/mL), 3,3,'5-Triiodo-L-Thyronine (T3 ) (10 µmol/L), selenium (50 µmol/L), hydrocortisone (1 µg/mL), and 10 ng/ml epidermal growth factor (EGF).

treatment_protocol: Cells were treated with the addition of 0.5uM gefitinib to culture media for 45 hours total.

value: nontransformed breast epithelial cells stably overexpressing HER-2

value: gefitinib


title: Gefitinib-treated_MCF10HER2_45hour

source_name: MCF-10HER-2 cell line, gefitinib, 45 hours

value: 45 hours


title: CP724,714-treated_MCF10HER2/E7_9hour

source_name: MCF-10HER-2/E7 cell line, CP724,714, 9 hours

value: 9 hours