title: Normal group A

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
NA


title: Normal group B

status: Public on Aug 04 2015

type: RNA

city: Shanghai，China

first: Xiangmei

last: Kong

address: 83 Fenyang Road, Xuhui District

department: Department of Ophthalmology

country: China

institute: Eye & ENT Hospital of Fudan University

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
NB

hyb_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform.

scan_protocol: Following the washing steps the slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA) and imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expression data were normalized using the median normalization.

molecule: total RNA

organism: Homo sapiens

source_name: normal group

label_protocol: Total RNAs (100 ng) were hy3-labeled using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

extract_protocol: At the beginning of the surgery the aqueous humor was collected as previously reported. After a corneal paracentesis, a 30-gauge needle on a tuberculin microsyringe was used to aspirate aqueous humor from the anterior chamber, not contacting any iris or lens tissue during the whole sample collection. Approximately 0.1-0.2ml of aqueous humor was collected from each patient, transferred to 1.5ml tubes, and immediately placed on dry ice. Then the samples were subsequently stored at −80°C until analysis.

tag: subject group

value: patients with cataract undergoing cataract surgery

tag: mean age

value: 67.8 years

tag: gender (male

value: female) ratio in the group:2:3

tag: tissue

value: Aqueous humor


title: Viremic Progressor_02S

city: Barcelona

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

country: Spain

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

description: non-coding small RNAs

hyb_protocol: Labeled samples were hybridized to the miRNA array at 48°C for 16 h and then washed and stained with a Streptavidin-PE solution prior to imaging.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affimetrix, Santa Clara, CA, USA).

data_processing: All microarray statistical analyses were performed using Bioconductor (http://www.bioconductor.org). After background correction, quantile normalization and median polish summarization the normalized data were fit to a linear model as implemented in bioconductor’s affy package.

label: biotin

source_name: CD8+ T-cells

label_protocol: All procedures were carried out according to the manufacturer's protocols. Briefly, 1 µg of each total RNA sample was poly-A tailed and the proprietary biotin-labeled dendramer molecule was joined to the 3´-end using the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were either isolated from fresh blood by Ficoll-Hypaque gradient centrifugation or used after thawing. PBMCs were cultured in RPMI medium containing 10% FBS and 2% gentamycin. CD8+ T-lymphocytes were isolated for RNA extraction after a positive selection with monoclonal antibodies.conjugated to microbeads AutoMACS (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA (enriched for small non-coding RNAs) was isolated according to manufacturer’s instructions using the ReliaPrep RNA Cell miniprep system kit (Promega, Fitchburg, WI, USA).

treatment_protocol: The isolated CD8+ population was used to generate resting and stimulated/activated pellets. CD8+ cell-subset was stimulated/activated using 10 ng/ml of CD3-OKT3 (ORTHO biotech Products, L.P., Raritan, NJ, USA) and 400 μg/ml of CD28 (kindly provided by Dr. R. Vilella (Laboratory of Immunology, Hospital Clinic, Barcelona, Spain) during three days.

tag: cell type

value: CD8+ T-cells

tag: patient type

value: Viremic Progressor

tag: resting/stimuli


title: Elite Controller_01R

description: non-coding small RNAs

value: Elite Controller

value: R


title: Uninfected Donor_01S

description: non-coding small RNAs

value: Uninfected Donor


title: Viremic Progressor_02R

description: non-coding small RNAs


title: Uninfected Donor_02S

description: non-coding small RNAs


title: 224a, biological replicate 2

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: MD Anderson Cancer Center

description: Gene expression data from DDLPS, 224a

hyb_protocol: Following fragmentation, 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package (12925520). For genes, which have represented by multiple probes on the array, maximum expression value was retained for further analyses. A gene is called as differentially expressed if FDR corrected p-value is less than 0.05, which is calculated with empirical Bayes method by eBayes function in Bioconductor’s limma package

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Plus reagent kit user manual (P/N 703210 Rev. 1) from 1 ug total RNA [Expression Analysis Technical Manual, 2009, Affymetrix (P/N 702232 Rev. 3)].

growth_protocol: LPS cell lines were cultures in DMEM containing 10% fetal bovine serum and maintained in standard tissue culture conditions (5% CO2, 37 degrees Celsius).

extract_protocol: Extraction of total RNA was performed using Qiagen RNaccording to the manufacturer's instructions.

treatment_protocol: Prior to extraction of total RNA, cells were treated with 0.25% trypsin and washed with PBS.

tag: cell line

value: DDLPS


title: Uninfected Donor_01R

description: non-coding small RNAs


title: Viremic Progressor_01S

description: non-coding small RNAs


title: Viremic Controller_02S

description: non-coding small RNAs

value: Viremic Controller


title: Viremic Controller_02R

description: non-coding small RNAs


title: Viremic Progressor_01R

description: non-coding small RNAs


title: 224a, biological replicate 1

description: Gene expression data from DDLPS, 224a


title: Primary gpen-angle glaucoma group B

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
PB

source_name: Primary open-angle glaucoma group

value: ocular hypertensive POAG patient group


title: Viremic Controller_01R

description: non-coding small RNAs


title: Viremic Controller_01S

description: non-coding small RNAs


title: 9263

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: 307-O/N NF 16/03/2010 - SP

hyb_protocol: 3μg labeled cDNA was hybridized on Human Whole Genome Gene Expression 4x44K MicroArray according to the One-Color microarray-Based Gene Expression Analysis User Manual v5.7, without fragmentation step.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1).

data_processing: The analysis is based on the expression values as obtained from the Agilent Feature Extraction software. Control probes and probes that were below background in all samples were removed. To decide whether a signal was significantly above background, we use the feature gIsPosAndSignif, also provided by the Agilent software. Signals were log2-transformed and then normalized with quantile normalization. Values for duplicated probes were subsequently averaged. The reported values are on log2-scale.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 2ng of total RNA was amplified and converted to single-stranded antisense cDNA using the NuGEN WT-Ovation Pico RNA Amplification System v1.0. All steps were carried out according to the manufacturers protocol (NuGEN). 2μg of purified, amplified cDNA were used as input into the Agilent Genomic DNA Enzymatic labeling according to the manufacturers instructions and labeled with cyanine 3-dUTP (Cy3). The Cy3-labeled cDNA was quantitated and dye incorporation determined by Nanodrop.

extract_protocol: Tumor samples were either immediately processed for flow-cytometric analysis after resection, or cryopreserved as small pieces, followed by storage at -196°C for later. Dissociated cells were processed for SP analysis. CD31¯/CD45¯ SP (purified SP or pSP) and pMP cells were sorted by FACS into cold lysis solution of the RNeasy Micro Kit (Qiagen, Venlo, The Netherlands). Total RNA was extracted immediately after cell collection according to the manufacturer’s guidelines. RNA samples were stored at -80°C until further processing for whole-genome expression profiling (in collaboration with the VIB Nucleomics Core, KU Leuven).

value: human pituitary adenoma

tag: type

value: non-functioning adenoma

tag: fraction

value: side population

tag: gender

value: male

tag: age


title: 9268

description: 356-O/N NF 28/06/2010 - MP

value: main population


title: Blood Normal 6 (Nsp)

type: genomic

city: Singapore

first: Muthulakshmi

last: Muthuswami

address: 8 College Road

department: Cancer and Stem cell Biology

country: Singapore

institute: Duke NUS Graduate Medical School

description: Hybridized to 250K_Nsp

hyb_protocol: As per the protocol specified for 500K SNP arrays by Affymetrix.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner GCS3000

data_processing: The data was analyzed using dChip software for normalization and copy number estimation.

molecule: genomic DNA

source_name: Blood Normal 6 (Nsp)

growth_protocol: All gastric cancer cell lines were grown in standard conditions.

extract_protocol: Genomic DNA was extracted using Qiagen DNA extraction kit according to manufacturer's instruction

value: blood

tag: sample type

value: Normal Male


title: Blood Normal 7 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 7 (Nsp)

label_protocol: As per the protocol specified for 500K SNP arrays by Affymetrix.


title: 9267

description: 353-Thawed NF 22/06/2010 - SP


title: 9261

description: 303-Thawed NF 02/12/2009 - SP


title: 9260

description: 302-Thawed NF 02/12/2009 - MP


title: 9266

description: 352-Thawed NF 22/06/2010 - MP


title: 9264

description: 342-Thawed NF 10/06/2010 - MP


title: 9269

description: 358-O/N NF 28/06/2010 - SP


title: 7987

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on Agilent Human Whole Genome 4x44K G4112F arrays followed by (manual) washing, according to the manufacturer's procedures

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent's Feature Extraction software (version 10.1.1.1 for samples of exp1016; version 10.5.1.1 for samples of exp1113).

label_protocol: RNA concentration and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 800 pg - 20 ng (samples of exp1016) and 3.8 ng - 10 ng (samples of exp1113) of total RNA was amplified in a 2-cycle amplification reaction as described by Baugh et al. (PMID: 11222780). During the second in vitro transcription reaction, the sample was amplified and labeled with Cyanine 3-CTP (Cy3) according to AgilentÕs protocol.

extract_protocol: Tumor samples were either immediately processed for flow-cytometric analysis after resection, or cryopreserved as small pieces, followed by storage at -196°C for later. Dissociated cells were processed for SP analysis. Total SP and MP cells were sorted by FACS into cold lysis solution of the RNeasy Micro Kit (Qiagen, Venlo, The Netherlands). Total RNA was extracted immediately after cell collection according to the manufacturer’s guidelines. RNA samples were stored at -80°C until further processing for whole-genome expression profiling. (in collaboration with the VIB Nucleomics Core, KU Leuven).

value: non-functioning pituitary adenoma

value: female


title: Blood Normal 3 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 3 (Nsp)

value: Normal Female


title: Blood Normal 2 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 2 (Nsp)


title: 7986


title: 9262

description: 305-O/N NF 16/03/2010 - MP


title: 7988


title: YCC9 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC9 Cell Line (Nsp)

value: Gastric Cell Line (YCC9)


title: 7985


title: YCC3 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC3 Cell Line (Nsp)

value: Gastric Cell Line (YCC3)


title: YCC11 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC11 Cell Line (Nsp)

value: Gastric Cell Line (YCC11)


title: 9265

description: 344-Thawed NF 10/06/2010 - SP


title: YCC16 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC16 Cell Line (Nsp)

value: Gastric Cell Line (YCC16)


title: 7984


title: YCC2 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC2 Cell Line (Nsp)

value: Gastric Cell Line (YCC2)


title: Blood Normal 5 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 5 (Nsp)


title: Blood Normal 4 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 4 (Nsp)


title: YCC1 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC1 Cell Line (Nsp)

value: Gastric Cell Line (YCC1)


title: YCC6 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC6 Cell Line (Nsp)

value: Gastric Cell Line (YCC6)


title: 7982

source_name: SP PitAd 6/07/09

value: human pituitary adenoma


title: Blood Normal 1 (Nsp)

description: Hybridized to 250K_Nsp

source_name: Blood Normal 1 (Nsp)


title: YCC7 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: YCC7 Cell Line (Nsp)

value: Gastric Cell Line (YCC7)


title: 6620

source_name: Pituitary AD MP

value: somatotropinoma


title: 6611

value: male


title: 6621

source_name: SP PitAd 13/3/08

value: main population


title: 7983


title: 6619

source_name: Pituitary AD SP

value: side population


title: SNU5 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: SNU5 Cell Line (Nsp)

value: Gastric Cell Line (SNU5)


title: 6618

source_name: SP PitAdAd 19/2


title: 6612


title: 6615

value: non-functioning pituitary adenoma


title: 7981

source_name: MP PitAd 6/07/09

value: female


title: SNU16 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: SNU16 Cell Line (Nsp)

value: Gastric Cell Line (SNU16)


title: 6617

source_name: MP PitAdAd 19/2


title: SNU1 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: SNU1 Cell Line (Nsp)

value: Gastric Cell Line (SNU1)


title: 2 Control THP 1

city: Omaha

first: Jessi

last: Winkler

state: Nebraska

address: DRC I

department: Exp Neuroscience and Pharmacology

institute: UNMC

description: Gene expression data from THP-1 cells treated with EZH2 inhibitor GSK126

hyb_protocol: Overnight hybridization using the Affymetrix hybridization over at 42oC. 500ng of cDNA was used

scan_protocol: Affymetrix GeneChip Scanner 3000 7G generated the resulting array image

data_processing: RMA normalization followed by Partek Genomic Suite 6.6 analysis

label_protocol: Biotinylated

growth_protocol: THP-1 cells were cultured in RPMI media supplemented with 10% FBS, 2.5mM glutamate, and 0.05mM 2-mercaptoethanol.

extract_protocol: Trizol

treatment_protocol: THP-1 cells were treated with 2uM GSK126 for 24 hours

tag: treatment

value: control


title: NCI-N87 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: NCI-N87 Cell Line (Nsp)

value: Gastric Cell Line (NCI-N87)


title: 6616


title: KATOIII Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: KATOIII Cell Line (Nsp)

value: KATOIII

value: Gastric Cell Line (KATOIII)


title: 3 Control THP 1


title: 1 Control THP 1


title: 2 THP 1

source_name: THP-1 plus 10uM EZH2 inhibitor GKS127

value: EZH2 inhibition


title: 3 THP 1

source_name: THP-1 plus 10uM EZH2 inhibitor GKS128


title: 1 THP 1

source_name: THP-1 plus 10uM EZH2 inhibitor GKS126


title: MKN7 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: MKN7 Cell Line (Nsp)

value: Gastric Cell Line (MKN7)


title: 10090510

city: Madrid

first: Nuria

last: Malats

state: Madrid

address: C/ Melchor Fernández Almagro 3

institute: CNIO

description: Gene expression data from bladder cancer tissue in humans

hyb_protocol: cDNA was hybridized to Human ST 1.0 Affymetrix arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed according to manufacturer's instructions (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned with GCS3000 autoloader scanner (Affymetrix, Santa Clara, CA)

data_processing: arrayQualityMetrics package from R was used to implement a background correction and to carry out normalization of expression levels across arrays (RMA algorithm). Application of QC steps resulted in 20,899 probes and 37 individuals. The affy library in R was used to annotate the probes.

label: bitotin

source_name: bladder tumoral tissue

label_protocol: 50 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 10 µg of cDNA were  subsequently fragmented and labeled using Human Mapping 10K SNP Kit (Affymetrix, Santa Clara, CA) , according to manufacturer's instructions.

extract_protocol: Samples obtained from patients were snap-frozen. RNA was extracted  using Trizol. cDNA synthesis and

value: bladder tumor

tag: tstage

value: TaGI


title: 30107919


title: 30108817


title: IM95 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: IM95 Cell Line (Nsp)

value: Gastric Cell Line (IM95)


title: Arid1a_KO_mouse2

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Mouse Genome 430 2.0 arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the affy package implemented in the R-statistical environment version 3.0.0. RMA was used to estimate log2 transformed expression values for each probe-set.

organism: Mus musculus

source_name: Ovarian carcinoma from Arid1a knockout mouse

label_protocol: 250-400 ng total RNA was reverse-transcribed, amplified and labeled, with the Affymetrix IVT express kits.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), and purified using Rneasy columns (Qiagen). Quality was checked with an Agilent 2100 Bioanalyzer.

tag: Sex

tag: genotype

value: APC-/- Pten-/- Arid1a-/-


title: Arid1a_KO_mouse1


title: 30108314


title: 30106114

value: TaGIII


title: 10093110


title: 30107414


title: Arid1a_WT_mouse3

source_name: Ovarian carcinoma from Arid1a wild-type mouse

value: APC-/- Pten-/-


title: Hs746T Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: Hs746T Cell Line (Nsp)

value: Gastric Cell Line (Hs746T)


title: Fu97 Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: Fu97 Cell Line (Nsp)

value: Gastric Cell Line (Fu97)


title: 10093510


title: Arid1a_KO_mouse3

value: female


title: 10093710


title: AGS Cell Line (Nsp)

description: Hybridized to 250K_Nsp

source_name: AGS Cell Line (Nsp)

value: AGS

value: Gastric Cell Line (AGS)


title: 10090110


title: 10091910


title: Arid1a_WT_mouse2


title: 30107610


title: 10094310


title: 10091710


title: 30105412


title: 10093010


title: 10092010


title: 10091810


title: 10090210


title: 10090910


title: 30108611


title: 30110214

description: DNA methylation data from bladder cancer tissue in humans

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: bladder tumoral tissue 53

label_protocol: Standard Illumina Protocol

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

value: TaGII


title: 10093310


title: 30106815


title: 30106516


title: 30108817

scan_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27

source_name: bladder tumoral tissue 50


title: 30107311


title: 30107713

source_name: bladder tumoral tissue 47


title: Arid1a_WT_mouse1


title: 30109911

source_name: bladder tumoral tissue 52


title: 30107610

source_name: bladder tumoral tissue 46


title: 10092810


title: 6622

source_name: MP PitAd 13/3/08

value: human pituitary adenoma

value: somatotropinoma

value: side population


title: 30105711


title: 30107919

source_name: bladder tumoral tissue 48


title: 30107012


title: 10094910


title: 10092310


title: 30106815

source_name: bladder tumoral tissue 43


title: 30107713


title: 30106712


title: 30106310

source_name: bladder tumoral tissue 39


title: 30106712

source_name: bladder tumoral tissue 42


title: 30109612

source_name: bladder tumoral tissue


title: 10094410


title: 30106619

source_name: bladder tumoral tissue 41


title: 30107012

source_name: bladder tumoral tissue 44


title: 30106516

source_name: bladder tumoral tissue 40


title: 30106619


title: 30106217

source_name: bladder tumoral tissue 38


title: 10093410


title: 10091310


title: 30104617


title: 30110214


title: 30109911


title: 10093210


title: 30110616


title: 30105412

source_name: bladder tumoral tissue 34


title: 30104411


title: 30104813

source_name: bladder tumoral tissue 33

value: Ta Benigne


title: 10094010


title: Blood Normal 7 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 7 (Sty)

value: male

value: blood

value: Normal Male


title: 10094510

source_name: bladder tumoral tissue 28

value: bladder tumor


title: 30105711

source_name: bladder tumoral tissue 36


title: 10094810

source_name: bladder tumoral tissue 30


title: Blood Normal 6 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 6 (Sty)


title: YCC3 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC3 Cell Line (Sty)

value: Gastric Cell Line (YCC3)


title: 10094910

source_name: bladder tumoral tissue 31


title: 10094610

source_name: bladder tumoral tissue 29


title: YCC7 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC7 Cell Line (Sty)

value: Gastric Cell Line (YCC7)


title: YCC2 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC2 Cell Line (Sty)

value: Gastric Cell Line (YCC2)


title: 10094410

source_name: bladder tumoral tissue 27


title: Blood Normal 1 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 1 (Sty)

value: Normal Female


title: Blood Normal 5 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 5 (Sty)


title: Blood Normal 3 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 3 (Sty)


title: 10094310

source_name: bladder tumoral tissue 26


title: 10094010

source_name: bladder tumoral tissue 24


title: YCC16 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC16 Cell Line (Sty)

value: Gastric Cell Line (YCC16)


title: YCC9 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC9 Cell Line (Sty)

value: Gastric Cell Line (YCC9)


title: 10094110

source_name: bladder tumoral tissue 25


title: YCC1 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC1 Cell Line (Sty)

value: Gastric Cell Line (YCC1)


title: YCC6 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC6 Cell Line (Sty)

value: Gastric Cell Line (YCC6)


title: Blood Normal 2 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 2 (Sty)

value: female


title: Blood Normal 4 (Sty)

description: Hybridized to 250K_Sty

source_name: Blood Normal 4 (Sty)


title: 10093510

source_name: bladder tumoral tissue 22

value: TaGI


title: 10093710

source_name: bladder tumoral tissue 23


title: SNU1 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: SNU1 Cell Line (Sty)

value: Gastric Cell Line (SNU1)


title: 10093410

source_name: bladder tumoral tissue 21


title: SNU16 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: SNU16 Cell Line (Sty)

value: Gastric Cell Line (SNU16)


title: IM95 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: IM95 Cell Line (Sty)

value: Gastric Cell Line (IM95)


title: SNU5 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: SNU5 Cell Line (Sty)

value: Gastric Cell Line (SNU5)


title: 10093110

source_name: bladder tumoral tissue 18


title: YCC11 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: YCC11 Cell Line (Sty)

value: Gastric Cell Line (YCC11)


title: 10093210

source_name: bladder tumoral tissue 19


title: Serum miRNA from binge female control rat replicate 4

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: miRNA expression data from rat blood serum

hyb_protocol: Affymetrix EukGE-WS2v4 Protocol

scan_protocol: Standard Affymetrix Genechip 7G Scanner

data_processing: RMA analysis using Affymetrix Expression Console software

organism: Rattus norvegicus

source_name: Rat blood serum

label_protocol: Affymetrix standard 1 cycle

extract_protocol: Qiagen total RNA

treatment_protocol: At postnatal day 29, Long Evans Hooded rats were split into four groups (two treatment and two control groups).  Two groups of rats were divided into pairs based on gender and body weight and weaned onto an ad lib liquid ethanol (6.7%)-containing diet or an isolcaloric liquid control diet (containing maltose instead of ethanol) for 3 weeks.  The other two groups of rats began receiving the same liquid ethanol or control diet in young adulthood (postnatal day 79) using a 3 week episodic binge-drinking paradigm (3 days liquid ethanol or control diet followed by 4 days ad lib solid chow). After the three week ethanol exposure period, all rats in each group were euthanized with CO2 and blood was collected into BD Vacutainer® SST™ tubes for serum miRNA isolation.

tag: strain

value: Long Evans Hooded rats

value: blood serum

tag: treatment age onset

value: adult

tag: animal pair

tag: exposure paradigm

value: episodic binge


title: NCI-N87 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: NCI-N87 Cell Line (Sty)

value: Gastric Cell Line (NCI-N87)


title: Hs746T Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: Hs746T Cell Line (Sty)

value: Gastric Cell Line (Hs746T)


title: Serum miRNA from binge female control rat replicate 3

tag: tissue


title: MKN7 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: MKN7 Cell Line (Sty)

value: Gastric Cell Line (MKN7)


title: Fu97 Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: Fu97 Cell Line (Sty)

value: Gastric Cell Line (Fu97)


title: 10092610

source_name: bladder tumoral tissue 14

value: bladder tumor


title: 10092910

source_name: bladder tumoral tissue 16


title: 10092810

source_name: bladder tumoral tissue 15

value: TaGII


title: Serum miRNA from binge female ethanol rat replicate 2

value: female


title: 10093010

source_name: bladder tumoral tissue 17

value: TaGI


title: 10093310

source_name: bladder tumoral tissue 20


title: Serum miRNA from binge female ethanol rat replicate 3


title: 10092510

source_name: bladder tumoral tissue 13


title: Serum miRNA from binge female control rat replicate 2


title: 10092210

source_name: bladder tumoral tissue 11


title: AGS Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: AGS Cell Line (Sty)

value: AGS

value: Gastric Cell Line (AGS)


title: KATOIII Cell Line (Sty)

description: Hybridized to 250K_Sty

source_name: KATOIII Cell Line (Sty)

value: KATOIII

value: Gastric Cell Line (KATOIII)


title: 10091910

source_name: bladder tumoral tissue 8


title: Serum miRNA from binge female ethanol rat replicate 1


title: Serum miRNA from binge female ethanol rat replicate 4


title: 10092110

source_name: bladder tumoral tissue 10

value: TaGIII


title: Serum miRNA from binge female control rat replicate 1

value: Long Evans Hooded rats


title: 10091710

source_name: bladder tumoral tissue 7


title: Serum miRNA from chronic daily male control rat replicate 6

source_name: Rat blood serum

value: blood serum

value: adolescent

value: male

value: daily


title: 10092010

source_name: bladder tumoral tissue 9


title: 4 - wt

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The data were analyzed according to the protocol described by Biemar, F., Nix, D.A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., Manak, J.R., and Levine, M.S. (2006). Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci USA 103, 12763–12768.
Expression values are RMA normalized log2 scale values.
matrix.txt is linked as a supplementary file on the Series record.

organism: Drosophila melanogaster

source_name: wt

label_protocol: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

extract_protocol:
100 larvae from the medium surface were put into replicate vials. For each assay, ten single-sex replicate vials for each line were obtained. The flies were starved for one hour in agar vials to reduce metabolites in the gut from any food they may have eaten. They were put to sleep under CO2 and weighed to 0.1 mg accuracy and stored at -80°C
RNA was isolated using Qiagen RNeasy Mini Kit from the thorax of 50 flies, following the manufacturer’s protocol.

treatment_protocol: Wildtype, CanA1 and CanA-14F mutant flies were maintained on standard cornmeal-molasses agar media in an incubator maintained at 25°C, 60-75% humidity, and a 12hr/12hr light/dark cycle.

tag: strain name

value: Isogenic wildtype w1118 strain (BL-6326)

tag: genotype/variation

value: wt

value: Whole thorax


title: Serum miRNA from chronic daily male ethanol rat replicate 5


title: Serum miRNA from chronic daily male control rat replicate 5


title: Serum miRNA from chronic daily male ethanol rat replicate 6


title: C177-CUT177

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: Subc Fat, Histology class 3

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Clinical sample prior bariatric surgery

extract_protocol: Rneasy kit (Qiagen)

treatment_protocol: Samples collected during bariatric surgery

tag: patientid

value: 52 year

tag: bmi

value: Subcutaneous fat


title: 3 - wt


title: Serum miRNA from chronic daily male ethanol rat replicate 4


title: 10091310

source_name: bladder tumoral tissue 6

value: bladder tumor


title: Serum miRNA from chronic daily male control rat replicate 4


title: C121-CUT121

source_name: Subc Fat, Histology class 2

value: 49 year

value: female


title: 10090510

source_name: bladder tumoral tissue 3

value: TaGI


title: C164-CUT164

source_name: Subc Fat, Histology class 1

value: 26 year


title: 1 - wt


title: C214-CUT214

source_name: Subc Fat, Histology class 4

value: 37 year


title: C096-CUT96

value: 53 year


title: Serum miRNA from chronic daily male ethanol rat replicate 3

value: Long Evans Hooded rats


title: 10090910

source_name: bladder tumoral tissue 4

value: TaGIII


title: V214-VIS214

source_name: Visceral Fat, Histology class 4

value: Visceral fat


title: Serum miRNA from chronic daily male control rat replicate 3

value: blood serum

value: adolescent

value: male


title: C119-CUT119

value: 46 year


title: 3 - CanA at 14-F mutant

source_name: CanA at 14-F mutant

value: CanA at 14-F mutant

value: Whole thorax


title: 4 - CanA at 14-F mutant


title: 2 - CanA at 14-F mutant


title: 10091210

source_name: bladder tumoral tissue 5


title: C095-CUT95

value: 39 year

value: Subcutaneous fat


title: 10090110

source_name: bladder tumoral tissue 1

value: bladder tumor


title: 10090210

source_name: bladder tumoral tissue 2


title: V205-VIS205

value: 44 year

value: female


title: Serum miRNA from chronic daily male ethanol rat replicate 2

value: daily


title: C205-CUT205


title: 1 - CanA at 14-F mutant


title: Serum miRNA from chronic daily male control rat replicate 2


title: 4 - Calcineurin A1 mutant

source_name: Calcineurin A1 mutant

value: Calcineurin A1 mutant


title: 2 - wt

value: Isogenic wildtype w1118 strain (BL-6326)

value: wt


title: Serum miRNA from chronic daily male control rat replicate 1

value: Long Evans Hooded rats


title: C073-CUT73

value: 23 year


title: V190-VIS190

source_name: Visceral Fat, Histology class 1

value: Visceral fat


title: Serum miRNA from chronic daily female ethanol rat replicate 5

source_name: Rat blood serum

value: blood serum

value: adolescent


title: Serum miRNA from chronic daily female control rat replicate 5


title: 1 - Calcineurin A1 mutant

value: male


title: Serum miRNA from chronic daily male ethanol rat replicate 1


title: 3 - Calcineurin A1 mutant


title: Serum miRNA from chronic daily female ethanol rat replicate 3


title: 2 - Calcineurin A1 mutant


title: Serum miRNA from chronic daily female control rat replicate 3


title: Serum miRNA from chronic daily female ethanol rat replicate 2


title: Serum miRNA from chronic daily female ethanol rat replicate 4


title: V170-VIS170

value: 26 year


title: C072-CUT72

value: 36 year


title: C198-CUT198

value: 60 year


title: C024-CUT24

value: Subcutaneous fat


title: V122-VIS122

source_name: Visceral Fat, Histology class 3


title: SF70-NASHF70

value: 49 year


title: Serum miRNA from chronic daily female ethanol rat replicate 1


title: Serum miRNA from chronic daily female control rat replicate 1


title: Serum miRNA from chronic daily female control rat replicate 4


title: Serum miRNA from binge male ethanol rat replicate 4

value: adult

value: episodic binge


title: Serum miRNA from chronic daily female control rat replicate 2

value: female

value: daily


title: KO.M.12

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

description:
A9
Gene expression data from placental tissue collected at day 18.5pc.

hyb_protocol: 3.5 ug of fragmented and labeled single-stranded cRNA were hybridized on Affymetrix MoGene 2.1 ST arrays and washed and stained following the Manual Target Preparation Guidelines for GeneChip® Whole Transcript (WT) Expression Arrays.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip scanner by the Ramaciotti Centre for Genomics, Sydney, Australia.

data_processing: The data were preprocessed, background subtracted and quantile normalised at the probe level using the Oligo package in R. Probesets were annotated using the Bioconductor mogene21sttranscriptcluster.db: Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) package.

source_name: Placenta, KO, M, day 18.5pc

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA following the Manual Target Preparation Guidelines for GeneChip® Whole Transcript (WT) Expression Arrays.

growth_protocol: Male and female mice heterozygous for the Vdr allele (Vdr knockout strain B6.129S4-Vdrtm1Mbd/J - The Jackson Laboratory) were mated at 10-12 weeks of age to generate offspring of the three genotype combinations: Vdr knockout, Vdr heterozygotes and Wild-type. Placentae from pregnant females were collected at day 18.5pc for gene expression analyses. Mice were raised on a standard chow diet.

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

treatment_protocol: Whole placentas were collected at day 18.5pc and fixed in RNAlater before RNA isolation.

tag: strain/background

tag: genotype/variation of offspring

value: Vdr knockout

tag: sex of offspring

value: M

value: placenta

tag: developmental stage

value: day 18.5pc


title: SF73-NASHF73

tag: age

value: 53 year

tag: gender


title: V152-VIS152

value: 25 year

value: Visceral fat


title: WT.M.125

description:
A7
Gene expression data from placental tissue collected at day 18.5pc.

source_name: Placenta, WT, M, day 18.5pc

value: wild-type


title: WT.F.12

description:
A8
Gene expression data from placental tissue collected at day 18.5pc.

source_name: Placenta, WT, F, day 18.5pc

value: F


title: WT.F.125

description:
A6
Gene expression data from placental tissue collected at day 18.5pc.


title: V210-VIS210

source_name: Visceral Fat, Histology class 2

value: 22 year


title: C152-CUT152


title: Serum miRNA from binge male control rat replicate 4

value: Long Evans Hooded rats

value: blood serum

tag: Sex

value: male


title: V095-VIS95

value: 39 year


title: Het.M.125

description:
A5
Gene expression data from placental tissue collected at day 18.5pc.

source_name: Placenta, Het, M, day 18.5pc

value: Vdr heterozygous


title: SF69-NASHF69

source_name: Subc Fat, Histology class 1

value: 41 year

value: female

value: Subcutaneous fat


title: V119-VIS119

value: 46 year


title: Serum miRNA from binge male control rat replicate 3

value: adult

value: episodic binge


title: Het.M.41_2

description:
A24
Gene expression data from placental tissue collected at day 18.5pc.

value: M

value: placenta

value: day 18.5pc


title: SF65-NASHF65

source_name: Subc Fat, Histology class 3

value: 54 year


title: Het.F.125

description:
A4
Gene expression data from placental tissue collected at day 18.5pc.

source_name: Placenta, Het, F, day 18.5pc

value: F


title: Serum miRNA from binge male ethanol rat replicate 2


title: KO.F.108

description:
A3
Gene expression data from placental tissue collected at day 18.5pc.

source_name: Placenta, KO, F, day 18.5pc

value: Vdr knockout


title: Het.M.41

description:
A22
Gene expression data from placental tissue collected at day 18.5pc.


title: V178-VIS178

value: 42 year

value: Visceral fat


title: Serum miRNA from binge male control rat replicate 2

value: Long Evans Hooded rats

value: blood serum

value: male


title: KO.M.41

description:
A23
Gene expression data from placental tissue collected at day 18.5pc.


title: Serum miRNA from binge male control rat replicate 1


title: V043-VIS43

value: 31 year


title: KO.F.41

description:
A21
Gene expression data from placental tissue collected at day 18.5pc.


title: Serum miRNA from binge male ethanol rat replicate 3


title: Mouse NSC treated with TGF replicate 5

description: miRNA expression data from mouse neural stem cells

source_name: Mouse NS5 neural stem cells

growth_protocol: A total of eighteen 10 cm dishes coated with poly-L-ornithine hydrobromide and laminin (Sigma) were plated with 3 million cells each and incubated at 37C for 24 hours in a Euromed-N maintenance medium (Euroclone).

treatment_protocol: Plates were separated into 4 groups and exposed to different media for 48 hours at 37C: maintenance media supplemented with 10 mg/ml FGF2 (Preprotech) or TGFβ1 (R&D Systems). In another set of dishes, 400 mg/dl of ethanol was added in each type of supplemented media. All dishes were placed inside airtight containers with a small container of either sterile water or 400 mg/dl ethanol to maintain constant concentration throughout the exposure period.

tag: cell line

tag: cell type

value: neural stem cells

tag: media supplement

value: TGF beta 1

tag: exposure

value: 10 mg/ml TGF beta 1


title: Serum miRNA from binge male ethanol rat replicate 1

tag: strain

tag: treatment age onset

value: adult

tag: animal pair

tag: exposure paradigm


title: SF57-NASHF57

source_name: Subc Fat, Histology class 2

tag: patientid

value: 32 year

value: female

tag: tissue

value: Subcutaneous fat


title: WT.M.41

description:
A20
Gene expression data from placental tissue collected at day 18.5pc.

tag: strain/background

value: wild-type

value: M

value: placenta

value: day 18.5pc


title: Mouse NSC treated with TGF replicate 3


title: Mouse NSC treated with TGF replicate 4


title: WT.F.21

description:
A19
Gene expression data from placental tissue collected at day 18.5pc.

tag: genotype/variation of offspring

value: F


title: C147-CUT147

source_name: Subc Fat, Histology class 4

value: 23 year

tag: bmi


title: KO.M.21

description:
A16
Gene expression data from placental tissue collected at day 18.5pc.

value: Vdr knockout

tag: sex of offspring

tag: developmental stage


title: SF53-NASHF53

tag: age

value: 50 year

tag: gender


title: Het.F.108

description:
A2
Gene expression data from placental tissue collected at day 18.5pc.

value: Vdr heterozygous


title: FN61-NASHF61-DupB

value: 58 year

value: Visceral fat


title: WT.M.21

description:
A18
Gene expression data from placental tissue collected at day 18.5pc.


title: SF55-NASHF55

value: 44 year


title: V147-VIS147

source_name: Visceral Fat, Histology class 4


title: Mouse NSC treated with TGF replicate 2

tag: cell line

value: neural stem cells

value: TGF beta 1

value: 10 mg/ml TGF beta 1


title: Mouse NSC treated with TGF replicate 1

tag: cell type


title: SF56-NASHF56

value: 39 year

value: female


title: Mouse NSC treated with TGF+ethanol replicate 4

tag: media supplement

value: 400 mg/dl ethanol + 10 mg/ml TGF beta 1


title: Mouse NSC treated with TGF+ethanol replicate 5

tag: exposure


title: KO.F.21

description:
A15
Gene expression data from placental tissue collected at day 18.5pc.


title: V096-VIS96

value: 53 year


title: KO.F.21_2

description:
A17
Gene expression data from placental tissue collected at day 18.5pc.

value: placenta


title: Het.M.21

description:
A14
Gene expression data from placental tissue collected at day 18.5pc.

value: M

value: day 18.5pc


title: Mouse NSC treated with TGF+ethanol replicate 3


title: FN76-NASHF76-DupB


title: Mouse NSC treated with TGF+ethanol replicate 2


title: Mouse NSC treated with TGF+ethanol replicate 1


title: FN70-NASHF70

value: 49 year


title: KO.M.14

description:
A13
Gene expression data from placental tissue collected at day 18.5pc.

value: Vdr knockout


title: Het.F.14

description:
A12
Gene expression data from placental tissue collected at day 18.5pc.

value: F


title: SW480_NFIL3_Rapamycin_1

city: Berlin

first: Jingjing

last: Qi

state: Outside the US or Canada

address: Robert-Roessle-str. 10

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

description:
SAMPLE 23
Biological replicate of NFIL3 treated with Rapamycin

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized with Illumina Genome Studio (v.2010.1) without background subtraction, data analysis and quality control were carried out using Partek® software (v.6.6).

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

extract_protocol: RNA from stable cells treated with indicated inhibitor or DMSO was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the protocol provided by the manufacturer.

value: colon cancer cells

tag: infected with

value: NFIL3 pBABE-puro retrovirus

tag: treated with

value: Rapamycin


title: Mouse NSC treated with FGF replicate 4

value: 10 mg/ml FGF2


title: WT.F.14

description:
A11
Gene expression data from placental tissue collected at day 18.5pc.

value: wild-type


title: SW480_NFIL3_Rapamycin_2

description:
SAMPLE 24
Biological replicate of NFIL3 treated with Rapamycin


title: FN65-NASHF65

value: 54 year

value: Visceral fat


title: Het.F.12

description:
A10
Gene expression data from placental tissue collected at day 18.5pc.

value: Vdr heterozygous


title: SF52-NASHF52

value: female

value: Subcutaneous fat


title: SW480_BOP1_DAPT_1

description:
SAMPLE 21
Biological replicate of BOP1 treated with DAPT

value: BOP1 pBABE-puro retrovirus

value: DAPT


title: FN64-NASHF64

value: 43 year

value: male


title: SW480_BOP1_DAPT_2

description:
SAMPLE 22
Biological replicate of BOP1 treated with DAPT


title: Mouse NSC treated with FGF replicate 3

description: miRNA expression data from mouse neural stem cells

value: neural stem cells


title: FN61-NASHF61-DupA

value: 58 year


title: FN53-NASHF53

value: 50 year


title: SW480_NFIL3_SB203580_1

description:
SAMPLE 19
Biological replicate of NFIL3 treated with SB203580

value: colon cancer cells


title: SW480_NFIL3_SB203580_2

description:
SAMPLE 20
Biological replicate of NFIL3 treated with SB203580

value: NFIL3 pBABE-puro retrovirus


title: FN79-NASHF79

value: 47 year


title: SW480_CKS2_SB203580_1

description:
SAMPLE 17
Biological replicate of CKS2 treated with SB203580

value: CKS2 pBABE-puro retrovirus


title: WT.F.108

description:
A1
Gene expression data from placental tissue collected at day 18.5pc.

value: wild-type

value: F

value: placenta

value: day 18.5pc


title: SW480_CKS2_SB203580_2

description:
SAMPLE 18
Biological replicate of CKS2 treated with SB203580


title: Mouse NSC treated with FGF replicate 2

value: 10 mg/ml FGF2


title: Mouse NSC treated with FGF+ethanol replicate 4

value: 400 mg/dl ethanol + 10 mg/ml FGF2


title: Mouse NSC treated with FGF replicate 1


title: Mouse NSC treated with FGF+ethanol replicate 3


title: Ma_hi_#1_9482913022_D

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description: Replicate 1

hyb_protocol: 1.5 µg of cDNA were hybridized for 17hrs at 55.4 °C on Illumina Mouse WG-6-Microarray

scan_protocol: Illumina iSCAN-Scanner according to Std Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). Microarray scanning was done using an iScan array scanner

data_processing: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampelís method). All remaining bead level data points are then quantile normalized [1]. As test for significance the studentís t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction [2] was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads. [1] Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001 [2] Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289ñ300.

source_name: Spleen from male mice

label_protocol: The NuGEN Ovation Pico WTA System (linear isothermal DNA amplification process) was used to generate single-stranded cDNA from small input amounts of 2.5 ng RNA. Labeled cRNA was prepared according to Nugene Encore BiotinIL Module.

extract_protocol: Spleen was harvested directly after euthanasia of mice and cells were FACS purified.

treatment_protocol: Mice were untreated

tag: strain

value: C57BL/6 Foxp3-GFP-DTR-CD90.1

value: Spleen


title: Mouse NSC treated with FGF+ethanol replicate 2


title: FN73-NASHF73

value: 53 year

value: female

value: Visceral fat


title: Mouse NSC treated with FGF+ethanol replicate 1

value: neural stem cells


title: FN57-NASHF57

value: 32 year


title: SW480_BOP1_SP600125_1

description:
SAMPLE 15
Biological replicate of BOP1 treated with SP600125

value: colon cancer cells

value: BOP1 pBABE-puro retrovirus


title: SW480_NFIL3_LY294002_2

description:
SAMPLE 14
Biological replicate of NFIL3 treated with LY294002

value: NFIL3 pBABE-puro retrovirus


title: FN76-NASHF76-DupA

source_name: Visceral Fat, Histology class 1

value: 44 year


title: SW480_CKS2_LY294002_2

description:
SAMPLE 12
Biological replicate of CKS2 treated with LY294002

value: CKS2 pBABE-puro retrovirus


title: Ma_int_#3_9482913022_C

description: Replicate 3

value: male


title: FN77-NASHF77

value: 48 year


title: FN56-NASHF56

value: 39 year


title: Ma_hi_#2_9482913022_E

description: Replicate 2


title: FA3

city: hang zhou

first: guifa

last: li

address: Zhejiang University School of Medicine Department of Neurobiology

department: Department of Neurobiology

institute: Zhejiang University School of Medicine

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: 3ppm FA_6hr_7 days

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: Mice are keep in temperature and light control, with food and water ad libitum

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs

treatment_protocol: The FA group exposed to 3ppm FA for six hours for consecutive 1 and 7days in a chamber which was described previously. The standard group was kept in same condition except the FA.

value: ICR

value: 8 weeks

tag: exposed to

value: 3ppm formaldehyde (FA) for 6hrs for 7 days

value: olfactory bulb


title: Ma_int_#2_9482913022_B

description: Replicate 2

value: C57BL/6 Foxp3-GFP-DTR-CD90.1

value: Spleen


title: FN69-NASHF69

tag: patientid

value: 41 year

value: female

value: Visceral fat


title: Ma_hi_#3_9482913022_F

description: Replicate 3

tag: tissue


title: SW480_NFIL3_LY294002_1

description:
SAMPLE 13
Biological replicate of NFIL3 treated with LY294002

value: colon cancer cells


title: FN71-NASHF71

value: 58 year


title: Ma_low_#2_9482913008_E

description: Replicate 2


title: Ma_int_#1_9482913022_A

description: Replicate 1


title: SW480_CKS2_LY294002_1

description:
SAMPLE 11
Biological replicate of CKS2 treated with LY294002


title: Ma_low_#1_9482913008_D

description: Replicate 1


title: Ma_low_#3_9482913008_F

description: Replicate 3


title: FA1


title: FA2


title: SW480_BOP1_LY294002_2

description:
SAMPLE 10
Biological replicate of BOP1 treated with LY294002

value: BOP1 pBABE-puro retrovirus


title: SW480_BOP1_LY294002_1

description:
SAMPLE 9
Biological replicate of BOP1 treated with LY294002


title: slide 176918

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description:
Sample 6
comparison of wild type and spo0A mutant at 0.7% agar concentration

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing:
Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.
Net{A} is the raw signal of channel A minus the local corner background signal of channel A
Net{B} is the raw signal of channel B minus the local corner background signal of channel B

organism: Bacillus subtilis subsp. natto

source_name: Net{A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using NucleoSpin Extract II columns

growth_protocol: B subtilis Natto (wild type or spo0A derivative) was spotted LB agar plate (with 0.7 or 1.5% agar concentrations) and grown at 37C overnight. Cells were harvested from the agar plate and RNA purification was performed on the samples.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 PMID: 17183215). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: no treatment

tag: genotype

value: wild type

tag: protocol

value: 0.7% agar

source_name: Net{B}


title: c4

source_name: 3ppm FA_6hr_1 day

value: male

value: 3ppm formaldehyde (FA) for 6hrs for 1 day


title: slide 176919

description:
Sample 7
comparison of wild type and spo0A mutant at 0.7% agar concentration


title: Fe_hi_#3_9482913008_C

description: Replicate 3

source_name: Spleen from female mice


title: c2


title: slide 176917

description:
Sample 5
comparison of wild type and spo0A mutant at 0.7% agar concentration


title: FN55-NASHF55

value: 44 year

tag: bmi


title: c1

value: ICR


title: N3

source_name: normal group

value: 8 weeks

value: none (control)


title: slide 176726

description:
Sample 4
comparison of wild type at 1.5% and 0.7% agar concentration

value: 1.5% agar


title: Fe_hi_#2_9482913008_B

description: Replicate 2

value: C57BL/6 Foxp3-GFP-DTR-CD90.1


title: SW480_CKS2_DMSO_2

description:
SAMPLE 6
Biological replicate of CKS2 treated with DMSO

value: CKS2 pBABE-puro retrovirus

value: DMSO


title: Fe_int_#2_9482913002_E

description: Replicate 2

value: Spleen

value: female


title: SW480_BOP1_DMSO_2

description:
SAMPLE 4
Biological replicate of BOP1 treated with DMSO

value: colon cancer cells


title: Fe_hi_#1_9482913008_A

description: Replicate 1


title: SW480_BOP1_DMSO_1

description:
SAMPLE 3
Biological replicate of BOP1 treated with DMSO


title: SW480_NFIL3_DMSO_1

description:
SAMPLE 7
Biological replicate of NFIL3 treated with DMSO

value: NFIL3 pBABE-puro retrovirus


title: N2

value: olfactory bulb


title: SW480_NFIL3_DMSO_2

description:
SAMPLE 8
Biological replicate of NFIL3 treated with DMSO


title: N1


title: Fe_low_#3_9482913002_C

description: Replicate 3


title: slide 176929

description:
Sample 2
comparison of wild type at 1.5% and 0.7% agar concentration

value: wild type


title: slide 176920

description:
Sample 1
comparison of wild type at 1.5% and 0.7% agar concentration

value: 0.7% agar


title: Fe_int_#3_9482913002_F

description: Replicate 3


title: Fe_int_#1_9482913002_D

description: Replicate 1


title: slide 176930

description:
Sample 3
comparison of wild type at 1.5% and 0.7% agar concentration


title: Fe_low_#1_9482913002_A

description: Replicate 1


title: SW480_Control_DMSO_1

description:
SAMPLE 1
Biological replicate of Control treated with DMSO

value: control pBABE-puro retrovirus


title: SW480_CKS2_DMSO_1

description:
SAMPLE 5
Biological replicate of CKS2 treated with DMSO


title: subject 20 unstimulated

status: Public on Aug 03 2015

city: Milan

first: Ferdinando

last: Clarelli

address: Via Olgettina 58

department: INSPE

country: Italy

institute: San Raffaele Scientific Institute

data_processing: The data were normalized using quantile normalization with R package Lumi

source_name: Peripheral blood mononuclear cells (PBMC)

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

treatment_protocol: Isolated PBMC extracted from healthy subjects and in vitro stimulated or not with with Interferon-β (Rebif44) at 100iU/mL for 18h

tag: disease state

value: healthy control

tag: individual

value: subject 20

value: Female

value: PBMC

tag: agent

value: control


title: subject 19 stimulated

value: subject 19

tag: gender

value: Male

value: IFN-beta


title: subject 14 stimulated

value: subject 14


title: subject 18 stimulated

value: subject 18


title: subject 15 stimulated

value: subject 15


title: subject 19 unstimulated


title: subject 17 stimulated

value: subject 17


title: SW480_BOP1_SP600125_2

description:
SAMPLE 16
Biological replicate of BOP1 treated with SP600125

tag: cell line

value: colon cancer cells

value: BOP1 pBABE-puro retrovirus


title: subject 16 stimulated

value: subject 16

tag: cell type


title: subject 15 unstimulated


title: subject 10 unstimulated

value: subject 10


title: subject 18 unstimulated


title: subject 14 unstimulated


title: subject 11 unstimulated

value: subject 11


title: subject 11 stimulated

value: healthy control


title: subject 13 unstimulated

value: subject 13


title: subject 12 stimulated

value: subject 12


title: subject 12 unstimulated

value: PBMC


title: subject 16 unstimulated

value: control


title: subject 13 stimulated

value: Female


title: subject 9 unstimulated

value: subject 9


title: subject 8 stimulated

value: subject 8

value: IFN-beta


title: subject 17 unstimulated

value: Male


title: subject 9 stimulated


title: subject 10 stimulated


title: subject 5 unstimulated

value: subject 5


title: subject 6 unstimulated

value: subject 6


title: subject 7 unstimulated

value: subject 7


title: subject 3 stimulated

value: subject 3


title: subject 1 unstimulated

value: subject 1


title: subject 3 unstimulated


title: subject 4 unstimulated

value: subject 4


title: colon_heme_repl1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization, washing and scanning of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet, replicate 1

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

extract_protocol: Total RNA was prepared from colonic scrapings 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 > 8.0).

treatment_protocol: Mice were fed a Westernized high fat control diet, or the same diet supplemented with 0.5 µmol heme/g diet. One group of control and one group of heme mice received a mixture of broad spectrum Antibiotics (Abx) (ampicilin, neomycin and metronidazole) in their drinking water. After 14 days of intervention, mice were killed and the colon was taken out. Mesenteric fat was removed from the colon. Colons were cut open longitudinally, washed in PBS, and scraped. RNA was isolated from scrapings and analysed by microarray.

tag: backgroud

value: male

tag: age

value: 11 weeks

value: colon

tag: diet


title: colon_heme_with Abx_repl2

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 2


title: colon_heme_with Abx_repl5

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 5


title: FN52-NASHF52

value: 49 year

value: female

value: Visceral fat


title: colon_heme_repl2

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet, replicate 2


title: subject 5 stimulated

value: healthy control

value: Female

value: PBMC


title: subject 6 stimulated

value: IFN-beta


title: subject 1 stimulated


title: colon_heme_repl3

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet, replicate 3


title: colon_heme_with Abx_repl1

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 1


title: colon_heme_repl4

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet, replicate 4


title: colon_heme_with Abx_repl6

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 6


title: subject 2 stimulated

value: subject 2


title: subject 7 stimulated

value: Male


title: colon_heme_with Abx_repl4

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 4


title: colon_control_with Abx_repl4

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 4


title: subject 8 unstimulated

value: subject 8

value: control


title: colon_heme_with Abx_repl3

source_name: colon of mouse, after 14 days on a Westernized high fat heme diet and Abx, replicate 3


title: subject 4 stimulated


title: shPLEKHA7-3

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

description: 20120321_20120320 antonis mirna_870_06.RCC

hyb_protocol: According to the manufacturer's protocol

scan_protocol: Data were collected using the NanoString nCounter Digital Analyzer

data_processing: Results were normalized for RNA input and background noise to internal positive and negative controls according to the manufacturer’s instructions.  A portion of readouts from NT-2 was lost due to an instrument error during detection; therefore this sample is not included until repeated.

label: nanoString probe

source_name: Caco2 cells_shPLEKHA9

extract_protocol: To obtain total RNA including small RNAs, cells were lysed using Trizol (Invitrogen) and subjected to the Trizol Plus Total Transcriptome Isolation protocol of the PureLink RNA mini kit (Ambion - Life Technologies). Final RNA concentrations were determined using a NanoDrop spectrophotometer.


title: colon_control_repl2

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 2


title: colon_control_with Abx_repl1

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 1


title: colon_control_with Abx_repl3

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 3


title: colon_control_repl1

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 1


title: colon_control_repl4

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 4


title: colon_control_with Abx_repl2

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet and Abx, replicate 2


title: colon_control_repl3

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 3


title: shPLEKHA7-2

description: 20120321_20120320 antonis mirna_860_05.RCC

source_name: Caco2 cells_shPLEKHA8


title: subject 2 unstimulated

source_name: Peripheral blood mononuclear cells (PBMC)


title: 48-FB#02-ins-UO-6h

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

institute: HHMI/University of Michigan

description: primary fibroblast, insulin treated for 6 hours in presence of U0126

hyb_protocol: cRNA was fragmented in 1X Fragmentation buffer (Ambion).  10 ug of cRNA were hybridized for 16 hours at 45C on GeneChip Human Genome HG-U133A_2 Arrays (GEO Platform GPL571). 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 data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: primary fibroblast, U0126 and insulin treated for 6 hour

label_protocol: 500ng of total RNA was used for each sample.  cRNA was amplified and biotin-labeled following manufacturer's protocol using MessageAmp™ Premier RNA Amplification Kits (Ambion).

growth_protocol: Primary fibroblasts were cultured at 37°C in 5% CO2 in MEM medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/ml streptomycin, and were passaged every 3 days.

extract_protocol: Total RNA was extracted from cells before or after treatment using RNeasy Micro Kit (QIAGEN).

treatment_protocol: To minimize technical variability, fibroblasts from the 35 individuals were passaged, treated and harvested in one batch for the signaling assays and microarray experiments.  Fibroblasts from 35 individuals were serum starved for 18 hours and treated with 100nM insulin for one hour and 6 hours.  In the ERK inhibition studies, cells from 4 individuals were treated with 10 uM UO126 (Cell Signaling) or DMSO (Sigma-Aldrich) for 1 hour before 100nM insulin or ddH2O (mock treatment) was added, and cells were incubated for another 1 hour or 6 hours before being harvested.

tag: individual id

value: primary fibroblast

value: U0126, insulin

tag: time point (insulin treatment)

value: 6 hour


title: NT-3

description: 20120321_20120320 antonis mirna_c70_03.RCC

source_name: Caco2 cells_NT


title: 26-FB#04-DMSO-ins-1h

description: primary fibroblast, insulin treated for 1 hour in presence of DMSO

source_name: primary fibroblast, DMSO and insulin treated for 1 hour

value: DMSO, insulin

value: 1 hour


title: 57-FB#04-DMSO-ss-6h

description: primary fibroblast, serum starved in presence of DMSO

source_name: primary fibroblast, DMSO and serum starved,

value: DMSO, no insulin

value: baseline


title: shPLEKHA7-1

description: 20120321_20120320 antonis mirna_850_04.RCC

source_name: Caco2 cells_shPLEKHA7


title: 56-FB#03-ins-UO-6h


title: 64-FB#04-ins-UO-6h


title: 40-FB#01-ins-UO-6h


title: NT-1

description: 20120321_20120320 antonis mirna_c50_01.RCC


title: 50-FB#03-DMSO-ins-6h

description: primary fibroblast, insulin treated for 6 hours in presence of DMSO

source_name: primary fibroblast, DMSO and insulin treated for 6 hour


title: 41-FB#02-DMSO-SS-6h


title: subject 20 stimulated

value: subject 20


title: 24-FB#03-ins-UO-1h

description: primary fibroblast, insulin treated for 1 hour in presence of U0126

source_name: primary fibroblast, U0126 and insulin treated for 1 hour


title: 49-FB#03-DMSO-ss-6h


title: 32-FB#04-ins-UO-1h


title: 34-FB#01-DMSO-ins-6h


title: Fe_low_#2_9482913002_B

description: Replicate 2

source_name: Spleen from female mice

tag: strain

value: C57BL/6 Foxp3-GFP-DTR-CD90.1

value: Spleen

value: female


title: 18-FB#03-DMSO-ins-1h


title: 58-FB#04-DMSO-ins-6h


title: 25-FB#04-DMSO-SS-1h


title: 42-FB#02-DMSO-ins-6h


title: SW480_Control_DMSO_2

description:
SAMPLE 2
Biological replicate of Control treated with DMSO

value: colon cancer cells

tag: infected with

value: control pBABE-puro retrovirus

tag: treated with

value: DMSO


title: 33-FB#01-DMSO-SS-6h


title: 10-FB#02-DMSO-ins-1h


title: 16-FB#02-ins-UO-1h


title: 9-FB#02-DMSO-SS-1h


title: 17-FB#03-DMSO-SS-1h


title: Placenta_GDM_Yes_ID55_rep 2_expression

city: Los Angeles

first: Alexandra

last: Binder

state: California

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

description: chart-reported case of gestational diabetes

hyb_protocol: 50 ng of high-quality RNA (260/280=1.8-2.0; RIN>6.0) was used to generate sense-strand cDNA with the Ambion® WT Expression Kit (Life Technologies), and then hybridised to the Affymetrix GeneChip® Human Transcriptome Array 2.0 using standard Affymetrix protocol

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner

data_processing: CEL files containing the measured expression intensities were processed using the Affymetrix Expression Console Software. Background correction was performed using Robust Multichip Analysis (RMA), probe values were then quantile normalized, and summarized into one gene-level expression measure using median polish (Expression Console Software Default Setting).

source_name: Placenta tissue from the maternal (decidual basalis) side near the umbilical cord

label_protocol: Affymetrix's GeneChip WT PLUS with the WT Terminal Labeling Kit

extract_protocol: RNA was isolated using the mirVANA RNA Isolation Kit (Ambion Inc., Austin, TX)

tag: tissue

value: placenta

tag: gestational diabetes

value: Yes


title: 8-FB#01-ins-UO-1h


title: 1-FB#01-DMSO-SS-1h


title: FB3180_360m_108

description: primary fibroblast, insulin treated for 6 hours

value: insulin


title: FB3178_360m_107

source_name: primary fibroblast, insulin treated for 6 hours

value: primary fibroblast


title: Placenta_GDM_Yes_ID25_expression


title: FB3180_60m_72

description: primary fibroblast, insulin treated for 1 hour


title: FB3178_0m_35

description: primary fibroblast, serum starved

source_name: primary fibroblast, serum starved

value: no insulin


title: Placenta_GDM_No_ID32_expression

value: No


title: FB3178_60m_71

source_name: primary fibroblast, insulin treated for 1 hour


title: 2-FB#01-DMSO-ins-1h

value: DMSO, insulin


title: Placenta_GDM_No_ID1_rep 1_expression


title: Placenta_GDM_No_ID1_expression


title: Placenta_GDM_Yes_ID24_expression

description: pregnancy without maternal complications


title: FB3180_0m_36

description: primary fibroblast, serum starved


title: FB3177_0m_34

description: primary fibroblast, serum starved


title: FB3177_360m_106

value: 6 hour


title: FB3177_60m_70

value: 1 hour


title: Placenta_GDM_No_ID48_expression


title: Placenta_GDM_Yes_ID34_expression


title: FB3176_60m_69


title: Placenta_GDM_Yes_ID41_expression


title: Placenta_GDM_No_ID1_rep 2_expression


title: Placenta_GDM_Yes_ID39_expression


title: Placenta_GDM_Yes_ID55_rep 1_expression


title: Placenta_GDM_No_ID7_expression


title: FB3176_360m_105


title: Placenta_GDM_Yes_ID22_expression


title: Placenta_GDM_Yes_ID14_expression


title: FB3176_0m_33

description: primary fibroblast, serum starved

value: baseline


title: Placenta_GDM_Yes_ID55_expression


title: FB3175_60m_68


title: FB3174_360m_103


title: FB3174_60m_67


title: Placenta_GDM_No_ID47_expression


title: Placenta_GDM_Yes_ID6_expression


title: FB3175_360m_104


title: FB3173_360m_102


title: FB3172_0m_29

description: primary fibroblast, serum starved


title: Placenta_GDM_No_ID23_expression


title: Placenta_GDM_No_ID31_expression


title: Placenta_GDM_No_ID42_expression


title: FB3173_60m_66


title: FB3172_60m_65


title: Placenta_GDM_No_ID38_expression


title: FB3173_0m_30

description: primary fibroblast, serum starved


title: FB3174_0m_31

description: primary fibroblast, serum starved


title: Placenta_GDM_No_ID15_expression


title: FB3172_360m_101


title: Placenta_GDM_No_ID33_expression


title: FB3170_60m_64


title: Placenta_GDM_No_ID5_expression


title: Placenta_GDM_No_ID40_expression


title: Placenta_GDM_Yes_ID54_expression


title: Placenta_GDM_Yes_ID30_expression


title: FB3170_360m_100


title: Placenta_GDM_No_ID52_rep 2_expression


title: Placenta_GDM_No_ID12_expression


title: Placenta_GDM_No_ID53_rep 2_expression


title: FB3170_0m_28

description: primary fibroblast, serum starved


title: FB3167_60m_63


title: Placenta_GDM_No_ID52_rep 1_expression


title: FB3175_0m_32

description: primary fibroblast, serum starved


title: FB3166_360m_98


title: Placenta_GDM_Yes_ID21_expression


title: FB3167_360m_99


title: Placenta_GDM_Yes_ID46_expression


title: FB3166_60m_62


title: FB3164_0m_25

description: primary fibroblast, serum starved


title: Placenta_GDM_Yes_ID45_expression


title: Placenta_GDM_No_ID37_expression


title: FB3166_0m_26

description: primary fibroblast, serum starved


title: FB3164_360m_97


title: FB3167_0m_27

description: primary fibroblast, serum starved


title: FB3163_360m_96


title: FB3163_0m_24

description: primary fibroblast, serum starved


title: FB3164_60m_61


title: Placenta_GDM_No_ID53_rep 1_expression


title: Placenta_GDM_Yes_ID13_expression


title: Placenta_GDM_Yes_ID20_expression


title: Placenta_GDM_No_ID16_expression


title: Placenta_GDM_Yes_ID51_expression


title: FB3163_60m_60


title: Placenta_GDM_No_ID52_expression


title: FB3162_60m_58


title: FB3162_0m_22

description: primary fibroblast, serum starved


title: FB3161_360m_95


title: FB3161_60m_59


title: Placenta_GDM_Yes_ID9_expression


title: Placenta_GDM_Yes_ID4_expression


title: FB3160_60m_57


title: Placenta_GDM_Yes_ID11_expression


title: FB3160_0m_21

description: primary fibroblast, serum starved


title: Placenta_GDM_No_ID28_expression


title: FB3162_360m_94


title: Placenta_GDM_No_ID53_expression


title: Placenta_GDM_No_ID8_expression


title: FB3161_0m_23

description: primary fibroblast, serum starved


title: Placenta_GDM_Yes_ID19_expression


title: Placenta_GDM_No_ID44_expression


title: FB3158_60m_56


title: Placenta_GDM_No_ID3_expression


title: FB3158_360_92


title: FB3158_0m_20

description: primary fibroblast, serum starved


title: Placenta_GDM_Yes_ID2_expression


title: FB3160_360_93


title: FB3157_360m_91


title: FB3157_60m_55


title: Placenta_GDM_Yes_ID29_expression


title: Placenta_GDM_Yes_ID27_expression


title: Placenta_GDM_Yes_ID43_expression


title: FB3156_360m_90


title: Placenta_GDM_No_ID35_expression


title: Placenta_GDM_Yes_ID49_expression


title: Placenta_GDM_No_ID18_expression


title: FB3150_0m_17

description: primary fibroblast, serum starved


title: FB3156_60m_54


title: FB3157_0m_19

description: primary fibroblast, serum starved


title: Placenta_GDM_Yes_ID17_expression


title: Placenta_GDM_Yes_ID26_expression


title: FB3150_360m_89


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica D

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #2

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)

data_processing: RMA of .CEL files using affy Bioconductor library and  Brainarray HGU133Plus2_Hs_ENTREZG_v17 custom cdf. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: YAP/TAZ depleted cells B

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.

growth_protocol: Cells were seeded at low confluence on day 1 in standard growth medium (DMEM/F12 with 2mM Glutamine, 17.5mM D-glucose, without antibiotics, 10% Fetal Bovine Serum).

extract_protocol: Trizol extraction of total RNA, followed by DNAseI digestion to reduce genomic DNA contaminations, was performed according to the manufacturer's instructions.

treatment_protocol: Cells were transfected on day 2 with siRNA oligonucleotides (final concentration 33nM) by using RNAi MAX (Life Technologies), following a direct transfection protocol as indicated by manifacturer's instructions. On day 3, medium was renewed. On day 4, cells were washed with 1XHBSS and harvested for RNA extraction.

value: breast cancer

tag: transfection construct

value: YAP/TAZ siRNA #2


title: FB3148_60m_51


title: FB3148_0m_15

description: primary fibroblast, serum starved


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica C


title: FB3156_0m_18

description: primary fibroblast, serum starved


title: Lame231 Area4

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicate 4 of 4

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

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

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Bos indicus

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

growth_protocol: Ovaries were collected immediately after slaughter and transported to the laboratory in saline solution (0.9% NaCl) supplemented with amikacine (250 µg/mL) at 35-36 °C. Cumulus oocyte complexes (COCs) were aspirated from follicles that were 3 to 8 mm in diameter. Only COCs with homogenous cytoplasm and at least three layers of cumulus cells were selected. After selection, the oocytes were washed and transferred to a 200-μL drop of maturation medium under silicone oil. The COCs were incubated for 22-24 hours at 39 °C with 5% CO2 in air. The maturation medium consisted of TCM-199 (Invitrogen, Carlsbad, CA, USA) supplemented with LH (1000 UI/mL), FSH (1 UI/mL), 10% fetal bovine serum (FBS – GIBCO®/Life Technologies, New York, USA), L-glutamine (10 mg/mL) and antibiotic (amikacin, 0.075 mg/mL). The matured oocytes were transferred to a 200-μL drop of fertilization medium, which consisted of TALP (Parrish et al., 1995) supplemented with penicillamine (2 mM), hypotaurine (1 mM), epinephrine (250 mM) and heparin (10 μg/mL). Frozen semen from a Bos indicus of proven fertility was used at a total concentration of 1x106 sperm cells/mL. Motile spermatozoa were obtained using a Percoll (GE Healthcare, Piscataway, NJ, USA) gradient (90:45%) in microtubes (Machado et al., 2009). The sperm and oocytes were co-incubated for 18 hours at 39 °C with 5% CO2 in air, and the day of in vitro insemination was considered as Day 0. After co-incubation, the presumptive zygotes were washed and transferred to 200-μL drops of SOFaaci medium (Holm et al., 1999) supplemented with 2.77 mM of myo-inositol and 5% FBS and cultured at 39 °C with 5% CO2.   Between D6 and D6.5 (144 to 156 hours post-insemination), the blastocysts (BL) were graded according to the criteria established by the International Embryo Transfer Society (IETS), and the grade I BLs were distributed equally into two groups: control (C) and vitrified (V).

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

treatment_protocol: The holding medium (HM), which was used for handling the embryos during vitrification and warming, was composed of HEPES-buffered TCM-199 (GIBCO®/Life Technologies) supplemented with 20% FBS. For vitrification, the groups of embryos were first washed three times in an equilibrium solution composed of 7.5% ethylene glycol and 7.5% dimethylsulfoxide (ME2SO) dissolved in HM for a minimum of 9 min. The embryos were transferred to a vitrification solution of 15% ethylene glycol, 15% ME2SO and 0.5 M of sucrose in HM where they were incubated for 45-60 sec. Next, the embryos were placed in a Cryotop device in sets of 3-5 under a stereomicroscope. Subsequently, the Cryotop device was immediately submerged into liquid nitrogen. Warming was performed after vitrification by immersing the end of the Cryotop into a drop of HM supplemented with 1 M sucrose that had been pre-warmed to 37 °C for 1 min. The embryos were transferred to HM supplemented with 0.5 M sucrose for 3 min and then finally transferred to the original HM. Afterwards, the embryos were placed in dishes and cultured for an additional 4 hours.  Control embryos were maintained on the bench in HM  at 37 ºC while the vitrification/warming was performed on the embryos of the vitrified group.   The vitrified embryos remained in the liquid N2 for at least 30 minutes before being warmed. The time required for vitrification/warming was approximately one hour. Subsequently, the embryos from both the C and V groups were returned to SOF medium and were cultured for an additional 4 hours. At the end of the culture period, the embryos were evaluated for re-expansion, and those that were considered to have a normal appearance were placed in RNAlater and stored at -20º C until RNA extraction.

tag: number per pool

tag: developmental stage

value: Blastocyst

tag: treatment

value: Control

value: Vitrified


title: Placenta_GDM_Yes_ID10_expression


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica A


title: MDA-MB-231 cells siYAP/TAZ#2, biological replica B


title: FB3147_0m_14

description: primary fibroblast, serum starved

tag: agent


title: FB3147_360m_86


title: Lame231 Area1

description: Biological replicate 1 of 4


title: Lame231 Area3

description: Biological replicate 3 of 4


title: FB3148_360m_87


title: FB3146_60m_49_2


title: FB3147_60m_50


title: Lame231 Area2

description: Biological replicate 2 of 4


title: Placenta_GDM_Yes_ID50_expression


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica D

description: Gene expression data from MDA-MB-231 cells depleted of endogenous YAP and TAZ by siRNA mix #1

source_name: YAP/TAZ depleted cells A

tag: cell line

value: YAP/TAZ siRNA #1


title: FB3146_360m_85

tag: cell type


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica C


title: Lame230 Area4

description: Biological replicate 4 of 4


title: FB3146_0m_12

description: primary fibroblast, serum starved


title: FB3144_360m_83


title: FB3144_60m_47


title: FB3144_0m_11

description: primary fibroblast, serum starved


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica B


title: Lame230 Area3

description: Biological replicate 3 of 4


title: FB3143_60m_52


title: FB3142_360m_82_2


title: FB3143_360m_88_2


title: MDA-MB-231 cells siControl, biological replica C

description: Gene expression data from control MDA-MB-231 cells

source_name: control cells

value: Control siRNA


title: MDA-MB-231 cells siControl, biological replica A


title: FB3143_0m_16

description: primary fibroblast, serum starved


title: MDA-MB-231 cells siControl, biological replica B


title: FB3141_0m_9

description: primary fibroblast, serum starved


title: MDA-MB-231 cells siYAP/TAZ#1, biological replica A


title: Lame230 Area2

description: Biological replicate 2 of 4


title: FB3142_60m_46


title: FB3139_60m_44


title: FB3142_0m_10

description: primary fibroblast, serum starved


title: E9.5 KO-3

city: San Francisco

first: Ron

last: Parchem

address: 35 Medical Center Way

institute: UCSF

description:
replicate 3
Sample24

data_processing: The data were preprocessed using Combat and quantile normalized in R (combat was used to normalize for batch effects across microarray plates)

source_name: mouse embryonic tissue

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 miRNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: miR-302 KO

tag: plate

value: anterior neural tissue


title: FB3138_360m_79

value: insulin


title: Lame230 Area1

description: Biological replicate 1 of 4


title: MDA-MB-231 cells siControl, biological replica D


title: Placenta_GDM_No_ID36_expression

value: placenta


title: FB3141_60m_45

value: primary fibroblast


title: FB3139_0m_8

description: primary fibroblast, serum starved

value: no insulin


title: E9.5 WT-4

description:
replicate 4
Sample21

value: WT


title: E9.5 KO-1

description:
replicate 1
Sample22


title: FB3138_60m_43


title: FB3139_360m_80

value: 6 hour


title: E9.5 KO-2

description:
replicate 2
Sample23


title: FB3138_0m_7

description: primary fibroblast, serum starved


title: E9.5 KO-4

description:
replicate 4
Sample25


title: FB3137_360m_78


title: FB3137_60m_42

value: 1 hour


title: HaHB11_rep2

city: Santa Fe

first: Jorge

middle: Ignacio

last: Giacomelli

state: Santa Fe

address: Ciudad Universitaria

department: LBV

country: Argentina

institute: Instituto de Agrobiotecnología del Litoral

description: overexpression replicate

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 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Helianthus annuus

source_name: Leaves from V3 stage sunflower

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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: Sunflower plants were grown in a controlled growth chamber under a long-day photoperiod (16-h light and 8-h dark at 25 °C) with an illumination of 130–150 μE m−2 s−1 and 40–65% relative humidity for 2–3 weeks

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen using the Trizol® method (Invitrogen, Argentina). The genomic DNA was eliminated after treatment with Dnase I for 20 min at RT using DNAse I® (Invitrogen, Argentina). RNA concentration was measured using an Implen nanophotometer (Implen GmbH, Munich, Germany). Purity and integrity of total RNA was determined by 260/280 nm ratio and the integrity was checked by electrophoresis in 1% agarose gel and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Sunflower disc from tissue obtained from leaves from V3 sunflower plants were obtained as described in Manavella and Chan, Nature Protocols 2009 (doi:10.1038/nprot.2009.178)

tag: construct

value: pBI121_35S Promoter::HaHB11

tag: genotype/variation

value: HaHB11 overexpression

value: sunflower leave disc


title: FB3141_360m_81_4

tag: individual id

tag: time point (insulin treatment)


title: HaHB11_rep3

description: overexpression replicate


title: HaHB11_rep1

description: overexpression replicate


title: E9.5 WT-3

description:
replicate 3
Sample20

tag: strain


title: E8.5 KO-2

description:
replicate 2
Sample16


title: E9.5 WT-1

description:
replicate 1
Sample18


title: FB3137_0m_6

description: primary fibroblast, serum starved

value: baseline


title: FB3136_360m_77


title: FB3135_0m_4

description: primary fibroblast, serum starved


title: E9.5 WT-2

description:
replicate 2
Sample19


title: uninfected.4h.2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description: uninfected BMDM at 4h p.i., biological replicate 2

hyb_protocol: 130µl hybridization mix prepared from biotin-labeled RNAs was hybridized to oligonucleotide arrays for 17h at 48°C. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: uninfected BMDM at 4h p.i.

label_protocol: 1µg of total RNA was labeled with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: BMDM from BALB/c mice were generated as previously described (Bringmann et al. 2013; PMID: 23587955), harvested and seeded in suspension culture plates at a cell concentration of 2*10^5*ml^-1 in RPMI-1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 10 mM hepes, 0.05 mM 2-mercaptoethanol, 100 U*ml^-1 penicillin, 50 µg*ml^-1 gentamycin and incubated for 4 h at 37°C.

extract_protocol: Total RNA was isolated with TRIzol (Life Technologies, Darmstadt, Germany) according to the manufacturer’s protocol.

treatment_protocol: BMDM were infected with L. major promastigotes (strain MHOM/IL/81/FE/BNI) at a parasite concentration of 3*10^6*ml^-1.

value: BALB/c

tag: infection

value: uninfected 4h


title: pBI121_rep3

description: control replicate

value: pBI121_35S Promoter::GUS

value: control

tag: tissue


title: uninfected.24h.2

description: uninfected BMDM at 24h p.i., biological replicate 2

source_name: uninfected BMDM at 24h p.i.

value: uninfected 24h


title: pBI121_rep2

description: control replicate


title: FB3150_60m_53

city: Ann Arbor


title: infected.24h.2

description: L. major infected BMDM at 24h p.i., biological replicate 2

source_name: L. major infected BMDM at 24h p.i.

value: Leishmania major infection at 24h


title: FB3136_60m_41

value: insulin