title: Cortex Replicate 3

description: Biological replicate 1 of 3. Naive mice

tag: tissue


title: WholeFish_Control_rep2D4

status: Public on Sep 01 2015

type: RNA

city: Davis

first: Ken

last: Jeffries

state: CA

address: One Shields Avenue

country: USA

institute: UC Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >13.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2.5 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

molecule: total RNA

organism: Hypomesus transpacificus

source_name: Whole Fish, Control

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrophotometer.

growth_protocol: Hypomesus transpacificus were allowed 24 hours to acclimatize to holding conditions at the Aquatic Toxicology Laboratory at the University of California Davis.

extract_protocol: At the termination of the 96 hour exposure period, fish were sacrificed by a lethal dose of MS-222 and whole fish were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Whole fish from the exposures were homogenized using a pestle in 1 ml of Trizol reagent following manufacturer’s protocols, which was followed by RNA Cleanup using RNeasy columns (Qiagen) with on-column DNAse digestion. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrophotometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Hypomesus transpacificus were exposed for 96 hours to measured concentrations of 0.69, 1.37, 2.56, 4.84 ug/L of permethrin, along with a control group handled identically to the other treatments.

tag: treatment

value: Control


title: WholeFish_0.025mg/L_repB8

description: Sample name: B8 - 0.025

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 80 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Menidia beryllina

source_name: Whole fish, 0.025 mg/L ibuprofen exposure

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Menidia beryllina were allowed four days to acclimatize to holding conditions at the Aquatic Toxicology Laboratory at the University of California Davis.

extract_protocol: At the termination of the 14 d exposure period, fish were sacrificed by a lethal dose of MS-222 and whole fish were immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Whole fish from the 14 d exposures were homogenized using a pestle in 1 ml of Trizol reagent following manufacturer’s protocols. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Menidia beryllina were exposed for 14 d to nominal concentrations of 0.025, 0.25 and 2.5 mg/L of ibuprofen, along with a control group handled identically to the other treatments.

value: ibuprofen

tag: treatment dose

value: whole fish


title: WholeFish_0.69 ug/L_rep9B1

source_name: Whole Fish, 0.69 ug/L

value: 0.69 ug/L permetrhin


title: siDDSR3,Biological Replicate3

city: Bethesda

first: Vivek

last: Sharma

state: MD

address: 41 Library Drive

department: CCR

institute: NCI

description: Gene expression data upon DDSR1 knockdown

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files from Affymetrix were imported into Partek Genomics Suite (Partek Incorporated) and RMA normalized.  Differentially expressed genes (DEG) were defined as genes having ≥ 1.5-fold change of expression in pair-wise comparison P value <0.05, unless otherwise stated (unadjusted p value).

label: Biotin

organism: Homo sapiens

source_name: hTERT immortalised Human Fibroblast cells

label_protocol: standard Affymetrix protocol

growth_protocol: Human Fibroblast cells were grown in 10 MEM supplemented with Penn/Strep and Glutamine

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen)

treatment_protocol: hTERT immotalised Human Fibroblast cells were transfected a non specific siRNA or siRNA against DDSR1,72 hours post transfection RNA was isolated and process for Microarray

tag: cell line

value: hTERT immortalised

tag: transfection

value: siRNA against DDSR1


title: siDDSR2,Biological Replicate2


title: WholeFish_0.025mg/L_repC3

description: Sample name: C3 - 0.025


title: WholeFish_0.69 ug/L_rep9A2

value: 0.69 ug/L permethrin


title: siNS1,Biological Replicate1

description: Gene expression data upon transcfection with siNS

value: non specific siRNA


title: siDDSR1,Biological Replicate1


title: siNS3,Biological Replicate2


title: WholeFish_0.25mg/L_repD2

description: Sample name: D2 - 0.25

source_name: Whole fish, 0.25 mg/L ibuprofen exposure


title: WholeFish_Control_rep2C1


title: Cortex Replicate 2

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description: Biological replicate 1 of 3. Naive mice

hyb_protocol: All the steps of hybridization, washing, scanning and feature extraction were performed following the Agilent protocols for methylated DNA immunoprecipitation analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B. Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: The extracted intensities were then analyzed using the R software environment for statistical computing (R Development Core Team, 2007). Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization (Bolstad et al., 2003) under the assumption that all samples have identical overall methylation levels.

molecule: genomic DNA

organism: Mus musculus

source_name: pooled DNA of frontal cortex

label_protocol: The amplified input and bound fractions were labeled for microarray hybridization with either Cy3-dUTP or Cy5-dUTP respectively using the SureTag Complete DNA Labeling Kit (Agilent) following the manufacturer’s instructions.

growth_protocol: Naïve male C57BL/6 mice of 2 months old

extract_protocol: Triplicates of 2μg of frontal cortex DNA pools of 3 mice were sonicated. Methylated DNA was then immunoprecipitated with 10 μg of anti-5methylCytosine antibody (Eurogentec, Cat. # BI-MECY) that does not recognize DNA hydroxymethylation. The DNA-antibody complex was immuno-precipitated with 50 ul of protein G. The input and bound fractions were then purified and amplified using the Whole Genome Amplification kit (Sigma).

tag: strain

tag: Sex

value: male

tag: age

value: 2 months

value: frontal cortex

tag: molecule subtype

value: input DNA

value: immunoprecipitated DNA


title: WholeFish_0.025mg/L_repB3

description: Sample name: B3 - 0.025


title: WholeFish_0.25mg/L_repA3

description: Sample name: A3 - 0.25


title: WholeFish_0.025mg/L_repA2

description: Sample name: A2 - 0.025


title: WholeFish_4.84 ug/L_rep12A1

source_name: Whole Fish, 4.84 ug/L

value: 4.84 ug/L permetrhin


title: WholeFish_0.025mg/L_repA3

description: Sample name: A3 - 0.025


title: WholeFish_Control_repA5

description: Sample name: A5 - Control

source_name: Whole fish, Control


title: WholeFish_0.25mg/L_repC8

description: Sample name: C8 - 0.25


title: WholeFish_Control_rep2B1


title: WholeFish_Control_repC8

description: Sample name: C8 - Control


title: WholeFish_Control_repC7

description: Sample name: C7 - Control


title: WholeFish_Control_rep2A1


title: WholeFish_Control_repD7

description: Sample name: D7 - Control


title: WholeFish_Control_repB4

description: Sample name: B4 - Control


title: WholeFish_Control_repB6

description: Sample name: B6 - Control


title: Pten KO DMSO, biological rep3

status: Public on Aug 31 2015

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: gene expression data from Pten KO HD-ΔPest NOTCH1 induced leukemias treated with DMSO

hyb_protocol: we hybridized on GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix) according to the manufacturer's protocol.

scan_protocol: Standard scan according to manufacturer's protocol

data_processing: Expression values were normalized with GC-RMA using the open-source Bioconductor software (www.bioconductor.org)

label: biotin

source_name: Pten KO NOTCH1 induced tumors treated with DMSO

label_protocol: RNA (1 µg) from Pten-positive and Pten-deleted leukemic cells treated with vehicle or DBZ was amplified and labeled using 3' IVT Express Kit (Affymetrix)

growth_protocol: We transplanted leukemia cells from primary recipients into secondary recipients, which were treated with vehicle or tamoxifen (to induce Pten deletion). We monitored the mice until they showed more than 70% of GFP positive cells in peripheral blood

extract_protocol: We isolated RNA from leukemic cells from spleen samples collected from mice acutely treated with Vehicle or DBZ using RNeasy plus mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Mice were treated twice, 16 hours apart, with vehicle only or DBZ (5 mg kg-1). 4 hours after the second treatment, mice were sacrificed and splenic samples were collected and subsequently snap-frozen

value: leukemia

tag: genotype

value: Pten KO HD-deltaPest NOTCH1


title: UA-10m

city: Cambridge

first: Tsute

last: Chen

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

description: treated with competence stimulating peptides (CSP) for 10 min

hyb_protocol: RNase-free BSA was added to the pre-hybridization solution and salmon sperm DNA was included in both pre-hybridization and hybridization solutions to block non-specific binding of RNA molecules  to the probes and surface of the microarray slides. Hybridization was conducted at a temperature of 42°C in the presence of 25% formamide.

scan_protocol: NimbleScan v2.5 software was used for spot feature extraction from the scanned images,

data_processing: Raw data were processed using a method based on a hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data (Yu, et al Bioinformatics 2010 26:1423-30)

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans UA159 wild type

label_protocol: RNA was fragmented and labelled using Mirus label IT µArray Cy3 labeling kit (Mirus), also described by Yu, et al BMC Molecular Biology 2011, 12:3

growth_protocol: Cultures of S. mutans were grown in TryptoneSoy Broth (TSB; Oxoid) at 37  ̊C in 5% CO2 and stored at -80  ̊C in TSB supplemented with 15%  glycerol

extract_protocol: The pellets were lysed with mutanolysin/lysozyme, followed by RNA extraction (mirVana miRNA isolation kit; Ambion). This kit was used to enhance the recovery rate of short transcripts (down to 10 nucleotides). The samples were then treated with Turbo DNase (Ambion), and  analysed for quality using Bioanalyzer. MICROBExpress kit was then used for mRNA enrichment (Ambion).

treatment_protocol: RNA samples were from the wild type and the comS deletion mutant, grown in the presence or absence of CSP in 100-ml volumes of TSB as described in the transformation assay.  For the wild type, culture samples were collected at 10 min and 100 min after CSP addition, and for the comS deletion mutant at 100 min. At each time, samples without CSP were included as controls. Two independent biological replicates were obtained for each condition, giving a total of 12 samples. Immediately after centrifugation (9000 g, 2,5 min, 4°C), the supernatants were discarded and the pellets frozen immediately  in liquid nitrogen.

tag: genotype/variation

value: wild type


title: WholeFish_0.025mg/L_repB1

description: Sample name: B1 - 0.025


title: Pten KO DBZ, biological rep3

description: gene expression data from Pten KO HD-ΔPest NOTCH1 induced leukemias treated with DBZ

source_name: Pten KO NOTCH1 induced tumors treated with DBZ


title: Pten WT DBZ, biological rep1

description: gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias treated with DBZ

source_name: Pten wild type NOTCH1 induced tumors treated with DBZ

value: Pten wild type HD-deltaPest NOTCH1


title: Pten KO DMSO, biological rep1


title: Lplantarum_4hrs

city: Atlanta

first: Rheinallt

middle: M

last: Jones

state: Georgia

address: 615 Michael

department: Pediatrics

institute: Emory Univeristy

hyb_protocol: Affymetrix GeneChip microarrays were hybridized according to standard manufacturer's protocols rotating at 60 rpm at 45 deg C for 16 hours and washed on an Affymetrix Fluidic Station

scan_protocol: Affymetrix GeneChip microarrays were scanned on a GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: CEL files were normalized using RMA normalization package in R using default settings

organism: Drosophila melanogaster

source_name: 40 midguts (monoassociated with Lactobacillus plantarum for 4 hours)

label_protocol: RNA was labeled using the Affymetrix GeneChip Eukaryotic Double Strand Whole Transcript Protocol for Arabadopsis, C. elegans, Drosophila, and Yeast Tiling Arrays

growth_protocol: Germ-free Drosophila

extract_protocol: RNA from forty dissected Drosophila midguts per sample was prepared using TRIzol reagent (Invitrogen, Carlsbad, California, USA), and cleaned using RNeasy kit (Qiagen) total RNA clean up protocol.

treatment_protocol: To assess gene expression associated with L. plantarum–induced cytoprotection, we employed microarray analysis on dissected larval midgut tissue following L. plantarum ingestion by germ-free Drosophila. Gene ontology analysis identified highly represented transcripts in L. plantarum fed larva (compared to germ-free)

tag: developmental stage

value: 3rd instar larvae

value: midgut


title: Pten WT DBZ, biological rep3


title: Pten WT DBZ, biological rep2


title: Pten KO DBZ, biological rep2


title: Pten KO DBZ, biological rep1


title: PBS_4hrs

source_name: 40 midguts (sterile PBS for 4 hours)


title: Pten WT DMSO, biological rep2

description: gene expression data from Pten wild type HD-ΔPest NOTCH1 induced leukemias treated with DMSO

source_name: Pten wild type NOTCH1 induced tumors treated with DMSO


title: Pten KO DMSO, biological rep2


title: Pooled CD11b+Gr1+ splenocytes from 3 healthy L2-Cre;p120+/f mice, biological rep3

city: Philadelphia

first: Anil

middle: K.

last: Rustgi

state: PA

address: 421 Curie Boulevard

department: Gastroenterology

institute: University of Pennsylvania

description:
Con_03
Forelimbs from Shh mutants 964 and 965

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. 5.5 micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Exon 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal. Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

data_processing:
All samples were carried out by doing background subtraction, normalization and summarizing probe sets from Affymetrix expression microarrays using Affymetrix Power tools (APT). The data were processed with RMA (Robust Multichip Average) and Probe Logarithmic Intensity Error (PLIER) Estimation methods in APT.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: control pool 3

label_protocol: The cDNA were fragmented, assessed by Bioanalyzer, and biotinylated  using terminal transferase end labeling.

growth_protocol: spleens were extracted from experimental and control mice

extract_protocol: Splenocytes were isolated by FACS sorting (CD11b+Gr1+ cells were collected) directly into the QIAzol lysis reagent (QIAGEN), and total RNA extraction was carried out according to the manufacturer's protocol.  Quality control check of the total RNA samples was performed using Agilent Bioanalyzer and Nanodrop spectrophotometry. All protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA.

treatment_protocol: not applicable

value: spleen

value: Shh -/-

value: mixed C57BL/6x129 background


title: Pten WT DMSO, biological rep3


title: serous 171

status: Public on Aug 13 2015

city: Manchester

first: Sacha

last: Howell

address: Oglesby Cancer Research Centre

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner settings.

data_processing: Probes were removed if they had less than 95% coverage across samples (as defined by detection p-value greater than 0.05). Probes with non-unique mappings and which map to SNPs were removed. Probes mapping to sex chromosomes were also removed.

label: Cy5 and Cy3

source_name: serous tumor sample

label_protocol: Standard Illumina Protocol for Infinium 450k Chip.

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions.

tag: histology

value: serous

tag: Stage

tag: grade


title: UA+100m

description: treated with competence stimulating peptides (CSP) for 100 min


title: Pooled CD11b+Gr1+ splenocytes from 3 healthy L2-Cre;p120+/f mice, biological rep2

description:
Con_02
Forelimbs from Shh mutants 954 and 955

source_name: control pool 2


title: serous 166


title: serous 169


title: clear cell 13

source_name: clear cell tumor sample

value: clear cell


title: undifferentiated 9

source_name: undifferentiated tumor sample

value: undifferentiated


title: serous 167


title: serous 168


title: serous 164


title: Pooled CD11b+Gr1+ splenocytes from 3 healthy L2-Cre;p120+/f mice, biological rep1

description:
Con_01
Forelimbs from Shh mutants 946 and 947

source_name: control pool 1


title: serous 163


title: serous 162


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep6

description:
Exp_06
posterior 2/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #11789

value: wild-type


title: clear cell 14


title: UA+10m

value: with competence stimulating peptides (CSP) for 10 min


title: 65-100m

source_name: Streptococcus mutans UA159 ∆comS::spc; SpcR

value: comS deletion mutant

value: with competence stimulating peptides (CSP) for 100 min


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep2

description:
Exp_02
anterior 1/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #1681


title: Pten WT DMSO, biological rep1


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep3

description:
Exp_03
anterior 1/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #1706


title: undifferentiated 8


title: clear cell 12


title: serous 170


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep4

description:
Exp_04
posterior 2/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #1780


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep5

description:
Exp_05
posterior 2/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #1808


title: 65+100m


title: UA-100m

source_name: Streptococcus mutans UA159 wild type


title: mucinous 9

source_name: mucinous tumor sample

value: mucinous


title: mucinous 8


title: endometrioid 18

source_name: endometrioid tumor sample

value: endometrioid


title: clear cell 11


title: mucinous 7


title: serous 158


title: serous 160


title: serous 156


title: serous 159


title: serous 157


title: serous 155


title: clear cell 10


title: endometrioid 17


title: undifferentiated 7


title: endometrioid 16


title: serous 154


title: serous 153


title: serous 152


title: undifferentiated 6


title: mucinous 6


title: undifferentiated 4


title: serous 151


title: undifferentiated 5


title: serous 165


title: serous 161


title: endometrioid 15


title: undifferentiated 3


title: clear cell 9


title: clear cell 8


title: serous 150


title: clear cell 6


title: clear cell 7


title: serous 149


title: clear cell 5


title: serous 148


title: clear cell 4


title: CD11b+Gr1+ splenocytes from tumor-bearing L2-Cre;p120f/f mouse, biological rep1

description:
Exp_01
anterior 1/3 of forelimb pooled litter

source_name: tumor-bearing L2-Cre;p120f/f mouse #1660


title: serous 144


title: serous 145


title: serous 146


title: serous 142


title: serous 141


title: clear cell 3


title: serous 143


title: serous 139


title: mucinous 5


title: serous 138


title: serous 140


title: endometrioid 14


title: serous 135


title: serous 136


title: serous 137


title: serous 134


title: serous 133


title: serous 132


title: endometrioid 13


title: serous 130


title: serous 147


title: serous 129


title: serous 131


title: serous 128


title: endometrioid 12


title: serous 124


title: serous 125


title: serous 126


title: serous 123


title: serous 122


title: mucinous 4


title: serous 120


title: serous 119


title: serous 118


title: serous 117


title: serous 114


title: serous 113


title: serous 112


title: serous 111


title: serous 110


title: mucinous 3


title: serous 116


title: serous 109


title: mucinous 2


title: clear cell 2


title: endometrioid 8


title: endometrioid 9


title: serous 106


title: endometrioid 10


title: serous 107


title: serous 108


title: serous 105


title: serous 127


title: serous 104


title: serous 103


title: endometrioid 11


title: serous 121


title: serous 102


title: endometrioid 7


title: serous 101


title: serous 115


title: mucinous 1


title: serous 100


title: serous 98


title: serous 96


title: serous 95


title: serous 97


title: serous 99


title: serous 94


title: serous 91


title: serous 92


title: serous 93


title: serous 88


title: serous 89


title: undifferentiated 2


title: serous 87


title: serous 90


title: serous 84


title: serous 81


title: serous 83


title: serous 80


title: serous 82


title: serous 79


title: serous 77


title: serous 78


title: endometrioid 5


title: serous 76


title: serous 75


title: serous 73


title: serous 74


title: serous 69


title: serous 68


title: serous 86


title: serous 85


title: serous 65


title: endometrioid 4


title: serous 71


title: serous 64


title: serous 62


title: serous 61


title: serous 72


title: endometrioid 6


title: undifferentiated 1


title: serous 66


title: serous 67


title: serous 56


title: serous 70


title: serous 59


title: serous 58


title: serous 55


title: serous 52


title: serous 53


title: serous 51


title: serous 54


title: serous 50


title: serous 49


title: serous 48


title: serous 46


title: serous 63


title: serous 47


title: serous 44


title: serous 43


title: serous 45


title: serous 41


title: serous 36


title: serous 40


title: serous 35


title: serous 39


title: serous 38


title: serous 34


title: serous 32


title: endometrioid 3


title: serous 33


title: serous 31


title: serous 29


title: serous 28


title: endometrioid 2


title: serous 42


title: serous 26


title: clear cell 1


title: serous 25


title: serous 23


title: serous 24


title: serous 37


title: serous 30


title: serous 27


title: serous 22


title: serous 20


title: serous 13


title: serous 15


title: serous 21


title: serous 18


title: serous 19


title: serous 14


title: serous 17


title: serous 16


title: serous 10


title: serous 8


title: serous 7


title: serous 5


title: serous 4


title: serous 9


title: serous 6


title: serous 3


title: serous 1


title: endometrioid 1


title: serous 12


title: serous 11


title: Modified ChIP against H3K4me1

status: Public on May 15 2015

type: SRA

city: Rotterdam

first: Raymond

middle: A

last: Poot

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus MC

library_source: genomic

data_processing:
Filtering against low complexity reads using prinseq-lite using options -lc_method dust and -lc_treshhold 7
mapping reads using bowtie 0.12.7 the options -n 2 -l 36 -e 70 -k 1 --best
Picard-tools-1.81 MarkDuplicates was used to remove the duplicates from the sam/bam file
MACS 1.4.2 was used for generating wig file using default settings
Genome_build: mm9

growth_protocol: Mouse embryonic stem cell line CGR8 was grown on gelatin coated dishes without feeders. Cells were cultured in Glasgow minimal essential medium supplemented with leukemia inhibitory factor, 15% fetal bovine serum, 0.25% sodium bicarbonate, 1mM glutamine, 1mM sodium pyruvate, nonessential amino acids, 50 μM beta-mercaptoethanol, and penicillin-streptomycin

extract_protocol: For each histone modification ChIP, 300x10^6 ESCs were used. For chromatin preparation, cells were washed on plate three times with PBS and incubated with 2 mM Disuccinimidyl glutarate (DSG, Thermo Scientific) in PBS for 45 min at room temperature. Subsequently, ESCs were washed in PBS three times, 0.1 volume of 11% formaldehyde (Merck) in 50 mM Hepes-KOH pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA was added, mixed and incubated for 12 min at room temperature, washed two times in 4 °C PBS and collected by centrifugation. All subsequent steps were performed on ice with pre-cooled buffers. Cell lysis was performed as described43. In brief, cells were collected and resuspended in LB1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). After 10 minutes incubation, cells were pelleted by centrifugation and resuspended in LB2 (10 mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). After 10 min incubation, cells were pelleted and resuspended in 3 ml freshly prepared LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) and sonicated on a Soniprep 150 (MSE), 27 cycles 15 s on, 45 s off on amplitude 7. After sonication, enriched DNA fragment size was confirmed to be between 200 and 1000 bp.  300 x 106 ESCs yielded approximately 10 mg chromatin (as measured by DNA content). To prevent immunoglobin elution and subsequent interference with the mass spectrometry analysis, 50 µg antibodies were crosslinked to 500 µl Protein A magnetic bead solution (15 mg beads, Life Technologies) with Dimethyl Pimelimidate (Sigma). Cross-linked antibody-bead complexes were equilibrated in LB3 buffer and subsequently blocked with 0.5 mg/ml BSA (New England Biolabs) and 0.2 mg/ml sonicated salmon sperm DNA (Stratagene) for one hour. The antibody-bead mixture was rotated overnight with approximately 10 mg chromatin at 4°C. Beads were transferred to 1.5 ml no stick tubes (Alpha laboratories) and washed five times 5 minutes in RIPA buffer (50 mM Hepes-KOH pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate).  Beads were washed once with 1 ml T50E10N50. Beads were eluted in 210 ul elution buffer and incubated for 30 minutes at 65 °C. Beads were discarded and supernatant was  incubated for 8 hours at 65 °C for decrosslinking. Subsequently the DNA was purified by two rounds of phenol extraction. DNA pellet was resolved in 60 ul of water. The library was prepared according to the illumina protocol. Briefly 10 ng of DNA ChIP material was end-repaired, ligated to adapters, size selected on gel (200 bp +-25 bp range) and PCR amplified using Phusion polymerase with 30 seconds incubation at 98 ᴼC, 18 cycles of 10 second 98 ᴼC , 30 seconds 65 ᴼC, 30 seconds 72ᴼC. Followed with 5 minutes of final extension at 72 ᴼC. Cluster generation was performed using the illumina genome analyzer II platform. Step-by-step protocol was uploaded to http://www.nature.com/protocolexchange/.

treatment_protocol: wt

tag: cell type

value: Embryonic Stem Cell

tag: chip antibody

value: H3K4me1 (ab8895, Abcam)


title: serous 2


title: Huh-7 untreated

status: Public on Jul 30 2015

city: Heidelberg

first: Volker

last: Lohmann

address: Im Neuenheimer Feld 345

department: Molecular Virology

country: Germany

institute: University of Heidelberg

description: MF7_Huh7 naiv Ko

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the Affymetrix Gene Expression Analysis Technical Manual.

scan_protocol: Arrays were scanned in the GeneArray scanner 2500 (Agilent, Palo Alto, CA)

data_processing: The data were analyzed with MAS 5.0 using Affymetrix default analysis settings and global scaling to a target intensity of 1000. RMA analysis was done by RMAexpress software

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Gene Expression Analysis Technical Manual starting from 13.5µg total RNA. Double-stranded cDNA was synthesized using an T7-oligo d(T)24 primer [5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAGA-(dT24)-3'] (MWG Biotech, Munich, Germany). After generation of double-stranded cDNA from the first-strand cDNA, biotinylated cRNA was synthesized by in vitro transcription using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, New York, NY).

growth_protocol: Huh6 and Huh7 cell lines were grown under standard cell culture conditions in DMEM supplemented with 10% FCS, NEA, L-Glut and Pen/Strep

extract_protocol: Total RNA was prepared using a GITC-based protocol (Chomczynski et al., 1987).

treatment_protocol: Cell lines were treated with 1000 IU/ml interferon-gamma for 24h or remained untreated

value: none (untreated control)


title: Huh6 IFNalpha

source_name: Huh6 cells, treated with IFNalpha

value: 1000 IU/ml IFNalpha


title: Huh6 IFNgamma

description: MF3_Huh6 naiv IFNg

source_name: Huh6_treated with IFNgamma

value: 1000 IU/ml IFNgamma for 24hrs


title: Huh-7 IFNgamma

description: MF9_Huh7 naiv IFNg

source_name: Huh-7_treated with IFNgamma


title: 037_Adenoma

status: Public on Feb 03 2015

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description:
Sample name: 037AD1
Patient 037 adenoma tissue

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Summarised data were exported from BeadStudio without normalisation and imported into R. After removing arrays with poor signal-to-noise ratio, remaining arrays were background corrected and normalised using the neqc method in the limma Bioconductor package.

source_name: Colon primary tissue

label_protocol: Standard Illumina protocol

growth_protocol: not applicable

extract_protocol: according to AllPrep kit from Qiagen

tag: gender

value: Male

tag: patient

tag: tissue

value: adenoma tissue


title: 041_Adenoma

description:
Sample name: 041AD1
Patient 041 adenoma tissue


title: Huh6 untreated

description: MF1_Huh6 naiv Ko

tag: cell line

tag: treatment


title: Huh-7 IFNalpha

source_name: Huh-7 cells, treated with IFNalpha


title: 009_Adenoma

description:
Sample name: 009AD5
Patient 009 adenoma tissue

value: Female


title: 038_tumor

description:
Sample name: 038T1
Patient 038 adenocarcinoma (tumor) tissue

value: adenocarcinoma (tumor) tissue


title: 011_tumor

description:
Sample name: 011T1
Patient 011 adenocarcinoma (tumor) tissue


title: 042_Adenoma

description:
Sample name: 042AD1
Patient 042 adenoma tissue


title: 042_tumor

description:
Sample name: 042T1
Patient 042 adenocarcinoma (tumor) tissue


title: 005_tumor

description:
Sample name: 005T1
Patient 005 adenocarcinoma (tumor) tissue


title: 041_tumor

description:
Sample name: 041T1
Patient 041 adenocarcinoma (tumor) tissue


title: 023_Adenoma

description:
Sample name: 023AD3
Patient 023 adenoma tissue


title: 002_tumor

description:
Sample name: 002T1
Patient 002 adenocarcinoma (tumor) tissue


title: 014_tumor

description:
Sample name: 014T1
Patient 014 adenocarcinoma (tumor) tissue


title: 007_tumor

description:
Sample name: 007T1
Patient 007 adenocarcinoma (tumor) tissue


title: 038_Normal_Close

description:
Sample name: 038NCOL
Patient 038 normal tissues taken close to tumor

value: normal tissues taken away (20cm) from the tumor


title: 039_tumor

description:
Sample name: 039T1
Patient 039 adenocarcinoma (tumor) tissue


title: 029_tumor

description:
Sample name: 029T1
Patient 029 adenocarcinoma (tumor) tissue


title: 020_Adenoma

description:
Sample name: 020AD1
Patient 020 adenoma tissue


title: 034_tumor

description:
Sample name: 034T1
Patient 034 adenocarcinoma (tumor) tissue


title: 039_Adenoma

description:
Sample name: 039AD1
Patient 039 adenoma tissue


title: 002_Normal_Close

description:
Sample name: 002NC
Patient 002 normal tissues taken close to tumor


title: 016_tumor

description:
Sample name: 016T1
Patient 016 adenocarcinoma (tumor) tissue


title: 017_tumor

description:
Sample name: 017T1
Patient 017 adenocarcinoma (tumor) tissue


title: serous 60

source_name: serous tumor sample

value: serous


title: serous 57


title: 001_tumor

description:
Sample name: 001T1
Patient 001 adenocarcinoma (tumor) tissue


title: CRC2_048_Adenoma2

description:
Sample name: CRC2_048Ad2
Patient 048 adenoma tissue

hyb_protocol: followed the Infinium-II-Assay guide

scan_protocol: Slides were scanned on an iScan

data_processing: BeadStudio was used to obtain the raw Signal_A and Signal_B values which were then read into R and processed using a custom script. Subsequently, locus methylation was calculated as an M value (log ratio of the Methylated versus Unmethylated channels) and separate quartile normalisation was applied to the probes annotated in the green or red channel.

label_protocol: Bisulfite conversion used the EZ-Gold kit (Zymo)

extract_protocol: according to Qiagen AllPrep kit

value: female


title: 001_Normal_Close

description:
Sample name: 001NC
Patient 001 normal tissues taken close to tumor


title: CRC2_048_Adenoma1

description:
Sample name: CRC2_048Ad1
Patient 048 adenoma tissue


title: CRC2_046_Tumour

description:
Sample name: CRC2_046T1
Patient 046 adenocarcinoma (tumour) tissue

value: male

value: adenocarcinoma (tumour) tissue


title: CRC2_049_Normal Close

description:
Sample name: CRC2_049Ncol
Patient 049 normal tissues taken close to tumour

value: normal tissues taken close to tumour


title: 001_Normal_Away

description:
Sample name: 001NA
Patient 001 normal tissues taken away (20cm) from the tumor


title: CRC2_045_Tumour

description:
Sample name: CRC2_045T1
Patient 045 adenocarcinoma (tumour) tissue


title: CRC2_047_Tumour

description:
Sample name: CRC2_047T1
Patient 047 adenocarcinoma (tumour) tissue


title: CRC2_045_Normal Close

description:
Sample name: CRC2_045Ncol
Patient 045 normal tissues taken close to tumour


title: CRC2_047_Adenoma1

description:
Sample name: CRC2_047AD1
Patient 047 adenoma tissue


title: CRC2_049_Tumour

description:
Sample name: CRC2_049T1
Patient 049 adenocarcinoma (tumour) tissue


title: CRC2_049_Adenoma1

description:
Sample name: CRC2_049Ad1
Patient 049 adenoma tissue


title: CRC2_048_Normal Close

description:
Sample name: CRC2_048Ncol
Patient 048 normal tissues taken close to tumour


title: CRC2_047_Normal Close

description:
Sample name: CRC2_047NCOL
Patient 047 normal tissues taken close to tumour


title: CRC2_046_Normal Close

description:
Sample name: CRC2_046Ncol
Patient 046 normal tissues taken close to tumour


title: CRC2_046_Adenoma1

description:
Sample name: CRC2_046Ad1
Patient 046 adenoma tissue


title: CRC2_044_Normal Close

description:
Sample name: CRC2_044NC
Patient 044 normal tissues taken close to tumour


title: CRC2_044_Normal Away

description:
Sample name: CRC2_044NA
Patient 044 normal tissues taken away (20cm) from the tumour


title: CRC2_045_Adenoma1

description:
Sample name: CRC2_045Ad1
Patient 045 adenoma tissue


title: CRC2_043_Tumour

description:
Sample name: CRC2_043T1
Patient 043 adenocarcinoma (tumour) tissue


title: CRC2_042_Normal Away

description:
Sample name: CRC2_042NA
Patient 042 normal tissues taken away (20cm) from the tumour


title: CRC2_044_Tumour

description:
Sample name: CRC2_044T1
Patient 044 adenocarcinoma (tumour) tissue


title: CRC2_041_Tumour

description:
Sample name: CRC2_041T1
Patient 041 adenocarcinoma (tumour) tissue


title: CRC2_042_Tumour

description:
Sample name: CRC2_042T1
Patient 042 adenocarcinoma (tumour) tissue


title: CRC2_042_Normal Close

description:
Sample name: CRC2_042NC
Patient 042 normal tissues taken close to tumour


title: CRC2_044_Adenoma1

description:
Sample name: CRC2_044AD1
Patient 044 adenoma tissue


title: CRC2_043_Normal Close

description:
Sample name: CRC2_043Ncol
Patient 043 normal tissues taken close to tumour


title: CRC2_041_Normal Close

description:
Sample name: CRC2_041NC
Patient 041 normal tissues taken close to tumour


title: CRC2_042_Adenoma1

description:
Sample name: CRC2_042Ad1
Patient 042 adenoma tissue


title: CRC2_043_Adenoma1

description:
Sample name: CRC2_043Ad1
Patient 043 adenoma tissue


title: CRC2_039_Normal Close

description:
Sample name: CRC2_039Ncol
Patient 039 normal tissues taken close to tumour


title: CRC2_039_Tumour

description:
Sample name: CRC2_039T1
Patient 039 adenocarcinoma (tumour) tissue


title: CRC2_040_Normal Close

description:
Sample name: CRC2_040NC
Patient 040 normal tissues taken close to tumour


title: CRC2_040_Tumour

description:
Sample name: CRC2_040T1
Patient 040 adenocarcinoma (tumour) tissue


title: CRC2_037_Normal Close

description:
Sample name: CRC2_037NC
Patient 037 normal tissues taken close to tumour


title: CRC2_039_Adenoma1

description:
Sample name: CRC2_039Ad1
Patient 039 adenoma tissue


title: CRC2_037_Adenoma1

description:
Sample name: CRC2_037AD1
Patient 037 adenoma tissue


title: CRC2_041_Adenoma1

description:
Sample name: CRC2_041AD1
Patient 041 adenoma tissue


title: CRC2_038_Adenoma1

description:
Sample name: CRC2_038Ad1
Patient 038 adenoma tissue


title: CRC2_038_Tumour

description:
Sample name: CRC2_038T1
Patient 038 adenocarcinoma (tumour) tissue


title: CRC2_038_Normal Close

description:
Sample name: CRC2_038Ncol
Patient 038 normal tissues taken close to tumour


title: CRC2_040_Adenoma1

description:
Sample name: CRC2_040AD1
Patient 040 adenoma tissue


title: CRC2_035_Tumour

description:
Sample name: CRC2_035T1
Patient 035 adenocarcinoma (tumour) tissue


title: CRC2_040_Normal Away

description:
Sample name: CRC2_040NA
Patient 040 normal tissues taken away (20cm) from the tumour


title: CRC2_037_Tumour

description:
Sample name: CRC2_037T1
Patient 037 adenocarcinoma (tumour) tissue


title: CRC2_041_Normal Away

description:
Sample name: CRC2_041NA
Patient 041 normal tissues taken away (20cm) from the tumour


title: CRC2_037_Normal Away

description:
Sample name: CRC2_037NA
Patient 037 normal tissues taken away (20cm) from the tumour


title: CRC2_035_Normal Close

description:
Sample name: CRC2_035NC
Patient 035 normal tissues taken close to tumour


title: CRC2_034_Tumour

description:
Sample name: CRC2_034T1
Patient 034 adenocarcinoma (tumour) tissue


title: CRC2_029_Normal Close

description:
Sample name: CRC2_029NC
Patient 029 normal tissues taken close to tumour


title: CRC2_035_Adenoma1

description:
Sample name: CRC2_035AD1
Patient 035 adenoma tissue


title: CRC2_034_Normal Close

description:
Sample name: CRC2_034Ncol
Patient 034 normal tissues taken close to tumour


title: CRC2_023_Normal Away

description:
Sample name: CRC2_023NA
Patient 023 normal tissues taken away (20cm) from the tumour


title: CRC2_029_Tumour

description:
Sample name: CRC2_029T1
Patient 029 adenocarcinoma (tumour) tissue


title: CRC2_035_Normal Away

description:
Sample name: CRC2_035NA
Patient 035 normal tissues taken away (20cm) from the tumour


title: CRC2_023_Tumour

description:
Sample name: CRC2_023T1
Patient 023 adenocarcinoma (tumour) tissue


title: CRC2_020_Tumour

description:
Sample name: CRC2_020T1
Patient 020 adenocarcinoma (tumour) tissue


title: CRC2_023_Normal Close

description:
Sample name: CRC2_023NC
Patient 023 normal tissues taken close to tumour


title: CRC2_020_Normal Away

description:
Sample name: CRC2_020NA
Patient 020 normal tissues taken away (20cm) from the tumour


title: CRC2_029_Normal Away

description:
Sample name: CRC2_029NA
Patient 029 normal tissues taken away (20cm) from the tumour


title: CRC2_020_Normal Close

description:
Sample name: CRC2_020NC
Patient 020 normal tissues taken close to tumour


title: CRC2_023_Adenoma1

description:
Sample name: CRC2_023Ad1
Patient 023 adenoma tissue


title: CRC2_020_Adenoma1

description:
Sample name: CRC2_020Ad1
Patient 020 adenoma tissue


title: CRC2_014_Adenoma1

description:
Sample name: CRC2_014Ad1
Patient 014 adenoma tissue


title: CRC2_010_Tumour

description:
Sample name: CRC2_010T1
Patient 010 adenocarcinoma (tumour) tissue


title: CRC2_017_Tumour

description:
Sample name: CRC2_017T1
Patient 017 adenocarcinoma (tumour) tissue


title: CRC2_029_Adenoma1

description:
Sample name: CRC2_029Ad1
Patient 029 adenoma tissue


title: CRC2_017_Normal Away

description:
Sample name: CRC2_017NA
Patient 017 normal tissues taken away (20cm) from the tumour


title: CRC2_017_Adenoma1

description:
Sample name: CRC2_017Ad1
Patient 017 adenoma tissue


title: CRC2_009_Normal Close

description:
Sample name: CRC2_009Ncol
Patient 009 normal tissues taken close to tumour


title: CRC2_017_Normal Close

description:
Sample name: CRC2_017NC
Patient 017 normal tissues taken close to tumour


title: CRC2_014_Normal Close

description:
Sample name: CRC2_014Ncol
Patient 014 normal tissues taken close to tumour


title: CRC2_034_Adenoma1

description:
Sample name: CRC2_034Ad1
Patient 034 adenoma tissue


title: CRC2_014_Tumour

description:
Sample name: CRC2_014T1
Patient 014 adenocarcinoma (tumour) tissue


title: CRC2_009_Adenoma4

description:
Sample name: CRC2_009Ad4
Patient 009 adenoma tissue


title: CRC2_009_Adenoma1

description:
Sample name: CRC2_009Ad1
Patient 009 adenoma tissue


title: CRC2_009_Adenoma2

description:
Sample name: CRC2_009Ad2
Patient 009 adenoma tissue


title: LNCaP_SIK2_KI_Myc_t12h_2

status: Public on Jan 12 2015

description: 8133182044_K: LNCaP transfected with SIK2-KI-Myc construct for 12h replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

Normalized data includes 784 controls (used for multiple testing correction) not represented in the HumanHT-12 V4.0 platform (GPL10558). Therefore, complete normalized data has been linked as a supplementary file (GSE45711_normalized.txt) to GSE45711 instead of creating the customary GEO sample tables.

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

growth_protocol: Cells were grown in RMPI + 10% Fbs in a 37°C + 5% CO2 incubator

extract_protocol: RNAs were extracted with RiboPure™ Kit according to manufacturer's instructions (Ambion). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with 10 µg DNA or 1 µM siRNA using AMAXA nulceofection or were treated with 10 µM Forskolin or equivalent Vehicle control.

value: LNCaP human cell line

tag: phenotype

value: kinase-dead SIK2 overexpression


title: LNCaP_EV_t96h_3

description: 8133182044_L: LNCaP transfected with empty vector construct for 96h replicate 3

value: Control overexpression


title: CRC2_010_Adenoma1

description:
Sample name: CRC2_010AD1
Patient 010 adenoma tissue

tag: Sex


title: CRC2_009_Adenoma3

description:
Sample name: CRC2_009Ad3
Patient 009 adenoma tissue


title: CRC2_010_Normal Close

description:
Sample name: CRC2_010NCOL
Patient 010 normal tissues taken close to tumour


title: CRC2_008_Adenoma2

description:
Sample name: CRC2_008Ad2
Patient 008 adenoma tissue


title: LNCaP_SIK2_Myc_t96h_1

description: 8133182044_H: LNCaP transfected with SIK2-Myc construct for 96h replicate 1

value: wild-type SIK2 overexpression


title: CRC2_002_Tumour

description:
Sample name: CRC2_002T1
Patient 002 adenocarcinoma (tumour) tissue


title: CRC2_002_Normal Close

description:
Sample name: CRC2_002NC
Patient 002 normal tissues taken close to tumour


title: CRC2_008_Normal Away

description:
Sample name: CRC2_008NA
Patient 008 normal tissues taken away (20cm) from the tumour


title: CRC2_008_Normal Close

description:
Sample name: CRC2_008NC
Patient 008 normal tissues taken close to tumour


title: CRC2_008_Adenoma3

description:
Sample name: CRC2_008Ad3
Patient 008 adenoma tissue


title: CRC2_008_Tumour

description:
Sample name: CRC2_008T1
Patient 008 adenocarcinoma (tumour) tissue


title: CRC2_001_Tumour

description:
Sample name: CRC2_001T1
Patient 001 adenocarcinoma (tumour) tissue


title: CRC2_002_Normal Away

description:
Sample name: CRC2_002NA
Patient 002 normal tissues taken away (20cm) from the tumour


title: CRC2_001_Normal Close

description:
Sample name: CRC2_001NC
Patient 001 normal tissues taken close to tumour


title: LNCaP_NT_siRNA_t24h_4

description: 8133182035_J: LNCaP transfected with non targeting siRNA for 24h replicate 4

value: Control silenced


title: LNCaP_SIK2_Myc_t12h_3

description: 8133182035_L: LNCaP transfected with SIK2-Myc construct for 12h replicate 3


title: LNCaP_Forskolin_t12h_1

description: 8133182035_K: LNCaP treated with forskolin for 12h replicate 1

source_name: LNCaP treated with forskolin for 12h


title: LNCaP_SIK2_siRNA_t96h_4

description: 8133182035_I: LNCaP transfected with SIK2 siRNA for 96h replicate 4

value: SIK2 silenced


title: HCT116_shRNA_TET2+3_2

description: Sample name: TET_KD_2.3_2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using a HiScan array scannner using standard recommended Illumina scanner setting

data_processing: Raw Infinium data were filtered by removing low quality data using a detection P-value threshold of 0.05. Cross-reactive probes (i.e. targeting several genomic locations) and probes containing SNPs were filtered out using the extended annotation provided by Price et al. [doi:10.1186/1756-8935-6-4]. Probes associated to X and Y chromosomes were removed from the analysis. Beta-values were computed using the formula Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta values were corrected for type I and type II bias using the peak-based correction method [doi: 10.1093/bib/bbt054 and doi: 10.2217/epi.11.105].

source_name: HCT116 cell culture, shRNA to TET2 and TET3_replicate2

label_protocol: Standard Illumina Protocol

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS, penicillin and streptomycin.

extract_protocol: DNA was purified by phenol:chloroform extraction.

treatment_protocol: Stable knockdown of TET2 in HCT116 used MISSION shRNA Lentiviral Transduction Particles (SHCLNV-NM_017628, Sigma) following manufacturers instructions and selection with 2ug/ml Puromycin (A11138-03, Life Technologies). For TET2C 10MOI of TRCN0000418976 and for TET2+3 5MOI each of TRCN0000418976 and TRCN0000246258 were used. shRNA control used 10MOI of MISSION pLKO.1-puro Non-Target shRNA Control Transduction Particles (SHC016V-1EA, Sigma).

value: shRNA to TET2 + TET3


title: LNCaP_SIK2_KI_Myc_t96h_1

description: 8133182035_D: LNCaP transfected with SIK2-KI-Myc construct for 96h replicate 1


title: LNCaP_SIK2_Myc_t96h_3

description: 8133182035_C: LNCaP transfected with SIK2-Myc construct for 96h replicate 3


title: LNCaP_CREB1_siRNA_t24h_3

description: 8133182035_A: LNCaP transfected with CREB1 siRNA for 24h replicate 3

value: CREB1 silenced


title: LNCaP_EV_t12h_1

description: 8133182044_I: LNCaP transfected with empty vector construct for 12h replicate 1


title: LNCaP_SIK2_siRNA_t24h_1

description: 8133182044_J: LNCaP transfected with SIK2 siRNA for 24h replicate 1


title: LNCaP_EV_t12h_3

description: 8133182029_K: LNCaP transfected with empty vector construct for 12h replicate 3


title: LNCaP_NT_siRNA_t96h_4

description: 8133182044_B: LNCaP transfected with non targeting siRNA for 96h replicate 4


title: LNCaP_SIK2_KI_Myc_t12h_1

description: 8133182035_H: LNCaP transfected with SIK2-KI-Myc construct for 12h replicate 1


title: LNCaP_t0h_1

description: 8133182044_C: LNCaP before transfection replicate 1

source_name: LNCaP before transfection


title: LNCaP_SIK2_KI_Myc_t96h_4

description: 8133182029_J: LNCaP transfected with SIK2-KI-Myc construct for 96h replicate 4


title: LNCaP_SIK2_KI_Myc_t96h_2

description: 8133182044_A: LNCaP transfected with SIK2-KI-Myc construct for 96h replicate 2


title: LNCaP_NT_siRNA_t24h_3

description: 8133182044_D: LNCaP transfected with non targeting siRNA for 24h replicate 3


title: HCT116_shRNA_TET2_2

description: Sample name: TET_KD_2C_2

source_name: HCT116 cell culture, shRNA to TET2_cell line C_replicate2

value: shRNA to TET2


title: LNCaP_t0h_3

description: 8133182029_G: LNCaP before transfection replicate 3


title: HCT116_shRNA_TET2_1

description: Sample name: TET_KD_2C_1

source_name: HCT116 cell culture, shRNA to TET2_cell line C_replicate1


title: LNCaP_EV_t96h_1

description: 8133182035_G: LNCaP transfected with empty vector construct for 96h replicate 1


title: HCT116_shRNA_emptyvector_2

description: Sample name: TET_KD_Plk_2

source_name: HCT116 cell culture, EmptyVectorControl_replicate2

value: EmptyVectorControl


title: LNCaP_t0h_4

description: 8133182028_L: LNCaP before transfection replicate 4


title: LNCaP_CREB1_siRNA_t24h_1

description: 8133182029_L: LNCaP transfected with CREB1 siRNA for 24h replicate 1


title: LNCaP_Vehicle_t12h_2

description: 8133182028_K: LNCaP treated with vehicle for 12h replicate 2

source_name: LNCaP treated with vehicle for 12h


title: LNCaP_SIK2_Myc_t12h_2

description: 8133182029_A: LNCaP transfected with SIK2-Myc construct for 12h replicate 2


title: LNCaP_CREB1_siRNA_t24h_2

description: 8133182028_F: LNCaP transfected with CREB1 siRNA for 24h replicate 2


title: LNCaP_Vehicle_t12h_4

description: 8133182029_I: LNCaP treated with vehicle for 12h replicate 4


title: LNCaP_SIK2_siRNA_t96h_1

description: 8133182029_B: LNCaP transfected with SIK2 siRNA for 96h replicate 1


title: HCT116_shRNA_TET2+3_1

description: Sample name: TET_KD_2.3_1

source_name: HCT116 cell culture, shRNA to TET2 and TET3_replicate1


title: LNCaP_SIK2_siRNA_t24h_2

description: 8133182028_C: LNCaP transfected with SIK2 siRNA for 24h replicate 2


title: CRC2_001_Normal Away

description:
Sample name: CRC2_001NA
Patient 001 normal tissues taken away (20cm) from the tumour


title: LNCaP_NT_siRNA_t96h_1

description: 8133182029_H: LNCaP transfected with non targeting siRNA for 96h replicate 1


title: LNCaP_EV_t12h_2

description: 8133182028_B: LNCaP transfected with empty vector construct for 12h replicate 2


title: LNCaP_Vehicle_t12h_3

description: 8133182035_E: LNCaP treated with vehicle for 12h replicate 3


title: LNCaP_Forskolin_t12h_4

description: 8133182028_A: LNCaP treated with forskolin for 12h replicate 4


title: LNCaP_NT_siRNA_t96h_2

description: 7927538069_L: LNCaP transfected with non targeting siRNA for 96h replicate 2


title: LNCaP_SIK2_KI_Myc_t12h_3

description: 7927538069_K: LNCaP transfected with SIK2-KI-Myc construct for 12h replicate 3


title: LNCaP_SIK2_Myc_t96h_2

description: 7927538069_J: LNCaP transfected with SIK2-Myc construct for 96h replicate 2


title: LNCaP_Forskolin_t12h_3

description: 7927538069_I: LNCaP treated with forskolin for 12h replicate 3


title: LNCaP_SIK2_siRNA_t24h_3

description: 8133182029_F: LNCaP transfected with SIK2 siRNA for 24h replicate 3


title: LNCaP_SIK2_KI_Myc_t12h_4

description: 8133182029_D: LNCaP transfected with SIK2-KI-Myc construct for 12h replicate 4


title: HCT116_shRNA_emptyvector_1

description: Sample name: TET_KD_Plk_1

source_name: HCT116 cell culture, EmptyVectorControl_replicate1


title: LNCaP_SIK2_Myc_t12h_4

description: 7927538069_D: LNCaP transfected with SIK2-Myc construct for 12h replicate 4


title: LNCaP_SIK2_siRNA_t96h_2

description: 8133182028_J: LNCaP transfected with SIK2 siRNA for 96h replicate 2


title: LNCaP_SIK2_siRNA_t96h_3

description: 7927538069_B: LNCaP transfected with SIK2 siRNA for 96h replicate 3


title: LNCaP_SIK2_siRNA_t24h_4

description: 7927538069_H: LNCaP transfected with SIK2 siRNA for 24h replicate 4


title: LNCaP_EV_t96h_2

description: 8133182028_H: LNCaP transfected with empty vector construct for 96h replicate 2


title: LNCaP_NT_siRNA_t24h_2

description: 7927538069_G: LNCaP transfected with non targeting siRNA for 24h replicate 2


title: LNCaP_NT_siRNA_t24h_1

description: 8133182028_I: LNCaP transfected with non targeting siRNA for 24h replicate 1


title: LNCaP_SIK2_KI_Myc_t96h_3

description: 8133182028_G: LNCaP transfected with SIK2-KI-Myc construct for 96h replicate 3


title: LNCaP_SIK2_Myc_t96h_4

description: 8133182028_E: LNCaP transfected with SIK2-Myc construct for 96h replicate 4


title: LNCaP_Vehicle_t12h_1

description: 7927538069_A: LNCaP treated with vehicle for 12h replicate 1


title: LNCaP_NT_siRNA_t96h_3

description: 8133182035_F: LNCaP transfected with non targeting siRNA for 96h replicate 3


title: LNCaP_EV_t12h_4

description: 7927538069_F: LNCaP transfected with empty vector construct for 12h replicate 4


title: LNCaP_SIK2_Myc_t12h_1

description: 8133182044_G: LNCaP transfected with SIK2-Myc construct for 12h replicate 1


title: LNCaP_CREB1_siRNA_t24h_4

description: 7927538069_C: LNCaP transfected withCREB1 siRNA for 24h replicate 4


title: LNCaP_t0h_2

description: 7927538069_E: LNCaP before transfection replicate 2


title: LNCaP_Forskolin_t12h_2

description: 8133182044_F: LNCaP treated with forskolin for 12h replicate 2


title: peripheral airway epithelial cells, smoker 28, rep1

status: Public on Jan 06 2015

city: new york

first: Jun-Chieh

middle: James

last: Tsay

address: 562 First Ave. NBV 7N27

department: Medicine

institute: NYU Langone Medical Center

hyb_protocol: Ten µg of cRNA was hybridized to the array, and was processed with the Affymetrix system, including GeneChip Hybridization Oven 640

scan_protocol: GeneChips scanned with Fluidics Station 450 and Scanner 3000.

data_processing: Normalization of Affymetrix array data was by Robust Multichip Average (RMA) through the RMexpress software package (http://rmaexpress.bmbolstad.com/).

source_name: peripheral airway epithelial cells_smoker

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

extract_protocol: extracted total RNA using Qiagen miRNeasy Mini Kit (Valencia, CA) according to the company protocol

treatment_protocol: The cytology brush was spun down and the cell pellet was collected and stored at -80° C until RNA extraction

tag: subject id

value: smoker 28

tag: age

tag: case

value: smoker

value: peripheral airway epithelial cells


title: 16.5 mM Glu + 12h + Met_rep3

status: Public on Dec 03 2014

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.

source_name: 16.5 mM Glu + normoxia 12h + Met

label_protocol: 250 ng total RNA was used as input for amplification using Ambion WT expression sense kit (Life Technilogies, Grand Island, NY, USA), Poly A control was added as suggested by WT expression kit manual. cDNA amplification products were fragmented and labeled with biotin using Affymetrix GeneChip WT terminal labeling kit, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit, and then washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol: RNA samples were isolated from HUVEC using the RNeasy Mini Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed (RIN > 9.0) on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Human umbilical vein endothelial cells (HUVECs)

tag: metformin added

value: YES

tag: oxygen level

value: normoxia

tag: glucose concentration

value: 16.5 mM (high)


title: 16.5 mM Glu + Met_rep3

source_name: 16.5 mM Glu + Met


title: peripheral airway epithelial cells, smoker 29, rep1

value: smoker 29

value: male


title: peripheral airway epithelial cells, smoker 8, rep1

value: smoker 8

value: female


title: peripheral airway epithelial cells, smoker 30, rep1

value: smoker 30


title: 5.5 mM Glu + Met + Hypoxia 12h_rep3

source_name: 5.5 mM Glu + Met + Hypoxia 12h

value: hypoxia

value: 5.5 mM (normal)


title: peripheral airway epithelial cells, smoker 7, rep1

value: smoker 7


title: peripheral airway epithelial cells, smoker 27, rep1

value: smoker 27


title: 16.5 mM Glu + Met + Hypoxia 3h_rep3

source_name: 16.5 mM Glu + Met + Hypoxia 3h


title: 5.5 mM Glu + Met + Hypoxia 1h_rep3

source_name: 5.5 mM Glu + Met + Hypoxia 1h


title: 16.5 mM Glu + 3h_No Met_rep3

source_name: 16.5 mM Glu + normoxia 3h_No Met

value: NO Met


title: 16.5 mM Glu_No Met_rep3

source_name: 16.5 mM Glu_No Met


title: 16.5 mM Glu + 12h_No Met_rep3

source_name: 16.5 mM Glu + normoxia 12h_No Met


title: 16.5 mM Glu + 1h_No Met_rep3

source_name: 16.5 mM Glu + normoxia 1h_No Met


title: 16.5 mM Glu + 3h + Met_rep3

source_name: 16.5 mM Glu + normoxia 3h + Met


title: 16.5 mM Glu + 1h + Met_rep3

source_name: 16.5 mM Glu + normoxia 1h + Met


title: peripheral airway epithelial cells, smoker 3, rep1

value: smoker 3


title: 16.5 mM Glu + Met + Hypoxia 1h_rep3

source_name: 16.5 mM Glu + Met + Hypoxia 1h


title: 16.5 mM Glu + Hypoxia 12h_No Met_rep3

source_name: 16.5 mM Glu + Hypoxia 12h_No Met


title: 5.5 mM Glu + Hypoxia 3h_No Met_rep3

source_name: 5.5 mM Glu + Hypoxia 3h_No Met


title: 16.5 mM Glu + Hypoxia 1h_No Met_rep3

source_name: 16.5 mM Glu + Hypoxia 1h_No Met


title: 5.5 mM Glu + Met + Hypoxia 3h_rep3

source_name: 5.5 mM Glu + Met + Hypoxia 3h


title: 16.5 mM Glu + 12h + Met_rep2


title: 16.5 mM Glu + Met + Hypoxia 12h_rep3

source_name: 16.5 mM Glu + Met + Hypoxia 12h


title: 5.5 mM Glu + Hypoxia 1h_No Met_rep3

source_name: 5.5 mM Glu + Hypoxia 1h_No Met


title: 5.5mmM Glu + Met_Normal_rep3

source_name: 5.5mmM Glu + Met_Normal


title: 16.5 mM Glu + 3h + Met_rep2


title: 16.5 mM Glu + 1h + Met_rep2


title: 16.5 mM Glu + Met + Hypoxia 1h_rep2


title: 5.5 mM Glu + Hypoxia 12h_No Met_rep3

source_name: 5.5 mM Glu + Hypoxia 12h_No Met


title: 16.5 mM Glu + 1h_No Met_rep2


title: 5.5mmM Glu_No Met_Normal_rep3

source_name: 5.5mmM Glu_No Met_Normal


title: 16.5 mM Glu + Met + Hypoxia 12h_rep2


title: 5.5mmM Glu + Met_Normal_rep2


title: 5.5 mM Glu + Met + Hypoxia 3h_rep2


title: 5.5 mM Glu + Met + Hypoxia 1h_rep2

source_name: 5.5 mM Glu + Met + Hypoxia 1h


title: 5.5 mM Glu + Met + Hypoxia 12h_rep2

source_name: 5.5 mM Glu + Met + Hypoxia 12h


title: 16.5 mM Glu + Hypoxia 3h_No Met_rep3

source_name: 16.5 mM Glu + Hypoxia 3h_No Met


title: 16.5 mM Glu + Met + Hypoxia 3h_rep2

source_name: 16.5 mM Glu + Met + Hypoxia 3h


title: LNCaP_EV_t96h_4

description: 8133182029_C: LNCaP transfected with empty vector construct for 96h replicate 4

value: LNCaP human cell line

value: Control overexpression


title: 5.5 mM Glu + Hypoxia 12h_No Met_rep2

value: Human umbilical vein endothelial cells (HUVECs)


title: 5.5 mM Glu + Hypoxia 1h_No Met_rep2


title: 16.5 mM Glu_No Met_rep2

source_name: 16.5 mM Glu_No Met


title: 5.5 mM Glu + Hypoxia 3h_No Met_rep2


title: 16.5 mM Glu + 12h_No Met_rep2

source_name: 16.5 mM Glu + normoxia 12h_No Met


title: 16.5 mM Glu + Hypoxia 1h_No Met_rep2


title: 16.5 mM Glu + Met_rep2

source_name: 16.5 mM Glu + Met

value: YES


title: 16.5 mM Glu + 3h_No Met_rep2

source_name: 16.5 mM Glu + normoxia 3h_No Met

value: normoxia


title: 5.5mmM Glu_No Met_Normal_rep2


title: 16.5 mM Glu + 3h + Met_rep1

source_name: 16.5 mM Glu + normoxia 3h + Met

value: 16.5 mM (high)


title: 16.5 mM Glu + Hypoxia 12h_No Met_rep2

source_name: 16.5 mM Glu + Hypoxia 12h_No Met


title: 16.5 mM Glu +Met + Hypoxia 1h_rep1

source_name: 16.5 mM Glu +Met + Hypoxia 1h


title: 16.5 mM Glu + Hypoxia 3h_No Met_rep2


title: 16.5 mM Glu + 1h + Met_rep1

source_name: 16.5 mM Glu + normoxia 1h + Met


title: 16.5 mM Glu + 12h + Met_rep1

source_name: 16.5 mM Glu + normoxia 12h + Met


title: 5.5 mM Glu + Met + Hypoxia 12h_rep1


title: 16.5 mM Glu + Met_rep1


title: 5.5 mM Glu +Met+ Hypoxia 3h_rep1

source_name: 5.5 mM Glu +Met+ Hypoxia 3h


title: 5.5 mM Glu + +Met+ Hypoxia 1h_rep1

source_name: 5.5 mM Glu + +Met+ Hypoxia 1h


title: 16.5 mM Glu + Met+ Hypoxia 3h_rep1

source_name: 16.5 mM Glu + Met+ Hypoxia 3h


title: 16.5 mM Glu + 12h_No Met_rep1


title: 16.5 mM Glu_No Met_rep1


title: 16.5 mM Glu + 3h_No Met_rep1


title: 16.5 mM Glu + 1h_No Met_rep1

source_name: 16.5 mM Glu + normoxia 1h_No Met


title: 16.5 mM Glu + Hypoxia 3h_No Met_rep1


title: 16.5 mM Glu + Met + Hypoxia 12h_rep1

source_name: 16.5 mM Glu + Met + Hypoxia 12h


title: 5.5mmM Glu + Met_Normal_rep1

source_name: 5.5mmM Glu + Met_Normal


title: 5.5 mM Glu + Hypoxia 3h_No Met_rep1

source_name: 5.5 mM Glu + Hypoxia 3h_No Met


title: 5.5 mM Glu + Hypoxia 1h_No Met_rep1

source_name: 5.5 mM Glu + Hypoxia 1h_No Met


title: C4-2 stably overexpressing nuclear ARRB1-GFP fusion protein-replicate 2

status: Public on Nov 26 2014

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: C4-2_nuclear ARRB1-GFP fusion protein overexpression

growth_protocol: C4-2 cells were cultured in RPMI supplemented with 10% FBS. C4-2 stable lines were maintained in 0.8 mg/ml G418 supplemented Media.

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

treatment_protocol: no treatments done.

value: immortalised prostate epithelial cells

tag: genotype/variation


title: 16.5 mM Glu + Hypoxia 12h_No Met_rep1


title: C4-2 stably overexpressing ARRB1-GFP fusion protein-replicate 1

source_name: C4-2_ARRB1-GFP fusion protein overexpression


title: PDAC 35 (gene level)

status: Public on Nov 10 2014

city: London

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

description: Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.

hyb_protocol: Affymetrix Standard Protocol.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: Exon array raw CEL files were processed using a pipeline based on the aroma.affymetrix R package. Only the "core" probesets were considered. The custom CDF file "HuEx-1_0-st-v2,coreR2,A20070914,EP.cdf" defining "core" units provided by aroma.affymetrix was used as the default annotation. Within the exon array pipeline, the RMA background correction and quantile normalisation were performed, followed by transcript-level and probeset-level intensity estimation and summarisation. FIRMA scores were also calculated for the alternative splicing analysis. The transcript cluster and probeset mapping to the human genome and gene symbol (hg19) was done using the Affymetrix NetAffx annotations (Release 32), e.g., "HuEx-1_0-st-v2.na32.hg19.transcript.csv" for transcript cluster annotation and "HuEx-1_0-st-v2.na32.hg19.probeset.csv" for probeset annotation. This was followed by intensity filtering as recommended by the Affymetrix exon array whitepaper.

source_name: PDAC

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

extract_protocol: Total RNA were extracted. Tumour samples from which the RNA was extracted consisted of at least 60% cancer cells with short and long time survival.

value: pancreatic ductal adenocarcinoma (PDAC)

tag: cellularity

value: F

tag: grading

tag: pt


title: PDAC 20 (gene level)

value: M


title: PDAC 21 (gene level)


title: PDAC 55 (gene level)


title: C4-2 stably overexpressing ARRB1-GFP fusion protein-replicate 2

tag: cell type


title: C4-2 GFP empty vector control-replicate 1

source_name: C4-2_GFP empty vector

value: transfected with GFP empty vector (control)


title: PDAC 24 (gene level)


title: 16.5 mM Glu + Hypoxia 1h_No Met_rep1

source_name: 16.5 mM Glu + Hypoxia 1h_No Met

value: hypoxia


title: parental C4-2 cell line-replicate 3

source_name: parental C4-2 cell line

value: parental control


title: PDAC 19 (gene level)


title: PDAC 32 (gene level)


title: parental C4-2 cell line-replicate 2


title: PDAC 27 (gene level)


title: PDAC 25 (gene level)


title: C4-2 GFP empty vector control-replicate 3


title: C4-2 GFP empty vector control-replicate 2


title: parental C4-2 cell line-replicate 1


title: PDAC 22 (gene level)


title: 5.5 mM Glu + Hypoxia 12h_No Met_rep1

source_name: 5.5 mM Glu + Hypoxia 12h_No Met

value: 5.5 mM (normal)


title: C4-2 stably overexpressing nuclear ARRB1-GFP fusion protein-replicate 1


title: 5.5mmM Glu_No Met_Normal_rep1

source_name: 5.5mmM Glu_No Met_Normal


title: Adjacent 42 (gene level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Unmatched sample.

source_name: adjacent pancreatic tissue

value: adjacent pancreatic tissue


title: PDAC 17 (gene level)


title: PDAC 23 (gene level)


title: PDAC 13 (gene level)


title: Adjacent 46 (gene level)


title: PDAC 14 (gene level)


title: Adjacent 34 (gene level)


title: Adjacent 27 (gene level)


title: PDAC 100 (gene level)


title: PDAC 46 (gene level)


title: PDAC 173 (gene level)


title: PDAC 102 (gene level)


title: PDAC 16 (gene level)


title: PDAC 60 (gene level)


title: PDAC 63 (gene level)


title: PDAC 54 (gene level)


title: PDAC 80 (gene level)


title: PDAC 163 (gene level)


title: Donor 1, rep2 (gene level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Rep2

source_name: normal pancreatic tissue

value: normal pancreas


title: PDAC 108 (gene level)


title: Donor 2 (gene level)


title: Donor 1, rep1 (gene level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Rep1


title: PDAC 64 (gene level)


title: PDAC 150 (gene level)


title: Blastocysts_INS10_treatment_rep-4

status: Public on Oct 31 2014

city: Uppsala

first: Denise

last: Laskowski

address: Postbox 7054

department: KV

country: Sweden

institute: SLU

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

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

growth_protocol: slaughterhouse derived ovaries collection, maturation, fertilization and culture according to standarized procedures at our IVF lab in Sweden with modofications during maturation in form of insulin treatment (reference IVF protocols Breed influences on in vitro development of  abattoir-derived bovine oocytes

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

treatment_protocol: bovine Insulin added to maturation media in High concentrations (10µg/ml medium) and Low concentration (0.1µg/ml medium) compared to control group with no insulin added

tag: compound added

tag: dose

value: 0 ug/ml

value: 10 ug/ml


title: Blastocysts_INS10_treatment_rep-2


title: Blastocysts_INS10_treatment_rep-1


title: Blastocysts_INS10_treatment_rep-3


title: TUMK0019

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

description: Ewing sarcoma, 5. rib

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: RMA normalization.

source_name: Ewing sarcoma, 5. rib

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

extract_protocol: RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer´s instructions.

tag: tissue

value: Ewing sarcoma, 5. rib


title: 2days_4OHT_Batch_D

status: Public on Jul 31 2014

description: 2d_D_MN 50

growth_protocol: cells were grown in DMEM medium supplemented with 10% Foetal Bovine Serum in an ambient atmosphere with 5% CO2 and passage was performed on the day before harvest using 0.125% Trypsin EDTA.

extract_protocol: Total RNA was extracted using Rneasy mini kit (Qiagen)

treatment_protocol: cells were treated with media supplemented with 100nM 4-OHT for indicated time.

tag: cell line background

value: expressing ER:RAS-G12V

tag: treated with

value: 100nM 4-OHT for 2 days


title: Blastocysts_INS0.1_treatment_rep-4

value: 0.1 ug/ml


title: TUMK0014

description: Ewing sarcoma, 2. & 3. rib

source_name: Ewing sarcoma, 2. & 3. rib

value: Ewing sarcoma, 2. & 3. rib


title: 24hrs_4OHT_Batch_D

description: 24h_D_MN 48

value: 100nM 4-OHT for 24hrs


title: TUMK0015

description: Ewing sarcoma, Os ileum

source_name: Ewing sarcoma, Os ileum

value: Ewing sarcoma, Os ileum


title: 4days_4OHT_Batch_A

description: 4d_A_MN 10

value: 100nM 4-OHT for 4 days


title: 2hrs_4OHT_Batch_B

description: 2h_B_MN 16

value: 100nM 4-OHT for 2hrs


title: 2hrs_4OHT_Batch_A

description: 2h_A_MN 2


title: 2hrs_4OHT_Batch_D

description: 2h_D_MN 44


title: Blastocysts_INS0.1_treatment_rep-3


title: TUMK0019M

description: Ewing sarcoma, lung metastasis

source_name: Ewing sarcoma, lung metastasis

value: Ewing sarcoma, lung metastasis


title: 24hrs_4OHT_Batch_A

description: 24h_A_MN 6


title: Blastocysts_INS0.1_treatment_rep-2


title: 2days_4OHT_Batch_A

description: 2d_A_MN 8


title: 0hr_control_Batch_B

description: 0hr_B_MN 15

value: none (0h control)


title: TUMK0017

description: Ewing sarcoma, femur

source_name: Ewing sarcoma, femur

value: Ewing sarcoma, femur


title: 0hr_control_Batch_D

description: 0hr_D_MN 43


title: PDAC 169 (gene level)

value: pancreatic ductal adenocarcinoma (PDAC)

tag: Sex

value: M


title: Blastocysts_INS0.1_treatment_rep-1


title: 2days_4OHT_Batch_B

description: 2d_B_MN 22


title: 0hr_control_Batch_A

description: 0hr_A_MN 1


title: 8days_4OHT_Batch_D

description: 8d_D_MN 56

value: 100nM 4-OHT for 8 days


title: 24hrs_4OHT_Batch_B

description: 24h_B_MN 20


title: 8hrs_4OHT_Batch_A

description: 8h_A_MN 4

value: 100nM 4-OHT for 8hrs


title: 8hrs_4OHT_Batch_B

description: 8h_B_MN 18


title: TUMK0018

description: Ewing sarcoma, perirenal

source_name: Ewing sarcoma, perirenal

value: Ewing sarcoma, perirenal


title: 8hrs_4OHT_Batch_D

description: 8h_D_MN 46


title: 4days_4OHT_Batch_D

description: 4d_D_MN 52


title: 8days_4OHT_Batch_B

description: 8d_B_MN 28


title: 6days_4OHT_Batch_D

description: 6d_D_MN 54

value: 100nM 4-OHT for 6 days


title: 6days_4OHT_Batch_A

description: 6d_A_MN 12

value: expressing ER:RAS-G12V


title: 4days_4OHT_Batch_B

description: 4d_B_MN 24


title: Neuroblastoma-MYCN/ALK.F1178L-Tum37

status: Public on Jun 24 2014

city: paris

first: Alex

last: Cazes

state: Please select...

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions. Samples were hybridized to Affymetrix MOE430.2 array

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.14.0.0, ENTREZG)

source_name: MYCN/ALK.F1178L tumor

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

extract_protocol: RNA was collected from tumors using the miRNeasy kit (Qiagen) according to the manufacturer's instructions.

tag: strain

value: Neuroblastoma


title: Neuroblastoma-MYCN-Tum35

source_name: MYCN tumor


title: 8days_4OHT_Batch_A

description: 8d_A_MN 14


title: Neuroblastoma-MYCN/ALK.F1178L-Tum28


title: Neuroblastoma-MYCN-Tum34


title: Neuroblastoma-MYCN/ALK.F1178L-Tum36


title: Neuroblastoma-MYCN-Tum33


title: 6days_4OHT_Batch_B

description: 6d_B_MN 26


title: Neuroblastoma-MYCN/ALK.F1178L-Tum38


title: Neuroblastoma-MYCN/ALK.F1178L-Tum31


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum18

source_name: MYCN/ALK.R1279Q tumor


title: Neuroblastoma-MYCN/ALK.F1178L-Tum29


title: Neuroblastoma-MYCN-Tum26


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum17


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum16


title: Neuroblastoma-MYCN/ALK.F1178L-Tum30


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum14


title: Neuroblastoma-MYCN-Tum32


title: Neuroblastoma-MYCN-Tum21


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum13


title: Neuroblastoma-MYCN/ALK.F1178L-Tum11


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum24


title: Neuroblastoma-MYCN/ALK.F1178L-Tum4


title: Neuroblastoma-MYCN-Tum23


title: Neuroblastoma-MYCN-Tum22


title: Neuroblastoma-MYCN-Tum25


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum19


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum8


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum9


title: Neuroblastoma-MYCN/ALK.F1178L-Tum1


title: Neuroblastoma-MYCN/ALK.F1178L-Tum2


title: LNCaP_pLVX_GABPa_Androgen_r2

status: Public on May 21 2014

data_processing: The data was log base 2 quantile normalised after artefact removal using the BASH and HULK algorithms in the R beadarray package

source_name: LNCaP cell line

label_protocol: cRNA was generated and biotin labelled using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: cells were grown in RPMI medium supplemented with 10% Foetal Bovine Serum and passage was performed at 80% confluence using 0.05% Trypsin EDTA.

extract_protocol: RNA was extracted using Trizol and isopropanol precipitation

treatment_protocol: cells were grown to 75-80% confluence and then transferred to media supplemented with charcoal-stripped serum for 48 hrs. Cells were then either treated with 1 nM methyltrienolone (R1881), a synthetic androgen, or an equal volume of ethanol.

tag: treatment

tag: condition

value: Androgen

tag: cell line

value: LNCaP


title: Neuroblastoma-MYCN-Tum3


title: LNCaP_NT_Control_r1

value: Control


title: Neuroblastoma-MYCN/ALK.R1279Q-Tum5


title: LNCaP_shGA_Androgen_r1

value: shGA


title: LNCaP_shGA_Androgen_r2


title: LNCaP_pLVX_EV_Androgen_r2


title: LNCaP_shGA_Control_r1


title: LNCaP_NT_Androgen_r1


title: LNCaP_pLVX_EV_Control_r1


title: LNCaP_pLVX_GABPa_Androgen_r1


title: LNCaP_pLVX_GABPa_Control_r2


title: LNCaP_shGA_Control_r2


title: LNCaP_pLVX_GABPa_Androgen_r1_TR


title: c42b_shGA_Androgen_r1

source_name: c42b cell line


title: LNCaP_pLVX_EV_Androgen_r1


title: c42b_shGA_Androgen_r2


title: LNCaP_pLVX_GABPa_Control_r1


title: c42b_pLVX_GABPa_Androgen_r1


title: LNCaP_NT_Control_r2


title: c42b_pLVX_GABPa_Androgen_r2_TR


title: LNCaP_pLVX_EV_Control_r2


title: LNCaP_shGA_Androgen_r1_TR


title: c42b_shGA_Control_r2


title: LNCaP_NT_Androgen_r2


title: c42b_pLVX_GABPa_Control_r1


title: c42b_pLVX_GABPa_Androgen_r2


title: c42b_shGA_Control_r1


title: c42b_pLVX_GABPa_Control_r2


title: c42b_pLVX_EV_Control_r2


title: c42b_pLVX_EV_Androgen_r2


title: c42b_NT_Androgen_r2_TR


title: LNCaP.FoxA1.6

status: Public on Jan 03 2014

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 6

hyb_protocol: Standard Illumina hybridisation procedure

scan_protocol: Standard Illumina scanning procedure

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

source_name: Prostate cancer cell line

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

growth_protocol: Cells were grown in RPMI + 10% FBS and standard antibiotics in a 37oC incubator with 5% CO2

extract_protocol: RNA was extracted using Qiagen RNEasy with on column DNaseI digestion according the the manufacturer's instructions.Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with 3μM pcDNA3.1_GFP (Control) or 3μM pcDNA3.1_FoxA1 using Lipofectamine2000 (Invitrogen). Cells were harvested 48h later.

tag: overexpression vector


title: c42b_pLVX_EV_Control_r1


title: c42b_pLVX_EV_Androgen_r1


title: c42b_NT_Control_r2


title: LNCaP.GFP.6

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 6

value: GFP


title: salivary gland

status: Public on Nov 01 2013

description: normal salivary gland pooled from 24 individuals (Clontech)

source_name: salivary gland

growth_protocol: Cell lines were grown in plastic cell culture flasks in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 10% heat-inactivated fetal bovine serum, 1% glutamine, 100 µg/mL gentamycin and 200 mg/dl D-glucose .

value: normal salivary gland


title: LNCaP.GFP.2

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 2


title: LNCaP.GFP.5

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 5


title: prostate

description: normal prostate pooled from 12 individuals (Clontech)

source_name: prostate

value: normal prostate


title: LNCaP.FoxA1.4

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 4


title: LNCaP.GFP.3

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 3


title: c42b_NT_Androgen_r2


title: c42b_NT_Control_r1


title: c42b_NT_Androgen_r1


title: LNCaP.FoxA1.2

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 2


title: LNCaP.FoxA1.3

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 3


title: LNCaP.GFP.1

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 1


title: LNCaP.FoxA1.1

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 1


title: LNCaP.FoxA1.5

description: FOXA1 overexpressing LNCaP prostate cancer cell line replicate 5


title: uterus

description: normal uterus pooled from 8 individuals (Clontech)

source_name: uterus

value: normal uterus


title: fetal brain

description: normal fetal brain pooled from 59 spontaneous abortions (Clontech)

source_name: fetal brain

value: normal fetal brain


title: fetal liver

description: normal fetal liver pooled from 63 spontaneous abortions (Clontech)

source_name: fetal liver

value: normal fetal liver


title: testis

description: normal testis pooled from 39 individuals (Clontech)

source_name: testis

value: normal testis


title: brain cerebellum

description: normal cerebellum pooled from 10 individuals (Clontech)

source_name: brain cerebellum

value: normal cerebellum


title: trachea

description: normal trachea pooled from 22 individuals (Clontech)

source_name: trachea

value: normal trachea


title: spinal cord

description: normal spinal cord pooled from 22 individuals (Clontech)

source_name: spinal cord

value: normal spinal cord


title: LNCaP.GFP.4

description: Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 4


title: skeletal muscle

description: normal skeletal muscle pooled from 2 individuals (Clontech)

source_name: skeletal muscle

value: normal skeletal muscle


title: brain (whole)

description: normal brain derived from 1 individual (Clontech)

source_name: brain (whole)

value: normal whole brail


title: lung

description: normal lung pooled from 3 individuals (Clontech)

source_name: lung

value: normal lung


title: stomach 2

description: patient derived normal stomach

source_name: stomach 2

value: normal stomach


title: small intestine

description: normal small intestine pooled from 5 individuals (Clontech)

source_name: small intestine

value: normal small intestine


title: thymus

description: normal thymus pooled from 2 males (Clontech)

source_name: thymus

value: normal thymus


title: normal PBMC

description: patient derived peripheral blood mononuclear cells (PBMC)


title: spleen

description: normal spleen pooled from 12 individuals (Clontech)

source_name: spleen

value: normal spleen


title: RD-ES

description: Ewing sarcoma cell line RD-ES, passage 12

source_name: Ewing sarcoma cell line RD-ES

value: Ewing sarcoma cell line RD-ES, wild type


title: MuET-MS

description: Ewing sarcoma, relapse

source_name: Ewing sarcoma, relapse

value: Ewing sarcoma, relapse

tag: subject

value: MuET-MS


title: MuET-DA

description: Ewing sarcoma, relapse

value: MuET-DA


title: stomach

description: normal stomach derived from 1 male (Clontech)

source_name: stomach


title: SK-N-MC

description: Ewing sarcoma cell line SK-N-MC with control siRNA treatment

source_name: Ewing sarcoma cell line SK-N-MC


title: liver

description: normal liver derived from 1 male (Clontech)

source_name: liver

value: normal liver


title: MuET-AP

description: Ewing sarcoma, relapse

value: MuET-AP


title: MuET-AP4R

description: Ewing sarcoma, 4th relapse

source_name: Ewing sarcoma, 4th relapse

value: Ewing sarcoma, 4th relapse


title: bone marrow

description: normal bone marrow pooled from 3 males (Clontech)

source_name: normal bone marrow

value: normal bone marrow


title: MuET-MJ

description: Ewing sarcoma, lung metastasis

source_name: Ewing sarcoma, lung metastasis

value: Ewing sarcoma, lung metastasis

value: MuET-MJ


title: MuET-KJ

description: Ewing sarcoma, lung metastasis

value: MuET-KJ


title: MuET-KE

description: Ewing sarcoma, relapse

value: MuET-KE


title: MuET-BS

description: Ewing sarcoma, lung metastasis

value: MuET-BS


title: E10 P2_BMP2.7 B

status: Public on Jun 24 2012

description:
4285752030_C
BMP2/7 treated replicate 2

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using GeneSpring GX software.

source_name: primary human keratinocytes treated with BMP2/7

growth_protocol: Primary human keratinocytes (line Lka, passage 2) were cultured in Keratinocyte Serum Free Medium.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. A DNase I digestion was included. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: vehicle (0.2% DMSO), the EGFR inhibitor AG1478 (10 uM), recombinant human BMP2/7 heterodimer (200 ng/ml) or a combination of AG1478+BMP2/7 (10 uM and 200 ng/ml, respectively) for 48 hours.

tag: cell

value: primary human keratinocytes


title: GV oocytes, XX, biological rep1

status: Public on Apr 02 2013

city: Tokyo

first: Feng

last: Cao

address: Sakuragaoka 1-1-1, Setagaya-ku

department: Bioscience

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression from Mouse GV oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner G3000.

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 100.

source_name: Mouse GV oocytes (XX)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol of 3' IVT expression Kit.

growth_protocol: XX, XY and XO females at 25–29 dpp were injected intraperitoneally each with 5 IU equine chorionic gonadotropin (Sigma, St Louis, MO), and sacrificed 45–47 hours later. Fully grown GV-stage oocytes surrounded by cumulus cells were isolated by puncturing large antral follicles with a pair of 26-gauge needles, and then denuded of cumulus cells by repeated pipetting through a fine glass needle. Only the oocytes with an intact GV and no apparent sign of degeneration were collected and stored at −80°C. Growing oocytes were collected from XX, XY, and XO females at 10 and 17 dpp.

extract_protocol: Total RNA were isolated from 10 oocytes each from 3 XY and 3 XX females using the RNeasy Micro Kit (Qiagen, Valencia, CA) and extracted in 11 µl RNase-free water. The Two-Cycle Eukaryotic Target Labeling Kit (Affymetrix) was used for synthesizing cRNA with oligo(dT) primers starting from 9 µl total RNA in solution

treatment_protocol: Ovaries were treated with 0.5 mg/ml each of testicular hyaluronidase (type IV), collagenase (B grade) and egg white lysozyme (all from Sigma) in M2 medium as previously reported. Oocytes with 40–60 µm diameter were collected with a fine glass needle, transferred in a group into a microcentrifuge tube, and stored at −80°C

tag: genotype

value: XX

value: Oocytes

tag: Stage

value: germinal vesicle (GV)


title: F9 P2_AG1478 A

description:
4285752030_D
AG1478 treated replicate 1

source_name: primary human keratinocytes treated with AG1478


title: GV oocytes, XX, biological rep3

description: Gene expression from Mouse GV oocytes


title: input DNA

data_processing: Sequence reads were aligned to the human genome (hg18) using the BWA alignment program

source_name: primary human keratinocytes (line Lka)

growth_protocol: Primary normal human keratinocytes, obtained from donor material with appropriate ethical approval and procedures, were cultured on feeders (irradiated J2-3T3 mouse fibroblasts) as described (Rheinwald, J. G. & Green, H. Serial cultivation of strains of human epidermal keratinocytes: the formation of keratinizing colonies from single cells. Cell 6, 331-343 (1975).)

extract_protocol: Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Schmidt et al, Methods. 2009 Jul;48(3):240-8. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Feeders were removed by washing cells with Versene (PBS, EDTA buffer) and keratinocytes were harvested by trypsinisation. Formaldehyde crosslinking (1% in PBS) for 10 minutes was followed by 5 minute quenching with Glycine. From here cells were kept on ice and chromatin was extracted as described (Connelly, J. T. et al. Nat Cell Biol 12, 711-718, 2010).

tag: passage

value: passage 2

tag: original body site

value: oral cavity (lip)

tag: antibody

value: none/input DNA


title: A10 P2_AG1478 BMP2.7 A

description:
4285752030_E
AG1478+BMP2/7 treated replicate 1

source_name: primary human keratinocytes treated with AG1478+BMP2/7


title: F10 P2_BMP2.7 C

description:
4285752030_F
BMP2/7 treated replicate 3


title: GV oocytes, XY, biological rep2

description: Gene expression from Mouse GV oocytes

source_name: Mouse GV oocytes (XY)

value: XY

tag: cell type


title: GV oocytes, XY, biological rep3

description: Gene expression from Mouse GV oocytes


title: GV oocytes, XY, biological rep1

description: Gene expression from Mouse GV oocytes


title: GV oocytes, XX, biological rep2

description: Gene expression from Mouse GV oocytes


title: G9 P2_AG1478 B

description:
4285752011_F
AG1478 treated replicate 2


title: B10 P2_AG1478 BMP2.7 B

description:
4285752030_A
AG1478+BMP2/7 treated replicate 2


title: E9 P2_vehicle C

description:
4285752030_B
vehicle treated replicate 3

source_name: primary human keratinocytes treated with vehicle


title: D9 P2_vehicle B

description:
4285752011_D
vehicle treated replicate 2


title: D10 P2_BMP2.7 A

description:
4285752011_E
BMP2/7 treated replicate 1


title: C10 P2_AG1478 BMP2.7 C

description:
4285752011_C
AG1478+BMP2/7 treated replicate 3


title: C9 P2_vehicle A

description:
4285752011_A
vehicle treated replicate 1


title: H9 P2_AG1478 C

description:
4285752011_B
AG1478 treated replicate 3


title: ING5 ChIP-seq

value: anti-ING5 (AbNova, mouse polyclonal, catalog# H00084289-B01P)


title: heart

description: normal heart pooled from 3 males (Clontech)

source_name: heart

tag: tissue

value: normal heart


title: colon w/ mucosa

description: normal colon w/ mucosa derived from 1 female (Clontech)

source_name: colon w/ mucosa

value: normal colon w/ mucosa