title: ribose and glucose, replicate 3

city: Helsinki

first: Elina

last: Jääskeläinen

address: P.O. Box 66 (Agnes Sjöbergin katu 2)

department: Food Hygiene and Environmental Health

institute: University of helsinki

description: Biological replicate 3 of 3 L. gasicomitatum type strain growth on ribose or glucose

hyb_protocol: Labeled amino allyl RNA (aaRNA) was fragmented at 60°C for 30 min using Gene Expression Hybridization kit (Agilent). Hybridization was performed at 65 °C with 20 rpm rotation for 16 h.

scan_protocol: Scanned on an Axon 4200 AL scanner

data_processing: R with limma package

organism: Leuconostoc gasicomitatum LMG 18811

source_name: middle of exponential phase cells in SDM + ribose

label_protocol: total RNA was used for poly(A) tailing reaction (Ambion/Applied Biosystems). Poly A labeled RNA was in vitro transcribed and labeled with cyanine 3 (Cy3, Invitrogen, Carlsbad, California) and cyanine 5 (Cy5, Invitrogen) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit

growth_protocol: SDM (20 ml) broth 25°C 20 rpm until cells were middle of exponential phase. SDM media (g/l):tween80 1g, Ammonium citrate 2g, Sodium acetate 5g, MgSO4 * 7H2O 0,1g, MnSO4 0,05g, K2HPO4 2g, Yeast extract 1,5g, Casamino acids 10g. Carbon source inosine, glucose or ribose 20 mM.

extract_protocol: Total RNA extacted using acid hot phenol-lithium chloride.

tag: carbon source

value: SDM + ribose

source_name: middle of exponential phase cells in SDM + glucose

value: SDM + glucose


title: CSS12, biological replicate 3

status: Public on Nov 11 2014

type: RNA

city: Montreal

first: Cynthia

last: Kanagaratham

state: Quebec

address: 1650 Cedar Ave.

department: Human Genetics

country: Canada

institute: McGill University

description: Gene expression data from mouse whole lung tissue

hyb_protocol: Hybridization of cartidge arrays was done using the Gene-Chip Hybridization, Wash and Stain Kit (Affymetrix) following the manufacturer's instructions.

scan_protocol: Followng hybridization gene chip was processed with the Hybridization Wash and Stain Kit (Affymetrix) following the manufacturer's instructions. Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was analyzed using the FlexArray software (McGill University). Data was normalized by Robust Multi-array Average (RMA) method for ST array. Strains were compared by cyber-T test and markers were deemed as significant if their fold change was <0.71 or >1.4 and p<0.05.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CSS12 whole lung tissue

label_protocol: cRNA was created using the Ambion WT expression Kit (Affymetrix) and cRNA was labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: All animals were house in a specific pathogen free facility in 12 hours of darkness and 12 hours of light, and with access to food and water ad libitum. Animals were sacrified by carbon dioxide overdose and lungs were collected in RNAlater stabilization reagent (Qiagen). Samples were left in RNAlater solution overnight at 4 degrees then at -80 degrees for long term storage. Lungs were collected from three different mice for each strain.

extract_protocol: All RNA samples were extracted at the same time in the same manner using the RNeasy mini kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: All animals were naïve and untreated.

tag: strain

tag: tissue

value: whole lung


title: Rice seedlings roots_V Replicate 1

city: Tainan

first: Hao-Jen

last: Huang

address: No.1, University Raod,

department: Life Sciences

country: Taiwan

institute: National Cheng Kung University

description: Biological replicate 1 of 3. Rice seedling roots with or without 1 mM-treated V

hyb_protocol: The fragmented labeled cRNA was then pooled and hybridized to the Rice Oligo DNA Microarray 44K RAP-DB (G2519F#15241; Agilent Technologies) 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.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 1 mM V

label_protocol: Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.

growth_protocol: Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.

extract_protocol: Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent  microarray analysis and semi-quantitative RT-PCR.

treatment_protocol: Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.

tag: cultivar

tag: age

value: 6 day

tag: treatment

value: exposed to 1 mM V

source_name: Rice seedlings roots were exposed to water

value: exposed to water


title: ribose and glucose, replicate 2

country: Finland

description: Biological replicate 2 of 3 L. gasicomitatum type strain growth on ribose or glucose


title: inosine and glucose, replicate 3

description: Biological replicate 3 of 4 L.gasicomitatum type strain growth on inosine or glucose

source_name: middle of exponential phase cells in SDM + inosine

value: SDM + inosine


title: inosine and glucose, replicate 2

description: Biological replicate 2 of 4 L. gasicomitatum type strain growth on glucose or inosine


title: CSS12, biological replicate 1


title: CSS12, biological replicate 2


title: ribose and glucose, replicate 1

description: Biological replicate 1 of 3 L. gasicomitatum type strain growth on ribose or glucose


title: L311

city: Ann Arbor

first: Elizabeth

middle: R.

last: Lawlor

state: MI

address: 1600 Huron Parkway

department: Pediatrics

country: USA

institute: University of Michigan

hyb_protocol: Affymetrix SOP

scan_protocol: Affymetrix GeneChip scanner

data_processing: Data were processed using Affymetrix Power Tools (APT). Robust Multi-array Average (RMA) was used to generate normalized gene-level signal intensity estimates. Only core probesets uniquely mapped to the genome were used.

organism: Homo sapiens

source_name: Primary tumor

label_protocol: Affymetrix SOP

extract_protocol: Total RNA was isolated using miRNAeasy kits (Qiagen, Valencia, CA). RNA concentrations were calculated using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE) and RNA integrity (RIN) was evaluated using the RNA 6000 PicoAssay (Agilent Technologies, Santa Clara, CA). RNA samples with RIN values of <4.0 were subjected to an RNA cleanup step using the mRNAeasy  kit (Qiagen, Valencia, CA).

tag: diagnosis

value: Ewing sarcoma

tag: study

tag: Sex

value: Male

tag: age at enrollment (days)

tag: primary tumor site

value: Extremity

tag: efs event

value: No event

tag: efs time (days)

tag: survival status

value: Alive

tag: survival time (days)

tag: experiment date

tag: tumor content


title: inosine and glucose, replicate 4

description: Biological replicate 4 of 4 L. gasicomitatum type strain growth on inosine or glucose

tag: carbon source


title: L308

value: Other


title: C57BL/6J, biological replicate 3

source_name: C57BL/6J whole lung tissue

tag: strain


title: C57BL/6J, biological replicate 2

tag: tissue


title: inosine and glucose, replicate 1

description: Biological replicate 1 of 4 L.gasicomitatum type strain growth on inosine or iglucose


title: EYFP-Actin

status: Public on Nov 10 2014

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

description: Gene expression of EYFP-actin expressed HeLa cell.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented and Hybrization using Gene Expression Hybridization Kit (Agilent) according to the user guide.

scan_protocol: Scanning images were obtained using Agilent Microarray Scanner G2565CA.

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

source_name: EYFP-Actin transfected cell, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA by using Low Input Quick Amp labeling kit, one-color (Agilent) according to the provided protocol.

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum and antibiotics (penicillin and streptomycin) at 37°C in 5% CO2 humidified atmosphere.

extract_protocol: Total RNA from cell lines was extracted using the Qiagen RNeasy kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Transfection of plasmids were performed with Fugene 6 (Promega) with 2 µg DNA according to manufacturer’s instructions.

tag: cell type

value: tumor cell

tag: cell line

value: HeLa


title: EYFP-NLS-Actin

description: Gene expression of EYFP-NLS-actin expressed HeLa cell.

source_name: EYFP-NLS-Actin transfected cell, replicate1


title: C57BL/6J, biological replicate 1


title: OsEREBP1 over expressed transgenic rice plant, biol rep. 1

city: Hyderabad

first: Rajeshwari

last: Ramanan

state: Andhra Pradesh

address: Uppal Road

department: Plant Science

country: India

institute: Centre for Cellular and molecular biology

description: Expression profile of OsEREBP1 over expressed transgenic rice plant

hyb_protocol: The biotinylated aRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rice Genome Array for 16h at 45oC and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450

scan_protocol: The gene chips were scanned on an Affymetrix Scanner 3000

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 12.6 - GX - PA  (Agilent Technology) for further analysis. The GC-RMA algorithm was used for data normalization

label: Biotin

source_name: 20 days old 4-3-1 rice seedlings

label_protocol: 150ng of total RNA was converted into biotinylated aRNA using Genechip 3' IVT Express Kit as per instructions of the manufacturer (Affymetrix)

growth_protocol: The seeds from non transgenic control rice plants (Kitaki) and OsEREBP1 over expressed transgenic rice plants  (4-3-1) were germinated in petri plates containing moistened filter paper. Three days old seedlings were transferred to plastic pots containing soil and were grown for 15 days in a green house. Two days before the actual treatment, the pots containing the rice seedlings were transferred to a growth chamber (28oC; 80% relative humidity with 12/12h light/dark cycle)

extract_protocol: 10-15 young leaves from Kitaki and 4-3-1 rice plants were harvested and subjected to total RNA isolation using Trizol (Invitrogen)

treatment_protocol: OsEREBP1  transcription factor over expressed transgenic plant comparison with non transgenic control

tag: genotype/variation

tag: line

tag: age

value: 20 day-old seedlings


title: OsEREBP1 over expressed transgenic rice plant, biol rep. 3


title: Non transgenic control, biol rep. 1

description: Expression profile of non transgenic control

source_name: 20 days old Kitaki rice seedlings

value: Non transgenic control

value: Kitaki


title: gastric normal 11 [miRNA]

city: Changchun

first: XiaoTian

last: Zhang

state: Jilin

address: No.126 of Xinmin street, College of Basic Medicine, Jilin University.

country: China

institute: Jilin University

hyb_protocol: Following fragmentation, 10 ug of cRNA  were hybridized at 45℃ and rotated at 60rpm for 17 h with Eukaryotic Hybridization Control Kit and Hybridization, Wash and Stain Kit(affymetrix),Fluidics washing is Hybridization, Wash and Stain KitFS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Data were processed using GeneBASE software.using RMA to get the gene core signal from each probe.

source_name: gastric normal 11

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: Tissues dissected from surgery patients

extract_protocol: Tissue RNA was isolated using Trizol and further isolated using the MirVanaTM miRNA lsolation Kit according to the manufacturer’s instructions.

treatment_protocol: All tissues were taken from surgery room and snap-frozen and stored in liquid nitrogen within 10 min after the resection, for RNA extraction.

tag: gender


title: gastric normal 6 [miRNA]

source_name: gastric normal 6

value: Female


title: gastric normal 13 [miRNA]

source_name: gastric normal 13


title: gastric normal 4 [miRNA]

source_name: gastric normal 4


title: gastric normal 14 [miRNA]

source_name: gastric normal 14


title: gastric normal 5 [miRNA]

source_name: gastric normal 5


title: gastric normal 8 [miRNA]

source_name: gastric normal 8


title: gastric normal 7 [miRNA]

source_name: gastric normal 7


title: gastric normal 10 [miRNA]

source_name: gastric normal 10


title: Non transgenic control, biol rep. 2


title: gastric normal 9 [miRNA]

source_name: gastric normal 9


title: gastric normal 3 [miRNA]

source_name: gastric normal 3


title: gastric cancer 15 [miRNA]

source_name: gastric cancer 15


title: gastric cancer 14 [miRNA]

source_name: gastric cancer 14


title: Non transgenic control, biol rep. 3


title: gastric cancer 12 [miRNA]

source_name: gastric cancer 12


title: gastric normal 1 [miRNA]

source_name: gastric normal 1


title: gastric normal 12 [miRNA]

source_name: gastric normal 12


title: gastric cancer 11 [miRNA]

source_name: gastric cancer 11


title: gastric cancer 13 [miRNA]

source_name: gastric cancer 13


title: gastric normal 2 [miRNA]

source_name: gastric normal 2


title: gastric normal 15 [miRNA]

source_name: gastric normal 15


title: OsEREBP1 over expressed transgenic rice plant, biol rep. 2

source_name: 20 days old 4-3-1 rice seedlings


title: gastric cancer 7 [miRNA]

source_name: gastric cancer 7


title: gastric cancer 8 [miRNA]

source_name: gastric cancer 8


title: gastric cancer 9 [miRNA]

source_name: gastric cancer 9


title: 6X-SuUR

type: genomic

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: Raw data was normailized LOESS normalized using the Ringo package in R.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: stage 13 egg chamber

label_protocol: DNA was labeled  by random priming and purified with an Amicon Ultra 30K column (Millipore)

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol: Egg chambers were resupended in genomic DNA extraction buffer (10mM Tris pH8.0, 1mM EDTA, 100mM NaCl, 0.5% SDS), dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.

treatment_protocol: Ovaries were hand dissected from females fattened for 2 days on wet yeast in EBR. Stage 13 egg chambers were isolated and transferred to EBR on ice until 100 egg chambers were collected. Egg chambers were stored at -20oC until all egg chambers from each genotype were collected.

tag: developmental stage

value: stage 13 egg chamber

source_name: Oregon R (Wild-type) embryonic 0-2h diploid gDNA

value: Wild-type (Oregon R)

value: embryonic 0-2h


title: gastric cancer 6 [miRNA]

source_name: gastric cancer 6


title: gastric cancer 4 [miRNA]

source_name: gastric cancer 4


title: OregonR (stage 13)


title: gastric cancer 5 [miRNA]

source_name: gastric cancer 5


title: SuUR-/-

value: SuUR-/-


title: gastric cancer 1 [miRNA]

source_name: gastric cancer 1


title: 4X-SuUR


title: gastric cancer 2 [miRNA]

source_name: gastric cancer 2


title: gastric cancer 10 [miRNA]

source_name: gastric cancer 10


title: gastric cancer 3 [miRNA]

source_name: gastric cancer 3


title: C26_heart 3

city: Sydney

first: David

middle: Cho Yau

last: Fung

state: New South Wales

address: Gate 10, Botany Street

country: Australia

institute: University of New South Wales

description: C26 colon cancer cell inoculated

hyb_protocol: According to the manufacturer’s protocol, Ambion® WT reagent kit (Life Technologies™, Carlsbad, CA, USA)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were collected using the GeneChip operating software (GCOS) v1.4 (Affymetrix, Santa Clara, CA, USA). Probe summarization and quantile normalization of log2 probe intensities using RMA were conducted with the use of Partek® Genomics Suite™ version 6.6 software (Partek, St. Louis, MO, USA) .
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: C26, whole heart

label_protocol: 250ng of total RNA from each sample were submitted to cDNA synthesis, biotin labeling, cDNA fragmentation, and hybridization with microarray probes using the Ambion® WT reagent kit (Life Technologies™, Carlsbad, CA, USA) according to the manufacturer’s protocol.

growth_protocol: C26 carcinoma cells (Amgen Inc., Thousand Oaks, California) were maintained in RPMI/Penicillin Streptomycin PS in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Frozen gastrocnemius and cardiac muscles were homogenized in TRIzol® reagent for the extraction of total RNA according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: For tumor inoculation, 1 x 10E6 C26 cells in 100 μl RPMI/PS were subcutaneously inoculated in the upper right flank of the mice.  Non-tumor-bearing (NTB) control mice were injected with 100 μl RPMI/PS. Whole gastrocnemius muscle and heart were extracted from separate cohorts of mice, snap-frozen in liquid nitrogen and stored at -80°C until further processing.

value: Balb/c-DBAj hybrid

value: 10-11 weeks

value: myocardium


title: NTB_skeletal 1

description: RPMI/PS inoculated

source_name: Normal gastrocnemius

value: gastrocnemius


title: NTB_skeletal 3

description: RPMI/PS inoculated


title: OregonR (stage 10B)

hyb_protocol: Slides were hybridized to genome-wide Agilent tiling arrays and washed as per Agilent recommendations

source_name: stage 10B egg chamber

label_protocol: DNA was labeled by random priming and purified with an Amicon Ultra 30K column (Millipore)

treatment_protocol: Ovaries were hand dissected from females fattened for 2 days on wet yeast in EBR. Stage 10B egg chambers were isolated and transferred to EBR on ice until 150 egg chambers were collected.

value: stage 10B egg chamber


title: NTB_heart 3

description: RPMI/PS inoculated

source_name: Normal heart


title: C26_skeletal 2

description: C26 colon cancer cell inoculated

source_name: C26, whole gastrocnemius


title: C26_skeletal 3

description: C26 colon cancer cell inoculated


title: NTB_skeletal 2

description: RPMI/PS inoculated


title: ENDO_replicate_2

city: Paris

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

country: France

institute: Inserm

description: maternal-fetal interface during pregnancy

hyb_protocol: 4 ug of Cy3-labelled cDNA was fragmented at 95°C for 5 minutes in a reaction volume of 12 µl containing  one of twelve specifics samples tracking controls. Only 6 µl was used for hybridization on 12*135K Nimblegen array into Nimblegen hybridization station for 17 hours at 42°C.  After hybridization, microarrays were manually washed according to manufacturer instruction then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the MS200 scanner (Roche)  using scan resolution of 2um.

data_processing: The scanned images were analyzed with DEVA Software (Roche) using 100718_HG18_opt_expr.ngd, 100718_HG18_opt_expr_HX12.ncd and 100718_HG18_opt_expr files. After bursting scanning image, we controled integrity of sample tracking control and  generated pair files. We used RMA for normalization.

source_name: endometriosis-affected women

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 50 ng of Total RNA using Ovation PicoSl WTA (Nugen) and NimbleGen Dual-Color DNA Labeling Kit  according to the manufacturer's instructions

extract_protocol: Total RNA was isolated from tissues, firstly crushed in Trizol (Life Technologies, Carlsbad, CA), using a Qiagen RNeasy Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: choriodecidua

tag: disease state

value: endometriosis


title: NTB_heart 2

description: RPMI/PS inoculated


title: NTB_heart 1

description: RPMI/PS inoculated


title: C26_heart 1

description: C26 colon cancer cell inoculated


title: ENDO_replicate_3


title: LineB BRD4mBD shBRD4

city: Bethesda

first: Tomohiko

last: Kanno

state: MD

address: Bldg.10/Room 11B15, NIH

department: NIAID

institute: NIH

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix).The arrays were then washed and stained on FS450 Fluidics Station.

scan_protocol: Array scanning was performed on a GeneChip Scanner 3000 7G according to the manufacturer's instruction.

data_processing: Affymetrix Expression Console software was used to generate expression values from the CEL files using the RMA expression measure.

source_name: 3T3 line B

label_protocol: Applause WT-Amp Plus ST System and Encore Biotin Module (NuGen) were used to generate biotinylated cDNA from 150 ng total RNA.

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics. The transduced cells were selected with G418 and puromycin.

extract_protocol: RNA was isolated from stably transduced cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with DNase I (Qiagen) to remove trace amounts of genomic DNA.

value: 3T3 line B

tag: shRNA

tag: rescue


title: C26_skeletal 1

description: C26 colon cancer cell inoculated


title: ENDO_replicate_1


title: LineD YFP shCONT

source_name: 3T3 line D

value: 3T3 line D

value: shCONT

value: YFP


title: LineB BRD4WT shBRD4


title: LineD YFP shBRD4


title: LineD BRD4WT shBRD4


title: LineB YFP shBRD4


title: LineB YFP shCONT


title: LineD BRD4mBD shBRD4


title: QC.Y40_2_2

city: Badalona

first: Miguel

middle: A

last: Peinado

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

country: Spain

institute: IGTP

description: Quadriceps muscle

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Quadriceps muscle replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit - Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary myoblast were cultured in growth medium (GM: Ham’s F-10 plus 20% FBS, 5 ng/ml bFGF, 100 U/ml penicillin and 100 µg/ml streptomycin) on 100 mg Collagen I rat tail (Becton and Dickinson) coated tissue culture dishes

extract_protocol: RNA  was isolated with miRNeasy Mini Kit  (Qiagen) according to the manufacturer's instructions.

treatment_protocol: To induce myotube formation, confluent proliferating primary myoblasts were grown on matrigel coated culture dishes (Basement Membrane Matrix, Becton and Dickinson) and switched to differentiation medium next day (DM: DMEM plus 2% horse serum, 100 U/ml penicillin and100 µg/ml streptomycin (Life technologies)) for 1,2 and 4 days.

value: Male

value: Quadriceps muscle


title: muscul_NOD3_1_1

description: Skeletal muscle

source_name: Skeletal muscle

value: NOD/ShiLtj

value: Skeletal muscle


title: CTRL_replicate_2

source_name: healthy subjects

value: healthy


title: CTRL_replicate_3


title: CTRL_replicate_1


title: C26_heart 2

description: C26 colon cancer cell inoculated


title: QC.Y28_2_2

description: Quadriceps muscle

source_name: Quadriceps muscle replicate 2


title: QC.Bl6_1_4

description: Quadriceps muscle

source_name: Quadriceps muscle replicate 1


title: MPC_26_D4_1_3

description: Muscle precursor cells in differentiation conditions at day 4

source_name: Primary myotubes differentiated for 4 day replicate 2

value: Primary myotubes

tag: growth protocol

value: differentiation conditions at day 4


title: MPC_28_D4_1_4

source_name: Primary myotubes differentiated for 4 day replicate 3


title: MPC_21_D2_2_1

description: Muscle precursor cells in differentiation conditions at day 2

source_name: Primary myotubes differentiated for 2 day replicate 1

value: differentiation conditions at day 2


title: MPC_21_D4_1_2

source_name: Primary myotubes differentiated for 4 day replicate 1


title: MPC_21_P_2_3

description: Muscle precursor cells in proliferation conditions at passage 8-10

source_name: Primary myoblasts in proliferation replicate 1

value: Primary myoblasts


title: MPC_28_P_2_1

source_name: Primary myoblasts in proliferation replicate 3

value: proliferation conditions at passage 8-10


title: MPC_26_P_1_1

source_name: Primary myoblasts in proliferation replicate 2


title: MPC_26_D2_1_4

source_name: Primary myotubes differentiated for 2 day replicate 2


title: E14tg2_2_2_2

description: Embryonic stem cell line

source_name: Technical replicate of Embryonic stem cell lineE14Tg2

value: Embryonic stem cells


title: MPC_28_D1S01_2_3

description: Muscle precursor cells in differentiation conditions at day 1

source_name: Primary myotubes differentiated for 1 day replicate 3

value: differentiation conditions at day 1


title: MPC_26_D1_2_1

source_name: Primary myotubes differentiated for 1 day replicate 2


title: SC_26_AP_2_3

description: Muscle precursor cells in proliferation conditions at passage 0

source_name: Primary myoblasts passage zero replicate 1

value: proliferation conditions at passage 0


title: SC_30_AP_1_3

source_name: Primary myoblasts passage zero replicate 2


title: RD1_1_3

description: Embryonic stem cell line

source_name: Embryonic stem cell line replicate 2


title: MPC_21_D1_2_4

source_name: Primary myotubes differentiated for 1 day replicate 1


title: SC_42_AP_2_4

source_name: Primary myoblasts passage zero replicate 3


title: MPC_28_D2_1_2

source_name: Primary myotubes differentiated for 2 day replicate 3


title: cGR8_1_1

description: Embryonic stem cell line

source_name: Embryonic stem cell line replicate 1


title: E14tg2_1_2_4

description: Embryonic stem cell line

source_name: Embryonic stem cell line replicate 3


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 1 [Mouse430_2]

status: Public on Nov 09 2014

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: tumor tissue includes mouse host stroma cells

hyb_protocol: Target cDNA generated from each sample was then processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).   Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization to Affymetrix Mouse Genome 430 2.0 arrays. Arrays were then washed and stained with streptavidin-phycoerythrin, before imaging on an Affymetrix GeneChip (3000) scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/Downloads/GeneChip_Hyb_Wash_Scan_Protocol-CR-UK_v4.pdf.

scan_protocol: Affymetrix GeneChip (3000) scanner

data_processing: Following scanning, .DAT files were processed using Affymetrix GCOS, 1.1.1.052, to generate .CEL files. Subsequent data processing was performed on these data using the affy, simpleaffy and GCRMA packages from BioConductor and R. mRNA was estimated using GCRMA and log2 values were used.

source_name: Bevacizumab treated

label_protocol: Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer’s recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, 10 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in ~100-fold amplification of RNA. A complete description of procedures is available at:  http://bioinf.picr.man.ac.uk/mbcf/Downloads/GeneChip_Target_Prep_Protocol-CR-UK_v4.pdf

growth_protocol: All protocols were carried out under Indiana University Institutional Animal Care and Use Committee (IACUC), and UK Home Office approved protocols and regulations. 107 U87 cells were implanted into 6- to 8-week-old female BALB/c SCID mice (Harlan Sprague Dawley, Inc.) subcutaneously (s.c.), as 100μL cell suspensions with an equal volume of Matrigel (BD Bioscience). Tumors were measured twice a week with a caliper, and volumes were calculated using the formula length x width2 x 0.5.

extract_protocol: Xenograft samples were placed in RNAlater (Ambion, USA) overnight before storage at -80oC. RNA was extracted using Tri-reagant (Sigma-Aldrich) and washed using the Qiagen Spin column (Qiagen). RNA quality and quantity were confirmed using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: Once the tumor volume reached 150-200 mm3, mice were randomized into two groups with starting cohort sizes of 5 mice per group and treatment of Bevacizumab injected intraperitoneally (i.p.) every 3 days at a dose of 10 mg/kg or saline control begun. Treatment was continued until tumors grew to approximately 15-30 mm diameter.

tag: specific-host

value: BALB/c SCID mouse

tag: tissue type

value: U87-EV human glioblastoma xenograft tumour


title: U87-EV human glioblastoma xenograft - Control  - 3 [Mouse430_2]

source_name: Control


title: U87-EV human glioblastoma xenograft - Control  - 2 [Mouse430_2]


title: U87-EV human glioblastoma xenograft - Control  - 1 [Mouse430_2]


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 2 [Mouse430_2]


title: Puerto Rican Children #108

status: Public on Nov 08 2014

city: Pittsburgh

first: Jerom

last: Lin

state: Pennsylvania

address: 4401 Penn Ave

institute: University of Pittsburgh

description: Total RNA was extracted from additional whole-blood samples collected in PaxGene tubes

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
Probeset signals were extracted from GenomeStudio software following the default quality control parameters. Background subtraction and quantile normalization were performed using the Lumi package implemented in R (version 3.0.1) for normalized data. Probes with more than 70% absent values were excluded for downstream analysis.
GenomeStudio Gene Expression Module v1.9.0

source_name: Puerto Rican Children

label_protocol: standard Illumina protocol

extract_protocol: Trizol

value: Whole Blood


title: Puerto Rican Children #117


title: U87-EV human glioblastoma xenograft - Bevacizumab treated  - 3 [Mouse430_2]


title: Puerto Rican Children #112


title: Puerto Rican Children #120


title: Puerto Rican Children #116


title: Puerto Rican Children #118


title: Puerto Rican Children #115


title: Puerto Rican Children #111


title: Puerto Rican Children #121


title: Puerto Rican Children #119


title: Puerto Rican Children #113


title: Puerto Rican Children #105


title: Puerto Rican Children #106


title: Puerto Rican Children #114


title: Puerto Rican Children #104


title: Puerto Rican Children #110


title: Puerto Rican Children #107


title: DNA_methylation_CTRL_replicate_1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Non-normalized data.txt file contains unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: healthy subjects

label_protocol: Standard Illumina Protocol

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

value: choriodecidua


title: Puerto Rican Children #103


title: Puerto Rican Children #102


title: Puerto Rican Children #101


title: Puerto Rican Children #99


title: Puerto Rican Children #100


title: Puerto Rican Children #97


title: Puerto Rican Children #109


title: DNA_methylation_CTRL_replicate_2


title: DNA_methylation_CTRL_replicate_3


title: DNA_methylation_ENDO_replicate_1

source_name: endometriosis-affected women


title: DNA_methylation_ENDO_replicate_3


title: Puerto Rican Children #95


title: DNA_methylation_ENDO_replicate_2


title: Puerto Rican Children #94


title: Puerto Rican Children #92


title: Puerto Rican Children #93


title: Puerto Rican Children #96


title: Puerto Rican Children #91


title: Puerto Rican Children #89


title: Puerto Rican Children #88


title: Puerto Rican Children #86


title: Puerto Rican Children #90


title: Puerto Rican Children #85


title: Puerto Rican Children #81


title: Puerto Rican Children #79


title: Puerto Rican Children #78


title: Puerto Rican Children #83


title: Puerto Rican Children #80


title: Puerto Rican Children #82


title: Puerto Rican Children #77


title: Puerto Rican Children #76


title: Puerto Rican Children #72


title: Puerto Rican Children #74


title: Puerto Rican Children #71


title: Puerto Rican Children #69


title: Puerto Rican Children #70


title: Puerto Rican Children #68


title: Puerto Rican Children #87


title: Puerto Rican Children #67


title: Puerto Rican Children #63


title: Puerto Rican Children #62


title: Puerto Rican Children #61


title: Puerto Rican Children #66


title: Puerto Rican Children #73


title: Puerto Rican Children #60


title: Puerto Rican Children #98


title: Puerto Rican Children #84


title: Puerto Rican Children #75


title: Puerto Rican Children #64


title: Puerto Rican Children #55


title: Puerto Rican Children #57


title: Puerto Rican Children #52


title: Puerto Rican Children #56


title: Puerto Rican Children #54


title: Puerto Rican Children #65


title: Puerto Rican Children #53


title: Puerto Rican Children #50


title: Puerto Rican Children #59


title: Puerto Rican Children #51


title: Puerto Rican Children #46


title: Puerto Rican Children #47


title: Puerto Rican Children #49


title: Puerto Rican Children #43


title: Puerto Rican Children #44


title: Puerto Rican Children #48


title: Puerto Rican Children #58


title: Puerto Rican Children #45


title: Puerto Rican Children #41


title: gastric normal 42

hyb_protocol: the labeled cDNA samples were used as probes to hybridize to the array chips by incubation at 45℃ and rotated at 60rpm for 17 h with Eukaryotic Hybridization Control Kit and Hybridization, Wash and Stain Kit(affymetrix),Fluidics washing is Hybridization, Wash and Stain KitFS450_0001

data_processing:
Data were processed using GeneBASE software.using RMA to get the gene core signal from each probe.
HuEx-1_0-st-v1.r2.pgf
HuEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: gastric normal 42

label_protocol: 1 μg RNA template was used to reversely transcribed into cDNA and cDNA samples were digested into cDNA fragments with endonucleases and then labeled with the IVT labeling Kit provided by Affymetrix

growth_protocol: tissues dissected from surgery patients

extract_protocol: Tissue RNA was isolated using Trizol and further purified using the RNeasy Mini kit according to the manufacturer’s instructions.

value: Female


title: Puerto Rican Children #42


title: Puerto Rican Children #39


title: gastric normal 43

source_name: gastric normal 43

value: Male


title: gastric normal 45

source_name: gastric normal 45


title: gastric normal 44

source_name: gastric normal 44


title: Puerto Rican Children #36


title: Puerto Rican Children #38


title: gastric normal 39

source_name: gastric normal 39


title: gastric normal 40

source_name: gastric normal 40


title: Puerto Rican Children #40


title: gastric normal 37

source_name: gastric normal 37


title: Puerto Rican Children #37


title: Puerto Rican Children #33


title: gastric normal 36

source_name: gastric normal 36


title: Puerto Rican Children #34


title: gastric normal 41

source_name: gastric normal 41


title: gastric normal 35

source_name: gastric normal 35


title: Puerto Rican Children #32


title: gastric normal 34

source_name: gastric normal 34


title: gastric normal 33

source_name: gastric normal 33


title: Puerto Rican Children #35


title: Puerto Rican Children #29


title: Puerto Rican Children #30


title: gastric normal 32

source_name: gastric normal 32


title: gastric normal 30

source_name: gastric normal 30


title: gastric normal 28

source_name: gastric normal 28


title: gastric normal 31

source_name: gastric normal 31


title: gastric normal 29

source_name: gastric normal 29


title: Puerto Rican Children #31

source_name: Puerto Rican Children


title: Puerto Rican Children #28


title: gastric normal 27

source_name: gastric normal 27


title: Puerto Rican Children #26


title: gastric normal 26

source_name: gastric normal 26


title: gastric normal 25

source_name: gastric normal 25


title: Puerto Rican Children #25


title: gastric normal 24

source_name: gastric normal 24


title: Puerto Rican Children #23


title: Puerto Rican Children #27


title: Puerto Rican Children #24


title: gastric normal 22

source_name: gastric normal 22


title: gastric normal 38

source_name: gastric normal 38


title: Puerto Rican Children #22


title: gastric normal 23

source_name: gastric normal 23


title: Puerto Rican Children #21


title: gastric normal 21

source_name: gastric normal 21


title: Puerto Rican Children #18


title: Puerto Rican Children #15


title: Puerto Rican Children #19


title: gastric normal 17

source_name: gastric normal 17


title: gastric normal 15

source_name: gastric normal 15


title: gastric normal 16

source_name: gastric normal 16


title: Puerto Rican Children #16


title: Puerto Rican Children #13


title: gastric normal 14

source_name: gastric normal 14


title: Puerto Rican Children #14


title: Puerto Rican Children #9


title: gastric normal 13

source_name: gastric normal 13


title: Puerto Rican Children #20


title: gastric normal 12

source_name: gastric normal 12


title: gastric normal 11

source_name: gastric normal 11


title: Puerto Rican Children #17


title: Puerto Rican Children #10


title: Puerto Rican Children #6


title: gastric normal 10

source_name: gastric normal 10


title: Puerto Rican Children #7

source_name: Puerto Rican Children


title: Puerto Rican Children #8


title: gastric normal 18

source_name: gastric normal 18


title: gastric normal 9

source_name: gastric normal 9


title: Puerto Rican Children #11


title: Puerto Rican Children #5


title: gastric normal 20

source_name: gastric normal 20


title: gastric normal 19

source_name: gastric normal 19


title: gastric normal 7

source_name: gastric normal 7


title: gastric normal 8

source_name: gastric normal 8


title: Puerto Rican Children #3


title: gastric normal 6

source_name: gastric normal 6


title: gastric normal 4

source_name: gastric normal 4


title: gastric normal 2

source_name: gastric normal 2


title: gastric normal 1

source_name: gastric normal 1


title: Puerto Rican Children #4


title: Puerto Rican Children #1


title: gastric normal 5

source_name: gastric normal 5


title: Puerto Rican Children #2


title: gastric cancer 34

source_name: gastric cancer 34


title: gastric cancer 43

source_name: gastric cancer 43


title: gastric cancer 37

source_name: gastric cancer 37


title: gastric cancer 41

source_name: gastric cancer 41


title: gastric cancer 42

source_name: gastric cancer 42


title: gastric cancer 36

source_name: gastric cancer 36


title: gastric cancer 40

source_name: gastric cancer 40


title: gastric cancer 38

source_name: gastric cancer 38


title: gastric cancer 44

source_name: gastric cancer 44


title: gastric cancer 33

source_name: gastric cancer 33


title: gastric cancer 45

source_name: gastric cancer 45


title: gastric normal 3

source_name: gastric normal 3


title: gastric cancer 32

source_name: gastric cancer 32


title: gastric cancer 39

source_name: gastric cancer 39


title: gastric cancer 31

source_name: gastric cancer 31


title: Puerto Rican Children #12

source_name: Puerto Rican Children


title: gastric cancer 29

source_name: gastric cancer 29


title: gastric cancer 25

source_name: gastric cancer 25


title: gastric cancer 23

source_name: gastric cancer 23


title: gastric cancer 26

source_name: gastric cancer 26


title: gastric cancer 28

source_name: gastric cancer 28


title: gastric cancer 35

source_name: gastric cancer 35


title: gastric cancer 27

source_name: gastric cancer 27


title: gastric cancer 22

source_name: gastric cancer 22


title: Scutellum_rep3

city: Tokyo

first: Jun-ichi

last: Itoh

state: Tokyo

address: Bunkyo, Yayoi 1-1-1

institute: The University of Tokyo

description: Gene expression of scutellum tissue of embryo at 7 DAP

hyb_protocol: At least 1,100 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with GenespringGX12(Agilent).

organism: Oryza sativa Japonica Group

source_name: 7DAP scutellum_rep3

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

extract_protocol: Total RNA was extracted from the each sample with a Pico-PureTM RNA isolation kit (Arcturus) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

tag: source organ

value: Embryo

value: scutellum tissue

value: 7 DAP


title: gastric cancer 21

source_name: gastric cancer 21


title: Epiblast_rep3

description: Gene expression of epiblast tissue of embryo at 7 DAP

source_name: 7DAP epiblast_rep3

value: epiblast tissue


title: gastric cancer 30

source_name: gastric cancer 30


title: gastric cancer 24

source_name: gastric cancer 24


title: Epiblast_rep2

source_name: 7DAP epiblast_rep2


title: Scutellum_rep2

source_name: 7DAP scutellum_rep2


title: Scutellum_rep1

source_name: 7DAP scutellum_rep1


title: Epiblast_rep1

source_name: 7DAP epiblast_rep1


title: Root_rep1

description: Gene expression of root tissue of embryo at 7 DAP

source_name: 7DAP root_rep1

value: root tissue


title: Root_rep2

source_name: 7DAP root_rep2


title: Root_rep3

source_name: 7DAP root_rep3


title: Shoot_rep3

description: Gene expression of shoot tissue of embryo at 7 DAP

source_name: 7DAP shoot_rep3

value: shoot tissue


title: gastric cancer 17

source_name: gastric cancer 17


title: gastric cancer 18

source_name: gastric cancer 18


title: gastric cancer 16

source_name: gastric cancer 16


title: gastric cancer 20

source_name: gastric cancer 20


title: Shoot_rep1

source_name: 7DAP shoot_rep1


title: gastric cancer 15

source_name: gastric cancer 15


title: Ventral_rep1

description: Gene expression of ventral part of embryo at 3 DAP

source_name: 3DAP ventral part embryo_rep1

value: ventral part

value: 3 DAP


title: Ventral_rep3

source_name: 3DAP ventral part embryo_rep3


title: Dorsal_rep2

description: Gene expression of dosal part of embryo at 3 DAP

source_name: 3DAP dosal part embryo_rep2

value: dosal part


title: Basal_rep3

description: Gene expression of basal part of embryo at 3 DAP

source_name: 3DAP basal part embryo_rep3

value: basal part


title: Dorsal_rep1

source_name: 3DAP dosal part embryo_rep1


title: Ventral_rep2

source_name: 3DAP ventral part embryo_rep2


title: Basal_rep2

source_name: 3DAP basal part embryo_rep2


title: gastric cancer 13

source_name: gastric cancer 13


title: Basal_rep1

source_name: 3DAP basal part embryo_rep1


title: gastric cancer 14

source_name: gastric cancer 14


title: Apical_rep3

description: Gene expression of apical part of embryo at 3 DAP

source_name: 3DAP apical part embryo_rep3

value: apical part


title: Dorsal_rep3

source_name: 3DAP dosal part embryo_rep3


title: gastric cancer 12

source_name: gastric cancer 12


title: Treated donor 6(T5D6)

city: Bergen

first: Ying

last: Xue

address: Årstadveien 19

department: Department of Dentistry

country: Norway

institute: University of Bergen

description: replicate 6

hyb_protocol: Hybridization was performed according to the Whole –Genome Gene Expression Direct Hybridization Assay Guide (3) from Illumina Inc. 1500 ng cRNA were hybridized at 58˚C for 17 hours.

scan_protocol: After scanning the iScan Reader calculates some quality parameters in order to know if the scanning has been successful. If the scan was successful the iScan Reader software extracts signal intensities and save all files for each BeadChip.

data_processing: All images from the scans were visually inspected by the staff at the NMC Core Facility lab in Bergen. As described in Part one of this report, the raw data from the scans were controlled in GenomeStudio, controls checked, and control plots made to look for outliers. The data was found to be of good quality and the SampleProbeProfile-text file was exported from GenomeStudio. In this export the control probes are removed. The SampleProbeProfile was loaded in to J-Express and further quality control of the data was performed. The quantile normalized data was analyzed by J express software.

source_name: Human bone marrow stromal cells_coculture with HUVECs

label_protocol: 250 ng of totalRNA from each sample was labelled using the Illumina TotalPrep RNA Amplification Kit. The samples were labelled by Solveig M. Angelskår and labelling was performed on an Eppendorf Mastercycler (reg. nr: 26963) and an Illumina hybridization oven, see table 1 for further details.

extract_protocol: After trypinization cells was collected and total RNA were extracted by using E.Z.N.A kits.

treatment_protocol: In this experiment human Bone Marrow Stem Cells (hBMSCs) are grown in co-culture with Human Umbilical Vein Endothelial Cells (HUVECs) for 5 days, HUVECs are removed by trypsination before call harvest. In parallel hBMSCs are grown in monoculture as a control for 5 days, and a sham trypsination performed before harvesting of the cells.

value: bone marrow stem cells

tag: culture method

value: coculture


title: Treated donor 5(T5D5)

description: replicate 5

growth_protocol: In this experiment human Bone Marrow Stem Cells (hBMSCs) are grown in co-culture with Human Umbilical Vein Endothelial Cells (HUVECs) for 5 days


title: Treated donor 3(T5D3)

description: replicate 3


title: gastric cancer 10

source_name: gastric cancer 10


title: Apical_rep1

source_name: 3DAP apical part embryo_rep1

tag: tissue


title: 4DAP_rep3

description: Gene expression of whole embryo at 4 DAP

source_name: 4DAP whole embryo_rep3

value: whole embryo at 4 DAP


title: Treated donor 4(T5D4)

description: replicate 4

tag: cell type


title: Apical_rep2

source_name: 3DAP apical part embryo_rep2


title: gastric cancer 11

source_name: gastric cancer 11


title: Treated donor 2(T5D2)

description: replicate 2


title: gastric cancer 7

source_name: gastric cancer 7

value: Female


title: 4DAP_rep2

source_name: 4DAP whole embryo_rep2


title: Treated donor 1(T5D1)

description: replicate 1


title: gastric cancer 5

source_name: gastric cancer 5

value: Male


title: Shoot_rep2

source_name: 7DAP shoot_rep2

value: Nipponbare


title: gastric cancer 6

source_name: gastric cancer 6


title: gastric cancer 9

source_name: gastric cancer 9


title: 4DAP_rep1

source_name: 4DAP whole embryo_rep1

value: Embryo


title: Control donor 6(C5D6)

description: replicate 6

source_name: Human bone marrow stromal cells_monoculture

value: monoculture


title: Control donor 4(C5D4)

description: replicate 4


title: Control donor 5(C5D5)

description: replicate 5


title: 3DAP_rep1

description: Gene expression of whole embryo at 3 DAP

source_name: 3DAP whole embryo_rep1

value: whole embryo at 3 DAP


title: gastric cancer 3

source_name: gastric cancer 3


title: 3DAP_rep2

source_name: 3DAP whole embryo_rep2


title: gastric cancer 8

source_name: gastric cancer 8


title: Control donor 2(C5D2)

description: replicate 2


title: 2DAP_rep3

description: Gene expression of whole embryo at 2 DAP

source_name: 2DAP whole embryo_rep3

value: whole embryo at 2 DAP


title: Control donor 3(C5D3)

description: replicate 3


title: gastric cancer 4

source_name: gastric cancer 4


title: 3DAP_rep3

source_name: 3DAP whole embryo_rep3


title: 2DAP_rep2

source_name: 2DAP whole embryo_rep2


title: Control donor 1(C5D1)

description: replicate 1


title: GM12146, gDNA

status: Public on Nov 07 2014

first: Tomi

middle: Markku

last: Pastinen

address: 740, Dr. Penfield Avenue

institute: McGill University and Génome Québec Innovation Centre

description: XC01334, maternal grandfather

hyb_protocol: according to manufacturer's instructions

data_processing: using GenomeStudio from illumina

label: Cy3 and Cy5

growth_protocol: The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), With 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2

extract_protocol: total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen. DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).

value: Lymphoblasts

tag: population

value: CEU


title: GM12878, cDNA

description: XC01463, daughter

scan_protocol: according to manufacturer's instructions


title: GM12146, cDNA

description: XC01334, maternal grandfather

label_protocol: according to manufacturer's instructions


title: GM11882, cDNA

description: XC01347, mother


title: GM12878, gDNA

description: XC01463, daughter


title: GM11881, cDNA

description: XC01347, father


title: gastric cancer 1

source_name: gastric cancer 1


title: gastric cancer 2

source_name: gastric cancer 2


title: GM10838, gDNA

description: XC01420, father


title: GM10838, cDNA

description: XC01420, father


title: MAT1A knockout at 15 month age, tumoral tissue, biological replicate 2

city: Alnarp

first: Itziar

last: Frades

address: Sundsvägen 14

department: Plant Protection Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

description:
MAT1A_T2
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.

hyb_protocol: Following fragmentation, 15 μg of cRNA was hybridized on Affymetrix GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Fluidics Station 450.

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

data_processing: The data were acquired with GCOS 1.4 instrument and processed using RMA normalization method.

source_name: Mouse liver tumoral tissue, MAT1A knockout, hepatocellular carcinoma, 15 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2μg of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: 2-4 mg of liver. The tissue received was pulverized in mortar with presence of liquid nitrogen. Total RNA was then extracted using Qiagen’s RNeasy Mini kit recovering each sample in 35μl of water.

tag: strain/background

tag: genotype/variation

value: MAT1A knockout

value: 15 months

value: liver, tumoral tissue

tag: disease status

value: hepatocellular carcinoma


title: MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 5

description:
MAT1A_NT5
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.

source_name: Mouse liver peritumoral tissue, MAT1A knockout, hepatocellular carcinoma, 15 months

tag: age

value: liver, peritumoral tissue


title: MAT1A knockout at 15 month age, tumoral tissue, biological replicate 3

description:
MAT1A_T3
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: Wild type used for MAT1A 15 month, replicate 3

description:
MAT1A_wt15_3
Gene expression data from the wild type used for MAT1A knockout at 15 month.

source_name: Mouse liver, wild type, healthy, 15 months

value: wild type

value: liver

value: healthy


title: 2DAP_rep1

source_name: 2DAP whole embryo_rep1


title: GM11882, gDNA

description: XC01347, mother

tag: gender

value: Female


title: MAT1A knockout at 15 month age, tumoral tissue, biological replicate 5

description:
MAT1A_T5
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 1

description:
MAT1A_NT1
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.


title: Wild type used for MAT1A 15 month, replicate 1

description:
MAT1A_wt15_1
Gene expression data from the wild type used for MAT1A knockout at 15 month.


title: MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 3

description:
MAT1A_NT3
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.


title: Wild type used for MAT1A 15 month, replicate 4

description:
MAT1A_wt15_4
Gene expression data from the wild type used for MAT1A knockout at 15 month.


title: Wild type used for MAT1A 15 month, replicate 5

description:
MAT1A_wt15_5
Gene expression data from the wild type used for MAT1A knockout at 15 month.


title: MAT1A knockout at 15 month age, tumoral tissue, biological replicate 1

description:
MAT1A_T1
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 4

description:
MAT1A_NT4
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.


title: Wild type used for MAT1A 15 month, replicate 2

description:
MAT1A_wt15_2
Gene expression data from the wild type used for MAT1A knockout at 15 month.


title: MAT1A knockout at 15 month age, tumoral tissue, biological replicate 4

description:
MAT1A_T4
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 2

description:
MAT1A_NT2
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.


title: GM19240, cDNA

extract_protocol: Total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen. DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).

value: Yoruba


title: GM11881, gDNA

description: XC01347, father

value: Male


title: GM19238, gDNA


title: GM19240, gDNA


title: GM19223, gDNA


title: GM19223, cDNA


title: GM19222, gDNA


title: GM19222, cDNA


title: GM19239, cDNA


title: GM19210, gDNA


title: GM19209, gDNA


title: GM19210, cDNA


title: GM19238, cDNA


title: GM19209, cDNA


title: GM19207, gDNA


title: GM19239, gDNA


title: GM19206, cDNA


title: GM19203, gDNA


title: GM19206, gDNA


title: GM19207, cDNA


title: GM19193, gDNA


title: GM19204, gDNA


title: GM19201, gDNA


title: GM19200, cDNA


title: GM19201, cDNA


title: GM19172, gDNA


title: GM19172, cDNA


title: GM19192, gDNA


title: GM19193, cDNA


title: GM19200, gDNA


title: GM19192, cDNA


title: GM19171, gDNA


title: GM19160, gDNA


title: gastric cancer 19

source_name: gastric cancer 19


title: GM19204, cDNA


title: GM19203, cDNA


title: GM19171, cDNA


title: GM19159, gDNA


title: GM19160, cDNA


title: GM19144, gDNA


title: GM19144, cDNA


title: GM19159, cDNA


title: GM19143, gDNA


title: GM19141, gDNA, duplicate #2


title: GM19143, cDNA


title: GM19141, cDNA, duplicate #2


title: GM19141, gDNA, duplicate #1


title: GM19141, cDNA, duplicate #1


title: GM19138, cDNA


title: GM19130, gDNA


title: GM19119, gDNA


title: GM19128, cDNA


title: GM19140, cDNA


title: GM19127, cDNA


title: GM19130, cDNA


title: GM19131, gDNA


title: GM19140, gDNA


title: GM19137, gDNA


title: GM19127, gDNA


title: GM19131, cDNA


title: GM19128, gDNA


title: GM19102, gDNA


title: GM19138, gDNA


title: GM19099, gDNA, duplicate #1


title: GM19093, cDNA


title: GM19093, gDNA


title: GM19098, gDNA


title: GM19098, cDNA


title: GM19119, cDNA


title: GM19137, cDNA


title: GM19101, cDNA


title: GM19099, cDNA, duplicate #1


title: GM19099, cDNA, duplicate #2


title: GM19099, gDNA, duplicate #2


title: GM19101, gDNA


title: GM19092, gDNA


title: GM19102, cDNA


title: GM19092, cDNA


title: GM18913, gDNA, duplicate #2


title: GM18912, gDNA


title: GM18913, cDNA, duplicate #1


title: GM18871, cDNA


title: GM18870, gDNA


title: GM18870, cDNA


title: GM18913, gDNA, duplicate #1


title: GM18871, gDNA


title: GM18859, cDNA


title: GM18859, gDNA


title: GM18861, gDNA


title: GM18858, cDNA


title: GM18853, gDNA


title: GM18855, gDNA


title: GM18855, cDNA


title: GM18856, cDNA


title: GM18861, cDNA


title: GM18853, cDNA


title: GM18852, gDNA, duplicate #1


title: GM18858, gDNA


title: GM18852, gDNA, duplicate #2


title: GM18856, gDNA


title: GM18852, cDNA, duplicate #1


title: GM18522, cDNA


title: GM18523, gDNA


title: GM18523, cDNA


title: GM18912, cDNA


title: GM18913, cDNA, duplicate #2


title: GM18517, gDNA


title: GM18508, gDNA


title: GM18517, cDNA


title: GM18507, cDNA


title: GM18852, cDNA, duplicate #2


title: GM18508, cDNA


title: GM18504, gDNA


title: GM18507, gDNA


title: GM18516, gDNA


title: GM18505, gDNA


title: GM12891, cDNA

description: XC01463, father


title: GM12892, cDNA

description: XC01463, mother


title: GM12891, gDNA

description: XC01463, father


title: GM12892, gDNA

description: XC01463, mother


title: GM18502, gDNA


title: GM12875, cDNA

description: XC01459, maternal grandmother


title: GM18505, cDNA


title: GM18501, gDNA


title: GM18502, cDNA


title: GM18504, cDNA


title: GM12873, gDNA

description: XC01459, paternal grandmother


title: GM12874, gDNA

description: XC01459, maternal grandfather


title: GM12873, cDNA

description: XC01459, paternal grandmother


title: GM12874, cDNA

description: XC01459, maternal grandfather


title: GM18501, cDNA


title: GM12872, gDNA

description: XC01459, paternal grandfather


title: GM18522, gDNA


title: GM12815, gDNA

description: XC01454, maternal grandmother


title: GM12814, gDNA

description: XC01454, maternal grandfather


title: GM18516, cDNA


title: GM12813, gDNA

description: XC01454, paternal grandmother


title: GM12812, gDNA

description: XC01454, paternal grandfather


title: GM12763, gDNA

description: XC01447, maternal grandmother


title: GM12763, cDNA

description: XC01447, maternal grandmother


title: GM12814, cDNA

description: XC01454, maternal grandfather


title: GM12762, gDNA

description: XC01447, maternal grandfather


title: GM12812, cDNA

description: XC01454, paternal grandfather


title: GM12761, cDNA

description: XC01447, paternal grandmother


title: GM12751, gDNA

description: XC01444, mother


title: GM12760, gDNA

description: XC01447, paternal grandfather


title: GM12750, cDNA

description: XC01444, father


title: GM12264, gDNA

description: XC01375, father


title: GM12750, gDNA

description: XC01444, father


title: GM12249, gDNA, duplicate#1

description: XC01416, mother


title: GM12249, cDNA, duplicate# 2

description: XC01416, mother


title: GM12239, cDNA

description: XC01334, maternal grandmother


title: GM12239, gDNA

description: XC01334, maternal grandmother


title: GM12762, cDNA

description: XC01447, maternal grandfather


title: GM12249, cDNA, duplicate#1

description: XC01416, mother


title: GM12264, cDNA

description: XC01375, father


title: GM12234, cDNA

description: XC01375, mother


title: GM12249, gDNA, duplicate#2

description: XC01416, mother


title: GM12156, gDNA

description: XC01408, maternal grandmother


title: GM12156, cDNA

description: XC01408, maternal grandmother


title: GM12234, gDNA

description: XC01375, mother


title: GM12155, gDNA

description: XC01408, maternal grandfather


title: GM12813, cDNA

description: XC01454, paternal grandmother


title: GM12155, cDNA

description: XC01408, maternal grandfather


title: GM12154, gDNA

description: XC01408, paternal grandfather


title: GM12761, gDNA

description: XC01447, paternal grandmother


title: GM12144, gDNA

description: XC01334, paternal grandfather


title: GM12154, cDNA

description: XC01408, paternal grandfather


title: GM12145, gDNA

description: XC01334, paternal grandmother


title: GM12751, cDNA

description: XC01444, mother


title: GM12760, cDNA

description: XC01447, paternal grandfather


title: GM12144, cDNA

description: XC01334, paternal grandfather


title: GM12057, gDNA

description: XC01344, mother


title: GM12057, cDNA

description: XC01344, mother


title: GM12043, cDNA

description: XC01346, father


title: GM11995, gDNA

description: XC01362, maternal grandmother


title: GM11832, gDNA, duplicate#2

description: XC01350, maternal grandmother


title: GM11832, gDNA, duplicate#1

description: XC01350, maternal grandmother


title: GM11994, cDNA

description: XC01362, maternal grandfather


title: GM11829, gDNA

description: XC01350, paternal grandfather


title: GM11829, cDNA

description: XC01350, paternal grandfather


title: GM11840, cDNA

description: XC01349, mother


title: GM11840, gDNA

description: XC01349, mother


title: GM11832, cDNA, duplicate#1

description: XC01350, maternal grandmother


title: GM11832, cDNA, duplicate#2

description: XC01350, maternal grandmother


title: GM11830, gDNA

description: XC01350, paternal grandmother


title: GM11994, gDNA

description: XC01362, maternal grandfather


title: GM11995, cDNA

description: XC01362, maternal grandmother


title: GM07357, gDNA

description: XC01345, father


title: GM07357, cDNA

description: XC01345, father


title: GM12145, cDNA

description: XC01334, paternal grandmother


title: GM07345, gDNA

description: XC01345, mother


title: GM07056, gDNA

description: XC01340, maternal grandmother


title: GM07056, cDNA

description: XC01340, maternal grandmother


title: GM12044, gDNA

description: XC01346, mother


title: GM07055, gDNA

description: XC01341, paternal grandmother


title: GM07055, cDNA

description: XC01341, paternal grandmother


title: GM12044, cDNA

description: XC01346, mother


title: GM07034, gDNA

description: XC01341, paternal grandfather


title: GM12043, gDNA

description: XC01346, father


title: GM07345, cDNA

description: XC01345, mother


title: GM07034, cDNA

description: XC01341, paternal grandfather


title: GM07022, cDNA

description: XC01340, maternal grandfather


title: GM07000, cDNA

description: XC01340, paternal grandmother


title: GM06994, gDNA

description: XC01340, paternal grandfather


title: GM06993, gDNA

description: XC01341, maternal grandfather


title: GM06985, gDNA

description: XC01341, maternal grandmother


title: GM06993, cDNA

description: XC01341, maternal grandfather


title: GM06994, cDNA

description: XC01340, paternal grandfather


title: GM06985, cDNA

description: XC01341, maternal grandmother


title: GM07022, gDNA

description: XC01340, maternal grandfather


title: WT-mesR mutant, biological replicate 3 of 3, dye swap.

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equal amounts of labeled cDNA from ETSU9 or ETSU9mesR were thoroughly mixed and used to hybridize microarray slides in Amersham microarray hybridization buffer.  Hybridization was carried out at 50C for 16 hr in the dark.

scan_protocol: After hybridization, the slides were washed in saline-sodium phosphate EDTA buffer and scanned with GenePix  4100A scanner and analyzed with GenePix Pro 5.0 software (Axon instruments)

data_processing: Data was subjected to two types of normalization, a ratio-based normalization so that the mean or median intensities are the same across the array, and a non-linear locally weighed scatterplot smoothing (LOWESS) normalization, which corrects intensity dependent variation in dye basis, before being combined into a single data set for further analysis.  Differential expression was defined as a minimum of two fold over or under expression of ETSU9mesR relative to ETSU9.  The data were further scrutinized so as to only include expression profiles that were observed in at least 4 of the 6 experiments and had a p<0.05 after one t-test analysis.

organism: Moraxella catarrhalis

source_name: O/N grown bacteria on BHI plates

label_protocol: Five micrograms of total RNA for cells grown O/N on BHI plates were used to generate cDNA using the Amino Allyl cDNA Labeling kit ragents (AmWT-mesR mutant, bion).  After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization.  The cDNAs were purified using the Qiaquick gel extraction columns (Qiagen).  After purification, Cy3 or Cy5 dye (GE Healthcare) was added following manufacturer's instructions.  The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal devices (Millipore) and labeling efficiency was determined using a Nanodrop spectrophotometer.

growth_protocol: Moraxella catarrhalis ETSU9  or ETSU9mesR strains were resucitated from frozen stock on BHI agar plates, and incubated ON at 37C in a humidified atmosphere containing 95% air and 5% CO2.

extract_protocol: Total RNA from the growth collected from 2 O/N BHI plates was extracted using the Ribopure Bacteria kit (AmWT-mesR mutant, bion) following manufacturer's instructions.

tag: strain

value: wild type ETSU9

value: ETSU9mesR mutant


title: NSC11 co-culture, rep2

first: Barbara

middle: Helen

last: Rath

address: 10 Center Drive B3B406

department: National Cancer Institute

institute: National Institute of Health

description: NSC11 - coculture 2

hyb_protocol: Following fragmentation, 100ng of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: GSCs isolated from human GBM surgical specimens_co-culture with astrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: GSCs were seeded into po/ln coated 6-wellplates (5x10^4 cells/cm2) with astrocytes (1.4x10^6 cells/cm2) onto the corresponding trans-well inserts with their respective culture medium and allowed to adhere overnight.

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

treatment_protocol: Co-cultures were initiated by combining the inserts and the 6-well plates; 48h later RNA was collected from GSCs

tag: patient id

value: patient 2

value: brain

tag: tumor

value: glioblastoma multiforme

tag: primary cell line

value: glioblastoma stem-like cells

tag: culture type

value: co-culture with astrocytes


title: NSC11 mono-culture, rep3

description: NSC11 - 3

source_name: GSCs isolated from human GBM surgical specimens_monoculture

value: alone (mono-culture)


title: NSC11 mono-culture, rep1

description: NSC11 - 1


title: NSC11 co-culture, rep1

description: NSC11 - coculture 1


title: GBAM1 co-culture, rep3

description: GBAM1 - coculture 3

value: patient 1


title: Lung_Emphysema_G3-3467#2

city: West Point

first: I-Ming

last: Wang

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck Research Lab

hyb_protocol: See detailed description in Lampe JW et al. Signatures of environmental exposures using peripheral leukocyte gene expression: tobacco smoke. Cancer Epidemiol Biomarkers Prev 2004;13:445–453.

scan_protocol: The two-colour microarrays were scanned using the Agilent scanner and proprietary image acquisition software as described in the reference above.

data_processing:
Experimental QC was performed in Matlab (mathworks, inc. Natick, ma, http://www.mathworks.com). Spiked-in exogenous mRNA hybridizations were examined for a large number of known problems, and attempts were made to explain any abnormal trends or outlier arrays. Expression data was loaded into the Resolver (Rosetta proprietary software database for transformation, http://www.rosettabio.com/products/resolver/default.htm), normalization and error modelling.  Fluor-reversed pairs for each sample were combined to give a single log-ratio and a p-value for technical variability for each biological sample compared to its appropriate control. Next, 1d and 2d clustering and classifier analysis was used to get an overview of the experiment.
The intensity of spots (about 100 m) were quantified from the 10-m pixels by frame-by-frame background subtraction and intensity averaging in each channel. Dynamic range of the resulting spot intensities was typically a ratio of 1,000 between the brightest spots and the background-subtracted additive error level. Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes. This procedure is nearly equivalent to normalization between channels using the intensity ratio of genomic DNA spots, but is possibly more robust, as it is based on the intensities of several thousand spots distributed over the array.

source_name: Pooled 8 GOLD0 Lung

label_protocol: mRNA from 8 of the GOLD 0 subjects (non-obstructed smokers) was pooled to form the reference mRNA (Channel 1).  This reference was used for competitive hybridization against all of the other samples (Channel 2) including the GOLD 0 samples which made up the reference pool.

growth_protocol: Immediately after resection, the lung or lobe was obtained from the operating room, and after the clinical specimens of the lesion, lymph nodes, and the resection margin were obtained, the lobes and lungs  were inflated using a 50% mixture of Cryomatrix (Shandon, Pittsburgh, PA) and saline and frozen in liquid nitrogen fumes. The frozen lungs and lobes were then cut into 7 to 15 2-cm-thick slices using a band saw  (Sears, Hoffman Estates, IL) and multiple randomly stratified blocks were acquired (1–3/slice) using a power-driven hole saw (Hobart, Troy, OH) fitted with a 1.5-cm diameter bit (11). The frozen ‘‘cores’’ were stored at 2808C for later cryosectioning and RNA extraction.

extract_protocol: RNA was extracted using a modification of the Qiagen RNeasy protocol. Briefly, lung tissue was homogenized in buffer containing the denaturant guanidine isothiocyanate and then centrifuged at 5,000 x g for 10 minutes.  One volume of 70% ethanol is then added to the supernatant and the sample applied by centrifugation onto a RNeasy midi column.  This was followed by on-column DNase digestion to remove DNA.  The column is then washed twice and RNA elution was performed twice with RNase-free water.  The quality of the RNA as revealed by the 28s/18s rRNA ratio (>1) was determined using an Agilent 2100 Bioanalyzer.  The RNA was then quantified (A260) and dilutions prepared for microarray profiling.

treatment_protocol: No additional treatment of lung samples was applied.

value: lung

tag: gold stage

value: Patient 3467

tag: sa/v

value: Low SA/V

tag: fev1 %p

tag: core with low s/v(cm2/ml)

tag: core with high s/v(cm2/ml)

tag: difference in s/v(cm2/ml)


title: GBAM1 mono-culture, rep3

description: GBAM1 - 3

tag: tissue


title: GBAM1 co-culture, rep1

description: GBAM1 - coculture 1


title: Lung_Emphysema_G2-3469#1

value: Patient 3469

value: High SA/V


title: GBAM1 mono-culture, rep2

description: GBAM1 - 2


title: Lung_Emphysema_G2-3469#2


title: NSC11 co-culture, rep3

description: NSC11 - coculture 3


title: WT-mesR mutant, biological replicate 1 of 3, dye swap.


title: WT-mesR mutant, biological replicate 2 of 3, dye swap.


title: WT-mesR mutant, biological replicate 2 of 3.


title: Lung_Emphysema_NS-3037#1

value: Non-smoker

value: Patient 3037


title: Lung_Emphysema_NS-3037#2


title: Lung_Emphysema_G3-3467#1


title: NSC11 mono-culture, rep2

description: NSC11 - 2


title: Lung_Emphysema_G2-3412#2

value: Patient 3412


title: GBAM1 co-culture, rep2

description: GBAM1 - coculture 2


title: WT-mesR mutant, biological replicate 3 of 3.

value: wild type ETSU9


title: WT-mesR mutant, biological replicate 1 of 3.

value: ETSU9mesR mutant


title: Lung_Emphysema_G3-6034#1

value: Patient 6034


title: Lung_Emphysema_G3-6034#2


title: Lung_Emphysema_G2-3380#2

value: Patient 3380


title: GBAM1 mono-culture, rep1

description: GBAM1 - 1

value: brain

value: glioblastoma multiforme


title: Lung_Emphysema_G2-3412#1


title: Lung_Emphysema_G2-3380#1


title: Lung_Emphysema_G1-6280#1

value: Patient 6280


title: siDJ-1 2

city: Toronto

first: Minna

last: Woo

state: Ontario

address: Room 10-601D, 101 College Street

institute: University of Toronto

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized by default algorithms in GeneSpring 12.6 software. 1, data transformation: set measurements less than 0.01 to 0.01. 2, normalize to 50th percentile per chip. 3, normalize to median per gene.

source_name: C2C12 myotubes, DJ-1 siRNA

label_protocol: Two hundred nanograms from each RNA sample were labelled using Illumina TotalPrep-96 RNA Amplification kit as per amplification protocol

growth_protocol: Murine C2C12 myoblasts (ATCC) were maintained in a growth medium consisting of Dulbecco’s modified Eagle’s medium (DMEM) (4.5 g/L D-glucose) supplemented with 10% (vol/vol) FBS (Gibco) and 100 U/mL penicillin and streptomycin (Gibco). Cells were cultured in a humidified incubator under an atmosphere of 5% CO2 at 37 °C. Differentiation was induced by switching to differentiation medium consisting of DMEM supplemented with 2% horse serum (Gibco) when cells reached confluency. Myotubes were used for experiments following 4 days of differentiation.

extract_protocol: Total RNA from C2C12 myotubes was isolated using the Trizol reagent (Invitrogen).

treatment_protocol: For siRNA transfection, cells cultured in growth medium were transfected with 60 nM siRNA using Lipofectamine RNAiMAX reagent (Invitrogen) according to the manufacturer’s reverse transfection protocol. 48 hours after transfection, cells were switched to differentiation medium and cultured for 96 hours

tag: cell type

value: Differentiated C2C12 myotubes


title: Scramble 1

description: replicate 1

source_name: C2C12 myotubes, scramble siRNA


title: Lung_Emphysema_G1-3385#2

value: Patient 3385


title: Lung_Emphysema_G1-6280#2

value: lung


title: Lung_Emphysema_G1-1984#1

value: Patient 1984


title: Lung_Emphysema_G2-3377#1

value: Patient 3377


title: Lung_Emphysema_G2-2427#2

value: Patient 2427

value: Low SA/V


title: Lung_Emphysema_G2-2427#1

value: High SA/V


title: Scramble 3

description: replicate 3


title: Lung_Emphysema_G1-2425#1

value: Patient 2425


title: Lung_Emphysema_G2-3377#2


title: Lung_Emphysema_G1-3385#1


title: siDJ-1 3

description: replicate 3


title: siDJ-1 1

description: replicate 1


title: Wild type used for MAT1A 8 month, replicate 3

description:
MAT1A_wt_8_3
Gene expression data from the wild type used for MAT1A knockout at 8 month.

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Mouse430_2.na21 platform. GeneChips were washed and stained in the Fluidics Station 450.

data_processing: The data were acquired with GCOS instrument and processed using RMA normalization method.

source_name: Mouse liver, wild type, healthy, 8 months

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

tag: strain/background

tag: genotype/variation

value: wild type

value: 8 months

value: liver

value: healthy


title: PGP1 with Mouse NEUROG1 and Mouse NEUROG2 replicate 1

city: La Jolla

first: Nathan

last: Lewis

state: CA

institute: University of California, San Diego

description: gene expression after 4 days of ectopic Ngn1 and Ngn2 (murine cDNA's) expression

hyb_protocol: 700ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented used Agilent Gene expression Hybridization kit ( part # 5188-5242 ) at 60°C for 30 minutes in a reaction volume of 25ul  following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent GEx hybridization buffer HI-RPM (part # 5188-5242) was added to the fragmentation mixture and hybridized to Agilent Suprint G3 Human GE 8X60K array (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds at room temperature with Stabilization and Drying Solution ( Agilent, part # 5185-5979) , then  Airdry for 5 minutes.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with Surescan High-Resolution Technology used one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data in the matrix table represent the non-normalized values imported directly from the raw files.

source_name: iPS cells, PGP1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng  RNA using the One-Color Microarray-Based Gene Expression Analysis, Low  Input Quick  Amplification Labeling kit (Agilent, Part # 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA, Part # 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PGP1 hiPS cells were grown in mTeSR-1 (Stem Cell Technologies) in Matrigel-coated in 6-well plates. The growth medium was changed daily. Doxycycline was added at a concentration of 500 ng/ml.

extract_protocol: The RNA extraction was performed using the mirVana Isolation Kit (AM1560, Ambion) following their protocol, omitting the last step for miRNA enrichment (resulting in total RNA extraction)

treatment_protocol: Cells were lysed in Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) and two wells were pooled per replicate for RNA extraction

value: Fibroblast derived iPS cells, differentiated neurons

tag: treatment


title: Lung_Emphysema_G1-1984#2


title: PGP1 rep3

description: gene expression after 4 days without ectopic expression

value: Fibroblast derived iPS cells

value: after 4 days without ectopic expression


title: PGP1 with Mouse NEUROG1 and Mouse NEUROG2 replicate 2

value: after 4 days of ectopic Ngn1 and Ngn2 (murine cDNA's) expression


title: PGP1 rep1


title: Wild type used for MAT1A 8 month, replicate 1

description:
MAT1A_wt_8_1
Gene expression data from the wild type used for MAT1A knockout at 8 month.

tag: age

tag: disease status


title: Wild type used for MAT1A 8 month, replicate 5

description:
MAT1A_wt_8_5
Gene expression data from the wild type used for MAT1A knockout at 8 month.


title: PGP1 with Mouse NEUROG1 and Mouse NEUROG2 replicate 3


title: Scramble 2

description: replicate 2

value: Differentiated C2C12 myotubes


title: Lung_Emphysema_G1-2425#2

tag: patient id


title: Wild type used for MAT1A 8 month, replicate 4

description:
MAT1A_wt_8_4
Gene expression data from the wild type used for MAT1A knockout at 8 month.


title: Wild type used for MAT1A 8 month, replicate 2

description:
MAT1A_wt_8_2
Gene expression data from the wild type used for MAT1A knockout at 8 month.


title: PGP1 rep2


title: MAT1A knockout at 8 month age, biological replicate 5

description:
MAT1A_8_5
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

source_name: Mouse liver, MAT1A knockout, non-alcoholic steatohepatitis, 8 months

value: MAT1A knockout

value: non-alcoholic steatohepatitis


title: Lung_Emphysema_G0-6091#2

value: lung

value: Patient 6091


title: PGP1 with Human NEUROG1 and Human NEUROG2 replicate 2

description: gene expression after 4 days of ectopic NGN1 and NGN2 expression


title: Lung_Emphysema_G0-5726#2

value: Patient 5726


title: Lung_Emphysema_G0-5954#1

value: Patient 5954


title: Lung_Emphysema_G0-5771#2

value: Patient 5771

value: Low SA/V


title: MAT1A knockout at 8 month age, biological replicate 1

description:
MAT1A_8_1
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.


title: Lung_Emphysema_G0-5771#1

value: High SA/V


title: MAT1A knockout at 8 month age, biological replicate 4

description:
MAT1A_8_4
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

value: 8 months


title: Lung_Emphysema_G0-5954#2


title: PGP1 with Human NEUROG1 and Human NEUROG2 replicate 3

value: after 4 days of ectopic NGN1 and NGN2 expression


title: MAT1A knockout at 3 month age, biological replicate 2

description:
MAT1A_3_2
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.

source_name: Mouse liver, MAT1A knockout, steatosis, 3 months

value: 3 months

value: liver

value: steatosis


title: Lung_Emphysema_G0-5726#1


title: Fibroblast derived iPS cells wt

value: Fibroblast derived iPS cells

value: after 4 days without ectopic expression


title: PGP1 with Human NEUROG2 replicate 3

description: gene expression after 4 days of ectopic NGN2 expression

value: Fibroblast derived iPS cells, differentiated neurons

value: after 4 days of ectopic NGN2 expression


title: PGP1 with Human NEUROG1 and Human NEUROG2 replicate 1


title: Wild type used for MAT1A 3 month, replicate 2

description:
MAT1A_wt_3_2
Gene expression data from the wild type used for MAT1A knockout at 3 month.

source_name: Mouse liver, wild type, healthy, 3 months

value: wild type

value: healthy


title: Wild type used for MAT1A 3 month, replicate 4

description:
MAT1A_wt_3_4
Gene expression data from the wild type used for MAT1A knockout at 3 month.


title: MAT1A knockout at 3 month age, biological replicate 3

description:
MAT1A_3_3
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.

value: MAT1A knockout


title: MAT1A knockout at 3 month age, biological replicate 5

description:
MAT1A_3_5
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.


title: Lung_Emphysema_G0-6091#1

value: lung

value: Patient 6091


title: Wild type used for MAT1A 3 month, replicate 5

description:
MAT1A_wt_3_5
Gene expression data from the wild type used for MAT1A knockout at 3 month.


title: PGP1 with Human NEUROG2 replicate 1


title: Wild type used for MAT1A 3 month, replicate 1

description:
MAT1A_wt_3_1
Gene expression data from the wild type used for MAT1A knockout at 3 month.


title: MAT1A knockout at 3 month age, biological replicate 4

description:
MAT1A_3_4
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.


title: PGP1 with Human NEUROG2 replicate 2


title: GNMT knockout at 8 month age, biological replicate 4

description:
GNMT_8ko4
Gene expression data from GNMT knockout at 8 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.

source_name: Mouse liver, GNMT knockout, hepatocellular carcinoma, 8 months

value: GNMT knockout

value: hepatocellular carcinoma


title: Wild type used for MAT1A 3 month, replicate 3

description:
MAT1A_wt_3_3
Gene expression data from the wild type used for MAT1A knockout at 3 month.


title: MAT1A knockout at 8 month age, biological replicate 2

description:
MAT1A_8_2
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

value: non-alcoholic steatohepatitis


title: MAT1A knockout at 3 month age, biological replicate 1

description:
MAT1A_3_1
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.


title: PGP1 with Human NEUROG1 replicate 3

description: gene expression after 4 days of ectopic NGN1 expression

value: after 4 days of ectopic NGN1 expression


title: Lung_Emphysema_G0-3491#1

value: Patient 3491

value: High SA/V


title: PGP1 with Human NEUROG1 replicate 2


title: Wild type used for GNMT 8 month, replicate 3

description:
GNMT_8WT3
Gene expression data from the wild type used for GNMT knockout at 8 month.

value: 8 months

value: liver


title: Lung_Emphysema_G0-3410#1

value: Patient 3410


title: Lung_Emphysema_G0-3381#2

value: Patient 3381

value: Low SA/V


title: GNMT knockout at 8 month age, biological replicate 2

description:
GNMT_8ko2
Gene expression data from GNMT knockout at 8 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: GNMT knockout at 8 month age, biological replicate 3

description:
GNMT_8ko3
Gene expression data from GNMT knockout at 8 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: GNMT knockout at 8 month age, biological replicate 1

description:
GNMT_8ko1
Gene expression data from GNMT knockout at 8 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.


title: Lung_Emphysema_G0-3491#2


title: Wild type used for GNMT 8 month, replicate 1

description:
GNMT_8WT1
Gene expression data from the wild type used for GNMT knockout at 8 month.


title: Lung_Emphysema_G0-3381#1


title: PGP1 with Human NEUROG1 replicate 1

value: Fibroblast derived iPS cells, differentiated neurons


title: Wild type used for GNMT 8 month, replicate 4

description:
GNMT_8WT4
Gene expression data from the wild type used for GNMT knockout at 8 month.

value: wild type


title: Lung_Emphysema_G0-1986#2

value: Patient 1986


title: Lung_Emphysema_G0-2028#1

value: Patient 2028


title: GNMT knockout at 3 month age, biological replicate 1

description:
GNMT_3ko1
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

source_name: Mouse liver, GNMT knockout, non-alcoholic steatohepatitis, 3 months

value: 3 months


title: GNMT knockout at 3 month age, biological replicate 4

description:
GNMT_3ko4
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.


title: Wild type used for GNMT 3 month, replicate 4

description:
GNMT_3WT4
Gene expression data from the wild type used for GNMT knockout at 3 month.

value: healthy


title: Wild type used for GNMT 8 month, replicate 5

description:
GNMT_8WT5
Gene expression data from the wild type used for GNMT knockout at 8 month.


title: GNMT knockout at 3 month age, biological replicate 5

description:
GNMT_3ko5
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

value: GNMT knockout


title: GNMT knockout at 3 month age, biological replicate 2

description:
GNMT_3ko2
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.


title: Wild type used for GNMT 3 month, replicate 2

description:
GNMT_3WT2
Gene expression data from the wild type used for GNMT knockout at 3 month.


title: Wild type used for GNMT 3 month, replicate 3

description:
GNMT_3WT3
Gene expression data from the wild type used for GNMT knockout at 3 month.


title: GNMT knockout at 3 month age, biological replicate 3

description:
GNMT_3ko3
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.


title: Lung_Emphysema_G0-3410#2

value: lung


title: Wild type used for GNMT 8 month, replicate 2

description:
GNMT_8WT2
Gene expression data from the wild type used for GNMT knockout at 8 month.


title: Lung_Emphysema_G0-2028#2


title: Wild type used for GNMT 3 month, replicate 5

description:
GNMT_3WT5
Gene expression data from the wild type used for GNMT knockout at 3 month.


title: Wild type used for GNMT 3 month, replicate 1

description:
GNMT_3WT1
Gene expression data from the wild type used for GNMT knockout at 3 month.


title: rcm1ko_totalRNA_90min_rep2

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: total cellular RNA of 90 min H2O2 treated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)

hyb_protocol: Hybridisation to Yeast (V2) 8 x 15K Gene Expression Microarrays (Agilent) and washing were performed following the manufactures instructions.

scan_protocol: Slides were scanned with the two laser Agilent microarray scanner (G2565A). For raw data generation Agilent feature extraction software (version 7.5) was used.

data_processing: Raw data were processed into R/Bioconductor. Intensities were log2 transformed, backgrounds were subtracted using normexp, and intensities were normalized within arrays by using the Loess method and between arrays by using Aquantile.

organism: Saccharomyces cerevisiae

source_name: exponentially growing yeast cells (OD = 0.6)

label_protocol: Samples were labelled using the Low Input Quick Amp Labeling Kit Two Color (Agilent) following the manufactures instructions.

growth_protocol: Wild-type and rcm1 knockout yeast were grown overnight in 3 mL SC medium at 28°C with shaking. On the next day, 100 ml SD were inoculated with the overnight culture to an OD600 of 0.003 and grown at 28°C with shaking until the OD600 reached 0.5 - 0.6.

extract_protocol: 125 µg/ml cycloheximide (Sigma) were added and the cells were incubated at 28°C with shaking for further 15 min. Afterwards the flasks were placed on ice for 15 min with shaking from time to time. After pelleting the cells at 3,500 rpm and 4°C for 5 min, the pellets were washed two times with 2 mL cooled TMNSH buffer (10 mM Tris pH 7.4, 50 mM NH4Cl, 10 mM MgCl2, 12.5 mM 2-mercaptoethanol) and resuspended in 1 mL of lysis buffer (10 mM Tris pH 7.4, 50 mM NH4Cl, 10 mM MgCl2, 12.5 mM 2-mercaptoethanol, 50 mM KCl, 1 mM PMSF, 125 μg/ml cycloheximid). Lysis was performed by transferring the suspensions to glass tubes and vortexing with glass beads (0.4 - 0.6 mm diameter) 8 times for 30 sec, with at least 30 sec recovery on ice between each cycle. Afterwards the crude lysates were centrifuged at 4,000 rpm at 4°C for 10 min to remove insoluble debris. The supernatants were transferred to fresh tubes and were supplemented with 100 μl Triton X-100 (10% v/v). After centrifugation at full speed in a tabletop centrifuge at 4°C for 10 min, the supernatants were carefully transferred to fresh vials and the OD260 was recorded for quantification. A volume equalling 15 OD260 was loaded onto a 10 mL linear 7-52 % sucrose gradient in TMNSH buffer containing 50 mM KCl and centrifuged at 37,000 rpm at 4°C for 3 h. The profiles were recorded from the bottom of the tubes with a UV detector set to 254 nm. 300 µl polysomal fractions or total lysate were mixed with 900 µl Trizol LS and RNA was extracted following the manufacture's protocol.

treatment_protocol: After the culture reached an OF of 0.5 - 0.6, 0.4 mM H2O2 were added to the medium for 30 min or 90 min.

tag: genotype

tag: h2o2 stress [min]

tag: assayed molecule

value: total cellular RNA

value: pool of wild-type and rcm1Δ

value: pool of 0, 30 and 90 min

value: pool of polysomal RNA and total RNA


title: rcm1ko_totalRNA_90min_rep1


title: wt_totalRNA_90min_rep1

description: total cellular RNA of 90 min H2O2 treated wild-type yeast (CY3) vs. common reference pool (CY5)

value: wild-type


title: wt_totalRNA_90min_rep2


title: rcm1ko_polysomes_90min_rep1

description: Polysome-associated RNA fraction of 90 min H2O2 treated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)

value: polysomal RNA


title: rcm1ko_totalRNA_0min_rep2

description: total cellular RNA of rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: rcm1ko_polysomes_30min_rep2

description: Polysome-associated RNA fraction of 30 min H2O2 treated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: rcm1ko_totalRNA_30min_rep1

description: total cellular RNA of 30 min H2O2 treated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: rcm1ko_totalRNA_0min_rep1

description: total cellular RNA of untreated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: rcm1ko_polysomes_90min_rep2


title: rcm1ko_totalRNA_30min_rep2


title: Lung_Emphysema_G0-1986#1

tag: gold stage

value: High SA/V


title: rcm1ko_polysomes_0min_rep1

description: Polysome-associated RNA fraction of untreated rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: wt_totalRNA_30min_rep1

description: total cellular RNA of 30 min H2O2 treated wild-type yeast (CY3) vs. common reference pool (CY5)


title: wt_polysomes_90min_rep2

description: Polysome-associated RNA fraction of 90 min H2O2 treated wild-type yeast (CY3) vs. common reference pool (CY5)


title: rcm1ko_polysomes_0min_rep2

description: Polysome-associated RNA fraction of rcm1 knockout yeast (CY3) vs. common reference pool (CY5)


title: wt_totalRNA_0min_rep2

description: total cellular RNA of untreated wild-type yeast (CY3) vs. common reference pool (CY5)


title: wt_totalRNA_30min_rep2


title: rcm1ko_polysomes_30min_rep1


title: wt_polysomes_30min_rep1

description: Polysome-associated RNA fraction of 30 min H2O2 treated wild-type yeast (CY3) vs. common reference pool (CY5)


title: wt_polysomes_30min_rep2


title: wt_polysomes_0min_rep2

description: Polysome-associated RNA fraction of untreated wild-type yeast (CY3) vs. common reference pool (CY5)


title: wt_polysomes_90min_rep1


title: wt_polysomes_0min_rep1


title: MAT1A knockout at 8 month age, biological replicate 3

description:
MAT1A_8_3
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

value: MAT1A knockout

value: 8 months

value: liver

value: non-alcoholic steatohepatitis