title: Hu1164_72hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
Hu1164_72hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hrs, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: CHC846T

status: Public on Dec 18 2013

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

description: Hepatocellular adenoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol. Log R Ratios exported from the Beadstudio software.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

tag: age

tag: Sex

value: F

tag: pathological diagnosis

value: dysplastic hepatocellular adenoma


title: placenta, FTB 4

type: RNA

city: Staten Island

first: Nanbert

last: Zhong

state: NY

address: 1050 Forest Hill Road

department: Human Genetics

country: USA

institute: New York State Institute fro Basic Research in Developmental Disabilities

description: FTB 4

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, Santa Clara, CA) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (Agilent Technology, Santa Clara, CA).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies, Santa Clara, CA). After normalization of the raw data, lncRNAs and mRNAs that have flags (“All Targets Value”) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (Version 12.1). Both “GO analysis” and “Pathway analysis” were performed in the standard enrichment computation method.

molecule: total RNA

source_name: FTB

extract_protocol: Total RNA isolated with Trizol.  mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE).

tag: tissue

value: placenta

tag: tissue source

value: Fresh tissue delivered from full term birth

tag: gestation


title: placenta, FTB 8

description: FTB 8

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, Santa Clara, CA) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, NE). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (Agilent Technology, Santa Clara, CA).


title: CHC517T

description: Hepatocellular adenoma


title: T2_Hu1153_12hr_0.01uM

city: Research Triangle Park

first: Patrick

middle: D

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

institute: The Hamner Institutes for Health Sciences

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T2_Hu1153_12hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization using Partek Genomics Suite

label: biotin

source_name: Human Hepatocyte cell

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: mirvana (AM1560)

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 0.01, Units of Dose or Concentration: uM

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: individual


title: T2_Hu1154_12hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T2_Hu1154_12hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 0.001, Units of Dose or Concentration: uM

tag: ratio


title: placenta, FTB 5

description: FTB 5


title: placenta, FTB 3

description: FTB 3


title: T2_Hu1153_2hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T2_Hu1153_2hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: T2_Hu1154_12hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T2_Hu1154_12hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: placenta, FTB 2

description: FTB 2


title: CHC464T

description: Hepatocellular adenoma


title: placenta, FTB 1

description: FTB 1


title: placenta, PPROM 10

description: PPROM 10

source_name: PPROM

value: Fresh tissue delivered from preterm premature rupture of membrane


title: 539-5

city: Toronto

first: Tobias

middle: Andreas

last: Beyer

state: ONT

address: 600 University Ave

department: Lunenfeld-Tannenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using median normalisation and log2 transformation with IlluminaGUI in R

source_name: WA09 siTEAD1-4

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

growth_protocol: WA09 grown on Matrigel/MEF conditioned DMEM/F12 20% KO-serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit including DNase I treatment . Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were transfected with siRNA using RNAi-MAX. Cells were harvested 48h after transfection

tag: cell line

tag: growth conditions

value: MEF conditioned medium/matrigel

tag: treatment

value: siTEAD1-4 (RNAi-MAX)

tag: timing

value: RNA harvested 48h after transfection


title: 539-8

description: Replicate 2

source_name: WA09 siTAZ/YAP

value: siTAZ/YAP (RNAi-MAX)


title: CHC1439T

description: Hepatocellular adenoma

tag: age

value: non dysplastic hepatocellular adenoma


title: T2_Hu1154_2hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T2_Hu1154_2hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: CHC1337T

description: Hepatocellular adenoma

tag: Sex


title: placenta, PPROM 9

description: PPROM 9


title: 539-1

description: Replicate 2

source_name: WA09 Mock

value: Mock transfection (RNAi-MAX)


title: 535-1

description: Replicate 1


title: 535-8

description: Replicate 1


title: T3_Hu1153_12hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_12hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: 535-5

description: Replicate 1


title: T3_Hu1153_24hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_24hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hr, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: CHC605T

description: Hepatocellular adenoma

tag: pathological diagnosis


title: CHC1424T

description: Hepatocellular adenoma


title: placenta, PPROM 8

description: PPROM 8

tag: tissue


title: CHC917T

description: Hepatocellular carcinoma

value: M

value: hepatocellular carcinoma developed on an adenoma


title: CHC624T

description: Hepatocellular adenoma


title: placenta, PPROM 6

description: PPROM 6

tag: tissue source


title: T3_Hu1153_24hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_24hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hr, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: T3_Hu1153_2hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_2hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: placenta, PPROM 7

description: PPROM 7

tag: gestation


title: CHC689T

description: Hepatocellular adenoma


title: CHC1915T

description: Hepatocellular carcinoma

value: not available


title: CHC462T

description: Hepatocellular adenoma


title: T3_Hu1153_2hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_2hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: Control, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 0, Units of Dose or Concentration: uM

tag: array type


title: placenta, PPROM 5

description: PPROM 5


title: CHC687T

description: Hepatocellular adenoma


title: placenta, PPROM 4

description: PPROM 4


title: T3_Hu1153_6hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_6hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hr, Dose or Concentration: 0.1, Units of Dose or Concentration: uM

tag: amount to core


title: CHC623T

description: Hepatocellular adenoma


title: T3_Hu1153_6hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_6hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: Control, Treatment Duration: 6, Units of Duration: hr, Dose or Concentration: 0, Units of Dose or Concentration: uM

tag: units of amount


title: CHC1916T

description: Hepatocellular adenoma


title: T3_Hu1153_6hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1153_6hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hr, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: placenta, PPROM 2

description: PPROM 2


title: CHC575T

description: Hepatocellular adenoma


title: T3_Hu1154_6hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1154_6hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: placenta, PPROM 3

description: PPROM 3


title: ulcerative colitis colon mucosa 509

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis treated with 6-mercaptopurine and mesalamine colon mucosa sample.

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software version 2010.3.0.30128

label: Cy5 and Cy3

source_name: colon mucosa 509, after treatment with 6-mercaptopurine and mesalamine

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.

tag: gender

value: Male

tag: age (y)

value: Colon mucosa

tag: disease state

value: ulcerative colitis

value: 6-mercaptopurine and mesalamine


title: CHC1488T

description: Hepatocellular adenoma

value: F


title: CHC578T

description: Hepatocellular adenoma


title: CHC1398T

description: Hepatocellular adenoma

data_processing: standard Illumina protocol. Beta values exported from Illumina Beadstudio software.


title: CHC1382T

description: Hepatocellular adenoma


title: CHC1489T

description: Hepatocellular adenoma


title: CHC1391T

description: Hepatocellular adenoma


title: CHC1383T

description: Hepatocellular adenoma


title: CHC1419T

description: Hepatocellular adenoma


title: CHC1124T

description: Hepatocellular adenoma

value: dysplastic hepatocellular adenoma


title: CHC1434T

description: Hepatocellular adenoma


title: CHC1343T

description: Hepatocellular adenoma


title: CHC1328T

description: Hepatocellular adenoma


title: CHC1023T

description: Hepatocellular adenoma


title: CHC1432T

description: Hepatocellular adenoma


title: T3_Hu1154_72hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1154_72hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hr, Dose or Concentration: 0.1, Units of Dose or Concentration: uM

value: ul


title: placenta, PPROM 1

description: PPROM 1

value: placenta

value: Fresh tissue delivered from preterm premature rupture of membrane


title: CHC1425T

description: Hepatocellular adenoma


title: CHC1020T

description: Hepatocellular adenoma


title: CHC979T

description: Hepatocellular adenoma


title: T3_Hu1154_72hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1154_72hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM

tag: individual


title: CHC1121T

description: Hepatocellular adenoma


title: CHC1329T

description: Hepatocellular adenoma


title: CHC955T

description: Hepatocellular adenoma


title: CHC918T

description: Hepatocellular adenoma


title: T3_Hu1156_24hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1156_24hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hr, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: notTreated_120hours_rep3

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours

hyb_protocol: cDNA was hybridized to Human Gene Expression 12x135K Arrays (Roche Nimblegen) in triplicate according to manufacturer’s protocol.

scan_protocol: The microarrays were scanned according to manufacturer’s instructions in Chapter 5 of NG_Expression_Guide_v5p1.pdf on a Nimblegen MS200 at 2-um resolution.

data_processing: From the scanned images .pair files were created using version 2.6.0.0 of the NimbleScan software. The same software was then used to normalize the expression matrix with the RMA method.

label_protocol: According to manufacturer’s instructions in Chapter 3 of NG_Expression_Guide_v5p1.pdf.

growth_protocol: MCF10A cells were cultured as described (Debnath et al., 2003, Pubmed ID 12798140). The human Snail-1 ORF with 6 Serine to Alanine mutations (Zhou et al., 2004, Pubmed ID 15448698) was fused with modified estrogen receptor (ER) and was cloned into the PBABEpuro retroviral expression vector. Retrovirus packaging, MCF10A transduction, puromycin selection were performed as described previously (Zhang et al., 2008, Pubmed ID 18413746)

extract_protocol: RNA was isolated using RNeasy Mini kit (Qiagen) 3 days or 7 days after viral infection. RNA samples were verified by Bioanalyzer. cDNA synthesis was performed using the Roche cDNA Synthesis System (11 17 831 001, Roche).

treatment_protocol: Treatment with either tamoxifen in ethanol or just ethanol

value: not Treated

tag: time (hours)

tag: cell line


title: T3_Hu1156_72hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1156_72hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hr, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: T3_Hu1156_2hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1156_2hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: treated_24hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 24 hours

tag: treatment

value: tamoxifen


title: treated_72hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 72 hours


title: T3_Hu1156_72hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1156_72hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: T3_Hu1154_72hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1154_72hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 72, Units of Duration: hr, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: notTreated_24hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 24 hours


title: treated_120hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours


title: CHC874T

description: Hepatocellular adenoma


title: T3_Hu1164_24hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_24hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC835T

description: Hepatocellular adenoma


title: CHC786T

description: Hepatocellular adenoma


title: CHC1428T

description: Hepatocellular adenoma


title: CHC846T

description: Hepatocellular adenoma


title: CHC1123T

description: Hepatocellular adenoma


title: CHC950T

description: Hepatocellular adenoma


title: T3_Hu1164_2hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_2hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC761T

description: Hepatocellular adenoma


title: notTreated_12hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 12 hours


title: treated_12hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 12 hours


title: treated_6hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours


title: T3_Hu1164_2hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_2hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: CHC749T

description: Hepatocellular adenoma


title: CHC754T

description: Hepatocellular adenoma


title: T3_Hu1164_6hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_6hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: T3_Hu1164_2hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_2hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 1, Units of Dose or Concentration: uM


title: CHC870T

description: Hepatocellular adenoma


title: notTreated_72hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 72 hours


title: notTreated_6hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: CHC756T

description: Hepatocellular adenoma


title: notTreated_3hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 3 hours


title: treated_3hours_rep3

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 3 hours


title: CHC663T

description: Hepatocellular adenoma


title: T3_Hu1164_6hr_1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_6hr_1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC605T

description: Hepatocellular adenoma


title: T3_Hu1164_72hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T3_Hu1164_72hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC603T

description: Hepatocellular adenoma


title: T4_Hu1153_2hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1153_2hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 2, Units of Duration: hr, Dose or Concentration: 0.01, Units of Dose or Concentration: uM


title: treated_120hours_rep2

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours


title: CHC574T

description: Hepatocellular adenoma


title: CHC621T

description: Hepatocellular adenoma


title: treated_72hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 72 hours


title: CHC536T

description: Hepatocellular adenoma


title: CHC535T

description: Hepatocellular adenoma


title: T4_Hu1154_12hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1154_12hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 0.1, Units of Dose or Concentration: uM


title: T4_Hu1154_12hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1154_12hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: Control, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 0, Units of Dose or Concentration: uM


title: CHC573T

description: Hepatocellular adenoma


title: CHC584T

description: Hepatocellular adenoma


title: CHC814T

description: Hepatocellular adenoma


title: T4_Hu1154_6hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1154_6hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 6, Units of Duration: hr, Dose or Concentration: 0.001, Units of Dose or Concentration: uM


title: CHC469T

description: Hepatocellular carcinoma


title: notTreated_72hours_rep2

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 72 hours


title: treated_24hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 24 hours


title: CHC582T

description: Hepatocellular adenoma


title: CHC471T

description: Hepatocellular adenoma


title: T4_Hu1154_72hr_0.01uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1154_72hr_0.01uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: T4_Hu1154_6hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1154_6hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC466T

description: Hepatocellular adenoma


title: notTreated_24hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 24 hours


title: CHC379T

description: Hepatocellular adenoma


title: CHC377T

description: Hepatocellular adenoma


title: treated_12hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 12 hours


title: CHC517T

description: Hepatocellular adenoma


title: notTreated_12hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 12 hours


title: notTreated_120hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: T4_Hu1156_24hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1156_24hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 24, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: T4_Hu1156_72hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1156_72hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: CHC465T

description: Hepatocellular adenoma


title: CHC747T

description: Hepatocellular adenoma


title: CHC364T

description: Hepatocellular adenoma


title: CHC375T

description: Hepatocellular adenoma


title: T4_Hu1164_24hr_0.1uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1164_24hr_0.1uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: treated_3hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 3 hours


title: notTreated_6hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: treated_6hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours


title: T4_Hu1164_12hr_10uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1164_12hr_10uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: GW7647, Treatment Duration: 12, Units of Duration: hr, Dose or Concentration: 10, Units of Dose or Concentration: uM


title: CHC344T

description: Hepatocellular adenoma


title: T4_Hu1164_72hr_0.001uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1164_72hr_0.001uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays


title: T4_Hu1164_72hr_0uM

description:
additional information: you may also contact Kathy Yarborough in my absence 5-1268
T4_Hu1164_72hr_0uM_(HT_HG-U133_Plus_PM): primary human hepatocytes from sandwich culture were treated with GW7647 (0,0.001, 0.01, 0.1, 1, 10 uM)  for 2, 6, 12, 24 or 72 hr; There are 5 biological replicates available, but only 4 will be run on arrays

treatment_protocol: in vitro Treatment: Control, Treatment Duration: 72, Units of Duration: hr, Dose or Concentration: 0, Units of Dose or Concentration: uM


title: CHC378T

description: Hepatocellular adenoma


title: Day 7 IL

city: Gainesville

first: Heather

middle: H

last: Ross

state: FL

institute: University of Florida

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, HPRT1 , LDHA, RPL13A.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. Fold Change worksheet reports test/control ratios.

label: SYBR GREEN

organism: Rattus norvegicus

source_name: Adult diaphragm injured side-7 days post-lesion

label_protocol: PCR assays were performed using the  SA Biosciences Rat Skeletal Muscle Development and Disease RT2 Profiler PCR Array (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with TRIzol reagent followed by DNase I treatment.

tag: strain

value: Sprague-Dawley

value: adult

tag: injury status

tag: lesion side

value: ipsi lesional

tag: timepoint


title: treated_120hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours


title: notTreated_3hours_rep2

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 3 hours


title: Day 1 CL

description: Test

source_name: Adult diaphragm, non-injured side 1 day post-lesion

tag: Sex

tag: age

value: contral lesional


title: Day 1 IL

description: Test

source_name: Adult diaphragm injured side-1 day post-lesion


title: Day 7 CL

description: Test

source_name: Adult diaphragm, non-injured side 7 days post-lesion


title: CHC575T

description: Hepatocellular adenoma

tag: pathological diagnosis

value: non dysplastic hepatocellular adenoma


title: Control

description: Control

source_name: Adult diaphragm, sham injury

value: control


title: CHC362T

description: Hepatocellular adenoma


title: CHC566N

description: normal liver

value: normal liver


title: CHC932N

description: normal liver


title: treated_72hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 72 hours


title: CHC934N

description: normal liver


title: notTreated_24hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 24 hours


title: notTreated_72hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 72 hours


title: treated_24hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 24 hours


title: treated_12hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 12 hours


title: notTreated_120hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: S288c vs 102 1

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

country: Spain

institute: Centro Superior de Investigaciones Científicas

description: comparison S288c vs 102 strain

hyb_protocol: Equal amounts of labeled DNA (1µ) were used as probes to hybridize to the PCR-amplified open reading frames (ORFs) of homoploid S. cerevisiae S288C DNA spotted onto microarrays (Eurogentec S.A., Belgium). Microarrays were pre-hybridized with 5 ml of pre-hybridization solution (3× SSC [1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate], 0.1% SDS, and 0.1 mg/ml BSA) at 42°C for 1 h. After washing slides with isopropanol and water, samples were centrifuged at 1300 rpm for 10 min at room temp. Then 10 µl of samples and 50 µl of hybridization solution (50 % (v/v) formamide, 5x SSC, 0.1% SDS and 0.1 mg/ml DNA from salmon sperm) were denatured (95ºC, 1 min) and added to the slides that were incubated for 16 h at 42ºC in a Gene Machines Hyb Chamber (Genomic Solutions). Slides were recovered and washed 5 min at 42ºC in 1 (2x SSC, 0.1% SDS), 2x10 min in solution 2 (0.1 x SSC, 0.1% SDS), 5x1min in solution 3 (0.1 x SSC) and 5 s in solution 4 (0.01 x SSC). Slides were centrifuged for 10 min at 1300 rpm.

scan_protocol: Images were acquired using GenePix 4100A (Axon Instruments, Molecular Devices Corp., USA) with a 10-µm resolution using the GenePix Pro 6.1 software (Axon Instruments, Molecular Devices Corp., USA)

data_processing:
Raw data were processed using Acuity 4.0 (Axon Instruments, Molecular Devices Corp., USA). All the slide data were normalized with a log2(ratio) average and filtered (signal of each channel > 350 and signal/noise ratio > 2.5). Poor or inconsistent signals were not considered for further analysis
Hybridization signals were depicted as the log2 hybridization signal ratio (test/reference). Genomic material obtained from three biological independent replicates was used to perform hybridizations two or three times, including a dye-swap, and the genes with signal intensities ± 0.5 were considered for further analysis. FDR<0.05 was used to select significant data.

organism: Saccharomyces cerevisiae

source_name: strain S288c

label_protocol: Before the labeling reaction, 4 μg of DNA were treated with RNAse A (1 mg/mL, Roche Diagnostics) for 1 h at 37ºC and with Proteinase K (1 mg/ml, Quiagen) for 1.5 h at 37ºC with agitation. Phenol extracted DNA was digested with MseI or RsaI (New England Biolabs, Inc.), according to the manufacturer's instructions, and digestions were mixed. The fragmented sample was purified using the QIA-quick gel extraction kit (Qiagen, Germany), heat denatured for 5 min at 100°C, and then cooled on ice. DNA was labeled in 21-μl reaction mixtures by random priming using the BioPrime® Array CGH Genomic Labeling System (Invitrogen). Unincorporated nucleotides are removed by filtration through a Qiaquick PCR Purification column (Qiagen)

growth_protocol: S. cerevisiae strains were cultured in YPD (1.0% yeast extract, 1.0% Bacto-peptone and 2.0% glucose)

extract_protocol: DNA was extracted from yeast strains grown from single colonies in YPD medium

source_name: strain 102


title: CHC591N

description: normal liver


title: S288c vs D14 1

description: comparison S288c vs D14 strain

source_name: strain D14


title: S288c vs 60 3

description: comparison S288c vs 60 strain, dye swap

source_name: strain 60


title: notTreated_12hours_rep1

description: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 12 hours


title: S288c vs 60 2

description: comparison S288c vs 60 strain


title: notTreated_6hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: S288c vs D14 2

description: comparison S288c vs D14 strain, dye swap


title: treated_3hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 3 hours


title: treated_6hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours


title: S288c vs 60 1

description: comparison S288c vs 60 strain


title: CHC341T

description: Hepatocellular adenoma

value: M


title: notTreated_3hours_rep1

source_name: non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 3 hours


title: S288c vs W303 3

description: comparison S288c vs W303 strain, dye swap

source_name: strain W303


title: SAOUHSC_02897 mutant

city: hefei

first: Yibo

last: You

state: Anhui

address: Huangshan street

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description:
Gene expression of biofilm formation at 12 hours
NCTC8325 SAOUHSC_02897::ermB

hyb_protocol: total of 600 ng cy5-labeled cDNA was used for hybridization sample using Gene Expression Hybridization Kit (Agilent p/n5188-4242) following the manufacturer’s instruction. 40 ul of the hybridization samples were added onto the microarray slide and hybridized in an Agilent hybridization oven to rotate at 10 rpm at 65 °C for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan resolution 5 um, Dye channel is set to Red and Red PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Quantity normalization were analyzed with GENESPRING 11.5 (Agilent).

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: Bacteria in the wells of biofilm formation at 12 hours

label_protocol: 5 ug RNA was used to synthesize cDNA, and labeled with cy5. This process was accomplished using FairPlay III Microarray Labeling Kit (Aglilent p/n252012). Labeled cDNA was purified and quantified with NanoDrop Spectrophotometer (Thermo G2939A).

growth_protocol: Overnight culture were diluted 1:100 in TSB and bacteria were grew statically in the 12-well plate at 12 hours.

extract_protocol: Total RNA was prepared using mirVana RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer’s instruction.

treatment_protocol: In order to lysis the cell wall, cells were collected and incubated in 37°C with 10 mg/ml lysozyme and 40 ug/ml lysostaphin for 5 minutes. Then, cells were centrifuged and resuspended in TRIzol immediately.

tag: genotype/variation

value: SAOUHSC-02897 mutant


title: NCTC8325 WT

description:
Gene expression of biofilm formation at 12 hours
NCTC8325 wild type

value: wild type


title: S288c vs W303 2

description: comparison S288c vs W303 strain


title: S288c vs W303 1

description: comparison S288c vs W303 strain


title: G4-NP8-W10_11551-6

city: Hamburg

first: Florian

last: Wegwitz

state: Hamburg

address: Martinistraße 52

department: Department of Tumor Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression data from mammary carcinoma developed in WAP-T-NP8 x WAP-W10 mouse line

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse Genome 430 2.0 GeneChip, washed and stained following the manufacturer’s recommendation.

scan_protocol: Microarrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: An alternative probe set mapping published by the AffyProbeMiner project (remapped transcript consistent cdf-file, using validated complete coding sequences in GenBank, version 1.0.0) was used to calculate probe set signals. dChip normalization were used.

label: Biotin

organism: Mus musculus

source_name: WAP-NP8 x WAP-W10 Mouse Mammary Carcinoma, high grade (grade 4)

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

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) followed by DNA digestion (TURBO DNA-free; Ambion) according to the manufacturer’s instructions. Total RNA from tumor samples and normal mammary gland was cleaned up using RNeasy mini kit according to the manufacturer’s instructions (Qiagen).

tag: strain background

value: Balb/c

value: WAP-T x WAP-mutp53R245W

tag: tissue

value: Mammary carcinoma

tag: tumour grade

value: Grade 4


title: G4-NP8-W10_11461-2


title: S288c vs 102 2

description: comparison S288c vs 102 strain, dye swap


title: G4-NP8-W10_11445-7


title: G3-NP8-W10_11560-1

source_name: WAP-NP8 x WAP-W10 Mouse Mammary Carcinoma, high grade (grade 3)

value: Grade 3


title: G3-NP8-W10_11551-2


title: G3-NP8-W10_11445-2


title: H3K4Me3_48_hours_rep2

description: H3K4Me3 CHiP after 48 hours of induction of Snail-1 expression

hyb_protocol: The amplified material was hybridized to Human 2.1 M Deluxe HG18 Promoter Arrays (Roche Nimblegen) in duplicates according to manufacturer’s protocol.

scan_protocol: The microarrays were scanned on a Nimblegen MS200 at 2-um resolution.

data_processing: From the scanned images .pair files were created using version 2.6.0.0 of the NimbleScan software. For each mark, the .pair files were preprocessed using the preprocess function of version 1.14.0 of the Ringo Bioconductor package (www.bioconductor.org) and quantile normalization was applied to the resulting matrix.

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

label_protocol: The  experimental (IP) and control (input) samples were labeled using the NimbleGen Dual-Color Labeling Kits according to manufacturer's protocol.

extract_protocol: The following antibodies were used for ChIP analyses: Snail-1 (AF3639, R&D Systems), H3K4Ac (07-539, Millipore), H3K27Ac (ab4729, Abcam), H3K4Me1 (ab8895, Abcam), H3K4Me2 (ab11946, Abcam), H3K4Me3 (ab8580, Abcam), H3K27Me3 (ab6002, Abcam). ChIP-chip was performed as described in Van Rechem et al. (Van Rechem et al., 2011, Pubmed ID 21757720). Snail-1, H3K4Ac, H3K27Ac, H3K4Me1, H3K4Me2, H3K4Me3 and H3K27Me3 immunoprecipitations were amplified with the WGA2 kit (Sigma).

tag: chip antibody

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours

tag: mark

tag: hours


title: H3K27Me3_0_hours_rep2

description: H3K27Me3 CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated

tag: time (hours)


title: H3K4Me3_48_hours_rep1

tag: cell line


title: H3K27Me3_48_hours_rep1

description: H3K27Me3 CHiP after 48 hours of induction of Snail-1 expression

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: H3K27Me3_120_hours_rep1

description: H3K27Me3 CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: H3K27Me3_0_hours_rep1


title: G4-NP8_12192-2

description:
reanalysis of GSM721097
Gene expression data from mammary carcinoma developed in WAP-T-NP8

source_name: WAP-T-NP8 Mouse Mammary Carcinoma, high grade (grade 4)

value: WAP-T


title: H3K4Me3_0_hours_rep1

description: H3K4Me3 CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated


title: H3K27Me3_6_hours_rep1

description: H3K27Me3 CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K27Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: H3K27Me3_120_hours_rep2


title: H3K27Me3_48_hours_rep2


title: H3K4Me3_0_hours_rep2


title: CHC786T

description: Hepatocellular adenoma


title: H3K4Me2_48_hours_rep2

description: H3K4Me2 CHiP after 48 hours of induction of Snail-1 expression

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: H3K4Me3_6_hours_rep1

description: H3K4Me3 CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: CHC964T

description: Hepatocellular adenoma

value: F


title: H3K4Me2_120_hours_rep1

description: H3K4Me2 CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: H3K4Me3_120_hours_rep2

description: H3K4Me3 CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K4Me3 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: CHC769T

description: Hepatocellular adenoma

value: dysplastic hepatocellular adenoma


title: H3K4Me2_6_hours_rep2

description: H3K4Me2 CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: High altitude pulmonary edema, PE_56

city: New Delhi

last: Sarkar

address: Lucknow Road, Timarpur.

country: India

institute: DIPAS

hyb_protocol: 10.0 µg of the labeled aRNA in 100 µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and was used for hybridization with the Human 40 K chip printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hrs on Tecan HS 4800 automated Hyb station.

scan_protocol: Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains (40, 50, 60).

data_processing: Intensity values obtained at 40, 50 and 60 PMT settings were averaged and used as raw data for Quantile normalization.

source_name: peripheral blood, high altitude pulmonary edema

label_protocol: Five microgram of total RNA was used for amplification using the Express Art® mRNA amplification Kit Message by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is reverse transcribed followed by second strand synthesis priming with an oligo (dT) primer bearing T7 promoter in a thermal cycler using the conditions described in the manual. The resulting cDNA was purified and then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA was then labelled with Cy3TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3 molecules were removed by a purification process.

extract_protocol: Blood samples were collected in PAXgene Blood RNA Tubes (PAXgene, PreAnalytiX, Hombrehtikon, Switzerland, distributed by Qiagen, catalog no. 762125 ex US) at high altitude in ambient temperature using a blood collection accessory (Beckton Dickinson) and stored at 4oC. The samples were transported on ice to laboratory at sea level. Isolation of total cellular RNA was done utilizing PAXgene Blood RNA kit (PreAnalytiX) as per manufacturer's protocol. An on-column DNase digestion was carried out for the removal of DNA using RNase-free DNase set (Qiagen) and purified RNA stored at -80oC. RNA concentration was evaluated by measuring an absorbance at 260 and 280 nm using a NanoDrop (NanoDrop, USA), and RNA quality was evaluated by electrophoretic analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA meeting the quality standards was released for probe generation.

treatment_protocol: Blood samples were collected from sea level sojourners (acclimatized, CN), high altitude natives (HN) and individuals with high altitude pulmonary edema (PE).

value: peripheral blood

tag: gender

value: male

tag: condition

value: high altitude pulmonary edema


title: H3K4Me2_48_hours_rep1


title: H3K4Me3_6_hours_rep2


title: H3K4Me2_120_hours_rep2


title: CHC711T

description: Hepatocellular adenoma


title: H3K4Me2_0_hours_rep2

description: H3K4Me2 CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K4Me2 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated


title: H3K4Me3_120_hours_rep1


title: CHC764T

description: Hepatocellular adenoma

value: non dysplastic hepatocellular adenoma


title: G3-NP8_12192-8

description:
reanalysis of GSM721093
Gene expression data from mammary carcinoma developed in WAP-T-NP8

source_name: WAP-T-NP8 Mouse Mammary Carcinoma, high grade (grade 3)


title: G3-NP8_12108-5

description:
reanalysis of GSM721092
Gene expression data from mammary carcinoma developed in WAP-T-NP8


title: High altitude pulmonary edema, PE_51


title: High altitude pulmonary edema, PE_47


title: G3-NP8_12212-2

description:
reanalysis of GSM721094
Gene expression data from mammary carcinoma developed in WAP-T-NP8


title: H3K4Me2_0_hours_rep1


title: CHC688T

description: Hepatocellular adenoma


title: High altitude pulmonary edema, PE_46


title: G3-NP8_11304-3

description:
reanalysis of GSM721095
Gene expression data from mammary carcinoma developed in WAP-T-NP8


title: G3-NP8_12109-1

description:
reanalysis of GSM721099
Gene expression data from mammary carcinoma developed in WAP-T-NP8


title: H3K4Me2_6_hours_rep1


title: CHC674T

description: Hepatocellular adenoma


title: 109490

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

hyb_protocol: Direct Hibridization Assay

scan_protocol: BeadArray TM Reader

data_processing: BRB arrayTools

source_name: metastatic colon cancer

label_protocol: Labeling steps of the proven GoldenGate Assay protocol

growth_protocol: Tissue stored in Formalin-Fixed Paraffin-Embedded Tissue

extract_protocol: RNeasy FFPE Kit (Qiagen, Hilden, D)

treatment_protocol: H&E sections were histologically reviewed and areas containing >50% tumor cells were marked; these were macrodissected from serial unstained sections at 8um after deparaffinization and submitted for RNA extraction.

value: Female

tag: grade

tag: stage tnm

value: IV

tag: death

value: No

tag: best response

value: PR

tag: eligible pfs


title: 109488

tag: Sex

value: Male

tag: age

value: SD


title: High altitude pulmonary edema, PE_67


title: 109485


title: High altitude pulmonary edema, PE_68


title: High altitude pulmonary edema, PE_66


title: 109483


title: High altitude pulmonary edema, PE_62


title: High altitude pulmonary edema, PE_61


title: 109479

value: CR


title: High altitude pulmonary edema, PE59_173


title: 109475


title: High altitude pulmonary edema, PE_63


title: H3K4Me1_120_hours_rep2

description: H3K4Me1 CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: High altitude pulmonary edema, PE_60


title: 109474

value: Yes

value: PD


title: CHC669T

description: Hepatocellular adenoma

tag: pathological diagnosis


title: High altitude pulmonary edema, PE_59

tag: tissue


title: H3K4Me1_48_hours_rep1

description: H3K4Me1 CHiP after 48 hours of induction of Snail-1 expression

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: CHC573T

description: Hepatocellular adenoma


title: 109470

value: IIIC


title: CHC574T

description: Hepatocellular adenoma

value: M


title: CHC485T

description: Hepatocellular adenoma

value: F


title: H3K4Me1_6_hours_rep1

description: H3K4Me1 CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: 109468


title: 109466


title: H3K4Me1_6_hours_rep2


title: High altitude pulmonary edema, PE_57


title: H3K4Me1_48_hours_rep2


title: H3K4Me1_120_hours_rep1


title: H3K4Me1_0_hours_rep1

description: H3K4Me1 CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K4Me1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated


title: CHC603T

description: Hepatocellular adenoma


title: CHC474T

description: Hepatocellular adenoma


title: High altitude pulmonary edema, PE127.38


title: CHC477T

description: Hepatocellular adenoma


title: 109464


title: CHC471T

description: Hepatocellular adenoma


title: High altitude pulmonary edema, PE_58


title: 109462


title: CHC464T

description: Hepatocellular adenoma

value: dysplastic hepatocellular adenoma


title: High altitude native, HN137

source_name: peripheral blood, high altitude native

value: peripheral blood

value: high altitude native


title: H3K27Ac_120_hours_rep2

description: H3K27Ac CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: High altitude native, HN134

value: male


title: H3K27Ac_48_hours_rep2

description: H3K27Ac CHiP after 48 hours of induction of Snail-1 expression

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: CHC466T

description: Hepatocellular adenoma

value: non dysplastic hepatocellular adenoma


title: CHC470T

description: Hepatocellular adenoma


title: 109454

value: Female

value: IIIB


title: High altitude native, HN_52


title: H3K4Me1_0_hours_rep2


title: 109449

value: unknown

value: IV

value: No


title: H3K27Ac_6_hours_rep2

description: H3K27Ac CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: High altitude native, HN135.49


title: 109451

value: Male

value: PR


title: H3K27Ac_0_hours_rep2

description: H3K27Ac CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K27Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated


title: High altitude native, HN133.47


title: CHC463T

description: Hepatocellular adenoma


title: 109447

value: Yes

value: CR


title: High altitude native, HN130


title: 109421

value: PD


title: 109440

value: IIIC


title: CHC461T

description: Hepatocellular adenoma

value: F


title: H3K27Ac_120_hours_rep1


title: H3K27Ac_48_hours_rep1


title: CHC454T

description: Hepatocellular adenoma

value: M


title: High altitude native, HN129

value: peripheral blood


title: High altitude native, HN120

value: high altitude native


title: H3K27Ac_6_hours_rep1


title: High altitude native, HN116

value: male


title: High altitude native, HN119


title: CHC452T

description: Hepatocellular adenoma

value: non dysplastic hepatocellular adenoma


title: H3K27Ac_0_hours_rep1


title: High altitude native, HN94


title: CHC382T

description: Hepatocellular adenoma


title: CHC383T

description: Hepatocellular adenoma


title: High altitude native, HN91


title: H3K4Ac_6_hours_rep2

description: H3K4Ac CHiP after 6 hours of induction of Snail-1 expression

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours


title: H3K4Ac_120_hours_rep2

description: H3K4Ac CHiP after 120 hours of induction of Snail-1 expression

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: High altitude native, HN80


title: H3K4Ac_48_hours_rep2

description: H3K4Ac CHiP after 48 hours of induction of Snail-1 expression

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: CHC378T

description: Hepatocellular adenoma

value: dysplastic hepatocellular adenoma


title: High altitude native, HN136.50


title: CHC379T

description: Hepatocellular adenoma


title: H3K4Ac_120_hours_rep1


title: CHC377T

description: Hepatocellular adenoma


title: CHC376T

description: Hepatocellular adenoma


title: Acclimatized control, CN72

source_name: peripheral blood, acclimatized control

value: acclimatized control


title: CHC372T

description: Hepatocellular adenoma


title: Acclimatized control, CN145


title: H3K4Ac_48_hours_rep1


title: CHC375T

description: Hepatocellular adenoma


title: Acclimatized control, CN128.39


title: Acclimatized control, CN144.43


title: CHC369T

description: Hepatocellular adenoma


title: SNAI1_120_hours_rep2

description: SNAI1 CHiP after 120 hours of induction of Snail-1 expression

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 120 hours

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 120 hours


title: Acclimatized control, CN141.40


title: Acclimatized control, CN143.42


title: H3K4Ac_6_hours_rep1


title: SNAI1_48_hours_rep2

description: SNAI1 CHiP after 48 hours of induction of Snail-1 expression

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 48 hours

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 48 hours


title: BDIX male

city: Essen

first: Andrea

last: Kindler-Röhrborn

address: Hufelandstr. 55

institute: Department of Pathology

data_processing: The data were normalized by subtracting background and rank invariant normalization using GenomeStudio Software 2010.

source_name: rat trigeminal nerve

label_protocol: Biotinylated cRNAs were prepared with the Illumina Total Prep RNA amplification kit (Ambion) according to manufacturer´s instructions.

extract_protocol: Total RNA from pooled trigeminal nerves was isolated using TRIzol Reagent (Invitrogen) according to manufacturer´s instructions. Quality and quantity of RNA was analysed using Peqlab Nanodrop spectrophotometer.

treatment_protocol: no treatment

tag: strain

value: BDIX

value: 85 days

tag: treatment

value: untreated

value: trigeminal nerve


title: CHC361TA

description: Hepatocellular carcinoma


title: SNAI1_6_hours_rep2

description: SNAI1 CHiP after 6 hours of induction of Snail-1 expression

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with tamoxifen in ethanol for 6 hours

tag: chip antibody

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen treated with ethanol for 6 hours

tag: mark


title: CHC364T

description: Hepatocellular adenoma


title: SNAI1_0_hours_rep2

description: SNAI1 CHiP after 0 hours of induction of Snail-1 expression

source_name: SNAI1 ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated

tag: time (hours)

tag: hours


title: CHC368T

description: Hepatocellular adenoma


title: BDIX female

tag: gender

value: female


title: A3R_d0_rep2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

description: highly aggressive A549 cell line

hyb_protocol: Bisulfite conversion of genomic DNA was performed using using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA). Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using HiScan instrument (Illumina Inc.) using standard recommended Illumina scanner setting

data_processing: Data preprocessing and methylation level extraction was performed using the Genome Studio software v2011.1 (Illumina Inc.) including the  Methylation module v1.9.0 and the Illumina Genome Viewer module v1.9.0.

source_name: A549 cell line

extract_protocol: genomic DNA extraction

tag: cell line

tag: rounds of in vivo selection

tag: 5-azacytidine status


title: A0R_d0_rep2

description: normal A549 cell line


title: BDIV female

value: BDIV


title: Acclimatized control, CN88

tag: condition


title: A0R_d0_rep1

description: normal A549 cell line


title: Acclimatized control, CN102


title: SNAI1_120_hours_rep1


title: BDIV male


title: BDIX.BDIV-Mss4a male


title: Acclimatized control, CN87


title: H3R_d0_rep2

description: highly aggressive HTB56 cell line

source_name: HTB56 cell line


title: Acclimatized control, CN96


title: CHC358T

description: Hepatocellular adenoma


title: CHC353T

description: Hepatocellular adenoma


title: SNAI1_48_hours_rep1


title: Acclimatized control, CN104


title: CHC343T

description: Hepatocellular adenoma


title: H3R_d0_rep1

description: highly aggressive HTB56 cell line


title: BDIX.BDIV-Mss4d female


title: H0R_d0_rep2

description: normal HTB56 cell line


title: BDIX.BDIV-Mss4d male


title: H0R_d0_rep1

description: normal HTB56 cell line


title: Salmonella inoculated, biological rep4

city: Madison

first: Jean-Michel

last: Ane

state: Wisconsin

address: 1575 Linden Drive

department: Agronomy

institute: University of Wisconsin Madison

description: Gene expression data from Medicago truncatula roots inoculated with Salmonella.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight on GeneChip Medicago Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GC3000 G7 scanner .

data_processing: The data were analyzed with AFX Expression Console v 1.1 using Affymetrix default analysis settings.

organism: Medicago truncatula

source_name: Medicago truncatula plants inoculated with Salmonella enterica

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp™ Premier IVT Manual version - P/N 4386269 Revision D used for all steps>  from 300 ng total RNA.

growth_protocol: Plants were grown in growth pouches at 25°C with 24 hour light cycle.

extract_protocol: Total RNA extraction was performed using Qiagen Rneasy® plant mini kit according to the manufacturer's instructions.

treatment_protocol: 1 day old plants were inoculated with 1x PBS, E. coli O157:H7(2 CFU/plant) and Salmonella (2 CFU/plant). Roots were harvested 10 days post inoculation and used for gene expression analyses.

value: Roots

value: inoculated with Salmonella enterica


title: SNAI1_6_hours_rep1


title: CHC340T

description: Hepatocellular adenoma

data_processing: standard Illumina protocol. Log R Ratios exported from the Beadstudio software.


title: Salmonella inoculated, biological rep3


title: DS_DAP_14C_Rep2

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Five Medicago truncatula plants were grown at controlled light/temperature conditions: 14/11°C, 16h light/dark from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 22 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, after abscission seeds were let in the same environmental conditions for one week.

extract_protocol: For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations

treatment_protocol: Medicago truncatula seeds developed at 14/11°C, 16h light/darkf rom 1 DAP to DS stage

tag: tissus

value: seed

tag: genetic background

tag: developmental stage

value: DS

tag: phenotype

value: Wild-type

value: Seeds developed at 15-13°C 16h

tag: harvest date


title: A3R_d0_rep1

description: highly aggressive A549 cell line


title: Acclimatized control, CN140

tag: tissue

value: peripheral blood


title: SNAI1_0_hours_rep1


title: CHC341T

description: Hepatocellular adenoma

extract_protocol: DNA was extracted from 3 mm3 frozen tumor samples using high salt precipitation (as described in PMID: 3344216).

tag: age

tag: Sex

value: M

tag: pathological diagnosis


title: BDIX.BDIV-Mss4a female

tag: strain

tag: treatment


title: CHC344T

description: Hepatocellular adenoma

value: F

value: non dysplastic hepatocellular adenoma


title: DS_DAP_14C_Rep1


title: CHC1020T

description: Hepatocellular adenoma


title: H3K4Ac_0_hours_rep2

description: H3K4Ac CHiP after 0 hours of induction of Snail-1 expression

source_name: H3K4Ac ChIP DNA from non-transformed, immortalized human mammary epithelial MCF10A cells engineered to express Snail-1 upon treatment with tamoxifen but un-treated

tag: chip antibody

tag: time (hours)

tag: mark

tag: hours


title: Abs_DAP_14C_Rep2

value: Abscission


title: Salmonella inoculated, biological rep2


title: ChIP-chip of Zip3-Flag from set1 del cells at 6 hr in meiosis

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

institute: Institut Curie

description: Zip3-Flag ChIP chip in set1 del meiotic cells (6 hr)

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then the ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

source_name: ChIP of Zip3-Flag

label_protocol:
ch1:two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling
ch2:1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 6 hr in meiosis

extract_protocol: 10ml (2*108 cells) were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Robine et al., 2007), using 2 µg of mouse monoclonal M2 anti-FLAG (Sigma) and 30 µl protein G magnetic beads suspension (New England Biolabs)

tag: time point

value: at 6 hr in meiosis

source_name: Whole cell extract


title: Salmonella inoculated, biological rep1


title: ChIP-chip of Zip3-Flag from set1 del cells at 7 hr in meiosis

description: Zip3-Flag ChIP chip in set1 del meiotic cells (7 hr)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 7 hr in meiosis

value: at 7 hr in meiosis


title: CHC1023T

city: Paris

last: Letouzé

institute: Ligue Contre Le Cancer

description: Hepatocellular adenoma

label_protocol: standard Illumina protocol

value: dysplastic hepatocellular adenoma


title: Abs_DAP_14C_Rep1


title: E. coli O157:H7 inoculated, biological rep4

description: Gene expression data from Medicago truncatula roots inoculated with E. coli O157:H7.

source_name: Medicago truncatula plants inoculated with Escherichia coli O157:H7


title: Acclimatized control, CN142.41

tag: gender

value: male

tag: condition

value: acclimatized control


title: H3K4Ac_0_hours_rep1

tag: cell line


title: ChIP-chip anti-Flag no tag control at 3 hr in meiosis

description: no tag ChIP chip control

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then the ratios from replicate #1 and replicate #2 were averaged, and the resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

source_name: ChIP anti-Flag

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 4 hr in meiosis

value: at 4 hr in meiosis


title: 65_DAP_14C_Rep2

tag: tissus

tag: genetic background

tag: developmental stage

value: 65_DAP maturation

value: 65 days after flowering


title: High altitude pulmonary edema, CN49(PE)

source_name: peripheral blood, high altitude pulmonary edema

tag: tissue

value: high altitude pulmonary edema


title: E. coli O157:H7 inoculated, biological rep2

value: Roots

value: inoculated with Escherichia coli O157:H7


title: 58_DAP_14C_Rep2

value: seed

value: 58_DAP maturation

tag: phenotype

value: Wild-type

value: Seeds developed at 15-13°C 16h

tag: age

value: 58 days after flowering

tag: harvest date


title: Mock treated control, biological rep4

description: Gene expression data from Medicago truncatula roots inoculated with 1xPBS (Mock treatment control).

source_name: Medicago truncatula plants mock inoculated with 1xPBS

value: mock inoculated with 1xPBS


title: ChIP-chip of Zip3-Flag from cells at 5 hr in meiosis

description: Zip3-Flag ChIP chip in meiotic cells (5 hr)

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then we computed a weighted average from the ratios from replicate #1 and replicate #2, wih the standard deviation of the chip as the weight. The resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 5 hr in meiosis

tag: strain

value: at 5 hr in meiosis


title: 65_DAP_14C_Rep1

tag: treatment


title: E. coli O157:H7 inoculated, biological rep1


title: E. coli O157:H7 inoculated, biological rep3


title: ChIP-chip of Zip3-Flag from spo11 del cells at 3 hr in meiosis

description: Zip3-Flag ChIP chip in spo11 del meiotic cells (3 hr)

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 3 hr in meiosis

value: at 3 hr in meiosis


title: ChIP-chip of Zip3-Flag from cells at 3 hr in meiosis

description: Zip3-Flag ChIP chip in meiotic cells (3 hr)


title: 58_DAP_14C_Rep1


title: IDI-PD 2 iPSc clone 3

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description:
iPS JR023-2
9256760080_H.AVG_Signal
single replicate

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: iPS_idiopathic PD patient

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: subject group

value: idiopathic Parkinson's Disease patients.

tag: subject id

value: IDI-PD 2

value: Male

tag: cell type

value: induced pluripotent stem cell line derived from dermal fibroblasts (iPS)

tag: culture conditions

value: mTeSR-1 + matrigel


title: Mock treated control, biological rep1


title: 46_DAP_14C_Rep1

value: 46_DAP maturation

value: 46 days after flowering


title: 46_DAP_14C_Rep2


title: 52_DAP_14C_Rep1

value: 52_DAP maturation

value: 52 days after flowering


title: Mock treated control, biological rep3

value: Roots


title: Acclimatized control, CN139

source_name: peripheral blood, acclimatized control

value: peripheral blood

value: male

value: acclimatized control


title: 40_DAP_14C_Rep2

value: seed

value: 40_DAP maturation

value: Wild-type

value: Seeds developed at 15-13°C 16h

value: 40 days after flowering


title: Mock treated control, biological rep2

value: mock inoculated with 1xPBS


title: GBA-PD 2 iPSc clone 1

description:
iPS MK088-1
9257259026_C.AVG_Signal
single replicate

source_name: iPS_PD patient [GBA N370S]

value: Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations

value: GBA-PD 2

value: Male


title: Obese-FBC-3

city: NEW YORK

first: Xiaoyuan

last: Xu

address: 1150 St Nicholas Ave.

department: Medicine

institute: Columbia University

description: Gene expression data from sorted FBC ( F4/80+, CD11b+, CD11c+) macrophages

hyb_protocol: Hybridization in AFFY Gene Chip HYB Oven 640 from AFFY for 16 hr at 45ºC and used EUKGE-WS2v5 wash protocol.

scan_protocol: GeneChips were scanned using the AFFY Gene Chip Scanner 3000 7G.

data_processing: Analyze on Expression Console

source_name: Adipose tissue macrophages from obese mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.  (GeneChip® Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Lean (C57BL/6J Lep +/+) and obese leptin-deficient (C57BL/6J Lep ob/ob) mice were obtained from the Jackson Laboratory.

extract_protocol: For whole AT samples, total RNA was extracted from the PGAT of individual mice. RNA was isolated from sorted FBC (F4/80+, CD11b+, and CD11c+) cells and FB (F4/80+, CD11b+, and CD11c−) cells with RNeasy micro kits (Qiagen) with a PicoPure RNA isolation kit and amplified for two rounds

treatment_protocol: Isolation stromal vascular cells: Adipose tissue was isolated from mice immediately after CO2 asphyxiation. Tissues were minced into fine (<10-mg) pieces and centrifuged at 500 g for 5 minutes to remove connective tissue debris. Minced samples were placed in a digestion solution of DMEM containing Liberase3 TM (0.14 units/ml) (Roche Applied Science), BSA 20 mg/ml, DNaseI, 50 U/ml (Sigma-Aldrich). The samples were then incubated at 37°C on an orbital shaker (185 rpm) for 30-45 minutes. Once digestion was complete, samples were passed through a sterile 250-μm nylon mesh (Sefar Filtration Inc.). The suspension was centrifuged at 500 g for 5 minutes. The pelleted cells were collected as the SVCs.The SVCs were resuspendedin erythrocyte lysisbuffer (BD Biosciences) and incubated at room temperature for 3 minutes. The erythrocyte-depleted SVCs were centrifuged at 500 g for 5 minutes and the pellet cells resuspendedin FACS buffer (PBS, 0.2%, fatty acid depleted-BSA, 5 mM EDTA) at a concentration of 7 x 106cells/ml for fluorescence activated cell sorting

value: Perigonadal

tag: genotype

value: 12~14 weeks of age

value: Macrophage of F4/80+, CD11b+, CD11c-+


title: IDI-PD 1 iPSc clone 3

description:
iPS MK024-3
9256760080_D.AVG_Signal
single replicate

value: idiopathic Parkinson's Disease patients.

value: IDI-PD 1

tag: gender

value: Female

value: induced pluripotent stem cell line derived from dermal fibroblasts (iPS)

value: mTeSR-1 + matrigel


title: GBA-PD 1 iPSc clone 1

description:
iPS MK071-1
9257259003_I.AVG_Signal
single replicate

value: GBA-PD 1


title: GBA-PD 1 iPSc clone 3

description:
iPS MK071-3
9257259003_J.AVG_Signal
single replicate


title: Obese-FBC-2

value: obese leptin-deficient (C57BL/6J Lep ob/ob)


title: 28_DAP_14C_Rep1

value: seed

value: 28_DAP maturation

value: Wild-type

value: 28 days after flowering


title: 34_DAP_14C_Rep2

value: 34_DAP maturation

value: Seeds developed at 15-13°C 16h

value: 34 days after flowering


title: 40_DAP_14C_Rep1

value: 40_DAP maturation

value: 40 days after flowering


title: Obese-FBC-4

value: Perigonadal

value: 12~14 weeks of age

value: Macrophage of F4/80+, CD11b+, CD11c-+


title: Obese-FBC-1


title: 34_DAP_14C_Rep1


title: SRSF1-targeting scramble siRNA-1

city: San Sebastian

first: Ravi

middle: Datta

last: Sharma

state: Gipuzkoa

address: Parque Tecnológico de San Sebastián, Paseo Mikeletegi, Nº 48,

department: Biomedical Engineering

institute: CEIT

description: A549 transfected with SRSF1 siRNA Experiment 1

hyb_protocol: Hybridization was performed by the Proteomics, Genomics and Bioinformatics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturer’s instructions.

scan_protocol: Affymetrix GeneChip 3000  Affymetrix® GeneChip® 3000  GeneChip® 3000

data_processing:
Background correction was processed with maximum likelihood estimation (mle). Quantile normalization was performed to adjust the experimental condition of the arrays. Summarized data by probesets.
probe group file: hjay.r1.pgf
meta-probeset file: hjay.r1.mps

source_name: A549 lung cancer cell line

label_protocol: Labeling was performed by the Proteomics, Genomics and Bioinformatics Core Facility of the Center for Applied Medical Research (CIMA) following manufacturer’s instructions.

growth_protocol: Cells were grown in RPMI supplemented with 2 mM glutamine, 10% Fetalclone, 100 U/ml of penicillin and 100 µg/ml of streptomycin

extract_protocol: Total RNA was extracted using the RNA/DNA Mini Kit (Qiagen)

treatment_protocol: Cells were transfected with a 30 nM solution of a non-targeting scramble siRNA (5´-ACGACACGCAGGTCGTCATtt-3´) or an SRSF1 siRNA (5´-TGAAGCAGGTGATGTATGTtt-3´) using lipofectamine

tag: transfection

value: SRSF1 siRNA


title: 28_DAP_14C_Rep2


title: SRSF1-targeting scramble siRNA-3

description: A549 transfected with SRSF1 siRNA Experiment 3


title: CHC222T

first: Eric

address: 15 rue de l'école de médecine

description: Hepatocellular adenoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

tag: Sex

value: M

tag: pathological diagnosis

value: non dysplastic hepatocellular adenoma


title: SRSF1-non-targeting scramble siRNA-3

description: A549 transfected with scramble siRNA Experiment 3

value: scramble siRNA


title: 22_DAP_14C_Rep2

tag: tissus

tag: genetic background

value: 22_DAP maturation

value: 22 days after flowering