title: CordBlood_CD4+_Act+IL4_72h_rep3

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: CD4+ cell culture from cord blood of human neonates

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.14.1). It was vst transformed and quantile normalized.

source_name: Human cord blood cell_CD4+_Act+IL4_72h

label_protocol: standard as recommended by illumina

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) according to manufacturers instructions.

value: cord blood

tag: cell type

value: CD4+ T cells


title: FG-3149 treated PKCe left ventricle, biological rep4

status: Public on Nov 20 2015

type: RNA

city: San Francisco

first: Mark

middle: D.

last: Sternlicht

state: CA

address: 409 Illinois Street

department: Molecular Biology

country: USA

institute: FibroGen, Inc.

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Affymetrix mouse genome 430A 2.0 microarrays using the Affymetrix GeneChip Hybridization, Wash, and Stain kit (P/N 901241) and standard protocol.  Hybridization was performed for 16hrs at 45°C, 60rpm in an Affymetrix GeneChip Hybridization Oven 640 and staining and washing were performed using an Affymetrix GeneChip Fluidics Station 450 using the manufacturer's recommended fluidics script for 430Av2 genechips (FS450_0002).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 7G.  Scanning was performed using AGCC software and resulting CEL files were exported to GCOS v1.4.0.036 to generate CEL files compatible with Agilent GeneSpring GX 7.3.1 analysis software.

data_processing: CEL data were preprocessed using the GC content-based Robust Multi-Array (GCRMA) algorithm and imported into GeneSpring GX 7.3.1.  Between-group gene expression comparisons were performed on median per-gene normalized data using parametric t-tests without assuming equal variances or correcting for multiple comparisons.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: FG-3149 treated PKCe left ventricle

label_protocol: Biotinylated cRNA were prepared from 250ng total RNA using the Affymetrix GeneChip 3'IVT Express kit (P/N 901229) according the manufacturer's standard protocol.

extract_protocol: Total RNA was isolated from frozen LV tissue using TRIzol Reagent (Invitrogen) and purified using the Qiagen RNeasy Mini RNA purification kit with DNase treatment per the manufacturer's recommended methods.  RNA quantity and integrity were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano assay kit.

treatment_protocol: All animal procedures were carried out in accordance with institutional and national guidelines.  Mice with cardiomyocyte-specific expression of a constitutively active (A159E) rabbit PKCε transgene driven by the mouse Myh6 gene promoter on an FVB/N background (PKCε mice) were kindly provided by Dr. Peipei Ping, University of California, Los Angeles.  Nontransgenic FVB/N mice (Charles River Laboratories) served as controls.  Three-month-old mice underwent baseline echocardiography and were randomly assigned to one of four groups: FVB/N mice that received nonimmune mouse immunoglobulin (IgG) (n=10), FVB/N mice that received the anti-CTGF antibody FG-3149 (n=12), PKCε mice that received IgG (n=10), or PKCε mice that received FG-3149 (n=12).  IgG and FG-3149 antibodies (FibroGen, San Francisco, CA) were administered by intraperitoneal injection twice weekly at 30 mg/kg for three months.  After three months of treatment, mice underwent echocardiography and LV catheterization, after which hearts were excised, rapidly frozen in liquid N2, and stored at -80C.

tag: mouse id

tag: strain background

value: FVB/N

tag: genotype/variation

value: PKCε transgenic

tag: gender

value: male

tag: treatment

value: anti-CTGF antibody FG-3149

tag: tissue

value: left ventricle


title: FG-3149 treated PKCe left ventricle, biological rep1

value: female


title: FG-3149 treated PKCe left ventricle, biological rep2


title: CordBlood_CD4+_Act+IL4_72h_rep1

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

organism: Homo sapiens


title: FG-3149 treated PKCe left ventricle, biological rep3


title: IgG treated PKCe left ventricle, biological rep10

source_name: IgG treated PKCe left ventricle

value: IgG


title: CordBlood_CD4+_Act+IL12_72h_rep3

source_name: Human cord blood cell_CD4+_Act+IL12_72h


title: CordBlood_CD4+_Act_72h_rep3

source_name: Human cord blood cell_CD4+_Act_72h


title: IgG treated PKCe left ventricle, biological rep5


title: IgG treated PKCe left ventricle, biological rep6


title: IgG treated PKCe left ventricle, biological rep4


title: CordBlood_CD4+_Act+IL4_72h_rep2


title: CordBlood_CD4+_Act_72h_rep1


title: CordBlood_CD4+_Act+IL12_72h_rep1


title: IgG treated PKCe left ventricle, biological rep7


title: CordBlood_CD4+_Act_72h_rep2


title: CordBlood_CD4+_naive_precursor_rep3

source_name: Human cord blood cell_CD4+_naive_precursor


title: IgG treated PKCe left ventricle, biological rep9


title: IgG treated PKCe left ventricle, biological rep8


title: IgG treated PKCe left ventricle, biological rep1


title: FG-3149 treated FVB/N left ventricle, biological rep9

source_name: FG-3149 treated FVB/N left ventricle

value: wild type


title: FG-3149 treated FVB/N left ventricle, biological rep12


title: IgG treated PKCe left ventricle, biological rep3


title: FG-3149 treated FVB/N left ventricle, biological rep10


title: IgG treated PKCe left ventricle, biological rep2


title: CordBlood_CD4+_naive_precursor_rep2


title: Muscle_d36_Treatment C (Phy1000) rep4

city: Village-Neuf

first: Jérôme

last: Schmeisser

address: 1, Boulevard d'Alsace

department: CRNA

country: France

institute: DSM Nutritional Products

description: Gene expression data from Pectoralis major of chicken receiving restricted diet supplemented with phytase

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C on ChiGene-1_0-st Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Affymetrix scanner 3000.

data_processing: The data were analyzed with the Expression console using Affymetrix GC-RMA normalization method.

label: Biotin

organism: Gallus gallus

source_name: Pectoralis major with restricted diet supplemented with phytase

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT plus kit, Affymetrix).

growth_protocol: 36 days of growth after chicks arrival (day 1), with 3 different diets (Normal, restricted in P and Ca, and restricted in P and Ca supplemented with phytase)

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

treatment_protocol: After sacrifice and dissection of the animals, the Pectoralis major muscle is removed and 100mg is stored in RNA later for RNA extraction

value: Pectoralis major

tag: strain

value: Ross PM3

tag: age

tag: diet

value: restricted supplemented with phytase


title: Muscle_d36_Treatment C (Phy1000) rep3


title: FG-3149 treated FVB/N left ventricle, biological rep6


title: Muscle_d36_Treatment B (NC) rep4

description: Gene expression data from Pectoralis major of chicken receiving restricted diet

source_name: Pectoralis major with restricted diet

value: restricted


title: FG-3149 treated FVB/N left ventricle, biological rep7


title: Muscle_d36_Treatment B (NC) rep3


title: Muscle_d36_Treatment B (NC) rep2


title: FG-3149 treated FVB/N left ventricle, biological rep8


title: FG-3149 treated FVB/N left ventricle, biological rep5


title: Muscle_d36_Treatment C (Phy1000) rep2


title: FG-3149 treated FVB/N left ventricle, biological rep3


title: CordBlood_CD4+_Act+IL12_72h_rep2


title: FG-3149 treated FVB/N left ventricle, biological rep4


title: FG-3149 treated FVB/N left ventricle, biological rep2


title: Muscle_d36_Treatment C (Phy1000) rep1


title: FG-3149 treated FVB/N left ventricle, biological rep1


title: Muscle_d36_Treatment B (NC) rep1


title: Muscle_d36_Treatment A (PC) rep4

description: Gene expression data from Pectoralis major of chicken receiving normal diet

source_name: Pectoralis major with normal diet

value: normal


title: IgG treated FVB/N left ventricle, biological rep10

source_name: IgG treated FVB/N left ventricle


title: Muscle_d36_Treatment A (PC) rep3


title: CordBlood_CD4+_Act+IL4_72h_rep3

hyb_protocol: Samples were hybridized to GeneChip Human Genome U133 plus 2.0 array with specific protocols for using the GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChip Scanner 3000 7G was used to scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control the GeneChip Fluidics station and scanner and in summarizing probe cell intensity data.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: human cord blood CD4+ cells_Act+IL4

label_protocol: Amplification was started from 250 ng of total RNA using the Affymetrix GeneChip 3'IVT Express Kit (P/N 901228), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to manufacturer's protocol.


title: FG-3149 treated FVB/N left ventricle, biological rep11


title: Muscle_d36_Treatment A (PC) rep1


title: Huh6 Con1 untreated

city: Heidelberg

first: Volker

last: Lohmann

address: Im Neuenheimer Feld 345

department: Molecular Virology

country: Germany

institute: University of Heidelberg

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

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

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

source_name: Huh6 Con1 (pool2) cells, untreated

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

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

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

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

tag: cell line

value: Huh6 Con1 (pool2)

value: untreated


title: CordBlood_CD4+_Act+IL4_72h_rep2

value: cord blood


title: CordBlood_CD4+_Act+IL12_72h_rep3

source_name: human cord blood CD4+ cells_Act+IL12

value: CD4+ T cells


title: CordBlood_CD4+_Act+IL4_72h_rep1


title: CordBlood_CD4+_Act+IL12_72h_rep2


title: Muscle_d36_Treatment A (PC) rep2


title: HFFs_E1a

city: Sanda

first: Kiyoshi

last: Ohtani

state: Hyogo

address: 2-1 Gakuen

department: Department of Bioscience

country: Japan

institute: Kwansei Gakuin University

description: Gene expression after 18 hr  in HFFs expressed with E1a

hyb_protocol: Cy3-labelled cRNA was hybridized to Agilent Whole Human Genome DNA Microarrays 4x44K v2 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with Gene Expression Wash Pack 5 (Agilent).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 7.

source_name: HFFs, E1a-expressed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick Amp Labeling Kit, one-color 3 (Agilent).

growth_protocol: Human normal fibroblasts (HFFs) were maintained in Dulbecco’s modified Eagle medium (DMEM) containing 10% fetal calf serum (FCS).

extract_protocol: Total RNA was extracted using Isogen (Nippon Gene) axcording to manufacturer's protocol.

treatment_protocol: HFFs were serum starved for 2 days, infected with recombinant adenovirus expressing E2F1 or the 2RG form of adenovirus E1a, which binds to all pRB family proteins but not to CBP/p300, or control virus at multiplicity of infection (MOI) of 200. Cells were further cultured in serum-free media and harvested after 18 h. To assess serum simulation, control virus-infected cells were re-stimulated with 10% serum or maintained in serum-free media, and similarly harvested after 18 h.

value: fibroblasts


title: CordBlood_CD4+_Act+IL12_72h_rep1


title: IgG treated FVB/N left ventricle, biological rep9

value: FVB/N


title: CordBlood_CD4+_Act_72h_rep3

source_name: human cord blood CD4+ cells_Act


title: Proband

type: genomic

city: Houston

first: Shen

last: Gu

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Hybridization controls were gender matched (HapMap individual NA10851 as male control and HapMap individual NA15510 as female control).

scan_protocol: Scanned array images were processed using Agilent Feature Extraction software (version 10).

data_processing: Extracted files were analyzed using Agilent Genomic Workbench (version 7.0.4.0)

molecule: genomic DNA

source_name: BAB7221 genomic DNA

label_protocol: Test individual labeled with Cy5 and control individual labled with Cy3

extract_protocol: Genomic DNA extracted using reagents from QIAGEN

tag: sample id

value: Peripheral blood

value: male

source_name: NA 10851 genomic DNA


title: IgG treated FVB/N left ventricle, biological rep8

value: left ventricle


title: Maternal grandmother

source_name: BAB8247 genomic DNA

value: female

source_name: NA 15510 genomic DNA


title: IgG treated FVB/N left ventricle, biological rep5

value: IgG


title: IgG treated FVB/N left ventricle, biological rep6

value: wild type


title: CordBlood_CD4+_Act_72h_rep2


title: HFFs_E2F1

description: Gene expression after 18 hr  in HFFs over-expressed with E2F1

source_name: HFFs, E2F1-overexpressed


title: HFF-Ser [HFFs_Serum]

description: Gene expression after 18 hr

hyb_protocol: Cy3- or Cy5-labelled cRNA was hybridized to Agilent Whole Human Genome DNA Microarrays 4x44K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with Gene Expression Wash Pack 5 (Agilent).

source_name: HFFs, control

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng RNA using the Quick Amp Labeling Kit (Agilent).

treatment_protocol: HFFs were serum starved for 2 days,  re-stimulated with 10% serum or maintained in serum-free media, and harvested after 18 h.

value: normal fibroblasts

source_name: HFFs, stimulated with serum


title: Maternal grandfather


title: IgG treated FVB/N left ventricle, biological rep3


title: Father

source_name: BAB7220 genomic DNA


title: CordBlood_CD4+_Act_72h_rep1


title: HFFs_Serum

description: Gene expression after 18 hr  in HFFs re-stimulated with serum


title: CordBlood_CD4+_naive_rep3

source_name: human cord blood CD4+ cells_naive


title: IgG treated FVB/N left ventricle, biological rep2


title: IgG treated FVB/N left ventricle, biological rep7


title: IgG treated FVB/N left ventricle, biological rep1


title: IgG treated FVB/N left ventricle, biological rep4


title: CordBlood_CD4+_naive_rep1


title: Mother

source_name: BAB7219 genomic DNA


title: HFFs_Control

description: Gene expression after 18 hr  in control HFFs


title: CordBlood_CD4+_naive_precursor_rep1

source_name: Human cord blood cell_CD4+_naive_precursor


title: Plasma, Esophageal Adenocarcinoma patient, 7

status: Public on Nov 19 2015

city: Utrecht

first: Jantine

last: van Baal

state: Utrecht

address: Heidelberglaan 100

department: Department of Gastroenterology and Hepatology

country: Netherlands

institute: University Medical Center Utrecht, The Netherlands

description: Esophageal Adenocarcinoma

data_processing:
For the normalization we used the average of 114 miRNAs present in all samples.
Target gene signals normalized to the average of 114 miRNAs; 2^deltaCt, where deltaCt = (Ct_norm - Ct_Target)]
Matrix normalized worksheet reports normalized signal (against normalization miRNAs).
Fold Change worksheet reports test/control (i.e., Barrett's esophagus/healthy control) ratios.

label: SYBR Green

molecule: other

source_name: plasma

label_protocol: PCR assays were performed using the Serum / Plasma Focus miRNA PCR panel (Exiqon, Denmark) following the Manufacturer’s instructions. Reverse transcription was performed using the miRCURY LNAtm Universal RT microRNA polymerase chain reaction (PCR), Polyadenylation and cDNA synthesis kit (all from Exiqon). Quantitative real-time PCR were performed (LightCycler® 480 Real-Time PCR System; Roche, Mannheim, Germany) with 45 cycles at 95 oC for 10 seconds and 60 oC for 60 seconds.

extract_protocol: miRNA were extracted with miRNeasy MiniKit from Qiagen (Venlo, The Netherlands).

tag: sample type

value: plasma

tag: disease state

value: Esophageal Adenocarcinoma

tag: barrett's esophagus size

tag: tumor stage

value: TxNxMx


title: Plasma, Esophageal Adenocarcinoma patient, 6

description: Esophageal Adenocarcinoma


title: Plasma, Esophageal Adenocarcinoma patient, 8

description: Esophageal Adenocarcinoma


title: Plasma, Esophageal Adenocarcinoma patient, 4

description: Esophageal Adenocarcinoma

value: unknown


title: Plasma, Esophageal Adenocarcinoma patient, 5

description: Esophageal Adenocarcinoma


title: Plasma, Esophageal Adenocarcinoma patient, 2

description: Esophageal Adenocarcinoma


title: CordBlood_CD4+_naive_rep2


title: Plasma, Barrett's esophagus patient, 8

description: Barrett's esophagus

value: Barrett's esophagus


title: Plasma, Barrett's esophagus patient, 7

description: Barrett's esophagus


title: Plasma, Barrett's esophagus patient, 5

description: Barrett's esophagus


title: Control (replicate 2) vs gill exposed to okadaic acid (replicate 2).

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

country: Spain

institute: INIBIC

description: Direct comparison: Control replicate 2 vs Treated replicate 2. Gill tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Mytilus galloprovincialis

source_name: MBC-1.5. Gill tissue.

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

extract_protocol: Total RNA was extracted from pooled tissue of 5 individuals per group using Trizol according to manufacturer's instructions

treatment_protocol:
Specimens were collected from the natural environment in an area free of dinoflagellate bloom at the time of collection; Valcobo beach, Galicia, Spain.
Sampled individuals were randomly divided into two groups; exposed to Prorocentrum lima (treated group) and non-exposed (control group). Both groups were kept in aerated tanks of seawater and fed with a combined diet of Tetraselmis suecica and Isochrysis galbana microalgae. After acclimation, the exposed group was fed with 200 cells/ml of a P. lima culture in exponential phase for 24 hours.

value: Non-exposed. Control.

tag: developmental stage

value: adult individuals

source_name: MBT-2.5. Gill tissue.

value: Exposed. 200 cells/ml P. lima.


title: Digestive gland exposed to okadaic acid (replicate 2) vs control (replicate 2).

description: Direct comparison: Treated replicate 2 vs Control replicate 2. Digestive gland tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.

source_name: MGT-2.5.Digestive gland tissue.

source_name: MGC-1.5.Digestive gland tissue.


title: Control (replicate 1) vs digestive gland exposed to okadaic acid (replicate 1).

description: Direct comparison: Control replicate 1 vs Treated replicate 1. Digestive gland tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.

source_name: MGC-1.4.Digestive gland tissue.

source_name: MGT-1.4.Digestive gland tissue.


title: Control (replicate 1) vs gill exposed to okadaic acid (replicate 1).

description: Direct comparison: Control replicate 1 vs Treated replicate 1. Gill tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.

source_name: MBC-1.4. Gill tissue

source_name: MBT-1.4. Gill tissue


title: Plasma, Barrett's esophagus patient, 3

description: Barrett's esophagus


title: Digestive gland exposed to okadaic acid (replicate 1) vs control (replicate 1).

description: Direct comparison: Treated replicate 1 vs Control replicate 1. Digestive gland tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.


title: Gill exposed to okadaic acid (replicate 2) vs control (replicate 2).

description: Direct comparison: Treated replicate 2 vs Control replicate 2. Gill tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.


title: Gill exposed to okadaic acid (replicate 1) vs control (replicate 1).

description: Direct comparison: Treated replicate 1 vs Control replicate 1. Gill tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.

source_name: MBT-1.4. Gill tissue.

source_name: MBC-1.4. Gill tissue.


title: Plasma, Barrett's esophagus patient, 2

description: Barrett's esophagus


title: Plasma, Barrett's esophagus patient, 1

description: Barrett's esophagus


title: Plasma, healthy control, 6

description: Healthy control

value: Healthy control


title: Plasma, Barrett's esophagus patient, 6

description: Barrett's esophagus


title: Plasma, Esophageal Adenocarcinoma patient, 3

description: Esophageal Adenocarcinoma


title: Plasma, healthy control, 5

description: Healthy control


title: Plasma, healthy control, 4

description: Healthy control


title: Plasma, healthy control, 1

description: Healthy control


title: Plasma, healthy control, 2

description: Healthy control


title: Plasma, healthy control, 3

description: Healthy control


title: Plasma, Esophageal Adenocarcinoma patient, 1

description: Esophageal Adenocarcinoma


title: Plasma, Barrett's esophagus patient, 4

description: Barrett's esophagus


title: Aborted fetus

source_name: BAB7218 genomic DNA

value: Fetus tissue

source_name: NA 10851 genomic DNA


title: LSK_KO_Mouse430

city: Beijing

first: dan

last: liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: standard Affymetrix protocol

source_name: Embryo cell

label_protocol: standard Affymetrix protocol

growth_protocol: primary fetal liver cells sorted by FASC

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen).

treatment_protocol: no treatment by Doxcycline or any other solutions

value: fetal liver

tag: doxcycline treatment

value: No

tag: genotype

value: ATF4 KO

tag: cell type

value: LSK


title: Venezuela.15

city: San Antonio

first: Ian

middle: Harry

last: Cheeseman

department: Genetics

institute: Texas Biomedical Research Institute

hyb_protocol: Standard NimbleGen except add Denhardts Solution

scan_protocol: Scanned on Nimblegen MS 200 Microarray at 2 micron resolution on 635 and 532 channels

data_processing: images scanned and Normalized using NimbleScan v2.5

organism: Plasmodium falciparum

label_protocol: Standard NimbleGen except use 65% AT-rich nonamers

growth_protocol: standard lab: Standard malaria parasite laboratory culture (Trager and Jensen, Science 1978) in O+ erythrocytes was performed

extract_protocol: Phenol-chloroform

tag: growth protocol

value: Standard Lab

growth_protocol: clinical: Parasites were obtained directly from the erythrocytes isolated from malaria infected individuals

value: Clinical


title: Venezuela.19


title: Venezuela.9


title: Venezuela.13


title: Control (replicate 2) vs digestive gland exposed to okadaic acid (replicate 2).

description: Direct comparison: Control replicate 2 vs Treated replicate 2. Digestive gland tissue, Mytilus galloprovincialis exposed to okadaic acid produced by dinoflagellate P. lima.


title: Venezuela.2


title: Venezuela.16


title: Venezuela.18


title: Venezuela.8


title: Venezuela.10


title: Venezuela.4


title: Venezuela

source_name: Venezuela

value: Venezuela


title: Peru.8


title: Venezuela.3


title: LSK_WT_Mouse430

value: wild type


title: Venezuela.14


title: Venezuela.12


title: Venezuela.11


title: Venezuela.17


title: Venezuela.5


title: Peru.7


title: Peru.9


title: Venezuela.1


title: Peru.12


title: Venezuela.6


title: Peru.13


title: Venezuela.7


title: Peru.4


title: Peru.2


title: Peru.1


title: Peru.11


title: Peru

source_name: Peru

value: Peru


title: Peru.10


title: Peru.3


title: Malawi.16


title: Malawi.18


title: Malawi.17


title: Malawi.20


title: Malawi.15


title: Malawi.12


title: Malawi.14


title: Malawi.13


title: Malawi.10


title: Peru.5


title: Malawi.7


title: Malawi.21


title: Gambia.39


title: Malawi.11


title: Peru.6


title: Malawi.4


title: Malawi.19


title: Malawi.5


title: Malawi.8


title: Malawi.9


title: Malawi

source_name: Malawi

value: Malawi


title: Gambia.35


title: Gambia.36


title: Gambia.34


title: Gambia.40


title: Malawi.6


title: Gambia.37


title: Malawi.3


title: Malawi.2


title: Gambia.28


title: Gambia.26


title: Gambia.24


title: Gambia.30


title: Gambia.32


title: Gambia.29


title: Gambia.31


title: Gambia.33


title: Gambia.38


title: Gambia.21


title: Gambia.23


title: Gambia.22


title: Malawi.1


title: Gambia.15


title: Gambia.8


title: Gambia.25


title: Gambia.9


title: M_Suflair_Cy3

city: Sao Paulo

first: Yuri

last: Moreira

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748 - Cidade Unersitária, São Paulo - SP, 05508-000, Brasil

department: Inst. Chemistry

country: Brazil

institute: USP

hyb_protocol: Labeled cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Slides were washed and processed according to the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol (Version 5.5) and scanned on a GenePix 4000 B scanner (Molecular Devices, Sunnyvale, CA, USA). Fluorescence intensities were extracted using Feature Extraction (FE) software (version 9.0; Agilent).

scan_protocol: Scanned on an GenePix 4000 B scanner Images were quantified using Agilent Feature Extraction (FE) software (version 9.0; Agilent)

data_processing: Averaged values of dye-swap technical replicates were used for further analysis.

organism: Canis lupus familiaris

label_protocol: Sample labeling and array hybridization were performed according to the Two-Color Microarray-Based Gene Expression Analysis—Low Input Quick Amp Labeling—protocol (Agilent Technologies) using the SurePrint Canine 4x44K (Agilent Technologies) Microarray (GEO Platform GPL11351). Samples were labeled with Cy5 and a single RNA from a normal individual was labeled with Cy3 and used as a common reference on all arrays. A dye-swap technical replicates approach was also applied, where all samples were labeled with cy3 and the reference RNA was labeled with cy5. Labeled cRNA was hybridized using Gene Expression Hybridization Kit

growth_protocol: RNA from muscle tissue was extracted

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

value: Muscle

value: DMD escaper

source_name: common reference

value: muscle

value: normal


title: Gambia.5


title: Gambia.14


title: Gambia.20


title: Gambia.10


title: M_Ringo_Cy5


title: M_Suflair_Cy5


title: M_Ringo_Cy3


title: Gambia.16


title: Gambia.3


title: Gambia.6


title: Gambia.13


title: Gambia.11


title: Gambia.4


title: Gambia.12


title: Gambia.7


title: Thailand.28


title: Gambia.1


title: A_Nix_Cy3

value: DMD affected


title: Gambia.2


title: A_Gaspar_Cy3


title: A_Toto_Cy3


title: A_Gaspar_Cy5


title: A_Nix_Cy5


title: Thailand.27


title: Normal Dog Bono_Cy5

source_name: Normal Dog Bono_Cy5


title: Thailand.25


title: Thailand.29


title: A_Hercules_Cy5


title: Gambia

source_name: Gambia

value: Gambia


title: A_Hercules_Cy3


title: Normal Dog Zorro_Cy3

source_name: Normal Dog Zorro_Cy3


title: A_Toto_Cy5


title: Thailand.24


title: Normal Dog Bono_Cy3

source_name: Normal Dog Bono_Cy3


title: S_Smc6 HU (SUP)

city: Milan

first: Demis

last: Menolfi

address: via Adamello 16

country: Italy

institute: IFOM

description: HY3170 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing HU 0.2M for 60 min

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

organism: Saccharomyces cerevisiae

source_name: S_Smc6 HU 60 min

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown YPDA or YP+Glucose 2% media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml

extract_protocol: ssDNA-BrdU-IP on chip profiles were determined as described in (Katou et al, 2003). Binding profiles by ChIP on chip were determined as described in (Bermejo et al., 2009).

treatment_protocol: G1 synchronization was performed by α−factor treatment (3-5 μg/ml) for 120 minutes at 25°C. Cells were pelleted, washed once with YP and released in media containing 20 μg/ml of nocodazole for G2/M synchronization or  0.2 M HU for the indicated time and fixed with 1% formaldehyde for 30 min at room temperature. For BrdU incorporation profiles cells were released from G1 arrest in media containing HU 0.2M and BrdU 200 μg/ml for 45 min and fixed with 0.1% Sodium Azide on ice for 30 minutes.

tag: strain genotype

tag: antibody

value: Anti-FLAG M2 F1804 (SIGMA)

value: HU 60 min


title: Thailand.23


title: Normal Dog Lua Cy5

source_name: Normal Dog Lua Cy5

tag: tissue


title: Normal Dog Lua Cy3

source_name: Normal Dog Lua Cy3


title: Normal Dog Zorro_Cy5

source_name: Normal Dog Zorro_Cy5


title: Smc6 HU (SUP)

description: HY2806 cells were arrested in G1 with alfa-factor for 2 h  and then released in media containing HU 0.2M for 60 min

source_name: Smc6 HU 60 min

tag: strain

value: W303 Mata SMC6-6HIS-3FLAG::KANMX4

tag: treatment


title: Thailand.19


title: Thailand.15


title: Thailand.18


title: Normal Dog Parru_Cy3

source_name: Normal Dog Parru_Cy3

tag: age


title: Smc6 HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1069_Smc6_HU_IP.CEL
R1069_Smc6_HU_SUP.CEL


title: Normal Dog Parru_Cy5

source_name: Normal Dog Parru_Cy5


title: Thailand.16


title: Thailand.26


title: G2_SMC6 Smc5 nocodazole (SUP)

description: HY3158 cells were arrested in G1 with alfa-factor for 2h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: G2_SMC6 Smc5 nocodazole

value: W303 Mata G2::NATNT2-SMC6 SMC5-9PK::HIS3MX6

value: Anti-PK SV5-Pk1 (AbD Serotech)

value: Nocodazole 150 min


title: G2_SMC6 Smc5 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R965_Smc5_G2_Smc6_noco_IP.CEL
R965_Smc5_G2_Smc6_noco_SUP.CEL


title: Thailand.17

value: Standard Lab

value: Clinical


title: AML control, rep 3

city: Salamanca

first: Elena

last: Diaz-Rodriguez

state: Salamanca

address: Campus Miguel de Unamuno, s/n

institute: Centro de Investigación del Cáncer

description: Gene expression data form AML xenografts

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

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

data_processing:
Data were processed using the RMA algorithm implemented in the Affimetrix Expression Console: Transcriptome Analysis console v3.0.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

source_name: AML xenografts

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

growth_protocol: Hel cells were injected into the right caudal flank of CB17-SCID mice and when tumors became palpable, animals were randomized to different groups to start the treatment.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturar´s intructions.

treatment_protocol: Aminals were daily (Monday to Friday) treated with 0.1 ml OOS/animla, by oral gabage.

tag: mouse model

value: acute myeloid leukemia mice model

tag: host strain

tag: injected with

value: HEL; AML cell line

tag: treated with

value: none (untreated)


title: Thailand.14


title: AML OOS treated, rep1

description: Gene expression data form AML xenografts treated with OOS

source_name: AML xenografts treated with OOS

value: Ocoxin Oral solution, daily


title: wt Smc5 nocodazole (SUP)

description: HY3156 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: wt Smc5 nocodazole

value: W303 Mata SMC5-9PK::HIS3MX6


title: Thailand.12


title: AML OOS treated, rep2


title: Thailand.22


title: S_Smc6 HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1071_S_Smc6_HU_IP.CEL
R1071_S_Smc6_HU_SUP.CEL


title: wt Smc5 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R965_Smc5_wt_noco_IP.CEL
R965_Smc5_wt_noco_SUP.CEL


title: Thailand.20


title: Thailand.13


title: AML control, rep 2


title: AML control, rep 1


title: Thailand.10


title: Thailand.8


title: AML OOS treated, rep3


title: G2_SMC6 Smc5 HU (SUP)

description: HY3158 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing HU 0.2M for 45 min

source_name: G2_SMC6 Smc5 HU 45 min

value: HU 45 min


title: Cebpg-/- MEF_REG replicate 3

city: Frederick

first: Peter

middle: F

last: Johnson

state: MD

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: NCI-Frederick

description: Gene expression data from Cebpg-/- MEFs after 3 hours of normal growth media

hyb_protocol: Three replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000

data_processing: Following QC checks, microarray probe level data were normalized, background adjusted, and summarized with the RMA algorithm (Robust Multichip Analysis)

source_name: Cebpg-/- MEFs cultured under normal conditions

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 1 ug total RNA.  RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled using Affymetrix One Cycle Target Labeling kit following manufacturer’s protocol

growth_protocol: MEFs for each genotype were isolated at E13.5 and passaged 2-3 times.  At time of experiment, cells were first plated in media for 24 hours and then replaced with either normal or AAD media for 3 hours, and RNA was prepared.

extract_protocol: MEFs were collected by scraping cells from the plate and RNA was extracted using RNeasy Mini Kits (Qiagen)

treatment_protocol: Amino acid deprivation of MEFs was achieved using Krebs-Ringer Buffer (with supportive supplementation) for 3 hours

value: Mouse embryonic fibroblast


title: Cebpg-/- MEF_AAD replicate 3

description: Gene expression data from Cebpg-/- MEFs after 3 hours of AAD growth media

source_name: Cebpg-/- MEFs cultured under AAD conditions


title: Thailand.9


title: G2_SMC6 Smc5 HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1150_Smc5_G2_Smc6_HU_IP.CEL
R1150_Smc5_G2_Smc6_HU_SUP.CEL


title: Thailand.11


title: Thailand.4


title: Thailand.7


title: Cebpg-/- MEF_AAD replicate 2


title: Thailand.21


title: Cebpg-/- MEF_REG replicate 2


title: wt Smc5 HU (IP)

description: HY3156 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing HU 0.2M for 45 min

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1150_Smc5_wt_HU_IP.CEL
R1150_Smc5_wt_HU_SUP.CEL

source_name: wt Smc5 HU 45 min


title: Atf4-/- MEF_REG replicate 3

description: Gene expression data from Atf4-/- MEFs after 3 hours of normal growth media

source_name: Atf4-/- MEFs cultured under normal media


title: Cebpg-/- MEF_AAD replicate 1


title: Cebpg-/- MEF_REG replicate 1


title: wt Smc5 HU (SUP)


title: Thailand.6


title: Rrm3 nocodazole (SUP)

description: HY4916 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: Rrm3 nocodazole

value: W303 Mata RRM3-10FLAG::KANMX4


title: Atf4-/- MEF_AAD replicate 3

description: Gene expression data from Atf4-/- MEFs after 3 hours of AAD growth media

source_name: Atf4-/- MEFs cultured under AAD media


title: Thailand.5


title: Atf4-/- MEF_REG replicate 2


title: Atf4-/- MEF_AAD replicate 2


title: Thailand.3


title: Thailand.2


title: Top3 nocodazole (SUP)

description: HY3807 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: Top3 nocodazole

value: W303 Mata TOP3-6HIS-3FLAG::KANMX4


title: Rrm3 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1142_Rrm3_noco_IP.CEL
R1142_Rrm3_noco_SUP.CEL

value: Anti-FLAG M2 F1804 (SIGMA)


title: Thailand.1


title: Top3 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1048_Top3_noco_IP.CEL
R1048_Top3_noco_SUP.CEL


title: S_Smc5 HU (SUP)

description: HY5324 cells were arrested in G2/M with Nocodazole 5μg/ml for 2 h and then released in media containing HU 0.2M for 120 min

source_name: S_Smc5 HU 120 min

value: HU 120 min


title: S_Smc5 HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1173_S_Smc5PK_HU_IP.CEL
R1173_S_Smc5PK_HU_SUP.CEL


title: Thailand

source_name: Thailand

value: Thailand


title: Smc5 HU (SUP)

source_name: Smc5 HU 120 min


title: Atf4-/- MEF_AAD replicate 1


title: Smc5 HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1173_Smc5Flag_HU_IP.CEL
R1173_Smc5Flag_HU_SUP.CEL


title: Atf4-/- MEF_REG replicate 1


title: Laos.34


title: Laos.33


title: WT MEF_REG replicate 3

description: Gene expression data from WT MEFs after 3 hours of normal growth media

source_name: WT MEFs cultured under normal media


title: WT MEF_REG replicate 1


title: WT MEF_AAD replicate 3

description: Gene expression data from WT MEFs after 3 hours of AAD growth media

source_name: WT MEFs cultured under AAD media


title: G2_SMC5 G2_SMC6 BrdU HU (SUP)

description: HY4896 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing BrdU 200μg/ml and HU 0.2M for 45 min

source_name: G2_SMC5 G2_SMC6 BrdU HU 45 min

value: W303 Mata ura3::URA3/GPD-TK(7X) G2::NATNT2-SMC6-6HIS-3FLAG::KANMX4 G2::NATNT2-SMC5-9PK-HIS3MX6

value: Anti-BrdU antibody MBL M1-11-3


title: 3T3-L1_si-Ctr_0hr_ExB

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

description: Gene expression before dexamethasone treatment

hyb_protocol: Biotinylated cRNA was hybridized  according to the standard Affymetrix protocol.

scan_protocol: Scanned by Affymetrix GeneChip scanner 3000 (Affymetrix).

data_processing: GeneChip Analysis Suite software program version 5.0 was (Affymetrix) was used.

source_name: 3T3-L1 preadipocytes treated with the negative control siRNA

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

growth_protocol: 3T3-L1 preadipocytes and 10Thalf mesenchymal stem cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. At day -5, 2×105 cells were seeded in 6-well plate. At day -3, the medium was replaced. At day 0, cells were treated with differentiation medium containing 0.25 μM dexamethasone (Dex). Cells were harvested before Dex treatment (0 hr) or after indicated time of treatment with Dex.

extract_protocol: Total RNA was extracted using ISOGEN (Nippongene) following manufacturer's protocol.

treatment_protocol: Stealth select small interfering RNAs (siRNAs, from Invitrogen) were transfected using RNAiMax reagent (Invitrogen) at day -5 and day 0.

tag: sirna

value: Negative control siRNA (si-Ctr)


title: 3T3-L1_si-Mbd1_0hr_ExB

description: Gene expression after 36 hrs treatment with dexamethasone

source_name: 3T3-L1 preadipocytes treated with Mbd1 specific siRNA

value: siRNA targeting Mbd1 (si-Mbd1, MSS206537)


title: WT MEF_AAD replicate 1


title: WT MEF_REG replicate 2


title: 10Thalf_si-Ctr_0hr

source_name: 10T1/2 mesenchymal stem cells treated with the negative control siRNA


title: 10Thalf_si-Ctr_48hr

description: Gene expression after 48 hrs treatment with dexamethasone

source_name: 10T1/2 cells treated with the negative control siRNA and dexamethasone


title: 3T3-L1_si-Setdb1_0hr_ExB

source_name: 3T3-L1 preadipocytes treated with Setdb1 specific siRNA

value: siRNA targeting Setdb1 (si-Setdb1, MSS234815)


title: 3T3-L1_si-Mcaf1_0hr_ExB

source_name: 3T3-L1 preadipocytes treated with Mcaf1 specific siRNA

value: siRNA targeting Mcaf1 (si-Mcaf1, MSS285128)


title: WT MEF_AAD replicate 2


title: 3T3-L1_si-Setdb1_36hr_ExA

source_name: 3T3-L1 cells treated with Setdb1 specific siRNA and dexamethasone


title: 10Thalf_si-Setdb1_0hr

source_name: 10T1/2 mesenchymal stem cells treated with Setdb1 specific siRNA


title: wt BrdU HU (SUP)

description: FY1110 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing BrdU 200μg/ml and HU 0.2M for 45 min

source_name: wt BrdU HU 45 min

value: W303 Mata ura3::URA3/GPD-TK(7X)


title: 10Thalf_si-Setdb1_48hr

source_name: 10T1/2 cells treated with Setdb1 specific siRNA and dexamethasone


title: Laos.32

value: Standard Lab

value: Clinical


title: Laos.30


title: G2_SMC5 G2_SMC6 BrdU HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1143_BrdU_G2_Smc56_IP.CEL
R1143_BrdU_G2_Smc56_SUP.CEL


title: 3T3-L1_si-Ctr_36hr_ExA

source_name: 3T3-L1 cells treated with the negative control siRNA and dexamethasone


title: 3T3-L1_si-Ctr_0hr_ExA


title: G2_Smc6 nocodazole (SUP)

description: HY3172 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: G2_Smc6 nocodazole

value: W303 Mata G2::NATNT2-SMC6-6HIS-3FLAG::KANMX4 G2::NATNT2-SMC5-9PK::HIS3MX6

value: Nocodazole 150 min


title: wt BrdU HU (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R1143_BrdU_wt_IP.CEL
R1143_BrdU_wt_SUP.CEL

value: HU 45 min


title: 3T3-L1_si-Setdb1_0hr_ExA


title: G2_Smc6 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R999_G2_Smc6_noco_IP.CEL
R999_G2_Smc6_noco_SUP.CEL


title: G2_Smc5 nocodazole (SUP)

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

source_name: G2_Smc5 nocodazole

value: Anti-PK SV5-Pk1 (AbD Serotech)


title: Laos.29

data_processing: images scanned and Normalized using NimbleScan v2.5


title: Smc6 nocodazole (SUP)

description: HY3447 cells were arrested in G1 with alfa-factor for 2 h and then released in media containing Nocodazole 20μg/ml for 150 min

source_name: Smc6 nocodazole

value: W303 Mata SMC6-6HIS-3FLAG::KANMX4 SMC5-9PK::HIS3MX6


title: Laos.31


title: Laos.26


title: Laos.28


title: Smc5 nocodazole (SUP)

source_name: Smc5 nocodazole


title: G2_Smc5 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R999_G2_Smc5_noco_IP.CEL
R999_G2_Smc5_noco_SUP.CEL


title: Smc5 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R999_Smc5_noco_IP.CEL
R999_Smc5_noco_SUP.CEL


title: Smc6 nocodazole (IP)

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

Input for BAR file production:
R999_Smc6_noco_IP.CEL
R999_Smc6_noco_SUP.CEL

value: Anti-FLAG M2 F1804 (SIGMA)


title: Laos.24


title: Laos.27


title: Laos.25


title: Laos.23


title: 5719882027G

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

description: Gene expression signature regulating co-cultured mesenchymal and neuroblastoma cells

hyb_protocol: Standard Illumina bead array protocol was used using MouseRef-8_V2_R0_11278551 array

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was bacground corrected using Bead studio Software (Illumina). The data were normalised using quantile normalisation with IlluminaGUI in R. detection scores were calculated in BeadStudio software.

label_protocol: RNA was amplified using illumina Total RNA amplification kit. Total RNA was reverse transcribed using T7 oligo dT primer to generate first strand of cDNA. Biotinylated cRNA was generated from double stranded cDNA templates via in vitro transcription.

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

tag: co-culture conditions

value: Human neuroblastoma

tag: dox treatment

value: yes


title: 5719882027H

value: THMYC

value: Mouse neuroblastoma


title: Laos.22


title: 5719882027E


title: Laos.21


title: Laos.18


title: 5719882027F


title: Laos.20


title: Laos.19


title: 5719882027B

value: no


title: Laos.17


title: 5719882027C


title: 5719882027D


title: Laos.16


title: 5719882025F


title: Laos.12


title: Laos.14


title: 5719882025G


title: 5719882025C


title: Laos.8


title: 5719882025E


title: Laos.10


title: 5719882027A


title: 5719882025B


title: 5719882025D


title: 5719882025H


title: Laos.13


title: Laos.9


title: Laos.11


title: Laos.15


title: Cambodia.16


title: Laos.7


title: Laos.1


title: 5719882025A


title: Cambodia.17


title: Laos.6


title: Laos.4


title: 5719882023G


title: 5719882023H


title: Laos.5


title: 5719882023F


title: Cambodia.15


title: BAG3-KD (siRNA for BAG3)-2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing:
GeneChip Analysis Suite
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.1.20

source_name: Human oral squamous cell carcinoma cell line HSC-3

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: HSC-3 cells were cultured in Eagle's Minimum Essential medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: HSC-3 cells were incubated in Opti-MEM® I Reduced Serum Medium containing 20 nM siRNA (for BAG3 or luciferase) and Lipofectamine™ RNAiMAX at 37°C. Six hours after transfection, the medium was exchanged for E-MEM medium supplemented with 10% FBS, and the cells were maintained at 37°C for 42 h.  HT treatment was carried out by immersing plastic culture vessels containing the attached cells in a water bath at 44°C for 90 min. After heat treatment, the cells were incubated for 6 h at 37°C.

tag: cell line

value: oral squamous carcinoma cells

tag: gender

value: male

value: 64 years

value: tongue

tag: life span

value: infinite

tag: morphology

value: epithelial-like

value: BAG3 siRNA


title: Laos

tag: growth protocol

value: Standard Lab

source_name: Laos

value: Laos

value: Clinical


title: HT-BAG3-KD (HT and siRNA for BAG3)-1

tag: cell type

value: Hyperthermia (HT) and BAG3 siRNA


title: 5719882023C


title: 5719882023D


title: HT-BAG3-KD (HT and siRNA for BAG3)-2

tag: tissue


title: 5719882023B

tag: strain


title: BAG3-KD (siRNA for BAG3)-1


title: HT-Control (HT and siRNA for luciferase)-2

value: Hyperthermia (HT) and luciferase siRNA


title: HT-Control (HT and siRNA for luciferase)-1


title: 5719882023E


title: Cambodia.13


title: Control (siRNA for luciferase)-2

value: siRNA for luciferase


title: Cambodia.14


title: Cambodia.10


title: 5719882023A


title: Cambodia.11


title: Control (siRNA for luciferase)-1


title: Cambodia.12


title: Cambodia.8


title: Laos.3


title: Laos.2


title: Cambodia.6


title: Cambodia.7


title: Lung_MWCNT, 90 days

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 90 days in MWCNT-instilled rat lungs

hyb_protocol: Cy3-labelled 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 o

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_F_20110906). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features fla

organism: Rattus norvegicus

source_name: Rat lungs, 90 days, MWCNT, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 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, Tokyo, Japan). Dye incorporation an

growth_protocol: Nine-week-old male Wistar rats purchased from Japan SLC, Inc. (Shizuoka, Japan) were divided into groups (n = 4 per group per time point). SWCNT or MWCNT were intratracheally administered into rats as a single injection, respectively. The vehicle control

extract_protocol: The right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturers instruct

treatment_protocol: 0.32 mg of SWCNT or MWCNT was suspended in 0.4 ml of 10mg/mL BSA. Each material suspension was intratracheally instilled once in rats. The animals were dissected at 1day, 3 days, 7 days, 30 days, and 90 days after instillation.

tag: post-instillation period

value: 90 days

value: lung


title: Lung_Control, 90 days (#2)

description: Gene expression after 90 days in vehicle control-instilled rat lungs

source_name: Rat lungs, 90 days, Vehicle control, replicate 4


title: Lung_SWCNT, 90 days

description: Gene expression after 90 days in SWCNT-instilled rat lungs

source_name: Rat lungs, 90 days, SWCNT, replicate 4


title: Lung_MWCNT, 30 days

description: Gene expression after 30 days in MWCNT-instilled rat lungs

source_name: Rat lungs, 30 days, MWCNT, replicate 4

value: 30 days


title: Lung_Control, 30 days (#2)

description: Gene expression after 30 days in vehicle control-instilled rat lungs

source_name: Rat lungs, 30 days, Vehicle control, replicate 4


title: Lung_MWCNT, 7 days

description: Gene expression after 7 days in MWCNT-instilled rat lungs

source_name: Rat lungs, 7 days, MWCNT, replicate 4

value: 7 days


title: Cambodia.2


title: Lung_SWCNT, 30 days

description: Gene expression after 30 days in SWCNT-instilled rat lungs

source_name: Rat lungs, 30 days, SWCNT, replicate 4


title: TO_MB92

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

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

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

data_processing: minfi package in the R statistical environment using Illumina normalization

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using proteinase K digestion followed by phenol:chloroform extraction and ethanol precipitation.

tag: disease state

value: Medulloblastoma

tag: molecular subtype

value: SHH


title: TO_MB91


title: Lung_SWCNT, 7 days

description: Gene expression after 7 days in SWCNT-instilled rat lungs

source_name: Rat lungs, 7 days, SWCNT, replicate 4

value: male


title: Cambodia.4


title: TO_MB85


title: Cambodia

source_name: Cambodia

value: Cambodia


title: Cambodia.5


title: Lung_MWCNT, 3 days

description: Gene expression after 3 days in MWCNT-instilled rat lungs

source_name: Rat lungs, 3 days, MWCNT, replicate 4

value: 3 days


title: TO_MB90


title: TO_MB82


title: TO_MB83


title: Lung_Control, 7 days (#2)

description: Gene expression after 7 days in vehicle control-instilled rat lungs

source_name: Rat lungs, 7 days, Vehicle control, replicate 4


title: TO_MB89


title: Cambodia.3


title: Lung_Control, 3 days (#2)

description: Gene expression after 3 days in vehicle control-instilled rat lungs

source_name: Rat lungs, 3 days, Vehicle control, replicate 4


title: Lung_MWCNT, 1 day

description: Gene expression after 1 day in MWCNT-instilled rat lungs

source_name: Rat lungs, 1 day, MWCNT, replicate 4

value: 1 day


title: TO_MB79


title: Lung_SWCNT, 3 days

description: Gene expression after 3 days in SWCNT-instilled rat lungs

source_name: Rat lungs, 3 days, SWCNT, replicate 4


title: TO_MB84


title: TO_MB76


title: TO_MB88


title: TO_MB80


title: Lung_SWCNT, 1 day

description: Gene expression after 1 day in SWCNT-instilled rat lungs

source_name: Rat lungs, 1 day, SWCNT, replicate 4


title: Lung_Control, 1 day

description: Gene expression after 1 day in vehicle control-instilled rat lungs

source_name: Rat lungs, 1 day, Vehicle control, replicate 4


title: Cambodia.1


title: TO_MB78


title: TO_MB86


title: TO_MB81


title: TO_MB74


title: TO_MB75


title: TO_MB71


title: TO_MB77


title: TO_MB70


title: TO_MB72


title: TO_MB63


title: TO_MB60


title: TO_MB66


title: TO_MB64


title: TO_MB69


title: TO_MB62


title: TO_MB65


title: TO_MB73


title: TO_MB67


title: TO_MB55


title: TO_MB68


title: TO_MB58


title: TO_MB54


title: TO_MB50


title: TO_MB57


title: TO_MB51


title: TO_MB52


title: tumor_xenograft_14_SSEA4+_replicate2 [miRNA]

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

hyb_protocol: Cy3-labeled RNA in hybridization buffer was hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v19 (Design ID 046064) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. The intensity data of the individual microarrays were subjected to probe summarization, thresholding (0.1), log2-transformation, and quantile normalization (GeneSpring v12.6, Agilent Technologies).

label_protocol: 100 ng of each RNA was used as template for sample labeling and according to the “miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011) using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

growth_protocol: Human breast cancer xenografts were established from patient’s primary tumor surgical specimens, by grafting tumor fragments into the interscapular fat pad of athymic nude mice, and maintained through in vivo passages as previously described (PMID: 17606733).

extract_protocol: Total RNA was isolated using the miRNeasy Kit (QIAGEN).

treatment_protocol: Whole tumors were dissected out together with the surrounding stromal tissue and were placed in a 50 mL falcon tube containing MACS® tissue storage solution (Miltenyi Biotec). Tumor tissue was dissociatied using the Tumor Dissociation Kit, human (Miltenyi Biotec). SSEA4+ and SSEA4- tumor cell subpopulations were isolated by magnetic activated cell sorting (MACS®). After dissociation and depletion of mouse cells, the cells were resuspended in PEB buffer (PBS, pH 7.2, 0.5% bovine serum albumin, and 2 mM EDTA; prepared by diluting MACS BSA Stock Solution 1:20 with autoMACS® Rinsing Solution) at a concentration of 1x10E7 cells per 100 µl. After adding 10 µl SSEA4-PE (Miltenyi Biotec) per 100 µl the suspension was incubated at 4°C under continuous agitation (MACSmix Tube Rotator, Miltenyi Biotec) for 10 min. Then the cells were pelleted at 300 g for 10 min, resuspended in 80 µl PEB per 1x10E7 cells, 20 µl of anti-PE MicroBeads (Miltenyi Biotec) were added and incubated at 4°C under continuous agitation for 15 min. Cells were washed in 1 ml PEB per 1x10E7 cells, pelleted and resuspended in 500 µl PEB per separation. SSEA4+ tumor cells were isolated using an MS-column (Miltenyi Biotec), SSEA4- tumor cells were isolated using an LD-column (Miltenyi Biotec). Purity of the isolated cells was evaluated using flow cytometry.

tag: host mouse strain

value: Hsd:Athymic Nude-Foxn1nu (athymic nude mice)

tag: host mouse gender

value: female

tag: xenograft tissue

value: human breast cancer

tag: xenograft batch

tag: cell fraction


title: TO_MB53


title: TO_MB42

value: WNT


title: tumor_xenograft_14_SSEA4-_replicate2 [miRNA]


title: TO_MB48


title: TO_MB61


title: tumor_xenograft_14_SSEA4+_replicate1 [miRNA]


title: TO_MB59


title: TO_MB43


title: tumor_xenograft_14_SSEA4-_replicate1 [miRNA]


title: TO_MB47


title: TO_MB40


title: TO_MB56


title: tumor_xenograft_10_SSEA4-_replicate2 [miRNA]


title: TO_MB37


title: TO_MB49


title: tumor_xenograft_10_SSEA4+_replicate2 [miRNA]


title: TO_MB39


title: TO_MB44


title: TO_MB45


title: TO_MB38


title: TO_MB46


title: tumor_xenograft_6_SSEA4+_replicate1 [miRNA]


title: tumor_xenograft_10_SSEA4-_replicate1 [miRNA]


title: TO_MB32


title: tumor_xenograft_6_SSEA4+_replicate2 [miRNA]


title: TO_MB87


title: TO_MB36


title: TO_MB33


title: tumor_xenograft_6_SSEA4-_replicate1 [miRNA]


title: tumor_xenograft_10_SSEA4+_replicate1 [miRNA]


title: TO_MB31


title: TO_MB35


title: TO_MB30

value: Group 4


title: TO_MB41


title: TO_MB34


title: TO_MB29


title: TO_MB26


title: TO_MB27


title: TO_MB28


title: TO_MB25


title: TO_MB20


title: Wild type ovaries at 14.5dpc, rep 2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

source_name: ovaries, wild type

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit).

growth_protocol: Mice were breeded in conventional animal facility in accordance with animal health care, ethics and current regulations.

extract_protocol: Gonads in RLT buffer were pooled and lysed with homogenizer before RNA extraction using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Pairs of fetal ovaries/post-natal testes were dissected from embryos/mouse that were previously weighed. Gonads were dissolved in 50µl RLT lysis buffer (Qiagen) and stored at -20°C before pools constitution. For males, testes were weighed and contralateral testes were fixed in Formol for histological analysis.

tag: strain/background

value: NMRI

tag: genotype/variation

value: wild type

value: ovaries

tag: age


title: TO_MB24


title: Meioc-/- ovaries at 14.5dpc, rep 1

source_name: ovaries, Meioc-/-

value: Meioc-/-

tag: gender


title: Meioc-/- ovaries at 14.5dpc, rep 2


title: TO_MB16


title: TO_MB15

value: Group 3


title: Wild type ovaries at 14.5dpc, rep 1


title: Meioc-/- testes at 8dpp, rep 2

source_name: testes, Meioc-/-

value: testes

value: 8 dpp


title: TO_MB12

value: Medulloblastoma


title: TO_MB18


title: Wild type testes at 8dpp, rep 2

source_name: testes, wild type

value: male


title: TO_MB19


title: TO_MB21


title: TO_MB9


title: TO_MB14


title: tumor_xenograft_14_SSEA4+_replicate2

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 8x60K v2 (Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.


title: Meioc-/- testes at 8dpp, rep 1


title: TO_MB17


title: tumor_xenograft_14_SSEA4+_replicate1


title: TO_MB5


title: TO_MB11


title: TO_MB7


title: TO_MB10


title: TO_MB2


title: TO_MB8


title: tumor_xenograft_14_SSEA4-_replicate2


title: tumor_xenograft_14_SSEA4-_replicate1


title: TO_MB1


title: C. jejuni NCTC 11168 treated with (-)-α-Pinene, replicate 4

city: Ljubljana

first: Jasna

last: Kovac

address: Jamnikarjeva 101

department: Department of Food Science and Technology

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

description:
C. jejuni NCTC 11168
Sample name: 1005
Biological replicate 4

hyb_protocol: The hybridization and wash were performed following (http://www.mycroarray.com/) standard protocol. Hybridization was for 24 hours at 42⁰C.

scan_protocol: Arrays were scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using GenePix 4100A (Molecular Devices, Sunnyvale, CA) following the manufacturer's protocol.

data_processing: Fluorescence intensities of each spot were extracted using GenePix Pro 7.0 (Molecular Devices). (i) After global background correction, the fluorescence intensity in each wavelength was log2 transformed and normalized using locally weighted linear regression (LOWESS) in statistical software R (http://www.r-project.org); (ii) for genes with more than one probe, only the genes with all the probes showing the same regulation trend were kept; (iii) T-test was performed to determine the differentially expressed genes.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

label_protocol: 5 µg of total RNA were primed with 2 µl of 3mg/ml random hexamer primer at 70°C for 10 min, then reversed transcribed at 42°C overnight in the presence of 400 U SuperScript III RTase (Invitrogen) and 0.6 ul 25mM labeling mix (2:3 aa-dUTP to dTTP). The purified aminoallyl-labeled cDNA was then dissolved in 4.5 ul 0.1 M sodium carbonate buffer pH 9.3 and incorporated with 4.5ul Cy3 or Cy5 dye.

growth_protocol: Stock of Campylobacter jejuni NCTC 11168 was taken from stock stored on -80 dC and plated on Mueller Hinton agar. Culture was incubated at 42 dC for 24 hours, replated and incubated again at 42 dC for 24 hours, both times in microaerobic conditions with 5% O2. After that the culture was resuspended in MHB and shaken in microaerobic conditions at 42 dC until it reached OD600=0.2.

extract_protocol: Total RNA was extracted using the RNeasy kit from Qiagen following manufacturer's instruction.

treatment_protocol: 62.5 ug/ml (-)-alpha pinene (dissolved in DMSO) was added to prepared culture (final concentration of DMSO was 0.048%). Culture was treated for 2 hours - shaking at 160 rpm, at 42 dC, microaerobically.

tag: treatment

value: (-)-α-Pinene


title: C. jejuni NCTC 11168 treated with (-)-α-Pinene, replicate 3

description:
C. jejuni NCTC 11168
Sample name: 967
Biological replicate 3


title: TO_MB3


title: TO_MB6


title: C. jejuni NCTC 11168 treated with (-)-α-Pinene, replicate 2

description:
C. jejuni NCTC 11168
Sample name: 966
Biological replicate 2


title: tumor_xenograft_6_SSEA4-_replicate2 [miRNA]


title: TO_MB13


title: C. jejuni NCTC 11168 treated with (-)-α-Pinene, replicate 1

description:
C. jejuni NCTC 11168
Sample name: 965
Biological replicate 1


title: tumor_xenograft_6_SSEA4+_replicate2


title: tumor_xenograft_10_SSEA4+_replicate2


title: TO_MB4


title: tumor_xenograft_10_SSEA4-_replicate1


title: tumor_xenograft_6_SSEA4+_replicate1


title: tumor_xenograft_10_SSEA4-_replicate2


title: tumor_xenograft_6_SSEA4-_replicate1


title: TO_MB23


title: patient 1 before lenalidomide

status: Public on Nov 18 2015

city: New York

first: Christian Matthias

last: Wilk

address: 1470 Madison Ave

department: Precision Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

description: Probe_02_Pat_1_Zyklus 0

hyb_protocol: A total of 20ng purified RNA was transcribed to cDNA anf amplified by using Ovation Pico WTA System (NuGen, Leek, Netherlands).  5µg cDNA were hybridized to the Human Genome U133A 2.0 chip (Affymetrix, Santa Clara, USA) following the manufacturer’s instructions.

scan_protocol: as indicated by the manufacturer

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 11.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples

source_name: MM patient before therapy_BM CD34+ HSPC

label_protocol: biotin labeling according to the manufacturers recommendations

extract_protocol: BM HCPCs were lysed in RLT buffer containing 1% beta-Mercaptoethanol and were cryopreserved at -20°C. RNA was prurified using Rneasy Micro Kit (Qiagen, Hilden, Germany).

tag: patient id

value: patient 1

tag: subject status

value: patients with Multiple Myeloma

tag: time point

value: before lenalidomide consolidation therapy.

value: bone marrow

value: CD34+ hematopoietic stem-progenitor cells (HSPCs)


title: patient 2 after lenalidomide

source_name: MM patient after therapy_BM CD34+ HSPC

value: patient 2

value: after lenalidomide consolidation therapy.

tag: tissue

tag: cell type


title: WM3248_Res_siCON_rep_1

city: Daejeon

first: Min Hwan

last: Kim

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: KAIST

description:
SAMPLE 13
replicate_1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Array probes transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using LPE (Local Pooled Error) test and fold change in which the null hypothesis was that no difference exists among groups.

source_name: PLX4032-resistant WM3248

label_protocol: Total RNA was amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (EPICENTRE) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 200 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP.

growth_protocol: SKMEL28 cells were grown in MEM supplemented with 10 % FBS, and WM3248 cells were grown in 4:1 combination of MCDB-153 and L-15 supplemented with 2 % FBS, 1.68 mM CaCl2, and 5 μg/ml insulin. SKMEL28 and WM3248 cells were continuously exposed to 2 μM of PLX4032 for 2 months for PLX4032 resistant clones generation

extract_protocol: total RNAs were extracted using the RNeasy kit (Qiagen). RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop), Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For sample 1~8, parental and resistant SKMEL28 and WM3248 cells were plated on culture dishes, and total RNAs were extracted.  For sample 9~16, Resistant SKMEL28 and WM3248 cells were transfected with either control siRNA or YAP/TAZ siRNAs for 72 hrs, and total RNAs were extracted

tag: cell line

value: PLX4032-resistant WM3248

tag: transfection

value: control siRNA

value: Melanoma cell line


title: patient 5 before lenalidomide

value: patient 5


title: patient 1 after lenalidomide

description: Probe_01_Pat_1_Zyklus 6


title: patient 4 after lenalidomide

value: patient 4


title: patient 5 after lenalidomide

description: Probe_10_Pat_5_Zyklus 6


title: patient 4 before lenalidomide


title: patient 3 before lenalidomide

value: patient 3


title: Liver wildtype, A888_54_L49

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

hyb_protocol: Affymetrix Mouse Gene 2.1 ST arrays were hybridized, washed and stained according to the protocol described in the Affymetrix GeneChip 3' IVT Express Kit Manual.

scan_protocol: The arrays were scanned using the Affymetrix GeneTitan Instrument, and raw data were extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: The Affymetrix GeneTitan Instrument was used for automated array processing. Raw data was generated and extracted from the scanned images for analysis with the Affymetrix GeneChip Command Console (AGCC) Software and Expression Console Software packages.

source_name: Liver, wildtype

label_protocol: For each sample, 100 ng of total RNA was processed according to the Affymetrix GeneChip 3' IVT Express Kit manual (P/N 702646 Revision 6) and hybridized to Affymetrix Mouse Gene 2.1 ST arrays.

extract_protocol: The manufacturer’s protocol for RNA isolation was performed. Upon RNA isolation, RNA clean-up was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany), including the DNase treatment step, according to the manufacturer’s protocol.

value: wildtype

tag: developmental stage

value: adult

value: liver


title: WM3248_Res_siYAP/TAZ_rep2

description:
SAMPLE 16
replicate_2

value: YAP/TAZ siRNAs


title: patient 2 before lenalidomide


title: patient 3 after lenalidomide


title: Liver wildtype, A888_56_L48

value: male


title: WM3248_Res_siYAP/TAZ_rep1

description:
SAMPLE 15
replicate_1


title: WM3248_Res_siCON_rep_2

description:
SAMPLE 14
replicate_2


title: SKMEL28_Res_siYAP/TAZ_rep2

description:
SAMPLE 12
replicate_2

source_name: PLX4032-resistant SKMEL28

value: PLX4032-resistant SKMEL28


title: Liver duplication carrier, A888_55_L21

source_name: Liver, duplication carrier

value: carrier of 16p11.2 duplication


title: Liver wildtype, A888_32_L17


title: SKMEL28_Res_siYAP/TAZ_rep1

description:
SAMPLE 11
replicate_1


title: SKMEL28_Res_siCON_rep_2

description:
SAMPLE 10
replicate_2


title: Control 4hrs_4

city: Ottawa

first: Nikolai

middle: L

last: Chepelev

state: Ontario

address: 50 Colombine Driveway

department: Environmental Health Science and Research Bureau

institute: Health Canada

hyb_protocol: Samples were hybridised to Agilent G3 Mouse GE 8x60K microarrays.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Control 4hrs

label_protocol: 200 ng of each sample was labelled with Cyanine 5-CTP (Cy5); universal reference total mouse RNA (Agilent Technologies) was labelled with Cyanine 3-CTP (Cy3).

extract_protocol: For all time points, the spleen was removed, flash-frozen in liquid nitrogen, and stored at -80°C.RNA was isolated, hybridized, and analyzed as described elsewhere (Malik, A. I., Rowan-Carroll, A., Williams, A., Lemieux, C. L., Long, A. S., Arlt, V. M., Phillips, D. H., White, P. A., and Yauk, C. L. (2013). Hepatic genotoxicity and toxicogenomic responses in MutaMouse males treated with dibenz[a,h]anthracene. Mutagenesis. 28, 543-554.)

treatment_protocol:
Adult male Muta™Mouse were administered Dibenzo[def,p]chrysene (DBC, CAS no. 191-30-0, purity ≥ 98%, Cambridge Isotopes, Tewksbury, MA) dissolved in highly refined olive oil (Sigma-Aldrich, Oakville, ON, Canada) at 0.005 ml/g body weight. The doses (2.0, 6.3, and 20.0 mg/kg-bw per day) were administered by oral gavage for three consecutive days.
There were 15 animals in each dose group (5 harvested per each of 3 time points [i.e., 4, 24, and 72 h after the last exposure]), as well as in the vehicle control groups. Five mice from each dose group (and control group) were anesthetized using isoflurane gas and then euthanized via cervical dislocation followed by chest cavity opening 4, 24, or 72 h after the final dose.

tag: strain

value: Muta Mouse

tag: ID

value: spleen

source_name: universal reference total mouse RNA

tag: manufacturer

value: Agilent Technologies


title: Liver deletion carrier, A888_53_L28

source_name: Liver, deletion carrier

value: carrier of 16p11.2 deletion


title: SKMEL28_Res_siCON_rep_1

description:
SAMPLE 9
replicate_1


title: Wild type testes at 8dpp, rep 1

value: NMRI

value: wild type

value: testes

value: 8 dpp


title: Mid Dose 4hrs_4

source_name: Mid Dose 4hrs


title: Liver wildtype, A888_08_L16


title: Liver deletion carrier, A888_29_L26


title: Liver duplication carrier, A888_31_L19


title: Low Dose 4hrs_5

source_name: Low Dose 4hrs


title: WM3248_Res_rep2

description:
SAMPLE 8
replicate_2

value: PLX4032-resistant WM3248

value: Melanoma cell line


title: High Dose 4hrs_5

source_name: High Dose 4hrs


title: Liver wildtype, A888_30_L29

value: wildtype


title: TO_MB22

tag: disease state

value: Medulloblastoma

tag: molecular subtype

value: Group 4


title: Control 24hrs_5

source_name: Control 24hrs


title: WM3248_Res_rep1

description:
SAMPLE 7
replicate_1


title: Liver wildtype, A888_06_L10

tag: strain/background

tag: genotype/variation

value: adult

value: liver


title: Liver duplication carrier, A888_07_L18

tag: gender

value: male


title: WM3248_Par_rep1

description:
SAMPLE 5
replicate_1

source_name: parental WM3248


title: SKMEL28_Res_rep2

description:
SAMPLE 4
replicate_2

value: PLX4032-resistant SKMEL28


title: High Dose 24hrs_5

source_name: High Dose 24hrs

value: Muta Mouse


title: Mid Dose 4hrs_3

value: spleen


title: SKMEL28_Res_rep1

description:
SAMPLE 3
replicate_1


title: Liver deletion carrier, A888_05_L11


title: Low Dose 24hrs_5

source_name: Low Dose 24hrs

value: Agilent Technologies


title: IRI_24h

city: Harbin

first: Wenliang

last: Zhu

state: Heilongjiang

address: Xuefu road 194

department: 1Institute of Clinical Pharmacology

institute: The Second Affiliated Hospital of Harbin Medical University

hyb_protocol: Cy3-labelled cRNA of 0.6 μg (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25 μl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-070156 Human  miRNA Microarray V19.0 8x60K(Agilent) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0 (Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: kidney tissue of AKI model mice after renal bilateral IRI surgery (24h)

label_protocol: Total RNA of 0.1 μg were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP (Cy3) using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Healthy male C57B/6 mice (20-25 g) were maintained under the standard animal room conditions (temperature 21±1 °C; humidity 55–60%) with food and water ad libitum for one week before in vivo experiment. Animals were suffered renal bilateral ischemia reperfusion injury (IRI). Warm ischemic time was 30 min. Sham-operated mice, which underwent the same surgical procedure without placement of the vascular clamp served as controls (Sham group). Mice were sacrificed at 6, 12, 24 and 48 hours after reperfusion (n = 8 per time point).

extract_protocol: Twenty mg of each renal tissue which had been stored in liquid nitrogen was obtained to extract RNA. Total RNA was extracted from each sample using Trizol reagent (Invitrogen, Shanghai, China).

value: kidney


title: IRI_12h

source_name: kidney tissue of AKI model mice after renal bilateral IRI surgery (12h)


title: SKMEL28_Par_rep2

description:
SAMPLE 2
replicate_2

source_name: parental SKMEL28


title: IRI_48h

source_name: kidney tissue of AKI model mice after renal bilateral IRI surgery (48h)


title: Low Dose 4hrs_4


title: Control 4hrs_3


title: IRI_6h

source_name: kidney tissue of AKI model mice after renal bilateral IRI surgery (6h)


title: Sham

source_name: kidney tissue of Sham-operated mice


title: Hippocampus deletion carrier, A888_71_H23

source_name: Hippocampus, deletion carrier

value: carrier of 16p11.2 deletion

value: hippocampus


title: Striatum wildtype, A888_70_S48

source_name: Striatum, wildtype

value: striatum


title: High Dose 4hrs_4

source_name: universal reference total mouse RNA


title: WM3248_Par_rep2

description:
SAMPLE 6
replicate_2


title: Hippocampus wildtype, A888_62_H56

source_name: Hippocampus, wildtype


title: AEII-3-static

city: Guangzhou

first: pu

last: mao

address: 151 Yanjiang Street West

institute: Guangzhou Institute of Respiratory Diseases

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (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: the 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: AEII_static control

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: Primary human AEII cells were cultured in small airway epithelial cell growth medium (Lonza, Walkersville, MD) at 37 °C in a humidified atmosphere of 5% CO2.

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. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Primary human AEII cells cells were seeded into BioFlex Culture 6-well plates (Flexcell International Corporation, Hillsborough, NC) at a density 5×105 cells/well in small airway epithelial cell growth medium containing 1% FBS for 24 h. The cells were then subjected to cyclic stretch for 48 h at a frequency of 20 cycles/min and 20% elongation (FX-5000; Flexcell International Corporation, Hillsborough, NC). Static cultured AEII cells were served as control.

value: lung cancer patient

tag: subject id

value: patient 3

value: primary alveolar epithelial type II (AEII) cells

tag: subjected to

value: Static resting


title: AEII-2-stretch

source_name: AEII_20% mechanical stretch

tag: subject status

value: patient 2

value: cyclic stretch for 48 h at a frequency of 20 cycles/min and 20% elongation


title: AEII-3-stretch


title: Low Dose 24hrs_4


title: Striatum wildtype, A888_58_S29

value: wildtype

value: adult


title: Striatum duplication carrier, A888_69_S54

source_name: Striatum, duplication carrier

value: carrier of 16p11.2 duplication

value: male


title: Control 24hrs_4

source_name: Control 24hrs

value: Muta Mouse


title: tumor_xenograft_10_SSEA4+_replicate1

tag: host mouse strain

value: Hsd:Athymic Nude-Foxn1nu (athymic nude mice)

tag: host mouse gender

value: female

tag: xenograft tissue

value: human breast cancer

tag: xenograft batch

tag: cell fraction


title: High Dose 24hrs_4

tag: tissue

value: spleen

value: Agilent Technologies


title: Hippocampus deletion carrier, A888_61_H26

value: carrier of 16p11.2 deletion

tag: developmental stage

value: hippocampus


title: SKMEL28_Par_rep1

description:
SAMPLE 1
replicate_1

tag: cell line

tag: transfection

tag: cell type

value: Melanoma cell line


title: Mid Dose 24hrs_4

source_name: Mid Dose 24hrs

tag: strain

tag: ID

tag: manufacturer


title: Striatum deletion carrier, A888_57_S28

source_name: Striatum, deletion carrier

tag: strain/background

tag: genotype/variation

tag: gender

value: striatum


title: Striatum wildtype, A888_60_S44


title: Hippocampus duplication carrier, A888_63_H45

source_name: Hippocampus, duplication carrier


title: Cerebellum wildtype, A888_52_C16

source_name: Cerebellum, wildtype

value: cerebellum


title: Striatum duplication carrier, A888_59_S47


title: High Dose 4hrs_3

source_name: High Dose 4hrs


title: Mid Dose 4hrs_2

source_name: Mid Dose 4hrs


title: Control 24hrs_3


title: Low Dose 4hrs_3

source_name: Low Dose 4hrs


title: High Dose 24hrs_3

source_name: High Dose 24hrs


title: Mid Dose 24hrs_3


title: Hippocampus wildtype, A888_64_H35


title: AEII-1-static

tag: subject status

value: lung cancer patient

tag: subject id

value: patient 1

value: primary alveolar epithelial type II (AEII) cells

tag: subjected to

value: Static resting


title: AEII-2-static

value: patient 2


title: AEII-1-stretch

value: cyclic stretch for 48 h at a frequency of 20 cycles/min and 20% elongation


title: Low Dose 24hrs_3

source_name: Low Dose 24hrs

value: Muta Mouse

value: male


title: Cerebellum duplication carrier, A888_51_C19

source_name: Cerebellum, duplication carrier

value: carrier of 16p11.2 duplication

value: adult


title: Cerebellum deletion carrier, A888_49_C17

source_name: Cerebellum, deletion carrier


title: Hippocampus wildtype, A888_46_H44

value: wildtype


title: Cerebellum wildtype, A888_50_C49


title: Hippocampus deletion carrier, A888_37_H11

source_name: Hippocampus, deletion carrier


title: Hippocampus wildtype, A888_45_H49

source_name: Hippocampus, wildtype


title: Hippocampus wildtype, A888_40_H16


title: Low Dose 4hrs_2

value: spleen

source_name: universal reference total mouse RNA

value: Agilent Technologies


title: Control 24hrs_2


title: Mid Dose 4hrs_1


title: High Dose 4hrs_1


title: Control 4hrs_2

source_name: Control 4hrs


title: Low Dose 24hrs_2


title: Striatum duplication carrier, A888_35_S21

source_name: Striatum, duplication carrier


title: Hippocampus duplication carrier, A888_39_H18

value: hippocampus


title: 35S:miR396, biological replicate 3

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

hyb_protocol: Affymetrix instructions

scan_protocol: Affymetrix instructions

data_processing: R/Bioconductor - GC-RMA

organism: Arabidopsis thaliana

source_name: microdissected meristems

label_protocol: GeneChip 3’ IVT Express Kit

growth_protocol: Plants were grown in long photoperiods (16 hr light/8 hr dark) at 21 °C vertically on 1X Murashige and Skoog salt mixture, 1% sucrose, and 2.3 mM 2-(Nmorpholino) ethanesulfonic acid (pH 5.8) in 1% agar.

extract_protocol: mirVana™ miRNA Isolation kit (Ambion).

treatment_protocol: No treatment

tag: organ

value: root

value: microdissected meristems

value: miR396 overexpression

tag: age

value: 7 days after sowing


title: High Dose 24hrs_1


title: Striatum wildtype, A888_36_S16

source_name: Striatum, wildtype

value: striatum


title: Low Dose 4hrs_1


title: High Dose 24hrs_2


title: Striatum wildtype, A888_34_S10


title: Hippocampus wildtype, A888_38_H6


title: Mid Dose 24hrs_2

source_name: Mid Dose 24hrs


title: High Dose 4hrs_2


title: tumor_xenograft_6_SSEA4-_replicate2

tag: host mouse strain

value: Hsd:Athymic Nude-Foxn1nu (athymic nude mice)

tag: host mouse gender

value: female

tag: xenograft tissue

value: human breast cancer

tag: xenograft batch

tag: cell fraction


title: 35S:miR396, biological replicate 1

tag: tissue


title: Sir3_alpha_factor_input

city: Fukui

first: Kay

last: Taniguchi

state: Fukui

address: 3-9-1, Bunkyo

institute: University of Fukui

hyb_protocol: Each hybridization mixutre contains the end-labbeled DNA, 50 pM Control Oligonucleotide B2 (affymetrix), 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml Acetylated BSA, 1X Hybridization Buffer. 2X hybridization Buffer was prepared as described in affymetrix Chromatin Immunoprecipitation Assay Protocol. Following denaturation at 99 ºC for 5 mins, cooling at 45 ºC for 5 min, and spin down, 200 µl of the hybridization mixture was hybridized at 45 ºC for 16 hrs using a hybridization oven 640 (affymetrix).

scan_protocol: Fluidics station 400 protocol EukGE-WS2v5 (affymetrix) was performed to wash and stain arrays. The arrays were scanned on GeneChip Scanner 3000 7G (affymetrix).

data_processing: ChIP-on-chip data was scanned using TAS (Tiling Analysis Software, Affymetrix) and IGB (Integrated Genome Browser)

source_name: Input DNA from alpha factor treated cells

label_protocol: The amplified DNA was digested with Dnase I to a mean size of 100 bp. The fragments were end-labelled with biotin-11-ddATP by terminal transferase.

extract_protocol: Immunoprecipitated DNA and Input DNA were amplified by random-priming, fragmented with DNase I, and end-labeled with biotin-ddATP as described elsewhere (Kugou et al, 2009).

tag: mating type

value: a

tag: strain background

tag: culture

value: G1 arrested cells

tag: antibody


title: 35S:miR396, biological replicate 2

tag: genotype/variation


title: Control 4hrs_1

tag: strain

value: Muta Mouse

tag: ID

tag: gender

value: male

tag: manufacturer


title: Sir3_alpha_factor

source_name: Sir3 ChIP DNA from alpha factor treated cells

value: anti-Myc monoclonal


title: Striatum deletion carrier, A888_33_S7

source_name: Striatum, deletion carrier

tag: strain/background

value: carrier of 16p11.2 deletion

tag: developmental stage

value: adult


title: Sir3_log_phase_input

source_name: Input DNA from log phase cells

value: log phase cells


title: Cerebellum wildtype, A888_28_C20

source_name: Cerebellum, wildtype

value: wildtype

value: cerebellum


title: Mid Dose 24hrs_1

value: spleen

value: Agilent Technologies


title: WT, biological replicate 3

tag: organ

value: root

value: microdissected meristems

value: WT

tag: age

value: 7 days after sowing


title: Cerebellum wildtype, A888_26_C25


title: Low Dose 24hrs_1


title: WT, biological replicate 2


title: Control 24hrs_1

source_name: Control 24hrs


title: WT, biological replicate 1


title: Hippocampus duplication carrier, A888_23_H47

source_name: Hippocampus, duplication carrier

value: carrier of 16p11.2 duplication

value: hippocampus


title: Cerebellum duplication carrier, A888_27_C45

source_name: Cerebellum, duplication carrier


title: CD4 T cell HFD d30 replicate 5

city: Toulouse

first: Lucile

last: Garidou

address: 1 Avenue J. Poulhes

institute: INSERM

description: Gene expression after 30 days of high fat diet diet

hyb_protocol: The Cy3-labeled cDNA were hybridized overnight (17hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarray 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray scanner System (Agilent technologies).

data_processing: The Agilent Feature Extraction Software was used to read and process the microarray image files. The software determines features intensities, reject outliers and calculate statistical confidences.

source_name: CD4 T cell HFD d30

label_protocol: 250 ng of cDNA was used as template for Cy3 labelling which was performed according to Myltenyi undisclosed protocol.

extract_protocol: Leukocytes were collected into SuperAmp lysis bufferTM and Super Amp RNA amplification was performed according to Miltenyi Biotec's undisclosed procedure.

treatment_protocol: Leukocytes from the lamina propria ofthe small intestine were isolated. CD4 T cells were sorted by flow cytometry.

value: small intestine

tag: cell type

value: lamina propria CD4 lymphocytes


title: CD4 T cell HFD d30 replicate 3

value: male


title: Sir3_log_phase

source_name: Sir3 ChIP DNA from log phase cells

value: a

value: anti-Myc monoclonal


title: Hippocampus duplication carrier, A888_15_H21

value: adult


title: Striatum deletion carrier, A888_21_S23

value: carrier of 16p11.2 deletion

value: striatum


title: CD4 T cell HFD d30 replicate 1


title: CD4 T cell HFD d30 replicate 4


title: Hippocampus wildtype, A888_16_H17

source_name: Hippocampus, wildtype

value: wildtype


title: CD4 T cell HFD d30 replicate 2


title: Hippocampus wildtype, A888_14_H29


title: Striatum wildtype, A888_22_S25


title: CD4 T cell HFD d10 replicate 4

description: Gene expression after 10 days of high fat diet diet

source_name: CD4 T cell HFD d10


title: CD4 T cell HFD d10 replicate 3