title: AK_2

city: Lund

first: Jenny

last: Karlsson

address: BMC C13

department: Clinical genetics

institute: Lund University

hyb_protocol: Illumina hybridization protocol (Manuel 11322187 Revision A)

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: Data was normalized with the quantile normalization algorithm in the BASE software (BASE - 2nd generation software for microarray data management and analysis, BMC Bioinformatics 2009)  BMC Bioinformatics 2009)

source_name: Non-neoplastic tissue

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v1.1)

extract_protocol: Total RNA was extracted with the RNeasy Lipid Tissue Mini Kit (Qiagen) followed by On-column DNase Digestion (Qiagen) according to the manufacturers´ instructions.

value: adult kidney


title: 23204

status: Public on Feb 04 2016

type: RNA

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

hyb_protocol: Biotin-double-stranded cDNA (3.75 μg) was hybridized, washed, stained, and scanned with the Affymetrix GeneTitan Instrument on an Affymetrix Human Gene 1.1 ST array plate (Affymetrix).  For some samples 200 ng of total RNA or 25 µg senseRNA or 5 µg double-stranded cDNA was not available.  In that case, all the available material was used.

scan_protocol: standard Affymetrix protocol

data_processing:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.download/HuGene11stv1_Hs_ENTREZG_15.1.0.zip
Raw Affymetrix gene expression data were pre-processed with RMA and summarized using the HU-gene11stv1hsentrezg 15.0.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FFPE tumor sample

label_protocol: A total of 25 μg SenseRNA was reverse transcribed and double-stranded cDNA was generated using the Biotin Labeling Kit for ST/Exon Arrays (Genisphere).  Using the same kit, 5 μg of double-stranded cDNA was fragmented and end-labeled with biotin.

extract_protocol: From each block four slices of 10 µm each were cut and transferred to a 1.5 ml Eppendorf tube.  Paraffin was removed using Deparaffinization Solution (Qiagen).  The tissue was then lyzed in proteinase K digestion (PKD) buffer (Qiagen).  RNA isolation was continued using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s instructions.  The RNA concentration of all the samples was determined on a Nanodrop-8000 UV-Vis Spectrophotometer (Thermo Scientific).  For a selection of samples, the RNA quality was determined with the RNA 6000 Nano LabChip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.  SenseRNA was generated from 200 ng of total RNA using the Sensation RNA Amplification Kit (Genisphere, Hatfield, PA, USA).

tag: tissue type

value: FFPE tumor sample

tag: panoptic il6


title: 39700


title: 51001


title: 38715


title: AK_1

country: Sweden

tag: tissue

tag: gender


title: FK_4

value: fetal kidney

value: pooled M/F


title: WT neurons endo-iPS12 2m r2

city: Moscow

first: Evgeny

last: Nekrasov

address: gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics

description:
SAMPLE 2
replicate 2
9345344033_B_Grn.idat

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalised using Genome Studio.

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

extract_protocol: RNA was extracted with the Qiagen QIAamp RNA Blood Mini Kit, followed by DNase I treatment and ethanol precipitation. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: wildtype

tag: age

value: 2 months

value: striatum-like

tag: cell type

value: iPSCs derived GABA MS-like neurons


title: WT neurons hESM01 3m r1

description:
SAMPLE 9
replicate 1
9345344033_I_Grn.idat

value: 3 months


title: 39762


title: Igorot15

type: genomic

city: Cambridge

first: Luca

last: Pagani

state: UK

address: Henry Wellcome Building, Fitzwilliam Street

department: Biological Anthropology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

source_name: Saliva

label_protocol: Followed Illumina standard protocol

extract_protocol: Extraction of genomic DNA from saliva was performed using standard extraction protocols.

value: M

tag: population

value: Kankanaey (Igorot)

tag: region

value: Philippines


title: 42355


title: Igorot14

value: F


title: FK_3


title: 39979


title: 36371


title: Igorot13


title: 38762


title: 32416


title: Igorot12


title: FK_2


title: 34160


title: Igorot11


title: 32829


title: 34149


title: CCSK_22

source_name: Tumor tissue

value: CCSK


title: 34259


title: 34265


title: WT43

value: Wilms tumor


title: Igorot1


title: FK_1


title: 41258


title: Dusun8

value: Dusun

value: Brunei


title: CCSK_19


title: Dusun7


title: 26702


title: Dusun6


title: AK6

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol

data_processing: GenomeStudio Software

label: Cy5 and Cy3

source_name: Fresh frozen non-malignant tissue from adult kidney

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted from fresh frozen tissue with the DNeasy Blood & Tissue Kit (Qiagen).


title: T47D untreated, day 5_rep1

hyb_protocol: A total of 4.5 µg fragmented biotin-labeled aRNA was hybridized on a HT Human Genome (HG)U219 96-array plate (Affymetrix).

scan_protocol: The plate was washed, stained, and scanned with the GeneTitan Instrument (Affymetrix).

data_processing: The microarray data were normalized with robust multi-array analysis (RMA; as per Irizarry et al, 2003) and summarized with the HG-U219H Entrezg 15.0.0 chip definition files (CDF).

source_name: T47D untreated_day 5

label_protocol: Biotin-labeled, amplified RNA (aRNA) was synthesized from 200 ng total RNA using the 3’IVT Express Kit (Affymetrix, Santa Clara, USA).  The aRNA was then purified using Agencourt RNAClean XP beads (Beckman Coulter Inc., Indianapolis, USA) on the BioMek Fx Workstation (Beckman Coulter Inc.).  Biotin-labeled aRNA was fragmented using the 3’IVT Express Kit (Affymetrix).

growth_protocol: Ten ERα-positive breast cancer cell lines, T47D, MDA-MB-134VI, BT474, BT-483, HCC1428, EFM-19, MCF-7, MDA-MB-175-VIIdsRed, MDA-MB-415 and ZR-751, were grown in TME-aligned 3D culture.

extract_protocol: After culturing, the media overlay was removed by aspiration and 150 μl Qiazol (Qiagen) immediately added to the cells plus BME to achieve lysis. This mixture was combined with an additional 600 μl Qiazol and stored at -80 °C until RNA isolation.  RNA isolation was performed using the miRNeasy 96 Kit (Qiagen). The RNA concentration of all the samples was determined on a Nanodrop-8000 UV-Vis Spectrophotometer (Thermo Scientific).

treatment_protocol: After establishment, the cells were grown in triplicate for 6 days in the absence or presence of 10 ng/ml IL-6, which was added on day 1. Sampling was performed on days 4, 5, and 6.  Five additional conditions were investigated in duplicate: (i) 10 ng/ml IL-6 added on day 0 + 50 μg/ml siltuximab added on day 1 (ii) 10 ng/ml IL-6 added on day 1 + 50 μg/ml siltuximab added on day 1 (iii) 50 μg/ml siltuximab added on day 0 (iv) human marrow stromal cell-conditioned media (hMSC-CM) (v) hMSC-CM + 50 μg/ml siltuximab.

tag: cell line

value: ERα-positive breast cancer cell line

tag: treatment

value: untreated

tag: time point (day)


title: WT41


title: Igorot10


title: WT42


title: AK5

value: Fresh frozen non-malignant tissue from adult kidney


title: WT40


title: Dusun5


title: Dusun3


title: Dusun4


title: Dusun23


title: Dusun22


title: 44971

value: FFPE tumor sample


title: Dusun21


title: AK4_B


title: Dusun2


title: AK3


title: Dusun20


title: AK4_C


title: WT38


title: AK2


title: AK1_B


title: Dusun19


title: WT35


title: FKm_C

source_name: commercially obtained DNA

value: commercially obtained DNA


title: WT33


title: AK1_C


title: WT36


title: WT31


title: Dusun18


title: WT19

source_name: Fresh frozen Wilms tumour tissue

value: Fresh frozen Wilms tumour tissue


title: FKf_C


title: FKm_A


title: WT34


title: WT18


title: WT37


title: WT29


title: Dusun17


title: FKf_A


title: WT32


title: Dusun16


title: WT30


title: WT17


title: WT28


title: WT27


title: Dusun15


title: HD neurons iPSHD22 2m r1

description:
SAMPLE 5
replicate 1
9345344033_E_Grn.idat

value: HD

value: 2 months

value: striatum-like


title: Dusun14


title: WT39

value: M


title: LP eosinophil_unstimulated

city: Pohang

first: Myoung Ho

last: Jang

address: 77 Cheongam-Ro

country: South Korea

institute: Academy of Immunology and Microbiology, Institute for Basic Science

description: Gene expression data from small intestinal lamina propria cells

hyb_protocol: The cDNA was hybridize for 16 hrs at 45°C on Affymetrix Murine Genome 430 2.0 microarray chips (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000 (Affymetrix).

data_processing: Microarray Suite software version 5.0 (Affymetrix) and GeneSpring software (Silicon Genetics) were used for data analysis.

organism: Mus musculus

source_name: Small intestinal lamina propria

label_protocol: Fragmented and biotinylated cDNA were synthesized from total RNA with Ovation Biotin System (Nugen) accroding to the manufacturer's protocol.

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

tag: strain

value: Small intestine

value: eosinophils

tag: cell markers

value: 8 weeks


title: Dusun13


title: WT26


title: Dusun12


title: Dusun11

description: Sample removed due to QC or inbreeding

value: F


title: WT15


title: WT25

value: Wilms tumor


title: WT24


title: LP DC_unstimulated

value: dendritic cells


title: WT14


title: WT11


title: WT10


title: WT12


title: Burm20

value: Burmese

value: Myanmar


title: Dusun1

value: Dusun

value: Brunei


title: Burm7


title: WT13


title: WT23


title: WT21


title: WT22


title: WT20


title: Burm19


title: Burm18


title: Dusun10


title: Burm17


title: WT16


title: WT9


title: WT6_A


title: WT7


title: Burm15


title: WT6_C


title: WT8


title: Burm16


title: WT9


title: WT5


title: Burm13


title: Fetal lung_2

city: Boston

first: Mauro

last: Longoni

state: MA

address: 185 Cambridge Street

department: Pediatric Surgical Research Laboratories

country: USA

institute: Massachusetts General Hospital

description: SAMPLE 2

hyb_protocol: Cy3 labeled samples were hybridized for 20 hours at 55oC with 20 rotation per minute

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Fetal Lung tissue, replicate 2

label_protocol: 100 ng total RNA was dephosphorylated and then labeled with Cyanine 3-pCp using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: Total RNA extraction of Fetal lung_1 and Fetal lung_2 was performed using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and the extraction was done according to the manufacturer’s instructions. The quantity and quality of each RNA sample was determined using NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) RNA Pico Kit.

treatment_protocol: Fetal lung_1 and _2 were obtained from termination of pregnancy

value: 9 week old

tag: developemental stage

value: pseudoglandular phase

value: fetal lung

value: uncultured


title: Fetal lung _Strategene_2

description: Total RNA from Strategene

source_name: Fetal Lung tissue_total RNA from Strategene

extract_protocol: RNA extraction and processing are available on the Stratagene website

treatment_protocol: Fetal lung _Strategene_1 and  _2 were commercial total RNA from Strategene

value: 18-20 week old

value: canalicular phase


title: WT11


title: WT2


title: Fetal lung _Strategene_1

description: Total RNA from Strategene


title: WT17

value: M


title: WT4

value: Fresh frozen Wilms tumour tissue


title: WT3_A


title: WT7


title: WT3_C


title: WT1


title: Burm12


title: WT3


title: LTL313BR - scr b 3a, scrb

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: SAMPLE 6

hyb_protocol: cRNAs were hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (AMDID 028004).

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner at a 3 µm scan resolution

data_processing: Data were processed with Agilent Feature Extraction 11.0.1.1. Processed signals were quantile normalized with Agilent GeneSpring 12.0

source_name: LTL313BR_Scrb ASO

label_protocol: The quality of the RNA samples was checked with the Agilent 2100 Bioanalyzer and NanoDrop ND-2000 UV-VIS spectrophotometer. Only samples with RNA Integrity Number (RIN) ≥8.0, A260/280 OD values between 1.8 and 2.0 and an A260/A230 OD value of 2.0 were used for one-color labelling using Agilent’s One-Colour Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling v6.0 (Agilent Technologies, Santa Clara, CA). Total RNA (100 ng) was used to generate cyanine-3-labeled cRNA.

extract_protocol: Qiagen RNeasy kit

tag: xenograft model

value: patient-derived xenograft (PDX) CRPC model

tag: tumor type

value: Prostate tumor, Patient derived xenograft

tag: tumor subtype

value: Adenocarcinoma

tag: treated with

value: Scrb ASO (i.p., 15mg/kg/day for 3 weeks, 5-day on, 2-day off)


title: Burm14


title: Burm11


title: Fetal lung_1

description: SAMPLE 1

source_name: Fetal Lung tissue, replicate 1

tag: tissue

tag: tissue type


title: Burm10

tag: gender


title: LTL313BR - scr b 5b, scrb

description: SAMPLE 8


title: CCSK37_C

source_name: Fresh frozen CCSK tissue

value: Fresh frozen CCSK tissue


title: LTL313BR - scr b 5a, scrb

description: SAMPLE 7


title: LTL313BR - scr b 1b, scrb

description: SAMPLE 5


title: Burm_9

value: Burmese


title: Burm_8

value: Myanmar


title: Burm_6


title: CCSK37_B


title: LTL313BR - 6w2 5b, 6w2

description: SAMPLE 4

source_name: LTL313BR_6w2 ASO

value: 6w2 ASO (i.p., 15mg/kg/day for 3 weeks, 5-day on, 2-day off)


title: Burm_4


title: WT2

value: F


title: CCSK36


title: LTL313BR - 6w2 4a, 6w2

description: SAMPLE 3


title: CCSK34


title: Burm_3


title: CCSK31


title: Burm_2


title: Burm_1


title: Bajo9KN

value: Bajo

value: Indonesia


title: CCSK35


title: Bajo9


title: WT16


title: LTL313BR - 6w2 1a, 6w2

description: SAMPLE 1


title: CCSK30


title: Burm_5


title: CCSK29


title: CCSK28


title: Bajo7KN


title: Bajo8


title: CCSK27


title: Bajo7


title: Bajo6KN


title: CCSK25


title: Bajo6


title: CCSK24


title: Bajo5KN


title: CCSK23


title: Bajo3KN


title: CCSK22


title: Bajo26KN


title: CCSK26


title: CCSK19_C


title: CCSK20


title: Bajo23KN


title: Bajo25KN


title: Bajo21KN


title: CCSK18_C


title: Bajo22KN

description: Sample removed due to QC or inbreeding


title: CCSK18_A


title: Bajo20KN


title: Bajo19KN


title: Bajo18KN


title: Bajo2KN


title: Bajo17KN


title: CCSK21


title: CCSK19_A


title: CCSK14


title: CCSK16


title: CCSK13


title: CCSK11


title: Bajo14KN


title: Bajo13


title: Bajo12KN


title: Bajo1KN


title: CCSK9


title: CCSK17


title: LTL313BR - 6w2 2b, 6w2

description: SAMPLE 2


title: Bajo16AKN


title: Bajo13KN


title: CCSK2


title: CCSK8


title: CCSK3_B


title: Bajo11KN


title: Bajo12


title: CCSK3_C


title: Bajo11


title: Bajo10KN


title: CCSK1


title: CCSK5


title: CCSK12


title: Bajo10


title: Bajo16BKN


title: Bajo15KN


title: liver_MDA low dose_5 day_rep 1

status: Public on Feb 03 2016

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

hyb_protocol: Fragmented, labeled cDNA were hybridized to Affymetrix RatGene 2.1 ST array plates on an Affymetrix GeneTitan following manufacturer’s instructions using the GeneTitan Hybridization, Wash and Stain Kit for WT array plates (Affymetrix, #901622).

scan_protocol: Array plates were scanned immediately after hybridization, wash and staining by the Affymetrix GeneTitan using default settings.

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the interPLIER gene level method (background = PM-GCBG, normalization method = Sketch-Quantile) in Affymetrix Expression Console software (Version 1.1).

organism: Rattus norvegicus

source_name: liver

label_protocol: An initial input of 100 ng total RNA per sample was synthesized to cDNA, fragmented, and labeled using Affymetrix's GeneChip WT Plus Reagent Kit Affymetrix #902281) according to manufacturer’s recommendations.

growth_protocol: Briefly, rats were housed under standard laboratory conditions in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility. Rats weighing 215-245 g (8 weeks old) were purchased from Charles River Laboratories (Raleigh, NC) and housed 2 per cage with a rat tunnel enrichment device (Bio-Serve, Frenchtown, NJ). Rats were fed a Purina Rodent Diet No. 5002 (Ralston Purina Co., St. Louis, MO), supplied ad libitum. Animals received reverse osmosis-treated tap water (City of Durham, NC) ad libitum, which was changed at least once weekly. Controls in the animal rooms were set to maintain temperatures between 20-25°C with a relative humidity of 30-70% and a 12-hour light/12-hour dark cycle, lights on at 6:00 AM.

extract_protocol: A portion of the frozen liver tissue was homogenized in QIAzol using Qiagen's TissueLyzer for 5 minutes at 50 Hz (Qiagen, GmbH, Germany). Total RNA was isolated from the homogenized liver tissue using Qiagen's miRNeasy 96 kits (Qiagen, GmbH, Germany) following the manufacturer's instructions. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Clinically healthy animals were assigned to dose groups using a procedure that stratifies animals across groups by body weight such that mean body weight of each group was not statistically different from any other group using analysis of variance (Statistical Analysis System version 9.2, SAS Institute, Cary, NC). Animals were dosed by oral gavage for five consecutive days (± 10 minutes from the previous day’s dose administration time). Volume was based upon daily body weight. Twenty-four hours after the final dose administration, animals were euthanized. Livers were harvested at necropsy and weighed to within 0.1 g. One half of the left lobe of the liver was fixed in 10% formalin. The remaining half of the left lobe of the liver was flash frozen in liquid nitrogen, then stored below -70°C. Liver specimens were frozen in less than three minutes from time of death.

value: Sprague Dawley

tag: Sex

value: male

tag: age

tag: toxicant

value: MDA

tag: dose

value: 22 mg/kg

value: liver


title: liver_MDA high dose_5 day_rep 1

value: 162 mg/kg


title: liver_MDA high dose_5 day_rep 3


title: liver_MDA mid dose_5 day_rep 2

value: 60 mg/kg


title: liver_dexamethasone high dose_5 day_rep 3

value: dexamethasone

value: 1 mg/kg


title: liver_MDA high dose_5 day_rep 2


title: liver_MDA/dex shared vehicle control_5 day_rep 3

value: MDA/dexamethasone

value: 0 mg/kg


title: liver_MDA low dose_5 day_rep 3


title: liver_dexamethasone high dose_5 day_rep 2


title: liver_MDA/dex shared vehicle control_5 day_rep 4


title: liver_MDA mid dose_5 day_rep 1


title: liver_MDA/dex shared vehicle control_5 day_rep 1


title: liver_carbon tetrachloride vehicle control_5 day_rep 5

value: carbon tetrachloride


title: liver_dexamethasone high dose_5 day_rep 1


title: liver_MDA mid dose_5 day_rep 3


title: liver_MDA low dose_5 day_rep 2


title: liver_MDA/dex shared vehicle control_5 day_rep 2


title: liver_MDA mid dose_5 day_rep 5


title: liver_MDA high dose_5 day_rep 5


title: liver_MDA/dex shared vehicle control_5 day_rep 5


title: liver_dexamethasone high dose_5 day_rep 4


title: liver_carbon tetrachloride vehicle control_5 day_rep 1


title: liver_MDA low dose_5 day_rep 5


title: liver_dexamethasone high dose_5 day_rep 5


title: liver_carbon tetrachloride vehicle control_5 day_rep 3


title: liver_carbon tetrachloride vehicle control_5 day_rep 2


title: liver_MDA high dose_5 day_rep 4


title: liver_MDA mid dose_5 day_rep 4


title: liver_carbon tetrachloride vehicle control_5 day_rep 4


title: liver_MDA low dose_5 day_rep 4


title: liver_carbon tetrachloride mid-high dose_5 day_rep 4

value: 93 mg/kg


title: liver_carbon tetrachloride mid dose_5 day_rep 1

value: 43 mg/kg


title: liver_carbon tetrachloride mid-high dose_5 day_rep 1


title: liver_carbon tetrachloride mid dose_5 day_rep 5


title: liver_carbon tetrachloride mid-high dose_5 day_rep 3


title: liver_carbon tetrachloride mid dose_5 day_rep 4


title: liver_carbon tetrachloride mid-high dose_5 day_rep 2


title: liver_carbon tetrachloride high dose_5 day_rep 2

value: 200 mg/kg


title: liver_carbon tetrachloride high dose_5 day_rep 3


title: liver_bromobenzene vehicle control_5 day_rep 3

value: bromobenzene


title: liver_carbon tetrachloride low dose_5 day_rep 3

value: 20 mg/kg


title: liver_carbon tetrachloride mid dose_5 day_rep 2

value: Sprague Dawley


title: liver_carbon tetrachloride low dose_5 day_rep 4

value: male


title: liver_bromobenzene vehicle control_5 day_rep 4


title: liver_bromobenzene mid-high dose_5 day_rep 3

value: 424 mg/kg


title: liver_carbon tetrachloride high dose_5 day_rep 4


title: liver_bromobenzene mid-high dose_5 day_rep 4


title: liver_bromobenzene vehicle control_5 day_rep 5


title: liver_carbon tetrachloride high dose_5 day_rep 5


title: liver_carbon tetrachloride low dose_5 day_rep 5


title: liver_carbon tetrachloride low dose_5 day_rep 1


title: liver_bromobenzene mid-high dose_5 day_rep 5


title: liver_carbon tetrachloride low dose_5 day_rep 2


title: liver_carbon tetrachloride high dose_5 day_rep 1


title: liver_bromobenzene mid-high dose_5 day_rep 1


title: liver_carbon tetrachloride mid-high dose_5 day_rep 5


title: liver_bromobenzene vehicle control_5 day_rep 2


title: liver_carbon tetrachloride mid dose_5 day_rep 3


title: liver_bromobenzene mid-high dose_5 day_rep 2


title: liver_bromobenzene mid dose_5 day_rep 4

value: 229 mg/kg


title: liver_bromobenzene mid dose_5 day_rep 5

value: liver


title: liver_bromobenzene mid dose_5 day_rep 3


title: liver_bromobenzene mid dose_5 day_rep 2


title: liver_bromobenzene low dose_5 day_rep 4

value: 124 mg/kg


title: liver_bromobenzene mid dose_5 day_rep 1


title: liver_bromobenzene low dose_5 day_rep 3


title: liver_bromobenzene low dose_5 day_rep 5


title: liver_bromobenzene high dose_5 day_rep 5

value: 785 mg/kg


title: liver_allyl alcohol vehicle control_5 day_rep 5

value: allyl alcohol


title: liver_allyl alcohol mid high dose_5 day_rep 4

value: 35 mg/kg


title: liver_allyl alcohol low dose_5 day_rep 5

value: 21 mg/kg


title: liver_allyl alcohol vehicle control_5 day_rep 2

value: 0 mg/kg


title: liver_allyl alcohol mid high dose_5 day_rep 1


title: liver_bromobenzene low dose_5 day_rep 1


title: liver_allyl alcohol vehicle control_5 day_rep 4


title: liver_allyl alcohol low dose_5 day_rep 4


title: liver_allyl alcohol mid high dose_5 day_rep 3


title: liver_bromobenzene high dose_5 day_rep 3


title: liver_bromobenzene low dose_5 day_rep 2


title: liver_bromobenzene high dose_5 day_rep 2


title: liver_allyl alcohol vehicle control_5 day_rep 3


title: liver_allyl alcohol mid dose_5 day_rep 5

value: 27 mg/kg


title: liver_allyl alcohol vehicle control_5 day_rep 1


title: liver_allyl alcohol mid dose_5 day_rep 3


title: liver_allyl alcohol mid dose_5 day_rep 2


title: liver_bromobenzene high dose_5 day_rep 1


title: liver_allyl alcohol low dose_5 day_rep 3


title: liver_allyl alcohol low dose_5 day_rep 2


title: liver_allyl alcohol mid dose_5 day_rep 4


title: liver_allyl alcohol mid high dose_5 day_rep 2


title: liver_bromobenzene high dose_5 day_rep 4


title: liver_allyl alcohol low dose_5 day_rep 1


title: Craniofacial microsomia 446

city: Beijing

first: Yong-Biao

last: Zhang

state: Select a State or Province

address: Beichen west road 1#

country: China

institute: Beijing Institute of Genomics

description: Genomic DNAs extracted from whole blood were genotyped using Illumina human Omni-zhonghua chips

hyb_protocol: according to the manufacturer’s specifications

scan_protocol: chips were scanned using iScan instrument

data_processing: We used Genomestudio to call the genotypes of SNPs, and performed association study using plink.

source_name: Craniofacial microsomia

growth_protocol: Extraction of genomic DNA from blood was performed using proteinase K and repeated phenol-chloroform extraction.

extract_protocol: genomic DNAs were extracted with DNA-extraction kits (Tiangen Biotech, Beijing, China)

treatment_protocol: the whole-blood was stored in -80 refrigerator

value: Male


title: liver_allyl alcohol high dose_5 day_rep 3

value: 45 mg/kg


title: liver_allyl alcohol high dose_5 day_rep 5


title: Craniofacial microsomia 443

label_protocol: according to the manufacturer’s specifications

value: Female


title: Craniofacial microsomia 445


title: Craniofacial microsomia 444


title: Craniofacial microsomia 438


title: Craniofacial microsomia 437


title: liver_allyl alcohol high dose_5 day_rep 1


title: Craniofacial microsomia 431


title: Craniofacial microsomia 441


title: Craniofacial microsomia 442


title: Craniofacial microsomia 433


title: Craniofacial microsomia 430


title: Craniofacial microsomia 436


title: Craniofacial microsomia 432


title: Craniofacial microsomia 434


title: Craniofacial microsomia 428


title: Craniofacial microsomia 423


title: Craniofacial microsomia 422


title: Craniofacial microsomia 427


title: Craniofacial microsomia 426


title: liver_allyl alcohol high dose_5 day_rep 4


title: Craniofacial microsomia 429


title: Craniofacial microsomia 435


title: Craniofacial microsomia 420


title: Craniofacial microsomia 440


title: Craniofacial microsomia 419


title: Craniofacial microsomia 439


title: Craniofacial microsomia 417


title: Craniofacial microsomia 418


title: Craniofacial microsomia 416


title: Craniofacial microsomia 415


title: Craniofacial microsomia 406


title: Craniofacial microsomia 414


title: Craniofacial microsomia 405


title: Craniofacial microsomia 425


title: Craniofacial microsomia 412


title: Craniofacial microsomia 424


title: Craniofacial microsomia 407


title: Craniofacial microsomia 409


title: Craniofacial microsomia 404


title: Craniofacial microsomia 402


title: Craniofacial microsomia 421


title: Craniofacial microsomia 400


title: Craniofacial microsomia 413


title: Craniofacial microsomia 408


title: Craniofacial microsomia 411


title: Craniofacial microsomia 398


title: Craniofacial microsomia 397


title: Craniofacial microsomia 396


title: Craniofacial microsomia 403


title: Craniofacial microsomia 401


title: Craniofacial microsomia 395


title: Craniofacial microsomia 410


title: Craniofacial microsomia 389


title: Craniofacial microsomia 394


title: Craniofacial microsomia 392


title: Craniofacial microsomia 393


title: Craniofacial microsomia 390


title: Craniofacial microsomia 388


title: Craniofacial microsomia 385


title: Craniofacial microsomia 380


title: Craniofacial microsomia 387


title: Craniofacial microsomia 382


title: Craniofacial microsomia 386


title: Craniofacial microsomia 379


title: Craniofacial microsomia 381


title: Craniofacial microsomia 383


title: Craniofacial microsomia 378


title: Craniofacial microsomia 384


title: Craniofacial microsomia 374


title: Craniofacial microsomia 375


title: Craniofacial microsomia 377


title: Craniofacial microsomia 373


title: Craniofacial microsomia 372


title: Craniofacial microsomia 371


title: Craniofacial microsomia 376


title: Craniofacial microsomia 370


title: Craniofacial microsomia 368


title: Craniofacial microsomia 367


title: Craniofacial microsomia 391


title: Craniofacial microsomia 399


title: Craniofacial microsomia 369


title: Craniofacial microsomia 366


title: Craniofacial microsomia 364


title: Craniofacial microsomia 361


title: Craniofacial microsomia 363


title: Craniofacial microsomia 360


title: Craniofacial microsomia 365


title: Craniofacial microsomia 359


title: Craniofacial microsomia 355


title: Craniofacial microsomia 353


title: Craniofacial microsomia 356


title: Craniofacial microsomia 354


title: Craniofacial microsomia 349


title: Craniofacial microsomia 345


title: Craniofacial microsomia 346


title: Craniofacial microsomia 351


title: Craniofacial microsomia 358


title: Craniofacial microsomia 343


title: Craniofacial microsomia 348


title: Craniofacial microsomia 347


title: Craniofacial microsomia 344


title: Craniofacial microsomia 342


title: Craniofacial microsomia 341


title: Craniofacial microsomia 350


title: Craniofacial microsomia 340


title: Craniofacial microsomia 339


title: Craniofacial microsomia 338


title: Craniofacial microsomia 335


title: Craniofacial microsomia 337


title: Craniofacial microsomia 336


title: Craniofacial microsomia 362


title: Craniofacial microsomia 334


title: Craniofacial microsomia 332


title: Craniofacial microsomia 333


title: Craniofacial microsomia 357


title: Craniofacial microsomia 331


title: Craniofacial microsomia 352


title: Craniofacial microsomia 330


title: Craniofacial microsomia 327


title: Craniofacial microsomia 329


title: Craniofacial microsomia 324


title: Craniofacial microsomia 328


title: Craniofacial microsomia 325


title: Craniofacial microsomia 322


title: Craniofacial microsomia 323


title: Craniofacial microsomia 318


title: Craniofacial microsomia 321


title: Craniofacial microsomia 320


title: Craniofacial microsomia 317


title: Craniofacial microsomia 315


title: Craniofacial microsomia 316


title: Craniofacial microsomia 314


title: Craniofacial microsomia 312


title: Craniofacial microsomia 326


title: Craniofacial microsomia 309


title: Craniofacial microsomia 308


title: Craniofacial microsomia 310


title: Craniofacial microsomia 307


title: Craniofacial microsomia 305


title: Craniofacial microsomia 306


title: Craniofacial microsomia 302


title: Craniofacial microsomia 319


title: Craniofacial microsomia 304


title: Craniofacial microsomia 301


title: Craniofacial microsomia 303


title: Craniofacial microsomia 300


title: Craniofacial microsomia 313


title: Craniofacial microsomia 299


title: Craniofacial microsomia 296


title: Craniofacial microsomia 295


title: Craniofacial microsomia 298


title: Craniofacial microsomia 291


title: Craniofacial microsomia 292


title: Craniofacial microsomia 297


title: Craniofacial microsomia 311


title: Craniofacial microsomia 288


title: Craniofacial microsomia 290


title: Craniofacial microsomia 293


title: Craniofacial microsomia 284


title: Craniofacial microsomia 286


title: Craniofacial microsomia 283


title: Craniofacial microsomia 287


title: Craniofacial microsomia 281


title: Craniofacial microsomia 289


title: Craniofacial microsomia 280


title: Craniofacial microsomia 282


title: Craniofacial microsomia 294


title: Craniofacial microsomia 285


title: Craniofacial microsomia 277


title: Craniofacial microsomia 276


title: Craniofacial microsomia 274


title: Craniofacial microsomia 275


title: Craniofacial microsomia 272


title: Craniofacial microsomia 273


title: Craniofacial microsomia 271


title: Craniofacial microsomia 270


title: Craniofacial microsomia 269


title: Craniofacial microsomia 268


title: Craniofacial microsomia 267


title: Craniofacial microsomia 265


title: Craniofacial microsomia 266


title: Craniofacial microsomia 262


title: Craniofacial microsomia 279


title: Craniofacial microsomia 264


title: Craniofacial microsomia 261


title: Craniofacial microsomia 259


title: Craniofacial microsomia 260


title: Craniofacial microsomia 258


title: Craniofacial microsomia 253


title: Craniofacial microsomia 254


title: Craniofacial microsomia 257


title: Craniofacial microsomia 252


title: Craniofacial microsomia 250


title: Craniofacial microsomia 256


title: Craniofacial microsomia 278


title: Craniofacial microsomia 255


title: Craniofacial microsomia 263


title: Craniofacial microsomia 246


title: Craniofacial microsomia 248


title: Craniofacial microsomia 247


title: Craniofacial microsomia 244


title: Craniofacial microsomia 242


title: Craniofacial microsomia 241


title: Craniofacial microsomia 243


title: Craniofacial microsomia 239


title: Craniofacial microsomia 240


title: Craniofacial microsomia 238


title: Craniofacial microsomia 237


title: Craniofacial microsomia 232


title: Craniofacial microsomia 235


title: Craniofacial microsomia 251


title: Craniofacial microsomia 236


title: Craniofacial microsomia 224


title: Craniofacial microsomia 225


title: Craniofacial microsomia 230


title: Craniofacial microsomia 229


title: Craniofacial microsomia 228


title: Craniofacial microsomia 249


title: Craniofacial microsomia 221


title: Craniofacial microsomia 222


title: Craniofacial microsomia 234


title: Craniofacial microsomia 231


title: Craniofacial microsomia 245


title: Craniofacial microsomia 226


title: Craniofacial microsomia 218


title: Craniofacial microsomia 223


title: Craniofacial microsomia 220


title: Craniofacial microsomia 216


title: Craniofacial microsomia 233


title: Craniofacial microsomia 219


title: Craniofacial microsomia 217


title: Craniofacial microsomia 214


title: Craniofacial microsomia 211


title: Craniofacial microsomia 210


title: Craniofacial microsomia 212


title: Craniofacial microsomia 208


title: Craniofacial microsomia 206


title: Craniofacial microsomia 205


title: Craniofacial microsomia 204


title: Craniofacial microsomia 207


title: Craniofacial microsomia 199


title: Craniofacial microsomia 203


title: Craniofacial microsomia 227


title: Craniofacial microsomia 201


title: Craniofacial microsomia 202


title: Craniofacial microsomia 200


title: Craniofacial microsomia 215


title: Craniofacial microsomia 197


title: Craniofacial microsomia 195


title: Craniofacial microsomia 198


title: Craniofacial microsomia 193


title: Craniofacial microsomia 192


title: Craniofacial microsomia 187


title: Craniofacial microsomia 191


title: Craniofacial microsomia 189


title: Craniofacial microsomia 209


title: Craniofacial microsomia 186


title: Craniofacial microsomia 188


title: Craniofacial microsomia 213


title: Craniofacial microsomia 182


title: Craniofacial microsomia 181


title: Craniofacial microsomia 196


title: Craniofacial microsomia 177


title: Craniofacial microsomia 178


title: Craniofacial microsomia 179


title: Craniofacial microsomia 176


title: Craniofacial microsomia 171


title: Craniofacial microsomia 194


title: Craniofacial microsomia 173


title: Craniofacial microsomia 166


title: Craniofacial microsomia 167


title: Craniofacial microsomia 190


title: Craniofacial microsomia 170


title: Craniofacial microsomia 165


title: Craniofacial microsomia 184


title: Craniofacial microsomia 169


title: Craniofacial microsomia 183


title: Craniofacial microsomia 172


title: Craniofacial microsomia 162


title: Craniofacial microsomia 163


title: Craniofacial microsomia 161


title: Craniofacial microsomia 180


title: Craniofacial microsomia 159


title: Craniofacial microsomia 158


title: Craniofacial microsomia 160


title: Craniofacial microsomia 164


title: Craniofacial microsomia 185


title: Craniofacial microsomia 175


title: Craniofacial microsomia 155


title: Craniofacial microsomia 153


title: Craniofacial microsomia 174


title: Craniofacial microsomia 156


title: Craniofacial microsomia 154


title: Craniofacial microsomia 152


title: Craniofacial microsomia 150


title: Craniofacial microsomia 148


title: Craniofacial microsomia 151


title: Craniofacial microsomia 145


title: Craniofacial microsomia 144


title: Craniofacial microsomia 147


title: Craniofacial microsomia 157


title: Craniofacial microsomia 141


title: Craniofacial microsomia 140


title: Craniofacial microsomia 146


title: Craniofacial microsomia 138


title: Craniofacial microsomia 136


title: Craniofacial microsomia 135


title: Craniofacial microsomia 142


title: Craniofacial microsomia 139


title: Craniofacial microsomia 143


title: Craniofacial microsomia 131


title: Craniofacial microsomia 134


title: Craniofacial microsomia 129


title: Craniofacial microsomia 130


title: Craniofacial microsomia 133


title: Craniofacial microsomia 125


title: Craniofacial microsomia 132


title: Craniofacial microsomia 168


title: Craniofacial microsomia 126


title: Craniofacial microsomia 123


title: Craniofacial microsomia 124


title: Craniofacial microsomia 127


title: Craniofacial microsomia 121


title: Craniofacial microsomia 117


title: Craniofacial microsomia 116


title: Craniofacial microsomia 119


title: Craniofacial microsomia 149


title: Craniofacial microsomia 115


title: Craniofacial microsomia 110


title: Craniofacial microsomia 113


title: Craniofacial microsomia 114


title: Craniofacial microsomia 128


title: Craniofacial microsomia 111


title: Craniofacial microsomia 104


title: Craniofacial microsomia 103


title: Craniofacial microsomia 112


title: Craniofacial microsomia 137


title: Craniofacial microsomia 99


title: Craniofacial microsomia 109


title: Craniofacial microsomia 107


title: Craniofacial microsomia 122


title: Craniofacial microsomia 96


title: Craniofacial microsomia 106


title: Craniofacial microsomia 102


title: Craniofacial microsomia 105


title: Craniofacial microsomia 100


title: Craniofacial microsomia 98


title: Craniofacial microsomia 95


title: Craniofacial microsomia 120


title: Craniofacial microsomia 93


title: Craniofacial microsomia 92


title: Craniofacial microsomia 108


title: Craniofacial microsomia 85


title: Craniofacial microsomia 88


title: Craniofacial microsomia 94


title: Craniofacial microsomia 83


title: Craniofacial microsomia 91


title: Craniofacial microsomia 90


title: Craniofacial microsomia 79


title: Craniofacial microsomia 89


title: Craniofacial microsomia 101


title: Craniofacial microsomia 84


title: Craniofacial microsomia 82


title: Craniofacial microsomia 81


title: Craniofacial microsomia 76


title: Craniofacial microsomia 74


title: Craniofacial microsomia 77


title: Craniofacial microsomia 80


title: Craniofacial microsomia 97


title: Craniofacial microsomia 73


title: Craniofacial microsomia 68


title: Craniofacial microsomia 69


title: Craniofacial microsomia 67


title: Craniofacial microsomia 66


title: Craniofacial microsomia 64


title: Craniofacial microsomia 87


title: Craniofacial microsomia 65


title: Craniofacial microsomia 75


title: Craniofacial microsomia 62


title: Craniofacial microsomia 70


title: Craniofacial microsomia 63


title: Craniofacial microsomia 78


title: Craniofacial microsomia 60


title: Craniofacial microsomia 61


title: Craniofacial microsomia 59


title: Craniofacial microsomia 72


title: Craniofacial microsomia 86


title: Craniofacial microsomia 55


title: Craniofacial microsomia 58


title: Craniofacial microsomia 56


title: Craniofacial microsomia 57


title: Craniofacial microsomia 54


title: Craniofacial microsomia 71


title: Craniofacial microsomia 52


title: Craniofacial microsomia 48


title: Craniofacial microsomia 47


title: Craniofacial microsomia 53


title: Craniofacial microsomia 118


title: Craniofacial microsomia 50


title: Craniofacial microsomia 44


title: Craniofacial microsomia 49


title: Craniofacial microsomia 51


title: Craniofacial microsomia 43


title: Craniofacial microsomia 41


title: Craniofacial microsomia 39


title: Craniofacial microsomia 40


title: Craniofacial microsomia 46


title: Craniofacial microsomia 38


title: Craniofacial microsomia 37


title: Craniofacial microsomia 36


title: Craniofacial microsomia 32


title: Craniofacial microsomia 30


title: Craniofacial microsomia 33


title: Craniofacial microsomia 34


title: Craniofacial microsomia 26


title: Craniofacial microsomia 35


title: Craniofacial microsomia 24


title: Craniofacial microsomia 21


title: Craniofacial microsomia 25


title: Craniofacial microsomia 18


title: Craniofacial microsomia 19


title: Craniofacial microsomia 22


title: Craniofacial microsomia 17


title: Craniofacial microsomia 29


title: Craniofacial microsomia 16


title: Craniofacial microsomia 27


title: Craniofacial microsomia 20


title: Craniofacial microsomia 42


title: Craniofacial microsomia 14


title: Craniofacial microsomia 11


title: Craniofacial microsomia 23


title: Craniofacial microsomia 9


title: Craniofacial microsomia 8


title: Craniofacial microsomia 10


title: Craniofacial microsomia 15


title: Craniofacial microsomia 5


title: Craniofacial microsomia 6


title: Craniofacial microsomia 3


title: Craniofacial microsomia 12


title: Craniofacial microsomia 31


title: Craniofacial microsomia 7


title: Craniofacial microsomia 2


title: Craniofacial microsomia 938


title: Craniofacial microsomia 937


title: Craniofacial microsomia 939


title: Craniofacial microsomia 935


title: Craniofacial microsomia 931


title: Craniofacial microsomia 933


title: Craniofacial microsomia 1


title: Craniofacial microsomia 932


title: Craniofacial microsomia 45


title: Craniofacial microsomia 936


title: Craniofacial microsomia 929


title: Craniofacial microsomia 927


title: Craniofacial microsomia 930


title: Craniofacial microsomia 928


title: Craniofacial microsomia 923


title: Craniofacial microsomia 4


title: Craniofacial microsomia 924


title: Craniofacial microsomia 934


title: Craniofacial microsomia 13


title: Craniofacial microsomia 925


title: Craniofacial microsomia 922


title: Craniofacial microsomia 920


title: Craniofacial microsomia 916


title: Craniofacial microsomia 915


title: Craniofacial microsomia 921


title: Craniofacial microsomia 917


title: Craniofacial microsomia 914


title: Craniofacial microsomia 912


title: Craniofacial microsomia 913


title: Craniofacial microsomia 911


title: Craniofacial microsomia 926


title: Craniofacial microsomia 918


title: Craniofacial microsomia 909


title: Craniofacial microsomia 910


title: Craniofacial microsomia 907


title: Craniofacial microsomia 908


title: Craniofacial microsomia 904


title: Craniofacial microsomia 906


title: Craniofacial microsomia 905


title: Craniofacial microsomia 919


title: Craniofacial microsomia 898


title: Craniofacial microsomia 900


title: Craniofacial microsomia 899


title: Craniofacial microsomia 901


title: Craniofacial microsomia 897


title: Craniofacial microsomia 894


title: Craniofacial microsomia 893


title: Craniofacial microsomia 896


title: Craniofacial microsomia 895


title: Craniofacial microsomia 889


title: Craniofacial microsomia 892


title: Craniofacial microsomia 891


title: Craniofacial microsomia 890


title: Craniofacial microsomia 886


title: Craniofacial microsomia 887


title: Craniofacial microsomia 888


title: Craniofacial microsomia 882


title: Craniofacial microsomia 884


title: Craniofacial microsomia 902


title: Craniofacial microsomia 903


title: Craniofacial microsomia 880


title: Craniofacial microsomia 881


title: Craniofacial microsomia 877


title: Craniofacial microsomia 876


title: Craniofacial microsomia 875


title: Craniofacial microsomia 873


title: Craniofacial microsomia 878


title: Craniofacial microsomia 871


title: Craniofacial microsomia 872


title: Craniofacial microsomia 870


title: Craniofacial microsomia 868


title: Craniofacial microsomia 865


title: Craniofacial microsomia 866


title: Craniofacial microsomia 867


title: Craniofacial microsomia 864


title: Craniofacial microsomia 861


title: Craniofacial microsomia 874


title: Craniofacial microsomia 883


title: Craniofacial microsomia 862


title: Craniofacial microsomia 860


title: Craniofacial microsomia 885


title: Craniofacial microsomia 859


title: Craniofacial microsomia 879


title: Craniofacial microsomia 855


title: Craniofacial microsomia 857


title: Craniofacial microsomia 854


title: Craniofacial microsomia 852


title: Craniofacial microsomia 856


title: Craniofacial microsomia 853


title: Craniofacial microsomia 850


title: Craniofacial microsomia 869


title: Craniofacial microsomia 851


title: Craniofacial microsomia 846


title: Craniofacial microsomia 848


title: Craniofacial microsomia 844


title: Craniofacial microsomia 863


title: Craniofacial microsomia 843


title: Craniofacial microsomia 845


title: Craniofacial microsomia 840


title: Craniofacial microsomia 839


title: Craniofacial microsomia 838


title: Craniofacial microsomia 858


title: Craniofacial microsomia 835


title: Craniofacial microsomia 834


title: Craniofacial microsomia 837


title: Craniofacial microsomia 842


title: Craniofacial microsomia 829


title: Craniofacial microsomia 832


title: Craniofacial microsomia 833


title: Craniofacial microsomia 827


title: Craniofacial microsomia 847


title: Craniofacial microsomia 831


title: Craniofacial microsomia 830


title: Craniofacial microsomia 849


title: Craniofacial microsomia 826


title: Craniofacial microsomia 841


title: Craniofacial microsomia 825


title: Craniofacial microsomia 822


title: Craniofacial microsomia 828


title: Craniofacial microsomia 821


title: Craniofacial microsomia 28


title: Craniofacial microsomia 824


title: Craniofacial microsomia 836


title: Craniofacial microsomia 819


title: Craniofacial microsomia 818


title: Craniofacial microsomia 816


title: Craniofacial microsomia 817


title: Craniofacial microsomia 810


title: Craniofacial microsomia 813


title: Craniofacial microsomia 814


title: Craniofacial microsomia 807


title: Craniofacial microsomia 809


title: Craniofacial microsomia 806


title: Craniofacial microsomia 808


title: Craniofacial microsomia 801


title: Craniofacial microsomia 805


title: Craniofacial microsomia 802


title: Craniofacial microsomia 803


title: Craniofacial microsomia 823


title: Craniofacial microsomia 800


title: Craniofacial microsomia 797


title: Craniofacial microsomia 799


title: Craniofacial microsomia 798


title: Craniofacial microsomia 796


title: Craniofacial microsomia 795


title: Craniofacial microsomia 794


title: Craniofacial microsomia 793


title: Craniofacial microsomia 815


title: Craniofacial microsomia 790


title: Craniofacial microsomia 789


title: Craniofacial microsomia 812


title: Craniofacial microsomia 820


title: Craniofacial microsomia 791


title: Craniofacial microsomia 811


title: Craniofacial microsomia 788


title: Craniofacial microsomia 786


title: Craniofacial microsomia 785


title: Craniofacial microsomia 782


title: Craniofacial microsomia 780


title: Craniofacial microsomia 787


title: Craniofacial microsomia 778


title: Craniofacial microsomia 781


title: Craniofacial microsomia 792


title: Craniofacial microsomia 777


title: Craniofacial microsomia 784


title: Craniofacial microsomia 775


title: Craniofacial microsomia 774


title: Craniofacial microsomia 771


title: Craniofacial microsomia 773


title: Craniofacial microsomia 769


title: Craniofacial microsomia 779


title: Craniofacial microsomia 772


title: Craniofacial microsomia 770


title: Craniofacial microsomia 776


title: Craniofacial microsomia 768


title: Craniofacial microsomia 767


title: Craniofacial microsomia 766


title: Craniofacial microsomia 765


title: Craniofacial microsomia 764


title: Craniofacial microsomia 763


title: Craniofacial microsomia 761


title: Craniofacial microsomia 760


title: Craniofacial microsomia 762


title: Craniofacial microsomia 783


title: Craniofacial microsomia 759


title: Craniofacial microsomia 758


title: Craniofacial microsomia 756


title: Craniofacial microsomia 755


title: Craniofacial microsomia 757


title: Craniofacial microsomia 752


title: Craniofacial microsomia 754


title: Craniofacial microsomia 751


title: Craniofacial microsomia 747


title: Craniofacial microsomia 746


title: Craniofacial microsomia 749


title: Craniofacial microsomia 745


title: Craniofacial microsomia 744


title: Craniofacial microsomia 743


title: Craniofacial microsomia 742


title: Craniofacial microsomia 750


title: Craniofacial microsomia 740


title: Craniofacial microsomia 748


title: Craniofacial microsomia 739


title: Craniofacial microsomia 738


title: Craniofacial microsomia 736


title: Craniofacial microsomia 741


title: Craniofacial microsomia 737


title: Craniofacial microsomia 735


title: Craniofacial microsomia 733


title: Craniofacial microsomia 804


title: Craniofacial microsomia 732


title: Craniofacial microsomia 734


title: Craniofacial microsomia 731


title: Craniofacial microsomia 730


title: Craniofacial microsomia 753


title: Craniofacial microsomia 729


title: Craniofacial microsomia 728


title: Craniofacial microsomia 727


title: Craniofacial microsomia 724


title: Craniofacial microsomia 726


title: Craniofacial microsomia 725


title: Craniofacial microsomia 719


title: Craniofacial microsomia 721


title: Craniofacial microsomia 716


title: Craniofacial microsomia 718


title: Craniofacial microsomia 717


title: Craniofacial microsomia 722


title: Craniofacial microsomia 714


title: Craniofacial microsomia 713


title: Craniofacial microsomia 711


title: Craniofacial microsomia 715


title: Craniofacial microsomia 712


title: Craniofacial microsomia 710


title: Craniofacial microsomia 709


title: Craniofacial microsomia 705


title: Craniofacial microsomia 704


title: Craniofacial microsomia 707


title: Craniofacial microsomia 703


title: Craniofacial microsomia 700


title: Craniofacial microsomia 701


title: Craniofacial microsomia 723


title: Craniofacial microsomia 702


title: Craniofacial microsomia 720


title: Craniofacial microsomia 696


title: Craniofacial microsomia 698


title: Craniofacial microsomia 694


title: Craniofacial microsomia 689


title: Craniofacial microsomia 693


title: Craniofacial microsomia 692


title: Craniofacial microsomia 690


title: Craniofacial microsomia 697


title: Craniofacial microsomia 688


title: Craniofacial microsomia 686


title: Craniofacial microsomia 685


title: Craniofacial microsomia 706


title: Craniofacial microsomia 684


title: Craniofacial microsomia 687


title: Craniofacial microsomia 682


title: Craniofacial microsomia 708


title: Craniofacial microsomia 683


title: Craniofacial microsomia 699


title: Craniofacial microsomia 679


title: Craniofacial microsomia 681


title: Craniofacial microsomia 680


title: Craniofacial microsomia 677


title: Craniofacial microsomia 676


title: Craniofacial microsomia 673


title: Craniofacial microsomia 674


title: Craniofacial microsomia 695


title: Craniofacial microsomia 675


title: Craniofacial microsomia 672


title: Craniofacial microsomia 671


title: Craniofacial microsomia 678


title: Craniofacial microsomia 670


title: Craniofacial microsomia 669


title: Craniofacial microsomia 691


title: Craniofacial microsomia 665


title: Craniofacial microsomia 663


title: Craniofacial microsomia 666


title: Craniofacial microsomia 668


title: Craniofacial microsomia 659


title: Craniofacial microsomia 655


title: Craniofacial microsomia 658


title: Craniofacial microsomia 662


title: Craniofacial microsomia 664


title: Craniofacial microsomia 660


title: Craniofacial microsomia 653


title: Craniofacial microsomia 650


title: Craniofacial microsomia 651


title: Craniofacial microsomia 657


title: Craniofacial microsomia 652


title: Craniofacial microsomia 654


title: Craniofacial microsomia 649


title: Craniofacial microsomia 648


title: Craniofacial microsomia 645


title: Craniofacial microsomia 646


title: Craniofacial microsomia 644


title: Craniofacial microsomia 647


title: Craniofacial microsomia 643


title: Craniofacial microsomia 642


title: Craniofacial microsomia 641


title: Craniofacial microsomia 656


title: Craniofacial microsomia 661


title: Craniofacial microsomia 667


title: Craniofacial microsomia 640


title: Craniofacial microsomia 639


title: Craniofacial microsomia 638


title: Craniofacial microsomia 636


title: Craniofacial microsomia 633


title: Craniofacial microsomia 634


title: Craniofacial microsomia 632


title: Craniofacial microsomia 635


title: Craniofacial microsomia 630


title: Craniofacial microsomia 629


title: Craniofacial microsomia 624


title: Craniofacial microsomia 626


title: Craniofacial microsomia 628


title: Craniofacial microsomia 625


title: Craniofacial microsomia 627


title: Craniofacial microsomia 623


title: Craniofacial microsomia 620


title: Craniofacial microsomia 619


title: Craniofacial microsomia 617


title: Craniofacial microsomia 622


title: Craniofacial microsomia 618


title: Craniofacial microsomia 615


title: Craniofacial microsomia 621


title: Craniofacial microsomia 609


title: Craniofacial microsomia 613


title: Craniofacial microsomia 612


title: Craniofacial microsomia 637


title: Craniofacial microsomia 611


title: Craniofacial microsomia 610


title: Craniofacial microsomia 614


title: Craniofacial microsomia 608


title: Craniofacial microsomia 606


title: Craniofacial microsomia 604


title: Craniofacial microsomia 631


title: Craniofacial microsomia 602


title: Craniofacial microsomia 601


title: Craniofacial microsomia 605


title: Craniofacial microsomia 599


title: Craniofacial microsomia 600


title: Craniofacial microsomia 596


title: Craniofacial microsomia 598


title: Craniofacial microsomia 595


title: Craniofacial microsomia 616


title: Craniofacial microsomia 597


title: Craniofacial microsomia 592


title: Craniofacial microsomia 590


title: Craniofacial microsomia 593


title: Craniofacial microsomia 594


title: Craniofacial microsomia 607


title: Craniofacial microsomia 589


title: Craniofacial microsomia 588


title: Craniofacial microsomia 591


title: Craniofacial microsomia 586


title: Craniofacial microsomia 584


title: Craniofacial microsomia 585


title: Craniofacial microsomia 583


title: Craniofacial microsomia 587


title: Craniofacial microsomia 582


title: Craniofacial microsomia 603


title: Craniofacial microsomia 581


title: Craniofacial microsomia 577


title: Craniofacial microsomia 578


title: Craniofacial microsomia 579


title: Craniofacial microsomia 575


title: Craniofacial microsomia 574


title: Craniofacial microsomia 571


title: Craniofacial microsomia 570


title: Craniofacial microsomia 572


title: Craniofacial microsomia 573


title: Craniofacial microsomia 568


title: Craniofacial microsomia 576


title: Craniofacial microsomia 569


title: Craniofacial microsomia 567


title: Craniofacial microsomia 566


title: Craniofacial microsomia 565


title: Craniofacial microsomia 560


title: Craniofacial microsomia 563


title: Craniofacial microsomia 561


title: Craniofacial microsomia 564


title: Craniofacial microsomia 555


title: Craniofacial microsomia 559


title: Craniofacial microsomia 562


title: Craniofacial microsomia 557


title: Craniofacial microsomia 580


title: Craniofacial microsomia 558


title: Craniofacial microsomia 554


title: Craniofacial microsomia 556


title: Craniofacial microsomia 551


title: Craniofacial microsomia 553


title: Craniofacial microsomia 550


title: Craniofacial microsomia 552


title: Craniofacial microsomia 548


title: Craniofacial microsomia 547


title: Craniofacial microsomia 545


title: Craniofacial microsomia 541


title: Craniofacial microsomia 542


title: Craniofacial microsomia 543


title: Craniofacial microsomia 539


title: Craniofacial microsomia 538


title: Craniofacial microsomia 537


title: Craniofacial microsomia 536


title: Craniofacial microsomia 535


title: Craniofacial microsomia 529


title: Craniofacial microsomia 528


title: Craniofacial microsomia 525


title: Craniofacial microsomia 533


title: Craniofacial microsomia 531


title: Craniofacial microsomia 524


title: Craniofacial microsomia 549


title: Craniofacial microsomia 532


title: Craniofacial microsomia 527


title: Craniofacial microsomia 530


title: Craniofacial microsomia 546


title: Craniofacial microsomia 526


title: Craniofacial microsomia 522


title: Craniofacial microsomia 521


title: Craniofacial microsomia 519


title: Craniofacial microsomia 520


title: Craniofacial microsomia 544


title: Craniofacial microsomia 518


title: Craniofacial microsomia 517


title: Craniofacial microsomia 540


title: Craniofacial microsomia 515


title: Craniofacial microsomia 516


title: Craniofacial microsomia 514


title: Craniofacial microsomia 513


title: Craniofacial microsomia 534


title: Craniofacial microsomia 511


title: Craniofacial microsomia 512


title: Craniofacial microsomia 510


title: Craniofacial microsomia 509


title: Craniofacial microsomia 507


title: Craniofacial microsomia 505


title: Craniofacial microsomia 506


title: Craniofacial microsomia 523


title: Craniofacial microsomia 504


title: Craniofacial microsomia 508


title: Craniofacial microsomia 502


title: Craniofacial microsomia 503


title: Craniofacial microsomia 498


title: Craniofacial microsomia 499


title: Craniofacial microsomia 501


title: Craniofacial microsomia 495


title: Craniofacial microsomia 500


title: Craniofacial microsomia 492


title: Craniofacial microsomia 497


title: Craniofacial microsomia 493


title: Craniofacial microsomia 491


title: Craniofacial microsomia 489


title: Craniofacial microsomia 485


title: Craniofacial microsomia 484


title: Craniofacial microsomia 487


title: Craniofacial microsomia 488


title: Craniofacial microsomia 480


title: Craniofacial microsomia 483


title: Craniofacial microsomia 496


title: Craniofacial microsomia 481


title: Craniofacial microsomia 479


title: Craniofacial microsomia 494


title: Craniofacial microsomia 476


title: Craniofacial microsomia 474


title: Craniofacial microsomia 475


title: Craniofacial microsomia 472


title: Craniofacial microsomia 477


title: Craniofacial microsomia 473


title: Craniofacial microsomia 470


title: Craniofacial microsomia 471


title: Craniofacial microsomia 469


title: Craniofacial microsomia 490


title: Craniofacial microsomia 467


title: Craniofacial microsomia 486


title: Craniofacial microsomia 468


title: Craniofacial microsomia 466


title: Craniofacial microsomia 482


title: Craniofacial microsomia 465


title: Craniofacial microsomia 464


title: Craniofacial microsomia 478


title: Craniofacial microsomia 462


title: Craniofacial microsomia 461


title: Craniofacial microsomia 459


title: Craniofacial microsomia 460


title: Craniofacial microsomia 458


title: Craniofacial microsomia 457


title: Craniofacial microsomia 456


title: Craniofacial microsomia 453


title: Craniofacial microsomia 463


title: DLP GFP+, biological rep 2

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

hyb_protocol: Standard hyb protocol per the Sequencing & Non-coding RNA facility at  MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

scan_protocol: Standard scan protocol per the Sequencing & Non-coding RNA facility at  MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

data_processing: Genes with statistically significant differences between test and control conditions (Ptenpc-/-Smad4pc-/- tumors vs Ptenpc-/- tumors or GFP+ vs. Tomato+) were generated using the following method: statistical analyses were performed on log scale data using parametric test and variances are not assumed equal (Welch t-test) with p-value cutoff 0.05. Additional fold change was applied to generate the final list of genes as indicated in the Figure legend. Gene filtering was performed by removing genes whose mean normalized test and control intensities are both less than the 20th percentile of the combined normalized signal intensities. The intensities reported below correspond to mean normalized test and control data rescaled to a median of 500.

source_name: DLP GFP+ cancer cells

label_protocol: Standard label protocol per the Sequencing & Non-coding RNA facility at  MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

growth_protocol: Ptenpc-/- Smad4pc-/- model were developed previously (Ding Z, Wu CJ, Chu GC, Xiao Y, Ho D, Zhang J, et al. SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression. Nature. 2011;470:269-73. ) and were backcrossed to the C57BL/6 background for more than 4 generations. B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J (“mTmG”) strain was obtained from Jackson Laboratory. Ptenpc-/- Smad4pc-/- mTmG+ mice were obtained through intercross. Mice were maintained in pathogen-free conditions at M.D. Anderson Cancer Center. All manipulations were approved under MD Anderson Cancer Center (MDACC) Institutional Animal Care and Use Committee (IACUC).

treatment_protocol: Mice were maintained to grow until 28 weeks when prominent prostate tumors developed. No further treatment was applied before tissue was harvested.

tag: prostate lobe

value: dorsolateral prostate (DLP)

tag: cell population

value: GFP+ sorted, cancer cells


title: DLP unsorted, biological rep 2

source_name: DLP unsorted cells

value: unsorted, both cancer and stromal


title: AP Tomato+, biological rep 2

source_name: AP tomato+ stromal cells

value: anterior prostate (AP)

value: Tomato+ sorted, stromal cells


title: Craniofacial microsomia 452


title: DLP Tomato+, biological rep 2

source_name: DLP tomato+ stromal cells


title: AP GFP+, biological rep 2

source_name: AP GFP+ cancer cells


title: DLP GFP+, biological rep 1


title: ESC-Men1-null-adipo 2

city: Bethesda

first: WeiPing

last: Chen

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

department: GCL

institute: NIDDK/NIH

description: 05-30-12_SAgarwal5_Mouse430_2_Men1-adipo-Null2.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek6.6

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

growth_protocol: Men1-null and WT mESCs were cultured in ESC maintenance medium with LIF (Millipopre) at 37˚C and 5% CO2.

extract_protocol: Total RNA was isolated using the RNAeasy kit according to the manufacturer's instructions (Qiagen) from 3 independent cultures of in vitro differentiated Men1-null and WT adipocytes

treatment_protocol: Men1-null and WT mESCs were differentiated into adipocytes by using the Adipogenesis kit (Millipore), and tested for adipocyte formation by oil red O staining

tag: cell type

value: adipocytes derived from mouse embryonic stem cells

tag: genotype/variation


title: Craniofacial microsomia 451


title: ESC-Men1-null-adipo 3

description: 05-30-12_SAgarwal6_Mouse430_2_Men1-adipo-Null3.CEL


title: AP Tomato+, biological rep 1


title: DLP Tomato+, biological rep 1


title: AP unsorted, biological rep 1

source_name: AP unsorted cells


title: Craniofacial microsomia 449


title: DLP unsorted, biological rep 1


title: Craniofacial microsomia 450


title: AP GFP+, biological rep 1


title: ESC-Men1-null-adipo 1

description: 05-30-12_SAgarwal4_Mouse430_2_Men1-adipo-Null1.CEL


title: ESC-WT-adipo 3

description: 05-30-12_SAgarwal3_Mouse430_2_Men1-adipo-WT3.CEL

source_name: ESC-WT-adipo

value: wild type


title: Craniofacial microsomia 447


title: AP unsorted, biological rep 2


title: ESC-WT-adipo 2

description: 05-30-12_SAgarwal2_Mouse430_2_Men1-adipo-WT2.CEL


title: ESC-WT-adipo 1

description: 05-30-12_SAgarwal1_Mouse430_2_Men1-adipo-WT1.CEL


title: Craniofacial microsomia 448


title: P/K OSE cells expressing homozygous Trp53 R172H mutation, Rep 2

first: Yi

last: Ren

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Gene expression data from tumor ovarian surface epithelial cells
trypsinized, plated, and unpassaged OSE cells

hyb_protocol: Standard Affymetrix hybridization

scan_protocol: GeneChips Scanner 3000

data_processing: RMA software

source_name: Mouse ovarian surface epithelial cells_homozygous _Trp63_R172H

label_protocol: Standard Affymetrix labeling

extract_protocol: RNeasy (Qiagen Sciences)

treatment_protocol:
OSE cells were trypsin-digested at 37 C for 30 min (Trypsin-EDTA: 0.25% w/v).
Trypsin-digested OSE cells were cultured in Dulbecco's modified Eagle's medium-F12 supplemented with 10% fetal bovine serum and 5% insulin-transferrin-selenium-A (Gibco).

value: ovary

value: ovarian surface epithelial cells

value: 4 weeks of age

tag: background strain

value: mixed


title: P/K OSE cells expressing wild-type p53 and Trp53 R172H mutation, Rep 2

source_name: Mouse ovarian surface epithelial cells_heterozygous_Trp53_R172H

value: 12 weeks of age


title: source A

city: Chapel Hill

first: Asma

last: Khan

state: NC

address: 1170 Old Dental Building CB 7450

department: Division of Endodontics

institute: UNC School of Dentistry

hyb_protocol: The cocktail for hybridization onto an Affymetrix Human Gene 2.1 ST peg plate was prepared using the Nugen Ovation PicoSL WT System V2 user guide’s cocktail assembly table. The hybridization cocktails were denatured and hybridized on the Human Gene 2.1 ST peg plate in the Affymetrix GeneTitan MC Instrument.

scan_protocol: Washing and scanning was also carried out on the Affymetrix GeneTitan MC Instrument.

data_processing: We  used  Affymetrix Expression Console Version 1.3.1.187 to generate the RMA normalization.

source_name: normal pulp

label_protocol: Briefly, 25 ng of total RNA was converted into amplified SPIA cDNA using the Nugen Ovation Pico WTA system V2 and accompanying user guide. The amplified SPIA cDNA was purified using the Qiagen QIAquick PCR purification kit. 2.5 ug of SPIA cDNA was fragmented and labeled using the Nugen Encore Biotin module and accompanying user guide.

extract_protocol: Total RNA was isolated using a commercial kit (Qiagen RNEasy Kit, Valencia, CA) following the manufacturer’s specifications. Quantity and purity of the total RNA was analyzed using Nano-DropTM (Thermo Scientific, Wilmington, DE) and BioanalyzerTM (Agilent Technologies, Sta. Clara, CA).

value: normal pulp

tag: pain intensity (vas)

tag: plate type

tag: probe array position

tag: barcode


title: source L

source_name: inflammed pulp

tag: diagnosis

value: irreversible pulpitis

value: inflammed pulp (pulpitis)

value: severe  (>30mm)


title: source E


title: P/K OSE cells expressing wild-type p53, Rep 2

source_name: Mouse ovarian surface epithelial cells_wildtype p53

tag: tissue

value: 9 weeks of age


title: source I

tag: tissue type

value: mild  (≤ 30mm)


title: source J

value: severe   (>30mm)


title: FXR1 knockdown

city: BOSTON

first: Shobha

last: Vasudevan

state: Massachusetts

department: Cancer Center, Medicine

description:
IB4
Gene expression data from G0 THP1 FXR1 knockdown cells

hyb_protocol: Following fragmentation, 41 ul of cDNA were hybridized for 16 hr at 45 C on GeneChip Human 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using RMA normalization.

label: Biotin

source_name: THP1_FXR1 knockdown_G0

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit Ambion WT, Lot # 1408041, followed by labeling 5.5 ug cDNA using kit Affymetrix GeneChip WT Terminal Labeling Kit, Lot #4236829

growth_protocol: FXR1 knockdown and shRNA control cells were induced with 1ug/ml of doxycycline continually to cause knockdown of FXR1; the cells were grown in serum for 3 days to induce the shRNAs, followed by 2 days of serum-starvation to induce G0.

extract_protocol: After harvesting, the cells were lysed in proteinase K buffer (Truesdell et al., 2012) and total RNA was isolated using Trizol (Invitrogen).

tag: cell line

value: THP1 (ATCC TIB202)

tag: cell line source

value: 1 year infant

tag: tissue origin

value: peripheral blood

value: human blood cell line

value: stably expressing FXR1 shRNA knockdown plasmid


title: source F


title: source H

value: mild (≤ 30mm)


title: source K


title: source G

value: mild (≤ 30mm )


title: source C


title: Control shRNA

description:
IB3
Gene expression data from G0 THP1 control shRNA cells

source_name: THP1_shRNA control_G0

value: stably expressing control shRNA (pTRIPZ) plasmid


title: P/K OSE cells expressing wild-type p53, Rep 1

value: ovary

value: ovarian surface epithelial cells

tag: age

value: mixed


title: source B

value: normal pulp


title: P/K OSE cells expressing wild-type p53 and Trp53 R172H mutation, Rep 1


title: source D


title: MEF (young, p3)_ rep1

city: Seoul

first: Dong-Hoon

last: Jin

address: 88 Olympicro-43gil, Songpa-gu

institute: Asan Medical Center

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Microarray. The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: MEF p3

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: mouse embryonic fibroblast (normal culture condition)

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

value: MEF (passage 3)

tag: strain


title: MEF (senescent, p11)_ rep1

source_name: MEF p11

value: MEF (passage 11)


title: Tumor dissociated A375-LM3 WT rep1

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

institute: KAIST

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina HumanHT-12 V4.0 Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScan scanner

data_processing: The data is analyzed using Illumina GenomeStudio software

source_name: Tumor dissociated A375-LM3 WT

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

growth_protocol: A375 LM3 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; JR Scientific, Woodland, CA) for 1 days. Tumor dissociated cells were isolated from primary tumor formed by A375-LM3. These cells were cultured for 3 passages.

extract_protocol: Total RNAs were isolated using Qiazol (Qiagen, Valencia, CA) followed by chloroform extraction.

tag: cell line/tissue

value: primary tumor formed by A375-LM3

value: expressing JMJD3

tag: cell/tissue type

value: Melanoma


title: Tumor dissociated A375-LM3 VEC rep2

source_name: Tumor dissociated A375-LM3 VEC

value: expressing vector


title: A375-LM3 WT rep2

source_name: A375-LM3 WT


title: Tumor dissociated A375-LM3 WT rep2


title: A375-LM3 VEC rep2

source_name: A375-LM3 VEC


title: Tumor dissociated A375-LM3 VEC rep1


title: Craniofacial microsomia 455

source_name: Craniofacial microsomia

tag: Sex

value: Male


title: IMR-90 iPSC-YAP mTeSR+2iFL naïve

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

institute: MRC Laboratory of Medical Sciences

hyb_protocol: biotinylated cRNA was produced from cDNA and hybridized to the Illumina HT-12 v4 gene exression chip O/N at 58oC

scan_protocol: scanned using iScan and expression data extracted using BeadStudio

data_processing:
Data were quantile normalised and log2 transformed using the R/Bioconductor package v.3.1.3 in Rstudio for Mac OSX
Normalised values are quantile normalised and log2 transformed intensities

source_name: human iPSCs YAP OE mTeSR naïve media

label_protocol: 100ng was used to generate labelled cDNA using the Illumina specific Ambion TotalPrep kit, stained with Streptavidin-Cy3

growth_protocol: Human primed ESCs and iPSCs were cultured on irradiated MEFs in primed medium (DF12+bFGF) consisting of 80% DMEM/F12, 20% Knockout serum replacement (KSR), 1 mM L-glutamax, 1% non-essential amino acids, 0.1 mM beta-mercaptoethanol, 1% penicillin-streptomycin and 8 ng/ml basic fibroblast growth factor (bFGF) (all from Invitrogen).

extract_protocol: total RNA was extracted with RNeasy mini Qiagen kit, and DNAse treated

treatment_protocol: Human PSCs were either grown in primed conditions as above, or switched to naïve media based on N2B27 or mTeSR. N2B27 medium consisted of: 1:1 mixture of DMEM/F12 and Neurobasal medium, with 1% N2 supplement, 2% B27 supplement, 1 mM L-glutamax, 0.1 mM beta-mercaptoethanol, 1x non-essential amino acids and 1x penicillin-streptomycin. N2B27 and mTeSR base media were supplemented with 2iFL: PD0325901 (Stemgent, 0.5 µM), CHIR99021 (Selleckchem, 3 µM), Forskolin (Sigma, 10 µM) and recombinant human LIF (EmdMillipore, 1 ng/ml). LPA (Sigma, 10 µM) was added to naïve media when indicated. The ROCK inhibitor Y-27632 (Stemgent, 5 µM) was used for the first three passages.

tag: cell type

value: iPSCs

tag: genotype/variation

value: Yap overexpression

tag: state

value: Naive


title: A375-LM3 WT rep1


title: IMR-90 iPSC primed

source_name: human iPSCs

value: Control

value: Primed


title: WT/Lhr-/- 4

first: Ariel

last: Poliandri

state: London

address: WHRI, Charterhouse Sq.

department: Endocrinology

institute: Queen Mary University

description:
Group 4 replicate 4
Lhr null rep4

hyb_protocol: Labelled RNA strands were hybridized in an overnight reaction to the bead on a BeadChip containing the complementary gene-specific sequence

scan_protocol: The BeadChip was imaged with Illumina HiScan

data_processing: Data was processed using Illumina GenomeStudio version 1.7.0 and quantile normalised

source_name: Lhr null ovaries

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

growth_protocol: Mice were kept under, and in accordance with, a Project License issued by the United Kingdom Home Office. Food and water were provided ad libitum.

extract_protocol: RNA was extracted using Trizol followed by clean up with Qiage RNeasy MinElute Cleanup Kit

treatment_protocol: Samples were collected from 12 week old mice.

value: FVB/N x C57/BL6 cross

tag: gender

value: female

value: 12 weeks

value: Lhr null

value: ovaries


title: WIBR3 mTeSR+2iFL+LPA naïve

source_name: WIBR-naïve cells in mTeSR naïve media

value: Yap activation by LPA


title: P/K OSE cells expressing homozygous Trp53 R172H mutation, Rep 1

source_name: Mouse ovarian surface epithelial cells_homozygous _Trp63_R172H

value: ovary

value: ovarian surface epithelial cells

value: 4 weeks of age

tag: background strain

value: mixed


title: WT/Lhr-/- 3

description:
Group 4 replicate 3
Lhr null rep3


title: H9-YAP N2B27+2iFL naïve

source_name: H9 ESCs, YAP OE, N2b27 naïve media

value: hESCs


title: H1-YAP primed

source_name: H1 ESCs, YAP OE


title: H9 mTeSR+2iFL+LPA naïve

source_name: H9 ESCs + LPA, mTeSR naïve media


title: H1 primed

source_name: H1 ESCs


title: Fshr-CAM/Lhr-/- 4

description:
Group 3 replicate 4
Fshr mutant/Lhr null rep4

source_name: Fshr mutant/Lhr null ovaries

value: Fshr mutant/Lhr null


title: A375-LM3 VEC rep1

value: expressing vector

value: Melanoma


title: WT/Lhr-/- 1

description:
Group 4 replicate 1
Lhr null rep1


title: WT/Lhr-/- 2

description:
Group 4 replicate 2
Lhr null rep2


title: Fshr-CAM/Lhr-/- 2

description:
Group 3 replicate 2
Fshr mutant/Lhr null rep2


title: Lung endothelial cell-Evi/Wls deleted-rep2

city: Heidelberg

first: Hellmut

middle: G

last: Augustin

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Center (DKFZ)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Microarray data were collected with an iScan array scanner

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

source_name: FACS sorted lung endothelial cell, Evi-iECKO mice

label_protocol: RNA is labeled according to standard Illumina labeling protocol based on biotin-tagged uracil bases

extract_protocol: RNA of FACS-sorted mouse EC was isolated using Arcturus®PicoPure®RNA isolation kit (Life Technologies). Quality and concentration of total RNA was checked by gel analysis using the Agilent RNA 6000 Pico Kit on an Agilent 2100 Bioanalyzer. RNA was reverse transcribed into cDNA. cDNA was amplified using NuGEN SPIA (Single Primer Isothermal Amplification) technology.

tag: mouse line

value: Evifl/fl x Cdh5CreERT2+

value: Lung endothelial cells

value: postnatal day 6


title: H9 primed

source_name: H9 ESCs

value: Control

value: Primed


title: Fshr-CAM/Lhr-/- 5

description:
Group 3 replicate 5
Fshr mutant/Lhr null rep5

value: FVB/N x C57/BL6 cross

value: female

value: 12 weeks


title: H9-YAP mTeSR+2iFL naïve

source_name: H9 ESCs, YAP OE, mTeSR naïve media

value: Yap overexpression

value: Naive


title: H9-YAP primed

source_name: H9 ESCs, YAP OE


title: IMR-90 iPSC-YAP primed

source_name: human iPSCs YAP OE

value: iPSCs


title: Lung endothelial cell-Evi/Wls deleted-rep1


title: Lung endothelial cell-Evi/Wls wildtype-rep3

source_name: FACS sorted lung endothelial cell, Evi-WT mice

value: Evifl/fl x Cdh5CreERT2-


title: Fshr-CAM/Lhr-/- 3

description:
Group 3 replicate 3
Fshr mutant/Lhr null rep3

value: ovaries


title: Lung endothelial cell-Evi/Wls wildtype-rep1


title: Craniofacial microsomia 454

source_name: Craniofacial microsomia

value: Male


title: Lung endothelial cell-Evi/Wls wildtype-rep2


title: Lung endothelial cell-Rspo3 wildtype-rep1

source_name: FACS sorted lung endothelial cell, Rspo3-WT mice

value: Rspo3fl/fl x Cdh5CreERT2-


title: Fshr-CAM/WT 2

description:
Group 2 replicate 2
Fshr mutant rep 2

source_name: Fshr mutant ovaries

value: Fshr mutant


title: WT/WT 4

description:
Group 1 replicate 4
Wild type rep 4

source_name: Wild type ovaries

value: Wild type


title: WT/WT 3

description:
Group 1 replicate 3
Wild type rep 3


title: H1-YAP mTeSR+2iFL naïve

source_name: H1 ESCs, YAP OE, mTeSR naïve media

value: hESCs


title: Lung endothelial cell-Rspo3 wildtype-rep2

value: Lung endothelial cells


title: WT/WT 2

description:
Group 1 replicate 2
Wild type rep 2


title: Lung endothelial cell-Rspo3 deleted-rep1

source_name: FACS sorted lung endothelial cell, Rspo3-iECKO mice

value: Rspo3fl/fl x Cdh5CreERT2+

value: postnatal day 6


title: Lung endothelial cell-Rspo3 deleted-rep3


title: Fshr-CAM/WT 1

description:
Group 2 replicate 1
Fshr mutant rep 1


title: Fshr-CAM/Lhr-/- 1

description:
Group 3 replicate 1
Fshr mutant/Lhr null rep1

value: Fshr mutant/Lhr null


title: Lung endothelial cell-Rspo3 deleted-rep2


title: WT/WT 1

description:
Group 1 replicate 1
Wild type rep 1

value: FVB/N x C57/BL6 cross


title: Cre- B2 cells replicate 2

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description: BH12_Cre- B2

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: sorted splenic CD19+CD43- cells

label_protocol: Biotinylated double strand cDNA targets were prepared from 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro  kit

value: spleen

value: B2 B lymphocyte subset

value: control

value: male


title: TEMO0%vs pool (exp)

city: Paterna

first: Elisabet

last: Navarro

address: avda Agustin Escardino 7

country: Spain

institute: Institute of Agrochemistry and Food Technology (IATA-CSIC)

hyb_protocol: Prehybridization step was performed in 3X SSC solution (Sigma), 0.1% SDS (Sigma) and 0.1 mg/ml BSA for 60 minutes at 50°C, in order to minimize background noise and remove the friable DNA probes. Competitive hybridization was carried out manually using equal quantity of the two labeled samples  (100-200 pmol) concentrated in a Concentrator Plus (EppendorfTM, Hamburg, Germany). The mixture was resuspended in hybridization solution ( 5xSSC , 0.1% SDS, 50% formamide and 0.1 mg/mL salmon sperm DNA) dropped onto the Yeast 6.4K Array (Microarray Centre, UHN, Toronto, Ontario, Canada) and covered with coverslips HybriSlip (Grace Bio-Labs, Sigma). Hybridization was conducted for 16 hours in  AHC chambers (Arraylt Corporation, CA, USA) immersed in a bath at 42°C and the labeled microarrays were washed manually with different solutions containing different SSC and SDS concentrations

scan_protocol: Signal intensities were acquired using an Axon GenePix 4100 scanner (Axon Instruments, Foster city, CA, USA), flawed or poor quality spots were manually removed from de dataset and a global background subtraction was performed by GenePix Pro 6.0 (Molecular Devices Corp., Union City; CA, USA).Raw microarray data were analyzed by Acuity 4.0 (Molecular Devices Corp.)

data_processing: Expression ratio values (Cy5/Cy3) were transformed into log2, the fluorescence intensity was normalized applying  a ratio-based normalization and quality control conditions were applied to removed unreliable data from the analysis. Replicates were combined and their medians were calculated, only spots with at least two replicates were considered.

organism: Saccharomyces cerevisiae

source_name: TEMOHAYA-26 strain, 0%etOH, exponential phase

label_protocol: we mixed 20 µg of total RNA and 2.5 µg oligo (dT)20 (Invitrogen) in 16 µl of DEPC water. Reverse transcription was carried out with SuperScript™ III Reverse Transcriptase, 334 µM aa-dUTP, 6 µM oligo (dT), 500 µM dATP, dCTP, dGTP, 166 µM dTTP and 10 µM DTT in a final volume of 13 µl. The reaction was incubated at 50°C for 12 hours and then with 10 µL of 1M NaOH and 10 µL of 0.5 M EDTA for 15 min at 70°C to degradate the original RNA. The pH were neutralized with 250 mM HCl. The coupling of dyes was performed for 2 hours at room temperature and darkness with CyDye NHS esters (Amersham Biosciences) and 0.13M Na2CO3.All samples were labeled with Cy5 dye, while a reference pool was labeled with Cy3.

growth_protocol: A single colony of each strain was picked from fresh GPY-agar plates and separately incubated for sixteen hours in 5 mL GPY pre-culture medium (5 g/L yeast extract, 5 g/L peptone, 20 g/L glucose) at 150 rpm and 28°C. These cultures were inoculated into sterile 250 mL Erlenmeyer flasks with cotton wool plugs, containing 100 mL of GPY in the absence or presence of ethanol, 0 and 10% (v/v) to achieve an initial OD600 of 0.1. Samples for RNA extraction were taken after 1 hour (adaptation phase) and mid-exponential phase (acclimation phase) after inoculation, both stressful conditions as non-stressful conditions.

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-chloroform (5:1) and phenol-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate.

tag: sampling

value: exponential phase

source_name: Total RNA pooled from all biological samples

value: PE35M and TEMOHAYA-26

value: 1 hour and exponential phase


title: PE35M0%vs pool (exp)

source_name: PE35M strain, 0%etOH, exponential phase


title: Cre+ B2 cells replicate 2

description: BH10_Cre+ B2

tag: tissue

value: induced deletion of Ikaros


title: TEMO0%vs pool (1h)

source_name: TEMOHAYA-26 strain, 0%etOH, 1h

value: 1 hour after inoculation


title: Cre- B1 cells replicate 2

description: BH11_Cre- B1

source_name: sorted splenic CD19+CD43+ cells

value: B1 B lymphocyte subset


title: PE35M10%vs pool (exp)

source_name: PE35M strain, 10%etOH, exponential phase


title: Cre+ B1 cells replicate 2

description: BH09_Cre+ B1


title: PE35M0%vs pool (1h)

source_name: PE35M strain, 0%etOH, 1h


title: Mouse IL-17 blocking antibodies.2

city: Baltimore

first: Florencia

last: McAllister

address: 401 N. Broadway

department: Sidney Kimmel Comprehensive Cancer Center

institute: The Johns Hopkins University

description: IL-17 Blocking antibodies

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

label_protocol: The Ambion WT Expression Kit (Ambion Life Technologies) was used as described in the manufacturer's manual.

growth_protocol: Mice with genotype Mist1Cretg/wt; Krastg/wt; mTmGtg/wt were injected with tamoxifen to activate Kras in the acinar cells (Time 0) and with cerulein for 3 weeks to induce chronic pancreatitis

extract_protocol: At week 7, mice were sacrificed, pancreas digested, and epithelial cells with Kras activation (GFP+) were sorted into RLT buffer (containing ME). On the same day, RNA was extracted using Qiagen RNA extraction kit and RNA stored at -80C.

treatment_protocol: At week 6, mice were injected with anti-IL-17 blocking antibodies (intraperitoneal injection, two times)

tag: genotype

value: Mist1Cretg/wt; Krastg/wt; mTmGtg/wt

value: pancreas

value: epithelial


title: PE35M10%vs pool (1h)

source_name: PE35M strain, 10%etOH, 1h


title: Cre+ B2 cells replicate 1

description: BH02_Cre+ B2

value: female


title: Mouse IL-17 blocking antibodies.1

description: IL-17 Blocking antibodies


title: TEMO10%vs pool (exp)

source_name: TEMOHAYA-26 strain, 10%etOH, exponential phase


title: TEMO10%vs pool (1h)

source_name: TEMOHAYA-26 strain, 10%etOH, 1h


title: Cre- B1 cells replicate 1

description: BH03_ Cre- B1


title: Cre- B2 cells replicate 1

description: BH04_Cre- B2


title: Mouse IL-17 blocking antibodies.3

description: IL-17 Blocking antibodies


title: Mouse IgG1 control antibody.1

description: Control antibodies


title: Mouse IgG1 control antibody.3

description: Control antibodies


title: mouse_#4_P9_mutant

status: Public on Feb 02 2016

city: Tempe

first: Jason

middle: M

last: Newbern

state: AZ

department: School of Life Sciences

institute: Arizona State University

hyb_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility

data_processing: Data were analyzed using Partek Genomics Suite Version 6

source_name: sensoricortex

extract_protocol: According to manufactory protocol (Qiagen miRNeasy kit)

value: sensoricortex

value: mutant (loss of function)

value: Postnatal day 9


title: mouse_#1_P9_mutant

scan_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility


title: Fshr-CAM/WT 3

description:
Group 2 replicate 3
Fshr mutant rep 3

value: FVB/N x C57/BL6 cross

value: 12 weeks

value: Fshr mutant

value: ovaries


title: Cre+ B1 cells replicate 1

description: BH01_Cre+ B1

value: spleen


title: mouse_#2_P9_control

label_protocol: According to manufactory protocol (Affymatrix) conducted by UNC functional genomics core facility

value: control (loss of function)


title: Mouse IgG1 control antibody.2

description: Control antibodies


title: Fshr-CAM/WT 4

description:
Group 2 replicate 4
Fshr mutant rep 4


title: STZ T1D with leptin W6

first: Qingchun

last: Tong

address: 1825 Pressler Street

institute: The Account Payable, University of Texas at Houston

description:
replicate 1
W6

hyb_protocol: We incubated the cRNA with HYB buffer with the BeadChips at 58C for 17 hours and washed according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: We incubated each BeadChip with Cy3-Streptavidin for 10 min, dried, and then scanned on an Illumina BeadArray Scanner.

data_processing: The raw data were processed with IlluminaGenomeStudio with no background correction.  The data were log2 transformed and quantile normalized.

source_name: STZ T1D with leptin - hypothalamus

label_protocol: Using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion #IL1791), we reverse-transcribed 300 ng of total RNA using a T7 oligo-dT primer, used the resulting cDNA to synthesize the complement strand, purified, and in vitro transcribed biotinylated cRNA.

growth_protocol: We extracted the hypothalamus of mice that were injected intraperitoneally twice as week with STZ, or infused continuously with leptin.

extract_protocol: Hypothalamic RNA was isolated with TRI Reagent following the manufacturer’s protocol.

treatment_protocol: Hypothalamic blocks were dissected from fresh brain tissue and stored immediately in RNALater.

value: hypothalamus

value: male

value: 12-15 weeks old

value: mixed


title: mouse_#11_mutant

source_name: mutant

value: Postnatal day 14


title: STZ T1D with leptin W7

description:
replicate 2
W7


title: mouse_#3_P9_control


title: mouse_#10_control

source_name: control


title: mouse_#9_mutant


title: Control Saline W5

description:
replicate 3
W5

source_name: Control Saline - hypothalamus


title: STZ-induced T1D W3

description:
replicate 1
W3

source_name: STZ-induced T1D - hypothalamus


title: STZ T1D with leptin W8

description:
replicate 3
W8


title: mouse_#12_control


title: HBEC PMX-Purom-GFP-mFAK + Pias1 rep2

city: Dallas

first: Jerfiz

middle: D

last: Constanzo

address: 6001 Forest Park Road

department: Hematology Oncology

institute: University of Texas Southwestern Medical Center

description: Cells are immortalized, non- oncogenic by transduction with CDK4, hTERT  (telomerase) and short hairpin knockdown of P53 tumor suppressor

hyb_protocol: We hybridized the productin step #4 to human HT12 v4.0 Expression BeadChip from Ilumina according to the manufacturer’s instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: We used R/Bioconductor package MBCB with default parameters to process raw data, background subtraction and quantile normalization. The linear value can be used for bar graph or further analysis according to study design base on normalized values higher than 120. After normalization value was transformed to Log (natural) value and median centered for Hierarchical Cluster analysis. For statistical analysis we utilized a false discovery rate (FDR) and benjamini hochberg test with a log ratio treshold of 0.6 and  p-value treshold of 0.3. Finaly values were analysed with Ingenuity Gene Set Enrichment sofrware (QIAGEN)

source_name: HBEC epithelial cell line

label_protocol: We processed 100 ng of total RNA with the Ambion TotalPrep Kit for Illumina arrays following manufacturers protocol

growth_protocol: Human bronchial epithelial cells  (HBECs) were transduced with retroviral particles containing PMX-Purom-GFP-emty or PMX-Purom-GFP-mFAK and positive clones selected with 2ug/mL Puromycing for 2 days.

extract_protocol: For total RNA extraction we used a RNA isolation kit (SIGMA) followed by DNase digestion and cleanup according to the manufacturer’s instructions

treatment_protocol: Gene expression profiles were obtained from exponentially growing HBEC cells in keratynocyte growth media supplemented with growth factors (Gibco)

tag: cell line

value: HBEC


title: MCF7/shNS cells_E2 treated_rep2

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

description:
8381653073_K
replicate 2

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio

source_name: MCF7/shNS cells

growth_protocol: cells were grown in phenol red free DMEM containing 10% charcoal stripped serum

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: treated with 10nM E2 or vehicle (ethanol)

value: MCF7, with Control Non-specific silencing

tag: treatment


title: MCF7/shNS cells_E2 treated_rep3

description:
8381653073_L
replicate 3


title: MCF7/shNS cells_E2 treated_rep1

description:
8381653073_J
replicate 1


title: Control Saline W4

description:
replicate 2
W4


title: mouse_#2_control


title: MCF7/shNS cells_Veh treated_rep3

description:
8381653073_I
replicate 3

value: Veh


title: STZ-induced T1D W1

description:
replicate 1
W1


title: HBEC PMX-Purom-GFP-mFAK + Pias1 rep1


title: mouse_#1_mutant

value: sensoricortex


title: MCF7/shNS cells_Veh treated_rep2

description:
8381653073_H
replicate 2


title: STZ-induced T1D W2

description:
replicate 2
W2


title: L1_50B over L1_90A

city: Ede

first: Jos

last: Boekhorst

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: Expression ratio of L1_50B and L1_90A

hyb_protocol: Hybridization was performed as described in van Melis et al., 2011

scan_protocol: Slides were scanned with Agilent G2505C scanner

data_processing: Microarrays were normalized using the approach reported previously (by van Melis et al 2011) for germinating spores involving the creation of so called synthetic microarrays. The background-corrected, raw signals (Cy3 and Cy5 channel) of all arrays were hierarchically clustered (Pearson correlation, complete linkage) using Genemaths XT. New synthetic arrays were defined from sample pairs showing the highest similarity in the clustering. The synthetic microarrays were Lowess normalized and all pairwise ratios were determined. The Lowess-normalized data are available on the series record in the file: cybert_ratios.xlsx.  The sample data table contains the normalized Cy5/Cy3 values that were used in the first step of the analysis.

organism: Bacillus cereus ATCC 14579

label_protocol: Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)

growth_protocol: Untreated and heat-treated (1 min 95C) B. cereus ATCC14579 spores were mixed with BHI and incubated with aeration (200rpm) at 30°C untill harvesting time (see overal design).

extract_protocol: RNA was extracted from samples in TRI-reagent by defrosting on ice, spores were mechanically disrupted by extensive bead beating in the presence of Lysing Matrix B beads. Direct-zol RNA MiniPrep was used according to the manufacturer’s instructions for on column RNA purification. Residual chromosomal DNA was removed by 30 min off column treatment of the samples with TURBO DNA-free Kit. The resulting mRNA was subsequently cleaned with RNeasy Mini Kit. The RNA quantity and quality were checked by UV spectroscopy and RNA 6000 Nanochip.

treatment_protocol: Cells were harvested at above mentioned timepoints (see overall design) by spinning down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen.

value: heat-treated spores 50 min after mixing with BHI

value: heat-treated spores 90 min after mixing with BHI


title: L1_150A over L1_50A

description: Expression ratio of L1_150A and L1_50A

value: heat-treated spores 150 min after mixing with BHI


title: L0_10B over L0_50A

description: Expression ratio of L0_10B and L0_50A

value: untreated spores 10 min after mixing with BHI

value: untreated spores 50 min after mixing with BHI