title: liver-lean-rep3

status: Public on Sep 02 2012

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

description: Biological replicate 3 of 4.

hyb_protocol: The labelled amples were hybridized using Agilent´s Gene Expression Hybridization Kit, according to the included instructions.

scan_protocol: After hybridization the arrays were washed, dried and immediately scanned using an Agilent DNA microarray scanner (Agilent Technologies). For each array, the photomultiplier tubes (PMT) and power of the laser was automatically set and as recommended by the company, images were scanned with both high (100%) and low (10%) eXtended Dynamic Range (XDR)

data_processing: Data from the image files were extracted using Agilent Feature Extration (FE) 10.7.3.1 software and imported into GeneSpring (Agilent) where the data was LOWESS normalized.

organism: Rattus norvegicus

source_name: liver from lean Zucker diabetic rat

label_protocol: 0.2 μg total RNA was labeled according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol - Low Input Quick Amp Labeling, including RNA spike in kit. Controls were labelled with Cy3 and treated samples with Cy5.

extract_protocol: Total RNA was isolated from frozen liver (100mg) by using SV Total RNA Isolation System (Promega) according to manufactory instructions. RNA concentration was quantified by NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc, USA, DE) spectrophotometrically at 260 nm and quality was determined using a 2100 Bioanalyzer and RNA 6000 nano LabChip kit  (Agilent Technologies, Palo Algo, CA).

treatment_protocol: The rats were treated subcutaneous (s.c.) with testosterone undecanoate (TU) (Bayer Schering Pharma AG, Germany, 1:5 proplyane glycol) at 20mg/kg body weight or vehicle control every three days for the first two weeks then thereafter once a week during the last two weeks.

value: lean Zucker diabetic fatty (fa/+) rat

value: 12 weeks

tag: treatment

value: vehicle control

value: Testosterone undecanoate (TU), s.c 20mg/kg body weight for 4 weeks.


title: A200_01_colonscr_OLF

status: Public on Sep 03 2012

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: scraping of the colon after 2 weeks low-fat diet, pooled sample of 8 old mice

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Male C57BL/6J mice of 12 weeks and 20 months of age were purchased from JANVIER SAS, Le Genest Saint Isle, France, and  housed individually in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice were fed standard lab chow (RMH-B; Arie Blok BV, Woerden, the Netherlands) and had free access to feed and water.

extract_protocol: Total RNA was prepared from colonic scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, RNA of 6-8 mice per group was subsequently pooled at a concentration of 500 ng/mouse.

treatment_protocol: After been fed for 1 week the lab chow, mice were given a semi-synthetic low-fat (10%) diet for 2 weeks. Subsequently, both age groups were split into two subgroups one of which received the low-fat diet for two more weeks while the other group received a high-fat (45%) diet for two weeks. Both diets were based on Research Diets’ formulas D12450B/D12451, with adaptations regarding type of fat (palm oil instead of lard) and carbohydrates. After this intervention period, mice were killed in the postprandial state and the colon was removed.

tag: strain

tag: gender

value: male

tag: age

value: 21 months

tag: tissue

value: colon


title: liver-obese-rep4

description: Biological replicate 4 of 4.

source_name: liver from obese Zucker diabetic rat

value: obese Zucker diabetic fatty (fa/fa) rat


title: primary KC, MED1flox/flox

city: Suita

first: Takeshi

last: Nakajima

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

description:
primary keratinocytes isolated from newborn mice
primary_KC,_control.CEL

hyb_protocol: The hybridization was performed (Hybridization Oven 640 110V, Affymetrix 800138) according to the manufacturer's instructions (Expression Analysis Technical Manual, 701021 Rev. 5, Section2 Eukaryotic Sample and Array Processing, Chapter2 Eukaryotic Target Hybridization, Affymetrix). GeneChips were washed and stained in the Fluidics Station 450 (Affymetrix 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix 00-0074).

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 (Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015).

source_name: primary murine keratinocytes derived from wild-type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Skin of newborn mice was excised after the mice were sacrificed with excessive anesthetic and were treated with dispase followed by trypsin to separate the epidermis from the dermis. Keratinocytes were seeded on type I collagen coated dishes, and were cultured in CnT07 conditioned culture medium (CELLnTEC, Bern, Switzerland).

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

treatment_protocol: Keratinocytes were used for experiment as a primary culture.

tag: cell type

value: cultured keratinocytes

tag: genotype/variation

value: derived from wild-type mice


title: liver-lean-rep1

description: Biological replicate 1 of 4.


title: liver-obese-rep1

description: Biological replicate 1 of 4.


title: liver-lean-rep2

description: Biological replicate 2 of 4.


title: liver-lean-rep4

description: Biological replicate 4 of 4.


title: liver-obese-rep3

description: Biological replicate 3 of 4.


title: liver-obese-rep2

description: Biological replicate 2 of 4.


title: PBC_1 tumor1

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

description:
Sample.1.cy3
raw data file: US22502676_251485056689_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: Hybridization was performed on a human GE 4x44K formatted expression array spotted with 60-mer oligonucleotides representing over 43,000 well-characterized coding and non-coding sequences (G4112F, Agilent Technologies, Amstelveen, The Netherlands).  Input: 825 ng RNA

scan_protocol: Scanning was performed using a microarray scanner G2505B (Agilent Technologies). Feature Extraction v9.5 using the manufacturers protocols (Agilent Technologies).

data_processing:
Preprocessing of the gene expression data comprised of RMA background correction, loess within-array normalization and A-quantile between-array normalization was performed in R. Single channel data were used to accommodate the unbalanced design. Ch1=cy3, ch2=cy5
The moderated t-test implemented in Limma, employing empirical Bayes estimation of the variance, was used to evaluate the difference in gene expression between the two groups. Sample origin and CyDye were taken along as possible confounders. The Benjamini-Hochberg procedure was applied to the raw p-values to control the False Discovery Rate (FDR).Tobacco use was classified as ‘none’ when the individual did not smoke for a period of at least half a year before sampling. Alcohol use was scored as ‘none’, when the individual drank no alcohol or if one had abstained from alcohol for more than half a year. Analysis was performed with and without correction for tobacco and alcohol consumption.
There were 28 patients with head and neck squamous cell carcinoma (HNSCC) with samples labeleld 'tumor''. There were 11 individuals without cancer that served as control, with samples labeled 'control'. Each patient and control has an unique number.
Although the hybridizations were dual channel (two samples per array), the data were analyzed as single channel (each sample independently).
Data for several Samples was not used in the analysis and are omitted from the processed data and Sample list: Sample 11 cy3, Sample 16 cy5, Sample 17 cy3, Sample 18 cy3, Sample 19 cy5, Sample 20 cy3, Sample 21 cy5, Sample 22 cy5, Sample 23 cy3, Sample 24 cy5, Sample 25 cy3

organism: Homo sapiens

source_name: Nucleated peripheral blood cells

label_protocol: cDNA synthesis and labeling were performed according to the recommendations of the manufacturer (Agilent Technologies, Amstelveen, The Netherlands), including quality controls (QCs)

extract_protocol: These PBC were lysed with RNA-bee (Campro Scientific bv., Veenendaal, the Netherlands)  and RNA was extracted according to the protocol of the manufacturer.

treatment_protocol: Blood collection was performed when the patient was under general anesthesia, before the surgical procedure had started. Blood samples by venipuncture were collected in heparin tubes. After lysis of the erythrocytes by osmotic shock, the nuclear cells were washed with Hanks buffered salt solution.

tag: cancer or control with number

tag: current tobacco consumption

value: yes

tag: current alchol consumption


title: HEK293 NFIL3 shRNA replicate 1

city: New York

first: Megan

middle: Erin

last: Keniry

state: New York

address: 1130 St. Nicholas Ave., room 407

department: Institute for Cancer Genetics

country: USA

institute: Columbia University

description: Biological replicate 1 of 4, HEK293 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1746s1c1) and selected.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Microarray data was extracted using Mean FG- Median BG (ch1=G, ch2=R), filtered: log (ch (1)*ch (2))/2>=.1, and normalized using Lowess normalization; the BASE database (Lund, Sweden) was utilized to extract, filter and normalize data.

source_name: human HEK293 cells infected with NFIL3 targeting shRNA

label_protocol: 2 µg of total RNA were labled using Agilent RNA Spike In Kit for Two color v4.0 according to manufacturer's protocol

growth_protocol: Human HEK293 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was prepared from cells using Qiagen Rneasy kit.

treatment_protocol: Cells were infected with lentivirus harboring control shRNA or shRNA targeting NFIL3.

tag: cell line

source_name: Universal Human Reference RNA Stratagene

tag: sample type

value: reference RNA


title: Transcriptome epiRIL98_Col vs WT_Col [ds1 and ds2]

city: PARIS

first: Vincent

last: Colot

address: 46 rue d'Ulm

country: France

institute: IBENS - CNRS UMR8197 - INSERM U1024

description:
Transcriptome analysis in dye-swap.
1st hybridization raw data:
epiRIL98=449775-2_635_A02.pair - WT=449775-2_532_A02.pair
swap raw data:
epiRIL98=449775-2_532_A01.pair - WT=449775-2_635_A01.pair

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biases.

label: Cy3, Cy5

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, 1 ug of total RNA were amplified with one round of in vitro transcription 10h at 37°C using the MessageAmp™ II aRNA Amplification Kit (Ambion). Double stranded cDNA synthesis was then performed on 2 ug of aRNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen).

growth_protocol: Seedlings 10 day-old plants grown in liquid 1/2MS media, 16 hours photoperiod.

extract_protocol: WT_Col:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.

treatment_protocol: no treatment

value: WT

tag: ecotype

value: 10 days

tag: developmental stage

value: whole seedlings

extract_protocol: epiRIL98_Col:10ug. Total RNA was extracted using Rneasy Plant Minikit (Qiagen) according to the supplier’s instructions.


title: HEK293 control (scr for scramble) shRNA replicate 3

description: Biological replicate 3 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.

source_name: human HEK293 cells infected with control (scr for scrambled) shRNA


title: HEK293 NFIL3 shRNA replicate 4

description: Biological replicate 4 of 4, HEK293 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1216s1c1) and selected.


title: HEK293 control (scr for scramble) shRNA replicate 1

description: Biological replicate 1 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: HEK293 control (scr for scramble) shRNA replicate 5

description: Biological replicate 5 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: HEK293 control (scr for scramble) shRNA replicate 2

description: Biological replicate 2 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: BT549 NFIL3 shRNA replicate 1

description: Biological replicate 1 of 2, BT549 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1216s1c1) and selected.

scan_protocol: Scanned on an Agilent G2539A scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

source_name: human BT549 cells infected with NFIL3 targeting shRNA

growth_protocol: Human BT549 cells were grown in DMEM supplemented with 10% FBS.

source_name: Universal Human Reference RNA (Stratagene)


title: BT549 NFIL3 shRNA replicate 2

description: Biological replicate 2 of 2, BT549 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1216s1c1) and selected.


title: HEK293 control (scr for scramble) shRNA replicate 6

description: Biological replicate 6 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: HEK293 NFIL3 shRNA replicate 3

description: Biological replicate 3 of 4, HEK293 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1216s1c1) and selected.


title: HEK293 control (scr for scramble) shRNA replicate 4

description: Biological replicate 4 of 6, HEK293 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: HEK293 NFIL3 shRNA replicate 2

description: Biological replicate 2 of 4, HEK293 cells infected with NFIL3 targeting shRNA (Clone ID: NM_005384.1-1746s1c1) and selected.


title: BT549 control shRNA replicate 2

description: Biological replicate 2 of 2, BT549 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.

source_name: human BT549 cells infected with control (scr for scrambled) shRNA


title: BT549 control shRNA replicate 1

description: Biological replicate 1 of 2, BT549 cells infected with scramble control shRNA (lenti-delivered pLKO.1-puro) and selected.


title: LE_KO2

status: Public on Sep 01 2012

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Gene expression from E15.5 MAP3K1 KO fetus leading edge

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer’s instructions

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF (Entrez Gene, version 14)

source_name: E15.5 MAP3K1 KO fetus leading edge

label_protocol: Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer’s instructions

growth_protocol: The heads of E15.5 wild type and knockout fetuses were embedded in Tissue-Tek OCT medium

extract_protocol: LCM was performed following the manufacturer’s protocol (Molecular Devices).

treatment_protocol: Eight µm coronal sections were mounted on plain uncoated glass slides, dehydrated and stained with HistoGene LCM frozen section staining kit

tag: genotype

value: KO

value: leading edge


title: LE_KO3


title: High Glucose vs. Control Glucose Area4

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol. PowerScanner with 2 lasers in auto-gain configuration was used to extract the signal from cye3 and cye 5 labbeled probed for each arrays.

data_processing: Data were processed by ArrayPro to mesure the intensity of scanned images. Using FlexArray, Intensities were corrected, normalized then compared using limma statistical test between HG and CTL samples.

organism: Bos taurus

source_name: Morula-CTL

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

treatment_protocol: In vitro culture used a 2 step synthetic oviductal fluid system. First step of culture spread from day 0 to day 3 and glucose concentration in the SOF medium is 0.2 mM in control condition or increased to 5 mM in HG condition by adding glucose to the medium. 2nd step of culture spread from day 3 to day 5 in control SOF medium.

value: in vitro

value: morulae

tag: time of embryo collection

value: 120 hpf (hours post-in-vitro fertilization)

tag: bsa source

value: Fatty-acid free BSA Sigma-Aldrich

tag: serum source

value: Hyclone, ThermoScientific

tag: agent

value: Glucose

tag: dose

tag: number per pool

tag: in vitro production

value: Yes

source_name: Morula-HG

value: 5 mM

tag: breed

value: Holstein


title: High Glucose vs. Control Glucose Area3


title: LE_KO1

tag: tissue


title: High Glucose vs. Control Glucose Area1


title: LE_WT3

description: Gene expression from E15.5 MAP3K1 WT fetus leading edge

source_name: E15.5 MAP3K1 WT fetus leading edge


title: IE_WT3

description: Gene expression from E15.5 MAP3K1 WT fetus inner epithelium

source_name: E15.5 MAP3K1 WT fetus inner epithelium

value: inner epithelium


title: LE_WT2


title: LE_WT1


title: IE_WT2


title: A197_09_SI3_OLF

source_name: scraping of the distal segment of the small intestine after 2 weeks low-fat diet, pooled sample of 8 old mice

extract_protocol: Total RNA was prepared from intestinal scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, RNA of 6-8 mice per group was subsequently pooled at a concentration of 500 ng/mouse.

treatment_protocol: After been fed for 1 week the lab chow, mice were given a semi-synthetic low-fat (10%) diet for 2 weeks. Subsequently, both age groups were split into two subgroups one of which received the low-fat diet for two more weeks while the other group received a high-fat (45%) diet for two weeks. Both diets were based on Research Diets’ formulas D12450B/D12451, with adaptations regarding type of fat (palm oil instead of lard) and carbohydrates. After this intervention period, mice were killed in the postprandial state and the small intestine was removed.

tag: strain

tag: gender

value: male

tag: age

value: 21 months

value: distal part small intestine


title: IE_KO3

description: Gene expression from E15.5 MAP3K1 KO fetus inner epithelium

source_name: E15.5 MAP3K1 KO fetus inner epithelium


title: High Glucose vs. Control Glucose Area2


title: rPLC-pYES2 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: Gene expression after 5 hour

hyb_protocol: 600ng of cy3 labeled samples were  fragmented and hybridized .  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C  and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX V 11 75th Percentile Normalization

organism: Saccharomyces cerevisiae

source_name: 5 hour induced

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity

growth_protocol: Cells were grown in synthetic minimal medium containing 0.67% yeast nitrogen base (Difco) supplemented with the appropriate amino acids, adenine and no uracil, and induced with 2% galactose for two or five hours as indicated.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit as per the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cell were harvested by centrifugation and stored in sigma RNAlater solution.

tag: genotype/variation


title: rPLC-pYES2 1

description: Gene expression after 2 hour

source_name: 2 hour induced


title: pYES2 1

description: Gene expression after 2 hour


title: pYES2 2

description: Gene expression after 5 hour


title: IE_KO2


title: Cell line KatoⅢ

type: genomic

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

institute: Sapporo medical university

description: Gastric cancer 13

hyb_protocol: Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Cell line KatoⅢ

label_protocol: Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and reference DNA was labeled with Cy3.

growth_protocol: A total of 46 human gastric mucosa and 10 gastric cancer were obtained from endoscopic biopsy.

extract_protocol: Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.

treatment_protocol: No treatment was carried out.

tag: cell line

value: KatoⅢ

source_name: Human Genomic DNA

tag: pathology

value: Normal Stomach

tag: sample type

value: reference DNA


title: INS1 Total2

city: San Francisco

first: Feroz

last: Papa

state: CA

address: 1700 4th Street

department: Medicine

institute: University of California, San Francisco

hyb_protocol: CyDye conjugated sample (24uL) was added to 30uL 2x hybridization buffer (50% formamide, 10X SSC, 0.2% SDS, H20), OligoDT(3uL), and COtI DNA(3uL-Invitrogen), and then probe was denatured at 95 degrees Celsius for 5 minutes. Tubes were quickly spun down and samples were kept at 42C until added to Pancchip 6.1 using the MAUI hybrization system (Biomicro systems) overnight at 42C. .

scan_protocol: Slides were washed and then scanned using an Axon scanner and data analyzed using the GenePixPro software.

data_processing: We normalized the data using the NOMAD database, and filtered to remove spots with low signal intensity (<2 fold above background) or inconsistent Cy5 to Cy3 signal ratios within the spot (R2 >0.7 for linear relationship between Cy5 vs. Cy3 signal). We then calculated the log2 ratio of the induced to uninduced signals (normalized to the Cy3 reference sample) for each target gene, and averaged the ratios from three independent experiments for each condition. We used Gene Cluster 3.0 to perform hierarchical clustering of genes induced and downregulated at least two-fold and used the Treeview software to visualize the clustered data.

source_name: INS-1 cells, untreated, total RNA

label_protocol: After cDNA purification, cDNA was labeled with either Cy3 (reference) or Cy5 (treated sample) using the Amersham Cy dye kit. 1 Dye tube was dissolved in 30uL DMSO, and 10uL Cy Dye was mixed with 10uL cDNA from sample. Samples were incubated for 1 hour in the dark, and then reactions were purified using the Qiagen MiniElute DNA purification columns, and eluted in 12uL H20. The untreated Cy3 sample was then mixed with the respective treated sample (Cy5), and incubated on ice until hybridization.

growth_protocol: INS-1 cells with doxycycline inducible expression of EGFP or EGFP-L10a fusion generated from INS-1/FRT/TO cells (#5-3.19) (Thomas et al., 2004) were grown in RPMI, 10% fetal calf serum, 1mM sodium pyruvate, 10mM HEPES, 2mM glutamine, 50µM b-mercaptoethanol, 10µg/ml blasticidin.

extract_protocol: Total RNA was extracted using Trizol. For Ribosomal immunoprecipiation, after treatment with Tg, cells were then treated with 100 μg/ml cycloheximide for 20 minutes, then washed twice with PBS containing 100 μg/ml cycloheximide. Lysis buffer was added (20mM HEPES [pH 7.4], 150mM KCL, 2M MgCl2, 1% NP-40—a non-ionic, non-denaturing detergent purchased from EMD Biosciences, San Diego, CA), and plates were incubated on ice for 10 minutes before detaching cells with cell lifters. Lysates were immediately homogenized in ice-cold polysome extraction buffer (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol (DTT), 100 μg/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors) using a motor-driven Teflon-glass homogenizer. Homogenates were centrifuged for 10 minutes at 2,000 × g, 4 °C, to pellet large cell debris, and NP-40 and 1,2-Diheptanoyl-sn-Glycero-3-Phosphocholine  (DHPC) (Avanti Polar Lipids, Alabaster, AL) were added to the supernatant at a final concentration of 1% and 30 mM, respectively, to extract polysomes. After incubation on ice for 5 minutes, the clarified lysate was centrifuged for 10 minutes at 13,000 ×g to pellet insoluble material. Goat anti-GFP (custom made in laboratory of Nathaniel Heintz, Rockefeller Univ.) coated protein G Dynal magnetic beads (Invitrogen Corporation, Carlsbad, CA) were added to the supernatant and the mixture was incubated at 4°C with end-over-end rotation for 30 minutes. Beads were subsequently collected on a magnetic rack, washed three times with high-salt polysome wash buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5mM dithiothreitol, 100 μg/ml cycloheximide) and immediately placed in TriZol-LS reagent (Invitrogen Corporation, Carlsbad CA) and chloroform to extract the bound rRNA and mRNA from polysomes. After extraction, RNA was precipitated with sodium acetate and Glycoblue (Ambion, Austin, TX) in isopropanol overnight at −80°C, washed twice with 70% ethanol, resuspended in water, followed by a DNase digestion, and ethanol purification, before being resuspended in water, and quantitated using a Nanodrop.

treatment_protocol: INS-1 cells were induced with 1ug/mL Doxycycline for 24 hours, then either left untreated for UT samples, or treated with 1uM Thapsigargin for 30 minutes.

value: INS-1 EGFP L10a

value: total RNA

tag: treatment

value: untreated

source_name: INS-1 cells, Tg treated, 30 min, total RNA

value: Total RNA

value: Thapsigargin


title: INS1 RIP2

source_name: INS-1 cells, untreated, immunoaffinity purified RNA

value: polyribosomal RNA

source_name: INS-1 cells,Tg treate,  30min, immunoaffinity purified RNA


title: Cell line MKN74

description: Gastric cancer 14

source_name: Cell line MKN74


title: INS1 RIP1


title: INS1 Total3


title: INS1 RIP3


title: IE_KO1

tag: genotype

value: KO


title: INS1 Total1


title: Cell line NUCG4

description: Gastric cancer 15

source_name: Cell line NUCG4


title: Cell line AGS

description: Gastric cancer 11

source_name: Cell line AGS

value: AGS


title: Human Stomach Tumor Tissue 53

description: Gastric cancer 7

source_name: human stomach tumor tissue

tag: tissue source

value: Diffuse type GC patients

value: F

tag: tissue type

value: gastric cancer


title: Cell line HSC44

description: Gastric cancer 12

source_name: Cell line HSC44


title: Human Stomach Tumor Tissue 55

description: Gastric cancer 9

value: Intestinal type GC patients

value: M


title: Human Stomach Tumor Tissue 54

description: Gastric cancer 8


title: Human Stomach Tumor Tissue 49

description: Gastric cancer 3


title: Human Stomach Tumor Tissue 48

description: Gastric cancer 2


title: Human Stomach Tumor Tissue 52

description: Gastric cancer 6


title: Human Stomach Tissue 46

description: Normal 46

source_name: human stomach tissue

value: noncancerous background gastric mucosa

tag: location of noncancerous gastric mucosa

value: Antrum


title: Human Stomach Tumor Tissue 47

description: Gastric cancer 1

value: Normal Stomach


title: Human Stomach Tumor Tissue 50

description: Gastric cancer 4

value: reference DNA


title: Human Stomach Tumor Tissue 56

description: Gastric cancer 10


title: Human Stomach Tissue 40

description: Normal 40


title: Human Stomach Tissue 45

description: Normal 45


title: Human Stomach Tissue 42

description: Normal 42


title: Human Stomach Tissue 43

description: Normal 43


title: Human Stomach Tissue 34

description: Normal 34

value: Healthy individuals (P or C)


title: Human Stomach Tumor Tissue 51

description: Gastric cancer 5


title: Human Stomach Tissue 31

description: Normal 31


title: Human Stomach Tissue 32

description: Normal 32


title: Human Stomach Tissue 35

description: Normal 35


title: Human Stomach Tissue 41

description: Normal 41


title: Human Stomach Tissue 37

description: Normal 37


title: Human Stomach Tissue 30

description: Normal 30

value: Healthy individuals (A)


title: Human Stomach Tissue 38

description: Normal 38


title: Human Stomach Tissue 44

description: Normal 44


title: Human Stomach Tissue 29

description: Normal 29


title: Human Stomach Tissue 33

description: Normal 33


title: Human Stomach Tissue 39

description: Normal 39


title: Human Stomach Tissue 36

description: Normal 36


title: Human Stomach Tissue 23

description: Normal 23

value: Body


title: Human Stomach Tissue 25

description: Normal 25


title: Human Stomach Tissue 26

description: Normal 26


title: Human Stomach Tissue 24

description: Normal 24


title: Human Stomach Tissue 19

description: Normal 19


title: Human Stomach Tissue 27

description: Normal 27


title: Human Stomach Tissue 20

description: Normal 20


title: Human Stomach Tissue 21

description: Normal 21


title: primary KC, MED1epi-/-

description:
primary keratinocytes isolated from newborn mice
primary_KC,_MED1_null.CEL

source_name: primary murine keratinocytes derived from keratinocyte-specific MED1 null mice

tag: cell type

value: cultured keratinocytes


title: Human Stomach Tissue 18

description: Normal 18


title: Human Stomach Tissue 22

description: Normal 22


title: Human Stomach Tissue 28

description: Normal 28


title: Human Stomach Tissue 14

description: Normal 14


title: Human Stomach Tissue 12

description: Normal 12


title: Human Stomach Tissue 15

description: Normal 15


title: Human Stomach Tissue 9

description: Normal 9


title: Human Stomach Tissue 7

description: Normal 7


title: Human Stomach Tissue 11

description: Normal 11


title: Human Stomach Tissue 6

description: Normal 6


title: Human Stomach Tissue 16

description: Normal 16


title: Human Stomach Tissue 8

description: Normal 8


title: Human Stomach Tissue 17

description: Normal 17


title: Human Stomach Tissue 10

description: Normal 10


title: Human Stomach Tissue 5

description: Normal 5


title: Human Stomach Tissue 2

description: Normal 2


title: Human Stomach Tissue 4

description: Normal 4


title: Human Stomach Tissue 13

description: Normal 13


title: FLAG-H2BE vs H3 signal

city: Cambridge

first: Stephen

middle: W.

last: Santoro

address: 16 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

hyb_protocol: Approximately 5 μg of biotin-labeled DNA was hybridized to each array using the Affymetrix hybridization kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: CEL file data was processed using Tiling Analysis Software (Affymetrix).

source_name: ChIP: FLAG-H2BE from Flag-H2be MOE

label_protocol: Samples were fragmented by sonication and biotin-labeled using the WT Labeling Kit (Affymetrix).

growth_protocol: Mice were housed under standard conditions in accordance with NIH standards and approved by the Harvard University Institutional Animal Care and Use Committee (IACUC)

extract_protocol: Chromatin immunoprecipitation (ChIP) and ligation-mediated PCR amplification of the purified DNA were performed essentially as described (Lee, T.I., Johnstone, S.E., and Young, R.A., 2006, Nature protocols 1, 729-748). Input chromatin was prepared from whole MOE tissue dissected from 5-week old male Flag-H2be mice using mouse anti-FLAG and rabbit anti-histone H3 antibodies.

value: 5 weeks

value: male

value: MOE

value: Flag-H2be transgenic

tag: antibody

value: FLAG M2 mouse monoclonal

source_name: ChIP: H3 from Flag-H2be MOE

value: H3 rabbit polyclonal


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate1- dye swap

city: Rehovot

first: Michal

last: Alon

address: Herzel St.

department: Department of Entomology

country: Israel

institute: Hebrew University of Jerusalem

hyb_protocol: The labeled cDNAs were purified by QIAquick PCR purification kit (QIAGEN) and mixed in 20XSSC with 20µg poly(A) and 0.15% v/v SDS and then hybridized to the microarray in a 65° C water bath for 16-18hr. The slides were washed for 2 minutes in each of the following solutions: 1.14 X SSC with 0.0285% SDS, then 1.14 X SSC, 0.228 X SSC and 0.057 X SSC. Next, the slides were dried at 1000 X g for 5 in a table-top centrifuge.

scan_protocol: Agilent automatic scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing:
ScanArray Express - Microarray Analysis System, version3 was used for data acquisition. (Perkin Elmer LAS, Inc, 2004)
The fluorescence intensity of the spots was quantified using the ScanArray software (Waltham, MA, USA). Statistical analysis was performed using the Limma (Linear Models for Microarray Data) package from the Bioconductor project (http://www.bioconductor.org). The gpr files (raw data) were read into limma using the function "read.maimages". Probes with flag values less than -74 were filtered out. Local background subtraction and lowess normalization were applied within arrays and a quantile normalization between arrays. Standard quality control was performed using the plot functions of Limma. The statistical analysis was performed using an approach called linear models for designed microarray experiments. We estimated the fold-changes and standard errors by fitting a linear model for each gene and applying empirical Bayes smoothing to the standard errors. FDR (false discovery rate) was used to correct for multiple comparisons. A 1.5-fold cut-off was considered as a filtering criterion for identifying B. tabaci ESTs that are significantly up- or down-regulated during short-term feeding (6 h) on PAP versus WT plants.

organism: Bemisia tabaci

source_name: Bemisia tabaci adults fed on wild type plants for 6hr

label_protocol: Cy3 and cy5 stnadard aminoallyl labeling

extract_protocol: TRIZOL

treatment_protocol: Feeding B.tabaci adults on PAP Purple transgenic plants for 6hr compared to wild type.

tag: developmental status

value: adult

tag: feeding

value: fed on wild type plants for 6hr

value: fed on PAP Purple plants for 6hr


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate3- dye swap


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type - Replicate2


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate1


title: Human Stomach Tissue 1

description: Normal 1

value: M

value: noncancerous background gastric mucosa


title: genomic DNA from normal adrenal tissue 3

city: New Haven

first: Annabelle

last: Fonseca

state: CT

address: 300 Cedar Street

department: Department of Surgery

institute: Yale University

description: Sample 45

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 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

label: Cy5 and Cy3

source_name: normal adrenal tissue

label_protocol: Standard Illumina Protocol

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

value: Male

tag: tissue

value: adrenal tissue

tag: disease state

value: normal adrenal tissue


title: Human Stomach Tissue 3

description: Normal 3

value: Healthy individuals (A)

tag: gender

value: F

value: Normal Stomach

value: reference DNA


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate2- dye swap


title: Bemisia tabaci adults fed on PAP Purple plants for 6hr vs wild type- Replicate3


title: genomic DNA from normal adrenal tissue 2

description: Sample 44

value: Female


title: genomic DNA from adrenocortical adenoma 27

description: Sample 42

source_name: adrenocortical adenoma

value: adenoma


title: genomic DNA from normal adrenal tissue 5

description: Sample 47


title: genomic DNA from normal adrenal tissue 1

description: Sample 43


title: genomic DNA from normal adrenal tissue 4

description: Sample 46


title: genomic DNA from normal adrenal tissue 6

description: Sample 48


title: genomic DNA from adrenocortical adenoma 24

description: Sample 39


title: genomic DNA from adrenocortical adenoma 25

description: Sample 40


title: genomic DNA from adrenocortical adenoma 26

description: Sample 41


title: M1+IL6 H3K4me3

city: Bethesda

first: Junfang

last: Zhang

state: MD

address: 37 Convent Dr.

department: NCI-CCR

institute: NIH

description: M1 cells treated with IL-6 for 5 days

hyb_protocol: A total of 3 µg of labeled ChIP and input DNA was cohybridized to the chip for 40 hours at 65°C

scan_protocol: scanned on an Agilent Scanner with Agilent Scan Control 7.0 software

data_processing: Data was extracted with Feature Extraction 9.1 software and analyzed using ChIP Analytics 1.3 software (Agilent).

source_name: M1+IL6 H3K4me3

label_protocol: A total of 2.5 µg of amplified DNA was labeled with Cy3 (input) or Cy5 (IP) dUTP (PerkinElmer Life and Analytical Sciences) using the CGH labeling kit (Invitrogen).

growth_protocol:
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
M1cells were seeded in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum and treated with interleukin-6 (IL-6) for5 days
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

extract_protocol: Chromatin immunoprecipitation assays was conducted as previously described (Paul, Bies et al. 2010). Cells were fixed in 0.8% formaldehyde for 6 minutes at room temperature. After lysis, samples were sonicated to a size range of 200 to 1000 bp. Chromatin (150-200 µg) was immunoprecipitated with antibodies for H3K4me3 (Abcam, ab8580), H3K4me1 (Abcam, ab8895), H3K9/14Ac (Upstate, 06-599), CTCF (Abcam, ab70303), H3K9me3 (Abcam, ab8898), H3K27me3 (Upstate,17-622),or rabbit IgG (Sigma-Aldrich, 15006). A 10% aliquot was removed as an input fraction. ChIP DNA and input DNA were amplified using WGA2 kit (Sigma-Aldrich).

treatment_protocol: For cell differentiation, M1 cells were seeded at a density of 1-2 x 105 cells / ml in medium containing interleukin-6 (IL-6) for 4-5 days.

tag: c-myb expression

value: No


title: Affy BCC TNF-treated - repeat 2

first: Babru

middle: Bahan

last: Samal

address: 9000 Rockville Pike

department: LCMR

institute: NIMH

description: No additional information.

hyb_protocol: Affy Hybridization Protocol Other: The hybridization cocktail containing the fragmented and labeled cDNAs was hybridized to the Bovine Genome Array Affymetrix GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Affy Scanning Protocol Other: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing:
Affy Data Processing Protocol
Calculation Method: The Affymetrix CEL files were analyzed using Expression Console (EC) following the vendor’s recommendation to create ‘Robust Multichips Analysis’ (RMA) normalized data.

source_name: TNF-treated BCC (Affy)

label_protocol:
Affy Labeling Protocol
Other: For the Affymetrix chips, the samples were prepared according to Affymetrix protocols (Affymetrix, Inc). 5 ug of total RNA was used per labeling reaction, in conjunction with the Affymetrix-recommended protocol ‘One-Cycle Target Labeling and Control Reagents’.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was isolated from cultured BCCs using RNeasy Mini Spin Columns (QIAGEN, Valencia, CA).

treatment_protocol:
Treatment type: compound
Agent: tumor necrosis factor alpha (TNF-alpha)
Treatment dose: 10 nM
Treatment time: 6 hours
Treatment temperature: 37C
In-vitro treatment: Primary cultures of BCCs were obtained after retrograde perfusion of bovine adrenal glands with 0.1% collagenase (Worthington Biochemical, Lakewood, NJ) and 30 U/ml DNase (Sigma-Aldrich), followed by dissociation of the digested adrenal medulla. The cells were cultured in DMEM (Invitrogen, Grand Island, NY) supplemented with 5% fetal calf serum and 100 U/ml penicillin-streptomycin, 2 mM glutamine, 10 µg/ml cytosine beta-D-arabinofuranoside, and 100 U/ml nystatin. Chromaffin cells were purified by differential plating as described previously (Anouar et al. 1994). Cells were then plated in the same medium as above at a density of 1 x 10^6 cells/ml, 2 ml/well, in poly-D-lysine-coated 6-well plates and treated with TNF-alpha(10 nM) for 6 hours.

value: adrenal glands

value: bovine chromaffin cell (BCC)


title: Affy BCC TNF-treated - repeat 1

description: No additional information.


title: AGL BCC TNF-treated - repeat 3

description: No additional information.

hyb_protocol: Agilent Hybridization Protocol Other: After purification, the labeled antisense RNAs were hybridized overnight to the Agilent Bovine (V2) Gene Expression Microarray, 4x44K oligo chips using the Agilent Two color hybridization protocol (Version 5.7). The slides are then washed according to the Agilent two-color buffers and temperatures.

scan_protocol: Agilent Scanning Protocol Other: A laser confocal Agilent Technologies Scanner G2505A US14702390(Agilent Technologies, Palo Alto, CA) was used to scan the hybridized Cy3 and Cy5 probes on the chips. The fluorescent intensities at the target locations on the array were extracted with the Agilent future extraction program.

data_processing:
Agilent Data Processing Protocol
Calculation Method: The fluorescent intensities at the target locations on the array were extracted with the Agilent Feature Extraction Software (Version 9.5.1.1). The spot values were normalized using the default linear-Lowess normalization.

source_name: Untreated BCC (AGL)

label_protocol:
Agilent Cy3 Labeling Protocol
Other: For the Agilent microarray slide processing, 1 ug of each RNA sample was reverse transcribed with an oligo dT-T7 and amplified using the Ambion MessageAmp(TM) II Kit (Ambion, Austin, TX). The aminoallyl UTP labeled RNAs generated were then coupled with Cy3 mono NHS ester CyDyes from GE Healthcare (Piscataway, NJ.).

source_name: TNF-treated BCC (AGL)

label_protocol:
Agilent Cy5 Labeling Protocol
Other: For the Agilent microarray slide processing, 1 ug of each RNA sample was reverse transcribed with an oligo dT-T7 and amplified using the Ambion MessageAmp(TM) II Kit (Ambion, Austin, TX). The aminoallyl UTP labeled RNAs generated were then coupled with Cy5 mono NHS ester CyDyes from GE Healthcare (Piscataway, NJ.).


title: Affy BCC TNF-treated - repeat 3

description: No additional information.


title: Affy BCC PACAP-treated - repeat 2

description: No additional information.

source_name: PACAP-treated BCC (Affy)

treatment_protocol:
Treatment type: compound
Agent: pituitary adenylate cyclase activating polypeptide (PACAP)
Treatment dose: 100 nM
Treatment time: 6 hours
Treatment temperature: 37C
In-vitro treatment: Primary cultures of BCCs were obtained after retrograde perfusion of bovine adrenal glands with 0.1% collagenase (Worthington Biochemical, Lakewood, NJ) and 30 U/ml DNase (Sigma-Aldrich), followed by dissociation of the digested adrenal medulla. The cells were cultured in DMEM (Invitrogen, Grand Island, NY) supplemented with 5% fetal calf serum and 100 U/ml penicillin-streptomycin, 2 mM glutamine, 10 µg/ml cytosine beta-D-arabinofuranoside, and 100 U/ml nystatin. Chromaffin cells were purified by differential plating as described previously (Anouar et al. 1994). Cells were then plated in the same medium as above at a density of 1 x 10^6 cells/ml, 2 ml/well, in poly-D-lysine-coated 6-well plates and treated with PACAP-38 (100 nM, Phoenix Pharmaceuticals, Burlingame, CA) for 6 hours.


title: AGL BCC PACAP-treated - repeat 2

description: No additional information.

source_name: PACAP-treated BCC (AGL)


title: 30-3-14 H3K4me3

description: myeloid leukemia cell line with virus integration in Mml1

growth_protocol:
Tumor cell were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum
Tumor cell were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

value: Yes


title: Affy BCC PACAP-treated - repeat 1

description: No additional information.


title: AGL BCC PACAP-treated - repeat 1

description: No additional information.


title: AGL BCC TNF-treated - repeat 2

description: No additional information.


title: Affy BCC Untreated Control - repeat 3

description: No additional information.

source_name: Untreated BCC (Affy)


title: AGL BCC PACAP-treated - repeat 3

description: No additional information.


title: genomic DNA from adrenocortical adenoma 21

description: Sample 36


title: Affy BCC PACAP-treated - repeat 3

description: No additional information.


title: G0, sample A

description:
Gene expression in G0 arrested myoblasts
Sample name: FC [G2]

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505B scanner and Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1)

data_processing: The normalization was done using GeneSpring GX 10 Software. Recommended Percentile Shift Normalization.

source_name: Sample A, Skeletal muscle myoblasts arrested in G0

label_protocol: The  samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Human muscle biopsies free of connective tissue were minced washed and dissociated with 0.05% trypsin-EDTA (Invitrogen) for 3x30 min. Harvested cells were pooled and Fetal Bovine Serum (FBS, Invitrogen) added as protease inhibitor. The isolated cells were seeded for up scaling (max 7 passages) on ECM-coated dishes (NUNC) after 15 min. of preplating and cultured in growth medium, GM (DMEM w. 10% FBS and 1% penicillin and streptomycin (PS), Invitrogen). Proliferating cells were G0 arrested in suspension medium (with 2% methyl cellulose (Sigma-Aldrich), 10% FBS and 1% PS), followed by reactivation in GM and finally differentiation in DM (DMEM with 2% FBS, 1% PS and 25 pmol Insulin (Actrapid from Novo Nordisk)) for 5-7 days.

extract_protocol: Cultured cells were rinsed twice in PBS and lysed in 1x Nucleic Acid Purification Lysis Solution (Applied biosystems, Foster City, CA, USA). Samples from suspension cultures were collected at various time points, washed twice in PBS and lysed with Lysis Solution. RNA was isolated using ABI PRISMTM 6100 Nucleic Acid PrepStation with Total RNA Chemistry kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s protocol.

value: muscle biopsy obtained from m. Vastus Lateralis

value: myoblast cell culture A

tag: culture condition


title: AGL BCC TNF-treated - repeat 1

description: No additional information.


title: genomic DNA from adrenocortical adenoma 22

description: Sample 37


title: 30-C-18 H3K4me3

tag: cell line

value: Tumor  30-C-18

source_name: 30-C-18 Input


title: genomic DNA from adrenocortical adenoma 23

description: Sample 38


title: Affy BCC Untreated Control - repeat 2

description: No additional information.


title: M1 H3K4me3

description: untreated myeloblastic M1 cells

source_name: M1 H3K4me3

growth_protocol:
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum
The murine myeloid cell line M1 was maintained in RPMI 1640 medium with 10% (v/v) heat-inactivated horse serum (Invitrogen). All tumor cell lines were cultured in Dulbecco modified Eagle medium with 10% (v/v) fetal bovine serum.

value: Myeloid M1


title: Affy BCC Untreated Control - repeat 1

description: No additional information.


title: 30-2-7 H3K4me3

description: myeloid leukemia cell line with virus integration in Mml3


title: M1 H3K9, 14ac

description: untreated myeloblastic M1 cells

source_name: M1 Input


title: genomic DNA from adrenocortical adenoma 20

description: Sample 35

value: Male


title: Differentiation after G0, Sample A

description:
Gene expression in differentiated myoblasts after G0 arrest
Sample name: FC [DG2]

source_name: Sample A, Skeletal muscle myoblasts differentiated after G0 arrest

value: Dif


title: G0, sample B

description:
Gene expression in G0 arrested myoblasts
Sample name: FC [G1]

source_name: Sample B, skeletal muscle myoblasts arrested in G0

value: myoblast cell culture B


title: genomic DNA from adrenocortical adenoma 19

description: Sample 34

value: adrenal tissue


title: genomic DNA from adrenocortical adenoma 18

description: Sample 33


title: genomic DNA from adrenocortical adenoma 16

description: Sample 31


title: Differentiation after G0, Sample B

description:
Gene expression in differentiated myoblasts after G0 arrest
Sample name: FC [DG1]

source_name: Sample B, skeletal muscle myoblasts differentiated after G0 arrest


title: Proliferation before G0, Sample B

description:
Gene expression in myoblasts proliferating before G0 arrest
Sample name: FC [BG1]

source_name: Sample B, Proliferating skeletal muscle myoblasts before G0 arrest


title: genomic DNA from adrenocortical adenoma 17

description: Sample 32


title: Proliferation before G0, Sample A

description:
Gene expression in myoblasts proliferating before G0 arrest
Sample name: FC [BG2]

source_name: Sampe A, Proliferating skeletal muscle myoblasts before G0 arrest


title: Reactivation after G0, sample A

description:
Gene expression in myoblasts proliferating af G0 arrest
Sample name: FC [AG2]

source_name: Sample A, Skeletal muscle myoblasts reactivation after G0 arrest


title: genomic DNA from adrenocortical adenoma 15

description: Sample 30

source_name: adrenocortical adenoma


title: Reactivation after G0, sample B

description:
Gene expression in myoblasts proliferating af G0 arrest
Sample name: FC [AG1]

source_name: Sample B, Skeletal muscle myoblasts reactivated after G0 arrest


title: genomic DNA from adrenocortical adenoma 13

description: Sample 28


title: genomic DNA from adrenocortical adenoma 14

description: Sample 29


title: P_infestans_NL07434_four_days_pos_inoculation_in_potato_biological_rep_1

city: Norwich

first: Liliana

middle: Maria

last: Cano

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Phytophthora infestans

source_name: Phytophthora infestans NL07434 infected potato leaves

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Mycelia of Phytophthora infestans 06_3928A and P. infestans NL07434 were harvested after growing for 10-12 days in V8 juice Agar or Rye Sucrose Agar (RSA), ground in liquid nitrogen and frozen prior RNA extraction.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: In addition to mycelia, we collected leaf discs infected by drop-inoculation with zoospores of P. infestans 06_3928A and P. infestans NL07434 at different days post inoculation: 2, 3 and 4 on potato.

tag: isolate

value: potato infected leaf 4 days post inoculation


title: P_infestans_NL07434_three_days_pos_inoculation_in_potato_biological_rep_2

value: potato infected leaf 3 days post inoculation


title: P_infestans_NL07434_four_days_pos_inoculation_in_potato_biological_rep_2


title: summer_2000-10

first: Yichi

last: Xu

state: NY

address: 1275 York Avenue

institute: MSKCC

description: liver tissue from summer active arctic ground squirrel

hyb_protocol: The hybridization was carried out for 18 hours at 42 °C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50 °C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55 °C.

scan_protocol: Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.

data_processing: Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.

organism: Urocitellus parryii

source_name: liver, summer active

label_protocol: Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.

extract_protocol: Total RNA was extracted from frozen tissues stored at -80 °C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen).  RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).

value: liver

tag: status

value: summer active


title: summer_98-79


title: genomic DNA from adrenocortical adenoma 11

description: Sample 26

value: Female

value: adenoma


title: P_infestans_NL07434_two_days_pos_inoculation_in_potato_biological_rep_2

value: potato infected leaf 2 days post inoculation


title: summer_20-52


title: genomic DNA from adrenocortical adenoma 12

description: Sample 27


title: genomic DNA from adrenocortical adenoma 10

description: Sample 25


title: P_infestans_NL07434_two_days_pos_inoculation_in_potato_biological_rep_1


title: genomic DNA from adrenocortical adenoma 8

description: Sample 23


title: P_infestans_NL07434_mycelia_V8_agar_rep_2

source_name: Phytophthora infestans NL07434 mycelia

value: mycelia grown in V8 agar


title: P_infestans_NL07434_three_days_pos_inoculation_in_potato_biological_rep_1


title: summer_04-78


title: summer_20-55


title: genomic DNA from adrenocortical adenoma 9

description: Sample 24


title: summer_2000-13


title: late_torpor_04-36

description: liver tissue from hibernating arctic ground squirrel

source_name: liver, hibernating

value: late torpor


title: genomic DNA from adrenocortical adenoma 7

description: Sample 22


title: P_infestans_NL07434_mycelia_rye_sucrose_agar_RSA_rep_1

value: mycelia grown in rye sucrose agar RSA


title: P_infestans_NL07434_mycelia_V8_agar_rep_1


title: summer_2000-2


title: genomic DNA from adrenocortical adenoma 5

description: Sample 20


title: genomic DNA from adrenocortical adenoma 4

description: Sample 19


title: genomic DNA from adrenocortical adenoma 6

description: Sample 21


title: P_infestans_NL07434_mycelia_rye_sucrose_agar_RSA_rep_2


title: genomic DNA from adrenocortical adenoma 3

description: Sample 18


title: P_infestans_06_3928A_four_days_pos_inoculation_in_potato_biological_rep_2

source_name: Phytophthora infestans 06_3928A infected potato leaves


title: P_infestans_06_3928A_four_days_pos_inoculation_in_potato_biological_rep_1


title: late_torpor_04-06


title: late_torpor_04-38


title: early_torpor_04-16

value: early torpor


title: late_torpor_20-39


title: early_torpor_2000-43


title: genomic DNA from adrenocortical adenoma 2

description: Sample 17


title: P_infestans_06_3928A_three_days_pos_inoculation_in_potato_biological_rep_2


title: P_infestans_06_3928A_two_days_pos_inoculation_in_potato_biological_rep_2


title: late_torpor_04-49


title: early_torpor_04-15


title: genomic DNA from adrenocortical adenoma 1

description: Sample 16


title: genomic DNA from adrenocortical carcinoma 14

description: Sample 14

source_name: adrenocortical carcinoma

value: carcinoma


title: genomic DNA from adrenocortical carcinoma 15

description: Sample 15


title: genomic DNA from adrenocortical carcinoma 13

description: Sample 13


title: P_infestans_06_3928A_three_days_pos_inoculation_in_potato_biological_rep_1


title: P_infestans_06_3928A_two_days_pos_inoculation_in_potato_biological_rep_1


title: early_torpor_04-81


title: genomic DNA from adrenocortical carcinoma 12

description: Sample 12


title: late_arousal_04-31

value: late arousal


title: late_arousal_2000-22


title: late_arousal_04-30


title: late_arousal_04-72


title: genomic DNA from adrenocortical carcinoma 8

description: Sample 8

value: Male


title: P_infestans_06_3928A_mycelia_rye_sucrose_agar_RSA_rep_1

source_name: Phytophthora infestans 06_3928A mycelia


title: P_infestans_06_3928A_mycelia_rye_sucrose_agar_RSA_rep_2


title: genomic DNA from adrenocortical carcinoma 10

description: Sample 10


title: genomic DNA from adrenocortical carcinoma 7

description: Sample 7


title: genomic DNA from adrenocortical carcinoma 11

description: Sample 11


title: early_arousal_04-43

value: early arousal


title: P_infestans_06_3928A_mycelia_V8_agar_rep_2


title: P_infestans_06_3928A_mycelia_V8_agar_rep_1


title: 3_nebulin_+/+ [miRNA]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: quadriceps total RNA of mouse WT3 with both nebulin alleles

hyb_protocol: according to the recommended protocol followed by washing at a Fluidics Station 450

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: Data were processed using the miRNAQC tool from Affymetrix following the recommended workflow from Genisphere (Background Detection -> RMA Global Background Correction -> Quantile Normalization -> Median polish Summarization); Statistical analysis was done using SAS JMP Genomics 4.0

label: Biotin

source_name: mouse WT3 wild type

label_protocol: Samples were labeled using the FlashTag™ Biotin HSR Kit from Genisphere starting with 1µg of totel RNA according to the protocol of the manufaturer

extract_protocol: total RNA was isolated from quadriceps using Trizol®-Reagent (Gibco brl).

tag: genotype/variation

value: nebulin +/+

value: quadriceps


title: early_arousal_04-21


title: genomic DNA from adrenocortical carcinoma 9

description: Sample 9

value: adrenal tissue


title: early_arousal_04-10


title: 3_nebulin_+/- [miRNA]

description: quadriceps total RNA of mouse HZ3 with one nebulin allele

source_name: mouse HZ3 heterozygous

value: Nebulin +/-


title: early_arousal_04-84

value: liver


title: Salmonella_typhimurium_LT2_control_rep1

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

description: This sample is of Salmonella typhimurium LT2 strain TA100 control unexposed. It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Two micrograms of the labeled DNA was used for subsequent hybridization to Nimblegen Bacterial Gene Expression Arrays for Salmonella typhimurium LT2 X4. The hybridized arrays were washed using the Nimblegen Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Microarray Scanner

data_processing: Microarray images were analyzed using Nimblescan v2.5.26 software (Nimblegen) and ArrayStar v4.0.0 (DNAstar, Madison, WI) software. Expression data were log2 transformed and statistical significance was determined using a moderated t-test for binary transcriptome comparisons (i.e. control vs. experimental). The P-value was set at 0.05 and only those genes induced or repressed at least fivefold were considered in this paper.  Differentially expressed transcripts were assigned to their functional classifications based on the Comprehensive Microbial Resource genome annotation from the J. Craig Venter Institute.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Salmonella typhimurium LT2 control unexposed rep 1

label_protocol: The cDNA was labeled with the One-Color DNA Labeling Kit (Nimblegen, Madison, WI) and the concentration verified using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA).

growth_protocol: Salmonella typhimurium LT2 TA100 controls were grown in Davis Mingioli media supplemented with glucose (4 g/L), biotin (0.5 mg/L), and histidine (20 mg/L) for 24 h at 30°C shaking at 150 rpm.Davis BD, Mingioli ES. 1950. Mutants of Escherichia coli requiring methionine or vitamin B12. Journal of bacteriology 60: 17-28.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and vortexing for 1 min. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer. The RNA was used to generate cDNA using the Superscript II Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s directions. At each step the quality of the RNA and cDNA was analyzed using the Agilent 2100 Bioanalyzer and DNA 1000 Kit (Agilent).

tag: treatment

value: unexposed


title: genomic DNA from adrenocortical carcinoma 4

description: Sample 4

value: Female


title: Salmonella_typhimurium_LT2_control_rep3

description: This sample is of Salmonella typhimurium LT2 strain TA100 control unexposed. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella typhimurium LT2 control unexposed rep 3


title: genomic DNA from adrenocortical carcinoma 2

description: Sample 2


title: Salmonella_typhimurium_LT2_control_rep2

description: This sample is of Salmonella typhimurium LT2 strain TA100 control unexposed. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella typhimurium LT2 control unexposed rep 2


title: 2_nebulin_+/+ [miRNA]

description: quadriceps total RNA of mouse WT2 with both nebulin alleles

source_name: mouse WT2 wild type


title: genomic DNA from adrenocortical carcinoma 3

description: Sample 3


title: Salmonella_typhimurium_LT2_C60_rep3

description: This sample is of Salmonella typhimurium LT2 strain TA100 exposed to 2 ppm C60. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella typhimurium LT2 exposed to C60 rep 3

growth_protocol: Salmonella typhimurium LT2 TA100 exposures were grown in Davis Mingioli media supplemented with glucose (4 g/L), biotin (0.5 mg/L), and histidine (20 mg/L) and 2 ppm C60 (median size 71 nm) for 24 h at 30°C shaking at 150 rpm.Davis BD, Mingioli ES. 1950. Mutants of Escherichia coli requiring methionine or vitamin B12. Journal of bacteriology 60: 17-28.

value: exposed to 2 ppm C60


title: genomic DNA from adrenocortical carcinoma 1

description: Sample 1


title: Salmonella_typhimurium_LT2_C60_rep2

description: This sample is of Salmonella typhimurium LT2 strain TA100 exposed to 2 ppm C60. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella typhimurium LT2 exposed to C60 rep 2


title: genomic DNA from adrenocortical carcinoma 6

description: Sample 6


title: Salmonella_typhimurium_LT2_C60_rep1

description: This sample is of Salmonella typhimurium LT2 strain TA100 exposed to 2 ppm C60. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: Salmonella typhimurium LT2 exposed to C60 rep 1


title: tomato_wild_type_3

city: Potsdam

first: Marc

last: Lohse

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP-Golm

hyb_protocol: Manufacturer standard protocol (Affymetrix)

data_processing: MAS5 normalization as implemented in the GCOS analysis software provided by affymetrix. The data were further normalized using the RMA method (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U,Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64. PubMed PMID: 12925520.).

organism: Solanum lycopersicum

source_name: leaf

extract_protocol: TriZol extraction according to manufacturer (Invitrogen, Life Technologies GmbH, Darmstadt, Germany)

tag: species

value: Solanum lycopersicum

tag: variety

value: MoneyMaker;

value: leaf

tag: age

value: 28 days


title: tomato_wild_type_4

scan_protocol: Manufacturer standard protocol (Affymetrix)


title: 1_nebulin_+/+ [miRNA]

description: quadriceps total RNA of mouse WT1 with both nebulin alleles

source_name: mouse WT1 wild type


title: 2_nebulin_+/- [miRNA]

description: quadriceps total RNA of mouse HZ2 with one nebulin allele

source_name: mouse HZ2 heterozygous


title: tomato_wild_type_2

label_protocol: Manufacturer standard protocol (Affymetrix)


title: tomato_wild_type_1


title: 1_nebulin_+/- [miRNA]

description: quadriceps total RNA of mouse HZ1 with one nebulin allele

source_name: mouse HZ1 heterozygous


title: tomato_OGDH_antisense_4


title: LCL-MRX3-Male-2

city: Adelaide

first: Mark

middle: A

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.4.0). It was vst transformed and quantile normalized.

source_name: Eppstien Barr virus immortalized lymphoblastoid cell line (LCL)

label_protocol: Labelling carried out by the Australian Genome Research Facility using standard protocols

growth_protocol: LCL were cultured in RPMI 1640 (Invitrogen, Australia) supplemented with 10% FCS, 2 mM L-glutamine, 0.017 mg/mL benzylpenicillin and grown at 37 oC with 5% CO2.

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

tag: Sex

value: male

tag: cell type

tag: affected status

value: Affected

tag: genotype

value: HCFC1 promoter mutation


title: tomato_OGDH_antisense_1

tag: tissue


title: tomato_OGDH_antisense_2


title: LCL-MRX3-Male-1

value: Eppstien Barr virus immortalized lymphoblastoid cell line (LCL)


title: MOE WT UNO-closed 5wk rep2

hyb_protocol: Labled samples were hybridized to Affymetrix Mouse Gene 1.0 ST Arrays according to the manufacturer's instructions

scan_protocol: Arrays were scanned using an Affymetrix 3000 7G Scanner according to the manufacturer's instructions

data_processing: CEL files were processed with the Affymetrix Expression Console software to generate probe level summarization files (CHP) using the iterative Probe Logarithmic Intensity Error Estimation (IterPLIER) and sketch-quantile normalization algorithms. Statistical analyses of differential expression between groups were carried out using the Bioconductor limma package implemented through the Bioconductor affylmGUI software to generate unadjusted P-values and false discovery rate (FDR) corrections for multiple comparisons.

source_name: MOE WT UNO-closed 5wk

label_protocol: RNA samples were labeled according to the standard Affymetrix protocol for Mouse Gene 1.0 ST Arrays

extract_protocol: RNA was isolated using Trizol Reagent (Invitrogen) and purified using an RNeasy Miniprep Kit (Qiagen)

treatment_protocol: Fourteen-day old mice were administered Buprenorphine (0.05 mg/kg), anesthetized using isoflurane (confirmed through a tail pinch), and subjected immediately to electrocautery for ~5 seconds on the right nostril under a dissecting microscope (with care taken to avoid contact of the electrocautery unit with any non-superficial tissues). Mice were administered additional doses of Buprenorphine 12 and 24 hours after the procedure and examined on a daily basis to ensure complete blockage of the right nostril through scar formation (typically ~3–5 days after the procedure) and normal mouse development and activity. RNA was prepared from freshly-dissected, MOE halves that were carefully removed from the medial bone.

value: MOE

value: WT

tag: manipulation

value: UNO

tag: uno side

value: closed

value: 6 mo


title: MOE WT UNO-closed 5wk rep3


title: tomato_OGDH_antisense_3


title: MOE H2be-KO UNO-closed 5wk rep3

source_name: MOE H2be-KO UNO-closed 5wk


title: MOE H2be-KO UNO-closed 5wk rep2


title: LCL-Control-Male-4

value: Unaffected

value: control


title: LCL-Control-Female-5

value: female


title: MOE WT UNO-open 5wk rep1

source_name: MOE WT UNO-open 5wk

value: open


title: MOE H2be-KO UNO-closed 5wk rep1


title: MOE WT UNO-closed 5wk rep1


title: MOE WT UNO-open 5wk rep3


title: MOE WT UNO-open 5wk rep2


title: LCL-Control-Female-3


title: LCL-Control-Female-2


title: LCL-Control-Female-4


title: LCL-Control-Male-3


title: LCL-Control-Male-1


title: LCL-Control-Female-1


title: LCL-Control-Male-2


title: MOE H2be-KO UNO-open 5wk rep2

source_name: MOE H2be-KO UNO-open 5wk


title: A809126 (mRNA)

city: Rochester

first: Virginia

middle: Bartleson

last: Hebl

state: MN

address: 200 1st St. SW

institute: Mayo Clinic

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina BeadArray Reader and the standard Illumina scanning protocol.

data_processing: Illumina BeadStudio processed without background correction or normalization for non-normalized data. Fastlo (PMID 15166021) normalized and log2 transformed for normalized data.

source_name: cardiac tissue, control

label_protocol: Standard Illumina labeling protocol.

extract_protocol: RNA was extracted using the QIAGEN MicroRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

tag: age (yrs)

value: cardiac

tag: sample type


title: MOE H2be-KO UNO-open 5wk rep1


title: A702013 (mRNA)


title: MOE WT 6mo rep6

source_name: MOE WT 6mo

treatment_protocol: RNA was prepared from freshly-dissected, whole MOE tissue


title: MOE H2be-KO UNO-open 5wk rep3


title: MOE WT 6mo rep3


title: MOE WT 6mo rep4


title: 5054 (mRNA)


title: MOE WT 6mo rep2


title: MOE H2be-KO 6mo rep5

source_name: MOE H2be-KO 6mo


title: A505654 (mRNA)


title: MOE WT 6mo rep5


title: 4095 (mRNA)


title: MOE H2be-KO 6mo rep4


title: MOE H2be-KO 6mo rep6


title: Adamts12 KO untreated

city: OVIEDO

first: ANGELA

last: MONCADA PAZOS

address: FERNANDO BONGERA

country: Spain

institute: UNIVERSIDAD DE OVIEDO

description: Gene expression data from distal colon of a healthy Adamts12-KO mouse

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Gene 1.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: After scanning, rawdata (Affymetrix Cel files) were processed with RMAExpress (http://RMAExpress.bmbolstad.com), using default settings

source_name: distal colon from Adamts12 KO mouse

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

growth_protocol: Mice were fed ad libitum and treatment started at 8-10 weeks of age

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

treatment_protocol: 2% DSS (dextran sodium sulfate) in drinking water during 8 days, followed by 1 day without treatment

value: Adamts12 KO

value: distal colon


title: 4021 (mRNA)


title: Adamts12 KO 2%DSS

description: Gene expression data from distal colon of an Adamts12-KO mouse with ulcerative colitis

source_name: distal colon from Adamts12 KO mouse after induction of ulcerative colitis with DSS

value: 2% DSS


title: MOE WT 6mo rep1


title: 4015 (mRNA)

value: male


title: 4102 (mRNA)


title: MOE H2be-KO 6mo rep2


title: 5033 (mRNA)


title: MOE H2be-KO 6mo rep3


title: 4152 (mRNA)


title: 4013 (mRNA)


title: 5048 (mRNA)


title: Adamts12 WT 2%DSS

description: Gene expression data from distal colon of an Adamts12-WT mouse with ulcerative colitis

source_name: distal colon from Adamts12 WT mouse after induction of ulcerative colitis with DSS

value: Adamts12 WT


title: 3162 (mRNA)


title: MOE WT 5wk rep6

source_name: MOE WT 5wk

value: 5 wk


title: SAT, biological replicate 3

city: PARIS

first: Alice

last: Pannérec

address: 105 boulevard de l'hopital

institute: INSERM 787

description: Gene expression data from young postnatal skeletal muscle

hyb_protocol: Following fragmentation, 600 ng of cRNA were hybridized for 16 hours at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 3 000 scanner.

data_processing: The data were analyzed with the BioConductor package of the R Software and normalization was performed using the GC-RMA algorithm.

source_name: satellite cells isolated from 1-week old muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA.

growth_protocol: Mice were bred in the laboratory animal facility

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Microkit, according to the manufacturer's instructions.

treatment_protocol: Hindlimb skeletal muscles were minced and enzymatically digested. Single cell suspensions were stained, and PICs and satellite cells were purified using flow cytometry based upon CD34 and Sca1 expression.

value: hindlimbs skeletal muscle

tag: strain

value: C57 black 6

value: 7 to 9 days old


title: Adamts12 WT untreated

description: Gene expression data from distal colon of a healthy Adamts12-WT mouse

source_name: distal colon from Adamts12 WT mouse


title: SAT, biological replicate 1


title: MOE H2be-KO 6mo rep1

value: MOE


title: MOE WT 5wk rep5

value: WT


title: SAT, biological replicate 2


title: 3145 (mRNA)


title: PICs, biological replicate 3

source_name: PICs isolated from 1-week old muscle


title: MOE WT 5wk rep4


title: 3131 (mRNA)


title: PICs, biological replicate 2


title: MOE WT 5wk rep2


title: PICs, biological replicate 1


title: MOE WT 5wk rep3


title: 3069 (mRNA)


title: 3108 (mRNA)


title: 3056 (mRNA)


title: MOE WT 5wk rep1


title: 2152 (mRNA)


title: 2158 (mRNA)


title: MOE H2be-GF 5wk rep4

source_name: MOE H2be-GF 5wk


title: MOE H2be-GF 5wk rep2


title: 2090 (mRNA)


title: T36_60hr, rep4

city: Boston

first: Youjin

last: Lee

state: MA

address: 4 Blackfan Circle, HIM#730

institute: Harvard Medical School/ Brigham Women's Hospital

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 in an Affymetrix GeneChip Hybridisation Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneTitan system.

data_processing: The data was normalized using the GenePattern software with the Robust Multi Array (RMA) algorithm.

source_name: Primary CD4 T cells, TGF-beta3/IL-6

label_protocol: Affymetrix 3' IVT Express kit (Affymetrix, 901228) using 100 ng total RNA as starting material for a single round of amplification using standard methods.

growth_protocol: Naïve CD4 T cells (CD4+, CD44low, CD62Lhigh) were sorted and cultured in tissue culture plates coated with anti-CD3/ anti-CD28 with their respective cytokines for 60 hours.

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

treatment_protocol: Cells were differentiated with activation alone (no cytokines) or Th17 conditions (IL-1beta-IL-6+/-IL-23, TGF-beta1-IL-6+/-IL-23, TGF-beta3-IL-6+/-IL-23).

value: 6-8 weeks

value: primary CD4 T cells

tag: cytokine activation

value: TGF-beta3, IL-6

tag: activation duration

value: 60 hours


title: 12799 (mRNA)

value: control


title: 4062 (mRNA)

value: cardiac


title: MOE H2be-GF 5wk rep3


title: MOE H2be-GF 5wk rep1


title: Lung T9 C3H-2 NNK

city: Irvine

first: William

last: Gordon

address: 839 Health sciences way

institute: University of CA Irvine

description: Gene expression data from NNK exposure before mature tumor formation

hyb_protocol: Affymetrix standard protcol performed UCI HTGC

data_processing: PLIER algorithm using Expression console software (Affymetrix)

source_name: Mouse Lung

growth_protocol: Mice were maintained under normal ligh dark conditions and with access to food and water in the UCI animal facility

extract_protocol: Trizol was used to extract total RNA followed by cleanup over Invitrogen RNA columns

treatment_protocol: NNK was injected at 100mg/kg once a week for four weeks

value: lung

tag: time after exposure

value: 9 weeks

value: NNK


title: 2089 (mRNA)

value: female


title: Lung T12 C3H-1 NNK

scan_protocol: Affymetrix standard protcol performed UCI HTGC

value: 12 weeks

tag: treatment


title: T36_60hr, rep3


title: T16_60hr, rep3

source_name: Primary CD4 T cells, TGF-beta1/IL-6

value: TGF-beta1, IL-6


title: NOCYTO_g_60HR, rep4

source_name: Primary CD4 T cells, no cytokine


title: 5603 (mRNA)

value: male


title: B623_60hr, rep4

source_name: Primary CD4 T cells, IL-1beta/IL-6/IL-23

value: IL-1beta, IL-6, IL-23


title: T16_60hr, rep4


title: NOCYTO_g_60HR, rep3


title: 1403 (mRNA)


title: Lung T12 C3H-2 NNK

label_protocol: Affymetrix standard protcol performed UCI HTGC


title: NOCYTO_60HR, rep2


title: Lung T9 C3H-1 NNK


title: B6_Il1_60hr, rep2

source_name: Primary CD4 T cells, IL-1beta/IL-6

value: IL-1beta, IL-6


title: B6_Il1_60hr, rep1


title: 91099 (mRNA)

source_name: cardiac tissue, control


title: 4049 (mRNA)


title: genomic DNA from adrenocortical carcinoma 5

description: Sample 5

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 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

source_name: adrenocortical carcinoma

label_protocol: Standard Illumina Protocol

tag: gender

value: Female

value: adrenal tissue

tag: disease state

value: carcinoma


title: Lung T6 C3H-2 NNK

value: 6 weeks


title: Lung T6 C3H-1 NNK


title: NOCYTO_60HR, rep1

tag: age

value: 6-8 weeks

value: primary CD4 T cells


title: B623_60hr, rep3

tag: Sex

value: 60 hours


title: 171102 (mRNA)

value: cardiac

value: control


title: 191002 (mRNA)


title: Lung T3 C3H-2 NNK

value: lung

value: 3 weeks


title: R5126 (mRNA)

value: female


title: Lung T12 C3H-1

value: 12 weeks


title: Lung T12 C3H-2


title: Lung T6 C3H-1


title: T3623_60hr, rep1

source_name: Primary CD4 T cells, TGF-beta3/IL-6/IL-23

tag: cell type

value: TGF-beta3, IL-6, IL-23


title: 5140 (mRNA)


title: Lung T3 C3H-2


title: Lung T6 C3H-2


title: Lung T9 C3H-1

value: 9 weeks


title: Lung T3 C3H-1 NNK

value: NNK


title: Lung T9 C3H-2


title: 22100 (mRNA)

value: male


title: R26309 (mRNA)


title: T3623_60hr, rep2


title: 0431840 (mRNA)


title: Lung T0 C3H-2

value: 0 weeks


title: 5059 (mRNA)


title: T16_60hr, rep2

value: TGF-beta1, IL-6


title: B623_60hr, rep2

value: IL-1beta, IL-6, IL-23


title: 5089 (mRNA)


title: R300305 (mRNA)


title: T16_60hr, rep1


title: 676236 (mRNA)

source_name: cardiac tissue, HCM

value: hypertrophic cardiomyopathy (HCM)

value: case


title: Lung T3 C3H-1


title: 627047 (mRNA)


title: Lung T12 AJ-2 NNK

value: A/J


title: B623_60hr, rep1

value: 6-8 weeks

value: primary CD4 T cells

value: 60 hours


title: lean_liver_ER_20080725

city: Bostn

first: Suneng

last: Fu

address: 665 Huntington Ave

department: Genetics and Complex Diseases

institute: Harvard School of Public Health

description: male, 3 months old,  wild type C57BL/6, overnight fasted, Diet 5058

hyb_protocol: Affymetrix GeneChip® Manual (rev. 1.3)

scan_protocol: Affymetrix GeneChip® Manual (rev. 1.3)

data_processing: Affymetrix GeneChip Operating Software , MAS5.0, R

label_protocol: GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis system (P/N 900431)

growth_protocol: 12-hour day/12-hour night cycle, Diet 5058 from Lab Diet, 3 months of age

extract_protocol: ER fractionation and Trizol LS extraction

treatment_protocol: with or without overnight fasting from 5pm-10am

value: 3 months old

value: liver

tag: rna subtype

value: Endoplasmic Reticulum-associated polysome mRNA

value: wild type

tag: diet

value: overnight fasted, Diet 5058


title: Lung T9 AJ-1 NNK

tag: tissue

value: lung

value: 9 weeks


title: obese_liver_ER_20080528

description: male, 3 months old, ob/ob in C57BL/6 background,ad libitum fed, Diet 5058

value: male

tag: genotype

value: ob/ob

value: ad libitum fed, Diet 5058


title: lean_liver_ER_20080528

description: male, 3 months old,  wild type C57BL/6, ad libitum fed, Diet 5058


title: Lung T12 AJ-1 NNK

value: 12 weeks

value: NNK


title: obese_liver_ER_20080725

description: male, 3 months old, ob/ob in C57BL/6 background, overnight fasted, Diet 5058


title: 655638 (mRNA)

value: cardiac

value: hypertrophic cardiomyopathy (HCM)

value: case


title: 639123 (mRNA)


title: R5144 (mRNA)

value: female

value: control


title: lean_liver_ER_20080808

value: 3 months old


title: R643724 (mRNA)


title: 673482 (mRNA)


title: lean_liver_ER_20080730

value: liver


title: obese_liver_ER_20080808

value: Endoplasmic Reticulum-associated polysome mRNA


title: 629740 (mRNA)


title: Lung T9 AJ-2 NNK

value: A/J


title: Lung T3 AJ-2 NNK

value: 3 weeks


title: Lung T6 AJ-2 NNK

value: lung

value: 6 weeks


title: Lung T6 AJ-1 NNK


title: obese_liver_ER_20080730

value: male


title: Lung T3 AJ-1 NNK


title: lean_liver_ER_20080604

description: male, 3 months old, wild type C57BL/6, overnight fasted, Diet 5058

value: wild type

value: overnight fasted, Diet 5058


title: 43 (mRNA)


title: R634935 (mRNA)


title: Lung T12 AJ-1

value: 12 weeks


title: 671852 (mRNA)


title: Lung T12 AJ-2


title: pregnant mammary gland of Elf5 KO animal, biological rep3

city: BUFFALO

first: SATRAJIT

last: SINHA

address: 701 ELLICOTT STREET

institute: SUNY AT BUFFALO

hyb_protocol: Biotinylated cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

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

data_processing: MAS5.0 algorithm in the Affy package of Bioconductor in the R statistical computing enviroment was used to generate expression summary values, followed by trimmed mean global normalization.

source_name: mouse MG p17

label_protocol: Total RNA was subjected to the standard Affymetrix labeling protocol to obtain biotinylated cRNA.

extract_protocol: Total RNA was extracted from wild type and Elf5 KO mammary gland using TRIzol (Invitrogen, Carlsbad, CA) and then purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

value: mammary gland

tag: developmental stage

value: pregnancy day 17

tag: genotype/variation

value: Elf5 KO


title: 28 (mRNA)

tag: age (yrs)

value: cardiac

value: hypertrophic cardiomyopathy (HCM)

tag: sample type

value: case


title: obese_liver_ER_20080604

description: male, 3 months old,ob/ob in C57BL/6 background, overnight fasted, Diet 5058

value: 3 months old

tag: strain

value: ob/ob


title: 39 (mRNA)

value: female


title: Lung T9 AJ-1

value: A/J

value: 9 weeks


title: 673368 (mRNA)


title: pregnant mammary gland of Elf5 KO animal, biological rep2


title: 639649 (mRNA)


title: pregnant mammary gland of wild type animal, biological rep3


title: R633573 (mRNA)


title: pregnant mammary gland of Elf5 KO animal, biological rep1


title: Lung T6 AJ-2

value: lung


title: Lung T9 AJ-2


title: Lung T6 AJ-1

value: 6 weeks


title: Lung T3 AJ-2

value: 3 weeks


title: Lung T0 AJ-2

value: 0 weeks


title: 631132 (mRNA)

value: male


title: primary tumor 4.27 months survival

city: São Paulo

first: Fatima

middle: Solange

last: Pasini

state: São Paulo

address: Av. Dr. Arnaldo, 455 sala 4115

department: Departamento de Radiologia e Oncologia

country: Brazil

institute: Faculdade de Medicina da USP

description: Gene expression data from gastric cancer of patient undergoing gastrectomy as a primary treatment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data normalization and probe summarization were performed by  Robust Multichip Analysis (RMA) using R Bioconductor software.

source_name: primary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Trizol extraction of total RNA and Clean-up (Quiagen) werw performed according to the manufacturers' instructions .

tag: age (y)

tag: histological type

value: Diffuse

tag: tumor stage (ajcc)

value: IIIb

tag: time (months) overall survival

tag: status

value: death

value: gastric cancer tumor


title: pregnant mammary gland of wild type animal, biological rep2

value: mammary gland

value: pregnancy day 17

value: wild type


title: primary tumor 4.37 months survival

tag: gender

value: IIIa


title: pregnant mammary gland of wild type animal, biological rep1


title: Lung T3 AJ-1

tag: time after exposure

tag: treatment


title: 3 (mRNA)

tag: Sex

value: cardiac

tag: disease state

value: hypertrophic cardiomyopathy (HCM)

value: case


title: 30 (mRNA)

value: female

tag: tissue


title: primary tumor 13.1 months survival


title: Lung T0 AJ-1

value: A/J

value: lung


title: primary tumor 17.3 months survival