title: WT;TLS+_+ biological rep 3

description: Gene expression data from the striatum of non-transgenic mice with normal gene dosage of  p62

source_name: Striatum at 8 weeks

value: mixed background (cross between B6CBAF1 female mice (HD) and C57BL/6J male mice (TLS+/-))

tag: genotype


title: CKF cell line 8 - culture replicate C

status: Public on Feb 12 2017

type: RNA

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Rabbit Agilent Custom Gene Expression Oligo Microarrays (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 042421_D_F_20120731). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Data has been normalized by the median after log transformation (replicated probes signal values have been averaged)

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: ES cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis 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 the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes a DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: CKF ES cell line

tag: dissociation protocol

value: Partial dissociation with collagenase

tag: culture condition

value: 20% KOSR and FGF2


title: WT;TLS+_+ biological rep 2

city: Tokyo

first: Yoshihiro

last: Kino

address: 2-522-1 Noshio, Kiyose

country: Japan

institute: Meiji Pharmaceutical University

hyb_protocol: 5 ug of Fragmented ssDNA were hybridized for 16 hr at 45C on GeneChip Mouse Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed by the RMA algorithm using AltAnalyze software at the default setting.
MoEx-1_0-st-v1.r2.pgf
Mm_gene_extended.mps

label: biotin

organism: Mus musculus

label_protocol: 100ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip® WT Terminal Labeling Kit) to fragment and labelled DNA.

extract_protocol: Samples were dissected and snap-frozen in liquid nitrogen. RNA extraction with Trizol and purification with RNeasy mini kit (Qiagen)

tag: strain


title: Col-0_cd_6_rep3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Transcriptomic profiling of Arabidopsis thaliana mutants in response to combined abiotic stress

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: Scanned on an Agilent scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 12 Software. 75th Percentile Shift Normalization

organism: Arabidopsis thaliana

source_name: leaf tissue_cd_6

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop.

extract_protocol: Trizol-RNA extraction

tag: tissue

value: leaf tissue


title: CKF cell line 8 - culture replicate A


title: CKF cell line 4 - culture replicate B


title: WT;TLS+_- biological rep 3

description: Gene expression data from the striatum of non-transgenic mice with genetic depletion of  p62


title: CKF cell line 4 - culture replicate C


title: AKSgff cell line 62 - culture replicate C

value: AKSgff ES cell line

value: Single cell dissociation with accutase

value: 10% KOSR; 10% FCS


title: AKSgff cell line 62 - culture replicate B


title: OoT2

city: Tarragona

first: Cristina

last: Reguant

state: Tarragona

address: Marcel·lí Domingo 1

department: Biochemistry and Biotechnology

country: Spain

institute: University Rovira i Virgili

description: Oenococcus oeni total RNA from cells after 2 hour after inoculation in wine like medium (12% ethanol v/v)

hyb_protocol: Cy3-labeled DNA was precipitated with 1 volume isopropanol. Hybridization mixture including 2mg labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). 090324_Ooen_exp Nimblegen arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed according to manufacturer's protocol

scan_protocol: Arrays were scanned on a Genepix 4000B scanner

data_processing: Pair reports (raw data) listing the probe  intensities of the arrays were extracted and processed using Nimblescan software v2.6

organism: Oenococcus oeni

source_name: Oenococcus oeni PSU-1

label_protocol: dsDNA was generated from 10 mg RNA following Nimblegen array user's guide protocol. 1mg dsDNA was labeled by Klenow random priming with Cy3 nonamers with Nimblegen One-color DNA labeling kit (cat.# 06370411001) following manufacturer's user's guide

growth_protocol: O. oeni PSU-1 was cultured at 28ºC in MRS broth medium supplemented with L-malic acid (4 g l-1) and fructose (5 g l-1) at pH 5.0.

extract_protocol: Total RNA extractions were performed using the Roche RNeasy kit according to the manufacturer’s instructions (Mannheim, Germany).

treatment_protocol: When cultures reached the late exponential phase (OD600nm ≈ 1,6) they were collected by centrifugation and inoculated in flasks of 5L with wine like medium (2 g/L fructose, 2 g/L tartaric acid, 0.5 g/L citric acid, 0.6 g/L L-malic acid, 5 g/L yeast extract, 0.1 g/L acetic acid, 5 g/L glycerol and 12 % ethanol v/v, it was adjusted to a pH 3.4 with NaOH 1N)


title: WT;TLS+_- biological rep 1


title: OoT1

description: Oenococcus oeni total RNA from cells after 1 hour after inoculation in wine like medium (12% ethanol v/v)


title: OoT8

description: Oenococcus oeni total RNA from cells after 8 hour after inoculation in wine like medium (12% ethanol v/v)


title: OoT6

description: Oenococcus oeni total RNA from cells after 6 hour after inoculation in wine like medium (12% ethanol v/v)


title: OoT4

description: Oenococcus oeni total RNA from cells after 4 hour after inoculation in wine like medium (12% ethanol v/v)


title: OoT0.5

description: Oenococcus oeni total RNA from cells after 0.5 hour after inoculation in wine like medium (12% ethanol v/v)


title: HD;TLS+_+ biological rep 3

description: Gene expression data from the striatum of HD transgenic mice with normal gene dosage of p62


title: OoT0

description: Oenococcus oeni total RNA from cells before inoculation in wine like medium (12% ethanol v/v, pH 3,4)


title: WT;TLS+_+ biological rep 1


title: WT;TLS+_- biological rep 2


title: HD;TLS+_- biological rep 3

description: Gene expression data from the striatum of HD transgenic mice with genetic depletion of p62


title: HD;TLS+_+ biological rep 1


title: HD;TLS+_+ biological rep 2


title: AKSgff cell line 3 - culture replicate B


title: AKSgff cell line 3 - culture replicate C


title: AKSL cell line 8 - culture replicate C

value: AKSL ES cell line

value: 10% KSOR, 10% FCS and LIF


title: AKSgff cell line 62 - culture replicate A


title: HD;TLS+_- biological rep 2


title: PDL60

city: Setagaya-ku

first: Mizuho

last: Sakaki

state: Tokyo

department: Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

hyb_protocol: The labeled RNAs were incubated at 100°C for 5min. Immediately transfer to an ice water for 5min. The treated RNAs were hybridized on the microarray at 55°C for 20hr.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505C.

data_processing: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

organism: Homo sapiens

source_name: TIG3 cells passaging until PDL60

label_protocol: Starting with 100  ng of the isolated RNA for each sample was labeled with cyanine 3 using miRNA Complete Labelling and Hyb Kit (Agilent) according to the manufacturer’s protocols.

extract_protocol: Total RNA was isolated with a ReliaPrep miRNA Cell and Tissue MiniPrep System (Promega) according to the manufacturer’s instructions.

tag: derived cell

tag: cell state

value: proliferating


title: PDL80

source_name: TIG3 cells passaging until PDL80

value: senescence


title: HD;TLS+_- biological rep 1


title: PDL78

source_name: TIG3 cells passaging until PDL78


title: AKSgff cell line 3 - culture replicate A


title: AKSL cell line 8 - culture replicate B


title: PDL44

source_name: TIG3 cells passaging until PDL44


title: AKSL cell line 8 - culture replicate A


title: AKSL cell line 4 - culture replicate C


title: AKSL cell line 4 - culture replicate B


title: AKSL cell line 4 - culture replicate A


title: AKSL cell line 20 - culture replicate C


title: AKSL cell line 20 - culture replicate B


title: Normal_58d_N5_re-analyzed

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Pool of five (5) jaws dissected from normal individuals

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

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5. Normalization procedures were performed using R statistical software. Microarray data were cyclic lowess (CL) normalized across all arrays and CL-normalized data were further adjusted for the known between-experiments batch effects by implementing parametric Combat correction in R. Data are expressed in Log2.

label: Cyanine 3

organism: Dicentrarchus labrax

source_name: 58 days old normal sea bass jaws

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

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: condition

value: Normal jaw

tag: age

value: 58 days

value: jaws


title: Normal_58d_N6


title: MI+433  1

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

country: China

institute: Shanghai University

description: To clarify whether and how miR-433 inhibition could prevent cardiac fibrosis in vivo

hyb_protocol: The purified cRNA were hybridized for 17 hr at 65°C on Agilent-028005 Array.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent).

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis.
Differentially expressed genes were then identified through fold change as well as P value calculated with t-test.

source_name: Heart,  miR-433 antagomir, 21 days post myocardial infarction

label_protocol: Total RNA were reverse transcribed into cDNA, labeled with Cyanine-3-CTP, and then synthesized to cRNA.

growth_protocol: Heart samples were harvested 21 days post myocardial infarction and snap frozen in liquide nitrogen.

extract_protocol: Total RNA were isolated using mirVanaTM RNA Isolation Kit according to the manufacturer's instructions.

value: C57BL/6 mice

value: heart

tag: gender

value: male

value: 8 weeks old


title: MI+433  3


title: OpAP2-3_1

description: Ap2/ERF overexpression lines

hyb_protocol: 1500ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent Tobacco Gene Expression  4x44k Array (AMADID: 021113). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.

organism: Nicotiana tabacum

source_name: seedlings

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Two weeks pot grown under control green house condition

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Control Condition

tag: cultivar

value: Xanthi

value: seedlings


title: Prognatous_58d_P3

description: Pool of five (5) jaws dissected from prognatous individuals

source_name: 58 days old prognatous sea bass jaws

value: Deformed jaw


title: VC2

description: Vector Control


title: MI+nc-7

description: 21 days post ligation of left anterior descending coronary artery (LAD)

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Affymetrix miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing:
Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization for Mm probesets. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

label: Biotin

source_name: Mouse heart, myocardial infarction, 21 days

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Heart tissues were collected and frozen immediately in liquid nitrogen.

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

tag: stress

value: myocardial infarction


title: AKSL cell line 20 - culture replicate A

value: Single cell dissociation with accutase


title: Normal_58d_N4_re-analyzed


title: MI+NC1

source_name: Heart,  scrambled control, 21 days post myocardial infarction


title: MI+433  2


title: Prognatous_58d_P7_re-analyzed


title: VC1

description: Vector Control


title: MI+NC3


title: OpAP2-3_2

description: Ap2/ERF overexpression lines


title: MI+NC2


title: AKSF cell line 19 - culture replicate C

value: AKSF ES cell line

value: 10% KOSR, 10% FCS and FGF2


title: MI+nc-5


title: AKSF cell line 26 - culture replicate A


title: Normal_58d_N2_re-analyzed


title: Prognatous_58d_P6_re-analyzed


title: Prognatous_58d_P5_re-analyzed


title: MI+nc-1


title: AKSF cell line 26 - culture replicate B


title: PDL85

type: genomic

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

scan_protocol: Arrays were imaged using the iScan system with standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.1
The methylation level of each of the >  450,000 sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using Normalization to Internal Controls and Background Subtraction options implemented in the Methylation Module 1.9.0.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: TIG3 cells passaging until PDL85

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated using the DNeasy Blood & Tissue (Qiagen) according to the manufacturer’s instructions.


title: Sham+nc-3

description: 21 days post sham surgery

source_name: Mouse heart, sham, 21 days

value: control


title: AKSF cell line 19 - culture replicate A


title: Prognatous_58d_P4_re-analyzed


title: AKSF cell line 19 - culture replicate B


title: AKF cell line 20 - culture replicate C

value: AKF ES cell line

value: 20% KOSR and FGF2


title: AKSF cell line 26 - culture replicate C


title: Sham+nc-4

description: 21 days post sham surgery


title: PDL36

source_name: TIG3 cells passaging until PDL36

value: proliferating


title: Normal_58d_N3_re-analyzed

value: Normal jaw

value: 58 days


title: Sham+nc-2

description: 21 days post sham surgery


title: AKF cell line 20 - culture replicate B


title: Normal_38d_N3_re-analyzed

description: Pool of five (5) heads dissected from normal individuals

source_name: 38 days old normal sea bass heads

value: whole head

value: normal

value: 38 days


title: Prognatous_38d_P3_re-analyzed

description: Pool of five (5) heads dissected from prognatous individuals

source_name: 38 days old prognathous sea bass heads

value: prognatous


title: MI+nc-4

value: male

value: 8 weeks old

value: heart


title: Prognatous_38d_P5_re-analyzed


title: Sham+nc-1

description: 21 days post sham surgery


title: AKF cell line 20 - culture replicate A

source_name: ES cell line


title: AKF cell line 5 - culture replicate B


title: Normal_38d_N6_re-analyzed


title: AKF cell line 5 - culture replicate C


title: Prognatous_38d_P6_re-analyzed


title: SVts8_38

hyb_protocol: The resultant cRNAs were fragmented for 30 min at 60°C in dark. The fragmented cRNAs (600 ng) were hybridized on the microarray at 65°C for 17 h.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

source_name: SVts8 cells cultured under 38°C

label_protocol: Starting with 200  ng of the isolated RNA for each sample, double stranded cDNA and cyanine 3 labeled cRNA were synthesized using low input quick amp labeling kit, one-color and RNA spike-in kit, one-color (Agilent).

extract_protocol: Total RNA was isolated with ReliaPrep RNA Cell MiniPrep System (Promega) according to the manufacturer’s instructions.

value: senescence


title: normal gingiva-3

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: normal gingiva

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

growth_protocol: Normal gingival tissue was collected from nine patients with a healthy gingiva who underwent surgical gingival resection for extraction of a supermumerary tooth, odontoma, or orthodontic reasons.

extract_protocol: Normal gingival tissues were homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from normal gingival tissues, according to the manufacturer's instructions.

treatment_protocol: The tissue was derived from the non-inflamed or hyperplastic gingiva of five males and four females with a mean age of 8.7-years. We combined three normal  gingival tissues into one sample to reduce sample vias.

value: gingiva

tag: disease status

value: healthy


title: Inner Cell Mass sample 4

source_name: Inner Cell Masses isolated by immunosurgery

tag: cell type

value: Day 4 Inner Cell Masses (ICM)

tag: embryonic compartment

value: Pool of 30 Inner cell masses obtained from in vivo developed Embryos recovered at 96 hours post-coitum from at least three different females


title: Inner Cell Mass sample 2

description: ICMB


title: SVts8_33.5

source_name: SVts8 cells cultured under 33.5°C


title: normal gingiva-2


title: Inner Cell Mass sample 3


title: Epiblast sample 2

source_name: Epiblasts dissected from the embryo

value: Day 6 Epiblasts

value: Pool of 10 epiblasts dissected from in vivo developed Embryos recovered from at least three different females


title: AKF cell line 5 - culture replicate A

value: AKF ES cell line

value: Single cell dissociation with accutase

value: 20% KOSR and FGF2


title: Normal_38d_N4_re-analyzed

value: whole head


title: Epiblast sample 4


title: pBabe-puro

source_name: TIG3 cells induced pBabe-puro

value: proliferating


title: pBabe-puro-H-RAS-V12

source_name: TIG3 cells induced pBabe-puro-H-RAS-V12


title: PDL85


title: Inner Cell Mass sample 1

description: ICMA


title: Epiblast sample 3


title: normal gingiva-1


title: Epiblast sample 1

value: Pool of 10 epiblasts dissected from in vivo developed Embryos recovered at 120 hours post-coitum from at least three different females


title: PDL36


title: 4_HIF1A_KD_H

status: Public on Feb 11 2017

city: Oulu

first: Irina

last: Raykhel

address: Aapistie 5

department: FBMM

country: Finland

institute: University of Oulu

description: Gene expression data from Madin-Darby canine kidney epithelial cells, KD for HIF1A, in hypoxia

hyb_protocol: cRNA was hybridized on GeneChip Canine Genome 2.0 Array  plates according to manufacturer's instructions (wash_stain_scan_cartridge_arrays_manual.pdf, Chapter2; WASH, STAIN AND SCAN PROTOCOL WITH USER PREPARED REAGENTS)

scan_protocol: 7GGeneChips were scanned on Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were normalized using pair-wise rank-invariant normalization in software dchip_2010_01.exe.

organism: Canis lupus familiaris

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix)

growth_protocol: Madin-Darby canine kidney epithelial cells (MDCKII) were incubated 24h in normoxic condition then additionally were incubated 24h in normoxic or hypoxic conditions

extract_protocol: Total RNA was extracted with RNeasy Kit (Qiagen) according to the manufacturer's instructions.

value: MDCKII cells (ATCC:CCL-34)

tag: genotype/variation

value: HIF1A KD

value: hypoxia


title: 1_HIF1A_WT_N

description: Gene expression data from Madin-Darby canine kidney epithelial cells, WT for HIF1A, in normoxia

value: HIF1A WT

value: normoxia


title: 3_HIF1A_WT_H

description: Gene expression data from Madin-Darby canine kidney epithelial cells, WT for HIF1A, in hypoxia


title: 2_HIF1A_KD_N

description: Gene expression data from Madin-Darby canine kidney epithelial cells, KD for HIF1A, in normoxia


title: GBM557

city: Harbin

first: Xuexin

last: Yu

address: Xuefu Road

department: College of Bioinformatics Science and Technology

institute: Harbin Medical University

description: gene expression of GBM survival patient

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GBM patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA).

tag: diagnosis

value: Glioblastoma Multiforme (GBM)

tag: survival_pfs (day)

tag: events_pfs (death = 1, alive = 0)

tag: os (day)

tag: events_os (death = 1, alive = 0)


title: 1_21B

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

institute: Sun Yat-sen University

description: Gene expression data from tongue tissue from 4NQO+IL-1Ra group

hyb_protocol: Gene expression profile was examined by rat genome oligonuleotide microarray (Affymetrix Gene Chip Rat Genome 230 2.0 Array) at Capitalbiochip Corporation (Beijing, China), where gene chip microarray service is certificated by Affymetrix. Briefly an aliquot of 2 µg of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged cRNA using the MessageAmpTM II-Biotin (Ambion, USA). The resulting bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix. The chip measures the expression of over 31,000 probe sets representing over 28,700 well-substantiated mouse genes. The protocol for microarray processing was carried out according to GeneChip® Expression Analysis Technical Manual (Affymetrix, 701021, Rev.5).

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

organism: Rattus norvegicus

source_name: tongue tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Briefly, A 0.05% stock solution of 4-nitroquinoline oxide (4-NQO; Sigma-Aldrich, Saint Louis, MO, USA) was prepared with distilled water and stored at 4℃ in a dark refrigerator. Thirty male SD rats were divided into two groups. In the experimental group (n=20), rats were daily fed with distilled water containing 0.002% 4NQO for 22 weeks, whereas animals in the control group (n=10) were fed with distilled water only. From week14 to week 22, ten experimental rats were sacrificed while visible lesions of tongue leukoplasia or squamous cell carcinoma (SCC) were developed respectively.

tag: tissue

value: tongue

tag: strain

value: Sprague Dawley

tag: treatment


title: 1_14B


title: 0_9B

description: Gene expression data from tongue tissue from 4NQO group


title: 1_20B


title: 0_11B


title: C_3B

description: Gene expression data from tongue tissue in normal condition

value: normal condition


title: 0_1B


title: C_2B


title: GBM596

description: gene expression of GBM survival patient


title: GBM489

description: gene expression of GBM survival patient


title: GBM218

description: gene expression of GBM survival patient


title: C_1B


title: GBM232

description: gene expression of GBM survival patient


title: leaf water infiltrated,under drought stress at 40% FC biological rep2

city: Delhi

first: Muthappa

last: Senthil-Kumar

state: New Delhi

address: Aruna Asaf Ali Road

department: Plant-microbe interaction

institute: National institute of plant genome research

description: Arabidopsis leaf mock infiltrated on drought stressed plants, rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Arabidospsis GeneChip® Gene 1.0 ST,  for 16 hr at 45C using Affymetrix GeneChip Hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw CEL files were processed through Affymetrix Expression Console software. The software uses the RMA algorithm.

source_name: 38-d-old Arabidopsis plants maintained at 40% FC, syringe infiltrated with water

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Seeds were sown in agropeat (Prakruthi Agro Tech, Karnataka, India): vermiculite (Keltech Energies Ltd, Maharashtra, India) mix (3:1 vol/vol, pre-weighed) and were stratified (for 48 h in dark at 4 °C). Plants were grown under short-day conditions (8 h of light, 16 h of dark) with 200 µE m-2s-1 light intensity, 75% humidity, and 20 °C constant temperature in growth chamber (PGR15, Conviron, Winnipeg, Canada). Plants were bottom irrigated with water or with Hogland solution (Cat # TS1094, Himedia Laboratories, Mumbai, India) every alternate day till the start of the stress treatments.

extract_protocol: Leaf tissue (100 mg fresh weight) from third tier of stressed and unstressed rosette was harvested at 24 hpt and immediately frozen in liquid nitrogen. leaves from 3 plants were grouped for one biological replicate. For each treatment two biological replicates have been sampled. Total RNA was isolated from leaf tissue using RNeasy plant mini kit (Cat # 74904, Qiagen, Hilden, Germany) as per the manufacturer’s instructions. RNA samples were treated with DNase I (Cat # 79254 RNeasy/QlAamp columns, Qiagen, Hilden, Germany) to remove DNA according to the manufacturer’s instructions. RNA quality and quantity were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA) with RNA 6000 Nano Chips (Cat # 5067-1511, Agilent Technologies, California, USA), following the manufacturer’s protocol. RNA integrity numbers (RIN) ranged from 7.0 to 7.5.

treatment_protocol: Drought stress was initiated by withholding water from potted A. thaliana plants (32-d-old, 8 leaf stage). Gravimetric method was followed for stress imposition. Briefly, potted plants were weighed twice a day (11:00 a.m. and 5:00 p.m.) and were brought down to a defined level of drought stress, 40% soil field capacity (FC) (Ψw = -3.9 MPa). Pathogen was infiltrated using needle-less syringe through abaxial surface of the leaves. Combined stressed treatment involved PStDC3000 infiltration at 5 X 103 CFU/mL concentration on drought stressed plants (DP). In another combined stressed treatment, PStDC3000 was infiltrated into the leaves (32-d-old–plants) and such plants were subjected to water withdrawal (PD). Drought stressed plants were re-watered and after 2 h of recovery plants were infiltrated with PStDC3000 (DRP). Individual drought stressed (D) and PStDC3000 infected (P) plants were separately maintained. PSta (non-host pathogen) was infiltrated at the concentration of 1 X 106 CFU/mL either individually (NH) or in combination with drought (DNH). Control plants were maintained at 100% FC (absolute control, C). The control healthy plants were infiltrated only with sterile water (mock inoculation, M). Drought stressed plants were mock infiltrated (DM) as control.

tag: ecotype

value: leaf

value: 38-d post germination


title: GBM354

description: gene expression of GBM survival patient


title: GBM260

description: gene expression of GBM survival patient


title: GBM292

description: gene expression of GBM survival patient


title: leaf under combined combined drought-non-host pathogen stress, biological rep2

description: Arabidopsis leaf non-host pathogen infiltration on drought stressed plants, rep2

source_name: 38-d-old Arabidopsis plants maintained at 40% FC, infiltrated with PSta, 1d

tag: age


title: GBM714

description: gene expression of GBM survival patient


title: leaf water infiltrated,under drought stress at 40% FC biological rep1

description: Arabidopsis leaf mock infiltrated on drought stressed plants, rep1


title: GBM699

description: gene expression of GBM survival patient


title: GBM231

description: gene expression of GBM survival patient


title: leaf under combined Drought recovery-pathogen stress, biological rep2

description: Arabidopsis leaf pathogen infiltration on drought recovered plants, rep2

source_name: 38-d-old Arabidopsis plants maintained at 40% FC, re-watered for 2h, infiltrated with PStDC3000, 1d


title: GBM683

description: gene expression of GBM survival patient


title: GBM462

description: gene expression of GBM survival patient


title: GBM822

description: gene expression of GBM survival patient


title: GBM684

description: gene expression of GBM survival patient


title: GBM331

description: gene expression of GBM survival patient


title: GBM454

description: gene expression of GBM survival patient


title: leaf under combined DP stress, biological rep2

description: Arabidopsis leaf PStDC3000 infiltration on drought stressed plants, rep2

source_name: 38-d-old Arabidopsis plants maintained at 40% FC, infiltrated with PStDC3000, 1d


title: leaf PSta infiltrated, biological rep2

description: Arabidopsis leaf non-host pathogen infiltrated, rep2

source_name: 38-d-old Arabidopsis plants maintained at 100% FC, syringe infiltrated with PSta, 1d


title: GBM664

description: gene expression of GBM survival patient


title: leaf under combined PD stress, biological rep2

description: Arabidopsis leaf PStDC3000 infiltrated plants exposed to drought stress, rep2

source_name: 38-d-old Arabidopsis plants syringe infiltrated with PStDC3000 and drought stress at 40%FC, 1d


title: leaf under combined combined drought-non-host pathogen stress, biological rep1

description: Arabidopsis leaf non-host pathogen infiltration on drought stressed plants, rep1


title: leaf PSta infiltrated, biological rep1

description: Arabidopsis leaf non-host pathogen infiltrated, rep1


title: GBM640

description: gene expression of GBM survival patient


title: GBM195

description: gene expression of GBM survival patient


title: GBM588

description: gene expression of GBM survival patient


title: leaf under combined PD stress, biological rep1

description: Arabidopsis leaf PStDC3000 infiltrated plants exposed to drought stress, rep1


title: leaf under combined DP stress, biological rep1

description: Arabidopsis leaf PStDC3000 infiltration on drought stressed plants, rep1


title: leaf PStDC3000 infiltrated 6d, biological rep2

description: Arabidopsis leaf PStDC3000 infiltrated for 6d, rep2

source_name: 38-d-old Arabidopsis plants maintained at 100% FC, syringe infiltrated with PStDC3000, 6 d


title: leaf PStDC3000 infiltrated, biological rep1

description: Arabidopsis leaf PStDC3000 infiltrated, rep1

source_name: 38-d-old Arabidopsis plants maintained at 100% FC, syringe infiltrated with PStDC3000, 1d


title: leaf PStDC3000 infiltrated, biological rep2

description: Arabidopsis leaf PStDC3000 infiltrated, rep2


title: GBM612

description: gene expression of GBM survival patient


title: GBM351

description: gene expression of GBM survival patient


title: leaf under combined Drought recovery-pathogen stress, biological rep1

description: Arabidopsis leaf pathogen infiltration on drought recovered plants, rep1


title: leaf under drought stress, biological rep2

description: Arabidopsis leaf 40% FC drought conditions, rep2

source_name: 38-d-old Arabidopsis plants maintained at 40% FC, 1d


title: GBM741

description: gene expression of GBM survival patient


title: leaf PStDC3000 infiltrated 6d, biological rep1

description: Arabidopsis leaf PStDC3000 infiltrated for 6d, rep1


title: GBM573

description: gene expression of GBM survival patient


title: leaf under drought stress, biological rep1

description: Arabidopsis leaf 40% FC drought conditions, rep1


title: leaf water infiltrated, biological rep1

description: Arabidopsis leaf mock infiltrated, rep1

source_name: 38-d-old Arabidopsis plants maintained at 100% FC, syringe infiltrated with water


title: leaf water infiltrated, biological rep2

description: Arabidopsis leaf mock infiltrated, rep2


title: GBM439

description: gene expression of GBM survival patient


title: GBM713

description: gene expression of GBM survival patient


title: GBM419

description: gene expression of GBM survival patient


title: GBM598

description: gene expression of GBM survival patient


title: GBM403

description: gene expression of GBM survival patient


title: leaf under control conditions, biological rep2

description: Arabidopsis leaf control conditions, rep2

source_name: 38-d-old Arabidopsis plants maintained at 100% FC


title: GBM508

description: gene expression of GBM survival patient


title: GBM606

description: gene expression of GBM survival patient


title: GBM287

description: gene expression of GBM survival patient


title: leaf under control conditions, biological rep1

description: Arabidopsis leaf control conditions, rep1


title: GBM575

description: gene expression of GBM survival patient


title: GBM549

description: gene expression of GBM survival patient


title: GBM342

description: gene expression of GBM survival patient


title: GBM654

description: gene expression of GBM survival patient


title: GBM775

description: gene expression of GBM survival patient


title: GBM104

description: gene expression of GBM survival patient


title: GBM308

description: gene expression of GBM survival patient


title: GBM225

description: gene expression of GBM survival patient


title: lncRNA Muscle_JEV_rep1

city: wuhan

first: li

middle: yun

last: chuan

state: hubei

address: No.1,Shizishan Street,Hongshan District

institute: Huazhong Agricultural University

description: the data in matrix template are lncRNA

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse Exon 1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Expression data were generated by Affymetrix APT software.

source_name: mouse infection JEV

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: Six adult BALB/C mice (six weeks old) were randomly assigned to two groups: the JEV-infected group and the control group.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: For the infection group, mice were inoculated intracranially with 200 PFU JEV (P3 strain) in 20μl DMEM, whereas mice belonging to the control group were injected intracranially with equal volume of DMEM.

value: brain

tag: group

value: JEV-infected


title: lncRNA Muscle_JEV_rep3

description: the data in matrix template are lncRNA


title: GBM437

description: gene expression of GBM survival patient


title: lncRNA Muscle_control_rep3

description: the data in matrix template are lncRNA

source_name: mouse infection without virus

value: control


title: GBM442

description: gene expression of GBM survival patient


title: GBM249

description: gene expression of GBM survival patient


title: GBM124

description: gene expression of GBM survival patient


title: lncRNA Muscle_control_rep2

description: the data in matrix template are lncRNA


title: GBM240

description: gene expression of GBM survival patient


title: GBM334

description: gene expression of GBM survival patient


title: lncRNA Muscle_JEV_rep2

description: the data in matrix template are lncRNA


title: GBM778

description: gene expression of GBM survival patient


title: GBM729

description: gene expression of GBM survival patient


title: GBM329

description: gene expression of GBM survival patient


title: GBM391

description: gene expression of GBM survival patient


title: GBM335

description: gene expression of GBM survival patient


title: GBM512

description: gene expression of GBM survival patient


title: lncRNA Muscle_control_rep1

description: the data in matrix template are lncRNA


title: GBM375

description: gene expression of GBM survival patient


title: GBM498

description: gene expression of GBM survival patient


title: CLL_MAC_CTRL_rep1

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: RNA was hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol.

scan_protocol: Scanning of the array was conducted by the MicroArray Department of the University of Amsterdam, and images were processed to obtain an intensity value for each oligonucleotide probe.

data_processing: Data were normalized and summarized to the probe set level using the robust multi-array average (RMA) method with default settings (function rma, package affy; version 1.44.0). Data of the two experiments (CD40L, macrophage) were normalized and analyzed separately.

label_protocol: Biotin-labeled cRNA probes were generated according to the manufacturer’s protocol.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) of CLL patients were isolated using ficoll (Pharmacia Biotech, Roosendaal, The Netherlands) and stored in liquid nitrogen. Expression of CD5 and CD19 (both Beckton Dickinson Biosciences [BD], San Jose, CA) on leukemic cells was assessed by flow cytometry (FACS Canto, BD) and analyzed with FACSDiva software (BD). All samples contained at least 90% CD5+/CD19+.

extract_protocol: RNA was isolated using TriReagent (Sigma) according to manufacturer’s instruction and RNA was further purified using the RNeasy micro kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instruction including a DNAse (Qiagen) treatment.

treatment_protocol: CD40L overexpressing NIH-3T3 cells (3T40) were generated by transduction as described in Pascutti et al, Blood, 2013 and macrophages were differentiated from healthy donor isolated monocytes for 72h using 10ng/mL IFN-γ (for M1 macrophages) or IL-4 (for M2 macrophages). Samples from 3 CLL patients were, in two different experiments, stimulated for 16h with either 3T40 cells (Experiment 1: CD40L) or M1 or M2 macrophages (Experiment 2: Macrophage) or left untreated and CLL cells were sorted to >99% purity using CD5/CD19 staining and FACS.

tag: subject status

value: chronic lymphocytic leukemia (CLL) patient

tag: subject/patient id

tag: experiment

value: Macrophage

tag: stimulus

value: CTRL (left untreated)

value: CD5+/CD19+ CLL cells


title: CLL_MAC_M2_rep3

tag: cell type


title: GBM364

description: gene expression of GBM survival patient


title: GBM203

description: gene expression of GBM survival patient


title: GBM345

description: gene expression of GBM survival patient


title: CLL_MAC_CTRL_rep3


title: CLL_MAC_CTRL_rep2


title: CLL_MAC_M1_rep3


title: dorsal root ganglion-mutant-rep3

city: Milwaukee

first: Cheryl

last: Stucky

state: WI

address: 8701 Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

hyb_protocol: 2.3 ug of fragmented, labeled ss-cDNA was hybridized to the chips overnight for 16 hours in a 45 degree oven rotating at 60 rpm. Chips were washed and stained on an Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data from .CEL files was imported into Genomics Suite 3 (Partek) and data was normalized using RMA background corrections. All chips containing epidermal samples were imported simultaneously for normalization purposes and to allow comparison between chips. All chips containing DRG samples were imported together for normalization.

source_name: dorsal root ganglia from naïve mutant mouse

label_protocol: 100 ng total RNA was amplified using the Affymetrix GeneChip WT Plus reagent cDNA synthesis kit. cDNA synthesis, cRNA biotinylation, fragmentation, and labeling were performed according to the manufacturer's instructions.

growth_protocol: Whole skin was dissected from mouse hindpaw immediately following euthanasia. The lumbar 1-6 dorsal root ganglia were also dissected from mouse following euthanasia.

extract_protocol: Tissues were mechanically dissociated in TRIzol, and RNA isolated using the PureLink RNA Micro Kit (LifeTechnologies) according to manufacturer's instructions.

treatment_protocol: Skin samples were treated with dispase for one hour, and the epidermis was peeled away and isolated.

value: DRG

tag: genotype

value: Mutant

tag: inflammation

value: Naïve


title: CLL_MAC_M2_rep2


title: dorsal root ganglion-mutant-rep1


title: dorsal root ganglion-wild type-rep3

source_name: dorsal root ganglia from naïve wild type mouse

value: WT


title: CLL_MAC_M1_rep2


title: dorsal root ganglion-wild type-rep2


title: CLL_MAC_M1_rep1


title: dorsal root ganglion-mutant-rep2


title: epidermis-naïve mutant-rep3

source_name: epidermis from naïve mutant mouse

value: Epidermis


title: CLL_MAC_M2_rep1


title: CLL_CD40L_CTRL_rep2


title: epidermis-CFA mutant-rep1

source_name: epidermis from inflamed mutant mouse

value: CFA


title: epidermis-CFA wild type-rep3

source_name: epidermis from inflamed wild type mouse


title: epidermis-CFA wild type-rep1


title: epidermis-naïve mutant-rep1


title: CLL_CD40L_3T40_rep1


title: epidermis-CFA mutant-rep3


title: epidermis-naïve mutant-rep2


title: dorsal root ganglion-wild type-rep1


title: epidermis-naïve wild type-rep3

source_name: epidermis from naïve wild type mouse


title: CLL_CD40L_CTRL_rep3


title: epidermis-CFA wild type-rep2


title: CLL_CD40L_CTRL_rep1


title: epidermis-naïve wild type-rep1


title: Subject Identifier_6, post-ingestion

city: Minato-ku

first: Yuriko

last: Oda

address: 7-3, Akasaka 9-Chome

institute: Fujifilm Corporation

description:
Sample name: T6
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

hyb_protocol: Following fragmentation, 10 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing:
Image data obtained with each probe were converted to intensity values (CEL files) using GeneChip® Operating Software ver1.4. The obtained data were normalized by the distribution-free weighting (DFW) method with R version 2.7.2.
The obtained data were normalized by the distribution-free weighting (DFW) method with R version 2.7.2. Intergroup comparison of the DFW-normalized data was performed by the rank products (RP) method of R version 2.14.2. Probe sets with a false discovery rate (FDR) < 0.05 were extracted and were gene annotation enrichment analysis based on Gene Ontology (GO) data according to biological functions using the Database for Annotation, Visualization and Integrated Discovery (DAVID ver. 6.7).

source_name: Human blood after ingestion of Salacia reticulata extract

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’ IVT PLUS Reagent Kit, P/N 703210 Rev. 1, Affymetrix).

extract_protocol: Blood samples collected in PAXgene RNA blood collection tubes were stored at 80°C. Total RNA was extracted from the samples with a PAXgene Blood RNA Kit (QIAGEN, Hilden, Germany). Globin RNA was removed from the samples with GLOBINclear Kit (Life Technologies, Gaithersburg, MD, USA) prior to microarray experiments.

treatment_protocol: The S. reticulata extract powder was ingested by the subjects as 60 mg (1 tablet = 250 mg) each before breakfast and lunch and 120 mg (2 tablets) before dinner with water or plain hot water. The test food consumption was monitored via a Web-based diary and subjects whose consumption rate was under 90% were excluded. Administration period was 4-weeks.

tag: subject

value: healthy male

tag: subject identifier

tag: agent

value: S.reticulata extract

tag: time

value: post-ingestion

value: Whole blood


title: epidermis-naïve wild type-rep2

tag: tissue


title: HepaRG_untransfected_FZ8CRD-AND-WNT3A-treated_replicate3

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 039494_D_F_20120411). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in any of the 8 experimental conditions (as defined in the characteristics of samples) had a detected flag (i.e. a positive and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which at least 100% of the values in any of the 8 experimental conditions (as defined in the characteristics of samples) were within the range of interest (i.e. 20-100th percentile).

label_protocol: Total RNA (150 ng) was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions.

growth_protocol: HepaRG cells were grown in William's E medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, and 50 μM hydrocortisone hemisuccinate.

extract_protocol: Total RNA was extracted and purified using the RNAeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s recommendations. Quality control of the extracted nucleic acids was performed by dosing the eluents with a NanoDrop spectrophotometer and by checking 28S/18S ratios by gel electrophoresis.

treatment_protocol: For Wnt3A and/or FZD8_CRD stimulations, mouse recombinant Wnt3a (R&D Systems, 200 ng/ml) and/or mouse FZD8_CRD (300 ng/ml, R&D Systems) were added for 72 hrs to serum-free HepaRG medium containing 0.1% BSA. For RNA interference experiments, HepaRG cells were detached by trypsinization, seeded at low density (2x104 cells/cm2), detached three days later and transfected in suspension with small interfering RNAs (siRNAs) by a MP100 Microporator (LabTech) and Neon™ Transfection System 100 µL Kit (Invitrogen) under optimized conditions (80 pmoles siRNA, 1500V, 20ms, 1 pulse). Silencer negative control (D-001810-10-05, Thermo Fisher) and β-catenin (HSS102460, Invitrogen) siRNAs were used.

tag: cell line

value: HepaRG

value: hepatocellular carcinoma cell line

tag: transfected with

value: none (untransfected control)

tag: stimulation type


title: HepaRG_transfected-CTRLsiRNA_WNT3A-treated_replicate3

value: Control-siRNA


title: Subject Identifier_7, post-ingestion

description:
Sample name: T7
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: Subject Identifier_5, post-ingestion

description:
Sample name: T5
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: HepaRG_untransfected_WNT3A-treated_replicate3


title: HepaRG_transfected-CTNNB1siRNA_WNT3A-treated_replicate3


title: Subject Identifier_2, post-ingestion

description:
Sample name: T2
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: HepaRG_transfected-CTRLsiRNA_untreated_replicate3

value: Untreated


title: Subject Identifier_6, pre-ingestion

description:
Sample name: B6
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

source_name: Human blood before ingestion of Salacia reticulata extract

value: control

value: pre-ingestion


title: Subject Identifier_4, post-ingestion

description:
Sample name: T4
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: HepaRG_untransfected_FZ8CRD-treated_replicate3


title: LPS E5 KM LPS2

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Probes were hybridised to the GeneChip MouseGene 1.0 ST arrays at 45°C for 16 hours. Hybridised arrays were then washed and stained on a Fluidics Station 450 using the Fluidics Station Program FS450_0007.

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G

data_processing: The image data were analysed with GeneChip Command Console software (Affymetrix, Santa Clara, CA, USA). To assess differential expression, CEL files were normalized by robust multiarray average to facilitate comparisons across arrays using the AltAnalyze 2.0.8 beta software suite (Gladstone Institutes, San Francisco, CA, USA) (14). Default analysis options were used, which included analysis of gene expression via an empirical Bayes moderated t-test with a Benjamini-Hochberg-adjusted p-value (15). Transcripts with a fold change of 1.5 or more and an adjusted p-value of less than 0.05 between the LPS- and PBS-treated groups were considered as being differentially expressed.

source_name: bone marrow (BM) cells

label_protocol: Probes for the GeneChip Mouse Gene 1.0 ST arrays were prepared and hybridized to the arrays according to the Ambion whole-transcript expression and the Affymetrix whole-transcript terminal labelling and control kit manuals. Briefly, for each sample, 300 ng of total RNA was reverse-transcribed into cDNA using a random hexamer oligonucleotide tagged with a T7 promoter sequence. After second strand synthesis, double-stranded cDNA was used as a template for amplification with T7 RNA polymerase to obtain antisense cRNA. Random hexamers were then used to reverse-transcribe the cRNA into single-stranded sense strand cDNA. The cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease 1. Fragment size was checked using the Agilent 2100 Bioanalyzer (fragment size between 50–200 bp). Fragmented sense cDNA was biotin-labelled with TdT

extract_protocol: Total RNA was extracted with TRIzol and quantified (Nanodrop). RNA quality was assessed using RNA 6000 NanoAssay with the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: For microarray analysis, mice were injected once i.p. with PBS and 50 µg LPS (1:1 mixture of E. coli K12 and S. minnesota) and analyzed 8 hours later

tag: strain

tag: treatment

value: LPS


title: LPS E5 KM LPS1


title: HepaRG_untransfected_untreated_replicate3


title: Subject Identifier_3, post-ingestion

description:
Sample name: T3
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: Subject Identifier_1, post-ingestion

description:
Sample name: T1
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: GBM377

description: gene expression of GBM survival patient

source_name: GBM patient

tag: diagnosis

value: Glioblastoma Multiforme (GBM)

tag: survival_pfs (day)

tag: events_pfs (death = 1, alive = 0)

tag: os (day)

tag: events_os (death = 1, alive = 0)


title: LPS E5 KM PBS1

value: PBS


title: Mature tendon cells, positive control, donor 9

city: Kuala Lumpur

first: Sik Loo

last: Tan

state: Federal Territory

address: Lembah Pantai

department: Department of Orthopaedic Surgery

country: Malaysia

institute: University of Malaya

description: Gene expression data from tenocyte primary culture without treatment (positive control).

hyb_protocol: The biotinylated cDNA samples (2.5 mg) were hybridized for 20 h at 60 rpm rotation and 45oC to Human GeneChip (Affymetrix Inc., Santa Clara, CA) in GeneChip® Hybridization Oven 640 (Affymetrix Inc., Santa Clara, CA). GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA) and Affymetrix GeneChip Command Console 3.2.3 (Affymetrix Inc., Santa Clara, CA) using default setting to get the CEL intensity files.

data_processing: The data were analyzed with the Affymetrix Power Tools. To decide whether a signal was significantly above background, the DABG detection calls were used.

source_name: Mature tendon cells from donor 9

label_protocol: Biotinylated cRNA were prepared with 200 ng of total RNA according to the sample preparation protocols as described in NuGEN Ovation manual (2009–2011 NuGEN Technologies, Inc) and Affymetrix GeneChip Expression Analysis Technical Manual (2001).

growth_protocol: Human bone marrow stromal cells (hMSCs) were isolated from bone marrow aspirate obtained from six adult donors undergoing intramedullary nailing in UMMC. Human tenocytes (hTeno) were isolated from human hamstring tendons free of pathology (N=6) and were obtained from donors who underwent ligamentous reconstruction of the knees and arthroplasty of the knee(s).

extract_protocol: Qiagen Allprep DNA/RNA/Protein kit was used for total RNA extraction, according to the manufacturer's protocols.

treatment_protocol: The hMSC primary cultures (at P2, n=6) were seeded in standard T25 culture flasks and supplemented with 100 ng/ml of recombinant GDF5 (Abcam, UK) for tenogenic differentiation for 4 and 10 days. Untreated hMSCs were used as negative control and hTeno (P2 or P3) were used as positive control. Cells were trypsinized with TrypLE Express (Invitrogen, Denmark), pelleted and snap frozen in liquid nitrogen prior to storage at -80oC.

tag: donor

tag: donor age

tag: donor gender

value: M

tag: cell type

value: primary tenocyte culture derived from hamstring tendon

tag: treatment to primary culture

value: untreated


title: HepaRG_transfected-CTNNB1siRNA_untreated_replicate3


title: GBM490

description: gene expression of GBM survival patient


title: Subject Identifier_7, pre-ingestion

description:
Sample name: B7
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

tag: subject

value: healthy male

tag: subject identifier

tag: agent

tag: time


title: HepaRG_untransfected_FZ8CRD-AND-WNT3A-treated_replicate2

tag: cell line

tag: transfected with

tag: stimulation type


title: HepaRG_transfected-CTNNB1siRNA_WNT3A-treated_replicate2


title: Mature tendon cells, positive control, donor 12

source_name: Mature tendon cells from donor 12


title: Mature tendon cells, positive control, donor 11

source_name: Mature tendon cells from donor 11


title: Mature tendon cells, positive control, donor 10

source_name: Mature tendon cells from donor 10

value: F


title: LPS E5 KM PBS3

tag: strain

tag: treatment


title: Subject Identifier_4, pre-ingestion

description:
Sample name: B4
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

tag: tissue


title: Mature tendon cells, positive control, donor 7

source_name: Mature tendon cells from donor 7


title: Mature tendon cells, positive control, donor 8

source_name: Mature tendon cells from donor 8


title: Subject Identifier_5, pre-ingestion

description:
Sample name: B5
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: Subject Identifier_3, pre-ingestion

description:
Sample name: B3
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).


title: HepaRG_untransfected_WNT3A-treated_replicate2


title: GDF5-induced hMSC, at day 10, donor 6

description: Gene expression data from hMSC primary culture treated with 100 ng/ml of GDF5 for 10 days.

source_name: GDF5-treated hMSC, at day 10, from donor 6

value: primary hMSC culture derived from bone marrow

tag: treatment duration

value: 10 days


title: Subject Identifier_2, pre-ingestion

description:
Sample name: B2
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

value: Whole blood


title: GDF5-induced hMSC, at day 10, donor 5

source_name: GDF5-treated hMSC, at day 10, from donor 5


title: plasma_pool_5patients

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
Cancer
2 males and 3 females.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were 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. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: pooled plasma, GSCC patients

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark).

extract_protocol: Total RNAs were extracted from plasma by using miRNeasy mini kit (Qiagen).

treatment_protocol: Anticoagulated whole blood collected in EDTA-containing vacutainer. Plasma was isolated within 4 hours of blood collection.

value: plasma

tag: disease status

value: gingival squamous cell carcinoma (GSCC)

tag: gender

value: pooled male and female

tag: age

value: 61 ~ 91 years


title: HepaRG_untransfected_untreated_replicate2

value: HepaRG

value: hepatocellular carcinoma cell line

value: none (untransfected control)

value: Untreated


title: GDF5-induced hMSC, at day 10, donor 2

source_name: GDF5-treated hMSC, at day 10, from donor 2

tag: donor

tag: donor age

tag: donor gender


title: HepaRG_transfected-CTRLsiRNA_WNT3A-treated_replicate2

tag: cell type

value: Control-siRNA


title: HepaRG_transfected-CTNNB1siRNA_untreated_replicate2


title: HepaRG_untransfected_FZ8CRD-treated_replicate2


title: GDF5-induced hMSC, at day 10, donor 1

source_name: GDF5-treated hMSC, at day 10, from donor 1

tag: treatment to primary culture


title: HepaRG_transfected-CTRLsiRNA_untreated_replicate2


title: plasma_pool_10controls

description:
Non-Cancer
4 males and 6 females.

source_name: pooled plasma, healthy controls

value: healthy

value: 60 ~ 92 years


title: GDF5-induced hMSC, at day 10, donor 4

source_name: GDF5-treated hMSC, at day 10, from donor 4


title: GDF5-induced hMSC, at day 10, donor 3

source_name: GDF5-treated hMSC, at day 10, from donor 3


title: HepaRG_transfected-CTNNB1siRNA_WNT3A-treated_replicate1


title: HepaRG_untransfected_FZ8CRD-treated_replicate1


title: HepaRG_untransfected_FZ8CRD-AND-WNT3A-treated_replicate1


title: GDF5-induced hMSC, at day 4, donor 6

description: Gene expression data from hMSC primary culture treated with 100 ng/ml of GDF5 for 4 days.

source_name: GDF5-treated hMSC, at day 4, from donor 6

value: 4 days


title: GDF5-induced hMSC, at day 4, donor 5

source_name: GDF5-treated hMSC, at day 4, from donor 5


title: HepaRG_transfected-CTRLsiRNA_untreated_replicate1


title: HepaRG_transfected-CTRLsiRNA_WNT3A-treated_replicate1


title: GDF5-induced hMSC, at day 4, donor 2

source_name: GDF5-treated hMSC, at day 4, from donor 2


title: GDF5-induced hMSC, at day 4, donor 1

source_name: GDF5-treated hMSC, at day 4, from donor 1


title: HepaRG_untransfected_untreated_replicate1


title: GDF5-induced hMSC, at day 4, donor 4

source_name: GDF5-treated hMSC, at day 4, from donor 4


title: HepaRG_transfected-CTNNB1siRNA_untreated_replicate1


title: GDF5-induced hMSC, at day 4, donor 3

source_name: GDF5-treated hMSC, at day 4, from donor 3


title: HepaRG_untransfected_WNT3A-treated_replicate1


title: Untreated hMSC, donor 4

description: Gene expression data from hMSC primary culture without treatment (negative control).

source_name: Untreated hMSC from donor 4

value: untreated


title: Untreated hMSC, donor 6

source_name: Untreated hMSC from donor 6

value: F


title: Subject Identifier_1, pre-ingestion

description:
Sample name: B1
The subjects were healthy males of at least 50 but less than 60 years of age. To match the lifestyles, only sedentary workers were included. The subjects were forbidden to take food and drugs that affect the intestinal microbiota, such as lactobacilli, oligosaccharides, and antibiotics, but instructed otherwise to maintain their usual lives (dietary, life rhythm, and sleep time).

source_name: Human blood before ingestion of Salacia reticulata extract

tag: subject

value: healthy male

tag: subject identifier

tag: agent

value: control

value: pre-ingestion


title: Untreated hMSC, donor 3

source_name: Untreated hMSC from donor 3

value: primary hMSC culture derived from bone marrow


title: epidermis-CFA mutant-rep2

source_name: epidermis from inflamed mutant mouse

value: Epidermis

tag: genotype

value: Mutant

tag: inflammation

value: CFA


title: Untreated hMSC, donor 1

source_name: Untreated hMSC from donor 1


title: Untreated hMSC, donor 5

source_name: Untreated hMSC from donor 5


title: AGS HIF-KD techRep3 Rep3

city: Berlin

first: Nadine

last: Rohwer

address: Augustenburger Platz 1

institute: Charité

hyb_protocol: Standard Illumina hybridization protocol using the Illumina BeadStation 500 platform

scan_protocol: Standard Illumina scanning protocol using the Illumina BeadStation 500 platform

data_processing: Raw image files were processed and analysed using the beadarray R package.The data was log (base 2) transformed, and quantile normalized.

source_name: AGS, stably transduced with shRNA against HIF-1α

label_protocol: 500 ng RNA were reverse transcribed to generate first-strand cDNA, followed by second-strand synthesis. Subsequently, the dscDNA was used for a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

growth_protocol: Human gastric cancer AGS cells were routinely cultured at 37°C and in 5% CO2 in DMEM supplemented with fetal bovine serum (10%), penicillin (100unit/ml), streptomycin (100μg/ml) and L-glutamine (2mM).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer´s instructions.

value: gastric cancer

tag: cell line

value: AGS

tag: shRNA


title: AGS HIF-KD techRep1 Rep3


title: Untreated hMSC, donor 2

source_name: Untreated hMSC from donor 2


title: AGS Scrambled techRep1 Rep3

source_name: AGS, stably transduced with control shRNA ("scrambled")

value: scrambled


title: Ulcerative colitis 8

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

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

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

data_processing:
BeadStudio software v3.2
The non_normalized.txt contains unmethylated and methylated signal intensities.

source_name: Ulcerative colitis

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the samples by Macrogen inc. according to standard instructions

tag: disease state

value: Ulcerative colitis


title: mRNA Muscle_control_rep1

description: the data in matrix template are mRNA

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

source_name: mouse infection without virus

tag: tissue

value: brain

tag: strain

value: BALB/C

tag: group


title: AGS Scrambled techRep2 Rep3


title: mRNA Muscle_JEV_rep2

description: the data in matrix template are mRNA

source_name: mouse infection JEV

value: JEV-infected


title: 3626_NRAS/BCL2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.mps

source_name: Sca-1+ splenocytes in AML mice

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

growth_protocol: Spleen cells were labelled with anti-Sca-1+ antibodies coupled with microbeads from Miltenyi  and then sorted using an AutoMacs separator (Miltenyi Biotec, Bergisch Gladbach,  Germany).

extract_protocol: 5x106 to 107 Sca-1+ sorted cells were used to extract total RNA using TRIzol  10  (Invitrogen, CA, USA). Quantification and quality of the RNAs were assessed using a  Nanodrop (Thermoscientific, USA).

value: AML

tag: treatment

value: transgenic mice in FVB/N

value: FVB/N

tag: genotype/variation

value: NRAS-BCL2 double transgenic

value: Sca1+ splenocyte


title: mRNA Muscle_JEV_rep1

description: the data in matrix template are mRNA


title: AGS HIF-KD techRep2 Rep3


title: mRNA Muscle_control_rep3

description: the data in matrix template are mRNA

value: control


title: 3518_NRAS/BCL2


title: 3386_BCL2

value: BCL2 transgenic


title: 3622_NRAS/BCL2


title: mRNA Muscle_control_rep2

description: the data in matrix template are mRNA


title: Skn-1 wild type mouse, biological rep3

city: Bunkyo-ku

first: Shota

last: Ushiama

address: 1-1-1 Yayoi

institute: The University of Tokyo

hyb_protocol: aRNA and microarray tip were hybridized at 45C for 16 h

scan_protocol: Fluorescence signals were scanned using the Affymetrix GeneChip System. Affymetrix GeneChip Command Console software was used to reduce the array images to the intensity of each probe (CEL files)

data_processing: The CEL files were quantified with the FARMS using statistical language R and Bioconductor.

source_name: WT mice after 18h fasting_gastrocnemius

label_protocol: Biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3′ IVT Express Kit. In addition, the aRNA was purified and fragmented according to the manufacturer's instructions

growth_protocol: Skn-1/Pou2f3-deficient mice with a mixed 129 x C57BL/6J background were generated and then backcrossed to C57BL/6J for more than 10 generations.All mice were fed a chow.

extract_protocol: RNA was extracted using Trizol reagent(Invitrogen) according to the manufacturer's instructions and purifed by using RNeasy Mini Kit.

treatment_protocol: All mice were fasted for 18 hours before dissection.

tag: strain background

value: mixed 129 x C57BL/6J

tag: Sex

value: male

tag: age

value: 12-16 weeks old

value: Wild type

value: gastrocnemius

tag: time point

value: after 18h fasting


title: Skn-1 wild type mouse, biological rep2


title: 3391_BCL2

tag: cell type


title: Skn-1 wild type mouse, biological rep1


title: Skn-1 wild type mouse, biological rep5


title: Ulcerative colitis 7

value: Ulcerative colitis


title: Ulcerative colitis 5


title: Ulcerative colitis 6


title: Human colon cancer cell

source_name: Human colon cancer cell

value: Human colon cancer cell


title: Skn-1 wild type mouse, biological rep4


title: mRNA Muscle_JEV_rep3

description: the data in matrix template are mRNA

value: brain

value: BALB/C


title: 8398_NRAS/tBCL2

value: AML

value: NRAS-tBCL2 double transgenic


title: 3012_BCL2

value: transgenic mice in FVB/N

value: FVB/N


title: Skn-1 deficient mouse, biological rep2

source_name: Skn-1 KO mice after 18h fasting_gastrocnemius


title: Normal 3

source_name: Normal

value: Normal


title: 8111_NRAS/tBCL2

value: Sca1+ splenocyte


title: Normal 2


title: Normal 1


title: Skn-1 deficient mouse, biological rep3


title: Ulcerative colitis 3


title: Ulcerative colitis 4


title: Ulcerative colitis 1


title: 7465_tBCL2

value: tBCL2 transgenic


title: 8019_NRAS/tBCL2


title: 8157_NRAS

value: NRAS transgenic


title: 7758_tBCL2


title: Skn-1 deficient mouse, biological rep1

value: mixed 129 x C57BL/6J

value: male


title: 8158_NRAS


title: 7466_tBCL2


title: AGS Scrambled Rep1

value: gastric cancer

value: AGS

value: scrambled


title: AGS HIF-KD Rep1


title: 8159_NRAS


title: Skn-1 deficient mouse, biological rep4

value: 12-16 weeks old

value: gastrocnemius

value: after 18h fasting


title: AGS Scrambled Rep2


title: Ulcerative colitis 2

value: Ulcerative colitis


title: AGS HIF-KD Rep2


title: 012-E1

status: Public on Feb 10 2017

city: Bogota

first: Diana

last: Ramirez

state: Bogota

address: Calle 53 Cra 37 Ed. 426

department: Medicine Faculty

country: Colombia

institute: Universidad Nacional de Colombia

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 1 with treatment ( E)

hyb_protocol: Approximately 5.5μg of target DNA marked was hybridized to the GeneChip at 45° C for 16 hours.

scan_protocol: The hybridized arrays were washed and stained in the fluidics station for GeneChip450 and scanned with the Scanner GCS3000 (Affymetrix). Signal values were computed using the GeneChip™ Comand Console® software.

data_processing:
Raw data were extracted automatically using the data extraction protocol included in the software Affymetrix® Expression Console™.  The statistical significance of the expression data was determined using fold change.  For each SDR set, hierarchical cluster analysis was performed using complete linkage and Euclidean distance as similarity measures.  Enrichment analysis of genes and functional annotation was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). Each term was assigned a score (EASA), which consists of the p-value modified by the Fisher Exact Test. If the value was less than 0.05 it was classified as enrichment.  All data analysis and visualization of differentially expressed genes were performed using R 3.1.2 (www.r-project.org). The genes obtained in functional annotations were grouped into clusters and those that had a fold change of2and significant p value were selected. Corrections of p value for the statistical significance of the findings were performed by using Bonferroni, Benjamini, and FDR tests.
After importing the CEL files, the data were summarized and normalized using the RMA method implemented in the Affymetrix® Expression Console™.  The results were exported using the RMA analysis and then the gene level protocol was performed for determining differentially expressed genes (DEG).

source_name: calvarial fibroblast

label_protocol: The cDNA sense was fragmented and biotinylated using TdT (terminal deoxynucleotidyl transferase) and using the GeneChip WT Terminal labeling kit.

growth_protocol: subperiosteal primary fibroblasts culture of 3 individuals with AS was made. The explant obtained from each patient was broken up into segments of approximately 2 to 3mm, placed in the middle of DMEM® culture medium supplemented with fetal bovine serum at 10% plus antibiotic Penicillin/Streptomycin at 1% at 37 ºC and 5%CO2, fibroblast growth was monitored by observation of the cell culture with an inverted microscope. Once confluence of 70-80% was obtained, subcultures (maximum 5) were performed in order to obtain the concentration of cells necessary for experiments. At the moment there is no availability of more cell cultures.

extract_protocol: Total RNA for each treatment culture was extracted using the extraction kit RNeasy® Mini Kit (74104: Quiagen®) according to manufacturer's conditions. Subsequently, it was quantified with Quibit® RNA Assay Kit (Q32852: Invitrogen®) and stored at -80° C to begin the process of reverse transcription. The purity and integrity of RNA used were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: In order to mimic the activation state of the mutated FGFR2, in 6- wellboxes,80,000 cells per well were sown in 1.600 µL of DMEM medium supplemented with FGF2 (0,069ng / µL) for 24 hours. After this the culture medium was removed from the wells that would go to treatment Idursulfase®, and these received supplemented DMEM plus Idursulfase® added at a concentration of 0.025mg/ml as reported in the literature (24), since there was no difference with the different concentrations used in the previous assay. The wells that served as control were left only with supplemented DMEM. Cells were incubated for 48 hours to proceed to the extraction of total RNA.

tag: diagnosis

value: Apert syndrome tissue

value: calvarial fibroblast

tag: gender


title: 012-E3

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 3 with treatment (E )


title: 004-E2

description:
male (YPM) - 1 year
First sample, culture 004 biological replica 2 with treatment (E )


title: 012-E2

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 2 with treatment ( E)


title: 012-ST2

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 2 without treatment (ST)


title: 008 E2

description:
female (KLT)-3 years
First sample, culture 008 biological replica 2 with treatment (E)

value: female


title: 004-E3

description:
male (YPM) - 1 year
First sample, culture 004 biological replica 3 with treatment (E )


title: IR_rep2

city: Atlanta

first: Adam

middle: I

last: Marcus

state: GA

address: 1365C Clifton Rd., N.E., Room 4092

institute: Emory University

hyb_protocol: Biotin labeled cDNA was hybridized to the Affymetrix Human Gene ST 2.0 gene expression microarray at 45 degrees C for 40 hours and further processed on the GeneChip Instrument System for Array Cartridges (Affymetrix, Santa Clara, CA).

scan_protocol: Hybridized microarrays were washed and stained on the Affymetrix GeneChip 450 fluidics station using the appropriate chip dependent fluidics script.  Arrays were scanned and intensity data extracted using the Affymetrix 7G scanner and the Command Console software suite.

data_processing:
CEL files were processed using Partek Genomics Suite v6.6
GC content adjusted, RMA background corrected, log2 transformed, quantile normalized, and mean probset

source_name: H1299-Dendra2 Cells_IR

label_protocol: Briefly, RNA from 1-20 cells was reverse transcribed using a proprietary RNA/DNA duplexed primer.  ss-cDNA was converted to ds-cDNA and linearly amplified in a single primer isothermal amplification reaction (SPIA).  Amplified cDNA was then fragmented and labeled.

extract_protocol: Cells were processed using the Ovation® One-Direct System and Encore® Biotin Module (NuGEN Technologies, Inc., San Carlos, CA).  All steps were carried out according to the manufacturer’s protocol.

value: H1299-Dendra2 Cells

tag: cell population

value: Invasive photoconverted cells


title: 004-ST1

description:
male (YPM) - 1 year
First sample, culture 004 biological replica 1 without treatment (ST)


title: 004-ST3

description:
male (YPM) - 1 year
First sample, culture 004 biological replica 3 without treatment (ST)


title: 012-ST1

description:
male (SAOM)-8 years
Third sample, culture 012 biological replica 1 without treatment (ST)


title: 004-E1

description:
male (YPM) - 1 year
First sample, culture 004 biological replica 1 with treatment ( E)


title: F_rep1

source_name: H1299-Dendra2 Cells_F

value: Follower cells


title: mirMM.464-MM95db

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: microRNA expression data from multiple myeloma newly-diagnosed primary tumor.

hyb_protocol: Byotin-labeled RNA samples were hybridized for 16 hours  at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning  of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website

source_name: Newly-diagnosed MM patient 464

label_protocol: 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.

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

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: multiple myeloma

value: primary tumor

tag: t(4;14) translocation

value: n


title: NG_rep3

source_name: H1299-Dendra2 Cells_NG

tag: cell line

value: Invasive non-photoconverted cells


title: IR_rep3


title: IR_rep1


title: F_rep2


title: L_rep3

source_name: H1299-Dendra2 Cells_L

value: Leader cells


title: NG_rep2


title: mirMM.449-MM95db

source_name: Newly-diagnosed MM patient 449


title: L_rep1


title: F_rep3


title: NG_rep1


title: mirMM.448-MM95db

source_name: Newly-diagnosed MM patient 448


title: mirMM.437-MM95db

source_name: Newly-diagnosed MM patient 437


title: mirMM.447-MM95db

source_name: Newly-diagnosed MM patient 447


title: mirMM.435-MM95db

source_name: Newly-diagnosed MM patient 435


title: Igrov 1 derived ovarian cancer cell line overexpressing ABCG2, biological rep 2

city: Albuquerque

first: Richard

last: Larson

state: New Mexico

address: 915 Camino de Salud NE

department: Office of Research

institute: University of New Mexico

hyb_protocol: Following fragmentation, 25ng/uL of fragmented and labeled DNA was hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0002.

data_processing: Data was analyzed using GeneSpring.

source_name: Immortal Human Ovarian Carcinoma Cell Line

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix GeneChip WT Terminal Labeling Kit protocol from 100ng of total RNA .

growth_protocol: Human solid tumor growth in a mouse

extract_protocol: Extracted RNA using Qiagen Rneasy Kit Protocol according to the manufactuer's instructions.

treatment_protocol: Tumor extracted from the mouse and homogenized RNA from the tissue.

tag: tissues

value: Solid Tumor from human ovarian cancer cells


title: mirMM.434-MM95db

source_name: Newly-diagnosed MM patient 434


title: Parental Igrov 1 Human cell lines, biological rep 2

value: Parental Igrov 1


title: Parental Igrov 1 Human cell lines, biological rep 1


title: Igrov 1 derived ovarian cancer cell line overexpressing ABCG2, biological rep 1


title: mirMM.430-MM95db

source_name: Newly-diagnosed MM patient 430


title: mirMM.433-MM95db

source_name: Newly-diagnosed MM patient 433


title: mirMM.429-MM95db

source_name: Newly-diagnosed MM patient 429


title: L_rep2


title: mirMM.424-MM95db

source_name: Newly-diagnosed MM patient 424


title: mirMM.423-MM95db

source_name: Newly-diagnosed MM patient 423


title: mirMM.425-MM95db

source_name: Newly-diagnosed MM patient 425


title: mirMM.422-MM95db

source_name: Newly-diagnosed MM patient 422


title: mirMM.414-MM95db

source_name: Newly-diagnosed MM patient 414


title: mirMM.413-MM95db

source_name: Newly-diagnosed MM patient 413


title: mirMM.411-MM95db

source_name: Newly-diagnosed MM patient 411


title: mirMM.402-MM95db

source_name: Newly-diagnosed MM patient 402


title: mirMM.362-MM95db

source_name: Newly-diagnosed MM patient 362


title: mirMM.398-MM95db

source_name: Newly-diagnosed MM patient 398


title: mirMM.382-MM95db

source_name: Newly-diagnosed MM patient 382


title: mirMM.385-MM95db

source_name: Newly-diagnosed MM patient 385


title: mirMM.387-MM95db

source_name: Newly-diagnosed MM patient 387


title: mirMM.340-MM95db

source_name: Newly-diagnosed MM patient 340


title: mirMM.407-MM95db

source_name: Newly-diagnosed MM patient 407


title: mirMM.321-MM95db

source_name: Newly-diagnosed MM patient 321


title: mirMM.314-MM95db

source_name: Newly-diagnosed MM patient 314


title: mirMM.327-MM95db

source_name: Newly-diagnosed MM patient 327


title: mirMM.308-MM95db

source_name: Newly-diagnosed MM patient 308


title: mirMM.301-MM95db

source_name: Newly-diagnosed MM patient 301


title: mirMM.300-MM95db

source_name: Newly-diagnosed MM patient 300


title: mirMM.280-MM95db

source_name: Newly-diagnosed MM patient 280


title: mirMM.278-MM95db

source_name: Newly-diagnosed MM patient 278


title: mirMM.261-MM95db

source_name: Newly-diagnosed MM patient 261


title: mirMM.286-MM95db

source_name: Newly-diagnosed MM patient 286


title: mirMM.267-MM95db

source_name: Newly-diagnosed MM patient 267


title: mirMM.282-MM95db

source_name: Newly-diagnosed MM patient 282


title: mirMM.274-MM95db

source_name: Newly-diagnosed MM patient 274

value: y


title: mirMM.243-MM95db

source_name: Newly-diagnosed MM patient 243


title: mirMM.253-MM95db

source_name: Newly-diagnosed MM patient 253


title: mirMM.330-MM95db

source_name: Newly-diagnosed MM patient 330


title: mirMM.239-MM95db

source_name: Newly-diagnosed MM patient 239


title: mirMM.219-MM95db

source_name: Newly-diagnosed MM patient 219


title: mirMM.317-MM95db

source_name: Newly-diagnosed MM patient 317


title: mirMM.177-MM95db

source_name: Newly-diagnosed MM patient 177


title: mirMM.159-MM95db

source_name: Newly-diagnosed MM patient 159


title: mirMM.212-MM95db

source_name: Newly-diagnosed MM patient 212


title: mirMM.131-MM95db

source_name: Newly-diagnosed MM patient 131


title: mirMM.066-MM95db

source_name: Newly-diagnosed MM patient 066


title: mirMM.050-MM95db

source_name: Newly-diagnosed MM patient 050


title: mirMM.074-MM95db

source_name: Newly-diagnosed MM patient 074


title: mirMM.087-MM95db

source_name: Newly-diagnosed MM patient 087


title: mirMM.043-MM95db

source_name: Newly-diagnosed MM patient 043


title: mirMM.042-MM95db

source_name: Newly-diagnosed MM patient 042


title: mirMM.039-MM95db

source_name: Newly-diagnosed MM patient 039


title: mirMM.027-MM95db

source_name: Newly-diagnosed MM patient 027


title: mirMM.262-MM95db

source_name: Newly-diagnosed MM patient 262


title: mirMM.034-MM95db

source_name: Newly-diagnosed MM patient 034


title: mirMM.036-MM95db

source_name: Newly-diagnosed MM patient 036


title: mirMM.015-MM95db

source_name: Newly-diagnosed MM patient 015


title: mirMM.026-MM95db

source_name: Newly-diagnosed MM patient 026


title: mirMM.016-MM95db

source_name: Newly-diagnosed MM patient 016


title: mirMM.004-MM95db

source_name: Newly-diagnosed MM patient 004


title: mirMM.229-MM95db

source_name: Newly-diagnosed MM patient 229


title: mirMM.143-MM95db

source_name: Newly-diagnosed MM patient 143