title: Case D34

city: Creteil

first: Roberto

last: Incitti

address: 51, av. du General de Lattre de Tassigny

institute: Universite Paris 12 (as of January 2010)

hyb_protocol: After purification, 10 µg of fragmented cRNA were hybridized to the Affymetrix GeneChip® Mouse Genome 430 2.0 Array, and the chips were automatically washed and stained with streptavidine-phycoerythrin using a fluidics station.

scan_protocol: Gene Chip Scanner 3000 (Affymetrix)

data_processing: To extract the expression values from the cell-probe values, we used the affy package of the R software with the rma2 implementation of the Robust Multiarray Averaging qspline, pmonly and liwong as methods of background correction, normalization, pm-correction and summarization, respectively.

source_name: mouse lung case

label_protocol: Affymetrix IVT labelling kit

extract_protocol: Total RNA was extracted from lung tissue using TRIzol reagent (Invitrogen, France), followed by purification using Rneasy columns (Qiagen, France)

value: inducible, lung-targeted FGF18-transgene (SP-C-rtTA and (teto)7-FGF18)

value: lung

tag: disease status

value: case


title: Control D50

status: Public on Jul 06 2011

type: RNA

country: France

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse lung control

tag: strain

value: FVB/N

tag: genotype/variation

tag: tissue

value: control


title: hnRNP K rep3

city: Albany

first: Ben

middle: Gregory

last: Szaro

state: NY

address: 1400 Washington Avenue

department: Biological Sciences

country: USA

institute: University at Albany, State University of New York

description:
anti-hnRNP K co-immunoprecipitated RNAs
Gene expression data of hnRNP K antibody, co-immunoprecipitated RNAs from juvenile frog brain

hyb_protocol: Standard Affymetrix protocol for Exon arrays.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: Raw data were corrected for background and transcripts scored as present or absent, using MAS 5.0 and further filtered to remove the bottom 30th percentile (GeneSpring GX 10).

organism: Xenopus laevis

source_name: Xenopus juvenile frog whole brain

extract_protocol:
The complete mRNP IP protocol is provided as a supplementary file on the Series record (GSE25207_IP_of_mRNP_complexes_protocol.txt).

RNA from Immunoprecipitated samples was isolated by phenol chloroform extraction and further purified on Qiagen Rneasy columns before performing quality control analysis on Agilent Bioanalyzer chips.

value: periodic albino

tag: developmental stage

value: juvenile

value: brain

tag: chip antibody

value: hnRNP K antibody


title: Control D58


title: Control D40


title: Pre-Tumor Liver 3

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.1 software.

data_processing:
Primary normalization and data extraction were done by the UCSF Microarray Core Facility. Briefly, raw log-intensities were normalized using the quantile normalization method (Bolstad et al., 2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
Normalized Log-intensities for each sample as well as the mean for the samples in each sample group are shown in the GSE28198_normalized_matrix.txt file.  For example, 'Cntrl.1' column heading represents an individual sample.  While 'meanCntrl' indicates the mean of all three CTRL samples.

source_name: LAP-tTA x TRE-MYC Transgenic Mouse 4-5 weeks off Doxy, liver tissue no tumor present

label_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com). RNA was amplified using the Sigma whole transcriptome amplification kit (Sigma-Aldrich), and subsequent Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc.). The labeled DNA was assessed using Nanodrop 8000, and equal amounts of Cy3 labeled target were hybridized to Agilent mouse whole genome 4x44K Ink-jet arrays.

growth_protocol: Mice were fed Doxycycline chow 200 mg/kg until >8 weeks of age and then doxy-chow was removed for the indicated time.  In the Early Tumor Regression Cohort doxy-chow was re-introduced into the mouse diet for 72 hrs.

extract_protocol: Liver and liver tumor tissues were frozen using liquid nitrogen and RNA was subsequently extracted (mirVanaTM mirna isolation kit, Ambion).  RNA quality was assessed using the Nanodrop ND-8000 (Nanodrop Technologies, Inc.) and a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies) and run on Agilent mouse whole genome 4x44K Ink-jet arrays.

value: LAP-tTA x TRE-MYC Transgenic Mouse


title: Case D48


title: hnRNP K rep1

label_protocol: Standard Affymetrix protocol for Exon arrays.


title: Case D04


title: Case D52


title: Pre-Tumor Liver 2


title: Pre-Tumor Liver 1


title: beta Galactosidase rep3

description:
anti-beta galactosidase co-immunoprecipitated RNAs
Gene expression data of control antibody, co-immunoprecipitated RNAs from juvenile frog brain

value: control antibody


title: Control D02


title: Pre-Tumor Liver 4


title: Mesentery_Estradiol benzoate_rep1

city: Vermillion

first: Kathleen

middle: M

last: Eyster

state: SD

address: 414 E. Clark St.

department: Basic Biomedical Sciences

institute: University of South Dakota

description: Protocol for dissecting the mesenteric arterial tree is detailed in Rodrigo MC et al., J Pharmacol Toxicol Methods 2002;47(2):87-92.

hyb_protocol: 10 micrograms of biotinylated cRNA were mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner.

data_processing: global median normalization, CodeLink Expression Analysis 4.1.0.4163

organism: Rattus norvegicus

source_name: Mesenteric arteries, treated with estradiol benzoate

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion from 2 micrograms total RNA starting material.

extract_protocol: The mesenteric arterial tree was dissected free from veins and adipose tissue under RNAlater (Ambion). The RNAlater was blotted off and the tissue was minced, then homogenized in TRI reagent (MRC).  The samples were centrifuged in the presence of bromochloropropane and sodium acetate.  The RNA-containing upper layer was removed and the RNA purified on an RNeasy extraction column (Qiagen).  The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen).  The purity and quantity of total RNA was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer.

value: Sprague Dawley

tag: age

value: 9 weeks

tag: gender

value: female

value: mesenteric artery

tag: agent

value: estradiol benzoate


title: Control Liver 1

source_name: LAP-tTA Transgenic Mouse control liver

value: LAP-tTA Transgenic Mouse


title: beta Galactosidase rep 1


title: beta Galactosidase rep2


title: Control Liver 2


title: tumor sample 84

status: Public on Jul 05 2011

city: Boston

first: Chunsheng

last: Zhang

address: 33 Avenue Louis Pasteur

institute: Merck

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin

organism: Homo sapiens

source_name: tumor

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: tumor liver


title: tumor sample 86


title: Control Liver 3


title: tumor sample 89


title: tumor sample 82


title: tumor sample 88


title: tumor sample 87


title: tumor sample 85


title: tumor sample 83


title: tumor sample 77


title: tumor sample 74


title: tumor sample 75


title: tumor sample 81


title: tumor sample 80


title: tumor sample 76


title: tumor sample 72


title: tumor sample 69


title: hnRNP K rep2


title: tumor sample 70


title: tumor sample 78


title: tumor sample 68


title: tumor sample 73


title: tumor sample 66


title: tumor sample 79


title: tumor sample 67


title: tumor sample 71


title: tumor sample 65


title: tumor sample 64


title: tumor sample 63


title: tumor sample 62


title: tumor sample 57


title: tumor sample 53


title: tumor sample 52


title: tumor sample 54


title: tumor sample 60


title: tumor sample 59


title: tumor sample 51


title: tumor sample 58


title: tumor sample 49


title: tumor sample 61


title: tumor sample 40


title: tumor sample 50


title: tumor sample 37


title: tumor sample 36


title: tumor sample 45


title: tumor sample 46


title: tumor sample 43


title: tumor sample 48


title: tumor sample 44


title: tumor sample 55


title: tumor sample 47


title: tumor sample 41


title: tumor sample 42


title: tumor sample 35


title: tumor sample 34


title: tumor sample 31


title: tumor sample 33


title: tumor sample 32


title: tumor sample 38


title: tumor sample 29


title: tumor sample 56


title: tumor sample 25


title: tumor sample 30


title: tumor sample 26


title: tumor sample 27


title: tumor sample 22


title: tumor sample 23


title: tumor sample 20


title: tumor sample 28


title: tumor sample 24


title: tumor sample 15


title: tumor sample 21


title: tumor sample 18


title: tumor sample 14


title: tumor sample 10


title: tumor sample 13


title: tumor sample 19


title: tumor sample 17


title: tumor sample 9


title: tumor sample 16


title: tumor sample 7


title: tumor sample 12


title: tumor sample 8


title: tumor sample 11


title: tumor sample 5


title: tumor sample 3


title: non_tumor sample 241

value: non_tumor liver


title: tumor sample 4


title: tumor sample 2


title: tumor sample 1


title: non_tumor sample 239


title: tumor sample 6


title: non_tumor sample 238


title: non_tumor sample 242


title: non_tumor sample 240


title: non_tumor sample 236


title: tumor sample 39


title: non_tumor sample 234


title: non_tumor sample 235


title: non_tumor sample 232


title: non_tumor sample 230


title: non_tumor sample 233


title: non_tumor sample 237


title: non_tumor sample 227


title: non_tumor sample 225


title: non_tumor sample 231


title: non_tumor sample 228


title: non_tumor sample 243


title: non_tumor sample 226


title: non_tumor sample 229


title: non_tumor sample 224


title: non_tumor sample 223


title: non_tumor sample 222


title: non_tumor sample 221


title: non_tumor sample 220


title: non_tumor sample 218


title: non_tumor sample 219


title: non_tumor sample 213


title: non_tumor sample 214


title: non_tumor sample 217


title: non_tumor sample 208


title: non_tumor sample 212


title: non_tumor sample 209


title: non_tumor sample 206


title: non_tumor sample 205


title: non_tumor sample 210


title: non_tumor sample 215


title: non_tumor sample 201


title: non_tumor sample 198


title: non_tumor sample 200


title: non_tumor sample 211


title: non_tumor sample 216


title: non_tumor sample 196


title: non_tumor sample 195


title: non_tumor sample 202


title: non_tumor sample 203


title: non_tumor sample 197


title: non_tumor sample 193


title: non_tumor sample 190


title: non_tumor sample 192


title: non_tumor sample 199


title: non_tumor sample 207


title: non_tumor sample 188


title: non_tumor sample 189


title: non_tumor sample 204


title: non_tumor sample 187


title: non_tumor sample 185


title: non_tumor sample 182


title: non_tumor sample 180


title: non_tumor sample 177


title: non_tumor sample 181


title: non_tumor sample 191


title: non_tumor sample 175


title: non_tumor sample 184


title: non_tumor sample 172


title: non_tumor sample 176


title: non_tumor sample 194


title: non_tumor sample 183


title: non_tumor sample 170


title: non_tumor sample 171


title: non_tumor sample 179


title: non_tumor sample 174


title: non_tumor sample 186


title: non_tumor sample 168


title: non_tumor sample 165


title: non_tumor sample 173


title: non_tumor sample 167


title: non_tumor sample 178


title: non_tumor sample 163


title: non_tumor sample 169


title: non_tumor sample 166


title: non_tumor sample 162


title: non_tumor sample 160


title: non_tumor sample 159


title: non_tumor sample 155


title: non_tumor sample 157


title: non_tumor sample 153


title: non_tumor sample 152


title: non_tumor sample 161


title: non_tumor sample 158


title: non_tumor sample 164


title: non_tumor sample 156


title: non_tumor sample 154


title: non_tumor sample 143


title: non_tumor sample 144


title: non_tumor sample 150


title: non_tumor sample 145


title: non_tumor sample 137


title: non_tumor sample 138


title: non_tumor sample 141


title: non_tumor sample 147


title: non_tumor sample 151


title: non_tumor sample 148


title: non_tumor sample 139


title: non_tumor sample 142


title: non_tumor sample 146


title: non_tumor sample 149


title: non_tumor sample 134


title: non_tumor sample 140


title: non_tumor sample 136


title: non_tumor sample 135


title: non_tumor sample 124


title: non_tumor sample 132


title: non_tumor sample 127


title: non_tumor sample 123


title: non_tumor sample 128


title: non_tumor sample 130


title: non_tumor sample 131


title: non_tumor sample 129


title: non_tumor sample 126


title: non_tumor sample 125


title: non_tumor sample 133


title: Array 2-2 [ARRAY2]

city: Rostock

first: Nikolai

last: Siemens

state: MV

address: Schillingallee 70

department: IMIKRO

country: Germany

institute: University of Rostock

description:
Array 2
Biological raplicate 2 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_2_2.txt

hyb_protocol: 200 ng of Cy3-labeled cDNA and 200 ng of Cy5-labeled cDNA were hybridizied together to the microarray (Custom Array GE 8x15K; Agilent). After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: data was analyzed using Gene Spring GX 11.0.2 software.

organism: Streptococcus pyogenes M49 591

source_name: wild type

label_protocol: cDNA synthesis was performed with 10 µg of total RNA. The RNA was mixed with ramdom primers (Promega) and spike-ins (Two-Color RNA Spike-In Kit, Agilent Technologies) followed by the incubation at 70°C for 10 min and 5 min on ice. Then, the following reagents were added: 10 µl of 5x First Strand Buffer (Invitrogen), 5 µl of 0.1 M DTT (Invitrogen), 0.5 µl of a dNTP mix (10 mM dATP, dGTP, and dTTP, 2.5 mM dCTP), 1.25 µl of Cy3-dCTP or Cy5-dCTP (GE Healthcare), and 2 µl of the SuperScript II reverse transcriptase (Invitrogen). The mixture was incubated at 42°C for 60 min and then heated to 70°C for 10 min, followed by incubation on ice for 5 min.  Then, the RNA was degraded by incubation with 2 units of RNaseH (Invitrogen) at room temperature for 30 min and labeled cDNA was purificated using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: GAS serotype M49 and its isogenic Δralp3 mutant were grown in Todd-Hewitt broth supplemented with 0.5% yeast extract to the transition phase (OD 600nm = 1.0) at 37°C under a 5% CO2 20% O2 atmosphere.

extract_protocol: Total RNA was isolated with FastRNA Pro Blue Kit (MP Biomedicals).

tag: serotype

value: wild type


title: Array 2-4 [ARRAY2]

description:
Array 2
Biological raplicate 4 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_2_4.txt


title: Array 1-3 [ARRAY2]

description:
Array 2
Biological raplicate 3 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_1_3.txt


title: non_tumor sample 114


title: non_tumor sample 121


title: Array 1-2 [ARRAY2]

description:
Array 2
Biological raplicate 2 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_1_2.txt


title: Array 1-4 [ARRAY2]

description:
Array 2
Biological raplicate 4 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_1_4.txt


title: Array 1-1 [ARRAY2]

description:
Array 2
Biological raplicate 1 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_1_1.txt


title: Array 2-4 [ARRAY1]

description:
Array 1
Biological raplicate 4 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_2_4.txt


title: Array 2-3 [ARRAY2]

description:
Array 2
Biological raplicate 3 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_2_3.txt


title: Array 2-3 [ARRAY1]

description:
Array 1
Biological raplicate 3 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_2_3.txt


title: non_tumor sample 119


title: non_tumor sample 122


title: non_tumor sample 117


title: non_tumor sample 116


title: Array 2-1 [ARRAY2]

description:
Array 2
Biological raplicate 1 of 4
mic_252555310005_S03_Green_Cropped_GE2_107_Sep09_2_1.txt


title: Array 1-4 [ARRAY1]

description:
Array 1
Biological raplicate 4 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_1_4.txt


title: non_tumor sample 115


title: Array 2-1 [ARRAY1]

description:
Array 1
Biological raplicate 1 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_2_1.txt


title: non_tumor sample 118


title: non_tumor sample 113


title: non_tumor sample 120


title: non_tumor sample 110


title: non_tumor sample 107


title: non_tumor sample 111


title: Array 2-2 [ARRAY1]

description:
Array 1
Biological raplicate 2 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_2_2.txt


title: non_tumor sample 106


title: non_tumor sample 109


title: Array 1-3 [ARRAY1]

description:
Array 1
Biological raplicate 3 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_1_3.txt


title: non_tumor sample 108


title: non_tumor sample 112


title: Array 1-1 [ARRAY1]

description:
Array 1
Biological raplicate 1 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_1_1.txt


title: non_tumor sample 105


title: non_tumor sample 104


title: Array 1-2 [ARRAY1]

description:
Array 1
Biological raplicate 2 of 4
mic_252555310008_S01_Green_Cropped_GE2_107_Sep09_1_2.txt


title: non_tumor sample 103


title: non_tumor sample 100


title: non_tumor sample 96


title: non_tumor sample 94


title: non_tumor sample 98


title: non_tumor sample 101


title: non_tumor sample 99


title: non_tumor sample 102


title: non_tumor sample 95


title: non_tumor sample 97


title: non_tumor sample 93


title: non_tumor sample 90


title: non_tumor sample 91


title: non_tumor sample 87


title: non_tumor sample 86


title: non_tumor sample 92


title: non_tumor sample 89


title: non_tumor sample 84


title: non_tumor sample 85


title: non_tumor sample 88


title: non_tumor sample 83


title: non_tumor sample 82


title: non_tumor sample 81


title: non_tumor sample 80


title: non_tumor sample 79


title: non_tumor sample 78


title: non_tumor sample 77


title: HKU_liver_tumor_345

type: genomic

description: genomic DNA was genotyped using Infinium HumanHap650-v3 Genotyping BeadChips (Illumina)

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland)

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina)

data_processing: Genomic DNA extracted from liver tumors was genotyped using Infinium HumanHap650-v3 Genotyping BeadChips (Illumina). Data were processed using Illumina BeadStudio (BSGT 3.3.7) according to the manufacturer's instructions

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1)

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction

tag: Sex

tag: diagnosis

tag: tumor stage

tag: hbsag


title: HKU_liver_tumor_330

value: m

value: tumor only

value: stage iva

value: positive


title: HKU_liver_tumor_339


title: non_tumor sample 76


title: HKU_liver_tumor_343


title: HKU_liver_tumor_342


title: non_tumor sample 75


title: non_tumor sample 74


title: HKU_liver_tumor_338


title: HKU_liver_tumor_325


title: HKU_liver_tumor_340


title: HKU_liver_tumor_344


title: non_tumor sample 73


title: HKU_liver_tumor_321

value: stage ii


title: non_tumor sample 72


title: HKU_liver_tumor_329

value: stage iiia


title: HKU_liver_tumor_337


title: HKU_liver_tumor_341


title: non_tumor sample 71


title: HKU_liver_tumor_320


title: non_tumor sample 70


title: HKU_liver_tumor_324

value: negative


title: non_tumor sample 67


title: non_tumor sample 68


title: HKU_liver_tumor_323

value: f


title: non_tumor sample 69


title: HKU_liver_tumor_276

value: hcc


title: HKU_liver_tumor_273


title: non_tumor sample 64


title: HKU_liver_tumor_271


title: non_tumor sample 65


title: HKU_liver_tumor_326

value: stage iii


title: HKU_liver_tumor_272


title: non_tumor sample 66


title: HKU_liver_tumor_274


title: non_tumor sample 63


title: HKU_liver_tumor_346


title: HKU_liver_tumor_328


title: HKU_liver_tumor_318


title: non_tumor sample 62


title: non_tumor sample 61


title: HKU_liver_tumor_270


title: non_tumor sample 60


title: non_tumor sample 58


title: HKU_liver_tumor_317


title: non_tumor sample 56


title: HKU_liver_tumor_275


title: non_tumor sample 57


title: non_tumor sample 54


title: non_tumor sample 55


title: non_tumor sample 59


title: non_tumor sample 53


title: non_tumor sample 51


title: HKU_liver_tumor_269


title: HKU_liver_tumor_268


title: non_tumor sample 50


title: non_tumor sample 52


title: non_tumor sample 49


title: HKU_liver_tumor_263

value: ltx-hcc


title: HKU_liver_tumor_266


title: non_tumor sample 48


title: non_tumor sample 47


title: HKU_liver_tumor_265


title: HKU_liver_tumor_262


title: HKU_liver_tumor_267


title: HKU_liver_tumor_260


title: non_tumor sample 45


title: non_tumor sample 43


title: non_tumor sample 44


title: HKU_liver_tumor_250


title: non_tumor sample 46


title: HKU_liver_tumor_258


title: HKU_liver_tumor_246


title: HKU_liver_tumor_261


title: HKU_liver_tumor_241


title: non_tumor sample 41


title: HKU_liver_tumor_244


title: non_tumor sample 42


title: HKU_liver_tumor_238


title: HKU_liver_tumor_248


title: HKU_liver_tumor_251


title: non_tumor sample 40


title: non_tumor sample 39


title: HKU_liver_tumor_249


title: non_tumor sample 37


title: HKU_liver_tumor_245


title: HKU_liver_tumor_232


title: HKU_liver_tumor_220


title: non_tumor sample 34


title: non_tumor sample 36


title: non_tumor sample 35


title: HKU_liver_tumor_229


title: HKU_liver_tumor_208


title: non_tumor sample 32


title: HKU_liver_tumor_216


title: HKU_liver_tumor_205


title: non_tumor sample 30


title: non_tumor sample 33


title: non_tumor sample 31


title: HKU_liver_tumor_225


title: non_tumor sample 28


title: non_tumor sample 29


title: HKU_liver_tumor_204


title: HKU_liver_tumor_207


title: non_tumor sample 27


title: HKU_liver_tumor_206


title: non_tumor sample 38


title: non_tumor sample 25


title: non_tumor sample 24


title: non_tumor sample 26


title: non_tumor sample 23


title: HKU_liver_tumor_202


title: HKU_liver_tumor_203


title: HKU_liver_tumor_199


title: non_tumor sample 22


title: non_tumor sample 21


title: HKU_liver_tumor_200


title: HKU_liver_tumor_198


title: HKU_liver_tumor_201


title: non_tumor sample 20


title: non_tumor sample 18


title: HKU_liver_tumor_197


title: non_tumor sample 17


title: non_tumor sample 19


title: HKU_liver_tumor_192


title: HKU_liver_tumor_196


title: non_tumor sample 14


title: non_tumor sample 13


title: non_tumor sample 16


title: non_tumor sample 15


title: HKU_liver_tumor_191


title: HKU_liver_tumor_189


title: HKU_liver_tumor_193


title: HKU_liver_tumor_188


title: HKU_liver_tumor_190


title: HKU_liver_tumor_185

value: stage i


title: HKU_liver_tumor_186


title: non_tumor sample 10


title: non_tumor sample 9


title: non_tumor sample 12


title: HKU_liver_tumor_184


title: HKU_liver_tumor_183


title: non_tumor sample 7


title: non_tumor sample 8


title: non_tumor sample 11


title: non_tumor sample 5


title: HKU_liver_tumor_180


title: HKU_liver_tumor_181


title: non_tumor sample 6


title: HKU_liver_tumor_179


title: HKU_liver_tumor_177


title: HKU_liver_tumor_175


title: non_tumor sample 3


title: non_tumor sample 2


title: non_tumor sample 4


title: HKU_liver_tumor_172


title: HKU_liver_tumor_174


title: non_tumor sample 1


title: HKU_liver_tumor_168


title: HKU_liver_tumor_171


title: cirrhotic sample 39

source_name: cirrhotic

value: cirrhotic liver


title: cirrhotic sample 40


title: cirrhotic sample 36


title: cirrhotic sample 37


title: HKU_liver_tumor_167


title: HKU_liver_tumor_182


title: HKU_liver_tumor_176


title: HKU_liver_tumor_169


title: HKU_liver_tumor_173


title: cirrhotic sample 31


title: HKU_liver_tumor_157


title: HKU_liver_tumor_158


title: HKU_liver_tumor_163


title: HKU_liver_tumor_164


title: cirrhotic sample 34


title: HKU_liver_tumor_165


title: cirrhotic sample 32


title: cirrhotic sample 38


title: cirrhotic sample 33


title: cirrhotic sample 30


title: HKU_liver_tumor_160


title: cirrhotic sample 28


title: cirrhotic sample 27


title: cirrhotic sample 29


title: cirrhotic sample 26


title: HKU_liver_tumor_153


title: HKU_liver_tumor_155


title: HKU_liver_tumor_170


title: HKU_liver_tumor_151


title: cirrhotic sample 23


title: HKU_liver_tumor_150


title: HKU_liver_tumor_149


title: cirrhotic sample 35


title: cirrhotic sample 25


title: HKU_liver_tumor_145


title: HKU_liver_tumor_144


title: HKU_liver_tumor_146


title: cirrhotic sample 21


title: cirrhotic sample 20


title: HKU_liver_tumor_156


title: cirrhotic sample 18


title: HKU_liver_tumor_140


title: cirrhotic sample 17


title: cirrhotic sample 22


title: cirrhotic sample 24


title: HKU_liver_tumor_154


title: HKU_liver_tumor_147


title: cirrhotic sample 16


title: cirrhotic sample 15


title: cirrhotic sample 13


title: cirrhotic sample 14


title: HKU_liver_tumor_135


title: HKU_liver_tumor_132


title: cirrhotic sample 12


title: cirrhotic sample 19


title: HKU_liver_tumor_159


title: HKU_liver_tumor_152


title: HKU_liver_tumor_134


title: cirrhotic sample 10


title: HKU_liver_tumor_131


title: HKU_liver_tumor_121


title: HKU_liver_tumor_126


title: HKU_liver_tumor_127


title: cirrhotic sample 9


title: cirrhotic sample 7


title: cirrhotic sample 8


title: cirrhotic sample 6


title: cirrhotic sample 4


title: cirrhotic sample 5


title: cirrhotic sample 11


title: HKU_liver_tumor_125


title: cirrhotic sample 3


title: HKU_liver_tumor_119


title: cirrhotic sample 1


title: healthy sample 6

source_name: healthy

value: healthy liver


title: healthy sample 5


title: HKU_liver_tumor_118

value: tumor liver


title: HKU_liver_tumor_115


title: cirrhotic sample 2


title: HKU_liver_tumor_114


title: HKU_liver_tumor_116


title: healthy sample 4


title: HKU_liver_tumor_117


title: healthy sample 1


title: healthy sample 2


title: healthy sample 3


title: HKU_liver_tumor_111


title: HKU_liver_tumor_113


title: HKU_liver_tumor_110


title: tumor sample 267


title: tumor sample 268


title: HKU_liver_tumor_122


title: HKU_liver_tumor_106


title: HKU_liver_tumor_128


title: HKU_liver_tumor_112


title: HKU_liver_tumor_95


title: tumor sample 265


title: tumor sample 264


title: HKU_liver_tumor_108


title: HKU_liver_tumor_101


title: HKU_liver_tumor_104


title: HKU_liver_tumor_96


title: tumor sample 266


title: tumor sample 262


title: tumor sample 263


title: HKU_liver_tumor_109


title: HKU_liver_tumor_93


title: tumor sample 259


title: HKU_liver_tumor_98


title: tumor sample 258


title: tumor sample 260


title: tumor sample 257


title: tumor sample 256


title: HKU_liver_tumor_92


title: HKU_liver_tumor_87


title: HKU_liver_tumor_91


title: tumor sample 255


title: HKU_liver_tumor_94


title: HKU_liver_tumor_86


title: tumor sample 254


title: tumor sample 252


title: tumor sample 253


title: HKU_liver_tumor_90


title: tumor sample 251


title: tumor sample 250


title: HKU_liver_tumor_89


title: tumor sample 249


title: tumor sample 261


title: HKU_liver_tumor_82


title: HKU_liver_tumor_105


title: HKU_liver_tumor_84


title: HKU_liver_tumor_102


title: tumor sample 248


title: tumor sample 246


title: tumor sample 247


title: tumor sample 244


title: tumor sample 243


title: HKU_liver_tumor_85


title: HKU_liver_tumor_80


title: tumor sample 242


title: tumor sample 245


title: HKU_liver_tumor_76


title: HKU_liver_tumor_73


title: tumor sample 241


title: HKU_liver_tumor_79


title: HKU_liver_tumor_78


title: HKU_liver_tumor_77


title: tumor sample 240


title: HKU_liver_tumor_72


title: HKU_liver_tumor_75


title: tumor sample 239


title: tumor sample 237


title: HKU_liver_tumor_74


title: tumor sample 238


title: HKU_liver_tumor_64


title: tumor sample 235


title: HKU_liver_tumor_70


title: HKU_liver_tumor_65


title: tumor sample 234


title: tumor sample 233


title: tumor sample 232


title: HKU_liver_tumor_67


title: tumor sample 230


title: tumor sample 229


title: HKU_liver_tumor_81


title: HKU_liver_tumor_58


title: tumor sample 236


title: tumor sample 228


title: HKU_liver_tumor_55


title: tumor sample 231


title: HKU_liver_tumor_54


title: tumor sample 227


title: tumor sample 226


title: HKU_liver_tumor_62


title: tumor sample 225


title: HKU_liver_tumor_51


title: HKU_liver_tumor_57


title: HKU_liver_tumor_56


title: tumor sample 223


title: HKU_liver_tumor_60


title: tumor sample 224


title: tumor sample 221


title: HKU_liver_tumor_46


title: tumor sample 220


title: HKU_liver_tumor_53


title: tumor sample 219


title: tumor sample 222


title: HKU_liver_tumor_50


title: tumor sample 218


title: HKU_liver_tumor_45


title: HKU_liver_tumor_49


title: HKU_liver_tumor_59

value: stage ivb


title: HKU_liver_tumor_47


title: HKU_liver_tumor_63


title: tumor sample 216


title: HKU_liver_tumor_68


title: tumor sample 215


title: HKU_liver_tumor_39


title: HKU_liver_tumor_43


title: HKU_liver_tumor_42


title: tumor sample 212


title: tumor sample 213


title: HKU_liver_tumor_38


title: tumor sample 214


title: tumor sample 217


title: tumor sample 211


title: HKU_liver_tumor_40


title: tumor sample 210


title: HKU_liver_tumor_36


title: HKU_liver_tumor_41


title: HKU_liver_tumor_33


title: tumor sample 205


title: HKU_liver_tumor_34


title: HKU_liver_tumor_29


title: tumor sample 208


title: tumor sample 207


title: HKU_liver_tumor_26


title: HKU_liver_tumor_32


title: tumor sample 209


title: tumor sample 204


title: tumor sample 206


title: tumor sample 202


title: HKU_liver_tumor_71


title: tumor sample 203


title: tumor sample 201


title: HKU_liver_tumor_22


title: HKU_liver_tumor_24


title: HKU_liver_tumor_21


title: HKU_liver_tumor_20


title: tumor sample 198


title: HKU_liver_tumor_19


title: tumor sample 196


title: tumor sample 195


title: HKU_liver_tumor_35


title: tumor sample 197


title: HKU_liver_tumor_17


title: tumor sample 194


title: HKU_liver_tumor_14


title: tumor sample 192


title: HKU_liver_tumor_15


title: tumor sample 199


title: tumor sample 200


title: tumor sample 193


title: HKU_liver_tumor_30


title: tumor sample 191


title: HKU_liver_tumor_13


title: tumor sample 190


title: tumor sample 188


title: tumor sample 187


title: HKU_liver_tumor_11


title: tumor sample 189


title: HKU_liver_tumor_18


title: tumor sample 186


title: HKU_liver_tumor_9


title: HKU_liver_tumor_23


title: HKU_liver_tumor_6


title: HKU_liver_tumor_8


title: tumor sample 185


title: HKU_liver_tumor_10


title: tumor sample 184


title: tumor sample 182


title: HKU_liver_tumor_4


title: HKU_liver_tumor_1


title: tumor sample 181


title: HKU_liver_non_tumor_342

value: non_tumor liver


title: tumor sample 179


title: HKU_liver_non_tumor_344


title: HKU_liver_non_tumor_345


title: tumor sample 178


title: HKU_liver_tumor_12

value: m


title: HKU_liver_tumor_2


title: HKU_liver_non_tumor_343


title: tumor sample 183


title: HKU_liver_non_tumor_346


title: HKU_liver_non_tumor_340


title: HKU_liver_non_tumor_341


title: tumor sample 177


title: HKU_liver_non_tumor_274


title: tumor sample 175


title: tumor sample 174


title: tumor sample 176


title: tumor sample 173


title: tumor sample 172


title: HKU_liver_non_tumor_275


title: HKU_liver_non_tumor_337


title: tumor sample 180


title: tumor sample 171


title: tumor sample 170


title: tumor sample 169


title: HKU_liver_non_tumor_272


title: tumor sample 168


title: HKU_liver_non_tumor_338


title: tumor sample 166


title: HKU_liver_non_tumor_339


title: tumor sample 165


title: HKU_liver_non_tumor_276


title: HKU_liver_non_tumor_273


title: tumor sample 164


title: HKU_liver_non_tumor_271


title: HKU_liver_non_tumor_270


title: tumor sample 167


title: tumor sample 162


title: tumor sample 161


title: tumor sample 160


title: HKU_liver_non_tumor_267


title: HKU_liver_non_tumor_266


title: tumor sample 163


title: tumor sample 158


title: tumor sample 159


title: HKU_liver_non_tumor_264


title: HKU_liver_non_tumor_265


title: HKU_liver_non_tumor_261


title: tumor sample 157


title: HKU_liver_non_tumor_268


title: tumor sample 156


title: tumor sample 155


title: tumor sample 154


title: HKU_liver_non_tumor_257


title: tumor sample 153


title: HKU_liver_non_tumor_209


title: HKU_liver_non_tumor_262


title: tumor sample 152


title: tumor sample 151


title: tumor sample 150


title: HKU_liver_non_tumor_207


title: tumor sample 148


title: tumor sample 149


title: HKU_liver_non_tumor_203


title: HKU_liver_non_tumor_208


title: HKU_liver_non_tumor_260


title: HKU_liver_non_tumor_258


title: tumor sample 147


title: HKU_liver_non_tumor_204


title: HKU_liver_non_tumor_201


title: HKU_liver_non_tumor_202


title: HKU_liver_non_tumor_198


title: tumor sample 144


title: tumor sample 143


title: HKU_liver_non_tumor_200


title: HKU_liver_non_tumor_205


title: HKU_liver_non_tumor_206


title: HKU_liver_non_tumor_199


title: tumor sample 145


title: tumor sample 146


title: tumor sample 142


title: tumor sample 141


title: HKU_liver_non_tumor_193


title: HKU_liver_non_tumor_190


title: tumor sample 140


title: tumor sample 139


title: tumor sample 138


title: tumor sample 137


title: HKU_liver_non_tumor_191


title: HKU_liver_non_tumor_197


title: HKU_liver_non_tumor_182


title: HKU_liver_non_tumor_188


title: tumor sample 135


title: tumor sample 134


title: tumor sample 133


title: HKU_liver_non_tumor_179


title: HKU_liver_non_tumor_189


title: HKU_liver_non_tumor_181


title: tumor sample 132


title: HKU_liver_non_tumor_186


title: tumor sample 130


title: HKU_liver_non_tumor_263


title: HKU_liver_non_tumor_185


title: tumor sample 129


title: tumor sample 136


title: HKU_liver_non_tumor_176


title: tumor sample 128


title: HKU_liver_non_tumor_177


title: tumor sample 127


title: tumor sample 131


title: HKU_liver_non_tumor_180


title: HKU_liver_non_tumor_174


title: tumor sample 125


title: tumor sample 126


title: HKU_liver_non_tumor_175


title: HKU_liver_non_tumor_173


title: tumor sample 124


title: tumor sample 123


title: tumor sample 122


title: HKU_liver_non_tumor_172


title: tumor sample 121


title: HKU_liver_non_tumor_167


title: tumor sample 119


title: HKU_liver_non_tumor_166


title: tumor sample 118


title: tumor sample 120


title: HKU_liver_non_tumor_169


title: HKU_liver_non_tumor_171


title: HKU_liver_non_tumor_170


title: tumor sample 116


title: tumor sample 114


title: HKU_liver_non_tumor_160


title: HKU_liver_non_tumor_163


title: tumor sample 113


title: tumor sample 117


title: HKU_liver_non_tumor_168


title: tumor sample 112


title: tumor sample 115


title: HKU_liver_non_tumor_164


title: HKU_liver_non_tumor_158


title: HKU_liver_non_tumor_153


title: HKU_liver_non_tumor_157


title: tumor sample 111


title: HKU_liver_non_tumor_154


title: tumor sample 110


title: tumor sample 109


title: HKU_liver_non_tumor_152


title: HKU_liver_non_tumor_151


title: tumor sample 108


title: HKU_liver_non_tumor_150


title: tumor sample 105


title: tumor sample 106


title: tumor sample 107


title: HKU_liver_non_tumor_156


title: tumor sample 104


title: tumor sample 103


title: tumor sample 101


title: HKU_liver_non_tumor_144


title: tumor sample 102


title: HKU_liver_non_tumor_148


title: HKU_liver_non_tumor_146


title: HKU_liver_non_tumor_149


title: HKU_liver_non_tumor_159


title: HKU_liver_non_tumor_165


title: tumor sample 100


title: tumor sample 98


title: tumor sample 97


title: HKU_liver_non_tumor_134


title: tumor sample 99


title: tumor sample 96


title: HKU_liver_non_tumor_127


title: tumor sample 94


title: HKU_liver_non_tumor_119


title: tumor sample 93


title: tumor sample 92


title: HKU_liver_non_tumor_145


title: HKU_liver_non_tumor_122


title: tumor sample 91


title: tumor sample 95


title: HKU_liver_non_tumor_128


title: HKU_liver_non_tumor_121


title: HKU_liver_non_tumor_116


title: tumor sample 90


title: HKU_liver_non_tumor_118


title: knockin replicate 1

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description:
FX-216_ki_replicate1
Gene expression data from mouse cells.

hyb_protocol: Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: Affymetrix Expression Console (Affymetrix, CA)

source_name: knockin, replicate 1

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: Bone marrow macrophages isolated from wild-type (WT) or knockin (KI) mice were plated in 60-mm tissue culture dishes.

extract_protocol:
Total RNA was isolated for microarray analysis
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent)

treatment_protocol: The cells were treated with M-CSF (44ng/ml) and RANKL (100ng/ml) for 24 hours.

value: knockin mutant

tag: cell type

value: bone marrow macrophages


title: HKU_liver_non_tumor_113

value: stage iva

value: positive


title: knock in replicate 3

description:
FX-251_ki_replicate3
Gene expression data from mouse cells.

source_name: knockI, replicate 3


title: HKU_liver_non_tumor_117

value: stage ii


title: knockin replicate 2

description:
FX-245_ki_replicate2
Gene expression data from mouse cells.

source_name: knockin, replicate 2


title: HKU_liver_non_tumor_140

value: stage iiia


title: HKU_liver_non_tumor_112

value: f

value: negative


title: HKU_liver_non_tumor_111

value: hcc


title: HKU_liver_non_tumor_110


title: wild type replicate 2

description:
FX-215_wt_replicate2
Gene expression data from mouse cells.

source_name: wild type, replicate 2

value: wild type


title: HKU_liver_non_tumor_106


title: fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 4

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

hyb_protocol: Following fragmentation, 1.5 ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.

scan_protocol: Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’.  Each array was analyzed for the following quality metrics:  3’/5’ signal ratio of house-keeping genes, signal intensity of species-specific house-keeping genes, signal intensities of Poly-A controls, signal intensities of hybridization controls, relative logarithmic probe cell intensity- and relative logarithmic expression signal values.

data_processing: Data was analyzed in GeneSpring GX 10.0 (Agilent Technologies, Santa Clara, CA).  Robust Multi-array Average (RMA) (Irizarry, 2003) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 42 samples) was run on data using logarithmic scale. All 42 samples passed quality control based on hybridization controls, 3'/5' ratios for internal controls, Pearson correlation and Principal Component Analysis (PCA). Probe sets were filtered by expression values based on percentiles. For pairwise comparisons, Student-Newman-Keuls (SNK) Post Hoc test was done on oneway ANOVA result to identify statistically significant (p-value cutoff 0.05), differentially expressed transcripts. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 10.0.

source_name: fibroblast

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).

growth_protocol: Female (wild-type) and TSG-6-KO (tumor-necrosis factor-alfa-stimulated protein-6: Tnfaip6-deficient) BALB/c mice were immunized intraperitonelly with the emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant. Arthtitic mice were sacrificed, synovial tissue dissected and cells released by pronase/collagenase combined digestion.

extract_protocol: Cells were washed with RNAse-free PBS, RNA isolated with TriZol reagent, and qulatiy measured by Agilent 2100 Bioanalyzer

treatment_protocol: Synovial fibroblasts were isolated by collagenase digestion and caltured up to 6 passages in 10% fetal calf serum (FCS) in DMEM (Dulbecco's Modified Minimal Essential Medium). Cells were serum depriviated (0.5% FCS) for overnignt and then treated or left untreated. Triplicate-quadraplicate synovial fibroblast cell cultures were treated either with 5 ng/ml TNFalfa, 200 ng/ml lipopolysaccharide, 120 ug recombinant mouse TSG-6/ml, 24 ug hyaluronan (HA)/ml, or 120 ug TSG-6 plus 24 ug/ml HA for 12 hours in serum depriviated DMEM.

value: BALB/c

value: female

tag: type

value: TSG-6 knockout

tag: treatment


title: fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 3


title: fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 1


title: HKU_liver_non_tumor_109


title: HKU_liver_non_tumor_105


title: HKU_liver_non_tumor_126


title: fibroblast, TSG6-knockout, HA-treated, biological replicate 4

value: HA-treated


title: fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 2


title: HKU_liver_non_tumor_96


title: HKU_liver_non_tumor_104


title: HKU_liver_non_tumor_114

value: stage i


title: HKU_liver_non_tumor_101

value: non_tumor liver


title: HKU_liver_non_tumor_131


title: wild type replicate 1

description:
FX-214_wt_replicate1
Gene expression data from mouse cells.

source_name: wild type, replicate 1


title: fibroblast, TSG6-knockout, HA-treated, biological replicate 2


title: fibroblast, TSG6-knockout, HA-treated, biological replicate 1


title: HKU_liver_non_tumor_95

value: m


title: fibroblast, TSG6-knockout, TSG6-treated, biological replicate 3


title: fibroblast, TSG6-knockout, HA-treated, biological replicate 3


title: HKU_liver_non_tumor_93


title: fibroblast, TSG6-knockout, TSG6-treated, biological replicate 2


title: fibroblast, TSG6-knockout, TSG6-treated, biological replicate 1


title: fibroblast, TSG6-knockout, LPS-treated, biological replicate 4

value: LPS-treated


title: HKU_liver_non_tumor_115


title: HKU_liver_non_tumor_89


title: fibroblast, TSG6-knockout, LPS-treated, biological replicate 2


title: HKU_liver_non_tumor_92


title: fibroblast, TSG6-knockout, LPS-treated, biological replicate 1


title: fibroblast, TSG6-knockout, TNFa-treated, biological replicate 4

value: TNFa-treated


title: fibroblast, TSG6-knockout, TNFa-treated, biological replicate 3


title: HKU_liver_non_tumor_108


title: wild type replicate 3

description:
FX-221_wt_replicate3
Gene expression data from mouse cells.

source_name: wild type, replicate 3

value: bone marrow macrophages


title: HKU_liver_non_tumor_90

value: positive


title: fibroblast, TSG6-knockout, LPS-treated, biological replicate 3


title: HKU_liver_non_tumor_87

value: stage ii


title: HKU_liver_non_tumor_85

value: stage iva


title: HKU_liver_non_tumor_94


title: Recovery Individual 7

city: Burnaby

first: Nicole

middle: Lisa

last: Quinn

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

hyb_protocol: Details of the microarray hybridization process can be found at the University of Victoria cGRASP website (http://web.uvic.ca/grasp/microarray/array.html) within the .pdf document entitled Invitrogen Indirect cDNA Labeling System version 3.

scan_protocol: Images were scanned on a ScanArray™ Express Microarray Scanner (Packard BioScience BioChip Technologies, model #ASCEX00). Slides were scanned at 74 and 72 PMT for Cy3 and Cy5, respectively, and spot intensity was calculated with ImaGene ver. 6.5.1.

data_processing: All statistical analyses of the microarray data were conducted using Genespring ver. 7.3.1. Signals were normalized per spot and per chip using an intensity-dependent (LOWESS) normalization, then per gene to normalize to the median. Spots were filtered on flags present, and only spots with signals greater or equal to the average base/proportional value of the raw channel were retained.

organism: Salvelinus alpinus

source_name: Arctic charr gill tissue whole RNA reverse transcribed to cDNA, after recovery

label_protocol: cDNA (300 ng) and aRNA (500 ng) were labeled with Cy5 and Cy3 (Amersham Biosciences), respectively, using Invitrogen’s SuperScript Indirect cDNA Labeling System following the manufacturer's instructions.

extract_protocol: Total RNA was isolated from gill tissues disrupted and homogenized in 1 ml TRIzol reagent using a Mixer-mill (Retch® MM 301) with tungsten carbide beads. Phase separation was conducted using 200 µl chloroform, and RNA was purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 200 Arctic charr were exposed to chronic, moderate heat stress (15-19ºC) for 72 hrs. 10 fish were sampled before (control), during (after 72 hrs of exposure) and after (12 hrs after returning to ambient temperature) heat exposure, then after 72 hrs of recovery time, representing the C, D, A and R treatment groups, respectively. Six randomly sampled fish from each treatment group were used for microarray analysis.

value: gill

tag: condition

value: after recovery at ambient temperature

tag: individual

organism: Salmo salar

source_name: reference aRNA

value: gonad, brain, spleen


title: Recovery Individual 9


title: HKU_liver_non_tumor_82

value: hcc

value: stage iiia


title: fibroblast, TSG6-knockout, TNFa-treated, biological replicate 1

tag: strain

value: BALB/c

value: female


title: Recovery Individual 5

tag: tissue


title: fibroblast, TSG6-knockout, TNFa-treated, biological replicate 2

value: TSG-6 knockout


title: fibroblast, TSG6-knockout, untreated, biological replicate 8


title: HKU_liver_non_tumor_86


title: HKU_liver_non_tumor_77


title: Recovery Individual 3


title: fibroblast, TSG6-knockout, untreated, biological replicate 7


title: HKU_liver_non_tumor_81


title: Recovery Individual 4


title: HKU_liver_non_tumor_80

value: negative


title: Recovery Individual 2


title: HKU_liver_non_tumor_84

value: non_tumor liver


title: HKU_liver_non_tumor_74

value: m


title: HKU_liver_non_tumor_75


title: fibroblast, TSG6-knockout, untreated, biological replicate 5


title: HKU_liver_non_tumor_76


title: HKU_liver_non_tumor_78


title: HKU_liver_non_tumor_98


title: HKU_liver_non_tumor_79

value: f


title: HKU_liver_non_tumor_71


title: HKU_liver_non_tumor_70


title: fibroblast, TSG6-knockout, untreated, biological replicate 3


title: After Individual 5

source_name: Arctic charr gill tissue whole RNA reverse transcribed to cDNA, immediately after cooling

value: immediately after cooling from moderate temperature stress


title: fibroblast, TSG6-knockout, untreated, biological replicate 4


title: HKU_liver_non_tumor_73


title: After Individual 6


title: fibroblast, TSG6-knockout, untreated, biological replicate 2


title: HKU_liver_non_tumor_91


title: After Individual 4


title: fibroblast, TSG6-knockout, untreated, biological replicate 6


title: HKU_liver_non_tumor_65


title: HKU_liver_non_tumor_67


title: fibroblast, TSG6-knockout, untreated, biological replicate 1


title: HKU_liver_non_tumor_63


title: After Individual 2


title: HKU_liver_non_tumor_60


title: After Individual 1


title: After Individual 3


title: HKU_liver_non_tumor_62


title: During Individual 8

source_name: Arctic charr gill tissue whole RNA reverse transcribed to cDNA, during temperature stress

value: during moderate temperature stress


title: HKU_liver_non_tumor_56


title: HKU_liver_non_tumor_58

value: positive


title: HKU_liver_non_tumor_54


title: fibroblast, wild-type, TSG6+HA-treated, biological replicate 2

value: Wild-type


title: HKU_liver_non_tumor_72


title: fibroblast, wild-type, TSG6+HA-treated, biological replicate 1


title: fibroblast, wild-type, HA-treated, biological replicate 2

value: HA-treated


title: HKU_liver_non_tumor_64


title: During Individual 6

value: gill


title: During Individual 5


title: fibroblast, wild-type, HA-treated, biological replicate 1


title: HKU_liver_non_tumor_55

value: stage ii


title: During Individual 4

value: gonad, brain, spleen


title: fibroblast, wild-type, TSG6-treated, biological replicate 2


title: During Individual 9


title: fibroblast, wild-type, TSG6-treated, biological replicate 1


title: HKU_liver_non_tumor_59

value: hcc

value: stage ivb


title: fibroblast, wild-type, LPS-treated, biological replicate 2

value: BALB/c

value: LPS-treated


title: During Individual 1


title: HKU_liver_non_tumor_47


title: HKU_liver_non_tumor_46

value: stage iiia


title: HKU_liver_non_tumor_51

value: stage iva


title: HKU_liver_non_tumor_50

value: non_tumor liver


title: HKU_liver_non_tumor_49

value: m


title: HKU_liver_non_tumor_43

value: f


title: HKU_liver_non_tumor_42


title: wrbA

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: 3 biological replicates

hyb_protocol: Prior to hybridization, the slides were treated with the background-reducing Pronto! Pre-Soak System (Corning Life Sciences). The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42°C and washed twice in 0.1xSSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5xSSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1xSSC, 0.1% SDS for 1 min and twice in 0.1xSSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800xg. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 ul of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5xSSC (1xSSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 ug of poly(A), and 1xDenhardt’s solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C. After hybridization was complete, the slides were washed in 2xSSC, 0.1% SDS at 42 °C for 2 min in 0.1xSSC, 0.1% SDS for 2 min at room temperature, and finally twice in 0.1xSSC for 2 min at room temperature. The microarray slides were dried by centrifugation for 5 min at 800g.

scan_protocol: Slides were scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing:
Genespring 7.3.1 was used to obtain LOWESS normalised data that represents the average of the three replicate experiments.
Processed data for each replicate is attached as a supplementary txt file

organism: Escherichia coli O157:H7

label_protocol: 20 ug total RNA was converted to Cy3-labelled cDNA using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE Healthcare) according to manufacturer’s instructions. Amino-allyllabelled nucleotides were incorporated into the cDNA by reverse transcription of the total RNA, followed by a direct chemical coupling of Cy3 NHS-dye esters to the amino-allyl-labelled cDNAs.

growth_protocol: Escherichia coli O157 TUV93-0 was grown at 37 degrees C to OD 0.7 in MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2.

extract_protocol: An RNeasy minikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd).

tag: genotype/variation

value: wild type

tag: growth characteristics

value: mid exponential culture grown in MEM-HEPES supplemented with Fe and Glucose

source_name: wrbA

value: wrbA mutant

tag: growth chararceristics


title: folX

description: 3 biological replicates

source_name: folX

value: folX mutant


title: HKU_liver_non_tumor_38

tag: age

value: positive


title: fibroblast, wild-type, TNFa-treated, biological replicate 2

tag: gender

value: female

value: Wild-type

value: TNFa-treated


title: tpx

description: 3 biological replicates

source_name: tpx

value: tpx mutant


title: fibroblast, wild-type, LPS-treated, biological replicate 1


title: HKU_liver_non_tumor_40

value: hcc

value: negative


title: HKU_liver_non_tumor_34

value: stage i


title: HKU_liver_non_tumor_53

value: stage ii


title: HKU_liver_non_tumor_68

value: stage iva


title: fibroblast, wild-type, TNFa-treated, biological replicate 1

value: BALB/c


title: HKU_liver_non_tumor_39

value: non_tumor liver

value: m


title: fibroblast, wild-type, untreated, biological replicate 5


title: HKU_liver_non_tumor_41


title: fibroblast, wild-type, untreated, biological replicate 4


title: HKU_liver_non_tumor_33

value: stage iiia


title: HKU_liver_non_tumor_30


title: HKU_liver_non_tumor_36


title: tpxC61S

description: 3 biological replicates

value: wild type

value: mid exponential culture grown in MEM-HEPES supplemented with Fe and Glucose

value: tpxC61S mutant


title: mytotubes #15, GFP vs FTO

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description:
Biological replicate 4.
350075

hyb_protocol: 1µg of labelled nucleic acid was hybridized at 62 degree_C during 17 hours.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were quantified using GenePix Pro 4.0.

data_processing: Normexp background correction (offset=50) and lowess normalization. A quantile normalization was added for between array normalization. Only spot with a flag=0 and SNR635 and SNR532 above 2 were considered.

source_name: mytotubes #15 infected with FTO

label_protocol: 1µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer’s instructions. Fluorescent probes were synthesized by chemical coupling of 4 µg of aminoallyl aRNA with cyanine (Cy)3 or Cy5 dyes.  Fluorescent probes were purified using Rneasy minikit (Qiagen).

growth_protocol: Myotubes were prepared from a human skeletal muscle biopsy.

extract_protocol: Total RNA extraction using Trizol following manufacturer's instructions.

treatment_protocol: After differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either GFP or FTO.

value: skeletal muscle

value: myotubes

tag: infection

value: FTO

source_name: mytotubes #15 infected with GFP

value: GFP


title: fibroblast, wild-type, untreated, biological replicate 3

value: female

value: Wild-type


title: mytotubes #186, GFP vs FTO

description:
Biological replicate 3.
350073

source_name: mytotubes #186 infected with FTO

source_name: mytotubes #186 infected with GFP


title: HKU_liver_non_tumor_32

tag: Sex

value: hcc

value: positive


title: HKU_liver_non_tumor_29

tag: diagnosis

value: stage ii


title: fibroblast, wild-type, untreated, biological replicate 2


title: DvH 480min 0 mM Peroxide gSet11

status: Public on Jul 04 2011

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 480 min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.  . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 480min. In sterile water

growth_protocol: Inoculate 200 ml of log-phase inoculum culture to 2000 ml of defined PIPES buffered medium LS4D (13, 27). Grow culture in six 2L glass bottles placed in the anaerobic chamber at 30 degree C till OD of ~0.3. Three bottles will be the control(Ph 7.0, sterile water added) and the other three bottles will be the varibles (1 mM hydrogen peroxide). Harvest 300 ml of cells from each of the six bottles for T0 sampling. Add 18.25 ml of 100 mM H2O2 to the three variable bottles for stress. Then harvest 300 ml of cells from each bottle at 30, 60, 120, 240 and 480 min after treatment. All sampling occur in the anaerobic chamber. Samples were chilled and pumped through stainless steel tubing in ice-water into centrifuge bottlessurrounded by ice. Harvested biomass was centrifuged at 11,000  g for 10 min at 4 degree C.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80 degree C until RNA isolation.

treatment_protocol: 480min. In sterile water

tag: time

value: 0mM Peroxide

value: Hildenborough


title: mytotubes #25, GFP vs FTO

description:
Biological replicate 2.
350072

source_name: mytotubes #25 infected with FTO

source_name: mytotubes #25 infected with GFP


title: mytotubes #184, GFP vs FTO

description:
Biological replicate 1.
350070

source_name: mytotubes #184 infected with FTO

source_name: mytotubes #184 infected with GFP


title: DvH 480min 1 mM Peroxide gSet12

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 480 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 480min. In 1mM H2O2

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 480min. 1mM H2O2

value: 1mM Peroxide


title: HKU_liver_non_tumor_26

value: non_tumor liver

value: f

tag: tumor stage

tag: hbsag


title: HKU_liver_non_tumor_35

value: m

value: stage iva


title: fibroblast, wild-type, untreated, biological replicate 1

source_name: fibroblast

value: BALB/c

tag: type


title: DvH 240min 0 mM Peroxide gSet9

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 240 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. In sterile water

extract_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 240min. In sterile water

tag: treatment


title: DvH 240min 1 mM Peroxide gSet10

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 240 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. In 1mM H2O2

treatment_protocol: 240min. 1mM H2O2


title: DvH 120min 1 mM Peroxide gSet8

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. In 1mM H2O2

treatment_protocol: 120min. 1mM H2O2


title: DvH 120min 0 mM Peroxide gSet7

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. In sterile water

treatment_protocol: 120min. In sterile water


title: DvH 60min 1 mM Peroxide gSet6

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. In 1mM H2O2

treatment_protocol: 60min. 1mM H2O2


title: DvH 60min 0 mM Peroxide gSet5

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. In sterile water

treatment_protocol: 60min. In sterile water


title: DvH 30min 1 mM Peroxide gSet4

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 30min. In 1mM H2O2

treatment_protocol: 30min. 1mM H2O2


title: HKU_liver_non_tumor_21

value: stage iiia

value: negative


title: DvH 30min 0 mM Peroxide gSet3

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 30min. In sterile water

treatment_protocol: 30min. In sterile water


title: HKU_liver_non_tumor_23

description: genomic DNA was genotyped using Infinium HumanHap650-v3 Genotyping BeadChips (Illumina)


title: HKU_liver_non_tumor_22


title: DvH 0min 1 mM Peroxide gSet2

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with 1mM H202.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. In 1mM H2O2

treatment_protocol: 0min. 1mM H2O2


title: DvH 0min 0 mM Peroxide gSet1

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with sterile water.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. In sterile water

treatment_protocol: 0min. In sterile water


title: HKU_liver_non_tumor_24


title: DvH 120min JW709 1 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW709 1 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. JW709 1 mM Peroxide

growth_protocol: Inoculate 100 ml of log-phase inoculum culture to 900 ml of defined PIPES buffered medium LS4D (13, 27). Grow culture in 1L glass bottles placed in the anaerobic chamber at 30 degree C till OD of ~0.3. Three bottles will be the control(Ph 7.0, sterile water added) and the other three bottles will be the varibles (1 mM hydrogen peroxide) fro wild type and deletion mutants respectively. Harvest 300 ml of cells from each bottle for T0 sampling. Add 7 ml of 100 mM H2O2 to the variable bottles for stress. Then harvest 300 ml of cells from each bottle at 120 min after treatment. All sampling occur in the anaerobic chamber. Samples were chilled and pumped through stainless steel tubing in ice-water into centrifuge bottlessurrounded by ice. Harvested biomass was centrifuged at 11,000  g for 10 min at 4 degree C.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80 degree C until RNA isolation.

treatment_protocol: 120min. JW709 1 mM Peroxide.

tag: genotype


title: DvH 120min WT 0 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with WT 0 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120Min. WT 0 mM Peroxide

treatment_protocol: 120Min. WT 0 mM Peroxide.

value: WT


title: DvH 120min WT 1 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with WT 1 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. WT 1 mM Peroxide

treatment_protocol: 120min. WT 1 mM Peroxide.


title: DvH 120min JW709 0 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW709 0 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120Min. JW709 0 mM Peroxide

treatment_protocol: 120Min. JW709 0 mM Peroxide.


title: HKU_liver_non_tumor_17


title: HKU_liver_non_tumor_45


title: HKU_liver_non_tumor_20


title: DvH 120min JW708 1 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW708 1 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. JW708 1 mM Peroxide

treatment_protocol: 120min. JW708 1 mM Peroxide.


title: DvH 120min JW708 0 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW708 0 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120Min. JW708 0 mM Peroxide

treatment_protocol: 120Min. JW708 0 mM Peroxide.


title: DvH 120min JW707 1 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW707 1 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. JW707 1 mM Peroxide

treatment_protocol: 120min. JW707 1 mM Peroxide.


title: DvH 120min JW707 0 mM Peroxide

description: This sample is one of a series of num_samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Peroxide. This sample was treated with JW707 0 mM Peroxide.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120Min. JW707 0 mM Peroxide

treatment_protocol: 120Min. JW707 0 mM Peroxide.


title: HKU_liver_non_tumor_11


title: HKU_liver_non_tumor_15


title: HKU_liver_non_tumor_19


title: DvH 0min WT 1 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. WT 1 mM Peroxide

treatment_protocol: 0min. WT 1 mM Peroxide.


title: HKU_liver_non_tumor_18


title: HKU_liver_non_tumor_12


title: Reference_61

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against an in house gDNA reference set of 61 normal females.

label_protocol: Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)

extract_protocol: Biopsied polar body, blastomere and trophectoderm samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

tag: reference

value: control gDNA

tag: patient number

tag: ploidy

tag: karyotype


title: HKU_liver_non_tumor_10

tag: tissue


title: DvH 0min WT 0 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. WT 0 mM Peroxide

treatment_protocol: 0min. WT 0 mM Peroxide.

tag: strain


title: Reference_59

description: Hybridized to 250K_Nsp


title: HKU_liver_non_tumor_13

tag: age


title: DvH 0min JW709 1 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW709 1 mM Peroxide

treatment_protocol: 0min. JW709 1 mM Peroxide.


title: HKU_liver_non_tumor_2


title: DvH 0min JW709 0 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW709 0 mM Peroxide

treatment_protocol: 0min. JW709 0 mM Peroxide.


title: HKU_liver_non_tumor_6


title: Reference_55

description: Hybridized to 250K_Nsp


title: DvH 0min JW708 1 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW708 1 mM Peroxide

treatment_protocol: 0min. JW708 1 mM Peroxide.


title: HKU_liver_non_tumor_9


title: Reference_53

description: Hybridized to 250K_Nsp


title: HKU_liver_non_tumor_8


title: HKU_liver_non_tumor_1


title: DvH 0min JW707 0 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW707 0 mM Peroxide

treatment_protocol: 0min. JW707 0 mM Peroxide.


title: Reference_60

description: Hybridized to 250K_Nsp


title: DvH 0min JW707 1 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW707 1 mM Peroxide

growth_protocol: Inoculate 100 ml of log-phase inoculum culture to 900 ml of defined PIPES buffered medium LS4D (13, 27). Grow culture in 1L glass bottles placed in the anaerobic chamber at 30 degree C till OD of ~0.3. Three bottles will be the control(Ph 7.0, sterile water added) and the other three bottles will be the varibles (1 mM hydrogen peroxide) from wild type and deletion mutants respectively. Harvest 300 ml of cells from each bottle for T0 sampling. Add 7 ml of 100 mM H2O2 to the variable bottles for stress. Then harvest 300 ml of cells from each bottle at 120 min after treatment. All sampling occur in the anaerobic chamber. Samples were chilled and pumped through stainless steel tubing in ice-water into centrifuge bottlessurrounded by ice. Harvested biomass was centrifuged at 11,000  g for 10 min at 4 degree C.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80 degree C until RNA isolation.

treatment_protocol: 0min. JW707 1 mM Peroxide.


title: Reference_54

description: Hybridized to 250K_Nsp


title: Fibroblasts not induced rep4

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: 22ng/mikL of fragmented and biotinilated cDNA was hybridizated for 16hours at 48°C on Affymetrix Mouse Gene 1.0 ST Arrays. We used FS0007 (labeling and washing script) protocol on Affymetrix Fluidic Station 450.

scan_protocol: Scanner 3000 7G (Affymetrix)

data_processing: Cel intensity values were computed using the Affymetrix Expression Console. Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied (Irizarry et al. 2003). Data were then filtered based on probe set intensity, so that only probesets that had intensity value >50 in at least half the arrays were retained. Statistical analysis was performed with limma (Smyth 2004). P-values were adjusted for multiple testing using Benjamini and Hochberg's method to control the false discovery rate (Hochberg and Benjamini 1990). Genes with adjusted P values below 0.01 were considered differentially expressed. Furthermore, a fold-change threshold cutoff was set to focus on genes whose expression level changes at least 2 times. Data were analyzed through DAVID Bioinformatics Resources v6.7 (Huang et al 2009, Dennis et al 2003).

source_name: E14,5 TH-GFP fibroblasts not infected

label_protocol: We used 10ng of total RNA with WT Ovation kit: Pico RNA amplification sys., Exon module, cDNA biotine module (according to NuGEN Technologies protocol).

growth_protocol: MEFs were isolated from TH-GFP knock-in mice embryos at E14.5 under a dissection microscope (Leica). The head, vertebral column (containing the spinal cord), dorsal root ganglia and all internal organs were removed and discarded to ensure the removal of all cells with neurogenic potential from the cultures. The remaining tissue was manually dissociated and incubated in 0.25% trypsin (Sigma) for 10–15 min to create a single cell suspension. The cells from each embryo were plated onto a 15-cm tissue culture dish in MEF media (Dulbecco’s Modified Eagle Medium; Invitrogen) containing 10% fetal bovine serum (FBS; Hyclone), b-mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate and penicillin/streptomycin (all from Invitrogen). In all experiments we used MEFs passaged no more than three times.

extract_protocol: All samples were resuspended in Trizol, and extracted according to manufacturer's protocol. All samples were Dnase I-treated, and checked by Bioanalyzer 2100 for quality control.

treatment_protocol: MEF cells were infected in MEF media, then 16–20 h in media containing lentivirus, the cells were switched into fresh MEF media containing doxycycline (2 mg/ml, Sigma) to activate expression of the transduced genes. After 48 h in MEF media with doxycycline the media was replaced with neuronal inducing media [(DMEM/F12 (Invitrogen), 25 μg/ml insulin (Sigma), 50 μg/ml transferrin (Sigma), 30 nM sodium selenite, 20 nM progesterone (Sigma), 100 nM putrescine (Sigma) and penicillin/streptomycin (Sigma)] containing doxycycline. The media was changed every 2–3 days for further 10 days.

tag: genotype/variation

value: TH-GFP knock-in

tag: developmental stage

tag: cell type

value: TH-GFP fibroblasts

tag: infection status

value: non-infected


title: DvH 0min JW708 0 mM Peroxide

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. JW708 0 mM Peroxide

treatment_protocol: 0min. JW708 0 mM Peroxide.

tag: time


title: Reference_58

description: Hybridized to 250K_Nsp


title: Reference_56

description: Hybridized to 250K_Nsp


title: Fibroblasts not induced rep3


title: HKU_liver_non_tumor_14

tag: Sex

tag: diagnosis

value: hcc

tag: tumor stage

value: positive


title: Reference_51

description: Hybridized to 250K_Nsp


title: ACC6_PC_Bulk

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using DNA Analytics 4.0.85 and the ADM2 step gram algorithm.

source_name: Frozen tissue biopsy

label_protocol: A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

growth_protocol: Tumor samples from patients with either pancreatic ductal adenocarcinoma, adrenocortical carcinoma, or prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting

extract_protocol: 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care).

value: Prostate Carcinoma

source_name: Reference pooled 46XX

value: pooled normal (46,XX) reference (Promega)


title: Reference_57

description: Hybridized to 250K_Nsp


title: Fibroblasts not induced rep1


title: Reference_52

description: Hybridized to 250K_Nsp


title: Reference_49

description: Hybridized to 250K_Nsp


title: Reference_48

description: Hybridized to 250K_Nsp


title: Reference_50

description: Hybridized to 250K_Nsp


title: B08 2N


title: Fibroblasts dopaminergic induced rep3

source_name: E14,5 TH-GFP fibroblasts infected

value: infected with lentiviruses expressing the three dopaminergic transcription factors  Ascl1, Lmx1a and Nurr1


title: ACC6_PC


title: Reference_47

description: Hybridized to 250K_Nsp


title: B07 AN


title: Reference_43

description: Hybridized to 250K_Nsp


title: Fibroblasts dopaminergic induced rep1


title: Fibroblasts not induced rep2


title: Reference_46

description: Hybridized to 250K_Nsp


title: B07 2N


title: Fibroblasts dopaminergic induced rep2


title: Reference_41

description: Hybridized to 250K_Nsp


title: Fibroblasts dopaminergic induced rep4


title: Reference_37

description: Hybridized to 250K_Nsp


title: Reference_44

description: Hybridized to 250K_Nsp


title: Reference_42

description: Hybridized to 250K_Nsp


title: ACC52

value: Adrenal Cortical Carcinoma


title: Reference_39

description: Hybridized to 250K_Nsp


title: B00 2N


title: Reference_38

description: Hybridized to 250K_Nsp


title: B00 AN


title: Reference_36

description: Hybridized to 250K_Nsp


title: B9 antimir-30

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: Gene expression after 4 days in adipogenic medium.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: hMADS cells, B9, antimir-30

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in the proliferation medium, which is composed of DMEM (low glucose) containing 10% fetal calf serum (FCS), 0.01 M HEPES, 100 U/ml penicillin and streptomycin.

extract_protocol: Total RNA was extracted with the Qiagen Rneasy kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: All transfections were performed with HighPerfect transfection reagent (Qiagen). Adipogenic medium was composed of DMEM/Ham’s F12 media supplemented with 10 µg/ml transferrin, 0.86 µM insulin, 0.2 nM triiodothyronine, 1 µM dexamethasone, 100 µM isobutyl-methylxanthine and 1 µM rosiglitazone. Three days later, the medium was changed (dexamethasone and isobutyl-methylxanthine were omitted).

value: human adipose tissue-derived stem cells

tag: clone

tag: agent


title: B9 antimir-neg

source_name: hMADS cells, B9, antimir-neg

value: control antimiR


title: Reference_34

description: Hybridized to 250K_Nsp

tag: reference


title: B7 antimir-30

source_name: hMADS cells, B7, antimir-30


title: ACC51


title: ACC47


title: B7 antimir-neg

source_name: hMADS cells, B7, antimir-neg


title: Reference_33

description: Hybridized to 250K_Nsp

tag: patient number


title: ACC48


title: Reference_35

description: Hybridized to 250K_Nsp

tag: ploidy


title: Reference_31

description: Hybridized to 250K_Nsp

tag: karyotype


title: Reference_45

description: Hybridized to 250K_Nsp


title: Reference_30

description: Hybridized to 250K_Nsp


title: B9 mir-30d

source_name: hMADS cells, B9, mir-30d


title: Reference_40

description: Hybridized to 250K_Nsp


title: B9 mir-30a

source_name: hMADS cells, B9, mir-30a


title: ACC45

tag: tissue


title: ACC35


title: ACC31


title: B9 mir-neg

source_name: hMADS cells, B9, mir-neg

value: control miRNA


title: Reference_32

description: Hybridized to 250K_Nsp


title: B7 mir-30d

source_name: hMADS cells, B7, mir-30d


title: Reference_27

description: Hybridized to 250K_Nsp


title: Reference_29

description: Hybridized to 250K_Nsp


title: ACC28


title: Reference_24

description: Hybridized to 250K_Nsp


title: Reference_28

description: Hybridized to 250K_Nsp


title: B7 mir-30a

source_name: hMADS cells, B7, mir-30a


title: Reference_25

description: Hybridized to 250K_Nsp


title: ACC27


title: Reference_22

description: Hybridized to 250K_Nsp


title: Reference_20

description: Hybridized to 250K_Nsp


title: B7 mir-neg

source_name: hMADS cells, B7, mir-neg


title: ACC26_AN2


title: ACC26_AN1


title: Reference_18

description: Hybridized to 250K_Nsp


title: Hypothalamus Furosemide Treated Gratified, Replicate 4

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

institute: Duke University

hyb_protocol: Sample and reference RNAs were pooled, mixed with 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS), COT-1 DNA, and poly-dA to limit nonspecific binding, and heated to 95°C for 2 minutes.  This mixture was pipetted onto a microarray slide by use of a Maui Mixer hybridization chamber (BioMicro Systems, Salt Lake City, UT) and hybridized overnight at 42°C on an automated Maui Hybridization Station (BioMicro Systems, Salt Lake City, UT).

scan_protocol: The array was then washed at increasing stringencies, and scanned on a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Within array Loess normalization was performed using the Limma package 3 to remove any bias that the intensity has on log-fold change.  Next, between array variance stabilization normalization was carried out, where both the red and green channel on the arrays are aligned to each other based on the assumption that most of the genes are constant across experiments4.  Spots not reaching the quality criterion were removed from further analysis.  Quality was determined in three ways.  1) There was insufficient red or green intensity to produce a reliable ratio.  2) The consistency of the ratio throughout the spot was low.  3) Other machine-annotated flags indicated the spot was not reliably read.  After filtering, if a particular spot was found only to be present on a small number of arrays (<15), then that spot was filtered for all arrays.  Spots measuring the same gene were combined into a final score for that transcript to avoid bias in a gene set analysis if the correlation between the was greater than 0.5 across all samples.

source_name: Total RNA from adult mouse hypothalamus

label_protocol: Add water first, then 1ul of oligo dT primer, then RNA samples.  Incubate at 65 degrees  for 10 mins, followed by 25 degrees for 5 mins.  Add 5x rxn buffer, .1M DTT, dNTP mix, Cy dCTP (3 or 5), Cy cUTP (3 or 5), and Superscript II.

growth_protocol: Adult Male Mice

extract_protocol: Total RNA was isolated from the hypothalamus and remainder of the brain from each animal using the TRIZOL-RNA-easy method, and RNA quality was assessed using spectrophotometry and micro-electrophoresis.

tag: strain

value: adult

tag: gender

value: male

value: Hypothalamus

tag: treatment

value: Furosemide Gratified

source_name: Universal Mouse Reference RNA, Stratagene

extract_protocol: Reference RNA purchased from Stratagene.

tag: reference rna vendor

value: Stratagene


title: Reference_26

description: Hybridized to 250K_Nsp

value: control gDNA


title: Reference_21

description: Hybridized to 250K_Nsp


title: Reference_14

description: Hybridized to 250K_Nsp


title: Reference_23

description: Hybridized to 250K_Nsp


title: ACC24


title: Hypothalamus Furosemide Treated Gratified, Replicate 2

tag: developmental stage


title: Hypothalamus Furosemide Treated Gratified, Replicate 1


title: Reference_15

description: Hybridized to 250K_Nsp


title: Reference_16

description: Hybridized to 250K_Nsp


title: Reference_19

description: Hybridized to 250K_Nsp


title: Reference_9

description: Hybridized to 250K_Nsp


title: Reference_10

description: Hybridized to 250K_Nsp


title: ACC18


title: Reference_13

description: Hybridized to 250K_Nsp


title: Hypothalamus Furosemide Treated Gratified, Replicate 3


title: Hypothalamus Furosemide Treated, Replicate 4

value: Furosemide


title: ACC23


title: ACC17


title: Hypothalamus Furosemide Treated, Replicate 2


title: Reference_7

description: Hybridized to 250K_Nsp


title: ACC16


title: Reference_11

description: Hybridized to 250K_Nsp


title: Reference_8

description: Hybridized to 250K_Nsp


title: Hypothalamus Furosemide Treated, Replicate 1


title: Reference_4

description: Hybridized to 250K_Nsp


title: ACC14


title: ACC15


title: Hypothalamus ACTH Treated Gratified, Replicate 6

value: ACTH Gratified


title: Reference_5

description: Hybridized to 250K_Nsp


title: Reference_12

description: Hybridized to 250K_Nsp


title: Hypothalamus Furosemide Treated, Replicate 3


title: Reference_3

description: Hybridized to 250K_Nsp


title: ACC13


title: Hypothalamus ACTH Treated Gratified, Replicate 5


title: Reference_6

description: Hybridized to 250K_Nsp


title: Reference_1

description: Hybridized to 250K_Nsp


title: Reference_2

description: Hybridized to 250K_Nsp


title: Reference_17

description: Hybridized to 250K_Nsp


title: Hypothalamus ACTH Treated Gratified, Replicate 3


title: ACC12


title: TE10E

description: Hybridized to 250K_Nsp

tag: cell type

value: Trophectoderm

value: Euploid

value: normal


title: ACC11

value: pooled normal (46,XX) reference (Promega)


title: Hypothalamus ACTH Treated Gratified, Replicate 4


title: Hypothalamus ACTH Treated Gratified, Replicate 2


title: TE10A

description: Hybridized to 250K_Nsp

value: Aneuploid


title: TE9E

description: Hybridized to 250K_Nsp


title: TE9A

description: Hybridized to 250K_Nsp


title: Hypothalamus ACTH Treated Gratified, Replicate 1


title: TE8A

description: Hybridized to 250K_Nsp


title: ACC9

value: Adrenal Cortical Carcinoma


title: Hypothalamus ACTH Treated, Replicate 5

value: ACTH


title: TE8E

description: Hybridized to 250K_Nsp


title: TE6A

description: Hybridized to 250K_Nsp


title: TE7A

description: Hybridized to 250K_Nsp


title: TE5E

description: Hybridized to 250K_Nsp


title: Hypothalamus ACTH Treated, Replicate 4


title: ACC1


title: TE6E

description: Hybridized to 250K_Nsp


title: Hypothalamus ACTH Treated, Replicate 3


title: TE4E

description: Hybridized to 250K_Nsp


title: TE2A

description: Hybridized to 250K_Nsp


title: TE7E

description: Hybridized to 250K_Nsp


title: Hypothalamus ACTH Treated, Replicate 2


title: P1009-1

value: Pancreatic Ductal Adenocarcinoma


title: TE4A

description: Hybridized to 250K_Nsp


title: PB9A

description: Hybridized to 250K_Nsp

value: Polar Body


title: Hypothalamus ACTH Treated, Replicate 1

value: adult


title: ACC10


title: TE5A

description: Hybridized to 250K_Nsp


title: P1021


title: TE3A

description: Hybridized to 250K_Nsp


title: Hypothalamus Control, Replicate 4

value: male


title: TE3E

description: Hybridized to 250K_Nsp


title: ACC2


title: Hypothalamus Control, Replicate 3

value: Hypothalamus


title: 1070263A5


title: 4080070A


title: Hypothalamus Control, Replicate 2


title: TE1E

description: Hybridized to 250K_Nsp


title: TE2E

description: Hybridized to 250K_Nsp


title: Hypothalamus Control, Replicate 1


title: PB7A

description: Hybridized to 250K_Nsp


title: PB9E

description: Hybridized to 250K_Nsp


title: 407104A


title: TE1A

description: Hybridized to 250K_Nsp


title: P1046.T1


title: PB8A

description: Hybridized to 250K_Nsp


title: P1027A


title: Whole Brain Furosemide Treated Gratified, Replicate 4

source_name: Total RNA from adult mouse whole brain

value: Whole Brain minus Hypothalamus

value: Furosemide Gratified


title: PB5A

description: Hybridized to 250K_Nsp


title: PB8E

description: Hybridized to 250K_Nsp


title: PB5E

description: Hybridized to 250K_Nsp


title: Whole Brain Furosemide Treated Gratified, Replicate 3

value: Stratagene


title: P1022V


title: 0710A192C


title: PB6E

description: Hybridized to 250K_Nsp


title: PB4E

description: Hybridized to 250K_Nsp


title: PB6A

description: Hybridized to 250K_Nsp


title: P1018R


title: Whole Brain Furosemide Treated Gratified, Replicate 2


title: PB3E

description: Hybridized to 250K_Nsp


title: PB7E

description: Hybridized to 250K_Nsp


title: P001


title: PB2A

description: Hybridized to 250K_Nsp


title: PB4A

description: Hybridized to 250K_Nsp


title: PB1E

description: Hybridized to 250K_Nsp


title: Whole Brain Furosemide Treated, Replicate 3

value: Furosemide


title: Blastomere9A

description: Hybridized to 250K_Nsp

value: Blastomere


title: P4511


title: Whole Brain Furosemide Treated, Replicate 4


title: Whole Brain Furosemide Treated Gratified, Replicate 1


title: PB3A

description: Hybridized to 250K_Nsp


title: P4029


title: PB1A

description: Hybridized to 250K_Nsp


title: Blastomere8Eii

description: Hybridized to 250K_Nsp


title: Whole Brain Furosemide Treated, Replicate 2


title: Blastomere8Aii

description: Hybridized to 250K_Nsp


title: P4028


title: Blastomere9E

description: Hybridized to 250K_Nsp


title: Whole Brain ACTH Treated Gratified, Replicate 5

value: ACTH Gratified


title: Whole Brain Furosemide Treated, Replicate 1


title: P1071