title: control amygdala, replicate1 (gene-level)

status: Public on May 31 2016

type: RNA

city: Hirosaki

first: Shinya

last: Ueno

state: Aomori  Pref.

address: 5 Zaifu-cho

department: Neurophysiology

country: Japan

institute: Hirosaki Univ Grad Sch of Med

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.2 μg each) hybridized on GeneChip® MTA 1.0 for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

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

data_processing:
The data were analyzed with Expression Console version 1.4.1 (Affymetrix) using default settings for background correction, normalization and summarization.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: control, brain, amygdala

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

growth_protocol: Mice were housed in plastic cages containing wood chips and covered with a wire lid. The cages were kept at 24±1 °C under a 12 h light/dark cycle (lights on at 8:00). The diet were standard laboratory food and water ad libitum.

extract_protocol: Total RNA was extracted from each source using RNeasy Lipid Tissue Mini Kit (QIAGEN) according to the manufacturer's protocol. 100 ng of total RNA was subsequently carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

treatment_protocol: Male mice of 8-week old were subjected to intraperitoneal injection of INTRALIPID or 5 mg/ml DZP at 8:00 and 18:00 for 10 days.

tag: strain

tag: gender

value: male

tag: age

value: 8 week-old

tag: agent

value: control

tag: tissue

value: brain

tag: tissue region

value: amygdala


title: DZP hippocampus, replicate2 (gene-level)

source_name: DZP, brain, hippocampus

value: DZP

value: hippocampus


title: DZP cerebral cortex, replicate1 (gene-level)

source_name: DZP, brain, cerebral cortex

value: cerebral cortex


title: DZP amygdala, replicate1 (gene-level)

source_name: DZP, brain, amygdala


title: DZP amygdala, replicate3 (gene-level)


title: control amygdala, replicate3 (gene-level)


title: control cerebral cortex, replicate3 (gene-level)

source_name: control, brain, cerebral cortex


title: control hippocampus, replicate3 (gene-level)

source_name: control, brain, hippocampus


title: DZP amygdala, replicate2 (gene-level)


title: control hippocampus, replicate2 (gene-level)


title: control cerebral cortex, replicate1 (gene-level)


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

label: Biotin

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male C57BL/6 mice (Harlan, Horst, The Netherlands), weighing approximately 20 g, were individually housed one week before start of the experiment. Mice were maintained on a 12 hour light:12 hour dark cycle in a climate-controlled room (21±1 0C). Standard diet (RMH-B, Arie Blok B.V, Woerden, The Netherlands) was available ad libitum during the entire experiment from one hour prior to dark phase until start of the light phase. Water was freely available 24 hours a day. Food intake, water intake and body weight were monitored daily from one week prior to the end of the experiment.

extract_protocol: Total RNA from the hypothalamus was isolated by using RNeasy Lipid tissue kit (Qiagen, Venlo, The Netherlands). RNA concentrations were measured by absorbance at 260 nm (Nanodrop). RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice were injected intraperitoneally (ip) with 50ul of saline (vehicle) (G-Biosciences, St.Louis, USA), TNFα (Peprotech, London, UK), IL-6 (Peprotech, London, UK), or both TNFα and IL-6. The study included 6 groups: Control, TNFα, IL-6 Low, IL-6 High, TNFα + IL-6 Low and TNFα + IL-6 High. Each group included 12 mice, of which 6 mice were used for determination of hypothalamic metabolites and 6 mice were used for hypothalamic gene expression analysis. Mice were injected one hour prior to the dark phase. Five hours after injection, blood was collected by cardiac puncture under general anaesthesia. After sacrifice, brain, hypothalamus and organs were weighted, and frozen in liquid nitrogen and stored at -80C.

tag: strain/background

value: hypothalamus

tag: treatment

value: TNFa+IL6 high


title: DZP cerebral cortex, replicate2 (gene-level)


title: DZP cerebral cortex, replicate3 (gene-level)


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 6

value: TNFa+IL6 low


title: hypothalamus, IL6 low, replicate 6

source_name: hypothalamus, IL6 low

value: IL6 low


title: DZP hippocampus, replicate3 (gene-level)


title: DZP hippocampus, replicate1 (gene-level)


title: hypothalamus, IL6 high, replicate 6

source_name: hypothalamus, IL6 high

value: IL6 high


title: control amygdala, replicate2 (gene-level)


title: control cerebral cortex, replicate2 (gene-level)


title: control hippocampus, replicate1 (gene-level)


title: Heart-ISO+IgG-rep1

type: protein

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

country: China

institute: Peking University Third Hospital

hyb_protocol: Antibody arrays were used according to the manufacturer’s instructions. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with HRP-conjugated streptavidin.

scan_protocol: Expose to x-ray film and detect signal using film developer or detect signal directly from membrane using chemiluminescene imaging system.

data_processing:
By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared.
IPP6.0 software computed normalized signal intensity

molecule: protein

source_name: heart, IgG at ISO 1hr

label_protocol: Samples were labeled according to the manufacturer’s instructions

extract_protocol: Weigh out tissue and cut into cubes. Prepare protein extraction reagent containing inhibitors. Add ice-cold Protein Extraction Reagent containing protease inhibitors. Grind in a blender on low power using 30-second bursts until fully homogenized. Allow material to cool for 1 minute between bursts. Centrifuge the lysate at 14,000xg for 15 minutes and transfer the supernatant to a new tube for further analysis.

treatment_protocol: Mice were subcutaneous injected with a single dose of  isoproterenol (ISO, 5 mg/kg body weight) or vehicle saline (10 ml/kg body weight). Hearts were harvested and immediately frozen in liquid nitrogen.

value: 10 weeks old

tag: Sex

value: Male

value: Heart


title: Heart-ISO+IL-18 nAbs-rep4

source_name: heart, IL18 nAbs at ISO 1hr


title: hypothalamus, TNFa low, replicate 6

source_name: hypothalamus, TNFa low

value: TNFa low


title: Heart-ISO+IL-18 nAbs-rep3


title: Heart-ISO+IL-18 nAbs-rep2


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 5

value: male


title: Heart-ISO+IL-18 nAbs-rep1


title: Heart-ISO-rep4

source_name: heart, ISO, 24hrs


title: hypothalamus, IL6 low, replicate 5


title: hypothalamus, IL6 high, replicate 5


title: Heart-ISO-rep3


title: hypothalamus, TNFa low, replicate 5


title: Heart-ISO-rep2


title: Heart-ISO+IgG-rep4


title: Heart-ISO-rep1


title: Heart-Vehicle-rep4

source_name: heart, vehicle


title: Heart-Vehicle-rep3


title: hypothalamus, control, replicate 5

source_name: hypothalamus, control

value: saline (vehicle)


title: Heart-Vehicle-rep2


title: Heart-ISO+IgG-rep3


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 4


title: Heart-Vehicle-rep1


title: Heart-ISO+IgG-rep2


title: hypothalamus, IL6 low, replicate 4


title: hypothalamus, TNFa low, replicate 4


title: hypothalamus, control, replicate 6


title: hypothalamus, IL6 high, replicate 4


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 3


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 4


title: hypothalamus, control, replicate 4


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 5


title: hypothalamus, IL6 high, replicate 3


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 3


title: hypothalamus, TNFa low, replicate 3


title: hypothalamus, IL6 low, replicate 3


title: hypothalamus, TNFa low, replicate 2


title: hypothalamus, control, replicate 3


title: hypothalamus, control, replicate 2


title: hypothalamus, IL6 low, replicate 2


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 2


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 2


title: hypothalamus, control, replicate 1


title: hypothalamus, combination 1 (TNF+IL6 low), replicate 1


title: hypothalamus, IL6 high, replicate 2


title: hypothalamus, TNFa low, replicate 1


title: HCT116 5aza Treated 2

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

country: USA

institute: University of Texas Southwestern

description: Gene expression data from 5-aza-2'-deoxycytidine treated HCT116 cells

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays.

scan_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control (RMA normalization).

organism: Homo sapiens

source_name: HCT116 cells treated with 5-aza-2'-deoxycytidine

label_protocol: The WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.

growth_protocol: HCT116 cells were grown in DMEM (Gibco) and split 1:3 every two days.

extract_protocol: Total RNA was isolated using Sigma GenElute RNA Isolation Kit

treatment_protocol: HCT116 cells were seeded in 10cm tissue culture dish at a 30% target density. Twenty four hours post seeding, media was replaced with 1μM 5-aza-2'-deoxycytidine. Forty eight hours post 5-aza-2'-deoxycytidine treatment, the cells were retreated. Seventy-two hours post 5-aza-2'-deoxycytidine treatment, total RNA was isolated from vehicle and 5-aza-2'-deoxycytidine treated cells.

tag: tumor-derived cell line

value: 5-aza-2'-deoxycytidine for 72 hours


title: BM-CD138+, diagnosis, rep1 [MM_90; re-analysis2]

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: re-analysis of GSM1401624

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model. (www.dchip.org, Li and Wong, 2001).

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

label_protocol: Samples with at least 30ng/uL RNA were labelled for gene expression profiling, using the Affymetrix One-cycle Gene Chip microarray system, according to the standard Affymetrix procedures.

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

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). B cell fractions were isolated both from mononuclear bone marrow and peripheral blood cells, obtained by Ficoll-Hypaque density gradient centrifugation using B-cell isolation kit on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). All cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: disease state

value: Multiple Myeloma

tag: cell type

value: BM-CD138+ cell fraction

tag: hh cluster


title: HCT116 5aza Treated 1


title: hypothalamus, combination 2 (TNF+IL6 high), replicate 1


title: HCT116 Vehicle Treated 1

description: Gene expression data from vehicle treated HCT116 cells

source_name: HCT116 cells treated with vehicle

value: vehicle


title: hypothalamus, IL6 low, replicate 1


title: hypothalamus, IL6 high, replicate 1


title: HCT116 Vehicle Treated 2


title: BM-CD138+, diagnosis, rep1 [MM_93; re-analysis2]

description: re-analysis of GSM1401627

value: test set (2)


title: BM-CD138+, diagnosis, rep1 [MM_98; re-analysis2]

description: re-analysis of GSM1401632


title: BM-CD138+, diagnosis, rep1 [MM_95; re-analysis2]

description: re-analysis of GSM1401629

value: test set (1)


title: BM-CD138+, diagnosis, rep1 [MM_91; re-analysis2]

description: re-analysis of GSM1401625


title: BM-CD138+, diagnosis, rep1 [MM_94; re-analysis2]

description: re-analysis of GSM1401628


title: BM-CD138+, diagnosis, rep1 [MM_88; re-analysis2]

description: re-analysis of GSM1401622


title: BM-CD138+, diagnosis, rep1 [MM_99; re-analysis]

description: re-analysis of GSM1684864


title: BM-CD138+, diagnosis, rep1 [MM_97; re-analysis2]

description: re-analysis of GSM1401631


title: BM-CD138+, diagnosis, rep1 [MM_96; re-analysis2]

description: re-analysis of GSM1401630


title: BM-CD138+, diagnosis, rep1 [MM_89; re-analysis2]

description: re-analysis of GSM1401623


title: BM-CD138+, diagnosis, rep1 [MM_92; re-analysis2]

description: re-analysis of GSM1401626


title: BM-CD138+, diagnosis, rep1 [MM_85; re-analysis2]

description: re-analysis of GSM1401620


title: BM-CD138+, diagnosis, rep1 [MM_86; re-analysis2]

description: re-analysis of GSM1401621


title: BM-CD138+, diagnosis, rep1 [MM_59; re-analysis2]

description: re-analysis of GSM1401617


title: BM-CD138+, diagnosis, rep1 [MM_83; re-analysis2]

description: re-analysis of GSM1401619


title: BM-CD138+, diagnosis, rep1 [MM_57; re-analysis2]

description: re-analysis of GSM1401615


title: BM-CD138+, diagnosis, rep1 [MM_55; re-analysis2]

description: re-analysis of GSM1401613


title: CeO2 treated roots, biological rep2

city: Bethesda

first: Laxminath

last: Tumburu

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

description: Gene expression data from 29 days old roots exposed to CeO2

hyb_protocol: Following fragmentation, quality of cRNA was evaluated on 2100 bionanalyzer, and  hybridized for overnight at 45°C to Affymetrix ATH1 GeneChips in an Affymetrix Model 640 GeneChip hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were washed and stained using an Affymetrix 450 fluidics station as per the manufacturer and then scanned on an Affymetrix Model 3000 scanner

data_processing: Raw scanning data files (Affymetrix.cel) were obtained using Affymetrix GeneChip Operating Software, v1.4, and then files were analyzed by Bioconductor SimpleAffy to assess data quality.  Data were normalized by quantile normalization and gene calls were generated using a robust multichip average algorithm.

organism: Arabidopsis thaliana

source_name: Arabidopsis plant, 29 day old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana wild-type ecotype Columbia (Col-0) seeds (Lehle Seeds) were surface-sterilized with 70 % (v/v) ethanol, further sterilized in 50 % (v/v) household bleach, and then washed four times with sterile water.  Seeds were stratified (4 °C for 8 h) and then placed on the surface of Arabidopsis potting media (PM-15-13, Lehle Seeds) contained in pots (5.7 cm diameter; 5.7 cm height). Pots were kept in a growth chamber for seed germination and plant growth (22 °C, light 100 μmol m-2 s-1, photoperiod 16 h/8 h light/dark).

extract_protocol: TRIzol®  extraction of total RNA was performed according to the manufacturer's (Life Technlogies, Inc) instructions.

treatment_protocol: For microarray analysis (n=3), nanoparticle suspensions were prepared at 0 (control) and 500 mg ENPs L-1 using 0.1 M KCl and millipore water, for nano-titania and nano-ceria, respectively.  Suspensions were indirectly sonicated for 30 min. The pH was adjusted to 5.4.  Mean physical particle sizes in stock suspensions and diluted suspensions were similar to (nano-titania) or smaller than (nano-ceria) sizes indicated by the manufacturer.  In all cases, particle sizes ranged from approximately10 nm to a small cohort exceeding 50 nm. For microarray analysis (n=3), plants were exposed by watering from above with control solution or the ENP treatment suspensions twice during the seed germination stage (Day 0-4) and for a third time during the primary rosette stage (Day 17).

tag: ecotype

value: Columbia (Col-0)

value: 29 days old

value: roots


title: BM-CD138+, diagnosis, rep1 [MM_56; re-analysis2]

description: re-analysis of GSM1401614


title: BM-CD138+, diagnosis, rep1 [MM_72; re-analysis2]

description: re-analysis of GSM1401618


title: Millipore Water treated roots, biological rep3

description: Gene expression data from 29 days old roots exposed to millipore water


title: CeO2 treated roots, biological rep1


title: Millipore Water treated roots, biological rep2


title: BM-CD138+, diagnosis, rep1 [MM_48; re-analysis2]

description: re-analysis of GSM1401610


title: CeO2 treated roots, biological rep3


title: BM-CD138+, diagnosis, rep1 [MM_44; re-analysis2]

description: re-analysis of GSM1401606


title: BM-CD138+, diagnosis, rep1 [MM_41; re-analysis2]

description: re-analysis of GSM1401603


title: BM-CD138+, diagnosis, rep1 [MM_40; re-analysis2]

description: re-analysis of GSM1401602


title: BM-CD138+, diagnosis, rep1 [MM_42; re-analysis2]

description: re-analysis of GSM1401604


title: Millipore Water treated roots, biological rep1


title: BM-CD138+, diagnosis, rep1 [MM_50; re-analysis2]

description: re-analysis of GSM1401612


title: BM-CD138+, diagnosis, rep1 [MM_38; re-analysis2]

description: re-analysis of GSM1401600


title: BM-CD138+, diagnosis, rep1 [MM_43; re-analysis2]

description: re-analysis of GSM1401605


title: BM-CD138+, diagnosis, rep1 [MM_47; re-analysis2]

description: re-analysis of GSM1401609


title: BM-CD138+, diagnosis, rep1 [MM_39; re-analysis2]

description: re-analysis of GSM1401601


title: BM-CD138+, diagnosis, rep1 [MM_37; re-analysis2]

description: re-analysis of GSM1401599


title: BM-CD138+, diagnosis, rep1 [MM_49; re-analysis2]

description: re-analysis of GSM1401611


title: BM-CD138+, diagnosis, rep1 [MM_36; re-analysis2]

description: re-analysis of GSM1401598


title: BM-CD138+, diagnosis, rep1 [MM_34; re-analysis2]

description: re-analysis of GSM1401596


title: BM-CD138+, diagnosis, rep1 [MM_35; re-analysis2]

description: re-analysis of GSM1401597


title: BM-CD138+, diagnosis, rep1 [MM_32; re-analysis2]

description: re-analysis of GSM1401594


title: BM-CD138+, diagnosis, rep1 [MM_33; re-analysis2]

description: re-analysis of GSM1401595


title: CeO2 treated rosette Leaves, biological rep2

description: Gene expression data from 29 days old rosette leaves exposed to CeO2

value: rosette leaves


title: Millipore Water treated rosette leaves, biological rep3

description: Gene expression data from 29 days old rosette leaves exposed to millipore water


title: TiO2 treated roots, biological rep3

description: Gene expression data from 29 days old roots exposed to 500mg/L TiO2


title: CeO2 treated rosette Leaves, biological rep3


title: CeO2 treated rosette Leaves, biological rep1


title: BM-CD138+, diagnosis, rep1 [MM_21; re-analysis2]

description: re-analysis of GSM1401589


title: BM-CD138+, diagnosis, rep1 [MM_28; re-analysis2]

description: re-analysis of GSM1401591


title: Millipore Water treated rosette leaves, biological rep2


title: BM-CD138+, diagnosis, rep1 [MM_30; re-analysis2]

description: re-analysis of GSM1401592


title: BM-CD138+, diagnosis, rep1 [MM_168; re-analysis2]

description: re-analysis of GSM1401586


title: TiO2 treated roots, biological rep2


title: BM-CD138+, diagnosis, rep1 [MM_22; re-analysis2]

description: re-analysis of GSM1401590


title: BM-CD138+, diagnosis, rep1 [MM_20; re-analysis2]

description: re-analysis of GSM1401588


title: BM-CD138+, diagnosis, rep1 [MM_19; re-analysis2]

description: re-analysis of GSM1401587


title: Millipore Water treated rosette leaves, biological rep1


title: TiO2 treated roots, biological rep1


title: BM-CD138+, diagnosis, rep1 [MM_164; re-analysis2]

description: re-analysis of GSM1401582


title: BM-CD138+, diagnosis, rep1 [MM_31; re-analysis2]

description: re-analysis of GSM1401593


title: BM-CD138+, diagnosis, rep1 [MM_165; re-analysis2]

description: re-analysis of GSM1401583


title: BM-CD138+, diagnosis, rep1 [MM_163; re-analysis2]

description: re-analysis of GSM1401581


title: BM-CD138+, diagnosis, rep1 [MM_167; re-analysis2]

description: re-analysis of GSM1401585


title: BM-CD138+, diagnosis, rep1 [MM_166; re-analysis2]

description: re-analysis of GSM1401584


title: KCl treated roots, biological rep3

description: Gene expression data from 29 days old roots exposed to 0.1mM KCl


title: BM-CD138+, diagnosis, rep1 [MM_162; re-analysis2]

description: re-analysis of GSM1401580


title: skn7∆_untreated (kc024)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description:
kc024
gene expression in untreated cells of skn7∆

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

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift. Gene based analysis was performed.

organism: Saccharomyces cerevisiae

source_name: skn7∆ cells

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

growth_protocol: Cells from overnight culture in YPD were innoculated at 0.1 OD in YPDcand grown upto OD ~0.4   at 30°C with 200rpm ; for the treated samples, 5mM DTT treatment was given. The untreated (control) and the DTT-treated were both kept at static 30°C for 3 hrs following treatment. Cells were harvested, stored in RNA later and shipped to Genotypic.

extract_protocol: Samples are subjected to RNA extraction , quality check and sample preparation for microarray by Genotypic

treatment_protocol: 5mM Dithiothretol (DTT) was given to the samples marked treated

tag: mating type

value: Mat α

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ026

tag: genotype/variation

value: untreated


title: BM-CD138+, diagnosis, rep1 [MM_156; re-analysis2]

description: re-analysis of GSM1401574


title: skn7∆_treated (kc019)

description:
kc019
skn7∆_treated with 5mM DTT for 3 hrs

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ025

value: DTT


title: BM-CD138+, diagnosis, rep1 [MM_161; re-analysis2]

description: re-analysis of GSM1401579


title: BM-CD138+, diagnosis, rep1 [MM_159; re-analysis2]

description: re-analysis of GSM1401577


title: KCl treated roots, biological rep2


title: KCl treated roots, biological rep1


title: TiO2 treated rosette Leaves, biological rep2

description: Gene expression data from 29 days old rosette leaves exposed to 500mg/L TiO2


title: BM-CD138+, diagnosis, rep1 [MM_158; re-analysis2]

description: re-analysis of GSM1401576


title: TiO2 treated rosette Leaves, biological rep3


title: skn7∆_untreated_repeat (kc014)

description:
kc014
gene expression in untreated cells of skn7∆

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ024


title: BM-CD138+, diagnosis, rep1 [MM_160; re-analysis2]

description: re-analysis of GSM1401578


title: BM-CD138+, diagnosis, rep1 [MM_152; re-analysis2]

description: re-analysis of GSM1401570


title: BM-CD138+, diagnosis, rep1 [MM_153; re-analysis2]

description: re-analysis of GSM1401571


title: BM-CD138+, diagnosis, rep1 [MM_155; re-analysis2]

description: re-analysis of GSM1401573


title: KCl treated rosette leaves, biological rep3

description: Gene expression data from 29 days old rosette leaves exposed to 0.1mM KCl


title: BM-CD138+, diagnosis, rep1 [MM_154; re-analysis2]

description: re-analysis of GSM1401572


title: BM-CD138+, diagnosis, rep1 [MM_157; re-analysis2]

description: re-analysis of GSM1401575


title: KCl treated rosette leaves, biological rep1


title: KCl treated rosette leaves, biological rep2


title: BM-CD138+, diagnosis, rep1 [MM_15; re-analysis2]

description: re-analysis of GSM1401567


title: BM-CD138+, diagnosis, rep1 [MM_149; re-analysis2]

description: re-analysis of GSM1401566


title: BM-CD138+, diagnosis, rep1 [MM_150; re-analysis2]

description: re-analysis of GSM1401568


title: TiO2 treated rosette Leaves, biological rep1


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #334]

type: genomic

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: The array image was acquired using Affymetrix Command Console, version 4.0. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping Console, version 4.0, software. Nexus, version 7.5 (BioDiscovery) was employed to perform CNAs comparisons; inferred copy number states were derived from segmentation algorithm implemented in Nexus.

molecule: genomic DNA

source_name: CD138+ cell fractions obtained from MM patients' BM

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from CD138+ plasma cells obtained from bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: patient id

value: MM patient #334

tag: tumor stage

value: diagnosis

value: mononuclear bone marrow cells

tag: cell subtype

value: CD138+ cell fractions


title: BM-CD138+, diagnosis, rep1 [MM_151; re-analysis2]

description: re-analysis of GSM1401569

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: 35sSIX4 roots, Fusarium treatment, replicate 4

city: Floreat

first: Louise

middle: Faye

last: Thatcher

state: WA

address: 147 Underwood Ave

department: Agriculture and Food

country: Australia

institute: CSIRO

description: Expression data from 35sSIX4 roots harvested 4 days post Fusarium inoculation.

hyb_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.

data_processing: The data was analyzed using GenespringGX 7.3.1. The raw CEL files were pre-processed using the RMA algorithm and the resulting expression values were normalized per chip to the median across all chips.

source_name: Root tissue from 4 week old Arabidopsis thaliana plants

growth_protocol: Plants were grown under short day conditions (8hrs light, 24C and 21C day night cycle) in plastic trays (20 cells) with one plant per cell for 4 weeks before treatment.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manfacturer's instructions.

treatment_protocol: Treatment involved lifting plants and rinsing off soil, placing roots in a spore suspension (1x106 spores/ml) for 1 minute, replanting, and covering tray with a clear plastic dome to maintain humidity. Plants were transferred to long  day conditions (16hrs light) at 28C. Samples were harvested after 4 days post inoculation.

value: Col-0 (35sSIX4)

tag: age

value: 4 week old

tag: inoculation

value: Fusarium


title: BM-CD138+, diagnosis, rep1 [MM_147; re-analysis2]

description: re-analysis of GSM1401564

value: test set (1)


title: WT_untreated (kc018)

description:
kc018
gene expression in untreated cells of  WT cells

source_name: WT

tag: strain

value: background strain is yMJ003

value: WT

tag: agent


title: sse2∆_untreated (kc015)

description:
kc015
gene expression in untreated cells of sse2∆

source_name: sse2∆ cells

value: Mat α

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ012


title: skn7∆_treated_repeat (KC002)

description:
KC002
skn7∆_treated with 5mM DTT for 3 hrs

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ019


title: 35sSIX4 roots, Fusarium treatment, replicate 3

scan_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.


title: WT_untreated (kc013)

description:
kc013
gene expression in untreated cells WT cells

value: untreated


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #429]

value: MM patient #429


title: BM-CD138+, diagnosis, rep1 [MM_146; re-analysis2]

description: re-analysis of GSM1401563


title: BM-CD138+, diagnosis, rep1 [MM_145; re-analysis2]

description: re-analysis of GSM1401562


title: BM-CD138+, diagnosis, rep1 [MM_143; re-analysis2]

description: re-analysis of GSM1401560


title: yap1∆_treated (KC023)

description:
KC023
yap1∆ treated with 5mM DTT

source_name: yap1∆ cells

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ018

value: DTT


title: sse2∆_treated_repeat (kc020)

description:
kc020
sse2∆ treated with 5mM DTT

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ015


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #174]

value: MM patient #174

value: diagnosis

value: mononuclear bone marrow cells

value: CD138+ cell fractions


title: BM-CD138+, diagnosis, rep1 [MM_148; re-analysis2]

description: re-analysis of GSM1401565

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: yap1∆_untreated_repeat (KC021)

description:
KC021
yap1∆ untreated after 6 hs of growth

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ016


title: 35sSIX4 roots, Fusarium treatment, replicate 2

label_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.

value: Col-0 (35sSIX4)

value: 4 week old

value: Fusarium


title: BM-CD138+, diagnosis, rep1 [MM_144; re-analysis2]

description: re-analysis of GSM1401561

value: test set (1)


title: Col-0 roots, Fusarium treatment, replicate 2

description: Expression data from Col-0 roots harvested 4 days post Fusarium inoculation.


title: Vma13∆_treated (kc016)

description:
kc016
vma13v treated with 5mM DTT

source_name: vma13∆ cells

value: Mat α

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ013


title: Col-0 roots, Fusarium treatment, replicate 4


title: Col-0 roots, Fusarium treatment, replicate 1


title: BM-CD138+, diagnosis, rep1 [MM_142; re-analysis2]

description: re-analysis of GSM1401559


title: daf-2_15deg_then_25deg(12hr)_(1)

city: Kobe

first: Atsushi

last: Kuhara

state: Hyogo

address: Okamoto8-9-1, Higashinada-ku

department: Biology,  Faculty of Science and Engineering

institute: Konan University

description: Gene expression cultivated at 25-degree for 12 hours after 15-degree in daf-2 adult

hyb_protocol: Each 1.65 μg cRNA was hybridized using a gene expression hybridization kit (Agilent; 5188-5242) to a C. elegans oligo DNA microarray (Ver2.0) (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one-color scan setting for 4×44 array slides (scan area 61×21.6 mm, scan resolution 5 μm, dye channel set to green PMT 100%).

data_processing: Data were analyzed using GeneSpring software. Data were normalized with the global normalization method. Scaling factor (SF), calculated as the mean of each array is adjusted to 2500. We performed three complete repetitions of culturing and microarray experiments.

organism: Caenorhabditis elegans

source_name: daf-2(e1370) mutant adults, 25-degree cultivated for 12 hours after 15-degree cultivated, replicate 1

label_protocol: Cy3-labeled cRNA was amplified using 100 ng aliquots of total RNA and the Low Input Quick Amp Labeling Kit (Agilent; 5190-2305).

growth_protocol: According to standard C. elegans culture methods, worms were grown with uncrowded and well-fed conditions until adult worms at disignated temperature

extract_protocol: Total RNA was isolated using RNeasy Mini kit(Qiagen; 74104) according to manufacturer’s instructions.

treatment_protocol: temperature changes only

tag: cultivated temperature

value: 25 degree for 12 hours after 15 degree grown


title: BM-CD138+, diagnosis, rep1 [MM_140; re-analysis2]

description: re-analysis of GSM1401557


title: Col-0 roots, Fusarium treatment, replicate 3


title: 35sSIX4 roots, Fusarium treatment, replicate 1


title: yap1∆_untreated (KC010)

description:
KC010
gene expression in untreated cells of yap1 ∆

value: background strain is yMJ003; contains RFP under Tef2 promoter, GFP under UPRE

value: untreated


title: sse2∆_treated (kc012)

description:
kc012
sse2∆ treated with 5mM DTT

value: DTT


title: Vma13∆_untreated_repeat (kc011)

description:
kc011
gene expression in untreated cells of vma13∆


title: WT_treated  (kc005)

description:
kc005
gene expression in WT cells treated with 5mM DTT

value: background strain is yMJ003

value: WT


title: BM-CD138+, diagnosis, rep1 [MM_14; re-analysis2]

description: re-analysis of GSM1401556


title: BM-CD138+, diagnosis, rep1 [MM_141; re-analysis2]

description: re-analysis of GSM1401558


title: MNDA-2xFV AP1 12h

city: Seattle

first: Daniel

middle: B

last: Stetson

address: 750 Republican St

department: Immunology

institute: University of Washington

description: replicate 1

hyb_protocol: Biotin-labelled cRNA was hybridized using the standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using an Illumina HiScan scanner.

data_processing: Data were normalized using quantile normalization with Illumina Genome Studio software

source_name: THP-1 cells

label_protocol: Biotin-labelled cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: THP1 cells were cultured in complete RPMI per standard protocol.

extract_protocol: Cells were harvested with RNA Stat60 (TelTest) and RNA was isolated per manufacturer’s instructions. To improve RNA quality, isolated RNA was then purified using the RNeasy kit (Qiagen) per manufacturers instructions.

treatment_protocol: THP1 cells were differentiated with PMA and seeded at a density of 3x10^5 cells per well in a 12-well plate; cells were treated with vehicle or 30nM AP1 (Clontech, also called ‘B/B Homodimerizer’) for 4 or 12 hours.

tag: treatment

value: AP1 dimerizer drug (12h)


title: N2_15deg_(1)

description: Gene expression cultivated at 15-degree in N2 adult

source_name: N2 adults, 15-degree cultivated, replicate 1

value: N2, Bristol

value: 15 degree


title: N2_15deg_then_25deg(12hr)_(1)

description: Gene expression cultivated at 25-degree for 12 hours after 15-degree in N2 adult

source_name: N2 adults, 25-degree cultivated for 12 hours after 15-degree cultivated, replicate 1


title: BM-CD138+, diagnosis, rep1 [MM_139; re-analysis2]

description: re-analysis of GSM1401555

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: Vma13∆_treated_repeat (KC008)

description:
KC008
gene expression in vma13v treated with 5mM DTT


title: PYHIN1-2xFV AP1 12h

description: replicate 1


title: yap1∆_treated_repeat (KC006)

description:
KC006
gene expression in yap1∆ treated with 5mM DTT


title: N2_15deg_then_25deg(3hr)_(1)

description: Gene expression cultivated at 25-degree for 3 hours after 15-degree in N2 adult

source_name: N2 adults, 25-degree cultivated for 3 hours after 15-degree cultivated, replicate 1

value: 25 degree for 3 hours after 15 degree grown


title: BM-CD138+, diagnosis, rep1 [MM_136; re-analysis2]

description: re-analysis of GSM1401552


title: IFI16-2xFV AP1 4h

description: replicate 1

value: AP1 dimerizer drug (4h)


title: N2_15deg_then_25deg(3hr)_(B)

source_name: N2 adults, 25-degree cultivated for 3 hours after 15-degree cultivated, replicate 2


title: Vma13∆_untreated (kc001)

description:
kc001
gene expression in untreated cells of vma13∆

value: contains RFP under Tef2 promoter, GFP under UPRE; background strain is yMJ003


title: daf-2_15deg_then_25deg(12hr)_(B)

source_name: daf-2(e1370) mutant adults, 25-degree cultivated for 12 hours after 15-degree cultivated, replicate 2


title: N2_15deg_(B)

source_name: N2 adults, 15-degree cultivated, replicate 2


title: N2_15deg_then_25deg(12hr)_(B)

source_name: N2 adults, 25-degree cultivated for 12 hours after 15-degree cultivated, replicate 2


title: sse2∆_untreated_repeat (KC004)

description:
KC004
gene expression in untreated cells of sse2∆


title: BM-CD138+, diagnosis, rep1 [MM_137; re-analysis2]

description: re-analysis of GSM1401553

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

value: test set (1)


title: BM-CD138+, diagnosis, rep1 [MM_135; re-analysis2]

description: re-analysis of GSM1401551


title: IFI16-2xFV AP1 12h

description: replicate 1


title: BFP AP1 12h

description: replicate 1


title: BM-CD138+, diagnosis, rep1 [MM_138; re-analysis2]

description: re-analysis of GSM1401554


title: BFP AP1 4h

description: replicate 1


title: N2_15deg_then_25deg(12hr)_(A)


title: Col-0_3_NO_180min_ctrl

city: Stuttgart

first: Jochen

last: Menz

address: Fruwirthstr. 20

department: Institute of Crop Science

country: Germany

institute: University of Hohenheim

description: Control, treated like -N but transferred to NO3--containing medium

data_processing: Raw data were analyzed with Limma (Smyth, 2005) package of in BioConductor for R. Within limma, data were background corrected with normexp function (offset=16) and quantile-normalized. Probes not at least 10 % brighter than negative-control probes were filtered. Differentially expressed genes were identified with eBayes function of limma.

source_name: root, Col-0, rep. 3, Nitrate, 180min ctrl

label_protocol: Conducted by OakLabs GmbH, Henningsdorf, Germany: 1st strand synthesis with oligo-dT Primer from 50 ng RNA. Approx. 5 µg cRNA derived, Approx. 17 pMol/µg Cy3 incorporated.

growth_protocol: Arabidopsis plants were grown 35 days hydroponically (Hoagland nutrient solution) under short day conditions (10h/22°C day, 14h/18°C night). After germination, 30 days on 1.5 mM NH4NO3 as N-source, last 5 days on 3 mM KNO3 or 1.5mM (NH4)2SO4, respectively.

extract_protocol: Frozen root material was ground. Out of approx. 100 mg per root sample RNA was extracted  with innuPREP Plant RNA Kit (Analytik Jena, Germany).

treatment_protocol: adult Nitrate/Ammonium adapted plants were transferred to N-depleted nutrient solution. Roots were harvested after 0 min, 15 min and 180 min in N-depleted nutrient solution. Roots of 6 plants were pooled, quickly rinsed, dried on paper towels and instantly frozen in liquid N2.

tag: tissue

value: root

tag: pre-treatment

value: Nitrate

tag: time in n-depletion

value: 180 min

value: moved to +N (NO3-)

tag: replicate


title: MNDA-2xFV Mock

description: replicate 1

value: Mock


title: BM-CD138+, diagnosis, rep1 [MM_134; re-analysis2]

description: re-analysis of GSM1401550

tag: disease state

tag: cell type

tag: hh cluster


title: BM-CD138+, diagnosis, rep1 [MM_132; re-analysis2]

description: re-analysis of GSM1401548


title: Col-0_3_NO_15min_ctrl

hyb_protocol: Conducted by OakLabs GmbH, Henningsdorf, Germany

source_name: root, Col-0, rep. 3, Nitrate, 15min ctrl

tag: ecotype

value: 15 min


title: PYHIN1-2xFV Mock

description: replicate 1


title: Col-0_2_NO_15min_ctrl

scan_protocol: Conducted by OakLabs GmbH, Henningsdorf, Germany

source_name: root, Col-0, rep. 2, Nitrate, 15min ctrl


title: N2_15deg_then_25deg(3hr)_(A)


title: BM-CD138+, diagnosis, rep1 [MM_133; re-analysis2]

description: re-analysis of GSM1401549


title: MNDA-2xFV AP1 4h

description: replicate 1


title: BM-CD138+, diagnosis, rep1 [MM_131; re-analysis2]

description: re-analysis of GSM1401547


title: BM-CD138+, diagnosis, rep1 [MM_130; re-analysis2]

description: re-analysis of GSM1401546


title: daf-2_15deg_then_25deg(12hr)_(A)

value: 25 degree for 12 hours after 15 degree grown


title: N2_15deg_(A)


title: IFI16-2xFV Mock

description: replicate 1


title: PYHIN1-2xFV AP1 4h

description: replicate 1


title: Col-0_3_NO_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 3, Nitrate, 180min

value: moved to -N


title: BM-CD138+, diagnosis, rep1 [MM_13; re-analysis2]

description: re-analysis of GSM1401545


title: BFP Mock

description: replicate 1


title: Col-0_1_NO_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 1, Nitrate, 180min


title: Col-0_2_NO_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 2, Nitrate, 180min


title: BM-CD138+, diagnosis, rep1 [MM_126; re-analysis2]

description: re-analysis of GSM1401542


title: Col-0_3_NO_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 3, Nitrate, 15min


title: BM-CD138+, diagnosis, rep1 [MM_128; re-analysis2]

description: re-analysis of GSM1401543


title: Col-0_1_NO_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 1, Nitrate, 15min


title: HUVEC + KSHV

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: Human umbilical vein endothelial cells (HUVEC)

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: The cells were maintained in DMEM/F-12 50/50 medium (Cellgro) supplemented with 5% FBS. All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: The cells were infected by KSHV (MOI=10) or transduced with the recombinant  adenoviral vector for 48 h

value: KSHV-infected cells

value: HUVEC


title: BM-CD138+, diagnosis, rep1 [MM_129; re-analysis2]

description: re-analysis of GSM1401544


title: HUVEC + Adv

value: AdV-control


title: HUVEC

value: mock cells


title: Col-0_2_NO_0min

source_name: root, Col-0, rep. 2, Nitrate, 0min

value: 0 min

value: harvested in +N (NO3-)


title: Col-0_1_NO_0min

source_name: root, Col-0, rep. 1, Nitrate, 0min


title: BM-CD138+, diagnosis, rep1 [MM_125; re-analysis2]

description: re-analysis of GSM1401541

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: Col-0_3_NO_0min

source_name: root, Col-0, rep. 3, Nitrate, 0min


title: BM-CD138+, diagnosis, rep1 [MM_121; re-analysis2]

description: re-analysis of GSM1401538


title: HUVEC + 147-Adv


title: BM-CD138+, diagnosis, rep1 [MM_123; re-analysis2]

description: re-analysis of GSM1401539


title: Col-0_2_NO_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 2, Nitrate, 15min


title: BM-CD138+, diagnosis, rep1 [MM_124; re-analysis2]

description: re-analysis of GSM1401540


title: BM-CD138+, diagnosis, rep1 [MM_120; re-analysis2]

description: re-analysis of GSM1401537


title: Col-0_3_NH_15min_ctrl

description: Control, treated like -N but transferred to NH4+-containing medium

source_name: root, Col-0, rep. 3, Ammonium, 15min ctrl

value: Ammonium

value: moved to +N (NH4+)


title: Col-0_3_NH_180min_ctrl

source_name: root, Col-0, rep. 3, Ammonium, 180min ctrl

value: root


title: BM-CD138+, diagnosis, rep1 [MM_118; re-analysis2]

description: re-analysis of GSM1401535


title: SK-N-Be(2)C-doxorubicin resistant 3

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

description:
replicate 3
bDR3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with bioconductor package lumi (v.2.13.3) in R (v.3.0.1).

source_name: SK-N-Be(2)C-doxorubicin resistant

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human neuroblastoma SK-N-Be(2)C cell lines were purchased from ATCC. Cells were grown in DMEM/F12 supplemented with 10% heat inactivated fetal bovine serum, penicillin 100 units/ml, and streptomycin 100µg/ml.

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

treatment_protocol:
Doxorubicin cell lines were generated by incubating the parental cells with stepwise concentrations of doxorubicin beginning 2 Log below the IC50. Cells were deemed resistant after surviving 5 passages in a concentration of drug approximately 2 Log above the IC50. The time course for this process occurred over 6-12 months and varied based on cell line doubling time.
Parallel cell lines, both wild type and wild type treated with doxorubicin, were intermittently exposed to the histone deacetylase inhibitor SAHA at their IC25 of SAHA at the time of each logarithmic increase in the dose of doxorubicin.

tag: cell line background

tag: tissue origin

value: bone marrow

value: human neuroblastoma cells

tag: genotype/variation

value: doxorubicin-resistant


title: Col-0_2_NH_15min_ctrl

source_name: root, Col-0, rep. 2, Ammonium, 15min ctrl

value: 15 min


title: SK-N-Be(2)C-doxorubicin resistant + treated with SAHA 3

description:
replicate 3
bDR+SAHA3

tag: treated with

value: histone deacetylase inhibitor SAHA


title: BM-CD138+, diagnosis, rep1 [MM_119; re-analysis2]

description: re-analysis of GSM1401536

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient


title: SK-N-Be(2)C-doxorubicin resistant + treated with SAHA 1

description:
replicate 1
bDR+SAHA1


title: SK-N-Be(2)C-doxorubicin resistant 2

description:
replicate 2
bDR2


title: SK-N-Be(2)C-doxorubicin resistant 1

description:
replicate 1
bDR1


title: Col-0_3_NH_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 3, Ammonium, 180min

value: 180 min

value: moved to -N


title: BM-CD138+, diagnosis, rep1 [MM_115; re-analysis2]

description: re-analysis of GSM1401533


title: Col-0_2_NH_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 2, Ammonium, 180min


title: BM-CD138+, diagnosis, rep1 [MM_117; re-analysis2]

description: re-analysis of GSM1401534


title: SK-N-Be(2)C-wild type treated with SAHA 2

description:
replicate 2
bWT+SAHA2

source_name: SK-N-Be(2)C-wild type treated with SAHA

value: wild type; parental


title: Col-0_1_NH_180min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 1, Ammonium, 180min


title: SK-N-Be(2)C-wild type treated with SAHA 3

description:
replicate 3
bWT+SAHA3


title: BM-CD138+, diagnosis, rep1 [MM_114; re-analysis2]

description: re-analysis of GSM1401532

value: test set (1)


title: Col-0_2_NH_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 2, Ammonium, 15min


title: Col-0_3_NH_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 3, Ammonium, 15min


title: SK-N-Be(2)C-doxorubicin resistant + treated with SAHA 2

description:
replicate 2
bDR+SAHA2


title: BM-CD138+, diagnosis, rep1 [MM_113; re-analysis2]

description: re-analysis of GSM1401531


title: BM-CD138+, diagnosis, rep1 [MM_111; re-analysis2]

description: re-analysis of GSM1401529


title: SK-N-Be(2)C-wild type treated with SAHA 1

description:
replicate 1
bWT+SAHA1


title: Col-0_1_NH_15min

description: transferred on N-depleted medium

source_name: root, Col-0, rep. 1, Ammonium, 15min


title: SK-N-Be(2)C-wild type 3

description:
replicate 3
bWT3

source_name: SK-N-Be(2)C-wild type


title: BM-CD138+, diagnosis, rep1 [MM_112; re-analysis2]

description: re-analysis of GSM1401530


title: Col-0_3_NH_0min

source_name: root, Col-0, rep. 3, Ammonium, 0min

value: harvested in +N (NH4+)


title: DZP amygdala, replicate3 (exon-level)

data_processing:
The data were analyzed with Expression Console version 1.4.1 (Affymetrix) using default settings for background correction, normalization and summarization.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0

source_name: DZP, brain, amygdala

tag: gender

value: male

value: 8 week-old

tag: age

value: DZP

value: brain

tag: tissue region

value: amygdala


title: BM-CD138+, diagnosis, rep1 [MM_110; re-analysis2]

description: re-analysis of GSM1401528

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: SK-N-Be(2)C-wild type 1

description:
replicate 1
bWT1

value: bone marrow


title: SK-N-Be(2)C-wild type 2

description:
replicate 2
bWT2

value: human neuroblastoma cells


title: Col-0_2_NH_0min

source_name: root, Col-0, rep. 2, Ammonium, 0min

value: root

value: Ammonium

value: 0 min


title: BM-CD138+, diagnosis, rep1 [MM_108; re-analysis2]

description: re-analysis of GSM1401527

value: test set (2)


title: Col-0_1_NH_0min

source_name: root, Col-0, rep. 1, Ammonium, 0min


title: SK-N-SH-doxorubicin resistant + treated with SAHA 2

description:
replicate 2
sDR+SAHA2

growth_protocol: Human neuroblastoma SK-N-SH cell lines were purchased from ATCC. Cells were grown in DMEM/F12 supplemented with 10% heat inactivated fetal bovine serum, penicillin 100 units/ml, and streptomycin 100µg/ml.

treatment_protocol:
Doxorubicin cell lines were generated by incubating the parental cells in stepwise concentrations of doxorubicin beginning 2 Log below the IC50. Cells were deemed resistant after surviving 5 passages in a concentration of drug approximately 2 Log above the IC50. The time course for this process occurred over 6-12 months and varied based on cell line doubling time.
Parallel cell lines, both wild type and wild type treated with doxorubicin, were intermittently exposed to the histone deacetylase inhibitor SAHA at their IC25 of SAHA at the time of each logarithmic increase in the dose of doxorubicin.

value: SK-N-SH

value: doxorubicin-resistant

value: histone deacetylase inhibitor SAHA


title: BM-CD138+, diagnosis, rep1 [MM_106; re-analysis2]

description: re-analysis of GSM1401525


title: BM-CD138+, diagnosis, rep1 [MM_105; re-analysis2]

description: re-analysis of GSM1401524


title: H37Rv detergent stimulon replicate 3

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Biological replicate 3 of 3

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: H37Rv detergent-grown

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Cultures were grown in minimal medium (MM) [KH2PO4 1 g/l, Na2HPO4 2.5 g/l, asparagine 0.5 g/l, ferric ammonium citrate 50 mg/l, MgSO4×7 H2O 0.5 g/l, CaCl2 0.5 mg/l, ZnSO4 0.1 mg/l, 0.1% (v/v) glycerol, and with or without Tyloxapol 0.05% (v/v; Sigma), pH 7.0]

extract_protocol: 10 ml mycobacterial cultures are pelleted and resuspended in 1ml Trizol and transferred to a Fast-Prep lysing matrix B tube. Tubes are processed in Fast-Prep apparatus for 45 seconds at 6.5 M per second then cooled on ice for 1 minute before debris is pelleted by centrifugation. RNA is then purified and sample is DNase-treated following Direct-zol kit manufacturer instructions.

treatment_protocol: M. tuberculosis was grown in MM with detergent for 6 days and then subcultured in fresh MM with or without detergent for 5 days.  Cultures were harvested when samples with detergent reached an OD600 nm= 0.3

tag: strain

source_name: H37Rv no detergent


title: BM-CD138+, diagnosis, rep1 [MM_107; re-analysis2]

description: re-analysis of GSM1401526


title: BM-CD138+, diagnosis, rep1 [MM_104; re-analysis2]

description: re-analysis of GSM1401523


title: SK-N-SH-doxorubicin resistant 3

description:
replicate 3
sDR3

source_name: SK-N-SH-doxorubicin resistant


title: SK-N-SH-doxorubicin resistant + treated with SAHA 3

description:
replicate 3
sDR+SAHA3


title: SK-N-SH-doxorubicin resistant + treated with SAHA 1

description:
replicate 1
sDR+SAHA1


title: SK-N-SH-doxorubicin resistant 2

description:
replicate 2
sDR2


title: Control DCs replicate 4

city: Sendai

first: Tohru

last: Fujiwara

address: 2-1 Seiryo-cho, Aoba-ku

department: Hematology and Rheumatology

institute: Tohoku University Graduate School of Medicine

description: Control DCs replicate 4

hyb_protocol: A sureprint G3 mouse GE microarray slide was used for hybridization according to the manufacturer's instructions(Agilent)

scan_protocol: After hybridization, slides were washed adequately and scanned immediately by using the Agilent DNA Microarray Scanner using one color scan setting

data_processing: Obtained scan data were analysed by using GeneSpring software (Agilent)

source_name: Control DC

label_protocol: Amplified samples were labeled with indocarbocyanine by using a Cy3 post-labeling reactive dye pack (Amersham)

growth_protocol: To induce DC differentiation from progenitors in vitro,  CMPs (5 × 10E3) were sorted from the BM of Gata2(f/f)/ER-Cre (CD45.2+) or Gata2(f/f) mice (CD45.2+). These progenitor cells were cocultured with BM feeder cells from SJL (CD45.1+) mice (1.5 × 105) in the presence of FLT3-L (200 ng/ml; 96-well culture plates).

extract_protocol: Total RNA was extracted from dendric cells in each condition by using Nucleospin® RNA XS (MACHEREY-NAGEL) and was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion)

treatment_protocol: Gata2(f/f) and Gata2(f/f)/ER-Cre mice were treated with tamoxifen on day 1,2,3,8,9,10. On day 20-22, CMP fractions were sorted and induced DC differeniation in vitro.

tag: strain background

value: Control

value: dendritic cell (DC)


title: H37Rv detergent stimulon replicate 2

description: Biological replicate 2 of 3


title: DZP amygdala, replicate2 (exon-level)

treatment_protocol: Male mice of 8-week old were subjected to intraperitoneal injection of INTRALIPID or 5 mg/ml DZP at 8:00 and 18:00 for 10 days.

value: male

tag: agent

value: 8 week-old

tag: tissue


title: H37Rv detergent stimulon replicate 1

description: Biological replicate 1 of 3


title: BM-CD138+, diagnosis, rep1 [MM_103; re-analysis2]

description: re-analysis of GSM1401522

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient


title: BM-CD138+, diagnosis, rep1 [MM_101; re-analysis2]

description: re-analysis of GSM1401520


title: Control DCs replicate 3

description: Control DCs replicate 3


title: Control DCs replicate 1

description: Control DCs replicate 1


title: SK-N-SH-doxorubicin resistant 1

description:
replicate 1
sDR1


title: BM-CD138+, diagnosis, rep1 [MM_100; re-analysis2]

description: re-analysis of GSM1401519


title: BM-CD138+, diagnosis, rep1 [MM_102; re-analysis2]

description: re-analysis of GSM1401521


title: SK-N-SH-wild type treated with SAHA 3

description:
replicate 3
sWT+SAHA3

source_name: SK-N-SH-wild type treated with SAHA

value: wild type; parental


title: DZP hippocampus, replicate3 (exon-level)

source_name: DZP, brain, hippocampus

value: DZP

value: brain

value: hippocampus


title: DZP amygdala, replicate1 (exon-level)

value: amygdala


title: DZP hippocampus, replicate2 (exon-level)


title: SK-N-SH-wild type treated with SAHA 1

description:
replicate 1
sWT+SAHA1

value: bone marrow

value: human neuroblastoma cells


title: SK-N-SH-wild type treated with SAHA 2

description:
replicate 2
sWT+SAHA2


title: DZP hippocampus, replicate1 (exon-level)


title: Control DCs replicate 2

description: Control DCs replicate 2


title: Gata2 knockout DCs replicate 3

description: Gata2 knockout DCs replicate 3

source_name: G2KD DC

value: Gata2 knockout


title: BM-CD138+, diagnosis, rep1 [MM_07; re-analysis2]

description: re-analysis of GSM1401517

value: Multiple Myeloma

value: BM-CD138+ cell fraction


title: Gata2 knockout DCs replicate 1

description: Gata2 knockout DCs replicate 1


title: SK-N-SH-wild type 2

description:
replicate 2
sWT2

source_name: SK-N-SH-wild type

value: SK-N-SH


title: BM-CD138+, diagnosis, rep1 [MM_06; re-analysis2]

description: re-analysis of GSM1401516

value: test set (2)


title: BM-CD138+, diagnosis, rep1 [MM_02; re-analysis2]

description: re-analysis of GSM1401513


title: Gata2 knockout DCs replicate 2

description: Gata2 knockout DCs replicate 2


title: BM-CD138+, diagnosis, rep1 [MM_05; re-analysis2]

description: re-analysis of GSM1401515


title: BM-CD138+, diagnosis, rep1 [MM_01; re-analysis]

description: re-analysis of GSM1684747

value: test set (1)


title: SK-N-SH-wild type 1

description:
replicate 1
sWT1


title: WT limb bud

city: Tokyo

first: Takahide

last: Matsushima

address: 1-5-45 Yushima, Bunkyo-ku

department: Systems BioMedicine

institute: Tokyo Medical and Dental University

description: Gene expression data from embryos limb bud

hyb_protocol: The cRNAs were hydrolyzed and hybridized to the GeneChip (R) Mouse Genome 430 2.0 array (Affymetrix).

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

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

source_name: Wildtype mouse embryo (E10.5) limb bud RNA

label_protocol: Total RNA (200 ng) was reverse-transcribed and biotinylated using the GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: The C57BL/6 line of wild-type and Bhlha9 knockout mice housed in an SPF environment was used for our analysis.

extract_protocol: ISOGEN (Nippongene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Whole limb bud were isolated from the E10.5 wild-type and Bhlha9 knockout embryos.

value: embryo limb bud

value: Wildtype


title: control amygdala, replicate2 (exon-level)

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.2 μg each) hybridized on GeneChip® MTA 1.0 for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

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

source_name: control, brain, amygdala

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

extract_protocol: Total RNA was extracted from each source using RNeasy Lipid Tissue Mini Kit (QIAGEN) according to the manufacturer's protocol. 100 ng of total RNA was subsequently carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

value: male

value: control


title: BDEsp-TDESM rep2

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

description: orthotopic cholangiocarcinoma obtained from bile duct inoculation of spontaneously-transformed rat cholangiocytes (BDEsp cells) in Fischer 344 young adult male rats.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

organism: Rattus norvegicus

source_name: Tumor arising from BDEsp cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: 3-dimensional (3-D) organotypic co-culture model of rat cholangiocarcinoma cells in diluted rat collagen type I gel.

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

treatment_protocol: TGFb inhibitors:  SB 431542 and LY2157299

tag: cell line origin

value: Clonal cancer-associated fibroblastic cell strain with Acta2 overexpression

tag: genetic background

value: Fischer 344


title: control amygdala, replicate3 (exon-level)

city: Hirosaki

first: Shinya

last: Ueno

address: 5 Zaifu-cho

institute: Hirosaki Univ Grad Sch of Med

value: 8 week-old

value: brain


title: BDEsp-TDESM rep1


title: BM-B cells, diagnosis, rep1 [MM7n]

description: Gene expression data from PBL-B cell fraction, obtained from newly diagnosed Multiple Myeloma patient

source_name: PBL-B cell fraction obtained from newly diagnosed Multiple Myeloma patient

value: PBL-B cell fraction


title: DZP cerebral cortex, replicate3 (exon-level)

source_name: DZP, brain, cerebral cortex

value: DZP

value: cerebral cortex


title: control amygdala, replicate1 (exon-level)

value: amygdala


title: DZP cerebral cortex, replicate2 (exon-level)


title: control hippocampus, replicate1 (exon-level)

source_name: control, brain, hippocampus

value: hippocampus


title: BDEsp-TDECC rep3

value: Clonal cholangiocarcinoma cell strain


title: control hippocampus, replicate2 (exon-level)


title: DZP cerebral cortex, replicate1 (exon-level)


title: BM-B cells, diagnosis, rep1 [MM6n]


title: BDEsp-TDECC rep2


title: BDEsp-TDESM rep3


title: BM-B cells, diagnosis, rep1 [MM5n]


title: Bhlha9 KO limb bud

source_name: Bhlha9 Knockout mouse embryo (E10.5) limb bud RNA

value: Bhlha9 Knockout


title: BM-B cells, diagnosis, rep1 [MM4n]


title: SK-N-SH-wild type 3

description:
replicate 3
sWT3

value: SK-N-SH

value: bone marrow

value: human neuroblastoma cells

value: wild type; parental


title: BDEsp-TDECC rep1


title: AIM2-/- BMM Mock

description:
replicate 1
10002897028_F

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMMs) and embryonic fibroblasts (MEFs) were generated and cultured as described (Lau et al., 2015, PMID 26405230).

treatment_protocol: BMMs and MEFs were seeded at a density of 7.5x10^5 and 1x10^5 per well, respectively, in a 12-well plate. Cells were transfected with 5μg calf thymus DNA (CT-DNA) per well using Lipofectamine 2000 (Life Technologies) for 4 or 8 hours.

value: AIM2-/- BMM

tag: treatment

value: mock


title: BM-B cells, diagnosis, rep1 [MM15n]

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). B cell fractions were isolated both from mononuclear bone marrow and peripheral blood cells, obtained by Ficoll-Hypaque density gradient centrifugation using B-cell isolation kit on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). All cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: cell type


title: control cerebral cortex, replicate1 (exon-level)

source_name: control, brain, cerebral cortex

growth_protocol: Mice were housed in plastic cages containing wood chips and covered with a wire lid. The cages were kept at 24±1 °C under a 12 h light/dark cycle (lights on at 8:00). The diet were standard laboratory food and water ad libitum.

value: male

value: control


title: BM-B cells, diagnosis, rep1 [MM13n]

tag: hh cluster


title: BM-B cells, diagnosis, rep1 [MM2n]


title: ALR-/- BMM Mock

description:
replicate 1
10002897028_D

value: ALR-/- BMM


title: ALR+/+ BMM Mock

description:
replicate 1
10002897028_E

value: ALR+/+ BMM


title: BM-B cells, diagnosis, rep1 [MM12n]

value: PBL-B cell fraction


title: ALR+/+ MEF CT-DNA 8h

description:
replicate 1
10002897028_B

source_name: embryonic fibroblasts

value: ALR+/+ MEF

value: CT-DNA

tag: time point


title: BM-B cells, diagnosis, rep1 [MM11n]


title: control cerebral cortex, replicate2 (exon-level)

value: 8 week-old

value: brain

value: cerebral cortex


title: BM-B cells, diagnosis, rep1 [MM10n]


title: AIm2-/- BMM CT-DNA 8h

description:
replicate 1
10002897022_F

value: AIm2-/- BMM


title: PBL-B cells, diagnosis, rep1 [MM1n]


title: ALR-/- MEF CT-DNA 8h

description:
replicate 1
10002897028_A

value: ALR-/- MEF


title: BM-B cells, diagnosis, rep1 [MM30n]

description: Gene expression data from BM-B cell fraction, obtained from newly diagnosed Multiple Myeloma patient

source_name: BM-B cell fraction obtained from newly diagnosed Multiple Myeloma patient

value: BM-B cell fraction


title: D15_DS_β-cateinin_activation_biological_replicate_3

city: Shanghai

first: Yi

middle: Xin

last: Tao

address: 1954 Huashan Road, Xuhui District, Shanghai (near Guangyuan Road West)

department: Life School

institute: Shanghai Jiao Tong University

description: SurePrint G3 Mouse GE 8x60K Microarray

hyb_protocol: 500ng Cy3-labelled cRNA (specific activity+B62 >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers` instructions. After the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression 8x60K Microarray (Agilent, G4852A, Design ID 028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B), using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Platform is SurePrint G3 Mouse GE 8x60K Microarray.Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass)

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from cΔex3 mice 4 and 5

label_protocol: 10ng input RNA samples were amplified and labeled to generate cRNA using Low RNA Input Linear Amplification Kit Plus, One-Color (Agilent Technologies). The generated cRNA was purified by using RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

extract_protocol: Total RNAs from FACS sorted cells were isolated by using TRIzol reagent (Invitrogen) according to the manufacturer`s protocol and quantified with the NanoDrop spectrophotometer (Thermo Scientific). RNA quality was assessed using Eukaryote Total RNA Pico 2.6 (Agilent Technologies) on a 2100 Bioanalyzer (Agilent Technologies) and samples with RNA integrity number (RIN) values of ~8 were analyzed further.

treatment_protocol: Mice were sacrificed according to the standard procedures. After single-cell suspensions of dermal cells was prepared, the samples were lebelled with with the following primary antibodies: CD34 eFluor660 (eBioscience), ITGα8 (R&D,goat), Alkaline Phosphatase (R&D,goat). The secondary antibody used was Donkey anti-goat IgG-PE (R&D). Before FACS sorting, 10μg/ml DAPI (Sigma) was added to exclude dead cells. Single cells were gated based on their pulse width. Sorting was performed using a FACSAria II cell sorter (BD Biosciences). Sorting parameters used were: sheath pressure 70 psi, nozzle 70 µm, frequency 87. Gates were set according to single stained positive and negative (isotype) controls.  The YFP+ve; CD34-ve; ALPL-ve; Itgα8-ve cell population was gated and sorted.

value: YFP+ve CD34-ve ALP-ve ITGα8-ve dermal sheath cells

value: Postnatal day 15


title: control cerebral cortex, replicate3 (exon-level)


title: AIM2-/- MEF CT-DNA 8h

description:
replicate 1
10002897028_C

value: AIM2-/- MEF


title: BM-B cells, diagnosis, rep1 [MM28n]


title: BM-B cells, diagnosis, rep1 [MM29n]


title: AIM2-/- BMM CT-DNA 4h

description:
replicate 1
10002897022_C

value: AIM2-/- BMM


title: ALR+/+ BMM CT-DNA 8h

description:
replicate 1
10002897022_E


title: ALR-/- BMM CT-DNA 8h

description:
replicate 1
10002897022_D


title: D15_DS_β-cateinin_activation_biological_replicate_4

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from cΔex3 mouse 6


title: control hippocampus, replicate3 (exon-level)

value: male

value: hippocampus


title: ALR+/+ BMM CT-DNA 4h

description:
replicate 1
10002897022_B


title: BM-B cells, diagnosis, rep1 [MM26n]


title: D15_DS_β-cateinin_activation_biological_replicate_2

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from cΔex3 mice 2 and 3


title: ALR-/- BMM CT-DNA 4h

description:
replicate 1
10002897022_A

value: ALR-/- BMM


title: D15_DS_control_biological_replicate_2

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from control mouse 2


title: D15_DS_control_biological_replicate_1

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from control mouse 1


title: BM-B cells, diagnosis, rep1 [MM25n]


title: AIM2-/- MEF CT-DNA 4h

description:
replicate 1
10001321027_F


title: Genomic DNA from central chondrosarcoma, MUT, sample_cytosnp_10

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

description: tumour sample

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip array according to the manufacturer's instructions.

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings.

data_processing: GenomeStudio software v2011.1. Standard GenomeStudio processed values.

label: C-Bio and A-DNP

source_name: central chondrosarcoma, MUT

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified using QiaAMP DNA Mini Kit according to standard instructions.

value: central chondrosarcoma

tag: idh status

value: MUT

tag: age at presentation

tag: Sex

value: M

tag: grade


title: Genomic DNA from central chondrosarcoma, MUT, sample_cytosnp_8

description: tumour sample


title: EK3

city: Lorenskog

first: Peder

last: Aabel

address: Sykehusvn. 27

department: ENT

country: Norway

institute: Akershus University Hospital

description: Purchased cells from ScienCell, HEK-a

hyb_protocol: Labeled sense strand DNA was hybridized to the GeneChip miRNA 3.0 Array  (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing:
The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.
miRNA-3_0-st-v3.pgf
miRNA-3_0.annotations.psname.20121203.probeset.csv

source_name: Epidermal keratinocyte

label_protocol: Total RNA (300 ng) from each sample was prepared using the Genisphere FlashTag HSR kit(Genisphere, Hatfield, PA)  according to manufacturer’s instructions.

extract_protocol: Total RNA from samples of cultivated TMK and EK cells was extracted using the miRNeasy mini kit from Qiagen

treatment_protocol: No treatment

value: epidermis

value: keratinocyte


title: Genomic DNA from central chondrosarcoma, WT, sample_cytosnp_5

description: tumour sample

source_name: central chondrosarcoma, WT

value: WT

value: F


title: BM-B cells, diagnosis, rep1 [MM24n]

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

institute: Institute of Hematology "L.A.Seràgnoli"

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model. (www.dchip.org, Li and Wong, 2001).

label_protocol: Samples with at least 30ng/uL RNA were labelled for gene expression profiling, using the Affymetrix One-cycle Gene Chip microarray system, according to the standard Affymetrix procedures.

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


title: Genomic DNA from central chondrosarcoma, MUT, sample_cytosnp_7

description: tumour sample


title: BM-CD138+, diagnosis, rep1 [MM23n]

description: Gene expression data from BM-CD138+ cell fraction, obtained from newly diagnosed Multiple Myeloma patient

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

value: BM-CD138+ cell fraction

value: test set (1)


title: ALR-/- MEF CT-DNA 4h

description:
replicate 1
10001321027_D

tag: genotype/variation

value: ALR-/- MEF

value: CT-DNA


title: Genomic DNA from central chondrosarcoma, MUT_Sample_cytosnp_6

description: tumour sample


title: EK1

description: Purchased cells from ScienCell, HEK-a


title: EK2

description: Purchased cells from ScienCell, HEK-a


title: D15_DS_control_biological_replicate_3

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from control mice 3 and 4

value: YFP+ve CD34-ve ALP-ve ITGα8-ve dermal sheath cells

tag: age

value: Postnatal day 15


title: TMK3

description: Primary cells from surgical patients

source_name: Tympanic membrane keratinocyte

value: tympanic membrane


title: D15_DS_β-cateinin_activation_biological_replicate_1

description: SurePrint G3 Mouse GE 8x60K Microarray

source_name: YFP+ve CD34-ve ALP-ve ITGα8-ve DS from cΔex3 mouse 1


title: BM-CD138+, diagnosis, rep1 [MM21n]


title: Genomic DNA from central chondrosarcoma, WT, sample_cytosnp_11

description: tumour sample


title: ALR+/+ MEF CT-DNA 4h

description:
replicate 1
10001321027_E

value: ALR+/+ MEF


title: AIM2-/- MEF Mock

description:
replicate 1
10001321027_C

value: AIM2-/- MEF

value: mock


title: ALR+/+ MEF Mock

description:
replicate 1
10001321027_B


title: BM-B cells, diagnosis, rep1 [MM27n]

value: BM-B cell fraction


title: BM-CD138+, diagnosis, rep1 [MM9n]


title: BM-CD138+, diagnosis, rep1 [MM20n]

value: test set (2)


title: Genomic DNA from central chondrosarcoma, WT, sample_cytosnp_4

description: tumour sample

value: central chondrosarcoma

value: M


title: ALR-/- MEF Mock

description:
replicate 1
10001321027_A


title: TMK2

description: Primary cells from surgical patients

value: keratinocyte


title: TMK1

description: Primary cells from surgical patients


title: BM-CD138+, diagnosis, rep1 [MM19n]


title: Genomic DNA from central chondrosarcoma, WT, sample_cytosnp_9

description: tumour sample

value: WT


title: Muscle_HFDcornoil_rep4

city: Gothenburg

first: Nikulkumar

middle: Kirtilal

last: Soni

state: Vastra Gotaland

address: Kemivagen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.18.0). It was vst transformed and quantile normalized.

source_name: high fat diet corn oil

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: 8 weeks

tag: gender

value: male

value: gastrocnemicus muscle


title: BM-CD138+, diagnosis, rep1 [MM17n]

value: BM-CD138+ cell fraction


title: Genomic DNA from central chondrosarcoma, MUT, sample_cytosnp_2

description: tumour sample

value: MUT


title: BM-CD138+, diagnosis, rep1 [MM16n]

value: test set (1)


title: Muscle_HFDEPADHA_rep4

source_name: high fat diet EPA/DHA

tag: strain


title: Muscle_controldiet_rep3

source_name: low fat diet


title: Genomic DNA from central chondrosarcoma, MUT, sample_cytosnp_1

description: tumour sample

value: F


title: BM-CD138+, diagnosis, rep1 [MM18n]


title: Genomic DNA from central chondrosarcoma, WT, sample_cytosnp_3

description: tumour sample


title: Muscle_controldiet_rep4


title: BHI+Bipy+Fe_t12 over BHI+Bipy+Fe_t12

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

description: Expression patterns were studied with and without iron starvation

hyb_protocol: Hybridization was performed as described in Mols et al., 2013.

scan_protocol: Slides were scanned with Agilent G2505C scanner

data_processing: Data were normalized using Lowess normalisation as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene was selected as the gene expression intensity.

organism: Bacillus cereus ATCC 10987

source_name: BHI+Bipy+Fe_t12: cells grown with both supplemented iron and the scavenger in BHI+Bipy until t12

label_protocol: Cy3 and Cy5 labeling of the cDNA was performed with CyScribe Post-Labeling kit (GE Healthcare)

growth_protocol: Liquid cultures of B. cereus ATCC 10987 were grown in BHI, BHI+Fe, BHI+Bipy and BHI+Fe+Bipy in 12-well plates statically at 30°C. 3ml was grown in each well and 8 such wells were pulled together for RNA isolation.

extract_protocol: Cultures were spinned down, resuspended in 1 ml TRI reagent (Ambion) and snap frozen in liquid nitrogen. RNA was extracted according to the RNAwiz (Ambion) protocol using Chloroform/isopropanol extraction. Residual DNA was enzymatically removed using the TURBO DNA-free (Ambion) kit following the instructions of the manufacturer.

treatment_protocol: Cells were harvested at t5 and t12 hours of growth.


title: BHI_t12 over BHI_t12

source_name: BHI_t12: cells grown in BHI as control until t12


title: BHI_t12 over BHI+Fe_t12 (2)

source_name: BHI+Fe_t12: cells grown with supplemented iron in BHI+Fe until t12


title: Muscle_HFDcornoil_rep3


title: BHI+Fe_t12 over BHI+Fe_t12


title: BHI+Bipy_t12 over BHI_t12 (2)

source_name: BHI+Bipy_t12: cells grown with iron starvation in BHI+Bipy until t12


title: BHI+Fe_t12 over BHI+Bipy+Fe_t12 (2)


title: Muscle_HFDEPADHA_rep3


title: BHI+Bipy_t12 over BHI+Bipy_t12


title: Muscle_HFDEPADHA_rep2


title: Muscle_HFDcornoil_rep2


title: G651

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Mouse liver RNA

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: Mouse liver was used for RNA isolation.

extract_protocol: We followed the instruction of the Ambion Purelink RNA mini kit. cDNA was synthesized from RNA template by using SuperScript III reverse transcriptase.

value: Rassf1a-/- Sav1+/-


title: Muscle_controldiet_rep1


title: BHI+Bipy_t12 over BHI_t12 (1)


title: BHI+Bipy+Fe_t12 over BHI+Bipy_t12 (1)


title: BHI+Fe_t12 over BHI+Bipy+Fe_t12 (1)


title: G650


title: BM-CD138+, diagnosis, rep1 [MM22n]


title: Muscle_HFDcornoil_rep1


title: Muscle_controldiet_rep2


title: Muscle_HFDEPADHA_rep1


title: G649


title: BHI_t12 over BHI+Fe_t12 (1)


title: BHI+Bipy+Fe_t5 over BHI+Fe_t5 (2)

source_name: BHI+Bipy+Fe_t5: cells grown with both supplemented iron and the scavenger in BHI+Bipy until t5

source_name: BHI+Fe_t5: cells grown with supplemented iron in BHI+Fe until t5


title: BHI+Bipy_t5 over BHI+Bipy_t5

source_name: BHI+Bipy_t5: cells grown with iron starvation in BHI+Bipy until t5


title: G647

description: SA


title: BHI_t5 over BHI_t5

source_name: BHI_t5: cells grown in BHI as control until t5


title: BHI_t5 over BHI+Bipy_t5 (2)


title: BHI+Fe_t5 over BHI+Fe_t5


title: BHI+Fe_t5 over BHI_t5 (2)


title: G645

description: SA


title: BHI+Bipy_t5 over BHI+Bipy+Fe_t5 (2)


title: G641

description: RA


title: BHI+Bipy+Fe_t5 over BHI+Bipy+Fe_t5


title: G644

description: SA


title: BHI+Bipy+Fe_t5 over BHI+Fe_t5 (1)


title: G648


title: G643

description: RA


title: BHI_t5 over BHI+Bipy_t5 (1)


title: G640

description: RA


title: BHI+Fe_t5 over BHI_t5 (1)


title: G646

description: SA


title: G639

description: WT

value: wildtype


title: G636

description: WT


title: G642

description: RA


title: G638

description: WT


title: BHI+Bipy_t5 over BHI+Bipy+Fe_t5 (1)


title: BHI+Bipy+Fe_t12 over BHI+Bipy_t12 (2)


title: E8.5 replicate 3

city: Manchester

first: Alexia

last: Eliades

address: Wilmslow Road

country: United Kingdom

institute: CRUK-Manchester Institute, The University of Manchester

hyb_protocol: Labeled RNA was hybridised to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix), following the manufacturer’s instructions

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Expression signals were generated with robust multichip average normalisation, followed by detection above background scoring, using the Affymetrix Power Tools software package (Affymetrix).

label_protocol: RNA was used to produce biotinylated sense-strand DNA with the Whole Transcript Sense Target Labelling Assay (Affymetrix)

growth_protocol: Timed matings were set up between ICR females and ETV2::GFP males.The morning the vaginal plug was observed was considered to be E0.5. Embryos were harvested at E7.5 and E8.5 developmental day

extract_protocol: RNA was isolated and amplified using the SuperAmp kit preparation kit (Miltenyi) according to the manufacturer's instructions

treatment_protocol: Embryos were trypsinized and stained with CD41-APC and FLK1-biotin conjugated anibody followed by Streptavidin-PECy7 staining. 50 cells for each replicate were sorted based on GFP+/FLK1+/CD41- immunophenotype in Myltenyi extraction buffer

tag: strain background

value: ICR (female) X ETV2::GFP (male)

tag: developmental stage


title: E8.5 replicate 2


title: G637

description: WT


title: E8.5 replicate 1


title: ME_2

city: Nanjing

first: Yan

last: Zhang

address: Xianlin Avenue

institute: Nanjing University

description: Gene expression data from mice liver after 90 days

hyb_protocol: Wash and stain the arrays with GeneChip® fluidics station 450.

scan_protocol: Scan the arrays with the GeneArray scanner 3000 by the GeneChip® Operating Software (GCOS) or Command Console® (AGCC) Software.

data_processing: Image analysis and quantification of probe values were performed using the GeneChip® Operating Software (Aff ymetrix). In our study, the Expression Console software of Affymetrix was used for RMA normalization.

source_name: liver, removed after 90-day

label_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays with GeneChip® hybridization oven 640.

growth_protocol: The mice were maintained in a 12-h light/12-h dark cycle at 25°C and 50% humidity, with free access to food and water.

treatment_protocol: The mice were randomly divided into two groups: the control group (n=10, treated with distilled water) and the ME group (n=10, treated with ME)

tag: exposure duration

value: municipal effluent


title: Control_3

value: control


title: ME_1


title: ME_3


title: E7.5 replicate 1


title: Control_2


title: CD8+ lymphocytes (ENK KO mice) 25

status: Public on May 30 2016

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: Spleen (ENK KO mice)

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Upon necropsy, cell were isolated using a cell sorter (FACSARIA) and subjeted to RNA extraction

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells were harvested with TRIzol Reagent (Invitrogen)

tag: tissue

value: spleen

value: ENK KO

value: Male

value: 9 Months


title: E7.5 replicate 3


title: Control_1


title: CD8+ lymphocytes (ENK KO mice) 31

value: 7 Months


title: CD8+ lymphocytes (WT mice) 34

source_name: Spleen (WT mice)

value: wild type


title: CD8+ lymphocytes (WT mice) 37


title: CD4+CD8+ lymphocytes (ENK KO mice) 1

source_name: Thymus (ENK KO mice)

value: thymus

value: Female

value: 2 Months


title: CD8+ lymphocytes (ENK KO mice) 6


title: CD8+ lymphocytes (WT mice) 22


title: CD4+CD8+ lymphocytes (WT mice) 32

source_name: Thymus (WT mice)


title: CD4+CD8+ lymphocytes (WT mice) 7


title: CD8+ lymphocytes (ENK KO mice) 3


title: CD8+ lymphocytes (WT mice) 40


title: colonic mucosa from MC group 5

city: Hangzhou

first: Shiyi

last: Wang

state: Zhejiang Province

address: No. 54, Youdian Road

department: Department of Gastroenterology

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

description:
Coding and non-coding gene expression data of colonic mucosa from MC group 5
STCa_(HTA-2_0)

hyb_protocol: After fragmentation, samples were hybridized in GeneChip® Hybridization Oven 645 according to the user manual of GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: After the wash protocols completing, the probe arrays were scanned by using the GeneChip® Scanner 3000 7G according to instructions for scanning probe arrays.

data_processing: The data were analyzed and standardized by SST-RMA algorithm using Affymetrix Expression Console™ Software (version 1.3).

source_name: MC patient_human colonic mucosa

label_protocol: Biotinylated samples were prepared according to the user manual of GeneChip® WT Terminal Labeling Kit.

growth_protocol: Fresh specimens of colon tissues form control patients were washed with RNAase free water and put into RNAlater(Qiagen) immediately and frozen in -80℃.

treatment_protocol: Fresh specimens of colon tissues form MC's patients were washed with RNAase free water and put into RNAlater(Qiagen) immediately and frozen in -80℃.

tag: subject group

value: melanosis coli (MC) patient group

value: colon biopsies from endoscopy


title: CD8+ lymphocytes (ENK KO mice) 28

value: 6 Months


title: CD4+CD8+ lymphocytes (ENK KO mice) 29


title: colonic mucosa from MC group 3

description:
Coding and non-coding gene expression data of colonic mucosa from MC group 3
STC4_(HTA-2_0)


title: E7.5 replicate 2


title: ifng + dexa_3

city: Cologne

first: Mario

last: Fabri

address: Kerpener Strasse 62

department: Dermatology

institute: University of Cologne

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G2595C Scanner

data_processing:
Genespring XII
Normalization: Shift to 75 percentile

source_name: ifng + dexa_3

label_protocol: Agilent low-Input QuickAmp Labeling Kit

extract_protocol: Trizol for RNA isolation

value: Monocyte-derived macrophages

tag: agent

value: dexamethasone/interferon-gamma


title: colonic mucosa from MC group 4

description:
Coding and non-coding gene expression data of colonic mucosa from MC group 4
STC6_(HTA-2_0)


title: ifng_3

tag: cell type

value: interferon-gamma


title: myometrium_cell line_30 hours_rep 6

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes (DEG) were identified by a two-way ANOVA, and p-values were adjusted using the FDR (false-discovery rate) method to correct for multiple comparisons. DEG were considered significant if p-value was £ 0.05 at a fold change (FC) of < -2 and > 2 with FDR <0.5.

source_name: myometrium, cell line, 30 hours

label_protocol: Total RNA according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Tissue was immediately plated in DMEM (as per treatment protocol). Cells were cultured in DMEM supplemented with 10% fetal calf serum and penicillin/streptomycin. Once confluent at passage 4, the media was refreshed to DMEM supplemented with penicillin/streptomycin alone and cultured as per 'treatment protocol'.

extract_protocol: Trizol extraction of total RNA was performed using a Trizol® Plus RNA Purification kit (Thermo Fisher Scientific, Ambion, Abgene Ltd., West Sussex, UK)

treatment_protocol: Tissue and cells were cultured for a period of 30 hours in DMEM supplemented with penicillin/streptomycin

tag: sample type

value: cell line

value: myometrium


title: CD4+CD8+ lymphocytes (WT mice) 38


title: colonic mucosa from MC group 1

description:
Coding and non-coding gene expression data of colonic mucosa from MC group 1
STC1_(HTA-2_0)


title: colonic mucosa from MC group 2

description:
Coding and non-coding gene expression data of colonic mucosa from MC group 2
STC2_(HTA-2_0)


title: dexa_3

value: dexamethasone


title: myometrium_cell line_30 hours_rep 5


title: colonic mucosa from control group 3

description:
Coding and non-coding gene expression data of colonic mucosa from control group 3.
con3_(HTA-2_0)

source_name: Control_human colonic mucosa

value: control patient group


title: colonic mucosa from control group 4

description:
Coding and non-coding gene expression data of colonic mucosa from control group 4.
con4_(HTA-2_0)


title: myometrium_cell line_30 hours_rep 4