title: Abdominal subcutaneous white adipose tissue, at study start, subject 61

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2).

source_name: abdominal subcutaneous white adipose tissue, VLCD, at study start

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Fifty-three overweight and obese individuals (BMI 28-35 kg/m2) were recruited by advertisement via local media. Exclusion criteria were smoking, cardiovascular disease, type 2 diabetes mellitus, liver or kidney disease, use of medication that influences body weight regulation, pregnancy, marked alcohol consumption (> 21 alcoholic units per week for men and >14 alcoholic units per week for women), elevated fasting glucose (>6.1 mmol/L), total cholesterol (>7.0 mmol/L) or triacylglycerol (>3.0 mmol/L) concentrations, or blood pressure (>160/100 mmHg). Furthermore, participants had to be weight stable (weight change <3.0 kg) for two months prior to the start of the study. This trial is registered with www.clinicaltrials.gov under the accession number NCT01559415.

extract_protocol: Total RNA was prepared from the frozen abdominal subcutaneous adipose biopsies (~150mg) using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).

treatment_protocol: The participants in our study followed a dietary intervention program that was divided in two phases (see also PDF describing the study design). First, participants were randomized to a 12-week low-calorie diet (LCD) period or a 5-week very-low-calorie diet (VLCD) period (weight loss (WL) period) and subsequently underwent a 4-week weight stable (WS) period. The WL period and WS period taken together was named the dietary intervention (DI) period. In the LCD group, participants underwent a 12-week diet providing 1250 kcal/day designed by the dietician. One meal was replaced by meal replacements, two meals were prepared by the participants themselves and three small in-between meal snacks were consumed. In the VLCD group, participants underwent a 5-week diet in which three meals per day were replaced by meal replacements, providing 500 kcal/day. During this period, participants were allowed to consume an unrestricted amount of low-calorie vegetables. Both groups subsequently underwent a 4-week WS period with a diet based on the energy requirement of the participants. The study dietician provided dietary advice to both groups to assist in weight loss during the WL period (five meetings) and in remaining weight stable throughout the WS period (four meetings). Abdominal subcutaneous AT needle biopsies (≈1 g) were collected 6-8 cm lateral from the umbilicus under local anesthesia (2% lidocaine) by needle biopsy after an overnight fast at study start and at the end of each period. Biopsies were immediately rinsed with sterile saline and visible blood vessels were removed with sterile tweezers. AT biopsies were snap-frozen in liquid nitrogen and stored at -80°C for further analysis.

value: abdominal subcutaneous white adipose

tag: treatment

value: very-low-calorie diet

tag: time point

value: at study start

tag: Sex

value: male

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi (kg/m2)

tag: body fat %


title: Abdominal subcutaneous white adipose tissue, at study start, subject 59

status: Public on Feb 07 2017

type: RNA

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: abdominal subcutaneous white adipose tissue, LCD, at study start

tag: tissue

value: low-calorie diet


title: hESC_Geldanamycin_16nM_48h_n3

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files

label: biotin

source_name: human embryonic stem cells

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of

growth_protocol: According to Pallocca et al. :Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. Arch Toxicol (2016) 90:159–180

extract_protocol: Total RNA from 2 days differentiated hESCs in the presence and absence of benchmark concentration (BMC) of toxicants has  been isolated with  Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

treatment_protocol: Human embryonic stem cells (hESC)-derived neural crest cells (NCC) have been treated for 48 hours with non-cytotoxic concentration of different toxicants (Arsenic trioxide, VPA,TSA, Geldanamycin, Triadimefon, PBDE-99, Interferon beta), known to inhibit NCC migration in vitro. Total RNA has been isolated after 48 h treatment and Affymetrix microarray analysis has been performed (for more informations see Pallocca et al. .Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration. Arch Toxicol (2016) 90:159–180)

tag: gender

value: female

value: human embryonic stem cells

tag: cell state

value: differentiated


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 59

source_name: abdominal subcutaneous white adipose tissue, LCD, after weight loss period

value: after weight loss period


title: hESC_Ctrl arsenic_0uM_48h_n1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 61

source_name: abdominal subcutaneous white adipose tissue, VLCD, after weight stable period

value: after weight stable period


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 56

source_name: abdominal subcutaneous white adipose tissue, LCD, after weight stable period


title: hESC_Geldanamycin_16nM_48h_n1


title: Abdominal subcutaneous white adipose tissue, at study start, subject 56


title: hESC_Ctrl 0.1%BSA_0pM_48h_n1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 55


title: Abdominal subcutaneous white adipose tissue, at study start, subject 55


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 54


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 52

source_name: abdominal subcutaneous white adipose tissue, VLCD, after weight loss period


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 51


title: Abdominal subcutaneous white adipose tissue, at study start, subject 52


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 50


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 54


title: Abdominal subcutaneous white adipose tissue, at study start, subject 51


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 55


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 53


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 51


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 52


title: Abdominal subcutaneous white adipose tissue, at study start, subject 53


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 50


title: Abdominal subcutaneous white adipose tissue, at study start, subject 50


title: PM04 post treatment

city: Urayasu-Shi

first: Takuya

last: Hirai

state: Chiba

address: 2-1-1, Tomioka

country: Japan

institute: Juntendo University Urayasu Hospital

description: The patients had no malignant tumors, analyzed by computerized tomography and gastrointestinal endoscopy.

hyb_protocol: Hybridized for 16 h at 37 ℃ with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: Hybridization images were scanned in a GenePix4400A device (Molecular Devices, Sunnyvale, CA, USA). The signal that caused the saturation was corrected as a result of the low PMT gain.

data_processing: The miRNA expression was assessed based on signal intensity calculated as the median of foreground signals minus local background, the obtained data were normalized to the average intensity levels using a per-chip 95th percentile method.

source_name: polymyositis

label_protocol: The extracted RNA was labeled using the 3D-Gene miRNA labeling kit (Toray Industries Inc.).

extract_protocol: Total RNA was extracted from 300 μl of plasma using the 3D-Gene RNA extraction kit (Toray Industries Inc., Tokyo, Japan) and miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands).

treatment_protocol: PM/DM patients recieved therapy with prednisolone, or, in case of prednisolone resistance or complications, with the combination of calcineurin inhibitors (cyclosporine or tacrolims) and/or pulse intravenous cyclophosphamide.

value: plasma

tag: status

value: post treatment

tag: age

value: 17 years

tag: diagnosis

value: polymyositis


title: PM04 pre treatment

value: pre treatment


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 48

value: no data


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 49


title: Abdominal subcutaneous white adipose tissue, at study start, subject 48


title: PM03 post treatment

value: 45 years


title: Abdominal subcutaneous white adipose tissue, at study start, subject 47

value: abdominal subcutaneous white adipose


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 48


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 47

value: very-low-calorie diet


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 46


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 46


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 49


title: Abdominal subcutaneous white adipose tissue, at study start, subject 49

value: at study start


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 47


title: PM02 post treatment

value: 83 years


title: PM03 pre treatment


title: PM01 post treatment

value: 52 years


title: PM01 pre treatment

value: female


title: PM02 pre treatment


title: DM04 post treatment

source_name: dermatomyositis

value: 40 years

value: dermatomyositis


title: DM04 pre treatment


title: DM03 pre treatment

value: 62 years

value: male


title: DM03 post treatment

value: plasma


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 43

value: after weight stable period


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 45


title: Abdominal subcutaneous white adipose tissue, at study start, subject 45


title: DM01 post treatment

value: post treatment

value: 32 years


title: DM01 pre treatment

value: pre treatment


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 45

value: after weight loss period


title: Abdominal subcutaneous white adipose tissue, at study start, subject 43


title: Abdominal subcutaneous white adipose tissue, at study start, subject 46


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 41

value: low-calorie diet


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 42

value: abdominal subcutaneous white adipose


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 42

value: very-low-calorie diet


title: Abdominal subcutaneous white adipose tissue, at study start, subject 42

value: at study start


title: DM02 pre treatment

value: 18 years


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 43


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 41


title: Abdominal subcutaneous white adipose tissue, at study start, subject 41


title: DM02 post treatment


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 40


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 40


title: Differentiated treatment

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

country: Taiwan

description:
A1-Control
3T3 adipocyte, differentiated cell

hyb_protocol: Samples were hybridized to Mouse Gene ST 1.0 arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty ul of hyb solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data generated were analyzed using Affymetrix Transcriptome Analysis Console software with Gene Level Differential Expression Analysis.
probe group file: MoGene-1_0-st-v1.na34.mm10.probeset.csv
meta-probeset file: MoGene-1_0-st-v1.na34.mm10.transcript.csv
Affymetrix Transcriptome Analysis Console 1.0.0.234

organism: Mus musculus

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: 3T3 fibroblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) with 10% calf serum at 37 °C in a water-saturated atmosphere of 95% air and 5% CO2. For differentiated 3T3 adipocyte from 3T3 fibroblast, 3T3 fibroblasts were grown till confluent before the initiation of differentiation. Differentiation was initiated by stimulation with induction media (10% FBS/DMEM with 115 μg/ml IBMX, 1 μg/ml insulin and 1 μmol/l dexamethasone). After 3 days of incubation, cells were maintained in insulin media (10% FBS/DMEM with 1 μg/ml insulin) for another 3 days.

extract_protocol: RNEasy Micro kit (Qiagen), following manufatcturer's instructions

treatment_protocol: For undifferentiated 3T3 fibroblast, cells were cotreated with 0.5 mM adenine or 0.5 mM AICAR for three days in Dulbecco's modified Eagle's medium (DMEM) with 10% calf serum. For differentiated 3T3 adipocyte from 3T3 fibroblast, induction media was added 0.5 mM adenine or 0.5 mM AICAR. After 3 days of induction, cells were maintained in insulin media only (10% FBS/DMEM with 1 μg/ml insulin) for another 3 days.

tag: cell line source

tag: cell type

value: fibroblasts

tag: treated with

value: none (control)

tag: cell subtype

value: differentiated adipocyte


title: Abdominal subcutaneous white adipose tissue, at study start, subject 40

tag: treatment

tag: time point

value: female


title: Undifferentiated treatment with AICAR

description:
AICAR
3T3 fibroblast culture with AICAR, undifferentiated cell

value: 0.5 mM AICAR for 3 days

value: undifferentiated fibroblast


title: Differentiated treatment with Adenine

description:
A1-Adenine
3T3 adipocyte culture with adenine, differentiated cell

value: 0.5 mM adenine for 3 days


title: Differentiated treatment with AICAR

description:
A1-AICAR
3T3 adipocyte culture with AICAR, differentiated cell


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 39

value: after weight stable period

tag: Sex

tag: age (yrs)


title: Undifferentiated Control

description:
Control
3T3 fibroblast, undifferentiated cell


title: Undifferentiated treatment with Adenine

description:
Adenine
3T3 fibroblast culture with adenine, undifferentiated cell


title: Abdominal subcutaneous white adipose tissue, at study start, subject 39

tag: height (cm)

tag: weight (kg)


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 38

tag: bmi (kg/m2)

tag: body fat %


title: Abdominal subcutaneous white adipose tissue, at study start, subject 38

tag: tissue


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 37


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 39


title: BL41 12h ctrl d3

city: Oslo

first: Thea

middle: Kristin

last: Vatsveen

address: Ullernschauseen 70

department: Cancer Research

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protoocol

data_processing: Limma package in R

source_name: Burkitt Lymphoma

label_protocol: Standard Illumina Protocol

growth_protocol: 0, 4 and 12 hours

extract_protocol: Total RNA was isolated using MiRNeasy (Qiagen, Hilden, Germany)

treatment_protocol: No treatment (control), or treatment with artesunate (5 µM).

tag: cell line

value: control


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 38


title: BL41 12h ctrl d1


title: BL41 0h ctrl d3


title: BL41 4h Art d3

value: artesunate (5 µM)


title: BL41 12h Art d3


title: BL41 12h Art d1


title: Su-4 0h ctrl d3

source_name: DLBCL-GCB


title: BL41 0h ctrl d1


title: Su-4 12h ctrl d1


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 37


title: Su-4 4h Art d3


title: Su-4 4h Art d1


title: Su-4 12h Art d1


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 36


title: BL41 4h Art d1


title: Su-4 12h ctrl d3


title: Ocily2 12h Art d3


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 36


title: Su-4 12h Art d3


title: Su-4 0h ctrl d1


title: Ocily2 12h ctrl d3


title: Ocily2 4h Art d3


title: Abdominal subcutaneous white adipose tissue, at study start, subject 37


title: Abdominal subcutaneous white adipose tissue, at study start, subject 36


title: Abdominal subcutaneous white adipose tissue, at study start, subject 35


title: Ocily2 0h ctrl d3


title: Ocily2 12h ctrl d1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 35


title: Ocily2 12h Art d1


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 34


title: hESC_Geldanamycin_16nM_48h_n2

tag: gender

value: human embryonic stem cells

tag: cell state

value: differentiated


title: Ocily2 0h ctrl d1


title: Abdominal subcutaneous white adipose tissue, at study start, subject 34

value: low-calorie diet


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 33

value: abdominal subcutaneous white adipose

value: male


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 31

value: after weight loss period


title: 14_siST3_2h_2

city: Bethesda

first: Ying

middle: E

last: Zhang

state: MD

address: 37 Convent Dr, Room 2056B

department: Center for Cancer Research

country: USA

institute: National Cancer Institute

description: Gene expression data from LX-2 cells transfected with STAT3  siRNA and treated with TGF-b for 2 hours

hyb_protocol: Samples were hybridized with GeneChip® Human Gene 2.0 ST Array (Affymetrix) and scanned at the Frederick National Laboratory for Cancer Research Microarray Core Facility.

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

data_processing: Data were processed using Partek Genomics Suite 6.6 software with guided Exon workflow for Gene-Level analysis.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: LX-2 cells were cultured in Dulbecco’s MEM supplemented with 10% fetal bovine serum and 100 units/ml penicillin-streptomycin.

extract_protocol: RNA was isolated from LX-2 cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: LX-2 cells were either untreated or treated with TGF-b (4 ng/ml) for 2 hours after culturing in DMEM with 0.2% fetal bovine serum for 4 hours

tag: sirna

value: 2 h

value: TGF-b


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 34


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 33


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 31


title: Abdominal subcutaneous white adipose tissue, at study start, subject 33

value: at study start


title: 15_siST3_2h_3

description: Gene expression data from LX-2 cells transfected with STAT3 siRNA and treated with TGF-b for 2 hours


title: Ocily2 4h Art d1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 30

value: very-low-calorie diet


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 30


title: Abdominal subcutaneous white adipose tissue, at study start, subject 30


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 29


title: Abdominal subcutaneous white adipose tissue, at study start, subject 29


title: Abdominal subcutaneous white adipose tissue, at study start, subject 31

value: female


title: Abdominal subcutaneous white adipose tissue, at study start, subject 28


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 28


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 35


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 27


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 29


title: 2_NS_0h_2

description: Gene expression data from LX-2 cells transfected with control siRNA and without TGF-b treatment

value: Control siRNA

value: 0 h


title: 11_siST3_0h_2

description: Gene expression data from LX-2 cells transfected with STAT3  siRNA and without TGF-b treatment


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 27


title: 4_NS_2h_1

description: Gene expression data from LX-2 cells transfected with control siRNA and treated with TGF-b for 2 hours


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 28


title: obese rat red TA, biological rep5

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

country: Canada

institute: University of Guelph

description: gene expression data from obese rat red TA

hyb_protocol: For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Rat Gene 2.1 ST array strips on the Affymetrix Hyb Oven 640, according to the manufacturer’s instructions. Strips were then washed and stained on the Affymetrix FS 450, according to the manufacturer’s instructions.

scan_protocol: Strips were scanned on the Affymetrix Scanner 3000 7G, following the manufacturer's default settings.

data_processing: RMA background correction and normalization.

organism: Rattus norvegicus

source_name: obese rat red TA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA according to the manufacturer's instructions.

growth_protocol: Male ZDF rats (Charles River, St-Constant, QC, Canada) were housed in individual cages, with a reverse 12h:12h light–dark cycle, and were provided with food and water ad libitum. Lean control rats were fed a standard chow (Purina 5008 diet; Purina, St Louis, MO, USA). Obese rats were provided a stock diet for 6 weeks.

extract_protocol: Tissue samples were homogenized using homogenizing beads and TRIzol (Thermo Fisher Scientific Inc., California, USA). Total RNA was then extracted using the RNeasy Mini Kit (Qiagen, Toronto, Canada), which included the optional DNase step, according to manufacturer instructions.

treatment_protocol: Samples were immediately frozen in liquid nitrogen after extraction from animals. Samples were thawed on ice immediately before commencing RNA extraction.

tag: strain

value: Zucker

value: red tibialis anterior (red TA)

tag: group

value: obese


title: obese rat red TA, biological rep3


title: obese rat red TA, biological rep4


title: Abdominal subcutaneous white adipose tissue, at study start, subject 27


title: 1_NS_0h_1

source_name: LX-2 cells transfected with control siRNA and without TGF-b treatment


title: obese rat red TA, biological rep2


title: 6_NS_2h_3

source_name: LX-2 cells transfected with control siRNA and treated with TGF-b for 2 hours


title: 13_siST3_2h_1

source_name: LX-2 cells transfected with STAT3  siRNA and treated with TGF-b for 2 hours


title: 10_siST3_0h_1

description: Gene expression data from LX-2 cells transfected with STAT3 siRNA and without TGF-b treatment


title: 5_NS_2h_2


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 26


title: 12_siST3_0h_3

source_name: LX-2 cells transfected with STAT3  siRNA and without TGF-b treatment


title: resveratrol rat red TA, biological rep4

description: gene expression data from resveratrol rat red TA

source_name: resveratrol rat red TA

value: resveratrol


title: Abdominal subcutaneous white adipose tissue, at study start, subject 26

source_name: abdominal subcutaneous white adipose tissue, VLCD, at study start


title: 3_NS_0h_3


title: Abdominal subcutaneous white adipose tissue, at study start, subject 25


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 24

value: after weight stable period


title: rosiglitazone rat red TA, biological rep5

description: gene expression data from rosiglitazone rat red TA

source_name: rosiglitazone rat red TA

value: rosiglitazone


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 25


title: rosiglitazone rat red TA, biological rep3


title: rosiglitazone rat red TA, biological rep4


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 24

value: low-calorie diet


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 23

value: abdominal subcutaneous white adipose


title: resveratrol rat red TA, biological rep2


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 25

value: male


title: Abdominal subcutaneous white adipose tissue, at study start, subject 24

source_name: abdominal subcutaneous white adipose tissue, LCD, at study start


title: resveratrol rat red TA, biological rep1


title: Abdominal subcutaneous white adipose tissue, at study start, subject 23


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 23

source_name: abdominal subcutaneous white adipose tissue, LCD, after weight loss period

value: after weight loss period


title: rosiglitazone rat red TA, biological rep2


title: resveratrol rat red TA, biological rep5


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 22

source_name: abdominal subcutaneous white adipose tissue, VLCD, after weight stable period

value: no data


title: lean control rat red TA, biological rep3

description: gene expression data from lean control rat red TA

source_name: lean control rat red TA

value: lean control


title: lean control rat red TA, biological rep4


title: Abdominal subcutaneous white adipose tissue, at study start, subject 22

value: at study start


title: lean control rat red TA, biological rep5


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 21

value: very-low-calorie diet


title: lean control rat red TA, biological rep2


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 22

source_name: abdominal subcutaneous white adipose tissue, VLCD, after weight loss period


title: rosiglitazone rat red TA, biological rep1


title: resveratrol rat red TA, biological rep3


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 21

value: female


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 18


title: obese rat red TA, biological rep1


title: Abdominal subcutaneous white adipose tissue, at study start, subject 21


title: Abdominal subcutaneous white adipose tissue, at study start, subject 19


title: Abdominal subcutaneous white adipose tissue, at study start, subject 18


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 19


title: Abdominal subcutaneous white adipose tissue, at study start, subject 20


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 20


title: lean control rat red TA, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 19

source_name: abdominal subcutaneous white adipose tissue, LCD, after weight stable period


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 26


title: obese rat liver, biological rep1

description: gene expression data from obese rat liver

source_name: obese rat liver

value: liver


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 20


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 14


title: resveratrol rat liver, biological rep3

description: gene expression data from resveratrol rat liver

source_name: resveratrol rat liver


title: rosiglitazone rat liver, biological rep4

description: gene expression data from rosiglitazone rat liver

source_name: rosiglitazone rat liver


title: obese rat liver, biological rep2


title: resveratrol rat liver, biological rep2


title: obese rat liver, biological rep5


title: rosiglitazone rat liver, biological rep3


title: resveratrol rat liver, biological rep1


title: resveratrol rat liver, biological rep5


title: obese rat liver, biological rep4


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 14


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 15


title: resveratrol rat liver, biological rep4


title: rosiglitazone rat liver, biological rep5


title: obese rat liver, biological rep3


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 15


title: Abdominal subcutaneous white adipose tissue, at study start, subject 14


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 13


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 13


title: lean control rat liver, biological rep4

description: gene expression data from lean control rat liver

source_name: lean control rat liver


title: Abdominal subcutaneous white adipose tissue, at study start, subject 13


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 12


title: lean control rat liver, biological rep5


title: lean control rat liver, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 12


title: obese rat blood, biological rep5

description: gene expression data from obese rat blood

source_name: obese rat blood

extract_protocol: RNA was extracted using the Mouse RiboPure-Blood RNA Isolation Kit (Thermo Fisher Scientific Inc., California, USA), according to manufacturer instructions.

value: blood


title: rosiglitazone rat liver, biological rep2

value: Zucker


title: lean control rat liver, biological rep3


title: Abdominal subcutaneous white adipose tissue, at study start, subject 11


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 11


title: rosiglitazone rat liver, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 11


title: obese rat blood, biological rep2


title: Abdominal subcutaneous white adipose tissue, at study start, subject 12


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 10


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 10


title: obese rat blood, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 9


title: obese rat blood, biological rep3


title: obese rat blood, biological rep4


title: resveratrol rat blood, biological rep5

description: gene expression data from resveratrol rat blood

source_name: resveratrol rat blood


title: resveratrol rat blood, biological rep2


title: lean control rat liver, biological rep2


title: resveratrol rat blood, biological rep4


title: resveratrol rat blood, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 8


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 8


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 9


title: Abdominal subcutaneous white adipose tissue, at study start, subject 9


title: Abdominal subcutaneous white adipose tissue, at study start, subject 10


title: Abdominal subcutaneous white adipose tissue, at study start, subject 6


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 6


title: Abdominal subcutaneous white adipose tissue, at study start, subject 8


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 6


title: rosiglitazone rat blood, biological rep3

description: gene expression data from rosiglitazone rat blood

source_name: rosiglitazone rat blood


title: rosiglitazone rat blood, biological rep2


title: rosiglitazone rat blood, biological rep4


title: resveratrol rat blood, biological rep3


title: lean control rat blood, biological rep5

description: gene expression data from lean control rat blood

source_name: lean control rat blood


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 5


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 5


title: rosiglitazone rat blood, biological rep1


title: rosiglitazone rat blood, biological rep5


title: Abdominal subcutaneous white adipose tissue, at study start, subject 5


title: lean control rat blood, biological rep2


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 4


title: lean control rat blood, biological rep1


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 4


title: ChrY-PWD-lung_rep3

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

hyb_protocol: Affymetrix® GeneChip® Hybridization Oven 645 at 45° C and 60 RPM for 16.5 hours overnight

scan_protocol: scanned with the 7G Affymetrix® GeneChip® Scanner 3000

data_processing: Raw intensity CEL files were imported into Expression Console software (Affymetrix, USA), and CHP files were generated for gene level level analysis. CHP files were imported into Transcriptome Analysis Console software (Affymetrix, USA)

label_protocol: Samples were then labeled with biotin using TdT (30U/µL), provided in the GeneChip® WT PLUS Reagent Kit;Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450

extract_protocol: RNEAsy Qiagen mini kit

treatment_protocol: intranasal influenza A virus infection


title: Pafah2-deficient BMMCs treated with omega-3 epoxides

city: Hongo, Bunkyo-ku

first: Yuta

last: Shimanaka

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: University of Tokyo

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: BMMCs

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: 8-12-wk-old Pafah2-deficient  mice (C57BL/6 background) were housed in climate-controlled (25 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) and water. ）

extract_protocol: Total RNA was purified using a GenElute Mammalian Total RNA Miniprep kit (Sigma-Aldrich) , and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Pafah2-deficient BMMCs were treated with a mixture of ω3 epoxides (17,18-EpETE/19,20-EpDPE = 2/3; 300 nM) or GW9662 (0.5 μM) for 12 hours. DMSO was used as vehicle.

tag: strain background

value: bone marrow derived mast cells (BMMCs)

tag: age


title: lean control rat blood, biological rep3


title: Pafah2-deficient BMMCs treated with GW9662


title: ChrY-PWD-lung_rep5


title: lean control rat blood, biological rep4


title: Abdominal subcutaneous white adipose tissue, at study start, subject 3

source_name: abdominal subcutaneous white adipose tissue, VLCD, at study start

tag: treatment


title: Abdominal subcutaneous white adipose tissue, at study start, subject 4

tag: time point


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 3

tag: Sex


title: Pafah2-deficient BMMCs treated with vehicle


title: B6-Lung_IAV_rep5


title: ChrY-PWD-lung_rep1


title: Abdominal subcutaneous white adipose tissue, at study start, subject 2

tag: age (yrs)


title: ChrY-PWD-lung_rep2


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 2

tag: height (cm)


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 2

tag: weight (kg)


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 3

tag: bmi (kg/m2)


title: B6-Lung_IAV_rep3


title: Test_MOLT_MG 2

city: Chennai

first: Rama

middle: Shanker

last: Verma

state: Tamilnadu

address: Bhupat and Jyoti Mehta School of Biosciences IITM

department: Biotechnology

country: India

institute: Indian Institute of Technology Madras

description: Gene expression data from RCCS Microgravity cultures of MOLT-4 cancer cell line

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

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

data_processing: The data were analyzed with Expression Console  using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: MOLT-4 cell line cultured in RCCS at 27RPM for 72h

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

growth_protocol: DLD-1 and MOLT-4 cells grown in 60mm Petri dishes(Static)

extract_protocol: Total RNA prepared using RNeasy Mini Kit - QIAGEN

treatment_protocol: DLD-1 and MOLT-4 cells grown in RCCS at 27RPM for 72h

tag: growth treatment

value: Non-adherent, Microgravity


title: Abdominal subcutaneous white adipose tissue, after weight stable period, subject 1

tag: tissue

tag: body fat %


title: ChrY-PWD-lung_rep4


title: Test_MOLT_MG 1

tag: cell line


title: Control_MOLT_ST 1

description: Gene expression data from Static suspension cultures of MOLT-4 Cancer cell line

source_name: MOLT-4 cell line cultured in Static suspension (60mm TCP) for 72h

value: Non-adherent, Static


title: Abdominal subcutaneous white adipose tissue, after weight loss period, subject 1


title: B6-Lung_IAV_rep2


title: Control_MOLT_ST 2


title: Test_DLD_MG 1

description: Gene expression data from RCCS Microgravity cultures of DLD-1 cancer cell line

source_name: DLD-1 cell line cultured in RCCS at 27RPM for 72h

value: adherent, Microgravity


title: Abdominal subcutaneous white adipose tissue, at study start, subject 1


title: Test_DLD_MG 2


title: Trsp-Ins1KO hypothlamus 2

status: Public on Feb 06 2017

city: Sendai

first: Akira

last: Uruno

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

institute: Tohoku University Graduate School of Medicine

hyb_protocol: Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner.

data_processing: The data were normalized by percentile shift and filtered by flag, using GeneSpring GX software (Silicon Genetics).

label_protocol: RNA samples were labeled with Cy3 using theLow Input Quick Amp Labeling Kits (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted using Sepazol-RNA I Super G RNA solution (Nakalai Tesque).

tag: gender

value: Male

value: 16 weeks

tag: genotype/variation

value: TrspFlox/Flox::Ins1-Cre (Trsp-Ins1KO)

value: Hypothlamus


title: Trsp-RIPKO hypothlamus 1

value: TrspFlox/Flox::RIP-Cre (Trsp-RIPKO)


title: TrspFF hypothlamus 2

value: TrspFlox/Flox (TrspFF)


title: Trsp-Ins1KO hypothlamus 1


title: B6-Lung_IAV_rep1

tag: strain


title: Trsp-Ins1KO islets 2

description: Gene expression in the islets of Trsp-Ins1KO mouse

source_name: Islets, Trsp-Ins1KO

value: ICR

value: pancreatic islets


title: Trsp-Ins1KO islets 1


title: Control_DLD_ST 2

description: Gene expression data from Static Monolayer cultures of DLD-1 cancer cell line

source_name: DLD-1 cell line cultured in monolayer for 72h

value: adherent, Static


title: Trsp-RIPKO hypothlamus 2


title: TrspFF islets 2

description: Gene expression in the islets of TrspFF mouse

source_name: Islets, TrspFF


title: TrspFF hypothlamus 1


title: Control_DLD_ST 1


title: Trsp-RIPKO islets 2

description: Gene expression in the islets of Trsp-RIPKO mouse

source_name: Islets, Trsp-RIPKO


title: TrspFF islets 1


title: Trsp-RIPKO islets 1


title: 5wks_KO nr. 6 24h IgE

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description: Sample name: 3998574028_F

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing: The data were normalised using quantile method

source_name: 5 weeks mouse Dnmt3a KO 24h IgE treatment

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

extract_protocol: RNA extraction was performed using a commercially available kit according to the manufactures recommendations. RNA quality was confirmed based on a RNA integrity number >8 by use of an electrophoresis bioanalyzer (2100 Agilent Bioanalyser).

treatment_protocol: treatment with IgE for 4hrs and 24hrs

tag: genotype

value: Dnmt3a KO

tag: cell type

value: mast

value: female

value: 24h IgE treatment


title: 5wks_KO nr. 6 4h IgE

description: Sample name: 3998574028_E

source_name: 5 weeks mouse Dnmt3a KO 4h IgE treatment

value: 4h IgE treatment


title: 5wks_WT nr 9 4h IgE

description: Sample name: 3998574028_B

source_name: 5 weeks mouse Dnmt3a WT 4h IgE treatment

value: wildtype


title: 5wks_WT nr. 9 24h IgE

description: Sample name: 3998574028_C

source_name: 5 weeks mouse Dnmt3a WT 24h IgE treatment


title: 5wks_WT nr. 9 US

description: Sample name: 3998574028_A

source_name: 5 weeks mouse Dnmt3a WT unstimulated

value: untreated


title: 5wks_Dnmt3aKO_no4_24h_IgE

description: Sample name: 3999574022_F

source_name: 5 weeks mouse n4 Dnmt3a KO 24h IgE treatment


title: 5wks_Dnmt3aKO_no4_4h_IgE

description: Sample name: 3999574022_E

source_name: 5 weeks mouse n4 Dnmt3a KO 4h IgE treatment


title: 5wks_Dnmt3aKO_no4_US

description: Sample name: 3999574022_D

source_name: 5 weeks mouse n4 Dnmt3a KO unstimulated


title: Type 2 diabetes monocytes, biological replicate 3

city: Brisbane

first: Katharine

last: Irvine

address: Translational Research Institute

country: Australia

institute: Mater Research Institute UQ

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Raw data were analysed using Expression Console

organism: Felis catus

source_name: peripheral blood monocytes from cat with type 2 diabetes

label_protocol: According to Affymetrix protocol

extract_protocol: Positive selection of CD14+ cells from whole blood using MACS beads followed by total RNA extraction using a Qiagen Rneasy kit with on-column DNA digestion.

tag: cat status

value: pet cat with type 2 diabetes

value: peripheral blood monocytes


title: 5wks_Dnmt3aWT_no8_24_hIgE

description: Sample name: 3999574022_C

source_name: 5 weeks mouse n8 Dnmt3a WT 24h IgE treatment

tag: treatment


title: 5wks_Dnmt3a_KO3 4h IgE

description: Sample name: 3998574042_F


title: 5wks_Dnmt3a_WT6 UT

description: Sample name: 3998574042_A

source_name: 5 weeks mouse Dnmt3a WT untreated


title: 5 wks_Dnmt3aWT_no8_4h_IgE

description: Sample name: 3999574022_B

source_name: 5 weeks mouse n8 Dnmt3a WT 4h IgE treatment


title: 5wks_Dnmt3a_KO3 UT

description: Sample name: 3998574042_D

source_name: 5 weeks mouse Dnmt3a KO untreated


title: Type 2 diabetes monocytes, biological replicate 2


title: Type 2 diabetes monocytes, biological replicate 1


title: 5wks_Dnmt3a_WT6 4h IgE

description: Sample name: 3998574042_C


title: Control monocytes, biological replicate 1

source_name: peripheral blood monocytes from control cat

value: non-diabetic control pet cat


title: 5wks_Dnmt3a_WT6 24h IgE

description: Sample name: 3998574042_B


title: 5wks_Dnmt3a_KO3 24h IgE

description: Sample name: 3998574042_E


title: Th9 repeat 3

city: CLEVELAND

first: ENGUANG

last: BI

state: OH

address: 9500 EUCLID AVE

department: CANCER BIOLOGY

institute: CLEVELAND CLINIC LERNER RESEARCH INSTITUTE

description:
8294816026_C_Grn.idat
replicate 3

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using average normalisation with Illumina GenomeStudio

source_name: CD4+ T cells

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

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

tag: age

value: 2 months

value: Spleen

value: Th9 cells


title: 5wks_Dnmt3aWT_no8_US

description: Sample name: 3999574022_A

source_name: 5 weeks mouse n8 Dnmt3a WT unstimulated


title: IL7 Th9 repeat 1

description:
8294816026_D_Grn.idat
replicate 1


title: IL7 Th9 repeat 2

description:
8294816026_E_Grn.idat
replicate 2


title: Control monocytes, biological replicate 3


title: CD4 IL7 24h Repeat 2

description:
3999889005_C_Grn.idat
replicate 2

value: CD4+ T cells


title: IL7 Th9 repeat 3

description:
8294816026_F_Grn.idat
replicate 3


title: Control monocytes, biological replicate 2


title: Th9 repeat 2

description:
8294816026_B_Grn.idat
replicate 2


title: CD4 IL7 6h Repeat 2

description:
3999889005_B_Grn.idat
replicate 2


title: B6-Lung_IAV_rep4


title: CD4 IL7 0h Repeat 2

description:
3999889005_E_Grn.idat
replicate 2


title: CD4 IL7 24h Repeat 1

description:
3999889005_F_Grn.idat
replicate 1


title: CD4 IL7 6h Repeat 1

description:
3999889005_A_Grn.idat
replicate 1


title: SH-SY5Y cells oxythiamine treatment_biological repicate 2

city: San Juan

first: Nataliya

last: Chorna

state: Puerto Rico

address: School of Medicine

department: Biochemistry

institute: University of Puerto Rico

description: Cell line SH-SY5Y cells differentiated with ATRA for 72 h. Treated with 1000 mM Oxythiamine for 72 h.

hyb_protocol: The arrays were prehybridized with continuous agitation for 1 h at 42°C in 5 mL hybridization solution (SpotHybTM Buffer; BD Biosciences Clontech) containing 0.1 mg/mL sheared salmon testes DNA (Sigma). Hybridization with biotin-labeled cDNA probes was performed overnight in 5 mL SpotHybTM Buffer at 42°C. The next day, membranes were washed with continuous agitation at 60°C in 2 × saline sodium citrate buffer (SSC), 1% (w/v) SDS (four times, each for 30 min) and then at 48°C in 0.1 × SSC (twice for 30 min). Probes were detected via labeling with IRDye-680RD-streptavidin (1:7000, Licor Biosciences).

scan_protocol: The arrays were visualized and quantified using the Odyssey Infrared Imaging System (LICOR Biosciences).

data_processing: The digital images were analyzed via AtlasImage 2.0 software (BD Biosciences Clontech)

source_name: Differentiated SH-SY5Y cells

label_protocol: 50 µg of the total RNA was reverse-transcribed using BD AtlasTM SpotLightTM Labeling Kit (BD Biosciences Clontech), to synthesize biotin-labeled probes with a pooled set of primers complementary to 205 human cDNAs spotted on the AtlasTM Human cDNA Apoptosis Array (BD Biosciences Clontech).

growth_protocol: DMEM/F12, 10% FCIII, 1% penicillin/streptomycin

extract_protocol: Total RNA was isolated using the TRIZOL® reagent (Thermofisher Sci) followed by DNase I treatment (Quiagen)

treatment_protocol: DMEM/F12, 1% FCIII, 1% penicillin/streptomycin differentiated with 15 μM ATRA for 72 h, followed with or without an additonal treatment with 1000 μM oxythiamine

tag: cell line backround

value: Neuroblastoma tumor cell line SH-SY5Y

tag: differentiated with

value: all trans retinoic acid (ATRA) for 72 h

value: 1000 μM Oxythiamine for 72hrs


title: SH-SY5Y cells control_biological replicate 2

description: Cell line SH-SY5Y cells differentiated with ATRA for 72 h. No additional treatment.

value: none (control)


title: PS3

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Oocyte RNA of Pecten maximus

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v10.7.3.1 and normalized by quantile normalization using R statistical software

label: Cyanine 3

organism: Pecten maximus

source_name: Stripped oocytes from an individual scallop

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Pecten maximus (mean weight±SD: 174±32g, mean length: 111±7mm) were caught from the bay of Brest at the beginning of their natural spawning period and transferred to the experimental hatchery of Ifremer (Argenton, France) where they were conditioned for 1 month under suitable conditions for germ cells maturation. Scallops were placed in experimental raceways supplied with 1 µm-filtered running seawater at 17 ± 1.0°C and fed with a mixed diet of two microalgae (Chaetoceros gracilis and Tisochrysis lutea).

extract_protocol: RNA was isolated by following the Extract-all manufacturer instructions and combining the RNeasy Mini Kit (Qiagen) for the nucleic acid purification. A DNAse treatment was also carried out (Qiagen).

tag: sample type

value: gamete stripping


title: SH-SY5Y cells control_biological replicate 1


title: SH-SY5Y cells oxythiamine treatment_biological repicate 1


title: PS5

description: Oocyte RNA of Pecten maximus


title: PS6

description: Oocyte RNA of Pecten maximus


title: T47D_decitabine-treated_96h_rep3

status: Public on Feb 05 2017

city: Philadelphia

first: Eric

middle: A.

last: Ariazi

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95) and Grid: 026652_D_F_20110325).  Mean Signals (without background subtraction) were quantile normalized. The following probes were removed: (i) Control probes; (ii) Probes which were absent across all arrays (gIsPosAndSignif, gIsWellAboveBG, and gIsFound not all TRUE); (iii) Probes lacking an Entrez identifier; (iv) All technical replicate probes except the first occurring of each probe identifier.

source_name: T47D/A18 cells, cultured in estrogenized media and treated with 1 μM decitabine for 96 h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were continuously cultured in estrogenized media (RPMI 1640 plus 10% whole FBS), estrogenized-media plus 100 nM fulvestrant, or estrogen-free media (phenol red-free RPMI 1640 plus 10% dextran-coated charcoal-stripped FBS) as indicated under 'Source name'.  Antihormone-resistant cells were maintained as polyclonal populations.

extract_protocol: Total RNA was purified using Qiagen’s RNeasy Plus kits. RNA samples were required to exhibit an RNA integrity number of 9.8-10.0 on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were treated with vehicle only (1:1,000 v/v ethanol) or 1 μM decitabine for 96 h where indicated under 'Source name'. Cells were collected for RNA purification at approximately 80% density in 60 mm dishes.

value: T47D/A18 cells

tag: time

tag: cell line status

value: wild-type breast cancer cell line


title: MCF7/FUL1_fulvestrant-treated_week21_rep2

description: MCF7/FUL wk21

source_name: MCF-7:WS8 cells, cultured in estrogenized media plus 100 nM fulvestrant for 21 weeks

value: MCF-7:WS8 cells

value: 21 weeks

value: fulvestrant-resistant breast cancer cell line


title: SH-SY5Y cells oxythiamine treatment_biological repicate 3


title: SH-SY5Y cells control_biological replicate 3


title: PS4

description: Oocyte RNA of Pecten maximus


title: T47D_decitabine-treated_96h_rep2

value: cultured in estrogenized media and treated with 1 μM decitabine


title: PP19_REL6

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 9.25 %)

value: spawning induction


title: T47D_decitabine-treated_96h_rep1


title: PP15_REL1

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 0.43 %)


title: PP16_REL7

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 11.20 %)


title: Th9 repeat 1

description:
8294816026_A_Grn.idat
replicate 1


title: PP18_REL3

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 0.88 %)


title: PP20_REL2

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 0.80 %)


title: PS2

description: Oocyte RNA of Pecten maximus


title: T47D_control-treated_96h_rep2

source_name: T47D/A18 cells, cultured in estrogenized media and treated with vehicle only (1:1,000 v/v ethanol) for 96 h


title: PP21_REL5

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 4.69 %)


title: T47D_control-treated_96h_rep3

value: cultured in estrogenized media and treated with vehicle only (1:1,000 v/v ethanol)


title: PS1

description: Oocyte RNA of Pecten maximus


title: CD4 IL7 0h Repeat 1

description:
3999889005_D_Grn.idat
replicate 1

value: 2 months


title: PP17_REL8

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 17.41 %)


title: MCF7/FUL1_fulvestrant-treated_week21_rep1

description: MCF7/FUL wk 21

value: cultured in estrogenized media plus 100 nM fulvestrant


title: 5wks_KO nr. 6 US

description: Sample name: 3998574028_D

source_name: 5 weeks mouse Dnmt3a KO unstimulated

value: Dnmt3a KO

value: mast

value: female

value: untreated


title: T47D_control-treated_96h_rep1


title: MCF7/FUL1_fulvestrant-treated_week8_rep2

description: MCF7/FUL wk 8

source_name: MCF-7:WS8 cells, cultured in estrogenized media plus 100 nM fulvestrant for 8 weeks

value: 8 weeks


title: MCF7_wild-type_rep1

source_name: MCF-7:WS8 cells, cultured in estrogenized media

value: cultured in estrogenized media


title: MCF7_wild-type_rep3


title: T47D/ED2/E2_estrogen-deprived_62weeks_E2-treated_24 weeks_rep1

description: T47D/ED2/E2 wk 24

source_name: T47D/A18 cells, cultured in estrogen-free media for 62 weeks and then treated with 1 nM 17β-estradiol for 24 weeks

value: 62 weeks (estrogen-free media), 24 weeks (1 nM 17β-estradiol)

value: estrogen deprivation-resistant, and then re-exposed to 17β-estradiol breast cancer cell line


title: T47D/ED2/E2_estrogen-deprived_62weeks_E2-treated_38 weeks_rep1

description: T47D/ED2/E2 wk 38

source_name: T47D/A18 cells, cultured in estrogen-free media for 62 weeks and then treated with 1 nM 17β-estradiol for 38 weeks

value: T47D/A18 cells

value: 62 weeks (estrogen-free media), 38 weeks (1 nM 17β-estradiol)


title: PP14_REL4

description: Oocyte RNA of Pecten maximus

source_name: Released oocytes from an individual scallop (D-larval rate = 4.53 %)


title: FUCH65M

status: Public on Feb 04 2017

type: genomic

city: San Francisco

first: Selene

last: Clay

state: California

address: 1001 Potrero Ave Rm 210

department: Ophthalmology

institute: University of California, San Francisco

description: Disease CE sample; Used in final analysis

hyb_protocol: Dispense fragmented and resuspended DNA samples onto Illumina Beadchips at 48C overnight in an Illumina Hybridization oven

scan_protocol: Illumina iScan system

data_processing: Raw intensity estimates were imported from the IDAT files and processed using the methylumi R package.  We corrected for color biases (adjColorBias.quantile function) and background intensity ("bgAdjust2C" method implemented in lumiMethyB) before quantile normalization (lumiMethyN).

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from corneal endothelial tissue

label_protocol: TEM reagent and Xstaining using Illumina chemistry

extract_protocol: genomic DNA was extracted and purified from corneal endothelial tissue using Macherey Nagel NucleoSpin Tissue XS according to manufacturer instructions

treatment_protocol: corneal endothelial tissue stored in RNAlater until DNA extraction

tag: Sex

value: Male

value: Diseased corneal endothelium (CE) tissue

tag: disease status

value: Fuchs Endothelial Corneal Dystrophy


title: CON70F

description: Control CE sample; Used in final analysis

value: Female

tag: tissue

value: Control corneal endothelium (CE) tissue

value: Healthy


title: FUCH73M


title: CON75M


title: FUCH_POOL

description: Pooled - excluded from analysis

value: Pooled (F, F, F)

value: Diseased corneal endothelium (CE) tissue (pooled)


title: CON46F


title: T47D/ED2/E2_estrogen-deprived_62weeks_E2-treated_38 weeks_rep2

description: T47D/ED2/E2 wk 38

tag: cell line

value: cultured in estrogen-free media for 62 weeks and then treated with 1 nM 17β-estradiol for 38 weeks


title: MCF7/FUL1_fulvestrant-treated_week8_rep3

description: MCF7/FUL wk 8

value: MCF-7:WS8 cells

value: cultured in estrogenized media plus 100 nM fulvestrant

value: fulvestrant-resistant breast cancer cell line


title: T47D/ED1_estrogen-deprived_52weeks_rep1

description: T47D/ED1 wk 52

source_name: T47D/A18 cells, cultured in estrogen-free media for 52 weeks

value: cultured in estrogen-free media

value: 52 weeks

value: estrogen deprivation-resistant breast cancer cell line


title: MCF7_wild-type_rep2

value: cultured in estrogenized media

value: wild-type breast cancer cell line


title: T47D/FUL_fulvestrant-treated_36weeks_rep2

description: T47D/FUL wk 36

source_name: T47D/A18 cells, cultured in estrogenized media plus 100 nM fulvestrant for 36 weeks

value: T47D/A18 cells

value: 36 weeks


title: T47D/FUL_fulvestrant-treated_36weeks_rep1

description: T47D/FUL wk 36


title: T47D_wild-type_rep2

source_name: T47D/A18 cells, cultured in estrogenized media


title: T47D/ED1_estrogen-deprived_52weeks_rep2

description: T47D/ED1 wk 52


title: T47D/ED2/E2_estrogen-deprived_62weeks_E2-treated_24 weeks_rep2

description: T47D/ED2/E2 wk 24

value: cultured in estrogen-free media for 62 weeks and then treated with 1 nM 17β-estradiol for 24 weeks

value: 62 weeks (estrogen-free media), 24 weeks (1 nM 17β-estradiol)

value: estrogen deprivation-resistant, and then re-exposed to 17β-estradiol breast cancer cell line


title: FUCH70F

description: Warned as low quality - excluded from analysis

value: Female

value: Diseased corneal endothelium (CE) tissue

value: Fuchs Endothelial Corneal Dystrophy


title: T47D/ED2_estrogen-deprived_62weeks_rep2

description: T47D/ED2 wk 62

source_name: T47D/A18 cells, cultured in estrogen-free media for 62 weeks

value: 62 weeks


title: CON49M

value: Male

value: Control corneal endothelium (CE) tissue

value: Healthy


title: FUCH75F

description: Used in final analysis


title: T47D/ED2_estrogen-deprived_62weeks_rep1

description: T47D/ED2 wk 62

value: cultured in estrogen-free media


title: FUCH76M

description: Used in final analysis


title: FUCH83F

description: Used in final analysis


title: FUCH47F

description: Used in final analysis


title: FUCH63M

description: Used in final analysis


title: FUCH77F

description: Warned as low quality, still used in analysis


title: FUCH75M

description: Excluded from analysis


title: T47D_wild-type_rep1


title: FUCH71M

description: Used in final analysis


title: AA2

status: Public on Feb 03 2017

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: AA mouse skin

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 1 µg total RNA sample and the RNA was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

extract_protocol: Total and small RNAs were isolated from the whole dorsal skin using the miRNeasy kit (Qiagen), and biotin labeled cRNA was generated through one round of in vitro transcription. Purified small RNAs were then subjected to global miRNA profiling using the µParaflo chips.

tag: sample group

value: spontaneous alopecia areata

value: Skin with hair loss


title: UA2

source_name: Unaffected mouse skin

value: unaffected; control

value: Normal haired skin


title: UA1


title: AA1


title: UA3


title: AA3


title: Ctrl 2

city: Modiin

first: Shiri

last: Klein

address: Migdal Halevanon 7

department: Gene Therapy

country: Israel

institute: Hebrew University

description: control

hyb_protocol: Following fragmentation, 5.5µg of Biotinylated ssDNA were hybridized for 17 hr at 45ºC on GeneChip Human Gene 1.0 ST Array.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The gene expression values were extracted using the Partek Genomics Suite 6.6 software and, after thresholding and filtering procedures, were submitted to fold change and cluster analyses.

source_name: Neuroblastoma tumor xenograft

label_protocol: biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: NSG mice, kept in a pathogen-free facility, under a 12 h light/dark cycle

extract_protocol: Tumors were removed and RNA was extracted using Trizol reagent.

treatment_protocol: 7 days following tumor cell injection mice were treated with BL-8040 (400ug) S.C. for 14 consecutive days.

value: Neuroblastoma tumor xenograft

value: NSG


title: Hippocampus_irradiated_2Gy

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: The mice were maintained in animal care facilities in a temperature-regulated room (23±1°C) with a 12 h light/dark cycle. All animals were fed water and standard mouse chow ad libitum.

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

treatment_protocol: The brain received whole-brain irradiation using six MV high energy photon rays (ELEKTA; Stockholm, Sweden) at a dose rate of 3.8 Gy/min. A radiation dosimeter (Semiflex Ionization Chamber 31013, PTW Co., Freiburg, Germany) was used to ensure that the radiation doses ranged from 99 to 100% at a point 3 cm below the surface of the simulated mouse head. We aligned the center of the head to the beam line center using the mouse holder. The distance of the skin from radiation source was 1 m.

tag: gender

value: male

value: hippocampus


title: Ctrl 3

description: control

tag: strain


title: Hippocampus_control


title: BL-8040 2

description: treated with CXCR4 inhibitor BL8040


title: BL-8040 3

description: treated with CXCR4 inhibitor BL8040


title: Centralbrain_DIP2 knockdown_rep1

city: Asahimachidori, Chuo-ku, Niigata-shi

first: Yohei

last: Nitta

state: Niigata

address: 757, Ichibancho,

institute: Niigata University

description: Gene expression profiles of DIP2 knockdown at 24hrs APF

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GE Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Drosophila Gene Expression Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Agilent Gene Expression Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The arrays were scanned using an Agilent G2565CA Microarray scanner (Agilent Technologies).

data_processing: Images were quantified using Feature Extraction 10.5.1.1 (Agilent Technologies). To identify candidate genes (p<0.05) whose expression levels were altered in the DIP2 RNAi brains, the data were analyzed using R statistical software

organism: Drosophila melanogaster

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 1

label_protocol: First strand synthesis and amplification of Cy3-labeled RNA were performed using an Agilent Low-Input QuickAmp Labeling Kit (Agilent Technologies), followed by RNeasy mini kit purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Experimental flies were raised at 29°C

extract_protocol: The total RNA was extracted from the central brains using an RNeasy Purification Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Experion (BIO-RAD).

value: central brain

value: female

tag: Stage

value: 24hrs APF

tag: genotype

value: DIP2 knockdown


title: BL-8040 1

description: treated with CXCR4 inhibitor BL8040


title: Ctrl 1

description: control


title: Centralbrain_DIP2 knockdown_rep4

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 4


title: Centralbrain_DIP2 knockdown_rep2

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 2


title: Centralbrain_DIP2 knockdown_rep3

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 3


title: Centralbrain_Control_rep4

description: Gene expression profiles of control at 24hrs APF

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 4

value: control


title: Centralbrain_Control_rep3

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 3


title: Centralbrain_Control_rep2

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 2


title: Centralbrain_Control_rep1

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 1


title: OX3 iPSc clone 6

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: single replicate

hyb_protocol: Standard Illumina hybridization protocol

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: induced pluripotent stem cell line derived from dermal fibroblasts, control donor OX3, clone 6

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

value: Male

tag: culture conditions

value: mTeSR-1 + matrigel


title: siP/CAF 1

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

description: SAMPLE 4_siP/CAF 1

data_processing: The data were normalised using quantile normalisation with GeneSpring GX v 10.0.2. Quantile normalization was performed for each sample individually and baseline was corrected to each probe across the samples in the experiment.

source_name: Rh30 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit  for Illumina array (HT12)

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

tag: cell type

value: Rhabdomyosarcoma Cell Line

tag: treatment

value: siP/CAF


title: OPA1P iPSc clone 5

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, OPA1 proband, clone 5

tag: age


title: siRNA 1

description: SAMPLE 1_siRNA 1


title: siP/CAF 2

description: SAMPLE 5_siP/CAF 2


title: siRNA 3

description: SAMPLE 3_siRNA 3


title: 13_1

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: The data were normalized using quantile normalisation in R.

source_name: Cervical endometrium

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: Samples of endometriosis, ovary cysts and cervical endometrium were obtained during surgical procedures. Tissues were placed in RNAlater solution immediately after removal and stored at -20°C. After removal of RNAlater solution samples were homogenized with 9 volumes of TRI Reagent (MRC), Direct-zol™ RNA MiniPrep (Zymo Research) was used for RNA extraction. RNA was quantified using Nanodrop (Thermo Fisher Scientific).

tag: individual

value: patient 13

value: cervical endometrium


title: 13_4

source_name: Capsule of endometrioid cyst of left ovary

value: ovary cyst


title: 13_3

source_name: Capsule of endometrioid cyst of right ovary


title: OPA1 iPSc clone 11

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, OPA1 mother, clone 11

value: Female


title: siRNA 2

description: SAMPLE 2_siRNA 2


title: Adult_Houston

city: MURCIA

first: Raul

last: Teruel-Montoya

address: Ronda Garay s/n

department: Hematology and Medical Oncology Deparment

country: Spain

institute: Centro Regional de Hemodonación, Morales Meseguer University Hospital, IMIB-Arrixaca

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC and 60 rpm on GeneChip Human Genome U133 Plus 2.0 Array using Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using  Affymetrix GeneChip Array Scanner 7G with autoloader.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Platelets

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 350 ng total RNA (Manual Target Preparation for GeneChip 3' Expression Arrays,P/N 703210 Rev1, 2013, Affymetrix).

value: platelets

tag: developmental stage

value: Adult


title: OPA1P iPSc clone 2

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, OPA1 proband, clone 2


title: Neonate_Houston

value: Neonate


title: Neonate_Murcia


title: MCF7/FUL1_fulvestrant-treated_week8_rep1

description: MCF7/FUL wk 8

source_name: MCF-7:WS8 cells, cultured in estrogenized media plus 100 nM fulvestrant for 8 weeks

value: MCF-7:WS8 cells

tag: time

value: 8 weeks

value: fulvestrant-resistant breast cancer cell line


title: 11_2

source_name: Peritoneal endometriosis

value: patient 11

value: endometriosis tissue


title: 13_2


title: Nr8_forsk+doxy

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: Gene expression data from MDA-MB-231 stably transfected with shLASP1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: MDA-MB-231-shLASP1 cells were grown 3 days in RPMI-1640 medium, supplemented with 10% FBS and Pen/Strep and -/+ 0.5 µg/ml doyxycycline.

extract_protocol: Cells were lysed in Trizol reagent and complete RNA was isolated according to manufacturers instructions.

treatment_protocol: Cultured MDA-MB-231-shLASP1 cells were treated 30 min with 5 µM forskolin prior to cell harvesting and RNA isolation to increase nuclear LASP1 localization

value: female

value: breast cancer


title: Nr6_forsk+doxy

source_name: MDA-MB-231 stably transfected with shLASP1


title: 11_1


title: 9_2

value: patient 9


title: 10_1

value: patient 10


title: 9_1

source_name: Retrocervical endometriosis


title: Nr4_forsk


title: 8_3

source_name: Capsule of ovarian endometrioid cyst

value: patient 8


title: Centralbrain_DIP2 knockdown_rep4

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 4

value: central brain

value: 24hrs APF

value: DIP2 knockdown


title: Adult_Murcia


title: Nr2_forsk


title: Centralbrain_DIP2 knockdown_rep3

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 3


title: Centralbrain_Control_rep4

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 4

value: control


title: Centralbrain_Control_rep3

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 3


title: OPA1P Fibroblasts [genomic]

description: HDF OPA1P

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: dermal fibroblasts, OPA1 proband

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: Male

value: ADMEM + 10% FCS


title: OPA1 iPSc clone 11 [genomic]

value: Female

value: mTeSR-1 + matrigel


title: OPA1 iPSc clone 9 [genomic]

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, OPA1 mother, clone 9


title: OX3 iPSc clone 6 [genomic]

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor OX3, clone 6


title: Centralbrain_DIP2 knockdown_rep2

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 2


title: 8_2


title: OPA1P iPSc clone 2 [genomic]

description: OPA1P _2


title: OX3 Fibroblasts [genomic]

description: HDF OX3

source_name: dermal fibroblasts, control donor OX3


title: OPA1P iPSc clone 5 [genomic]

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, OPA1 proband, clone 5


title: 10_2

source_name: Cervical endometrium

value: cervical endometrium


title: OPA1 Fibroblasts [genomic]

description: HDF OPA1

source_name: dermal fibroblasts, OPA1 mother


title: 7_1

value: patient 7

value: ovary cyst


title: Centralbrain_Control_rep2

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 2


title: Centralbrain_DIP2 knockdown_rep1

source_name: elav-Gal4/UAS-dicer2;DIP2-IR, DIP2 knockdown, 24hrs APF, replicate 1


title: Centralbrain_Control_rep1

source_name: elav-Gal4/UAS-dicer2, control, 24hrs APF, replicate 1


title: siP/CAF

description: SAMPLE 6_siP/CAF

source_name: Rh30 cell line

value: Rhabdomyosarcoma Cell Line

value: siP/CAF


title: 8_1


title: HM3722_I3

status: Public on Feb 02 2017

city: Iowa City

first: Miles

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

institute: University of Iowa

description: treated

hyb_protocol: According to UCLA Neuroscience Genomics Core (UNGC) protocol

data_processing: Bioconductor lumi/limma

source_name: patient from Children's Oncology Group

growth_protocol: All cells were geown in RPMI plus 10% FBS with no antibiotics

extract_protocol: Qiagen miRNAeasy

treatment_protocol: Cells were treated with 1µM dexamethasone for 4 hours or 0.1% ethanol as a vehicle control

value: primary human B-ALL (high risk B-ALL)

tag: chemotherapy treatment

value: standard chemotherapy

tag: dex treatment

value: dexamethasone

tag: treatment response

value: Relapsed, unknown relapse response

tag: diagnostic or relapse

value: relapse


title: HM3722_U3

description: control

scan_protocol: According to UCLA Neuroscience Genomics Core (UNGC) protocol


title: HM3722_U2

description: control


title: HM2872_I2

description: treated

value: Unknown

value: diagnostic


title: KRY_B_I2

description: treated

source_name: Blood

value: normal B cells

value: NA - normal B cells


title: HM3722_U1

description: control

value: control


title: HM2872_U1

description: control


title: HM2872_I3

description: treated


title: HM3722_I1

description: treated


title: HM3722_I2

description: treated


title: HM2872_I1

description: treated


title: 7_2

tag: tissue


title: KRY_B_I1

description: treated


title: HM2872_U2

description: control


title: KRY_B_I3

description: treated


title: KRY_B_U1

description: control


title: KRY_B_U3

description: control


title: HM3101_U3

description: control

value: primary human B-ALL

value: did not respond to chemotherapy, dexamethsone resistant


title: REH_I6

description: treated

source_name: DSMZ cell line

tag: cell line

value: B cell ALL cell line

value: dexamethasone resistant


title: HM3101_I3

description: treated


title: HM3101_I2

description: treated


title: HM3101_I1

description: treated


title: REH_I5

description: treated


title: HM3101_U1

description: control


title: Metastatic GIST-51

city: Boston

first: Jonathan

last: Fletcher

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital and Harvard Medical School

hyb_protocol: As per manufacturer's instructions (Affymetrix).

scan_protocol: Hybridized chip arrays were scanned according to the manufacturer's protocol.

data_processing: The positions and intensities of the fluorescence emissions were analyzed using Affymetrix Chromosome Analysis Suite 2.0.

source_name: Small intestine GIST

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Snap-frozen tumor biopsies were collected with institutional review board approval.

extract_protocol: High molecular weight genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, Valencia, CA, USA) and analyzed by Affymetrix Cytoscan HD 2,600K-SNP array (Affymetrix, Santa Clara, CA, USA) with Affymetrix Chromosome Analysis Suite 2.0.

tag: gender

value: Female

tag: tumor type

value: KIT-mutant gastrointestinal stromal tumor

tag: primary/metastasis

value: Metastasis


title: REH_I4

description: treated


title: REH_U6

description: control


title: REH_U5

description: control


title: KRY_B_U2

description: control


title: Metastatic GIST-56

value: Male


title: HM3101_U2

description: control

value: standard chemotherapy


title: MHH_CALL4_D2

description: treated

value: dexamethasone

value: dexamethasone sensitive


title: Primary GIST-46

value: Primary


title: B1_I4

description: treated


title: B1_U4

description: control


title: REH_U4

description: control


title: MHH_CALL4_D3

description: treated


title: B1_I5

description: treated


title: B1_U5

description: control


title: Primary GIST-44

source_name: Gastric GIST

value: KIT/PDGFRA/NF1 wild-type gastrointestinal stromal tumor


title: Mutz5_D3

description: treated


title: MHH_CALL4_D1

description: treated


title: MHH_CALL4_U2

description: control


title: MHH_CALL4_U1

description: control


title: C1 Synchronous Paraganglioma one

city: Melbourne

first: Aidan

middle: John

last: Flynn

state: Victoria

address: 305 Grattan St

department: Research

institute: Peter MacCallum Cancer Center

description:
Fresh Frozen DNA, CytoscanHD
C1-PGL1

hyb_protocol: Affymetrix CytoscanHD/OncoScan standard protocol

data_processing: Chromosome Analysis Suite (ChAS) with internal reference

extract_protocol: DNA was extracted from fresh frozen tissue samples with the Qiagen Dneasy blood and tissue kit, or from formalin-fixed parrafin-embedded tissue using the Qiagen QIAamp FFPE DNA kit

tag: Sex

tag: Stage

value: benign


title: Primary GIST-70

value: NF1-associated gastrointestinal stromal tumor


title: Mutz5_U1

description: control


title: Mutz5_D1

description: treated


title: Mutz5_U3

description: control


title: Mutz5_U2

description: control


title: Mutz5_D2

description: treated


title: Kasumi2_I2

description: treated


title: Kasumi2_I3

description: treated


title: Primary GIST-28


title: Primary GIST-33


title: C1 Synchronous Paraganglioma four

description:
Fresh Frozen DNA, CytoscanHD
C1-PGL4

scan_protocol: Affymetrix CytoscanHD/OncoScan standard protocol


title: C5 cervical metastasis from primary one

description:
Fresh Frozen DNA, CytoscanHD
C5-T1M

source_name: Medullary thyroid carcinoma, cervical node metastasis

label_protocol: Affymetrix CytoscanHD/OncoScan standard protocol

value: metastatic


title: 697_I3

description: treated

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


title: 697_U3

description: control

value: control


title: Primary GIST-3

value: PDGFRA-mutant gastrointestinal stromal tumor


title: B1_I3

description: treated


title: 697_I1

description: treated


title: 697_U2

description: control


title: B1_I1

description: treated


title: Metastatic GIST-8

source_name: Metastatic GIST


title: B1_I2

description: treated


title: Kasumi2_U3

description: control


title: MHH_CALL4_U3

description: control


title: B1_U2

description: control


title: 697_U1

description: control


title: B1_U3

description: control


title: Kasumi2_U2

description: control


title: Kasumi2_I1

description: treated


title: SUP_B15_I2

description: treated


title: C5 Primary one

description:
Fresh Frozen DNA, CytoscanHD
C5-T1

source_name: Medullary thyroid carcinoma, frist primary tumour


title: SUP_B15_I3

description: treated


title: C1 Synchronous Paraganglioma three

description:
Fresh Frozen DNA, CytoscanHD
C1-PGL3


title: B1_U1

description: control


title: S_set 2

city: Bethesda

first: Christina

last: Annunziata

address: 10 Center Drive, Room 4B54

department: Women's Malignancies Branch

institute: National Cancer Institute

description: expression levels for cells obtained from adherent cultures and expanded in ultra-low attachment flasks with stem cell media

hyb_protocol: All replicates of experimental samples were prepared, labeled and hybridized to Affymetrix H133 Plus 2.0 gene chips

scan_protocol: Gene chips were scanned using an Affymetrix GeneChip scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Raw microarray (CEL) data was processed using robust multi-array analysis (RMA) using the oligo package in Bioconductor

source_name: S - adherent cells in low attachment flask with serum-free stem cell media (DMEM/F12 with growth factors)

label_protocol: RNA (1ug) was reverse transcribed with T7-oligo (dT) primers and labeled with biotin using the Affymetrix One Cycle Target Labeling Kit

growth_protocol: ovarian cancer cells were seeded in traditional adherent flasks or ultra-low attachment flasks with traditional culture medium of DMEM/F12 containing 10% FBS and 1% penicillin/streptomycin or serum-free stem cell medium of DMEM/F12 containing 20 ng/ml EGF,  10 ng/ml FGF, 1% penicillin/streptomycin, 1% Knock-out serum replacement, 0.4% bovine serum albumin, and 0.1% insulin-transferin-selenium

extract_protocol: Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) as described by the manufacturer’s protocol and treated with DNAse to remove contaminating DNA. RNA quality checked on an Agilent Bioanalyzer; only samples having a high quality score (RIN>9) were used for microarray analysis.

tag: date rna collect


title: SUP_B15_I1

description: treated


title: SUP_B15_U1

description: control


title: SUP_B15_U2

description: control


title: REH_I3

description: treated


title: F_set 2

description: expression levels for floating cells obtained from adherent cultures that were expanded in ultra-low attachment flasks with stem cell media

source_name: F - Floating cells in low attachment flask with serum-free stem cell media (DMEM/F12 with growth factors)


title: S_set 1


title: AS_set 2

description: expression levels for cells expanded in adherent flasks in stem cell media

source_name: AS - Adherent cells in high attachment flask with serum-free stem cell media (DMEM/F12 with growth factors)


title: S_set 3


title: REH_U1

description: control


title: RS_4_11_U3

description: control


title: F_set 3


title: A_set 2

description: expression levels for cells expanded in adherent flasks in traditional media

source_name: A - adherent cells in high attachment flask with 10% FBS (DMEM/F12 base medium)


title: AS_set 3


title: REH_I2

description: treated


title: A_set 1


title: REH_U3

description: control


title: Kasumi2_U1

description: control


title: SUP_B15_U3

description: control


title: RS_4_11_U2

description: control


title: RCH_ACV_U3

description: control


title: RS_4_11_U1

description: control


title: RCH_ACV_U2

description: control


title: REH_U2

description: control


title: AS_set 1


title: RCH_ACV_I3

description: treated


title: 697_I2

description: treated


title: REH_I1

description: treated