title: Bangladesh132


title: Bangladesh115

status: Public on May 28 2014

type: genomic

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

country: USA

institute: University of Maryland School of Medicine

hyb_protocol: described in Jacob et al, 2014

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner using autogain setting per manufacturer's protocol (www.NimbleGen.com)

data_processing: data were processed by both a previously published method (PMCID: PMC3218861), and by a custom algorithm (Jacob et al, 2014, Submitted)

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: clincal isolate

label_protocol: described in Jacob et al, 2014

extract_protocol: all samples were extracted using a Qiagen blood extraction mini prep (qiagen.com)

tag: country

value: Bangladesh


title: Bangladesh126


title: Bangladesh114


title: Bangladesh131


title: Bangladesh130


title: Bangladesh121


title: Bangladesh118


title: Bangladesh112


title: Bangladesh123


title: Bangladesh124


title: Bangladesh119


title: Bangladesh110


title: Bangladesh116


title: Bangladesh111


title: Bangladesh113


title: Bangladesh109


title: Bangladesh105


title: Bangladesh125


title: Bangladesh106


title: Bangladesh117


title: Bangladesh122


title: Bangladesh104


title: Bangladesh107


title: Bangladesh108


title: Bangladesh133


title: Bangladesh120


title: Bangladesh136


title: Bangladesh103


title: Bangladesh101


title: Bangladesh100


title: Bangladesh98


title: Bangladesh96


title: Bangladesh95


title: Bangladesh99


title: Bangladesh84


title: Bangladesh94


title: Bangladesh81


title: Bangladesh83


title: Bangladesh74


title: Bangladesh89


title: Bangladesh91


title: Bangladesh72


title: Bangladesh77


title: Bangladesh87


title: Bangladesh97


title: Bangladesh80


title: Bangladesh73


title: Bangladesh85


title: Bangladesh82


title: Bangladesh76


title: Bangladesh92


title: Bangladesh78


title: Bangladesh93


title: Bangladesh71


title: Bangladesh86


title: Bangladesh75


title: Bangladesh70


title: Bangladesh102


title: Bangladesh69


title: Bangladesh79


title: Bangladesh67


title: Bangladesh68


title: Bangladesh90


title: Bangladesh65


title: Bangladesh61


title: Bangladesh53


title: Bangladesh62


title: Bangladesh88


title: Bangladesh55


title: Bangladesh54


title: Laos17

value: Laos


title: Laos18


title: Bangladesh56


title: Bangladesh63


title: Bangladesh59


title: Laos13


title: Laos16


title: Laos12


title: Bangladesh57


title: Bangladesh58


title: Laos14


title: Bangladesh60


title: Laos7


title: Laos15


title: Laos9


title: Laos10


title: Laos6


title: Laos5


title: Laos8


title: Laos3


title: Laos4


title: Cambodia190

value: Cambodia


title: Laos2


title: Laos1


title: Cambodia188


title: Cambodia189


title: Cambodia184


title: Cambodia185


title: Cambodia183


title: Cambodia179


title: Cambodia180


title: Cambodia187


title: Cambodia176


title: Cambodia182


title: Cambodia186


title: Cambodia177


title: Cambodia168


title: Cambodia169


title: Cambodia174


title: Bangladesh64


title: Cambodia173


title: Cambodia172


title: Cambodia166


title: Cambodia167


title: Cambodia178


title: Cambodia162


title: Cambodia165


title: Cambodia175


title: Cambodia171


title: Cambodia164


title: Cambodia161


title: Cambodia163


title: Laos11


title: Cambodia170


title: Cambodia156


title: Cambodia160


title: Cambodia157


title: Cambodia158


title: Cambodia155


title: Cambodia159


title: Cambodia154


title: Bangladesh66


title: Thailand42

value: Thailand


title: Cambodia153


title: Thailand37


title: Thailand38


title: Thailand40


title: Thailand24


title: Thailand34


title: Thailand27


title: Thailand39


title: Thailand35


title: Thailand23


title: Thailand32


title: Thailand41


title: Thailand29


title: Thailand30


title: Thailand31


title: Thailand43


title: Thailand36


title: Thailand26


title: Thailand28


title: Thailand22


title: Thailand20


title: Thailand33


title: Thailand17


title: Thailand16


title: Thailand18


title: Thailand21


title: Cambodia181


title: Thailand13


title: Thailand12


title: Thailand25


title: Thailand6


title: Cambodia152


title: Thailand15


title: Thailand10


title: Cambodia151


title: Thailand5


title: Cambodia147


title: Cambodia145


title: Thailand4


title: Cambodia146


title: Cambodia150


title: Thailand3


title: Thailand7


title: Thailand14


title: Thailand2


title: Thailand9


title: Thailand11


title: Cambodia149


title: Cambodia139


title: Cambodia142


title: Thailand1


title: Thailand8


title: Thailand19


title: Cambodia143


title: Cambodia148


title: Cambodia140


title: Cambodia141


title: Cambodia138


title: Cambodia144


title: Cambodia121


title: Cambodia113


title: Cambodia128


title: Cambodia123


title: Cambodia130


title: Cambodia111


title: Cambodia137


title: Cambodia116


title: Cambodia125


title: Cambodia119


title: Cambodia129


title: Cambodia117


title: Cambodia133


title: Cambodia136


title: Cambodia132


title: Cambodia124


title: Cambodia112


title: Cambodia118


title: Cambodia131


title: Cambodia114


title: Cambodia108


title: Cambodia120


title: Cambodia126


title: Cambodia134


title: Cambodia109


title: Cambodia110


title: Cambodia115


title: Cambodia127


title: Cambodia122


title: Cambodia107


title: Cambodia135


title: Cambodia105


title: Cambodia103


title: Cambodia106


title: Cambodia102


title: Cambodia97


title: Cambodia98


title: Cambodia104


title: Cambodia100


title: Cambodia96


title: Cambodia84


title: Cambodia93


title: Cambodia95


title: Cambodia85


title: Cambodia88


title: Cambodia82


title: Cambodia86


title: Cambodia101


title: Cambodia92


title: Cambodia83


title: Cambodia99


title: Cambodia80


title: Cambodia94


title: Cambodia90


title: Cambodia81


title: Cambodia91


title: Cambodia89


title: Cambodia77


title: Cambodia79


title: Cambodia87


title: Cambodia78


title: Cambodia72


title: Cambodia74


title: Cambodia76


title: Cambodia75


title: Cambodia71


title: Cambodia69


title: Cambodia66


title: Cambodia73


title: Cambodia63


title: Cambodia64


title: Cambodia60


title: Cambodia61


title: Cambodia67


title: Cambodia65


title: Cambodia57


title: Cambodia51


title: Cambodia50


title: Cambodia52


title: Cambodia46


title: Cambodia62


title: Cambodia70


title: Cambodia68


title: Cambodia59


title: Cambodia53


title: Cambodia49


title: Cambodia44


title: Cambodia42


title: Cambodia47


title: Cambodia48


title: Cambodia56


title: Cambodia54


title: Cambodia45


title: Cambodia58


title: Cambodia41


title: Cambodia40


title: Cambodia39


title: Cambodia43


title: Cambodia38


title: Cambodia36


title: Cambodia35


title: Cambodia34


title: Cambodia30


title: Cambodia33


title: Cambodia31


title: Cambodia29


title: Cambodia55


title: Cambodia32


title: Cambodia25


title: Cambodia28


title: Cambodia18


title: Cambodia26


title: Cambodia15


title: Cambodia21


title: Cambodia16


title: Cambodia19


title: Cambodia13


title: Cambodia12


title: Cambodia22


title: Cambodia10


title: Cambodia17


title: Cambodia23


title: Cambodia24


title: Cambodia5


title: Cambodia6


title: Cambodia11


title: Cambodia20


title: Cambodia9


title: Cambodia7


title: Cambodia8


title: Bangladesh52


title: Cambodia14


title: Cambodia1


title: Bangladesh50


title: Cambodia3


title: Bangladesh49


title: Cambodia4


title: Bangladesh48


title: Cambodia37


title: Bangladesh46


title: Bangladesh47


title: Bangladesh43


title: Bangladesh51


title: Bangladesh41


title: Bangladesh44


title: Bangladesh37


title: Bangladesh38


title: Bangladesh39


title: Bangladesh31


title: Bangladesh36


title: Bangladesh35


title: Bangladesh34


title: Bangladesh42


title: Bangladesh33


title: Bangladesh32


title: Bangladesh29


title: Cambodia2


title: Bangladesh30


title: Bangladesh26


title: Bangladesh24


title: Bangladesh20


title: Bangladesh28


title: Bangladesh25


title: Bangladesh19


title: Bangladesh27


title: Bangladesh23


title: Bangladesh16


title: Bangladesh21


title: Bangladesh15


title: Bangladesh22


title: Bangladesh13


title: Bangladesh14


title: Bangladesh17


title: Bangladesh5


title: Bangladesh11


title: Bangladesh40


title: Bangladesh45


title: Bangladesh9


title: Bangladesh6


title: Vietnam100

value: Vietnam


title: Bangladesh3


title: Vietnam99


title: Bangladesh18


title: Bangladesh8


title: Cambodia27


title: Vietnam103


title: Bangladesh10


title: Bangladesh7


title: Bangladesh12


title: Vietnam101


title: Vietnam102


title: Vietnam105


title: Vietnam104


title: Vietnam96


title: Bangladesh2


title: Vietnam95


title: Vietnam106


title: Bangladesh4


title: Vietnam98


title: Bangladesh1


title: Vietnam97


title: Vietnam94


title: Vietnam93


title: Vietnam91


title: Vietnam92


title: Vietnam81


title: Vietnam82


title: Vietnam83


title: Vietnam80


title: Vietnam90


title: Vietnam85


title: Vietnam73


title: Vietnam86


title: Vietnam72


title: Vietnam74


title: Vietnam89


title: Vietnam66


title: Vietnam77


title: Vietnam67


title: Vietnam64


title: Vietnam76


title: Vietnam87


title: Vietnam68


title: Vietnam62


title: Vietnam63


title: Vietnam75


title: Vietnam65


title: Vietnam88


title: Vietnam70


title: Vietnam69


title: Vietnam61


title: Vietnam59


title: Vietnam60


title: Vietnam79


title: Vietnam71


title: Vietnam56


title: Vietnam84


title: Vietnam54


title: Vietnam57


title: Vietnam58


title: Vietnam52


title: Vietnam50


title: Vietnam53


title: Vietnam55


title: Vietnam47


title: Vietnam78


title: Vietnam43


title: Vietnam49


title: Vietnam44


title: miRNA_Control ASM cells_rep4

type: RNA

city: London

first: Mark

last: Perry

address: Dovehouse Street

department: Airway Disease

country: United Kingdom

institute: NHLI, Imperial College London

description: Gene expression after 24h

hyb_protocol: miRNA-enriched RNA samples (100 ng) used in the microRNA microarrays were labeled with the Labeling Spike-In solution using Agilent’s miRNA Complete Labeling and Hyb Kit and then the samples were dephosphorylated by incubation at 37 oC on a heat block for 30 min. DMSO was added to the dephosphorylated RNA for denaturation for 10 min, followed by the assembly of the Labeling Reaction, where samples were incubated with Cyanine 3-pCp and allowed to ligate for 2 h at 16 oC. The labeled RNA was purified using Micro Bio-Spin 6 columns (Bio-Rad) and the desalted samples were dried up in a vacuum concentrator at 50 oC for 1 h to remove DMSO. Samples were resuspended in Hybridization Mix using Hyb Spike-In solution and Hybridization Buffer and were loaded onto Agilent Human miRNA microarrays and hybridized at 55 oC for 20 h at 20 rpm using Agilent’s Hybridization oven and SureHyb chamber. The microarrays were then disassembled and washed in GE Wash Buffer 1 (Agilent) for 60 sec at RT, followed by GE Wash Buffer 2 for 60 sec at 37 oC. The microarrays were scanned with the Agilent Microarray Scanner G2565BA using the profile for miRNA microarrays (AgilentHD_miRNA) at 2 μm resolution, dye channel Green, Scan Area 61 x 21.6 mm.

scan_protocol: Scanned on an Agilent Sureprint G3 scanner.

data_processing: Agilent Feature Extraction Software

molecule: total RNA

organism: Homo sapiens

source_name: ASM, 24hr

label_protocol: miRNA samples were labeled using cy3

growth_protocol: Confluent cells were growth-arrested by FCS deprivation for 24 h before being treated with dexamamethasone for 60 min, and then stimulated with FCS for a further 24 h.

extract_protocol: Total RNA was extracted using the mirVana™miRNA isolation kit (Ambion Europe). RNA was eluted in 50 μl RNase-free water (Promega UK, Southampton, UK) and stored at -80 °C. RNA content and purity was measured using a BioTek PowerWave XS (SSi Robotics, Tustin, CA, U.S.A.) spectrophotometer.

tag: tissue

value: Airway Smooth Muscle


title: miRNA_Control ASM cells_rep3

description: Gene expression after 24h


title: Vietnam41


title: miRNA_2.5 % FCS_rep3

description: Gene expression after 24h


title: Vietnam35


title: Vietnam38


title: Vietnam33


title: miRNA_2.5 % FCS + Dex 10-7 M_rep4

description: Gene expression after 24h


title: miRNA_2.5 % FCS + Dex 10-7 M_rep3

description: Gene expression after 24h


title: Vietnam39


title: Vietnam36


title: Vietnam34


title: miRNA_2.5 % FCS_rep4

description: Gene expression after 24h


title: Vietnam48


title: Vietnam45


title: Vietnam42


title: Vietnam40


title: Vietnam32


title: Vietnam46


title: Vietnam30


title: Vietnam31


title: miRNA_2.5 % FCS + Dex 10-7 M_rep2

description: Gene expression after 24h


title: Vietnam51


title: Vietnam37


title: Vietnam28


title: miRNA_2.5 % FCS + Dex 10-7 M_rep1

description: Gene expression after 24h


title: miRNA_Control ASM cells_rep2

description: Gene expression after 24h


title: Vietnam27


title: miRNA_Control ASM cells_rep1

description: Gene expression after 24h


title: miRNA_2.5 % FCS_rep2

description: Gene expression after 24h


title: miRNA_2.5 % FCS_rep1

description: Gene expression after 24h


title: Vietnam25


title: Vietnam21


title: Sibling WT_shoot_biological rep2

city: Changchun

first: Ningning

last: Wang

state: Jilin

address: 2888, Xinchen Street

country: China

institute: Jilin Agricultural University

description: Gene expression data from sibling WT.

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

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

data_processing: The data were analyzed with Expression Console using RMA as normalization method.

label: biotin

organism: Oryza sativa

source_name: Sibling WT in rice, shoot

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

growth_protocol: Seeds of the two genotypes were thoroughly washed with distilled water and then germinated in the dark in Petri dishes containing distilled water at 28℃. After a 2-day incubation, germinated seeds were transferred to a greenhouse at 26℃ under 16 h/8 h light/dark regime about 48 hours to harvest.

extract_protocol: Total RNA was isolated from the same seedlings with the Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Tos17 insert mutant.

tag: variety

value: Hitomebore

tag: genotype/variation

value: wild type

value: shoot-tip


title: Vietnam23


title: Vietnam26


title: Osrdr1_shoot_biological rep2

description: Gene expression data from Osrdr1 mutant.

source_name: Osrdr1 mutant in rice, shoot

value: Osrdr1 mutant


title: Vietnam20


title: Sibling WT_shoot_biological rep3

description: Gene expression data from sibling WT.


title: Sibling WT_shoot_biological rep1

description: Gene expression data from sibling WT.


title: Osrdr1_shoot_biological rep3


title: MoDC Aged_3

city: Irvine

first: Sudhir

last: Gupta

state: CA

address: Med Sci Buld I, C240

department: Medicine

institute: University of California, Irvine

description: Gene expression data in MoDC from aged donor

hyb_protocol: 2 ug of  fragmented target single-stranded cRNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix  array.  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.to produce cell intensity files (CEL).  CEL were analyzed with Microarray Suite 5.0

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: MoDC from age_78 donor

label_protocol: The single-stranded cRNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 70 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: To induce differentiation of DCs, purified CD14+ monocytes were cultured in RPMI 1640 10% fetal bovine serum. Supplemented with human rGM-CSF,50ng/ml  and 10 ng/ml human rIL-4 in 37C incubator with 5% CO2 for 6 days.

extract_protocol: Total RNA was extracted from MoDCs  using the TRI Reagent kit (Molecular Research Center Inc., Cincinnati, OH, USA), following the manufacturer’s protocol.

treatment_protocol: Purified CD14+ monocytes were cultured in RPMI 1640 10% fetal bovine serum.  Supplemented with human rGM-CSF,50ng/ml and 10 ng/ml human rIL-4.

tag: individual

value: aged donor

tag: age

tag: cell type

value: monocyte derived dendritic cells (MoDC)


title: Osrdr1_shoot_biological rep1


title: Vietnam18


title: MoDC Aged_5

source_name: MoDC from age_87 donor


title: Vietnam16


title: MoDC Aged_4

source_name: MoDC from age_81donor


title: MoDC Aged_2

source_name: MoDC from age_77 donor


title: Vietnam17


title: MoDC Aged_1

source_name: MoDC from age_84 donor


title: MoDC Young_4

description: Gene expression data in MoDC from young donor

source_name: MoDC from age_20 donor

value: young donor


title: MoDC Young_3

source_name: MoDC from age_27 donor


title: Vietnam19


title: MoDC Young_2

source_name: MoDC from age_25 donor


title: Vietnam15


title: Vietnam29


title: Vietnam14


title: MoDC Young_1

source_name: MoDC from age_22 donor


title: Vietnam13


title: Vietnam10


title: Vietnam11


title: Vietnam12


title: Vietnam8


title: Vietnam9


title: Vietnam22


title: Rice seedlings roots_Hg long exposures Replicate 2

city: Tainan

first: Wen-Chang

last: Chi

state: Taiwan

address: No.1, University Road, Tainan City

department: Life Science

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 2 of 3. Rice seedling roots with or without 25mM Hg during long (24 h) exposures

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: Roots of rice seedlings were exposed to 25mM Hg during long (24 h) exposures

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after Hg treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.

growth_protocol: 6-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Control and rice seedlings were exposed to to 25mM Hg during short (pooled from 1- and 3-h treatments) exposures or long (24 h) exposures

tag: cultivar

value: Oryza sativa L. cv. TN-67

value: 6 day

source_name: Rice seedlings roots were exposed to water


title: Vietnam7


title: Rice seedlings roots_Hg long exposures Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 25mM Hg during long (24 h) exposures


title: Rice seedlings roots_Hg long exposures Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 25mM Hg during long (24 h) exposures


title: Vietnam5


title: Rice seedlings roots_Hg short exposures Replicate 3

description: Biological replicate 3 of 3. Rice seedling roots with or without 25mM Hg short (pooled from 1- and 3-h treatments) exposures

source_name: Roots of rice seedlings were exposed to 25mM Hg during short (pooled from 1- and 3-h treatments) exposures


title: DN4_Thymus_CTL_rep1

city: La Jolla

first: Sylvia

last: Evans

address: 9500 Gilman Drive

institute: University of California San Diego

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: plier

molecule: polyA RNA

organism: Mus musculus

source_name: Thymocyte, Control, DN4

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were sorted into ice-cold PBS plus 2% heat-inactivated FBS. RNA was extracted according to manufacturer's instructions (Qiagen RNeasy Mini Kit).

treatment_protocol: Thymocytes were manually dissociated in ice-cold PBS, filtered (70uM), labeled with antibodies on ice for 20 minutes, washed twice, and resuspened in ice-cold PBS plus 2% heat-inactivated FBS prior to FACS.

tag: gender

value: female

tag: strain

value: mixed

value: thymus

value: 1 week

tag: developmental stage


title: Vietnam6

source_name: clincal isolate


title: ISP_Thymus_KO_rep1

source_name: Thymocyte, Knockout, ISP

value: ISP


title: ISP_Thymus_CTL_rep1

source_name: Thymocyte, Control, ISP


title: pBABE_plasmid_with_steA_L4_rep1

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

hyb_protocol: Labelled cDNA was hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix) following the manufacturer’s instructions

scan_protocol: The arrays were scanned in a 3000 7G Scanner from Affymetrix.

data_processing:
Image analysis, fluorescent data quantification and quality control was carried out with LIMMA package
All procedures and preliminary data analysis, including fluorescent data processing, normalization using Robust Multi-array Average (RMA) algoritm

source_name: HeLa cells (line 4) transfected with steA plasmid

label_protocol: Biotinylated single-stranded cDNA was prepared from 100 ng per sample of total intact RNA extracted from 9 independent samples (3 from HeLa pBABE Puro, 3 from HeLa pBABE Puro-SteA-3xFLAG L2, and 3 from HeLa pBABE Puro-SteA-3xFLAG L4).

growth_protocol: HeLa cells (ECAC no. 93021013) were cultured in DMEM supplemented with 10% foetal calf serum. 2 mM L-glutamine, 100 U/ml penicillin and 100 g/ml streptomycin were included in the culture media

extract_protocol: Total RNA from HeLa cells stably transfected with pBABE Puro or their derivatives encoding the SteA-3xFLAG fusion was isolated in triplicate using 1 ml of TRIzol reagent (Invitrogen) according to the protocol supplied by the manufacturer. An additional purification step was carried out by using the RNeasy MinElute Cleanup Kit from Qiagen

treatment_protocol: All cells were maintained in a 5% CO2 humidified atmosphere at 37ºC. For transient transfection assays, 1x107 HeLa cells/assay were suspended in 200 ul of 15 mM Hepes-buffered serum-containing medium, mixed with 50 l of 210 mM NaCl containing 5-10 ug of plasmid DNA and electroporated using a BTX Electrocell Manipulator 600 set at 240 V, 720 , 950 F. Cells were processed 24 hours after electroporation.

tag: cell line

value: HeLa L4

value: steA


title: DN4_Thymus_KO_rep1

source_name: Thymocyte, Knockout, DN4


title: Rice seedlings roots_Hg short exposures Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 25mM Hg short (pooled from 1- and 3-h treatments) exposures


title: Rice seedlings roots_Hg short exposures Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 25mM Hg short (pooled from 1- and 3-h treatments) exposures


title: Vietnam1

value: Vietnam


title: pBABE_plasmid_with_steA_L4_rep2


title: Vietnam2


title: pBABE_plasmid_with_steA_L4_rep3


title: Vietnam24


title: Vietnam4


title: pBABE_plasmid_with_steA_L2_rep2

source_name: HeLa cells (line 2) transfected with steA plasmid

value: HeLa L2


title: pBABE_plasmid_with_steA_L2_rep1


title: pBABE_plasmid_without_steA_rep3

source_name: HeLa cells transfected with control plasmid

value: HeLa

value: control


title: pBABE_plasmid_without_steA_rep2


title: Vietnam3


title: pBABE_plasmid_without_steA_rep1


title: liver_CL diet_0.005%  β-cryptoxanthin_rep 5

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

country: Japan

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from liver after 12 week feeding of CL diet containing 0.005% β-cryptoxanthin

hyb_protocol: Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner 3000; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

source_name: liver, fed CL diet containing 0.005% β-cryptoxanthin for 12 weeks

label_protocol: Fragmented biotin-labeled aRNA was synthesized from total RNA of each mouse using GeneChip® 3′ IVT Express Kit (Affymetrix Japan KK, Tokyo, Japan)

growth_protocol: Mice were housed in colony cages with a 12-hour light/12-hour dark cycle and allowed food and water at libitum.

extract_protocol: The mice were killed and liver tissue were immediately removed and weighted.  A large portion of each liver was snap-frozen in liquid nitrogen. Total RNA was isolated from frozen liver using a GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich Japan, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: Eight-week old male C57BL/6J mice were fed for 12 weeks on a CRF-1 standard chow (control), a high-cholesterol and high-fat diet (CL diet; 38.23% CRF-1, 60% cocoa butter, 1.25% cholesterol, 0.5% sodium cholate) or a CL diet containing 0.003% β-cryptoxanthin.

value: male

value: liver


title: liver_CL diet_0.005%  β-cryptoxanthin_rep 2


title: liver_CL diet_0.005%  β-cryptoxanthin_rep 1


title: liver_CL diet_rep 4

description: Gene expression data from liver after 12 week feeding of CL diet

source_name: liver, fed CL diet  for 12 weeks


title: liver_CL diet_0.005%  β-cryptoxanthin_rep 4


title: liver_CL diet_rep 5


title: pBABE_plasmid_with_steA_L2_rep3


title: case-9_Germline DNA

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

hyb_protocol: Microarrays were hybridized using the Sure Hyb chamber in a rotisserie oven at 65°C for 40 h.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version11.0.1.1).

data_processing: Analysis and visualization were performed with DNA Analytics software (version 4.081, Agilent)

source_name: peripheral blood

label_protocol: Patient’s DNA and reference DNA samples were labeled by random priming with either, Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS

extract_protocol: Genomic DNA was obtained using proteinase K/RNAse treatment and phenol-chloroform extraction according to standard procedures.

value: peripheral blood

value: F

source_name: pooled healthy donor

value: M


title: liver_CL diet_rep 3


title: case-6_Germline DNA


title: liver_CL diet_0.005%  β-cryptoxanthin_rep 3


title: liver_CL diet_rep 2


title: case-3_Germline DNA


title: M990115

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

description: MeDIP on M990115 melanoma cells

hyb_protocol: Samples were hybridized at 42°C for 20 hours

scan_protocol: Arrays were scanned with MS 200 Microarray Scanner according to manufactorer's protocol

data_processing: Arrays were processed with Nimblescan 2.5 standard protocol for MeDIP

source_name: Input DNA from M990115 melanoma cells

label_protocol: 1.5 ug of MeDIP DNA and 1.5 ug of input DNA were labellled with Cy5 and Cy3 respectively by Nimblegen Dual-Color DNA Labeling Kit

growth_protocol: RPMI1640 + 10%FCS + 5 mM glutamine

extract_protocol: Genomic DNA was extracted by Dneasy Blood & Tissue Kit (QIAGEN), sheared into 300-500bp fragments by sonication (Covaris), and aliquots 5 ug were incubated with 10 uL of anti-5-methylcytidine antibody (Eurogentec) overnight at 4°C. Antibody-bound DNA was precipated with 40uL of Dynabeeds (M-280 sheep antibody to mouse IgG, Invitrogen) at 4°C for 2 h on a rotating wheel. Bound DNA was eluted by proteinase K incubation for 3 hours at 50°C and purified by standard phenol/chloroform procedure.

value: primary melanoma cells

tag: phenotype

value: Invasive

source_name: MeDIP DNA from M990115 melanoma cells


title: case-1_Germline DNA


title: case-9_cNF DNA

source_name: cutaneous neurofibroma

value: cutaneous neurofibroma


title: case-4_Germline DNA


title: M010119

description: MeDIP on M010119 melanoma cells

source_name: Input DNA from M010119 melanoma cells

source_name: MeDIP DNA from M010119 melanoma cells


title: M080201

description: MeDIP on M080201 melanoma cells

source_name: Input DNA from M080201 melanoma cells

source_name: MeDIP DNA from M080201 melanoma cells


title: case-5_Germline DNA


title: case-7_Germline DNA


title: case-8_cNF DNA


title: case-7_cNF DNA


title: case-2_Germline DNA


title: case-8_Germline DNA


title: case-6_cNF DNA


title: M050829

description: MeDIP on M050829 melanoma cells

source_name: Input DNA from M050829 melanoma cells

value: Proliferative

source_name: MeDIP DNA from M050829 melanoma cells


title: M080310

description: MeDIP on M080310 melanoma cells

source_name: Input DNA from M080310 melanoma cells

source_name: MeDIP DNA from M080310 melanoma cells


title: case-5_cNF DNA


title: case-4_cNF DNA


title: M080423

description: MeDIP on M080423 melanoma cells

source_name: Input DNA from M080423 melanoma cells

source_name: MeDIP DNA from M080423 melanoma cells


title: liver_control diet_rep 5

description: Gene expression data from liver after 12 weeks feeding of control CRF-1 chow

source_name: liver, fed control CRF-1 chow  for 12 weeks


title: liver_CL diet_rep 1

source_name: liver, fed CL diet  for 12 weeks


title: Control ASM cells_rep3

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_4.txt (Cy3)
Sample 3 OX125 Control

hyb_protocol: Total RNA samples (50 ng) used in lncRNA and mRNA microarrays were initially labeled with Spike-In control A (for Cyanine 3-CTP) or B (for Cyanine 5-CTP). Labelled samples were then used for cDNA synthesis using the cDNA Master Mix (Agilent) and were incubated for 2 h at 40 oC followed by 15 min at 70 oC to inactivate the AffinityScript enzyme. The synthesized cDNA was then used for cRNA synthesis and amplification using the Transcription Master Mix with either Cyanine 3 or Cyanine 5 and incubated at 40 oC for 2 h. Labeled and amplified RNA was then purified using the RNeasy Mini Kit (Qiagen) and quantified using the NanoDrop Spectrophotometer’s Microarray Measurement function. The Cyanine 3 or Cyanine 5 concentrations and the cRNA concentration were used to calculate the yield (μg) and the specific activity (pmol Cy3 or Cy5 per μg cRNA) of each sample. For each microarray reaction, 300 ng of Cyanine 3- and 300 ng of Cyanine 5-labelled, linearly amplified cRNA samples were mixed and incubated together with Fragmentation buffer for 30 min, followed by the addition of Hybridization buffer. Samples were loaded onto SurePrint G3 (8 x 60 K) microarray slides (Agilent) and hybridized at 65 oC for 17 h at 10 rpm using Agilent’s Hybridization oven and SureHyb chamber. The microarrays were then disassembled and washed in GE Wash Buffer 1 (Agilent) for 60 sec at RT, followed by GE Wash Buffer 2 for 60 sec at 37 oC, followed by an acetonitrile wash (10 sec at RT) and the final wash in Stabilization and Drying solution for 30 sec at RT, to improve microarray results by preventing ozone-mediated fluorescent signal degradation. The microarrays were scanned with the Agilent Microarray Scanner G2565BA using the profile for 2-colour microarrays (AgilentG3_GX_2Color) at 5 μm resolution, dyes channel Red&Green, Scan Area 61 x 21.6 mm.

source_name: Human primary airway smooth muscle cultured for 24 h

label_protocol: mRNA samples were dual labeled using either cy3 or cy5

growth_protocol: Confluent cells were growth-arrested by FCS deprivation for 24 h in DMEM supplemented with sodium pyruvate (1 mM), L-glutamine (2 mM), nonessential amino acids (1:100), penicillin (100 U/ml)/streptomycin (100 μg/ml), amphotericin B (1.5 μg/ml), and bovine serum albumin (0.1 %). Cells were stimulated with 2.5 % FCS for 24 h.

value: Airway Smooth Muscle


title: liver_control diet_rep 2


title: liver_control diet_rep 3


title: 2.5 % FCS_rep4

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_3.txt (Cy5)
Sample 4 OXI13 FCS


title: Control ASM cells_rep2

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_4.txt (Cy5)
Sample 2 OX120 Control


title: 2.5 % FCS_rep3

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_3.txt (Cy3)
Sample 3 OX125 FCS


title: 2.5 % FCS + Dex 10-7 M_rep3

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_2.txt (Cy3)
Sample 3 OX125 Dex+FCS


title: 2.5 % FCS_rep2

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_3.txt (Cy5)
Sample 2 OX120 FCS


title: 2.5 % FCS + Dex 10-7 M_rep2

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_2.txt (Cy5)
Sample 2 OX120 Dex+FCS


title: 2.5 % FCS + Dex 10-7 M_rep4

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_2.txt (Cy5)
Sample 4 OXI13 Dex+FCS


title: IMR32, MSX1, t=48, control, rep3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Neuroblastoma were transfected with MSX1.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: IMR32, MSX1, t=48, control

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: To induce MSX1 in IMR32, doxycycline was addded to the medium. Controls were identically grown but without doxycycline.

value: Neuroblastoma

tag: msx1 expression

value: inducible


title: IMR32, MSX1, t=24, rep3


title: liver_control diet_rep 1


title: Control ASM cells_rep4

description:
Raw data: US91903684_252800413362_S01_GE2_105_Dec08_1_4.txt (Cy5)
Sample 4 OXI13 Control


title: M000921

description: MeDIP on M000921 melanoma cells

source_name: Input DNA from M000921 melanoma cells

source_name: MeDIP DNA from M000921melanoma cells


title: case-3_cNF DNA

source_name: cutaneous neurofibroma

source_name: pooled healthy donor


title: liver_control diet_rep 4


title: 2.5 % FCS + Dex 10-7 M_rep1

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_2.txt (Cy3)
Sample 1 OXI12 Dex+FCS


title: IMR32, MSX1, t=8, rep3

source_name: IMR32, MSX1, t=8


title: Wild-type embryos, biological rep4

city: New York

first: Hidetaka

last: Niizuma

state: NY

address: 1275 York Ave

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

description: 3 embryos (littermates) were pooled in this sample

hyb_protocol: Following fragmentation, ~10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 A2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed with Expression Console (Affymetrix), normalized by RMA algorithm. The signal intensity data were transformed to linear values for subsequent GSEA analyses.

source_name: E14.5 Mouse fetal liver HSCs

label_protocol: RNA samples were subjected to reverse transcription, linear amplification, and production and fragmentation of biotinylated cRNA using 3' IVT Express kit.

growth_protocol: TFIIAα-βnc/+ male and female mice were crossed for timed pregnancy. Embryos were grown until they reach embryonic day 14.5.

extract_protocol: Sorted HSCs were lysed in TRIzol reagent, and total RNA was isolated according to the manufacturer's instruction.

treatment_protocol: Embryos were quickly genotyped by PCR using DNAs extracted from their tails. Fetal liver single cell suspensions of the same genotype were pooled into a single sample. The samples were stained with following antibodies: a Lineage antibody cocktail (CD3, CD4, CD8a, B220, TER-119 and Gr-1) Pacific Blue, Sca-1 PE, c-Kit APC/Alexa750,CD150 PE/Cy7. Lineage-Sca-1+c-Kit+CD150+ cells (HSCs) were double sorted for RNA isolation.

tag: genotype

value: Wild-type


title: 2.5 % FCS_rep1

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_3.txt (Cy3)
Sample 1 OXI12 FCS


title: case-2_cNF DNA


title: IMR32, MSX1, t=0, rep3

source_name: IMR32, MSX1, t=0


title: Control ASM cells_rep1

description:
Raw data: US91903684_252800413360_S01_GE2_105_Dec08_1_4.txt (Cy3)
Sample 1 OXI12 Control


title: M010817

description: MeDIP on M010817 melanoma cells

source_name: Input DNA from M010817 melanoma cells

source_name: MeDIP DNA from M010817 melanoma cells


title: M980513

description: MeDIP on M980513 melanoma cells

source_name: Input DNA from M980513 melanoma cells

source_name: MeDIP DNA from M980513 melanoma cells


title: M080307

description: MeDIP on M080307 melanoma cells

source_name: Input DNA from M080307 melanoma cells

source_name: MeDIP DNA from M080307 melanoma cells


title: case-1_cNF DNA


title: Lactococcus chungangensis CAU 28T

city: Seoul

first: Maytiya

last: Konkit

address: 84, Heukseok-ro, Dongjak-ku

department: Microbiology

country: South Korea

institute: Chung-Ang University

description: This sample is of type strain L. chungangensis CAU 28T  .

hyb_protocol: Hybridization were carried out according to NimbleGen protocols.

scan_protocol: Arrays were scanned using the NimbleGen MS 200 Microarray Scanner

data_processing: Array data export processing and analysis was performed using NimbleScan v2.5  (RMA algorithm)  correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Pseudolactococcus chungangensis

source_name: Lactococcus chungangensis CAU 28T

label_protocol: cDNA were prepared from 10 ug total RNA using the SuperScript double-stranded cDNA synthesis kit(Invitrogen). Labeling were carried out according to NimbleGen protocols.

growth_protocol: L. lactis KCTC 3769T, L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T and L. chungangensis CAU 28T were grown on Tryptic Soy Agar (TSA)(Bacto,Dickinson and company, Sparks, U.S.A) incubated at 30°C for 18 hours excepted L. piscium  DSM 6634T was incubated under aerobic condition

extract_protocol: Total RNA was extracted using RiboPure Bacteria Kit (Ambion, UK) following manufacturer’s instructions. RNA quality and concentration was determined by analysis with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: CAU 28T

value: normal


title: Lactococcus fujiensis JSM 16395T

description: This sample is of type strain L. fujiensis JSM 16395T.

organism: Lactococcus fujiensis

source_name: Lactococcus fujiensis JSM 16395T


title: Lactococcus plantarum DSM 20686T

description: This sample is of type strain L. plantarum DSM 20686T.

organism: Pseudolactococcus plantarum

source_name: Lactococcus plantarum DSM 20686T


title: Lactococcus garvieae KCTC 3772T

description: This sample is of type strain L. garvieae KCTC 3772T .

organism: Lactococcus garvieae

source_name: Lactococcus garvieae KCTC 3772T

value: KCTC 3772T


title: IMR32, MSX1, t=0, rep2


title: TFIIAα-βnc/nc embryos, biological rep3

description: 4 embryos (littermates) were pooled in this sample

value: TFIIAα-βnc/nc


title: IMR32, MSX1, t=48, control, rep2

source_name: IMR32, MSX1, t=48, control


title: Lactococcus raffinolactis DSM 20443T

description: This sample is of type strain L. raffinolactis DSM 20443T.

organism: Pseudolactococcus raffinolactis

source_name: Lactococcus raffinolactis DSM 20443T


title: TFIIAα-βnc/nc embryos, biological rep1

description: 2 embryos (littermates) were pooled in this sample


title: Wild-type embryos, biological rep3


title: TFIIAα-βnc/nc embryos, biological rep2


title: IMR32, MSX1, t=48, rep2


title: IMR32, MSX1, t=8, rep2


title: IMR32, MSX1, t=48, rep3


title: Lactococcus piscium DSM 6634T

description: This sample is of type strain L. piscium DSM 6634T .

organism: Pseudolactococcus piscium

source_name: Lactococcus piscium DSM 6634T

value: DSM 6634T


title: Lactococcus lactis KCTC 3769T

description: This sample is of type strain L. lactis KCTC 3769T.

organism: Lactococcus lactis

source_name: Lactococcus lactis KCTC 3769T

value: KCTC 3769T


title: Wild-type embryo, biological rep1

description: 1 embryo in this sample


title: IMR32, MSX1, t=48, control, rep1


title: Wild-type embryo, biological rep2

description: 1 embryo in this sample


title: IMR32, MSX1, t=24, rep1


title: IMR32, MSX1, t=8, rep1

source_name: IMR32, MSX1, t=8


title: IMR32, MSX1, t=48, rep1


title: IMR32, MSX1, t=24, rep2


title: IMR32, MSX1, t=0, rep1


title: Sh-Ctr, replicate 1

status: Public on May 27 2014

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

hyb_protocol: Affymetrix Human gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) were hybridized with fragmented, biotin-labeled target in hybridization cocktail. Target denaturation: 2 min at 99°C, 5 min at 45°C, 18h hybridization.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Background correction and normalization with Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA).

source_name: control NP cells

label_protocol: ST-cDNAs were fragmented and biotin-labeled to generate biotinylated ST-cDNA with FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: Human nucleus pulposus cells were isolated from intervertebral discs and maintained in DMEM with 10% FBS and antibiotics.

extract_protocol: Total RNA was extracted using RNAeasy mini columns (Qiagen) and treated with DNase1. cDNA amplification was performed with Ovation Pico WTA-system V2 RNA amplification system (NuGen Technologies, Inc.).

treatment_protocol: Cells were transduced with lentivirus expressing either control or FIH-1 specific shRNA.

value: nucleus pulposus


title: PBMCs-1

city: Cartagena

first: Niradiz

last: Reyes

address: Campus de Zaragocilla. Facultad de Medicina

country: Colombia

institute: Universidad de Cartagena

description: PBMCs were cultured for 24H at the same conditions than treated samples

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: dChip v 1.3 was used for normalization, model-based gene expression estimatation and outlier detection.

source_name: PBMCs cultured for 24H before RNA extraction

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets according to standard Affymetrix protocols.

extract_protocol: standard Affymetrix procedures were used on total RNA extracted from samples

value: peripheral blood mononuclear cell

tag: exposure

value: control


title: H37Ra-2

description: PBMCs were exposed to H37Ra at a MOI=10

source_name: PBMCs exposed to H37Ra for 24H


title: Sh-FIH-1, replicate 3

source_name: FIH-1 silenced NP cells


title: PBMCs-2


title: Sh-FIH-1, replicate 1


title: Sh-Ctr, replicate 3


title: Sh-FIH-1, replicate 2


title: H37Ra-3

description: PBMCs were exposed to H37Ra at a MOI=10


title: PBMCs-3


title: H37Ra-1

description: PBMCs were exposed to H37Ra at a MOI=10


title: Sh-Ctr, replicate 2


title: genomic DNA from brain tumor 259

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

institute: Duke University

description: SAMPLE 45

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan

data_processing:
Data were interpreted in GenomeStudio v2011.1 Methylation Module 1.9.0 and exported for analysis
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: biotin nucleotide or dinitrophenyl labeled

source_name: brain tumor 45

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications

extract_protocol: Genomic DNA was extracted usingWizard® Genomic DNA Purification Kit (Cat.No.A1125, Promega, USA). Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications

value: M

tag: tumor location

value: Thalamus

tag: idh1/h3f3a mutation status

value: H3F3A MUT


title: genomic DNA from brain tumor YD-4

description: SAMPLE 35

hyb_protocol: Followed the manufacturer's (Illumina) specifications

source_name: brain tumor 35

value: Supratentorial

value: IDH1 MUT


title: genomic DNA from brain tumor 242

description: SAMPLE 37

source_name: brain tumor 37

value: F

value: Brainstem


title: genomic DNA from brain tumor 252

description: SAMPLE 38

source_name: brain tumor 38

value: IDH1/H3F3A WT


title: genomic DNA from brain tumor YD-26

description: SAMPLE 40

source_name: brain tumor 40

value: IDH1 hemizygous MUT


title: genomic DNA from brain tumor BST-14

description: SAMPLE 34

source_name: brain tumor 34


title: genomic DNA from brain tumor 241

description: SAMPLE 31

source_name: brain tumor 31


title: genomic DNA from brain tumor 249

description: SAMPLE 44

source_name: brain tumor 44


title: genomic DNA from brain tumor H1190

description: SAMPLE 32

source_name: brain tumor 32


title: genomic DNA from brain tumor 261

description: SAMPLE 30

source_name: brain tumor 30


title: genomic DNA from brain tumor YD-18

description: SAMPLE 36

source_name: brain tumor 36


title: genomic DNA from brain tumor YD-25

description: SAMPLE 41

source_name: brain tumor 41


title: genomic DNA from brain tumor 234

description: SAMPLE 42

source_name: brain tumor 42


title: genomic DNA from brain tumor YD-39

description: SAMPLE 21

source_name: brain tumor 21


title: genomic DNA from brain tumor 243

description: SAMPLE 43

source_name: brain tumor 43


title: genomic DNA from brain tumor YD-37

description: SAMPLE 39

source_name: brain tumor 39


title: genomic DNA from brain tumor YD-24

description: SAMPLE 26

source_name: brain tumor 26


title: genomic DNA from brain tumor YD-67

description: SAMPLE 25

source_name: brain tumor 25


title: genomic DNA from brain tumor 244

description: SAMPLE 33

source_name: brain tumor 33


title: genomic DNA from brain tumor 237

description: SAMPLE 20

source_name: brain tumor 20


title: genomic DNA from brain tumor BST-17

description: SAMPLE 28

source_name: brain tumor 28


title: genomic DNA from brain tumor YD-21

description: SAMPLE 23

source_name: brain tumor 23


title: genomic DNA from brain tumor YD-62

description: SAMPLE 24

source_name: brain tumor 24


title: genomic DNA from brain tumor 235

description: SAMPLE 27

source_name: brain tumor 27


title: genomic DNA from brain tumor 254

description: SAMPLE 16

source_name: brain tumor 16


title: genomic DNA from brain tumor BST-15

description: SAMPLE 29

source_name: brain tumor 29


title: genomic DNA from brain tumor YD-44

description: SAMPLE 19

source_name: brain tumor 19


title: genomic DNA from brain tumor 246

description: SAMPLE 18

source_name: brain tumor 18


title: genomic DNA from brain tumor 260

description: SAMPLE 17

source_name: brain tumor 17


title: genomic DNA from brain tumor 247

description: SAMPLE 22

source_name: brain tumor 22


title: PLE-2

city: Ilan

first: Jyh-Yih

last: Chen

address: 23-10, Dahuen Rd., Jiaushi, Ilan

institute: Academia Sinica

description: Gene expression in liver after 24 hours for injected epinecidin-1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA were fragmented and hybridized to Agilent Mouse Whole Genome Oligo 4×44K (G4122F) according to Agilent protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies Scanner G2505A) using default one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  All data were entered into Agilent GeneSpring GX12 (Agilent Technologies). Quntile normalization was applied to bring singal distribution of each array to a similar range. Then the baseline of each gene was transformed to the median value of each gene of all samples. Features with signal intensity lower than 100, or flagged as Not detected or Compomised,  in one condition were excluded. T-test unpaired was performed to find features with p-value <= 0.05. Genes with an expression level change of ≥ 2-fold (average ratio of biological duplicates of ≥ 2 or ≤ 0.5) were considered to be significantly affected by treatment. Functional enrichment of ≥ 2-fold genes was tested on David Microarray Analysis Platform (Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 ), and further data mining was done with Pathway Studio software (Ariadne Genomics, Rockville, MD, USA).

source_name: mice treated with epinecidin-1

label_protocol: Total RNA (0.5 μg) from each sample was amplified and labeled with cyanine-3 (Cy3), according to the 1-color labeling protocol of a Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Trizol reagent and Qiagen Rneasy Mini kit were used to extract RNA from the livers of mice treated with epinecidin-1 or PBS alone. Two independent RNA replicates were obtained and stored separately. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The mice were treated with epinecidin-1 or PBS for 24 hours

value: BALB/c

tag: tissue

value: liver

value: male

tag: agent


title: genomic DNA from brain tumor YD-43

description: SAMPLE 13

source_name: brain tumor 13


title: PLE-1


title: genomic DNA from brain tumor 248

description: SAMPLE 15

source_name: brain tumor 15


title: genomic DNA from brain tumor YD-2

description: SAMPLE 7

source_name: brain tumor 7


title: genomic DNA from brain tumor 239

description: SAMPLE 11

source_name: brain tumor 11


title: Mu_NL219_lung_d3_2

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

source_name: lung, NL219, d3

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol:
Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.
All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

tag: strain/background

value: lung

tag: infection

tag: timepoint


title: Mu_VN1203_lung_d5_2

source_name: lung, VN1203, d5


title: Mu_Mex4482_lung_d3_3

source_name: lung, Mex4482, d3


title: Mu_VN1203_lung_d3_3

source_name: lung, VN1203, d3


title: Mu_NL219_lung_d5_2

source_name: lung, NL219, d5


title: Mu_NL219_lung_d3_4


title: N-2

description: Gene expression in liver after 24 hours for injected PBS

source_name: mice treated with PBS

value: PBS


title: Mu_NL219_lung_d5_3


title: Mu_Mex4482_lung_d1_3

source_name: lung, Mex4482, d1


title: Mu_VN1203_lung_d5_3


title: Mu_Anhui01_lung_d3_4

source_name: lung, Anhui01, d3


title: Mu_VN1203_lung_d3_5


title: genomic DNA from brain tumor YD-23

description: SAMPLE 4

source_name: brain tumor 4

tag: age


title: Mu_Mex4482_lung_d1_2


title: N-1


title: genomic DNA from brain tumor 250

description: SAMPLE 3

source_name: brain tumor 3


title: Mu_Anhui01_lung_d1_4

source_name: lung, Anhui01, d1


title: genomic DNA from brain tumor 245

description: SAMPLE 14

source_name: brain tumor 14


title: Mu_NL219_lung_d1_5

source_name: lung, NL219, d1


title: genomic DNA from brain tumor 258

description: SAMPLE 10

source_name: brain tumor 10


title: genomic DNA from brain tumor 313

description: SAMPLE 6

source_name: brain tumor 6


title: genomic DNA from brain tumor YD-1

description: SAMPLE 9

source_name: brain tumor 9


title: Mu_NL219_lung_d1_1


title: Mu_Anhui01_lung_d5_3

source_name: lung, Anhui01, d5


title: Mu_Mex4482_lung_d5_1

source_name: lung, Mex4482, d5


title: Mu_mock_lung_d3_2

source_name: lung, mock, d3

value: mock


title: genomic DNA from brain tumor YD-16

description: SAMPLE 5

source_name: brain tumor 5


title: Mu_Mex4482_lung_d3_2

source_name: lung, Mex4482, d3


title: genomic DNA from brain tumor H1377

description: SAMPLE 8

source_name: brain tumor 8


title: Mu_Mex4482_lung_d1_5


title: Mu_mock_lung_d1_2

source_name: lung, mock, d1


title: Mu_Mex4482_lung_d5_3


title: Mu_mock_lung_d1_1


title: Mu_Anhui01_lung_d1_3


title: Mu_VN1203_lung_d3_1

source_name: lung, VN1203, d3


title: Mu_Anhui01_lung_d5_4


title: Mu_NL219_lung_d3_5

source_name: lung, NL219, d3


title: Mu_mock_lung_d5_1

source_name: lung, mock, d5


title: Mu_Anhui01_lung_d5_5


title: Mu_NL219_lung_d5_5

source_name: lung, NL219, d5


title: Mu_NL219_lung_d1_3


title: Mu_Anhui01_lung_d3_3

source_name: lung, Anhui01, d3


title: Mu_NL219_lung_d5_1


title: genomic DNA from brain tumor 240

description: SAMPLE 2

source_name: brain tumor 2


title: Mu_Mex4482_lung_d5_5


title: genomic DNA from brain tumor BST-2

description: SAMPLE 1

source_name: brain tumor 1


title: Mu_Anhui01_lung_d3_5


title: Mu_Mex4482_lung_d1_1

source_name: lung, Mex4482, d1


title: Mu_Anhui01_lung_d3_1


title: Mu_Mex4482_lung_d5_2


title: Mu_Mex4482_lung_d3_1


title: Mu_mock_lung_d5_2


title: Mu_mock_lung_d1_3


title: Mu_Anhui01_lung_d1_1

source_name: lung, Anhui01, d1


title: Mu_VN1203_lung_d1_1

source_name: lung, VN1203, d1


title: Mu_mock_lung_d3_3


title: Mu_NL219_lung_d1_2

source_name: lung, NL219, d1


title: brain tumor BST-17

hyb_protocol: Array hybridization and wash was performed using GeneChipR Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization  Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station  450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer's instructions.

scan_protocol: Slides were scanned by GeneChipR Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Robust Multichip Average (RMA) method by R was used for data processing and normalization

source_name: brain tumor 20

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3'IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer's instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018¡ALife technologies, Carlsbad, CA, US)following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: IDH1/H3F3A wild type


title: Mu_VN1203_lung_d1_4


title: Mu_VN1203_lung_d1_3


title: brain tumor 245

source_name: brain tumor 17


title: Mu_VN1203_lung_d5_1

source_name: lung, VN1203, d5


title: brain tumor 244

source_name: brain tumor 16


title: brain tumor 246

source_name: brain tumor 12


title: brain tumor 252

source_name: brain tumor 18


title: Mu_Mex4482_lung_d5_4

source_name: lung, Mex4482, d5


title: brain tumor 247

source_name: brain tumor 13


title: brain tumor 237

source_name: brain tumor 15


title: Mu_NL219_lung_d5_4

source_name: lung, NL219, d5


title: brain tumor BST-2

source_name: brain tumor 10


title: brain tumor BST-14

source_name: brain tumor 11


title: Mu_Mex4482_lung_d3_4

source_name: lung, Mex4482, d3


title: brain tumor 261

source_name: brain tumor 9


title: brain tumor BST-15

source_name: brain tumor 19


title: Mu_VN1203_lung_d1_2

source_name: lung, VN1203, d1


title: brain tumor 260

source_name: brain tumor 14


title: brain tumor 258

source_name: brain tumor 21


title: genomic DNA from brain tumor 251

description: SAMPLE 12


title: brain tumor 250

source_name: brain tumor 8


title: Mu_Anhui01_lung_d5_2

source_name: lung, Anhui01, d5


title: Mu_VN1203_lung_d1_5


title: brain tumor 241

source_name: brain tumor 7


title: brain tumor 235

source_name: brain tumor 6


title: brain tumor 248

source_name: brain tumor 2


title: brain tumor 259

source_name: brain tumor 5


title: Mu_Anhui01_lung_d3_2

source_name: lung, Anhui01, d3


title: brain tumor 249

source_name: brain tumor 3


title: Mu_Anhui01_lung_d1_2

source_name: lung, Anhui01, d1


title: Mu_mock_lung_d3_1

source_name: lung, mock, d3


title: brain tumor 254

source_name: brain tumor 4


title: Mu_mock_lung_d5_3

source_name: lung, mock, d5


title: Mu_NL219_lung_d3_3

source_name: lung, NL219, d3


title: Mu_Mex4482_lung_d1_4

source_name: lung, Mex4482, d1


title: brain tumor 243

source_name: brain tumor 1


title: second_trimester_euploid_male2 [microarray]

city: Boston

first: Lillian

last: Zwemer

state: MA

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

description:
GSM ID (previous GEO IDs for same sample): GSM1128150
gene expression data from normal second trimester fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: cell-free RNA from second trimester amniotic fluid supernatant

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 10 mL amniotic fluid supernatant (centrifugation at 350g, 4C, 10, min).All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: source


title: Mu_VN1203_lung_d3_2

source_name: lung, VN1203, d3


title: second_trimester_euploid_male3 [microarray]

description:
GSM ID (previous GEO IDs for same sample): GSM1128151
gene expression data from normal second trimester fetus

tag: gender

value: second trimester amniotic fluid supernatant


title: second_trimester_euploid_female1 [microarray]

description:
GSM ID (previous GEO IDs for same sample): GSM1128147
gene expression data from normal second trimester fetus

value: female


title: second_trimester_euploid_female2 [microarray]

description:
GSM ID (previous GEO IDs for same sample): GSM1128148
gene expression data from normal second trimester fetus


title: second_trimester_euploid_male1 [microarray]

description:
GSM ID (previous GEO IDs for same sample): GSM1128149
gene expression data from normal second trimester fetus


title: Mu_Mex4482_lung_d3_5

source_name: lung, Mex4482, d3


title: Mu_Anhui01_lung_d1_5


title: human endomyocardIA/IgGl biopsy Co4

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip System Confocal Scanner 3000.

data_processing: Expression raw data were transferred to Rosetta Resolver 7.2 (Rosetta Inpharmatics LLC) and MAS 5.0 extraction algorithm was performed. For further analyses probe sets  exhibiting p<0.05 were used. The pipeline calculates expression summaries using MAS5 via Affymetrix Power Tools from scans using both the perfect-match (PM) and mis-match (MM) probes. It returns only sequence-level results. The resulting P-values may be used as a guideline to decide expression presence or absence. This pipeline combines the expression values for individual profiles using an arithmetic average and computes the error of the result. P-value is the geometric mean of the profile-level P-values. Results are computed from sequence-level data using group processing. All profiles in the experiment definition are normalized together.

source_name: human endomyocardIA/IgGl biopsy Co4

label_protocol: Two round T7 RNA polymerase mediated linear amplification was performed with 14-25ng RNA starting amount according to the Affymetrix manufacturers Two Cycle Target Labelling protocol

extract_protocol: Column based RNA extraction (Qiagen) was performed following the manufacturers instructions for total RNA isolation from fibrous tissues, including purifications step using Charge Switch Total RNA Cell Kit. RNA integrity was checked using RNA 6000 Pico LabChip on a Bioanalyzer 2100 (Agilent)

tag: sample type

value: endomyocardial biopsy

tag: lvef

tag: lvidd

tag: virus

value: negative

tag: inflammation (cd68+ + cd3+)

tag: bmi


title: human endomyocardIA/IgGl biopsy Co14

source_name: human endomyocardIA/IgGl biopsy Co14


title: human endomyocardIA/IgGl biopsy Co19

source_name: human endomyocardIA/IgGl biopsy Co19


title: Mu_VN1203_lung_d5_4

source_name: lung, VN1203, d5


title: human endomyocardIA/IgGl biopsy Co12

source_name: human endomyocardIA/IgGl biopsy Co12


title: human endomyocardIA/IgGl biopsy Co18

source_name: human endomyocardIA/IgGl biopsy Co18


title: Mu_NL219_lung_d3_1


title: human endomyocardIA/IgGl biopsy Co13

source_name: human endomyocardIA/IgGl biopsy Co13


title: human endomyocardIA/IgGl biopsy Co10

source_name: human endomyocardIA/IgGl biopsy Co10


title: Mu_NL219_lung_d1_4

source_name: lung, NL219, d1


title: Mu_Anhui01_lung_d5_1

source_name: lung, Anhui01, d5


title: DCM_human endomyocardIA/IgGl biopsy P20  IA/IgG_baseline

description: P20  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P28  IA/IgG_baseline

description: P28  IA_BL

value: EBV


title: Mu_VN1203_lung_d3_4


title: DCM_human endomyocardIA/IgGl biopsy P41  IA/IgG_baseline

description: P41  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P19  IA/IgG_baseline

description: P19  IA_BL


title: human endomyocardIA/IgGl biopsy Co11

source_name: human endomyocardIA/IgGl biopsy Co11


title: DCM_human endomyocardIA/IgGl biopsy P24  IA/IgG_baseline

description: P24  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P49  IA/IgG_baseline

description: P49  IA_BL


title: WSB_MEF_18h_Mock_c

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

data_processing: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K Mouse Whole Genome Gene Expression Microarray (ID G4122F).Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. Extracted raw data was background corrected using the norm-exp method and quantile normalized using R and the limma Bioconductor package.

source_name: Mouse strain, cell type (MEF), timepoint (18h p.i.), treatment/stimulation, biological replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Mouse embryonic fibroblasts obtained from the eight Founder mouse strains of the Collaborative Cross were maintained in DMEM (Dulbecco’s minimal essential medium) with 10% fetal bovine serum (FBS) and 1% P/S.

extract_protocol: After 16 hours, cells were washed once with 1X DPBS and harvested in 500 μl of QIAzol Lysis Reagent. Samples were stored at -80C prior to processing RNAs. Total RNA was extracted following the miRNeasy Mini kit’s procedure (Qiagen, Valencia, CA), and sample quality was tested on a 2100 Bioanalyzer (Agilent, Palo Alto, CA). A total of 1500 ng Cy3-labeled probe was used for microarray slide hybridizations, thereby normalizing for the input RNA amount.  Samples were measured with 4x44K Mouse Whole Genome Gene Expression Microarray (Agilent Technologies).

treatment_protocol: Mouse embryonic fibroblasts cell lines were treated with either mouse recombinant Interferon-α4 (50 units/ml; PBL InterferonSource, 12110-1), Interferon-β (100 units/ml; PBL InterferonSource, 12400-1), Interferon-γ (10 ng/ml; Sigma, I5517) or Interleukin-28β/Interferon-λ3 (25 ng/ml; PBL InterferonSource, 12820-1). Treatments were done in replicates of three and at 16 hr post-treatment samples were collected for RNA extraction.

tag: cell line founder animal

value: WSB

tag: treatment

value: Mock


title: DCM_human endomyocardIA/IgGl biopsy P56  IA/IgG_baseline

description: P56  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P42  IA/IgG_baseline

description: P42  IA_BL


title: BL6_MEF_18h_Mock_b


title: DCM_human endomyocardIA/IgGl biopsy P55  IA/IgG_baseline

description: P55  IA_BL

value: HHV6B, EBV


title: DCM_human endomyocardIA/IgGl biopsy P54  IA/IgG_baseline

description: P54  IA_BL


title: PWK_MEF_18h_Mock_a

value: PWK


title: DCM_human endomyocardIA/IgGl biopsy P53  IA/IgG_baseline

description: P53  IA_BL

value: HHV6 A


title: PWK_MEF_18h_Mock_b


title: DCM_human endomyocardIA/IgGl biopsy P50  IA/IgG_baseline

description: P50  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P51  IA/IgG_baseline

description: P51  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P52  IA/IgG_baseline

description: P52  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P48  IA/IgG_baseline

description: P48  IA_BL


title: NZO_MEF_18h_Mock_c

value: NZO


title: WSB_MEF_18h_Mock_b


title: WSB_MEF_18h_Mock_a


title: AJ_MEF_18h_Mock_c

value: AJ


title: AJ_MEF_18h_Mock_a


title: NZO_MEF_18h_Mock_b


title: DCM_human endomyocardIA/IgGl biopsy P43  IA/IgG_baseline

description: P43  IA_BL

value: male


title: DCM_human endomyocardIA/IgGl biopsy P46  IA/IgG_baseline

description: P46  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P40  IA/IgG_baseline

description: P40  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P47  IA/IgG_baseline

description: P47  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P45  IA/IgG_baseline

description: P45  IA_BL


title: PWK_MEF_18h_Mock_c


title: DCM_human endomyocardIA/IgGl biopsy P39  IA/IgG_baseline

description: P39  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P44  IA/IgG_baseline

description: P44  IA_BL


title: NOD_MEF_18h_Mock_c

value: NOD


title: DCM_human endomyocardIA/IgGl biopsy P37  IA/IgG_baseline

description: P37  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P36  IA/IgG_baseline

description: P36  IA_BL

value: EBV,


title: DCM_human endomyocardIA/IgGl biopsy P38  IA/IgG_baseline

description: P38  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P32  IA/IgG_baseline

description: P32  IA_BL


title: AJ_MEF_18h_Mock_b


title: DCM_human endomyocardIA/IgGl biopsy P35  IA/IgG_baseline

description: P35  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P34  IA/IgG_baseline

description: P34  IA_BL


title: 129_MEF_18h_Mock_a


title: CAST_MEF_18h_Mock_b

value: CAST


title: DCM_human endomyocardIA/IgGl biopsy P31  IA/IgG_baseline

description: P31  IA_BL


title: STC6

city: Wuhan

first: Congqing

last: Jiang

state: Hubei

address: 169 Donghu Road, Wuchang District

department: Department of Colorectal Surgery

institute: Zhongnan Hospital of Wuhan University

description: STC6 (张永清DL)

hyb_protocol: Standard Agilent protocol.

scan_protocol: After hybridization, the microarrays were washed and scanned with a laser confocal scanner (G2565BA, Agilent Technologies, Palo Alto, CA, US) according to the manufacturer’s instructions.

data_processing:
The intensities of fluorescence were calculated by Agilent Feature Extraction (FE) software version 9.5.3 and analyzed with Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).
The Gene Spring software generated unique values for each miRNA species and determined the average of the results from six spots. The samples were normalized using the on-chip median normalization feature of Gene Spring software. MiRNAs with an altered expression were identified using the filter of the n-fold-change tool. An analysis of variance (ANOVA) was used to compare the average values obtained with miRNA probes in all samples.

source_name: Full-thickness colonic specimen, STC

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Agilent Technologies p/n 5190-0456, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was isolated from frozen histologic specimens using a mirVana™ RNA isolation Kit (Applied Biosystems p/n AM1556, Foster City, CA, US) according the manufacturer’s instructions.

tag: disease state

value: severe STC

value: colon


title: NC5

description: NC5 (2_1)

source_name: Full-thickness colonic specimen, control

value: control

value: female

tag: tissue


title: DCM_human endomyocardIA/IgGl biopsy P11  IA/IgG_baseline

description: P11  IA_BL

value: endomyocardial biopsy


title: STC5

description: STC5 (2_2)


title: DCM_human endomyocardIA/IgGl biopsy P13  IA/IgG_baseline

description: P13  IA_BL

value: negative


title: DCM_human endomyocardIA/IgGl biopsy P30  IA/IgG_baseline

description: P30  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P27  IA/IgG_baseline

description: P27  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P15  IA/IgG_baseline

description: P15  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P25  IA/IgG_baseline

description: P25  IA_BL


title: 129_MEF_18h_Mock_c


title: DCM_human endomyocardIA/IgGl biopsy P16  IA/IgG_baseline

description: P16  IA_BL


title: NC6

description: NC6 (张永清Nor)


title: BL6_MEF_18h_Mock_c


title: STC3

description: STC3 (11.9D)


title: STC4

description: STC4 (2_4)


title: DCM_human endomyocardIA/IgGl biopsy P21  IA/IgG_baseline

description: P21  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P23  IA/IgG_baseline

description: P23  IA_BL


title: DCM_human endomyocardIA/IgGl biopsy P18  IA/IgG_baseline

description: P18  IA_BL


title: CAST_MEF_18h_Mock_a


title: DCM_human endomyocardIA/IgGl biopsy P22  IA/IgG_baseline

description: P22  IA_BL


title: 129_MEF_18h_Mock_b


title: NC4

description: NC4 (2_3)


title: NOD_MEF_18h_Mock_a


title: NC2

description: NC2 (11.2N)


title: STC2

description: STC2 (11.2D)


title: STC1

description: STC1 (11.12D)


title: NC3

description: NC3 (11.9N)


title: NC1

description: NC1 (11.12N)


title: BL6_MEF_18h_Mock_a


title: BL6_MEF_18h_IFNb_c

value: IFNb


title: CAST_MEF_18h_IFNb_c


title: NZO_MEF_18h_Mock_a

value: Mock


title: WSB_MEF_18h_IFNb_c

value: WSB


title: VN3040.7_sample 32

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

description: SAMPLE 32

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

organism: Macaca mulatta

source_name: Bronchial Brush

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA was extracted from bronchial brushes with the RNeasy Mini Kit (Qiagen, Hilden, Germany)  following the manufacturer's recommendation.

treatment_protocol: Tissue from brushes were placed in the RNA stabilization reagent RNAlater (Ambion, CA) and stored at -80°C. All tissues were thawed together and homogenized (2 minutes at 30Hz) by using a TissueLyser (Qiagen, Hilden, Germany), following the manufacturer’s instructions.

tag: animal number

tag: influenza strain

tag: time (days post infection)

value: Bronchial Brush


title: VN3040.7_sample 46

description: SAMPLE 46


title: VN3040.Pre_sample 28

description: SAMPLE 28

value: Pre


title: VN3040.5_sample 26

description: SAMPLE 26


title: NOD_MEF_18h_Mock_b


title: AJ_MEF_18h_IFNb_a


title: VN3040.3_sample 44

description: SAMPLE 44


title: VN3040.1_sample 24

description: SAMPLE 24


title: VN3040.7_sample 27

description: SAMPLE 27


title: VN3040.3_sample 30

description: SAMPLE 30


title: 129_MEF_18h_IFNb_b


title: WSB_MEF_18h_IFNb_a


title: VN3040.Pre_sample 2

description: SAMPLE 2


title: NOD_MEF_18h_IFNb_a


title: PWK_MEF_18h_IFNb_c

value: PWK


title: VN3040.1_sample 29

description: SAMPLE 29


title: VN3040.5_sample 31

description: SAMPLE 31


title: VN3040.3_sample 25

description: SAMPLE 25


title: WSB_MEF_18h_IFNb_b


title: BL6_MEF_18h_IFNb_a


title: VN3040.5_sample 45

description: SAMPLE 45


title: NOD_MEF_18h_IFNb_b


title: BL6_MEF_18h_IFNb_b


title: VN3040.1_sample 43

description: SAMPLE 43


title: VN30259.3_sample 15

description: SAMPLE 15


title: 129_MEF_18h_IFNb_c


title: VN30259.7_sample 6

description: SAMPLE 6


title: VN30259.5_sample 16

description: SAMPLE 16


title: VN30259.1_sample 14

description: SAMPLE 14


title: VN3040.Pre_sample 23

description: SAMPLE 23


title: VN30259.5_sample 5

description: SAMPLE 5


title: NZO_MEF_18h_IFNb_a

value: NZO


title: AJ_MEF_18h_IFNb_c

value: AJ


title: VN30259.3_sample 4

description: SAMPLE 4


title: CAST_MEF_18h_Mock_c


title: CAST_MEF_18h_IFNb_a


title: PWK_MEF_18h_IFNb_a


title: CAST_MEF_18h_IFNa_b

value: IFNa


title: PWK_MEF_18h_IFNb_b


title: AJ_MEF_18h_IFNb_b


title: VN30259.Pre_sample 13

description: SAMPLE 13


title: NZO_MEF_18h_IFNb_b


title: NOD_MEF_18h_IFNb_c

value: NOD


title: NOD_MEF_18h_IFNa_a


title: NZO_MEF_18h_IFNb_c


title: CAST_MEF_18h_IFNb_b

value: CAST


title: VN30259.7_sample 17

description: SAMPLE 17


title: VN30259.1_sample 3

description: SAMPLE 3


title: NZO_MEF_18h_IFNa_a


title: VN30259.Pre_sample 7

description: SAMPLE 7


title: Asalm_delta_iron_rep6

city: Tromsoe

first: Espen

middle: Mikal

last: Robertsen

address: Breivika

department: Chemistry

country: Norway

institute: University of Tromsoe

description: Sample 6

hyb_protocol: Samples were hybridized to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 2×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.). Images were quantified using the GenePix v6.1 software

data_processing: The quantified signals were background corrected using “normexp” (LIMMA) with offset value 50 and normalized using print-tip loess and between-array quantile normalization. The expression data were analyzed using the LIMMA package in Bioconductor (http://www.bioconductor.org).

organism: Aliivibrio salmonicida LFI1238

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 18 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

growth_protocol: Six individual colonies (i.e. biological replicates)  of Aliivibrio salmonicida LFI1238 were grown in lysogen broth containing 1% NaCl at 200 rpm at 8°C until they reached an Optical denisty at 600nm at 0.5. Before treatment each relicate was split in two new flasks keeping one halv of the culture as as an untreated control and one halv was treated with 2,2-dipyridyl.

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

treatment_protocol: Each of the six replicates were split in two halves at OD600nm 0.5, keeping one halv of each replicate as control (still growing while the treated samles were growing with 2,2-dipyridyl treatment) while the other halv was treated with 50µM 2,2-dipyridyl for 15 minutes. Cells were then spun at 4000 rpm at 4°C for 10 minutes, supernatant were removed and cells flash frozen and then kept at -70°C.

value: Chelation


title: VN30259.5_sample 40

description: SAMPLE 40


title: Asalm_delta_iron_rep5

description: Sample 5


title: VN30259.3_sample 39

description: SAMPLE 39


title: VN30259.1_sample 38

description: SAMPLE 38


title: NZO_MEF_18h_IFNa_b


title: VN30259.7_sample 41

description: SAMPLE 41


title: NZO_MEF_18h_IFNa_c


title: CAST_MEF_18h_IFNa_a


title: NOD_MEF_18h_IFNa_c


title: VN30259.Pre_sample 1

description: SAMPLE 1


title: Asalm_delta_iron_rep3

description: Sample 3


title: Asalm_delta_iron_rep2

description: Sample 2


title: AJ_MEF_18h_IFNa_c


title: Asalm_delta_iron_rep4

description: Sample 4


title: VN3028II.7_sample 37

description: SAMPLE 37


title: VN3028II.1_sample 34

description: SAMPLE 34


title: CAST_MEF_18h_IFNa_c


title: VN3028II.7_sample 22

description: SAMPLE 22


title: VN3028II.3_sample 35

description: SAMPLE 35


title: VN3028II.5_sample 36

description: SAMPLE 36


title: Asalm_delta_iron_rep1

description: Sample 1


title: VN3028II.Pre_sample 33

description: SAMPLE 33


title: VN3028II.5_sample 21

description: SAMPLE 21


title: WSB_MEF_18h_IFNa_b


title: VN3028II.1_sample 19

description: SAMPLE 19


title: VN3028II.3_sample 20

description: SAMPLE 20


title: WSB_MEF_18h_IFNa_a


title: BL6_MEF_18h_IFNa_c


title: AJ_MEF_18h_IFNa_b


title: VN3028II.7_sample 11

description: SAMPLE 11


title: Small cell lung cancer from transgenic mouse CK5-PAP-2303.2, Biological replicate 2

city: Baronissi (SA)

first: Rosanna

last: Martinelli

address: Via Allende

department: Medicine and Surgery

country: Italy

institute: Salerno University

description: Biological replicate 2

hyb_protocol: Equal amounts of cRNA (825ng) from control and from transgenic mouse were combined in a total volume of  55 μL and incubated at 60°C for 30 min. Mix of samples and 55 μL of 2X GEx Hybridization buffer HI-RPM (Agilent Technology) were applied to the arrays and incubate at 65° C for 17 hours with rotation at 10 rpm, using the Agilent microarray hybridization chambers SureHyb, in a hybridization oven with rotation. Microarray slide were washed with Gene Expression Wash buffer 1 at room temperature for 1 min and Gene Expression Wash buffer 2 at 37°C for 1 min. Finally to dry the slides and prevent ozone degradation arrays were treated with the Stabilization and Drying Solution for 30 seconds at room temperature (Agilent Technologies).

scan_protocol: Microarrays were scanned on Agilent DNA Microarray Scanner (Agilent Technologies) and raw data extracted using Feature Extraction software 9.5.1 (Agilent Technologies).

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

source_name: Transgenic SCLC

label_protocol: Total RNAs were labelled using the Agilent low RNA Input Fluorescence Linear Amplification kit (Agilent Technologies), following instruction manual.

extract_protocol: Lung tissues were homogenised in guanidine thiocyanate-phenol solution (QIAzolTM Lysis Reagent; Qiagen) by rotor-stator and total RNA was purified using Rneasy mini kit (Qiagen), according to the manufacturer’s protocol.  RNAs concentrations and purity was evaluated by NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNAs integrity was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: mouse model

tag: strain

value: HPV16-E6/E7 transgenic

source_name: Normal Lung

value: Littermate


title: PWK_MEF_18h_IFNa_a


title: VN3028II.Pre_sample 18

description: SAMPLE 18


title: BL6_MEF_18h_IFNa_a


title: 129_MEF_18h_IFNa_c


title: Small cell lung cancer from transgenic mouse CK5-PAP-2303.1, Technical Replicate of Biological Replicate 1


title: Small cell lung cancer from transgenic mouse CK5-PAP-2303.2, Technical Replicate of Biological Replicate 2


title: VN3028II.5_sample 10

description: SAMPLE 10


title: 129_MEF_18h_IFNa_a


title: WSB_MEF_18h_IFNa_c


title: Small cell lung cancer from transgenic mouse CK5-PAP-2303.1, Biological replicate 1

description: Biological replicate 1


title: PWK_MEF_18h_IFNa_c


title: PWK_MEF_18h_IFNa_b


title: 129_MEF_18h_IFNa_b


title: 8224

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

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

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1 for samples hyb6370, hyb6371, hyb6384 and hyb6385; version 10.5.1.1 for samples hyb8221, hyb8222, hyb8223 and hyb8224).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.5.1.1). Intensities were base 2 log-transformed. Control probes were removed.

label_protocol: RNA concentration and RNA integrity were assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 20 ng (hybs 6370, 6371, 6384, 6385) and 1.8ng - 8ng (hybs 8221, 8222, 8223, 8224) of total RNA was amplified in a 2-cycle amplification reaction as described by Baugh et al. (PMID: 11222780). During the second in vitro transcription reaction, the sample was amplified and labeled with Cyanine 3-CTP (Cy3) according to Agilent's protocol.

extract_protocol: RNeasy Micro Kit (Qiagen) with additional, on-column DNase digestion (Qiagen)

value: female

tag: age

tag: melanoma subtype

value: SSMM

tag: breslow depth

tag: clarck level

tag: cell type

value: melanoma side population


title: VN3028II.3_sample 9

description: SAMPLE 9


title: 8222

tag: gender


title: 8223

value: melanoma main population


title: 6384

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.1.1.1). Intensities were base 2 log-transformed. Control probes were removed.


title: VN3028II.1_sample 8

description: SAMPLE 8


title: 6385


title: 8221


title: 6371


title: VN3028II.Pre_sample 12

description: SAMPLE 12


title: AJ_MEF_18h_IFNa_a


title: NOD_MEF_18h_IFNa_b


title: BL6_MEF_18h_IFNa_b


title: Huh7 shDNMT1 LD G4 replicate 2

status: Public on May 26 2014

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

description:
replicate 2
Sample 56

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.9.0 in Genome Studio V2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: shDNMT1 KO Low Density 4th Generation

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.

extract_protocol: Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: Liver samples from male animals were collected at various time-points ranging from 0 weeks to 3 weeks. Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.

tag: cell line

value: Huh7 Liver Cancer Cell Line


title: Huh7 shDNMT1 HD G3 replicate 3

description:
replicate 3
Sample 54

source_name: shDNMT1 KO High Density 3rd Generation


title: Huh7 shDNMT1 LD G4 replicate 1

description:
replicate 1
Sample 55


title: Huh7 shDNMT1 LD G3 replicate 2

description:
replicate 2
Sample 50

source_name: shDNMT1 KO Low Density 3rd Generation


title: Huh7 shDNMT1 HD G4 replicate 2

description:
replicate 2
Sample 59

source_name: shDNMT1 KO High Density 4th Generation


title: Huh7 shDNMT1 HD G4 replicate 3

description:
replicate 3
Sample 60


title: Huh7 shDNMT1 HD G4 replicate 1

description:
replicate 1
Sample 58


title: Huh7 shDNMT1 HD G3 replicate 1

description:
replicate 1
Sample 52


title: Huh7 shDNMT1 HD G3 replicate 2

description:
replicate 2
Sample 53


title: Huh7 shDNMT1 HD G1 replicate 2

description:
replicate 2
Sample 47

source_name: shDNMT1 KO High Density 1st Generation


title: Huh7 shDNMT1 LD G4 replicate 3

description:
replicate 3
Sample 57


title: Huh7 shDNMT1 HD G1 replicate 1

description:
replicate 1
Sample 46


title: Huh7 shDNMT1 LD G1 replicate 2

description:
replicate 2
Sample 44

source_name: shDNMT1 KO Low Density 1st Generation


title: 6370


title: Huh7 shDNMT1 LD G3 replicate 1

description:
replicate 1
Sample 49


title: Huh7 shDNMT1 LD G1 replicate 3

description:
replicate 3
Sample 45


title: PLC Sph LDZ G3 replicate 2

description:
replicate 2
Sample 38

source_name: Sphare Low Density ZEB treated 3rd Generation

value: PLC Liver Cancer Cell Line

value: Zebularine (ZEB)


title: PLC Sph LDZ G4 replicate 1

description:
replicate 1
Sample 40

source_name: Sphare Low Density ZEB treated 4th Generation


title: Huh7 shDNMT1 LD G1 replicate 1

description:
replicate 1
Sample 43


title: Huh7 shDNMT1 LD G3 replicate 3

description:
replicate 3
Sample 51


title: PLC Sph LDZ G4 replicate 2

description:
replicate 2
Sample 41


title: PLC Sph LDZ G4 replicate 3

description:
replicate 3
Sample 42


title: Huh7 shDNMT1 HD G1 replicate 3

description:
replicate 3
Sample 48


title: PLC Sph LDZ G3 replicate 1

description:
replicate 1
Sample 37


title: GC_STAT6ko_Nbd14

city: Erlangen

first: Adriana

last: Turqueti Neves

state: Bavaria

address: Wasserturmstrasse 3/5

department: Department of Infection Biology

institute: Universitätsklinikum Erlangen

hyb_protocol: 10µg labeled RNA in hybridization cocktail, heated 5 min 99°C, cool to 45°C, centrifuge, hybridization 17h over night at 45°C on mouse Gene ST

scan_protocol: GeneChips were scanned using the Gene Scanner 3000 from Affymetrix

data_processing: Raw data analysis was performed with the Affymetrix Expression Console software, using RMA-sketch for normalization

source_name: STAT6ko GC sorted from LN of STAT6ko/WT chimera after N.brasiliensis infection

label_protocol: Gene Chip Whole Transcript Sense target labelling from Affymetrix using 200ng total RNA/Array

extract_protocol: Total cellular RNA was isolated from sorted germinal center B cells using a RNA isolation kit according to the manufacturer's instructions

treatment_protocol: Mice were infected with 500 Nippostrongylus brasiliensis larvae (L3) subcutaneously.Total RNA of draining lymph nodes was extracted 14 days after infection.

value: STAT6ko/WT mixed bone marrow chimera in the BALB/c background

tag: genotype/variation

value: WT

tag: infection

value: Nippostrongylus brasiliensis larvae

value: Lymph node

value: germinal center B cells

tag: sorted cell fraction


title: PLC Sph LDZ G3 replicate 3

description:
replicate 3
Sample 39

tag: treatment


title: PLC Sph HDZ G1 replicate 3

description:
replicate 3
Sample 36

source_name: Sphare High Density ZEB treated 1st Generation


title: PLC Sph HDZ G1 replicate 2

description:
replicate 2
Sample 35


title: GC_WT_Nbd14

source_name: WT GC sorted from LN of STAT6ko/WT chimera after N.brasiliensis infection

tag: tissue


title: PLC Sph HDU G1 replicate 1

description:
replicate 1
Sample 31

source_name: Sphare High Density ZEB untreated 1st Generation


title: PLC Sph LDZ G1 replicate 1

description:
replicate 1
Sample 28

source_name: Sphare Low Density ZEB treated 1st Generation


title: PLC Sph LDZ G1 replicate 3

description:
replicate 3
Sample 30


title: PLC Sph LDZ G1 replicate 2

description:
replicate 2
Sample 29


title: PLC Sph HDU G1 replicate 3

description:
replicate 3
Sample 33


title: BF2S vs BF2 rep 1

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (  >2-fold) in both microarray were selected as differentially expressed genes

hyb_protocol: Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and mixed into 80uL hybridization solution (3×SSC, 0.2%SDS, 5×Denhart’s, 25%  formamide). DNA in hybridization solution was denatured at 95°C for 3 min before loading onto a microarray. The array was hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS，2×SSC at 42°C for 5 min, and 0.2×SSC for 5 min at room temperature).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a LuxScan3.0 fluorescent scanner (Capital Bio Corp. Beijing, China), and image intensity data were extracted and analyzed with a GenePix Pro 4.0 (Axon Instruments, Foster City, CA).

data_processing: A space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency (both above 2-fold) in both microarray were selected as differentially expressed genes.

organism: Saccharomyces cerevisiae

source_name: BF2S:bdf1∆bdf2∆[BDF2 L][SIR2 H] under salt treatment

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Bio-Sciences, Piscataway, NJ, USA) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. The total RNA was purified using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany). Because  oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.

extract_protocol: Total yeast RNA was isolated using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany).

tag: genotype

value: BF2S:bdf1∆bdf2∆[BDF2 L][SIR2 H]

value: salt stress

source_name: BF2:bdf1∆[pYX242][pRS316] under salt treatment


title: Huh7 Sph LDZ G4 replicate 2

description:
replicate 2
Sample 26


title: PLC Sph HDU G1 replicate 2

description:
replicate 2
Sample 32


title: BF2S vs BF2 rep 2


title: PLC Sph HDZ G1 replicate 1

description:
replicate 1
Sample 34


title: Huh7 Sph LDZ G4 replicate 3

description:
replicate 3
Sample 27


title: Huh7 Sph LDZ G4 replicate 1

description:
replicate 1
Sample 25


title: Huh7 Sph LDZ G3 replicate 3

description:
replicate 3
Sample 24


title: BF2B vs BF2 rep 1

description: For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency ( > 2-fold) in both microarray were selected as differentially expressed genes

source_name: BF2B:bdf1∆bdf2∆[BDF2 L][pYX242] under salt treatment

value: BF2B:bdf1∆bdf2∆[BDF2 L][pYX242]


title: thoraric aorta, SCD, biological repl. 4

city: Graz

first: Birgit

last: Gallé

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

description: Gene expression data from thoracic aortic tissue from mice fed a standard chow diet

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays; Affymetrix GeneChip HT Hybridization, Wash and Staining Kit; Affymetrix Fluidics station 450: protocol FS_450_0007 for Cartridge Arrays

scan_protocol: Affymetrix scanner: GCS3000

data_processing:
Affymetrix Geneexpression Console (1.3.1) using Affymetrix default analysis settings for generating CEL.files
Data pre-processing and filtering (Partek Genomic Suite Software v 6.6): RMA (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summerization), ANOVA

source_name: thoraric aorta, SCD

label_protocol: NuGen Applause WT Amp Plus ST System and NuGen Biocore Biotin Module

growth_protocol: DBA/2NCrl mice were 8 weeks old at the start of the experiment.

extract_protocol: For RNA isolation the aorts were disrupted and homogenized in RLT-buffer (Qiagen)using MagNA lyzer green beads and MagNa lyzer tissue disrupter. Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer´s protocol.

treatment_protocol: DBA/2NCrl mice were fed either a high-phosphate diet (HPD) containing 20.2 g phosphorus per kg or a standard chow diet (SCD) containing 7.0 g phosphorus per kg.for 5 days, respectively.

value: thoracic aorta


title: BF2B vs BF2 rep 2


title: abdominal aorta, SCD, bioloogical repl. 4

description: Gene expression data from abdominal aortic tissue from mice fed a standard chow diet

source_name: abdominal aorta, SCD

value: abdominal aorta


title: thoaric aorta, HPD, biological repl. 2

description: Gene expression data from thoracic aortic tissue from mice fed a high phosphate diet

source_name: thoaric aorta, HPD


title: Huh7 Sph LDZ G3 replicate 2

description:
replicate 2
Sample 23