title: treatment cultivar 4 vs control cultivar 1 replicate 3

city: Dublin

first: Mauro

last: Di Fenza

address: Belfield

country: Ireland

institute: University College Dublin

description: Biological replicate 3 of 3. Treatment cultivar 4 was hybrized with the control cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

hyb_protocol: Hybridization was carried out according to a direct comparative loop design

scan_protocol: Image acquisition was performed with a GenePix® scanner and quantified with the in-built software

data_processing:
Data were background corrected with the minimum method, print-tip lowess (within-array) normalized and scaled (between-array) from log2 of processed red signal/processed green signal
Quality check was performed with the MapMan Robin software. Data were processed and analysed with the web-based application CarmaWeb
Data Analysis: The normalized intensities within an array and between replicates were averaged to one single value per gene. Differentially expressed genes were determined with the limma paired moderate t-test. Adjusted p-values were generated according to the Benjamini and Hochberg (BH) method.

organism: Zea mays

source_name: Seedlings grown in climate chambers

label_protocol: RNA samples were labelled with Cy3/Cy5 fluorophores by the manufacturer

growth_protocol: In growth chambers: Control (18°C/16h, 12°C/6h, dark) - Cold treatment (12°C/16h, 6°C/8h, dark)

extract_protocol: Total RNA was extraced from roots with a Qiagen Rneasy© Plant Mini Kit

tag: variety

value: Codisco

tag: treatment

value: cold-treated

value: primary root

value: 8 days post-germination

value: Fergus

value: control


title: Valpha14 tg stage 1 NKT, biological replicate 2

status: Public on May 24 2016

type: RNA

city: Chicago

first: Aiping

last: Mao

state: IL

address: 929 East 57th street

department: Pathology

country: USA

institute: University of Chicago

description:
NKT st1 2
thymic stage 1 NKT from pooled Valpha14 TCR tg mice

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize the labeled DNA to Mouse Genome 430 2.0 arrays

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: RMA normalization was performed using Expression Console

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Valpha14 tg stage 1 NKT

label_protocol: The WT-Ovation Pico RNA Amplification System (NuGEN Technologies) was used to generate amplified single-stranded cDNA that was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies)

growth_protocol: Mouse thymus from C57BL/6J background

extract_protocol: RNA was extracted from FACS-sorted lymphocytes using TRIzol (Thermo Fisher Scientific) followed by Rneasy Mini Kit (Qiagen) column purification

treatment_protocol: Not applicable

tag: strain background

tag: age

value: 4-6 weeks

tag: genotype/variation

value: Valpha14 tg

tag: tissue

value: thymus

tag: cell type

value: FACS-sorted stage 1 NKT (CD1d tetramer+ CD24low CD44- NK1.1-)


title: PLZF-deficient Luxoid Valpha14 tg stage 1 NKT, biological replicate 1

description:
LuxNKT st1 1
thymic stage 1 NKT from pooled PLZF-deficient Luxoid Valpha14 TCR tg mice

value: Luxoid Valpha14 tg


title: DLBCL Patient No.17, lymph node sample

type: genomic

city: Shanghai

first: Fan

last: YANG

address: 197, Rui Jin Er Road

country: China

institute: Shanghai Institute of Hematology

description: Genomic DNA extracted from lymph node tissue was genotyped using Human610W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Regions were determined based on the Log R Ratio (LRR) of the signal intensity and B allele frequency (BAF) of genotyping call using platform of GenomeStudio V2011.1 with CnvPartition 3.1.6 (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: lymph node 17, at diagnosis

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA was extracted using Wizard Genomic DNA Purificaiton Kit (Promega, WI, USA) according to the manufacturer's protocol.

tag: tumor

value: Diffuse large B cell lymphoma

tag: Sex

value: Female


title: PMM rep3 [array]

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

hyb_protocol: Fragmentation was carried out by incubation at 60 °C for 30 min in a fragmentation buffer (Agilent  Technologies), and the process was stopped by the addition of an equal volume of hybridization  buffer (Agilent Technologies). The fragmented target was applied to an Agilent Pig Gene  Expression Oligo Microarray (Version 2). Hybridization was carried out at 60 °C for 17 h in a  hybridization oven (Robbins Scientific).

scan_protocol: The hybridized single channel array was scanned with an  Agilent microarray scanner. The TIFF image generated was loaded into Feature Extraction  Software (Agilent Technologies) for feature data extraction

data_processing:
Data analysis was performed with MultiExperiment Viewer
In order to identify differentially expressed (DE) mRNAs (P < 0.01) for the clustering analysis,  we used one way ANOVA for comparisons of more than two groups or Student’s t-test for two  groups comparisons, with each group corresponding to one of the seven DMR types. Resulting P  values of above tests were corrected with adjusted Bonferroni method (FDR < 0.01, 1,000  permutations)

organism: Sus scrofa

source_name: psoas major

label_protocol: The labeling procedure was carried out using an RNA Fluorescent Linear Amplification Kit (Agilent Technologies). The sample was labeled with Cy3 dye only.

growth_protocol: Three female Landrace pigs, no direct and collateral blood relationship within the last 3 generations, were uesd in this study. All pigs were housed in some environment and fed twice a day with the some diet from weaning (28-day-old) to slaughter (210-day-old). The diets formulas meet the National Research Council (NRC 1998) recommendations for the different growth phase. During experiment preiods, the animals were allowed access to feed and water ad libitum and lived under the same normal conditions

extract_protocol: Total RNA was extracted from adipose tissues using TRIzol (Invitrogen) and further purified with RNeasy columns (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: When being slaughtered, the pigs were kept off feed but given free access to water for 24 h, and then electrically stunned, exsanguinated, scalded and rinsed. Samples were obtained from the intermediate section of the longissimus dorsi and psoas major immediately after exsanguination, and rapidly frozen in liquid nitrogen for sequencing analysis.

tag: breed

value: Landrace

tag: gender

value: female

value: 210 days old

value: psoas major muscle


title: Valpha14 tg stage 1 NKT, biological replicate 1

description:
NKT st1 1
thymic stage 1 NKT from pooled Valpha14 TCR tg mice


title: C57BL/6J (8-week 4NQO 100ug/ml treated) Tongue replicate 3

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

hyb_protocol: Hybridization was performed according to the Affymetrix protocols. 12.5 ug of fragmented cRNA was used in a 250-ul hybridization mixture containing herring-sperm DNA (0.1 mg/ml;Promega),plus bacterial and phage cRNA controls to serve as internal controls for hybridization efficiency. Aliquots of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridizaiton Oven 640 (Affymetrix).

scan_protocol: Scaning were performed according to the Affymetrix protocols. Arrays wre scaned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities.

data_processing: Data pre-processing was carried out in R with Bioconductor package biocLite for quality fitering and data normalization.

source_name: Tongue tissue of C57BL/6J mouse

label_protocol: Biotinylated cRNA were generated from cDNAs by in vitro transcription and amplied by using the Biorray T7 RNA polymerase labeling kit (Enzo Diagnostics).

growth_protocol: C57BL/6J mice were given 4NQO (100ug/ml in drink) for 8 weeks; Non-treated control samples were used for comparison.

extract_protocol: Tongues were dissected and snap-frozen for extraction of total RNA. Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, CarIsbad,CA)

value: Adult

tag: strain

value: Tongue


title: PMM rep2 [array]


title: control cultivar 4 vs treatment cultivar 4 replicate 3

description: Biological replicate 3 of 3. Control cultivar 4 was hybrized with the treatment cultivar 4 on the spotted oligo-array as a part of a microarray loop design.

value: Codisco

value: primary root

value: cold-treated


title: UC_1

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic mucosal gene expression data

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 17h at 45°C on Affymetrix human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

source_name: Colonic mucosal biopsy from active UC patient before probiotics intake

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

treatment_protocol: Endoscopically-derived biopsies were immersed in RNAlater® (Applied Biosystems, Lennik, Belgium) and stored at -80°C for RNA isolation

value: colonic mucosa

tag: time point

value: before probiotics intake


title: PMM rep1 [array]


title: LDM rep3 [array]

source_name: longissimus dorsi

value: longissimus dorsi muscle


title: DLBCL Patient No.14, lymph node sample

source_name: lymph node 14, at diagnosis

value: Male


title: treatment cultivar 3 vs control cultivar 4 replicate 3

description: Biological replicate 3 of 3. Treatment cultivar 3 was hybrized with the control cultivar 4 on the spotted oligo-array as a part of a microarray loop design.

value: 8 days post-germination

value: control


title: C57BL/6J (8-week 4NQO 100ug/ml treated) Tongue replicate 1


title: treatment cultivar 2 vs control cultivar 3 replicate 3

description: Biological replicate 3 of 3. Treatment cultivar 2 was hybrized with the control cultivar 3 on the spotted oligo-array as a part of a microarray loop design.

value: Picker


title: C57BL/6J (Negative control) Tongue replicate 3


title: C57BL/6J (8-week 4NQO 100ug/ml treated) Tongue replicate 2


title: LDM rep1 [array]


title: control cultivar 3 vs treatment cultivar 3 replicate 3

description: Biological replicate 3 of 3. Control cultivar 3 was hybrized with the treatment cultivar 3 on the spotted oligo-array as a part of a microarray loop design.


title: DLBCL Patient No.16, lymph node sample

source_name: lymph node 16, at diagnosis

value: Diffuse large B cell lymphoma


title: DLBCL Patient No.12, lymph node sample

source_name: lymph node 12, at diagnosis

value: Female


title: GFP+cell_shEZH2_rep3

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

country: Spain

institute: IBMB

description: Gene expression data from shRNA EZH2 electroporated neural tube cells

hyb_protocol: 3.75 µg of ssDNA were hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: CEL files were generated from DAT files using GCOS software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using Genespring Software. This software uses RMA summarization algorithm to normalize CEL data.

organism: Gallus gallus

source_name: chick embryo spinal cord

label_protocol: 25 ng total RNA was amplified using the Ovation® RNA Amplification System V2 Kit (Nugen; catalog #3100-60) and subsequently labeled using EncoreTM Biotin Module Kit (Nugen; catalog # 4200-12), according to manufacturer's instructions.

growth_protocol: Eggs from White-Leghorn chickens were incubated at 38.5ºC and 70% humidity. Embryos were staged following Hamburger and Hamilton (HH)

extract_protocol: mRNA from GFP positive cells from dissected shRNA-control or shRNA-EZH2 electroporated neural tubes was extracted by TRIZOL (Invitrogen) protocol with 2 µl of pellet paint co-precipitant (Novagene).

treatment_protocol: Chick embryos were electroporated with purified plasmid DNA at 0.25-3 µg/µl in H2O with 50 ng/ml of fast Green. Plasmid DNA was injected into the lumen of HH10, electrodes were placed at both sides of the neural tube and embryos were electroporated by an IntracelDual Pulse (TSS-100) electroporator delivering five 50 ms square pulses of 20-25 V. Electroporated embryos were dissected out 48h after electroporation and trypsinized for 5-10 min in 0.5% Trypsin-EDTA (Sigma). Trypsinization was stopped by 20% horse serum in PBS-0.1% glucose solution. GFP+ cells from cell suspension were sorted by flow cytometry using a MoFlo flow cytometer (DakoCytomation, Fort Collins, CO).

tag: transfection

value: neuroepithelium

value: White-Leghorn


title: C57BL/6J (Negative control) Tongue replicate 2


title: control cultivar 2 vs treatment cultivar 2 replicate 3

description: Biological replicate 3 of 3. Control cultivar 2 was hybrized with the treatment cultivar 2 on the spotted oligo-array as a part of a microarray loop design.


title: DLBCL Patient No.13, lymph node sample

source_name: lymph node 13, at diagnosis


title: GFP+cell_shEZH2_rep2


title: eKCs animal 3

city: Innsbruck

first: Piotr

last: Tymoszuk

state: Tirol

address: Anichstrasse 35

department: University Clinic of Internal Medicine VI

country: Austria

institute: Medical University of Innsbruck

description: Gene expression data from embryonic Kupffer cells

hyb_protocol: Labeled cDNA samples (6 γg/sample) were hybridized at 45°C for 16 h on separate Affymetrix Mouse Gene 2.0 ST Arrays. GeneChips were washed and stained in the GeneChip® 3000 Fluidics Station

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

data_processing: The data were analyzed with CARMAweb 1.5 software. The raw data files are preprocessed using the RMA method

label: Biotin

source_name: FACS-sorted CD45+ CD11b- F4/80+ GFP- tdTomato+ Kupffer cells

label_protocol: 2 ng total RNA per sample was used processed with the Affymetrix GeneChip® WT PICO Reagent Kit according to manufacturer's instructions

extract_protocol: total RNA was extracted with the Rneasy Micro Kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: eKCs (CD45+ CD11b- F4/80+ GFP- tdTomato+) and mKCs (CD45+ CD11b- F4/80+ GFP+ tdTomato-) were FACS-sorted into cooled RLT buffer-containing Eppendorf tubes (50000 cells each) and frozen at -80 degree prior to RNA extraction

tag: strain/background

value: liver

value: Kupffer

tag: genotype

value: CX3CR1-CreERT+/+ Stopfl/fl tdTomato mice

tag: cell markers

tag: kupffer cell derivation

value: embryonic


title: DLBCL Patient No.10, lymph node sample

source_name: lymph node 10, at diagnosis


title: treatment cultivar 1 vs control cultivar 2 replicate 3

description: Biological replicate 3 of 3. Treatment cultivar 1 was hybrized with the control cultivar 2 on the spotted oligo-array as a part of a microarray loop design.

tag: variety

value: Fergus

tag: treatment

value: primary root


title: DLBCL Patient No.15, lymph node sample

source_name: lymph node 15, at diagnosis


title: DLBCL Patient No.8, lymph node sample

source_name: lymph node 8, at diagnosis


title: C57BL/6J (Negative control) Tongue replicate 1

tag: age

value: Adult

value: Tongue


title: DLBCL Patient No.11, lymph node sample

source_name: lymph node 11, at diagnosis


title: control cultivar 1 vs treatment cultivar 1 replicate 3

description: Biological replicate 3 of 3. Control cultivar 1 was hybrized with the treatment cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

source_name: Seedlings grown in climate chambers

value: cold-treated


title: treatment cultivar 4 vs control cultivar 1 replicate 2

description: Biological replicate 2 of 3. Treatment cultivar 4 was hybrized with the control cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

value: Codisco


title: GFP+cell_shEZH2_rep1


title: LDM rep2 [array]

value: Landrace

value: female

value: 210 days old

value: longissimus dorsi muscle


title: GFP+cells_shC_rep2

description: Gene expression data from shRNA control electroporated neural tube cells

value: shRNA-control


title: eKCs animal 2

value: FACS-sorted CD45+ CD11b- F4/80+ GFP- tdTomato+ Kupffer cells


title: mKCs animal 3

description: Gene expression data from monocyte-derived Kupffer cells

source_name: FACS-sorted CD45+ CD11b- F4/80+ GFP+ tdTomato- Kupffer cells

value: monocyte


title: treatment cultivar 3 vs control cultivar 4 replicate 2

description: Biological replicate 2 of 3. Treatment cultivar 3 was hybrized with the control cultivar 4 on the spotted oligo-array as a part of a microarray loop design.

value: 8 days post-germination

value: control


title: GFP+cells_shC_rep1

value: neuroepithelium

value: White-Leghorn


title: H9

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Hybridized to Affymetrix DMET array

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Data were processed using the Affymetrix DMET Console Analysis Software

source_name: WiCell cell line WA09, alias H9

label_protocol: For microarray hybridization, DNA was processed for hybridization to Affymetrix DMET Plus Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: DNA was isolated from cell lines using Qiagen (Valencia, CA) DNeasy blood and tissue kit according to manufacturer's recommendations.

tag: cell line

value: WiCell H9

value: Human embryonic stem cells


title: eKCs animal 1

tag: tissue

value: liver

value: Kupffer

value: CX3CR1-CreERT+/+ Stopfl/fl tdTomato mice

value: embryonic


title: mKCs animal 1

tag: cell type

value: FACS-sorted CD45+ CD11b- F4/80+ GFP+ tdTomato- Kupffer cells


title: control cultivar 3 vs treatment cultivar 3 replicate 2

description: Biological replicate 2 of 3. Control cultivar 3 was hybrized with the treatment cultivar 3 on the spotted oligo-array as a part of a microarray loop design.

value: primary root

value: cold-treated


title: treatment cultivar 2 vs control cultivar 3 replicate 2

description: Biological replicate 2 of 3. Treatment cultivar 2 was hybrized with the control cultivar 3 on the spotted oligo-array as a part of a microarray loop design.

value: Picker


title: DLBCL Patient No.5, lymph node sample

description: Genomic DNA extracted from lymph node tissue was genotyped using Human610W-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: lymph node 5, at diagnosis

tag: tumor

value: Diffuse large B cell lymphoma

value: Male


title: DLBCL Patient No.6, lymph node sample

source_name: lymph node 6, at diagnosis

tag: Sex


title: H7

description: Hybridized to Affymetrix DMET array

source_name: WiCell cell line WA07, alias H7

value: WiCell H7


title: DLBCL Patient No.9, lymph node sample

source_name: lymph node 9, at diagnosis

value: Female


title: control cultivar 2 vs treatment cultivar 2 replicate 2

description: Biological replicate 2 of 3. Control cultivar 2 was hybrized with the treatment cultivar 2 on the spotted oligo-array as a part of a microarray loop design.

value: control

value: 8 days post-germination


title: DLBCL Patient No.4, lymph node sample

source_name: lymph node 4, at diagnosis


title: DLBCL Patient No.3, lymph node sample

source_name: lymph node 3, at diagnosis


title: GFP+cells_shC_rep3

value: shRNA-control

value: neuroepithelium

tag: breed

value: White-Leghorn


title: H14

description: Hybridized to Affymetrix DMET array

source_name: WiCell cell line WA14, alias H14

value: WiCell H14

value: Human embryonic stem cells


title: H1

description: Hybridized to Affymetrix DMET array

source_name: WiCell cell line WA01, alias H1

value: WiCell H1


title: H13

description: Hybridized to Affymetrix DMET array

source_name: WiCell cell line WA13, alias H13

value: WiCell H13


title: DLBCL Patient No.2, lymph node sample

source_name: lymph node 2, at diagnosis


title: control cultivar 1 vs treatment cultivar 1 replicate 2

description: Biological replicate 2 of 3. Control cultivar 1 was hybrized with the treatment cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

value: Fergus


title: DLBCL Patient No.7, lymph node sample

source_name: lymph node 7, at diagnosis


title: treatment cultivar 4 vs control cultivar 1 replicate 1

description: Biological replicate 1 of 3. Treatment cultivar 4 was hybrized with the control cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

value: Codisco

value: primary root


title: treatment cultivar 1 vs control cultivar 2 replicate 2

description: Biological replicate 2 of 3. Treatment cultivar 1 was hybrized with the control cultivar 2 on the spotted oligo-array as a part of a microarray loop design.

value: cold-treated

value: Picker


title: control cultivar 4 vs treatment cultivar 4 replicate 1

description: Biological replicate 1 of 3. Control cultivar 4 was hybrized with the treatment cultivar 4 on the spotted oligo-array as a part of a microarray loop design.


title: mKCs animal 2

value: liver

value: Kupffer

value: CX3CR1-CreERT+/+ Stopfl/fl tdTomato mice

value: FACS-sorted CD45+ CD11b- F4/80+ GFP+ tdTomato- Kupffer cells

value: monocyte


title: treatment cultivar 3 vs control cultivar 4 replicate 1

description: Biological replicate 1 of 3. Treatment cultivar 3 was hybrized with the control cultivar 4 on the spotted oligo-array as a part of a microarray loop design.

value: 8 days post-germination

value: control


title: Saos2 Off vs Ref rep 1

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Saos Off vs Ref replicate 1

hyb_protocol: Tumors and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned using a laser scanner from Agilent Technologies

data_processing: Agilent Feature Extraction Software was used for spot quality filtering and normalization

source_name: Saos2 Off vs Ref

label_protocol: standard Agilent protocol

growth_protocol: All cell lines were maintained in DMEM (Invitrogen) with 10% FCS (Invitrogen), 2mM l-glutamine (Invitrogen), and 100μg/ml penicillin and streptomycin (Invitrogen) at 37°C and 5% CO2

extract_protocol: Genomic DNA was extracted using TRIzol and purified by chloroform extraction and subsequent ethanol precipitation.

treatment_protocol: Tet-ON inducible cell lines were treated with 1μg/ml Doxycycline (Applichem)

tag: sample type

value: Tet OFF cells

value: Reference HG


title: PLZF tg CD4SP, biological replicate 3

description:
PLZF tg CD4SP 3
thymic CD4SP from pooled PLZF transgenic mice

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize the labeled DNA to Mouse Exon 1.0 ST arrays

data_processing:
RMA normalization was performed using Expression Console
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.na31.mm9.probeset.csv

source_name: PLZF transgenic CD4SP

label_protocol: The Ambion WT Expression Kit was used to generate amplified sense-strand cDNA that was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit

tag: strain background

value: 4-6 weeks

value: PLZF transgenic

value: thymus

value: FACS-sorted CD4+ CD8- (CD4SP) lymphocytes


title: control cultivar 4 vs treatment cultivar 4 replicate 2

description: Biological replicate 2 of 3. Control cultivar 4 was hybrized with the treatment cultivar 4 on the spotted oligo-array as a part of a microarray loop design.

value: Codisco


title: Saos2 Off vs Ref rep 2

description: Saos Off vs Ref replicate 2


title: DLBCL Patient No.1, lymph node sample

source_name: lymph node 1, at diagnosis

value: Diffuse large B cell lymphoma

value: Female


title: Saos2 Escape vs Ref rep 2

description: Saos Esc vs Ref replicate 2

source_name: Saos2 Escape vs Ref

value: Tet ON cells


title: PPI-049  BM_last

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description: 1321524; 22940.CEL

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Copy number analysis from the SNP arrays was performed using Partek Genomics Suite (Partek, Inc),

source_name: last tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: panobinostat plus decitabine on the EOT (end of treatment) samples.  Pre-study = none.

tag: subject status

value: myelodysplastic syndromes (MDS) patient

tag: subject id

tag: tissue type

value: bone marrow tumor

tag: time point

value: at the end of treatment


title: control cultivar 3 vs treatment cultivar 3 replicate 1

description: Biological replicate 1 of 3. Control cultivar 3 was hybrized with the treatment cultivar 3 on the spotted oligo-array as a part of a microarray loop design.

source_name: Seedlings grown in climate chambers

value: primary root

value: cold-treated


title: control cultivar 2 vs treatment cultivar 2 replicate 1

description: Biological replicate 1 of 3. Control cultivar 2 was hybrized with the treatment cultivar 2 on the spotted oligo-array as a part of a microarray loop design.

value: Picker

value: 8 days post-germination


title: PPI-049  BM pre-study

description: 1227590; 22939.CEL

source_name: tumor pre-study

value: at pre-study


title: PLZF tg CD4SP, biological replicate 1

description:
PLZF tg CD4SP 1
thymic CD4SP from pooled PLZF transgenic mice

tag: genotype


title: PPI-035  BM_last

description: 1224826; 22938.CEL


title: treatment cultivar 2 vs control cultivar 3 replicate 1

description: Biological replicate 1 of 3. Treatment cultivar 2 was hybrized with the control cultivar 3 on the spotted oligo-array as a part of a microarray loop design.

value: control


title: PLZF tg CD4SP, biological replicate 2

description:
PLZF tg CD4SP 2
thymic CD4SP from pooled PLZF transgenic mice

value: 4-6 weeks


title: Saos2 Escape vs Ref rep 1

description: Saos Esc vs Ref replicate 1

value: Reference HG


title: WT CD4SP, biological replicate 1

description:
WT CD4SP 1
thymic CD4SP from pooled wiildtype mice

source_name: wild-type CD4SP

value: wild type

value: thymus


title: control cultivar 1 vs treatment cultivar 1 replicate 1

description: Biological replicate 1 of 3. Control cultivar 1 was hybrized with the treatment cultivar 1 on the spotted oligo-array as a part of a microarray loop design.

value: Fergus


title: PPI-035  BM pre-study

description: 1224813; 22937.CEL


title: WT CD4SP, biological replicate 2

description:
WT CD4SP 2
thymic CD4SP from pooled wiildtype mice

value: FACS-sorted CD4+ CD8- (CD4SP) lymphocytes


title: treatment cultivar 1 vs control cultivar 2 replicate 1

description: Biological replicate 1 of 3. Treatment cultivar 1 was hybrized with the control cultivar 2 on the spotted oligo-array as a part of a microarray loop design.


title: PPI-031  BM_last

description: 1224805; 22936.CEL


title: Reactive Hyperplasia Patient No.8, lymph node sample

description: Genomic DNA extracted from lymph node tissue was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: lymph node 53, at diagnosis

value: Reactive hyperplasia

value: Male


title: Subject 10 AE+RE

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Skeletal muscle after resistance  and aerobic exericse, Subject 10

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HuGene-2_1-st array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the 'oligo' package (Bioconductor project).

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 10

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

extract_protocol: Biopsies were obtained from the vastus lateralis muscle using the Bergström needle technique. The biopsies were immediately stored in liquid nitrogen until processing. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Vastus lateralis

value: Resistance  and aerobic exericse

tag: gender

tag: subject

value: Subject 10


title: PPI-031  normal

description: 1107078; 22934.CEL

source_name: skin as normal

value: myelodysplastic syndromes (MDS) patient

value: skin as normal


title: PPI-035  normal

description: 1114602; 22933.CEL


title: Subject 10 RE

description: Skeletal muscle after resistance exercise, Subject 10

source_name: Human Vastus lateralis after resistance exercise, Subject 10

tag: treatment

value: Resistance exercise


title: DLBCL patient WGW with GSTT1 deletion

description: Gene expression data from lymph node of WGW at diagnosis

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 GeneChip® Scanner 3000 and GeneChip® Command Console Software (AGCC)

data_processing: The data were analyzed with Partek Genomics Suite 6.5 under default procedure for background correction on the PM values, quantile normalization across all the chips in the experiment and Log2 transformation

source_name: Lymph node tissue from WGW

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

value: Lymph node

value: Diffuse large B cell lymphoma


title: DLBCL patient WMZ with normal GSTT1

description: Gene expression data from lymph node of WMZ at diagnosis

source_name: Lymph node tissue from WMZ


title: DLBCL patient HYD with GSTT1 deletion

description: Gene expression data from lymph node of HYD at diagnosis

source_name: Lymph node tissue from HYD


title: TCL Patient No.19, lymph node sample

source_name: lymph node 44, at diagnosis

value: T cell lymphoma

value: Female


title: DLBCL patient ZXQ with GSTT1 deletion

description: Gene expression data from lymph node of ZXQ at diagnosis

source_name: Lymph node tissue from ZXQ


title: PPI-049  normal

description: 1227754; 22932.CEL


title: Subject 9 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 9

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 9

value: Subject 9


title: Subject 9 RE

description: Skeletal muscle after resistance exercise, Subject 9

source_name: Human Vastus lateralis after resistance exercise, Subject 9


title: PPI-031  BM pre-study

description: 1224783; 22935.CEL

value: bone marrow tumor

value: at pre-study


title: DLBCL patient BSW with normal GSTT1

description: Gene expression data from lymph node of BSW at diagnosis

source_name: Lymph node tissue from BSW


title: DLBCL patient WBB with normal GSTT1

description: Gene expression data from lymph node of WBB at diagnosis

source_name: Lymph node tissue from WBB


title: PPI-023  BM_last

description: 1321521; 22929.CEL

source_name: last tumor

value: at the end of treatment


title: Subject 7 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 7

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 7

value: Subject 7


title: DLBCL patient SHF with normal GSTT1

description: Gene expression data from lymph node of SHF at diagnosis

source_name: Lymph node tissue from SHF


title: PPI-050  BM_last

description: 1321527; 22931.CEL


title: Subject 8 RE

description: Skeletal muscle after resistance exercise, Subject 8

source_name: Human Vastus lateralis after resistance exercise, Subject 8

value: Subject 8


title: Subject 8 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 8

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 8

value: Male


title: TCL Patient No.17, lymph node sample

source_name: lymph node 42, at diagnosis


title: Subject 7 RE

description: Skeletal muscle after resistance exercise, Subject 7

source_name: Human Vastus lateralis after resistance exercise, Subject 7

value: Vastus lateralis


title: PPI-005  BM pre-study

description: 1222278; 22927.CEL

source_name: tumor pre-study


title: PPI-050  BM pre-study

description: 1227593; 22930.CEL


title: TCL Patient No.18, lymph node sample

source_name: lymph node 43, at diagnosis


title: TCL Patient No.20, lymph node sample

source_name: lymph node 45, at diagnosis


title: PPI-010  BM_last

description: 1321516; 22926.CEL


title: TCL Patient No.15, lymph node sample

source_name: lymph node 40, at diagnosis


title: PPI-005  BM_last

description: 1321517; 22924.CEL


title: PPI-010  normal

description: 1003568; 22925.CEL

source_name: skin as normal


title: Subject 6 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 6

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 6

value: Resistance  and aerobic exericse

value: Subject 6


title: PPI-010  BM pre-study

description: 1222296; 22928.CEL

value: myelodysplastic syndromes (MDS) patient


title: PPI-005  normal

description: 820773; 22923.CEL

value: skin as normal


title: Subject 6 RE

description: Skeletal muscle after resistance exercise, Subject 6

source_name: Human Vastus lateralis after resistance exercise, Subject 6

value: Resistance exercise


title: Subject 5 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 5

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 5

value: Subject 5


title: TCL Patient No.16, lymph node sample

description: Genomic DNA extracted from lymph node tissue was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: lymph node 41, at diagnosis


title: PPI-023  normal

description: 1003556; 22921.CEL


title: PPI-023  BM pre-study

description: 1019878; 22922.CEL


title: DLBCL patient YGA with GSTT1 deletion

description: Gene expression data from lymph node of YGA at diagnosis

source_name: Lymph node tissue from YGA

value: Lymph node

value: Diffuse large B cell lymphoma


title: Subject 4 RE

description: Skeletal muscle after resistance exercise, Subject 4

source_name: Human Vastus lateralis after resistance exercise, Subject 4

value: Subject 4


title: Subject 3 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 3

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 3

value: Subject 3


title: Melanoma Patient I (un-irradiated)

city: Cleveland

first: Nikki

last: Harter

state: Ohio

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

description: Human miRNA Card B

data_processing:
Raw Ct values were obtained by using Applied Biosystems TaqMan SDS v2.4 software. These values were then imported into Applied Biosystems RQ manager or Expression Suite software to quantify the relative expression of miRNAs in each of the un-irradiated and irradiated samples. Both software packages use the comparative CT method (Delta Delta CT), which translates into an RQ value.
RQ values are represented as log2-transformed RQ values, and values > than 1.2 or < than 0.5 are considered significant.

label: Flourescence from FAM/SYBR green

source_name: LCM-derived melanocytes (un-irradiated)

extract_protocol: Total RNA was extracted from the microdissected melanocytes using the RNAqueous-Micro RNA isolation Kit

treatment_protocol: An area (6 mm circle) on the posterior shoulder of each volunteer received an ssUVR (UVA+UVB) dose of 4.0 times their baseline MED, and after 24 h, this spot was again exposed to the same amount of ssUVR. The following day (24 h later), the irradiated site, along with an adjacent non-exposed site, was removed by using a skin biopsy punch. Afterwards, the irradiated and un-irradiated tissues were immediately snap frozen in Tissue-Tek Optimal Cutting Temperature (OCT) embedding medium, and sectioned accordingly.  Laser Capture Microdissection was used to capture a pure population of melanocytes from the respective tissues.  After total RNA extraction, TaqMan human microRNA arrays consisting of cards A and B were used for profiling the microRNAs in the irradiated and un-irradiated tissue samples of both healthy and melanoma patients by using Applied Biosystems 7900 HT Fast Real-Time PCR system.

value: Female

value: LCM-derived melanocytes

tag: diagnosis

value: Melanoma


title: TCL Patient No.13, lymph node sample

source_name: lymph node 38, at diagnosis

value: T cell lymphoma


title: Melanoma Patient I (irradiated)

description: Human miRNA Card B

source_name: LCM-derived melanocytes (irradiated )


title: Subject 3 RE

description: Skeletal muscle after resistance exercise, Subject 3

source_name: Human Vastus lateralis after resistance exercise, Subject 3


title: TCL Patient No.14, lymph node sample

source_name: lymph node 39, at diagnosis


title: Melanoma Patient I (irradiated)

description: Human miRNA Card A

source_name: LCM-derived melanocytes (irradiated)


title: Subject 4 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 4

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 4


title: Melanoma Patient H (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient I (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient H (un-irradiated)

description: Human miRNA Card B


title: TK-10_cordyceps

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: TK-10 renal cells were treated with cordyceps 750 ug/mL for 48hrs

hyb_protocol: Complementary RNA was hybridized using the Agilent`s Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing: The scanned images were analyzed Agilent's GeneSpring Software.

source_name: TK-10 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

growth_protocol: TK-10 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 10 mM nicotinamide, 10 μM troglitazone, and 16.7 μM zinc sulfate. Cells were cultured in humidified incubator at 37℃ and 5% CO2.

extract_protocol: RNA was prepared using theTrizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TK-10 renal cells were treated with 0.1% DMSO, cordyceps 750 ug/mL, and sunitinib 10uM for 48hrs.

tag: cell line

tag: agent

value: cordyceps 750 ug/mL


title: Subject 1 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 1

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 1

tag: tissue

value: Male

value: Subject 1


title: Subject 1 RE

description: Skeletal muscle after resistance exercise, Subject 1

source_name: Human Vastus lateralis after resistance exercise, Subject 1

value: Vastus lateralis


title: TK-10_control

description: TK-10 renal cells were treated with 0.1% DMSO for 48hrs

value: 0.1% DMSO


title: Melanoma Patient H (irradiated)

description: Human miRNA Card B

tag: cell type


title: TK-10_sunitinib

description: TK-10 renal cells were treated with sunitinib 10uM for 48hrs

value: sunitinib 10uM


title: A549_cordyceps

description: A549 lung cancer cells were treated with cordyceps 100 ug/mL for 48hrs

source_name: A549 cells

growth_protocol: A549 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 10 mM nicotinamide, 10 μM troglitazone, and 16.7 μM zinc sulfate. Cells were cultured in humidified incubator at 37℃ and 5% CO2.

treatment_protocol: A549 lung cancer cells were treated with 0.1% DMSO, cordycepin 60 ug/mL, and cordyceps 100 ug/mL for 48hrs.

value: cordyceps 100 ug/mL


title: Subject 2 RE

description: Skeletal muscle after resistance exercise, Subject 2

source_name: Human Vastus lateralis after resistance exercise, Subject 2

value: Resistance exercise

value: Subject 2


title: A549_control

description: A549 lung cancer cells were treated with 0.1% DMSO for 48hrs


title: WholeBlood_HC_2

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: FB-04, New Biological Sciences, Indian Institute of Science

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

description: Gene expression from whole blood of healthy controls

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4858A-039494) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The  data was processed using the limma package in R where it was log2 transformed and quantile normalized.

source_name: Whole Blood_Healthy control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNA was isolated using the Ribopure RNA isolation kit (Ambion Inc.) according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: healthy control

tag: age

value: male

value: whole blood


title: WholeBlood_HC_1


title: WholeBlood_LTB

description: Gene expression from whole blood of latent tuberculosis patient

source_name: Whole Blood_Latent TB patient

value: tuberculosis (TB) patient

value: female


title: Subject 2 AE+RE

description: Skeletal muscle after resistance  and aerobic exericse, Subject 2

source_name: Human Vastus lateralis after resistance  and aerobic exericse, Subject 2

value: Resistance  and aerobic exericse


title: Melanoma Patient G (un-irradiated)

description: Human miRNA Card B

value: Female

value: LCM-derived melanocytes

value: Melanoma


title: KG1a PLZF ChIP-seq

type: SRA

library_source: genomic

data_processing:
Base calling was performed using Illumina software pipeline
ChIP-seq reads were aligned to hg19 genome
Peaks were called using MACS with P value cutoff 1e-5
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS; bed files contained the peaks called by MACS

source_name: KG1a PLZF ChIP-seq

growth_protocol: KG1a cells were grown in IMDM with 20% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and PLZF-DNA complexes were isolated with PLZF antibody.
Libraries were prepared according to Illumina TruSeq DNA Sample Preparation Guide (Part# 15026486).

treatment_protocol: PLZF antibody

tag: chip antibody

value: anti-PLZF (R&D Systems; AF2944)


title: Melanoma Patient G (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient G (irradiated)

description: Human miRNA Card B


title: Melanoma Patient H (irradiated)

description: Human miRNA Card A


title: WholeBlood_TB_3

description: Gene expression from whole blood of Tuberculosis patients at diagnosis

source_name: Whole Blood_Pulmonary TB patient at diagnosis


title: Melanoma Patient F (un-irradiated)

description: Human miRNA Card B

source_name: LCM-derived melanocytes (un-irradiated)


title: Melanoma Patient F (irradiated)

description: Human miRNA Card A


title: Melanoma Patient F (irradiated)

description: Human miRNA Card B


title: TCL Patient No.12, lymph node sample

description: Genomic DNA extracted from lymph node tissue was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: lymph node 37, at diagnosis

tag: tumor

value: T cell lymphoma

tag: Sex


title: WholeBlood_TB_pooled

description: Gene expression of pooled RNA from TB patients 1-4.

source_name: Whole Blood_Pulmonary TB patients at diagnosis

tag: subject status


title: WholeBlood_TB_4


title: WholeBlood_TB_2


title: Melanoma Patient E (un-irradiated)

description: Human miRNA Card B


title: Melanoma Patient E (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient E (irradiated)

description: Human miRNA Card A


title: Melanoma Patient E (irradiated)

description: Human miRNA Card B

source_name: LCM-derived melanocytes (irradiated )


title: Melanoma Patient D (un-irradiated)

description: Human miRNA Card B


title: Melanoma Patient F (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient D (un-irradiated)

description: Human miRNA Card A


title: Melanoma Patient D (irradiated)

description: Human miRNA Card B


title: glc_24h_repl3

city: VTT, Espoo

first: Merja

last: Oja

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre of Finland

description: 24.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo42, one of the three biological replicate cultivations on glucose used in this study.

hyb_protocol: The labelled cDNAs were hybridized to the S. cerevisiae Expr 12x135K Arrays (Roche NimbleGen, USA) according to the instructions of the manufacturer.

scan_protocol: The arrays were scanned using a Roche NimbleGen Microarray scanner according to the instructions of the manufacturer.

data_processing: Data was exported from NimbleScan v2.5 Software as X, Y, and Signal report (.xys files) that contains the fluorescence intensity and position of each feature on the array. Data was processed in R, version 2.10.1, (http://www.r-project.org/) using Bioconductor (http://www.bioconductor.org/). Bioconductor package pdInfoBuilder  was used to create a platform design information package for the Nimblegen array, based on the design file (.ndf). Functions read.xysfiles and rma from the oligo package were used to read in and normalize the data. The rma-normalized data is presented as log2 intensities. Each gene was presented by three probesets on the microarray. The signals from the three probesets were averaged after rma normalization.  To retain the information of the three different probesets, the .ndf file provided by NimbleGen was modified by adding an inidicator b1, b2 or b3 to probeset identifiers based on the container (BLOCK1, BLOCK2, or BLOCK3) the probe was located in. Sample xN46-09 with overall low intensities was deemed to be of too low quality and was removed before normalizing the data with rma, thus this sample is missing from the processed data.

organism: Saccharomyces cerevisiae

source_name: 24.5h time point in 20g/l glucose cultivation

label_protocol: 1 µg of cDNA from each sample was labelled with Cy3 by using a NimbleGen One-Color DNA Labeling Kit (Roche NimbleGen, USA) according to the instructions of the manufacturer.

growth_protocol: The S. cerevisiae strain used in the study was VTT C-10883 originating from VTT C-10880, i.e. [CEN.PK113-1A (URA3. HIS3. LEU2. TRP1. MAL2-8c. SUC2), ura3::XYL1 XYL2, xks1::XKS1]. In this strain the XYL1 and XYL2 genes of S. stipitis were chromosomally integrated into the URA3 locus under PGK1 and ADH1 promoters. The integration cassette was constructed as described earlier (Toivari et al. Metab Eng 3:236-249, 2001). However, VTT C-10883 was cured for its uracil auxotrophy by integrating URA3 next to the XYL1-XYL2 cassette.  For the gene expression level studies, triplicate anaerobic batch cultivations with S. cerevisiae strain VTT C-10883 were performed with either glucose or a mixture of glucose and xylose. All cultivations were carried out in 2 l volume in a Braun Biostat B bioreactor (Sartorius AG, Germany) and monitored with MFCS software (Sartorius AG, Germany). The minimal mineral medium (Verduyn et al. 1992) used in the inocula and the bioreactor cultivations contained 5 g (NH4)2SO4 l-1, 3 g KH2PO4 l-1, 0.5 g MgSO4·7H2O l-1, 15 mg C10H14N2Na2O8·2H2O (EDTA) l-1, 4.5 mg ZnSO4·7H2O l-1, 0.84 mg MnCl2·2H2O l-1, 0.3 mg CoCl2·6H2O l-1, 0.3 mg CuSO4·5H2O l-1, 0.4 mg Na2MoO4·2H2O l-1, 4.5 mg Na2MoO4·2H2O l-1, 3.0 mg FeSO4·7H2O l-1, 1.0 mg H3BO3 l-1, 0.1 mg KI l-1, 0.05 mg biotin l-1, 1.0 mg CaPantothenate l-1, 5 mg nicotinic acid l-1, 25 mg myo-inositol l-1, 1.0 mg thiamine HCl l-1, 1.0 mg pyridoxol HCl l-1, and 0.2 mg p-aminobenzoic acid l-1. In addition the cultivation medium contained in three cultivations 20 g glucose l-1 and in three cultivations 20 g glucose l-1 and 50 g xylose l-1 as the main carbon sources. The inocula were prepared by transferring cells from a YPD-plate to 25 ml mineral medium in 100 ml Erlenmeyer-flasks and incubating on a plate shaker (150 rpm, 30 °C) for 24 h. The inocula were transferred into 75 ml mineral medium in 250 ml Erlenmeyer-flasks and incubated (150 rpm, 30 °C) for 12 h. The inocula were centrifuged (3000 rpm, 4 °C, 5 min) and the cells re-suspended into 40 ml of salt solution containing 5 g (NH4)2SO4 l-1, 3 g KH2PO4 l-1 and 0.5 g MgSO4·7H2O l-1. Initial cell dry weight in the cultivations was 0.15 g/l. All cultivations were kept anaerobic by flushing the head space of the reactor with N2 at a gas flow rate of 0.25 vvm. Agitation was 200 rpm; temperature was 30 °C; pH was kept at 5 with 1 M NaOH.

extract_protocol: Total RNA was extracted from the cells by breaking them using glass beads in Trizol reagent (Gibco BRL, Life Technologies, USA). After the extraction, RNA was precipitated by isopropyl alcohol and the RNA pellet was rinsed with 80 % (v/v) ethanol and resuspended in RNAse-free water. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). 100 µg of RNA from each sample was further purified with RNeasy columns according to the instructions of the manufacturer (Qiagen, USA) and the RNA integrity was verified using a Bioanalyzer 2100 (Agilent, USA). 10 µg of RNA was used for the cDNA synthesis with SuperScript™ Double-Stranded cDNA Synthesis Kit (Invitrogen, USA) according to the instructions of the manufacturer.

treatment_protocol: Samples (15 ml) for gene expression analysis were taken at 3.5 h, 6.5 h, 9.5 h, 12.5 h and 24.5 h after inoculation, from cultivations with strain VTT-C10883, samples were mixed into 35 ml of ice cold 10 mM sodium phosphate buffer and centrifuged immediately (3000 rpm, 4 °C, 10 min). The supernatant was discarded and the cells were frozen in liquid nitrogen before storing at -80 °C until analysis.

tag: time

tag: cultivationname

tag: group

tag: carbonsource

value: 20g/L GLC

tag: oxygen

value: anaerobic


title: glc_09h_repl3

description: 9.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo42, one of the three biological replicate cultivations on glucose used in this study.

source_name: 9.5h time point in 20g/l glucose cultivation


title: Melanoma Patient C (un-irradiated)

description: Human miRNA Card B

tag: gender


title: glc_12h_repl3

description: 12.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo42, one of the three biological replicate cultivations on glucose used in this study.

source_name: 12.5h time point in 20g/l glucose cultivation


title: WholeBlood_TB_1

description: Gene expression from whole blood of tuberculosis patients at diagnosis


title: Melanoma Patient C (un-irradiated)

description: Human miRNA Card A


title: glc_03h_repl3

description: 3.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo42, one of the three biological replicate cultivations on glucose used in this study.

source_name: 3.5h time point in 20g/l glucose cultivation


title: Melanoma Patient C (irradiated)

description: Human miRNA Card B


title: Melanoma Patient C (irradiated)

description: Human miRNA Card A

source_name: LCM-derived melanocytes (irradiated)


title: Melanoma Patient B (un-irradiated)

description: Human miRNA Card B


title: glc_24h_repl2

description: 24.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo41, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient D (irradiated)

description: Human miRNA Card A


title: glc_06h_repl3

description: 6.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo42, one of the three biological replicate cultivations on glucose used in this study.

source_name: 6.5h time point in 20g/l glucose cultivation


title: Melanoma Patient B (un-irradiated)

description: Human miRNA Card A


title: glc_12h_repl2

description: 12.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo41, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient B (irradiated)

description: Human miRNA Card A


title: glc_09h_repl2

description: 9.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo41, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient A (un-irradiated)

description: Human miRNA Card A


title: glc_03h_repl2

description: 3.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo41, one of the three biological replicate cultivations on glucose used in this study.


title: glc_06h_repl2

description: 6.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo41, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient A (irradiated)

description: Human miRNA Card B


title: glc_24h_repl1

description: 24.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo40, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient A (irradiated)

description: Human miRNA Card A


title: Healthy Person H (un-irradiated)

description: Human miRNA Card B

value: Healthy


title: Healthy Person H (un-irradiated)

description: Human miRNA Card A


title: glc_09h_repl1

description: 9.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo40, one of the three biological replicate cultivations on glucose used in this study.


title: Melanoma Patient B (irradiated)

description: Human miRNA Card B


title: Melanoma Patient A (un-irradiated)

description: Human miRNA Card B


title: glc_12h_repl1

description: 12.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo40, one of the three biological replicate cultivations on glucose used in this study.


title: Healthy Person H (irradiated)

description: Human miRNA Card A


title: glc_06h_repl1

description: 6.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo40, one of the three biological replicate cultivations on glucose used in this study.


title: Healthy Person G (un-irradiated)

description: Human miRNA Card B


title: Healthy Person H (irradiated)

description: Human miRNA Card B


title: xyl_24h_repl3

description: 24.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo46, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 24.5h time point in 20g/l glucose and 50g/l xylose cultivation

value: 20g/L GLC and 50g/L XYL


title: Healthy Person G (irradiated)

description: Human miRNA Card B


title: Healthy Person G (irradiated)

description: Human miRNA Card A


title: xyl_09h_repl3

description: 9.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo46, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 9.5h time point in 20g/l glucose and 50g/l xylose cultivation


title: Healthy Person F (un-irradiated)

description: Human miRNA Card B


title: Healthy Person F (un-irradiated)

description: Human miRNA Card A


title: Subject 5 RE

description: Skeletal muscle after resistance exercise, Subject 5

source_name: Human Vastus lateralis after resistance exercise, Subject 5

value: Vastus lateralis

tag: treatment

value: Resistance exercise

value: Male

tag: subject

value: Subject 5


title: Melanoma Patient G (irradiated)

description: Human miRNA Card A

tag: diagnosis


title: Spent_Fe_rep2

first: Anupama

last: Khare

state: NY

address: 1150 St. Nicholas Ave., Room 406

institute: Columbia University

description:
Iron-supplemented spent-media treated cells vs. untreated cells; Replicate 2
Biological Replicate 2 of 2

hyb_protocol: Hybridization was carried out as per the Low Input Quick Amp labeling kit protocol

scan_protocol: Images were quantified using the Agilent Feature Extraction Software (version 9.5) using the GE2-v5_95_Feb07_nospikein protocol

data_processing: probes were filtered using the IsFound, IsFeatNonUnif, IsBGNonUnif, ISFeatPopnOL, and IsBGPopnOL flags, and discarded if the first flag had a value of 0, or any of the others had a value of 1. log10 ratios were averaged for identical probes

organism: Escherichia coli

source_name: E. coli cells, 45% WT spent-media + 100µM ferric citrate

label_protocol: RNA was polyadenylated, and then 300ng of the RNA was labeled using the Low Input Quick Amp labeling kit from Agilent (using Cy3 for the control and Cy5 for the treated sample)

growth_protocol: WT E. coli cells were grown in modified M63 media

extract_protocol: RNA was extracted using the Norgen Total RNA Extraction Kit using the manufacturer's recommendations for bacteria

treatment_protocol: Cells in early log phase were treated with 45% WT P. aeruginosa spent media + 100µM ferric citrate for 20 minutes, and cells were collected at 0 min (control) and 20 min.

source_name: E. coli cells, untreated

value: Untreated


title: Healthy Person F (irradiated)

description: Human miRNA Card B


title: MYC OE

city: New Haven

first: Eriona

last: Hysolli

state: CT

address: 10 Amistad Street

department: Genetics

institute: Yale University

description:
Bisulfite-treated gDNA
SAMPLE 14

hyb_protocol: Bisulfite-converted gDNAs were hybridized according to manufacturer’s protocol using the Illumina’s Infinium HumanMethylation450 BeadChip kit (cat# WG-314-1003)

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: IDAT files were preprocessed and converted into beta value by minfi Bioconductor package

label: Cy3, Cy5

source_name: D551 fibroblast

label_protocol: Standard Illumina labelling protocol

growth_protocol: Detroit 551 (D551) human fibroblasts cells (ATCC CCL-110) were cultured with 10%FBS in DMEM

extract_protocol: PureLink Kit from Life Technologies (cat# K1820-02)

treatment_protocol: Retrovirus or lentivirus are treated for 3 days with MOI2.5-5.0

value: MYC OE for 3 days


title: Healthy Person G (un-irradiated)

description: Human miRNA Card A


title: Healthy Person F (irradiated)

description: Human miRNA Card A


title: xyl_06h_repl3

description: 6.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo46, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 6.5h time point in 20g/l glucose and 50g/l xylose cultivation


title: Healthy Person E (un-irradiated)

description: Human miRNA Card B

source_name: LCM-derived melanocytes (un-irradiated)


title: glc_03h_repl1

description: 3.5h time point of the cultivation with glucose as the carbon source. It is from cultivation Nemo40, one of the three biological replicate cultivations on glucose used in this study.


title: OCT4 OE

description:
Bisulfite-treated gDNA
SAMPLE 11

value: OCT4 OE for 3 days


title: KLF4 OE

description:
Bisulfite-treated gDNA
SAMPLE 13

value: KLF4 OE for 3 days


title: Healthy Person E (irradiated)

description: Human miRNA Card B

value: Female


title: xyl_12h_repl3

description: 12.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo46, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 12.5h time point in 20g/l glucose and 50g/l xylose cultivation


title: xyl_03h_repl3

description: 3.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo46, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 3.5h time point in 20g/l glucose and 50g/l xylose cultivation


title: SOX2 OE

description:
Bisulfite-treated gDNA
SAMPLE 12

value: SOX2 OE for 3 days


title: Spent-media treated cells vs. untreated cells; Replicate 2

description: Biological Replicate 2 of 2

source_name: Spent-media treated cells

label_protocol: RNA was polyadenylated, and then 300ng of the RNA was labeled using the Low Input Quick Amp labeling kit from Agilent (using Cy3 for the control and Cy5 for the treated sample

treatment_protocol: Cells in early log phase were treated with 20% WT P. aeruginosa spent media for 20 minutes, and cells were collected before (control) and after the treatment

value: 20% WT spent-media

source_name: Untreated cells


title: Healthy Person D (un-irradiated)

description: Human miRNA Card B

value: LCM-derived melanocytes


title: xyl_24h_repl2

description: 24.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo45, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: Healthy Person D (un-irradiated)

description: Human miRNA Card A


title: xyl_12h_repl2

description: 12.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo45, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: Tet3 OE

description:
Bisulfite-treated gDNA
SAMPLE 8

value: Tet3 OE for 3 days


title: Spent_Fe_rep1

description:
Iron-supplemented spent-media treated cells vs. untreated cells; Replicate 1
Biological Replicate 1 of 2

value: 45% WT spent-media + 100µM ferric citrate


title: PPI-050  normal

description: 1222211; 22920.CEL

source_name: skin as normal

value: myelodysplastic syndromes (MDS) patient

tag: subject id

tag: tissue type

value: skin as normal


title: Healthy Person D (irradiated)

description: Human miRNA Card B

source_name: LCM-derived melanocytes (irradiated )

tag: cell type

value: Healthy


title: Empty vector

description:
Bisulfite-treated gDNA
SAMPLE 3

value: Empty vector for 3 days


title: Spent-media treated cells vs. untreated cells; Replicate 1

description: Biological Replicate 1 of 2


title: Healthy Person D (irradiated)

description: Human miRNA Card A


title: 20 ng/ml tacrolimus, biological rep3

city: Hangzhou

first: Qi

last: Ling

state: Zhejiang

address: 79 Qingchun road

department: Suegery

institute: Zhejiang University

description: Gene expression data from HepG2 cells treated with 20 ng/ml tacrolimus (high-dose group) for 24 hr.

hyb_protocol: The procedure was performed according to the manufacturer's instructions

scan_protocol: GeneChips were scanned using the affymetrix GeneChip2 Scanner 3000 7G.

data_processing: Gene-Cloud of Biotechnology Information (https://www.gcbi.com.cn/gclib/html/index) was used to performed microarray data analysis

source_name: HepG2 cells treated with 20 ng/ml tacrolimus for 24 hr

label_protocol: Microarray profiles were obtained using a human Affymetrix GeneChip miRNA 4.0 Array (Affymetrix Technologies, USA) in different concentrations (0, 5, 20 ng/ml) of TAC treated HepG2 cells.

growth_protocol: cells were cultured in DMEM (Life technologies) containing 1.0 g/L of glucose and 10% FBS at 37 °C in a humidified atmosphere of 5% CO2

treatment_protocol: HepG2 cells were treated with 0, 5, 20 ng/ml tacrolimus for 24 hrs and RNA was extracted. The expression of mirnas were compared between low-dose tacrolimus group and control, high-dose tacrolimus and control.

value: liver cancer cells


title: Healthy Person C (un-irradiated)

description: Human miRNA Card B


title: xyl_09h_repl2

description: 9.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo45, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

value: 20g/L GLC and 50g/L XYL

value: anaerobic


title: Healthy Person E (un-irradiated)

description: Human miRNA Card A


title: DNMT3B OE

description:
Bisulfite-treated gDNA
SAMPLE 5

value: DNMT3B OE for 3 days


title: DNMT3A OE

description:
Bisulfite-treated gDNA
SAMPLE 4

value: DNMT3A OE for 3 days


title: OSKM poly OE

description:
Bisulfite-treated gDNA
SAMPLE 10

value: OSKM poly OE for 3 days


title: Ctrl sponge

description:
Bisulfite-treated gDNA
SAMPLE 2

value: Ctrl sponge for 3 days


title: Healthy Person C (un-irradiated)

description: Human miRNA Card A

value: Female


title: 20 ng/ml tacrolimus, biological rep1


title: Healthy Person C (irradiated)

description: Human miRNA Card B


title: TDG OE

description:
Bisulfite-treated gDNA
SAMPLE 9

value: TDG OE for 3 days


title: Healthy Person C (irradiated)

description: Human miRNA Card A

source_name: LCM-derived melanocytes (irradiated)


title: 20 ng/ml tacrolimus, biological rep2


title: Healthy Person B (un-irradiated)

description: Human miRNA Card B


title: xyl_06h_repl2

description: 6.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo45, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: Healthy Person B (un-irradiated)

description: Human miRNA Card A


title: xyl_03h_repl2

description: 3.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo45, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: Tet2 OE

description:
Bisulfite-treated gDNA
SAMPLE 7

value: Tet2 OE for 3 days


title: xyl_24h_repl1

description: 24.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo39, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: xyl_12h_repl1

description: 12.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo39, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: 5 ng/ml tacrolimus, biological rep1

description: Gene expression data from HepG2 cells treated with 5 ng/ml tacrolimus (low-dose group) for 24 hr.

source_name: HepG2 cells treated with 5 ng/ml tacrolimus for 24 hr


title: Healthy Person B (irradiated)

description: Human miRNA Card B

value: LCM-derived melanocytes


title: Healthy Person A (un-irradiated)

description: Human miRNA Card B


title: TET1 OE

description:
Bisulfite-treated gDNA
SAMPLE 6

value: TET1 OE for 3 days


title: 0 ng/ml tacrolimus, biological rep3

description: Gene expression data from HepG2 cells treated with 0 ng/ml tacrolimus (control group) for 24 hr.

source_name: HepG2 cells treated with 0 ng/ml tacrolimus for 24 hr


title: Healthy Person A (irradiated)

description: Human miRNA Card A


title: A549_cordycepin

description: A549 lung cancer cells were treated with cordycepin 60 ug/mL for 48hrs

source_name: A549 cells

tag: cell line

tag: agent

value: cordycepin 60 ug/mL

tag: time point


title: Healthy Person E (irradiated)

description: Human miRNA Card A


title: Healthy Person A (irradiated)

description: Human miRNA Card B


title: miR29a/b/c sponge

description:
genomic DNA
SAMPLE 1

value: miR29a/b/c sponge for 3 days


title: Healthy Person B (irradiated)

description: Human miRNA Card A


title: xyl_09h_repl1

description: 9.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo39, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

source_name: 9.5h time point in 20g/l glucose and 50g/l xylose cultivation


title: xyl_06h_repl1

description: 6.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo39, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.


title: Healthy Person A (un-irradiated)

description: Human miRNA Card A


title: 0 ng/ml tacrolimus, biological rep2


title: 40mM Glucose-HUVEC-24hrs

status: Public on May 23 2016

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

country: Singapore

institute: National University of Singapore

hyb_protocol: Hybridization on miRCURY LNA™ Arrays, using MAUI® hybridization system at 56C for 16-18 hr.

scan_protocol: Hybridization images were scanned and digitized using InnoScan 700 microarray scanner (Innopsys, France).

data_processing: miRNA microarray data were analyzed by subtracting the background signal (B532nm) from the test signal (F532nm).

source_name: 40mM Glucose -24hrs

label_protocol: LNA-modified oligonucleotide (Exiqon, Denmark) probes for human miRNAs annotated in miRBase version 11.0 were used in the microarray analysis. Total RNA (1 µg) was 3′-end –labeled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark).

growth_protocol: Human Umbilical vein endothelial cells (HUVECs) were purchased from ATCC (CRL-1730) and grown in a T75 flask using 5mM glucose Dulbecco’s Modified Eagle Medium DMEM (Thermo Fisher Scientific, MA USA) supplemented with 2mM L-glutamine, 10% fetal bovine serum (FBS) and 1% penicillin (100 IU/ml) and streptomycin (100 µg/ml) (Thermo Fisher Scientific, MA USA) in the presence of 5% CO2 at 37C. Media were changed every 48 hours until the cells reached 80-90% confluence. The cells (between passages 3 to 6) were used and they were seeded at a density of 6 x10^4 cells/well in 24 well plates (Greiner bio-one, Cell star, Austria) and serum starved in 5mM glucose DMEM containing 1% FBS for another 24 hours before treating them glucose.

extract_protocol: After each treatment time interval, the cells in culture were washed with 1x PBS (3x) and lysed using 1ml of TRIzol per 3 wells of 24 well plate. The samples were stored in -80C untill futher analysis. Total RNA (+ miRNAs) was extracted from the cells by using Trizol Reagent (Invitrogen, Life Technologies, CA, USA). The RNA concentration and purity were measured using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del). The ratios of 260/280 were always kept within the range of 1.9 – 2.0 and RNA integrity was observed using denatured 1% agarose gel and 15% polyacrylamide gel electrophoresis.

treatment_protocol: HUVECs grown in the presence of 5mM glucose in DMEM containing 1% FBS were treated with different concentrations of glucose (5, 10, 25 and 40mM) for 6, 12, 24 and 48 hr time intervals.

value: HUVECs

value: glucose

tag: dose

tag: protocol

value: Treatment


title: 40mM Glucose-HUVEC-48hrs

source_name: 40mM Glucose-48hrs

tag: time


title: xyl_03h_repl1

description: 3.5h time point of the cultivation with glucose-xylose mixture as the carbon source. It is from cultivation Nemo39, one of the three biological replicate cultivations on glucose-xylose mixture used in this study.

tag: cultivationname


title: 40mM Glucose-HUVEC-12hrs

source_name: 40mM Glucose-12hrs


title: 5 ng/ml tacrolimus, biological rep2

value: liver cancer cells


title: 10mM Glucose-HUVEC-12hrs

source_name: 10mM Glucose-12hrs


title: 10mM Glucose-HUVEC-6hrs

source_name: 10mM Glucose-6hrs


title: 25mM Glucose-HUVEC-12hrs

source_name: 25mM Glucose-12hrs


title: 25mM Glucose-HUVEC-48hrs

source_name: 25mM Glucose-48hrs


title: 0 ng/ml tacrolimus, biological rep1


title: 40mM Glucose-HUVEC-6hrs

source_name: 40mM Glucose-6hrs


title: 10mM Glucose-HUVEC-24hrs

source_name: 10mM Glucose -24hrs


title: 25mM Glucose-HUVEC-24hrs

source_name: 25mM Glucose -24hrs


title: 10mM Glucose-HUVEC-48hrs

source_name: 10mM Glucose-48hrs


title: 1mM Glucose-HUVEC-24hrs


title: TatHB-METH-3 [methylation]

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol

data_processing:
Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.
-log10 scaled (peak value of NimbleScan Peak value)

source_name: Methylated Genomic DNA

label_protocol: DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.

extract_protocol: DNA was extracted  using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).

value: METH

tag: genotype/variation

value: TatHB

tag: strain

source_name: Total Genomic DNA


title: 1mM Glucose-HUVEC-48hrs


title: 5mM Glucose-HUVEC-12hrs

source_name: 5mM Glucose-12hrs

value: Control


title: 5mM Glucose-HUVEC-24hrs

source_name: 5mM Glucose -24hrs


title: 1mM Glucose-HUVEC-12hrs


title: 0mM Glucose-HUVEC-12hrs

value: control


title: 1mM Glucose-HUVEC-6hrs


title: 0mM Glucose-HUVEC-48hrs


title: TatHB-METH-2 [methylation]


title: 5mM Glucose-HUVEC-48hrs

source_name: 5mM Glucose-48hrs


title: 5mM Glucose-HUVEC-6hrs

source_name: 5mM Glucose-6hrs


title: 0mM Glucose-HUVEC-24hrs


title: TatHB-Saline-3 [methylation]

value: Saline


title: TatHB-METH-1 [methylation]


title: 0mM Glucose-HUVEC-6hrs


title: WT-METH-3 [methylation]

value: WT


title: TatHB-Saline-1 [methylation]


title: WT-METH-2 [methylation]


title: 5 ng/ml tacrolimus, biological rep3

source_name: HepG2 cells treated with 5 ng/ml tacrolimus for 24 hr


title: TatHB-Saline-2 [methylation]


title: WT-Saline-1 [methylation]


title: WT-METH-1 [methylation]


title: WT-Saline-2 [methylation]


title: MCAT-AZT-3 [methylation]

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001) following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.

data_processing:
Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.
.gff files include -log10 scaled peak score.

source_name: Heart, MCAT overexpressing, AZT treated, methylated genomic DNA

extract_protocol: DNA was extracted using a MagNAPure DNA Extraction System (Roche), quantitated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA were amplified using whole genome amplification (Sigma-Aldrich).

tag: strain/background

value: MCAT overexpressing

tag: tissue

value: left ventricle

value: AZT

tag: sample type

value: methylated genomic DNA

source_name: Heart, MCAT overexpressing, AZT treated, total genomic DNA

value: total genomic DNA


title: MCAT-AZT-4 [methylation]

tag: treatment


title: MCAT-AZT-1 [methylation]


title: WT-AZT-4 [methylation]

source_name: Heart, WT, AZT treated, methylated genomic DNA

value: wild-type

source_name: Heart, WT, AZT treated, total genomic DNA


title: MCAT-Veh-1 [methylation]

source_name: Heart, MCAT overexpressing, vehicle treated, methylated genomic DNA

value: vehicle (1%CMC)

source_name: Heart, MCAT overexpressing, vehicle treated, total genomic DNA


title: MCAT-Veh-3 [methylation]


title: WT-AZT-3 [methylation]


title: MCAT-Veh-4 [methylation]


title: WT-AZT-1 [methylation]


title: WT-Veh-4 [methylation]

source_name: Heart, WT, vehicle treated, methylated genomic DNA

source_name: Heart, WT, vehicle treated, total genomic DNA


title: WT-AZT-2 [methylation]


title: WT-Veh-2 [methylation]


title: WT-Veh-1 [methylation]


title: WT-Veh-3 [methylation]


title: WT-Saline-3 [methylation]


title: MCAT-AZT-2 [methylation]


title: 25mM Glucose-HUVEC-6hrs

source_name: 25mM Glucose-6hrs

value: HUVECs


title: 16_weeks_tenotomy_rat_162_SOL_R

city: Ankara

first: Cetin

last: Kocaefe

state: Sihhiye

address: Hacettepe University School of Medicine

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University School of Medicine

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. Standard Affymetrix 3'IVT protocol for RAE_230 2.0 chips was pursued

scan_protocol: Standard Affymetrix scan protocol for RGU_230 2.0 chips using Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Affymetrix .cel files were analysed using Affymetrix microarray software suite 5.0 (MAS 5.0) using default analysis setting and global scaling as normalization method. ExpressionStat affymetrix-algorithm-version = 5.0
Algorithm: ExpressionStat 5.0

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 12 hr day/night + ad libitum accesto food and water

extract_protocol: Standard RNA extraction using Trizol reagent

treatment_protocol: Muscle samples were freshly homogenized in trisol using a bead beater and stored at -80 prior to extraction

value: Sprague Dawley

tag: gender

value: male

tag: sample group

value: long-term immobilized

tag: immobilization duration

value: 16 weeks

value: skeletal muscle


title: Organoid DNMT1 KD

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: DNMT1 knockdown

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Polyp of ApcMin mice

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Organoid culture was performed in matrigel with serum-free medium including EGF and Noggin.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: Tumor organoids were treated with 1 uM of 5-Aza-CdR. Lentivirus-mediated knockdown of DNMT1 was performed in tumor organoids.

value: ApcMin


title: DcpS-inh (D156844)_3

city: Lausanne

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: SAMPLE 7

hyb_protocol: Labelled samples hybridized at 55 °C for 20 h at 20 rpm.  Array has design ID 046064.

scan_protocol: After washing, the fluorescent signal intensities were detected on a PowerScanner (Tecan, Mannedorf, Switzerland) and analyzed with Array-Pro Analyzer software (MediaCybernetics, Bethesda, MD, USA). To evaluate the efficiency of labeling and hybridization, Agilent microRNA Spike-In were added in the appropriate steps.

data_processing: Arrays are Agilent DesignID 046064. Raw intensity text files were processed using limma. Briefly, we first subtracted the background using the "subtract" method. We then normalized and log2 transformed the background subtracted data using quantile normalization. Finally, since there are multiple times the same probe on the array, we averaged the signals of the indentical probes. The log2 quantile normalized data are available on the series record.

source_name: HEK293T DcpS-inh treated cells replicate 3

label_protocol: Briefly, 100 ng of total RNA were treated with alkaline calf intestine phosphatase and labeled with Cyanine 3-pCp.

growth_protocol: HEK293T cells were grown in Dulbecco modified Eagle medium (DMEM) supplemented with 10% of fetal bovine serum (FBS) and 5% of antibiotics at 37°C in 5% CO2. 3x10^5 cells were seeded in 6-well plates. Medium was changed at Day 2 with the addition of 500 nM final of DcpS-inh D156844 or DMSO. 18h after treatment cells were harvested and RNA or proteins were extracted.

extract_protocol: Total RNA, including miRNAs, was isolated with Absolutely RNA miRNA Kit (Agilent Technologies) according to the manufacturer’s protocol.


title: 4_weeks_tenotomy_rat_42_SOL_R

value: short-term immobilized

value: 4 weeks


title: control_rat_61_SOL_L

value: control

value: none (control)


title: 1_week_tenotomy_rat_13_SOL_R

value: 1 week


title: 3_weeks_tenotomy_rat_32_SOL_R

value: 3 weeks


title: control_rat_161_SOL_L


title: control_rat_163_SOL_L


title: 22_weeks_tenotomy_rat_221_SOL_R

value: 22 weeks


title: Id2WT Tfh Day 7 biological rep2

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 GIlman Drive.

department: Biological Sciences

institute: University of California, San Diego

description:
Gene expression data from Id2WT Tfh cells 7 days post LCMV infection
SM.WTSLAMlo.D7#2

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: RMA, Genepattern, The Sample Data table contains raw expression data post RMA, excluding unlabeled probes or duplicate probes (that showed identical value).

source_name: Splenocytes 7 days post LCMV

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

treatment_protocol: 1x10^4 Id2WT or Id2KO SMARTA CD4+ T cells were transferred into congenically distinct hosts and infected with LCMV the next day. On day 7 of infection, cells were purified by FACS Aria sorting.

tag: age

value: 10 weeks

tag: infection

value: LCMV

tag: cell type

value: splenocyte

tag: cell subtype

value: Tfh


title: Id2WT Th1 Day 7 biological rep2

description:
Gene expression data from Id2WT Th1 cells 7 days post LCMV infection
SM.WTSLAMhi.D7#2


title: Organoid 5AZA control

description: control for 5AZA treatment


title: DcpS-inh (D156844)_4

description: SAMPLE 8

source_name: HEK293T DcpS-inh treated cells replicate 4

tag: cell line


title: 6_weeks_tenotomy_rat_61_SOL_R

value: Sprague Dawley

value: 6 weeks


title: control_rat_62_SOL_L

value: male


title: Id2KO Tfh Day 7 biological rep3

description:
Gene expression data from Id2KO Tfh cells 7 days post LCMV infection
SM.Id2KOSLAMlo.D7#3


title: Organoid 5AZA treatment

description: 5AZA treatment


title: Organoid Mock control

description: control for DNMT1 knockdown


title: Id2KO Th1 Day 7 biological rep2

description:
Gene expression data from Id2KO Th1 cells 7 days post LCMV infection
SM.Id2KOSLAMhi.D7#2


title: Id2WT Tfh Day 7 biological rep3

description:
Gene expression data from Id2WT Tfh cells 7 days post LCMV infection
SM.WTSLAMlo.D7#3


title: Id2WT Th1 Day 7 biological rep3

description:
Gene expression data from Id2WT Th1 cells 7 days post LCMV infection
SM.WTSLAMhi.D7#3


title: MCAT-Veh-2 [methylation]

value: MCAT overexpressing

value: left ventricle

value: vehicle (1%CMC)

value: methylated genomic DNA

value: total genomic DNA


title: 2_weeks_tenotomy_rat_25_SOL_R

value: short-term immobilized

value: 2 weeks

value: skeletal muscle


title: 2_weeks_tenotomy_rat_27_SOL_R


title: 1_week_tenotomy_rat_12_SOL_R

value: 1 week


title: Id2KO Tfh Day 7 biological rep2

description:
Gene expression data from Id2KO Tfh cells 7 days post LCMV infection
SM.Id2KOSLAMlo.D7#2


title: 6_weeks_tenotomy_rat_62_SOL_R

value: long-term immobilized


title: DcpS-inh (D156844)_1

description: SAMPLE 5

source_name: HEK293T DcpS-inh treated cells replicate 1


title: DcpS-inh (D156844)_2

description: SAMPLE 6

source_name: HEK293T DcpS-inh treated cells replicate 2


title: DMSO_4

description: SAMPLE 4

source_name: HEK293T DMSO treated cells replicate 4


title: Id2KO Th1 Day 7 biological rep3

description:
Gene expression data from Id2KO Th1 cells 7 days post LCMV infection
SM.Id2KOSLAMhi.D7#3

value: 10 weeks


title: DMSO_3

description: SAMPLE 3

source_name: HEK293T DMSO treated cells replicate 3


title: DMSO_2

description: SAMPLE 2

source_name: HEK293T DMSO treated cells replicate 2


title: DMSO_1

description: SAMPLE 1

source_name: HEK293T DMSO treated cells replicate 1


title: WT-METH-4 [gene expression]

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: Total RNA from WT-METH Left Ventricle

label_protocol: DNA labeling was completed using NimbleGen labeling Kit following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies).  cDNA quality was determined using a Spectramax 190 plate reader ( ) for A260 and A280 absorbance determination along with gel electrophoresis.

value: WT

value: METH


title: Posterior-High-2

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

description:
Post.High_2
Delaminating cell population (RFP-positive, MMP1-GFP-positive).

hyb_protocol: Affymetrix Drosophila Genome 2.0 arrays were hybridized with 8 ug of labeled dsDNA, washed, stained and scanned according to the protocol described in 3’IVT express kit User Manual.

scan_protocol: Arrays scanning and CEL files generation were performed using an Affymetrix GeneChip Scanner 3000.

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package.

organism: Drosophila melanogaster

source_name: Wing discs, delaminating cell population

label_protocol: Amplified cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Drosophila larvae expressing p35, a dsRNA form of asp and RFP under the control of the en-gal4 driver and carrying an MMP1-GFP reporter construct were grown until ~8 days old.

extract_protocol: RNA extraction and cDNA amplification were performed as described in Gonzalez-Roca E et al. (Plos One, 2010). cDNA library was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2).

treatment_protocol: Drosophila wing imaginal discs were dissected, dissociated with trypsin and cells were sorted by FACS.

tag: developmental stage

value: 8-day-old larvae

value: wing imaginal discs

tag: cell population

value: RFP-positive, MMP1-GFP-positive


title: TatHB-METH-1 [gene expression]

department: Pathology

source_name: Total RNA from TatHB-METH Left Ventricle

value: TatHB


title: Posterior-Low-1

description:
Post.Low_1
Cells from the posterior compartment (RFP-positive, MMP1-GFP-negative).

source_name: Wing discs, posterior compartment cells

value: RFP-positive, MMP1-GFP-negative


title: Anterior-3

description:
Ant_3
Cells from the anterior compartment (RFP-negative, MMP1-GFP-negative).

source_name: Wing discs, anterior compartment cells

value: RFP-negative, MMP1-GFP-negative


title: Anterior-2

description:
Ant_2
Cells from the anterior compartment (RFP-negative, MMP1-GFP-negative).


title: Anterior-1

description:
Ant_1
Cells from the anterior compartment (RFP-negative, MMP1-GFP-negative).


title: Posterior-High-1

description:
Post.High_1
Delaminating cell population (RFP-positive, MMP1-GFP-positive).


title: Posterior-High-3

description:
Post.High_3
Delaminating cell population (RFP-positive, MMP1-GFP-positive).


title: TatHB-METH-2 [gene expression]


title: Posterior-Low-2

description:
Post.Low_2
Cells from the posterior compartment (RFP-positive, MMP1-GFP-negative).


title: Posterior-Low-3

description:
Post.Low_3
Cells from the posterior compartment (RFP-positive, MMP1-GFP-negative).


title: TatHB-Saline-2 [gene expression]

source_name: Total RNA from TatHB-Saline Left Ventricle

value: Saline


title: TatHB-Saline-3 [gene expression]


title: WT-METH-3 [gene expression]


title: ALDH high QGP1 cells

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description: Gene expression profile of ALDH high QGP1 cells

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: Human pNET cell line QGP1

label_protocol: aRNA was prepared using 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 7.0.

treatment_protocol: ALDH high QGP1 cells were obtained by FACS sorting


title: TatHB-METH-4 [gene expression]


title: TatHB-Saline-1 [gene expression]


title: WT-METH-2 [gene expression]


title: TatHB-METH-3 [gene expression]


title: TatHB-Saline-4 [gene expression]


title: Control QGP1 cells

description: Gene expression profile of Control QGP1 cells


title: WT-METH-1 [gene expression]


title: MCAT-AZT-2 [expression]

source_name: Heart, MCAT overexpressing, AZT treated

label_protocol: DNA labeling was completed using NimbleGen labeling Kit (Cat # 06370438001) following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies). cDNA quality was determined using a Spectramax 190 plate reader for A260 and A280 absorbance determination along with gel electrophoresis.

treatment_protocol: All heart samples were obtained fresh. Each sample was quickly flash frozen in liquid nitrogen and stored at -80°C until needed.

value: MCAT transgenic

value: left ventricle

value: AZT


title: MCAT-AZT-1 [expression]


title: MCAT-AZT-4 [expression]


title: MCAT-Veh-3 [expression]

source_name: Heart, MCAT overexpressing, Vehicle treated

value: vehicle (1%CMC)


title: MCAT-AZT-3 [expression]


title: MCAT-Veh-2 [expression]


title: WT-Saline-3 [gene expression]

source_name: Total RNA from WT-Saline Left Ventricle


title: WT-Saline-1 [gene expression]


title: MCAT-Veh-1 [expression]


title: colo205-culture_2

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: SAMPLE 23

hyb_protocol: Standard Illumina hybridization protocol. Hybridization performed in AROS (Denmark) http://arosab.com/services/microarrays/gene-expression/

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized using lumi library in R 3.1.1, separately for xenograft samples (1-21) and cell culture samples (22-24)

source_name: colo205 cell line (control)

label_protocol: Standard Illumina labeling protocol

extract_protocol: Following extraction tumors were preserved in RNAlater (Qiagen) and stored at -80°C. A scoop of a tumor (~25mg) was homogenized with pestle under liquid nitrogen and immediately processed according to RNeasy Mini Kit protocol (Qiagen). RNA concentration was measured with NanoDrop spectrophotometer and stored at -80°C. Prior to microarray analyses the quality of the RNA samples was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

tag: protocol

value: cell culture


title: miR-211 overexpressed MCF7

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

institute: dongguk unversity

description:
SAMPLE 6
mammary gland, breast; derived from metastatic site: pleural

hyb_protocol: Following fragmentation, 0.75ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Genomestudio v2011.1 (Gene Expresion Module v1.9.0)

source_name: miR-211 overexpressed MCF7

label_protocol: Biotinylated cRNA were prepared from 0.55ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

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

value: female

value: breast

value: breast cancer cell line MCF-7

value: epithelial

tag: genotype/variation

value: miR-211 overexpression


title: WT-AZT-3 [expression]

source_name: Heart, WT, AZT treated

value: wild-type


title: WT-Saline-4 [gene expression]

value: WT

tag: strain


title: colo205-culture_1

description: SAMPLE 22


title: colo205-culture_3

description: SAMPLE 24