title: 557247A06 - HA-FIT-8_10µMFe_BR3 vs HA-FIT-8_0µMFe_BR3

hyb_protocol: HA-FIT-8_0µMFe_BR3 Cy5 / HA-FIT-8_10µMFe_BR3 Cy3 : 30pmol.


title: 557247A08 - HA-FIT-8_0µMFe_BR1 vs col_0µMFe_BR1

status: Public on Feb 14 2015

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Analyse the responses to bHLH39 overexpression. bHLH39 is one of the transcription factors regulating iron homeostasis responses.

hyb_protocol: col_0µMFe_BR1 Cy5 / HA-FIT-8_0µMFe_BR1 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Media=Hoagland-agar hygrometry Temperature=21°C Light=16 hours light

extract_protocol: col_0µMFe_BR1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:0µM Fe - abiotic stress - compound starvation,fe:quantity 0uM . Col-0 (wild type, named C), HA-FIT 8 (a strong 2xpCAMV35S-driven HA7-tagged FIT overexpressor, named H) and fit-3 (fit knock-out mutant, named F) plants were grown as follows: Seeds were sterilized and stratified for two days at 4 °C in the dark. Hydroponic growth was carried out as previously described (Klatte et al., 2009). Plants were hydroponically grown for five weeks in ¼ Hoagland medium with 10 µM Fe under long-day conditions. The medium was refreshed every seven days. The fit-3 mutants were weekly sprayed with iron. Then the rosettes were showered intensively with ddH2O and the roots were rinsed with quarter-strength Hoagland medium with 0 μM Fe to remove residual iron and then the plants of each line were split into two fractions. During the sixth week half of the plants were exposed to the same medium (+Fe control, named +) while the other half was exposed to iron-sufficient conditions (-Fe, ¼ Hoagland, 0 Fe, named -).

tag: tissue

value: seedling

tag: treatment

value: 0 µMFe

tag: genotype

value: wild type

tag: genetic background

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

tag: arabidopsis thaliana (columbia)  mutant (col-0) -  dev.stage (boyes et al. plant cell 2001)


title: 557247A07 - col_0µMFe_BR1 vs HA-FIT-8_0µMFe_BR1

hyb_protocol: HA-FIT-8_0µMFe_BR1 Cy5 / col_0µMFe_BR1 Cy3 : 30pmol.


title: 0186_rep1

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

country: USA

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

description:
0186 A
This sample is of Gordonia sp. KTR9 0186 Mutant under carbon starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Two micrograms of the labeled DNA was used for subsequent hybridization to custom Nimblegen Bacterial Gene Expression Arrays for Gordonia sp. KTR9. The hybridized arrays were washed using the Nimblegen Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Microarray Scanner

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

organism: Gordonia sp. KTR9

source_name: 0186 under carbon starvation rep1

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

growth_protocol:
Gordonia sp. KTR9 and KTR9 mutant 0186 were grown in mineral salts media supplemented with succinate (10 mM), gluconate (10 mM), fructose (10 mM) and ammonium chloride (18 mM) for 72 h at 30°C shaking at 150 rpm. This was used as a starter culture to inoculate triplicates of KTR9 and KTR9 mutant 0186.
Triplicates of KTR9 and KTR9 mutant 0186 were inoculated at an OD600 of 0.015 and grown in mineral salts media  supplemented with succinate (10 mM), gluconate (10 mM), fructose (10 mM) and ammonium chloride (18 mM) for 72 h at 30°C shaking at 150 rpm.
For nitrogen starvation, cultures were spun down, rinsed in PBS buffer, and resuspended in mineral salts media with succinate (10 mM), gluconate (10 mM), and fructose (10 mM) and incubated at 30C for 48h.
After nitrogen starvation, cultures were exposed to carbon starvation. Cultures were spun down, rinsed in PBS buffer, and resuspended in mineral salts media with ammonium chloride (18 mM) and incubated at 30C for 72h.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and bead beating for 30s. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer. The RNA was used to generate cDNA using the Superscript II Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s directions. At each step the quality of the RNA and cDNA was analyzed using the Agilent 2100 Bioanalyzer and DNA 1000 Kit (Agilent).

tag: genotype/variation

value: KTR9_0186 disruptant

tag: exposed to

value: carbon starvation


title: KTR9_rep3

description:
KTR9 C
This sample is of Gordonia sp. KTR9 under carbon starvation conditions. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 under carbon starvation rep3


title: KTR9_rep1

description:
KTR9 A
This sample is of Gordonia sp. KTR9 under carbon starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 under carbon starvation rep1


title: Control, biological rep2 (E16.5)

city: Irvine

first: Xing

last: Dai

state: Ca

address: Med Sci I D288

institute: UC Irvine

description:
Gene expression data from isolated skin
TRE-Ovol2-Flag or TRE-Ovol2-Flag;K5-tTA

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

label: biotin

organism: Mus musculus

source_name: skin from mice

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Littermates were raised in the same cages.

extract_protocol: Trizol extraction of total RNA followed by column purification (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Control (TRE-Ovol2-Flag or wild type, 2 mice/array) and Ovol2 overexpression in epidermis (TRE-Ovol2-Flag;K5-tTA (Ovol2 BT), 2 mice/array)

tag: strain

value: Skin

tag: gender

value: female

tag: age

value: control


title: Control, biological rep1 (E17.5)

treatment_protocol: Control (TRE-Ovol2-Flag, or wild type 2 mice/array) and Ovol2 overexpression in epidermis (TRE-Ovol2-Flag;K5-tTA (Ovol2 BT), 2 mice/array)

value: Control


title: 557247A05 - HA-FIT-8_0µMFe_BR3 vs HA-FIT-8_10µMFe_BR3

hyb_protocol: HA-FIT-8_10µMFe_BR3 Cy5 / HA-FIT-8_0µMFe_BR3 Cy3 : 30pmol.

treatment_protocol: no treatment

value: 10 µMFe


title: Ovol2 BT, biological rep1 (E16.5)

value: FVB/N

value: Ovol2 overexpression (Ovol2 BT)


title: 557247A03 - HA-FIT-8_0µMFe_BR2 vs HA-FIT-8_10µMFe_BR2

hyb_protocol: HA-FIT-8_10µMFe_BR2 Cy5 / HA-FIT-8_0µMFe_BR2 Cy3 : 30pmol.


title: 557247A02 - HA-FIT-8_10µMFe_BR1 vs HA-FIT-8_0µMFe_BR1

hyb_protocol: HA-FIT-8_0µMFe_BR1 Cy5 / HA-FIT-8_10µMFe_BR1 Cy3 : 30pmol.


title: Ovol2 BT, biological rep2 (E16.5)


title: 557231A12 - HA-FIT-8_10µMFe_BR3 vs col_10µMFe_BR3

hyb_protocol: col_10µMFe_BR3 Cy5 / HA-FIT-8_10µMFe_BR3 Cy3 : 30pmol.


title: Control, biological rep1 (E16.5)


title: Ovol1/2 DKO, biological rep1 (no calcium)

description:
Gene expression data from isolated keratinocytes from skin
Ovol2flox/+; Ovol1+/- or Ovol1-/- or Ovol2flox/-;K14-Cre; Ovol1-/-

source_name: isolated keratinocytes from mouse skin

treatment_protocol: Control (Ovol2flox/+; Ovol1+/- or Ovol2flox/+;K14-Cre, 2 mice/array) and Ovol1 knockout (Ovol1-/-, 2 mice/array) and Ovol1/2 double conditional knockout (Ovol2flox/-;K14-Cre; Ovol1-/-, 2 mice/array)

tag: cell type

value: keratinocyte

value: Ovol1/2 DKO


title: Ovol1 KO, biological rep1 (no calcium)

value: Ovol1 KO


title: Control, biological rep2 (no calcium)


title: Ovol1/2 DKO, biological rep2 (no calcium)


title: 557231A11 - col_10µMFe_BR3 vs HA-FIT-8_10µMFe_BR3

hyb_protocol: HA-FIT-8_10µMFe_BR3 Cy5 / col_10µMFe_BR3 Cy3 : 30pmol.


title: 557231A06 - col_10µMFe_BR3 vs col_0µMFe_BR3

hyb_protocol: col_0µMFe_BR3 Cy5 / col_10µMFe_BR3 Cy3 : 30pmol.

extract_protocol: col_0µMFe_BR3:10ug. (Qiagen_RNeasy.pdf)


title: KTR9_rep2

description:
KTR9 B
This sample is of Gordonia sp. KTR9 under carbon starvation conditions. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: KTR9 under carbon starvation rep2


title: 557247A04 - HA-FIT-8_10µMFe_BR2 vs HA-FIT-8_0µMFe_BR2

hyb_protocol: HA-FIT-8_0µMFe_BR2 Cy5 / HA-FIT-8_10µMFe_BR2 Cy3 : 30pmol.


title: Ovol1 KO, biological rep2 (no calcium)


title: 557231A09 - col_10µMFe_BR2 vs HA-FIT-8_10µMFe_BR2

hyb_protocol: HA-FIT-8_10µMFe_BR2 Cy5 / col_10µMFe_BR2 Cy3 : 30pmol.


title: 557231A07 - col_10µMFe_BR1 vs HA-FIT-8_10µMFe_BR1

hyb_protocol: HA-FIT-8_10µMFe_BR1 Cy5 / col_10µMFe_BR1 Cy3 : 30pmol.


title: Ovol1/2 DKO, biological rep1 (with calcium)

value: calcium


title: M683

status: Public on Feb 13 2015

type: genomic

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2; The 'Heptromics_raw_signal_intensities.txt' contains unmethylated and methylated signal intensities
The  'Heptromics_avrg_beta.txt' contain average beta values

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

tag: subject group

value: HCC (hepatocellular carcinoma) resected patient

value: liver


title: M695


title: B301


title: M617


title: B175


title: 557231A05 - col_0µMFe_BR3 vs col_10µMFe_BR3

hyb_protocol: col_10µMFe_BR3 Cy5 / col_0µMFe_BR3 Cy3 : 30pmol.

value: seedling

value: 0 µMFe


title: 557231A10 - HA-FIT-8_10µMFe_BR2 vs col_10µMFe_BR2

hyb_protocol: col_10µMFe_BR2 Cy5 / HA-FIT-8_10µMFe_BR2 Cy3 : 30pmol.

value: wild type


title: M637


title: Ovol1 KO, biological rep1 (with calcium)


title: M593


title: Ovol1 KO, biological rep2 (with calcium)


title: 557231A08 - HA-FIT-8_10µMFe_BR1 vs col_10µMFe_BR1

hyb_protocol: col_10µMFe_BR1 Cy5 / HA-FIT-8_10µMFe_BR1 Cy3 : 30pmol.


title: Ovol1/2 DKO, biological rep2 (with calcium)


title: Control, biological rep1 (no calcium)


title: 557231A04 - col_10µMFe_BR2 vs col_0µMFe_BR2

hyb_protocol: col_0µMFe_BR2 Cy5 / col_10µMFe_BR2 Cy3 : 30pmol.

extract_protocol: col_0µMFe_BR2:10ug. (Qiagen_RNeasy.pdf)


title: M723


title: M209


title: M783


title: B181


title: M797


title: M467


title: M757


title: Control, biological rep2 (with calcium)


title: M673


title: M773


title: Control, biological rep1 (with calcium)


title: 557247A01 - HA-FIT-8_0µMFe_BR1 vs HA-FIT-8_10µMFe_BR1

hyb_protocol: HA-FIT-8_10µMFe_BR1 Cy5 / HA-FIT-8_0µMFe_BR1 Cy3 : 30pmol.


title: M425


title: 557231A03 - col_0µMFe_BR2 vs col_10µMFe_BR2

hyb_protocol: col_10µMFe_BR2 Cy5 / col_0µMFe_BR2 Cy3 : 30pmol.


title: M649


title: M777


title: M371


title: B319


title: 557231A02 - col_10µMFe_BR1 vs col_0µMFe_BR1

hyb_protocol: col_0µMFe_BR1 Cy5 / col_10µMFe_BR1 Cy3 : 30pmol.


title: B215


title: M237


title: 557231A01 - col_0µMFe_BR1 vs col_10µMFe_BR1

hyb_protocol: col_10µMFe_BR1 Cy5 / col_0µMFe_BR1 Cy3 : 30pmol.


title: M393


title: M577


title: M271


title: M573


title: B109


title: M257


title: M619


title: M213


title: M655


title: M493


title: M543


title: M595


title: M749


title: M591


title: M217


title: M379


title: M733


title: M459


title: M537


title: M679


title: M305


title: M803


title: B299


title: M539


title: M743


title: M607


title: M711


title: M363


title: M703


title: B239


title: M629


title: M553


title: M357


title: B167


title: M613


title: M517


title: M339


title: M479


title: B307


title: M503


title: M547


title: B159


title: M735


title: M781


title: M587


title: M311


title: M729


title: M603


title: M269


title: M501


title: M609


title: M405


title: M707


title: M519


title: M421


title: M677


title: M491


title: M747


title: M789


title: M533


title: B179


title: M569


title: M261


title: M751


title: M585


title: M795


title: M657


title: M345


title: M761


title: M615


title: M611


title: M753


title: M571


title: M623


title: M785


title: M535


title: M337


title: M505


title: M631


title: M235


title: M635


title: M693


title: M369


title: M451


title: M667


title: M549


title: M559


title: B135


title: B153


title: M755


title: M411


title: M233


title: M529


title: M523


title: M719


title: M685


title: M775


title: M745


title: M391


title: M229


title: M627


title: M397


title: M423


title: M597


title: M663


title: B317


title: M321


title: M439


title: M665


title: M675


title: B111


title: M759


title: M713


title: M589


title: M275


title: M793


title: M483


title: M741


title: M313


title: M697


title: M689


title: M243


title: M671


title: M521


title: M481


title: M725


title: M335


title: M625


title: B161


title: M727


title: B209


title: M737


title: M531


title: M373


title: M687


title: M653


title: M353


title: B231


title: M699


title: M325


title: M799


title: M807


title: M579


title: M709


title: M701


title: M215


title: M633


title: M651


title: M565


title: B265


title: M563


title: M329


title: M399


title: M551


title: B151


title: M515


title: M581


title: M669


title: M513


title: M385


title: M247


title: M461


title: M545


title: M765


title: M605


title: Melmet5 S100A4 rep3

city: Oslo

first: Lina

last: Prasmickaite

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

description:
replicate 3
A4#46A42011.24#4Melmet5S100A4

hyb_protocol: A total of 750ng of biotin-labeled cRNA was hybridized followingstandard Illumina protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw microarray data was preprocessed and quantile normalized in Illumina Genome Studio v2011.1 at transcript level. The data was imported into J-Express v2012 (www.molmine.com) and log2-transformed

source_name: Melanoma cell line Melmet5

label_protocol: standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit In short, 500ng of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: Total RNA was isolated using the TRI Reagent® (Invitrogen, Carlsbad, CA) using the manufacturer protocol. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer

tag: cancer type

value: Melanoma

tag: phenotype

value: Proliferative

tag: tissue origin

value: Metastases lymph node

value: stimulated with rS100A4 protein for 48hrs


title: M769


title: Melmet5 S100A4 rep1

description:
replicate 1
A42011.16#8Melmet5S100A4


title: Melmet5 control rep2

description:
replicate 2
A4#41A42011.24#3Melmet5ctrl

value: non-stimulated


title: Melmet5 control rep3

description:
replicate 3
A4#45A42011.24#3Melmet5ctrl


title: Melmet1 S100A4 rep3

description:
replicate 3
A4#44A42011.24#2Melmet1S100A4

source_name: Melanoma cell line Melmet1

value: Invasive

value: Metastases subcutaneous


title: Melmet5 control rep1

description:
replicate 1
A42011.16#7Melmet5ctrl


title: Melmet1 control rep2

description:
replicate 2
A4#39A42011.21#1Melmet1ctrl


title: MSC_Ctrl

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

country: Japan

institute: National Center for Global Health and Medicine

description: CD45- Ter-119- CD140a+ CD51+ cells as mesenchymal stem cells (MSC) control group

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used according to the manufacturer's instruction

scan_protocol: DNA Microarray Scanner (Agilent) was used according to the manufacturer's instruction

data_processing: The scaned images were analyzed with Feature Extraction Ver.9.5.3 (Agilent). Normalization method was 75 percentile shift for each sample, followed by baseline to median of all sample for each gene. Normalized data were again changed to linear scale.

source_name: MSC control group

label_protocol: Gene Expression Hybridization Kit (5188-5242 : Agilent) was used according to the manufacturer's instruction

extract_protocol: Qiagen RNeasy mini kit (74104 : Qiagen) was used according to the manufacturer's instruction

treatment_protocol: Mice were treated with PBS (Ctrl) or 200nmol c-di-GMP (cdG) and cells were collected after 3 days of injection

value: Male

value: 10 week old

value: Bone marrow

value: MSC

tag: agent

value: Ctrl


title: EC_cdG

description: CD45- Ter-119- CD31+ cells as endothelial cells (EC) cdG group

source_name: EC cdG group

tag: tissue

value: EC

value: cdG


title: Melmet5 S100A4 rep2

description:
replicate 2
A4#42A42011.24#4Melmet5S100A4

tag: treatment


title: HSC_Ctrl

description: CD150+ CD41- CD48- CD34- Flt3- LSK cells as hematopoietic stem cells (HSC) control group

source_name: HSC control group

value: HSC


title: M527

value: HCC (hepatocellular carcinoma) resected patient

value: liver


title: pgr016_corr (Ctnnb1-mut;p53fl)

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

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

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 using the RMA method batch correction for amplficiation assay followed using the three repeated samples assayed by both methods in STATA/SE 11.  Data provided in the spreadsheet are the corrected data. The Median Absolute Deviation (MAD) was calculated for each probe and then ranked to identify the 1000 most varying genes within the dataset (Following samples not included in calculation: dka040, 042 and 044 as these samples are not tumors; dka012, dka016 and dka049 since these were duplicate samples used for correction). Spotfire was used for two-way unsupervised hierarchical clustering and principal component analyses. Initial unsupervised hierarchical analysis used dka012, dka016 and dka049 and found them to cluster with or near their duplicate, so these were not used in the remainder of the analyses.

label: Biotin (One cycle kit)

source_name: Genetically-engineered WNT medulloblastoma model

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction. Biotinylated cRNA were prepared according to the standard Affymetrix one-Cycle protocol).  Some samples were amplified and labeled using the Affyexpress method. Three samples were amplified by both method to serve as basis for batch correction

growth_protocol: Spontaneous SHH medulloblastomas [dka001-005, 009, 033 and 034] and [dka050-057] were isolated from [Nestin-Cre; Cdkn2c-/-; Trp53fl/fl] and [Cdkn2c-/-; Ptch1+/-] mice (Uziel et al.,2005 Genes Dev). Spontaneous WNT medulloblastomas [pgr003, 016 and 066] were dissected from [Blbp-Cre; Ctnnb1+/lox (ex3); Trp53fl/fl] mice (Gibson et al., 2010, Nature). Group3 medulloblastomas [dka013-16, 049 and 065-067] were generated by overexpressing Myc in P6 cerebellar granule neuron progenitors (GNPs) from [Cdkn2c-/-, Trp53-/-] mouse pups prior to orthotopic injection into immunocompromised nude mice (Kawauchi et al, 2012, Cancer Cell). Cell-lineage specific Group3 medulloblastomas [dka072-075] and [dka077-081] were generated as in Kawauchi and colleagues (2012) except GNPs were isolated from Cre-recombined postnatal day 6 [Atoh1-CreER;Trp53fl/-] or [Prom1-CreER; Trp53fl/-] mouse pups (tamoxifen administered on P0-1), respectively. In situ Group3 medulloblastomas were generated by electroporating plasmids containing Myc and dominant negative Trp53 flanked by loxP sites into the fourth ventricle of E13.5 mouse embryos of Blbp-Cre [dka081, 087, 089, 090, 091 and blm121], Gad2-IRES-Cre [blm128-130 and blm134] or Ptf1a-Cre [blm135-137] mice.  FACS-sorted GFP-positive [dka040, 042, 044] GNPs were obtained from P6 [Cdkn2c-/-, Trp53-/-, Atoh1-GFP] mouse pups.

extract_protocol: Total RNAs were extracted with Trizol reagent (Invitrogen) according to a supplied RNA isolation protocol.

treatment_protocol: Tumor cells were dissociated and purified by percoll-gradient before RNA extraction.

value: Blbp-Cre; Ctnnb1+/lox (ex3); Trp53fl/fl


title: pgr066_corr (Ctnnb1-mut;p53fl)


title: dka091  (Blbp-MYC_25085)

label: Biotin (Affyexpress)

source_name: Electroporation-based Group3 medulloblastoma model

value: Blbp-Cre electroporated with Myc and dominant negative p53


title: Melmet1 S100A4 rep2

description:
replicate 2
A4#40A42011.21#2Melmet1S100A4

value: Melanoma


title: dka090  (Blbp-MYC_25087)


title: M223


title: HSC_cdG

description: CD150+ CD41- CD48- CD34- Flt3- LSK cells as hematopoietic stem cells (HSC) cdG group

source_name: HSC cdG group


title: Melmet1 S100A4 rep1

description:
replicate 1
A42011.16#4Melmet1S100A4

value: stimulated with rS100A4 protein for 48hrs


title: dka087  (Blbp-MYC_25077)


title: dka089   (Blbp-MYC_25078)


title: pgr003_corr (Ctnnb1-mut;p53fl)


title: EC_Ctrl

description: CD45- Ter-119- CD31+ cells as endothelial cells (EC) control group

source_name: EC control group


title: Melmet1 control rep3

description:
replicate 3
A4#43A42011.24#1Melmet1ctrl

value: non-stimulated


title: MSC_cdG

description: CD45- Ter-119- CD140a+ CD51+ cells as mesenchymal stem cells (MSC)  cdG group

source_name: MSC cdG group


title: dka081  (Prom1-CreER_Myc_124)

source_name: Cell-lineage specific orthotopic Group3 medulloblastoma model

value: Prom1-CreER, p53floxed/- infected with mcMyc/mRFP


title: M455


title: M645


title: M331


title: Melmet1 control rep1

description:
replicate 1
A42011.16#3Melmet1ctrl

value: Invasive

value: Metastases subcutaneous


title: M567


title: B157


title: M477


title: M375


title: B325


title: M557


title: M805


title: dka072 (Atoh1-CreER_Myc_13309)

value: Atoh1-CreER, p53floxed/- infected with mcMyc/mRFP


title: dka079  (Prom1-CreER_Myc_15239)


title: M599


title: M639


title: M771


title: dka077  (Prom1-CreER_Myc_15934)


title: dka073 (Atoh1-CreER_Myc_13333)


title: dka075 (Atoh1-CreER_Myc_16599)


title: dka067 (MycRFP_1448)

source_name: Orthotopic Group3 medulloblastoma model

value: p53-/-, Cdkn2c-/-, Math1-GFP infected with mcMyc/mRFP


title: dka065 (MycRFP_84905)


title: dka074 (Atoh1-CreER_Myc_15173)


title: M691


title: dka066 (MycRFP_87531)


title: M433


title: M253


title: M489


title: M715


title: dka055_corr (Ptch;Cdkn2c_82981)

source_name: Genetically-engineered SHH medulloblastoma model

value: Ptc+/-, Cdkn2c-/-


title: dka057_corr (Ptch;Cdkn2c_89130)


title: M295


title: B237


title: dka051_corr  (Ptch;Cdkn2c_45728)


title: M561


title: dka054_corr (Ptch;Cdkn2c_82260)


title: M661


title: M473


title: dka080  (Prom1-CreER_Myc_123)


title: M681


title: B247


title: dka053_corr (Ptch;Cdkn2c_47064)


title: dka050_corr (Ptch;Cdkn2c_45672)


title: M265


title: dka052_corr (Ptch;Cdkn2c_46926)


title: dka049_corr (MycRFP_1448)

description: dka049 is repeated measure of dka067


title: M787


title: M319


title: dka056_corr (Ptch;Cdkn2c_84324)


title: dka042_corr (P6 Atoh1-GFP+ GNPs)

source_name: Control for the Myc infected GNPs (prepared from FACS-sorted GFP+ cells from P6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella)

value: p53-/-, Cdkn2c-/-, Math1-GFP FACS sort for GFP+


title: M659


title: M279


title: dka044_corr (P6 Atoh1-GFP+ GNPs)


title: dka040_corr (P6 Atoh1-GFP+ GNPs)


title: dka034_corr (Nestin-Cre;p53fl_86898)

value: p53floxed, Nestin-Cre, Cdkn2c-/-


title: M443


title: dka033_corr (Nestin-Cre;p53fl_84046)


title: dka016_corr (MycRFP_87531)

description: dka016 is repeated measure of dka066


title: dka012_corr (Myc-RFP_84905)

description: dka012 is repeated measure of dka065


title: dka014_corr (MycRFP_87224)


title: B214

value: Cirrhotic patient


title: M435


title: dka015_corr (MycRFP_87228)


title: B178


title: B174


title: B156


title: M407


title: B152


title: dka005_corr (Nestin-Cre;p53fl_83559)


title: dka009_corr (Nestin-Cre;p53fl_86113)


title: B134


title: B110


title: B108


title: B150


title: dka004_corr (Nestin-Cre;p53fl_84565)


title: dka003_corr (Nestin-Cre;p53fl_85176)


title: NY108

value: normal individual


title: NY107


title: dka013_corr (MycRFP_86416)


title: dka001_corr (Nestin-Cre;p53fl_86583)


title: NY106


title: blm136 (Ptf1a-MYC_DK016)

value: Ptf1a-Cre electroporated with Myc and dominant negative p53


title: NY104

value: liver


title: dka002_corr (Nestin-Cre;p53fl_84557)


title: blm137 (Ptf1a-MYC_DK020)


title: NY103


title: blm135 (Ptf1a-MYC_DK015)


title: NY101


title: blm130 (Gad2-MYC_DK013)

value: Gad2-IRES-Cre electroporated with Myc and dominant negative p53


title: blm134 (Gad2-MYC_DK014)


title: blm128 (Gad2-MYC_DK011)


title: B46


title: B51


title: B44


title: B43


title: blm121 (Blbp-MYC_LL13-04)

value: Blbp-Cre electroporated with Myc and dominant negative p53


title: Hippocampus_Random-Antisense_Age 12mo_SAMP8, Biological Replicate 3

city: St. Louis

first: Harvey

middle: J

last: Armbrecht

state: MO

address: #1 Jefferson Barracks Drive

department: Division of Geriatric Medicine & Department of Molecular Microbiology & Immunology

institute: St. Louis Veterans Affairs Medical Center , & Saint Louis University School of Medicine

description:
Random-AS_SAMP8__3
Gene Expression Data from Random-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age

hyb_protocol: Following fragmentation, 12.5μg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were normalized using gc-RMA algorithms, which consist of background adjustment and quantile normalization, accounting for probe GC content; executed using  the R statistical environment and the BioConductor package.  A One-way ANOVA (4 conditions, N=4 independent biological replicates per condition)  was performed on GCRMA-normalized log2 transformed signal intensities to assess gene expression variability with regard to Treatment (Not Treated, Random-Antisense, and AβPP Antisense) and Strain (Control (50% SAMP8) vs SAMP8) (FDR ≤ 0.1).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 μg total RNA per sample (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: The 'Control' mice were a 50% backcross of the SAMP8 (senescence-accelerated) mice with CD-1 mice (50% SAMP8 mice).  These mice were closely related to SAMP8 mice but exhibited no memory deficits at 4 or 12 months.  The SAMP8 mice had memory deficits at 12 months but not at 4 months.

extract_protocol: Total RNA was extracted from the hippocampus of individual mice using the Qiagen RNeasy Lipid Extraction Mini Kit.

treatment_protocol: AβPP Antisense and Random Antisense were administered peripherally (IV) in these studies, a clinically relevant route.  In order to assess memory and cognitive function in each mouse, T-maze foot shock avoidance and novel object recognition were measured as described in the manuscript.  T-maze is a declarative memory task that requires an intact hippocampus.

value: SAMP8 (senescence-accelerated) mice

value: 12 month-old

value: male

tag: treated with

value: Random-Antisense

value: Hippocampus


title: Hippocampus_Not Treated_Age 12mo_SAMP8, Biological Replicate 3

description:
NT_SAMP8__3
Gene Expression Data from Untreated hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age

source_name: Hippocampus_Not Treated_Age 12mo_SAMP8

value: none (control)


title: Hippocampus_AβPP-Antisense_Age 12mo_SAMP8, Biological Replicate 3

description:
AS_SAMP8__3
Gene Expression Data from AβPP-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age

value: AβPP-Antisense


title: blm129 (Gad2-MYC_DK012)


title: Hippocampus_Random-Antisense_Age 12mo_SAMP8, Biological Replicate 2

description:
Random-AS_SAMP8__2
Gene Expression Data from Random-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: Hippocampus_AβPP-Antisense_Age 12mo_SAMP8, Biological Replicate 2

description:
AS_SAMP8__2
Gene Expression Data from AβPP-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: cNK PLZF+/+ rep1 tech-rep

city: Chicago

first: Albert

last: Bendelac

state: IL

address: 929 East 57th Street, GCIS W506

department: Pathology

institute: The University of Chicago

description: cNK WT replicate 1 technical replicate

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The non-normalized array data were extracted using GenomeStudio (version GSGX 1.9.0). Background correction, variance stabilization, and quantile normalization were performed in R/Bioconductor using the 'lumi' package.

source_name: Mouse Liver

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNeasy mini kit (Qiagen) to extract total RNA from cells stored in Trizol (Life Technologies)

tag: genotype

value: PLZF+/+

value: cNK

value: 4-10 weeks

value: Liver

tag: gating


title: Hippocampus_AβPP-Antisense_Age 12mo_SAMP8, Biological Replicate 1

description:
AS_SAMP8__1
Gene Expression Data from AβPP-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: ILC1 PLZF+/+ rep2

description: ILC1 WT replicate 2


title: cNK PLZF+/+ rep1

description: cNK WT replicate 1


title: Hippocampus_AβPP-Antisense_Age 12mo_SAMP8, Biological Replicate 4

description:
AS_SAMP8__4
Gene Expression Data from AβPP-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: Hippocampus_Not Treated_Age 12mo_SAMP8, Biological Replicate 4

description:
NT_SAMP8__4
Gene Expression Data from Untreated hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: ILC1 PLZF-/- rep1 tech-rep

description: ILC1 KO replicate 1 technical replicate

value: PLZF-/-


title: Hippocampus_Random-Antisense_Age 12mo_SAMP8, Biological Replicate 4

description:
Random-AS_SAMP8__4
Gene Expression Data from Random-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: ILC1 PLZF-/- rep2

description: ILC1 KO replicate 2


title: Hippocampus_Not Treated_Age 12mo_SAMP8, Biological Replicate 2

description:
NT_SAMP8__2
Gene Expression Data from Untreated hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: ILC1 PLZF+/+ rep1 tech-rep

description: ILC1 WT replicate 1 technical replicate


title: Hippocampus_Not Treated_Age 12mo_SAMP8, Biological Replicate 1

description:
NT_SAMP8__1
Gene Expression Data from Untreated hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: PAMAM dendrimer-NH2_72 h, replicate1

city: tsukuba

first: Yang

last: Zeng

state: ibaraki

address: Onogawa 16-2

institute: NIES

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions.  microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Microarray Scanner, Scan resolution3μm.

data_processing: The scanned images were analyzed with Agilent Feature Extraction 10.7.3.1 using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: human neural progenitor cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low Input Quick Amp Labeling Kit (Agilent  Technologies)

growth_protocol: The hNPCs were cultured in NEM (ENStem-A) supplemented with 0.05% b-FGF and 1% L-glutamine (Sigma-Aldrich, St. Louis, MO, US) on poly-ornithine-coated (Sigma-Aldrich, St. Louis, MO, US) and laminin-111-coated (Sigma-Aldrich, St. Louis, MO, US) dishes. On day 0 (d0), the cells were transferred to 96-well round bottom plates (Nunc, Falcon) at a density of 6,000 cells per well to allow neurosphere formation. On day 2 (d2), the developed neurospheres were gently transferred to a 48-well plate that was pre-coated with laminin-511 and contained neural differentiation media (Neurobasal Medium, NDM), supplemented with 1× B27, 1× N2, and 10 ng/mL BDNF (Invitrogen, Carlsbad, CA).

extract_protocol: RNA was prepared using the RNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. RNA was quantified using  the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: On day 4 (d4), NDM mixed with PAMAM dendrimers was gently replaced, incubated for 72 hours.

tag: cell line

value: hNPCs

tag: treatment time


title: Hippocampus_Random-Antisense_Age 12mo_SAMP8, Biological Replicate 1

description:
Random-AS_SAMP8__1
Gene Expression Data from Random-Antisense Treatment hippocampus of 12-month-old SAMP8 mice, which exhibit memory deficits at 12 months, but NOT 4 months of age


title: ILC1 PLZF-/- rep1

description: ILC1 KO replicate 1


title: PAMAM dendrimer-NH2_72 h, replicate2


title: Hippocampus_Not Treated_Age 12mo_50% SAMP8, Biological Replicate 2

description:
NT_Control__2
Gene Expression Data from Untreated hippocampus of 12-month-old 50% SAMP8 mice, which exhibit NO memory deficits at 4 or 12 months of age

value: 50% backcross of the SAMP8 mice with CD-1 mice


title: Control12 [set 2]

status: Public on Feb 12 2015

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: non-heart failure subject

hyb_protocol: hybridized on miRCURY LNA™ Arrays, using MAUI® hybridization system

scan_protocol: Chips were scanned on Innopsys Scan 700, microarray scanner at 532 nm

data_processing:
miRNA microarray data were analyzed by subtracting the mean background signal (B532nm) from the test signal (F532nm). All the 3 versions (v12; v16; 6thGEn chips and v18; 7thGen Chips) of Exiqon miRNA microarray probes were matched to the v18 miRNA name. Subsequently the collated data was analysed for further interpretations.
Raw signal values in the non-normalised matrix  and quantile normalised  data in the normalised matrix spread sheet respectively. The quantile normalization of the probes were carried out on PartekÒ Genomics Suite™ 6.6 software.

label_protocol: LNA-modified oligonucleotide (Exiqon) probes for human, mouse and rat miRNAs annotated in miRBase version 12.0, 16.0, 18.0 were used in the microarray. Total RNA (1 μg) was 3’-end –labeled with Cy3 dye using the miRCURY LNA ™ Power Labeling Kit (Exiqon)

extract_protocol: Total RNA (plus miRNAs) was isolated using a modification of the RiboPure™-Blood kit from Ambion (Austin,TX) according to the manufacturer’s protocol. The concentration of total RNA and integrity were determined by using Nano-Drop ND-1000 Spectrophotometry (NanoDrop Tech, Rockland, Del) and gel electrophoresis respectively.

tag: sample group

value: control (no past history of heart failure/disease)

value: peripheral blood

tag: molecule subtype

value: microRNA


title: Control11 [set 2]

description: non-heart failure subject


title: hfPEF5 [set 2]

description: preserved ejection fraction

value: patients with heart ailment (hfPEF)

tag: % of left ventricular ejection fraction

value: preserved left ventricular ejection fraction (hfPEF)


title: hfPEF4 [set 2]

description: preserved ejection fraction


title: hfPEF6 [set 2]

description: preserved ejection fraction


title: Control10 [set 2]

description: non-heart failure subject


title: ILC1 PLZF+/+ rep1

description: ILC1 WT replicate 1

tag: strain

tag: age


title: Hippocampus_Not Treated_Age 12mo_50% SAMP8, Biological Replicate 3

description:
NT_Control__3
Gene Expression Data from Untreated hippocampus of 12-month-old 50% SAMP8 mice, which exhibit NO memory deficits at 4 or 12 months of age

value: 12 month-old

tag: gender

value: male


title: Control9 [set 2]

description: non-heart failure subject


title: Control7 [set 2]

description: non-heart failure subject


title: Control8 [set 2]

description: non-heart failure subject


title: hfPEF3 [set 2]

description: preserved ejection fraction


title: hfREF15 [set 2]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)


title: hfREF14 [set 2]

description: reduced ejection fraction


title: hfREF12 [set 2]

description: reduced ejection fraction


title: hfREF13 [set 2]

description: reduced ejection fraction


title: Control6 [set 2]

description: non-heart failure subject


title: Hippocampus_Not Treated_Age 12mo_50% SAMP8, Biological Replicate 1

description:
NT_Control__1
Gene Expression Data from Untreated hippocampus of 12-month-old 50% SAMP8 mice, which exhibit NO memory deficits at 4 or 12 months of age

value: none (control)

value: Hippocampus


title: hfREF11 [set 2]

description: reduced ejection fraction


title: No treatment, replicate2


title: Control4 [set 2]

description: non-heart failure subject


title: Control5 [set 2]

description: non-heart failure subject


title: Hippocampus_Not Treated_Age 12mo_50% SAMP8, Biological Replicate 4

description:
NT_Control__4
Gene Expression Data from Untreated hippocampus of 12-month-old 50% SAMP8 mice, which exhibit NO memory deficits at 4 or 12 months of age


title: hfREF9 [set 2]

description: reduced ejection fraction


title: hfREF10 [set 2]

description: reduced ejection fraction


title: Control2 [set 2]

description: non-heart failure subject


title: No treatment, replicate1


title: hfREF8 [set 2]

description: reduced ejection fraction


title: hfREF7 [set 2]

description: reduced ejection fraction


title: hfREF5 [set 2]

description: reduced ejection fraction


title: hfPEF1 [set 2]

description: preserved ejection fraction


title: hfREF3 [set 2]

description: reduced ejection fraction


title: hfPEF2 [set 2]

description: preserved ejection fraction


title: hfREF6 [set 2]

description: reduced ejection fraction


title: hfREF4 [set 2]

description: reduced ejection fraction


title: hfREF2 [set 2]

description: reduced ejection fraction


title: hfREF1 [set 2]

description: reduced ejection fraction


title: Control3 [set 2]

description: non-heart failure subject


title: RWPE-1_Cells_rep3

first: Nina

middle: Pettersen

last: Hessvik

department: Department for Biochemistry

institute: The Norwegian Radium Hospital, Oslo University Hospital

description: Biological replicate 3 of 3. RWPE-1 cells harvested after 24 h incubation in the absense of bovine pituitary extract.

hyb_protocol: Exiqon protocol – miRCURY LNA microRNA Array Instruction Manual, 6th generation arrays, hsa, mmu, rno. Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA). Ozone free environment

data_processing: Image analysis by ImaGene® (miRCURY LNA microRNA Array Analysis Software, Exiqon, Denmark). Background correction using Normexp with an offset value of 10. No normalization. Median centration.

source_name: RWPE-1 cell lysates

label_protocol: Exiqon protocol - miRCURY LNA microRNA Hi-Power Labeling. 750ng was labeled.

growth_protocol: RWPE-1 cells were cultured in Keratinocyte Serum Free Medium supplemented with 0.05 mg/ml bovine pituitary extract, 5 ng/ml human recombinant epidermal growth factor, 100 units/ml penicillin and 100 µg/ml streptomycin, in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol: Total RNA extracted using mirVana RNA isolation kit (Ambion) following manufacturer's instructions.

treatment_protocol: RWPE-1 cells were incubated for 24 h in the absence of bovine pituitary extract.

tag: sample source

value: RWPE-1 cells

source_name: Total RNA from pooled sample 1-9

tag: sample type

value: reference


title: PC-3_Exosomes_rep2

description: Biological replicate 2 of 3. Exosomes isolated from cell culture media from PC-3 cells after 24 h incubation using ultracentrifugation.

source_name: Exosomes from PC-3 cells

growth_protocol: PC-3 cells were cultured in Ham’s F-12/ Dulbecco’s Modified Eagle’s Medium (1:1 mixture) with Glutamax supplemented with 7% foetal calf serum (FCS), 100 units/ml penicillin and 100 µg/ml streptomycin, in a humidified 5% CO2 atmosphere at 37 °C.

treatment_protocol: PC-3 cells were incubated for 24 h under serum free conditions, and exosomes were isolated from conditioned media by ultracentrifugation.

value: Exosomes


title: PC-3_Exosomes_rep1

description: Biological replicate 1 of 3. Exosomes isolated from cell culture media from PC-3 cells after 24 h incubation using ultracentrifugation.


title: PC-3_Cells_rep3

description: Biological replicate 3 of 3. PC-3 cells harvested after 24 h incubation under serum free conditions.

source_name: PC-3 cell lysates

treatment_protocol: PC-3 cells were incubated for 24 h under serum free conditions.

value: PC-3 Cells


title: RWPE-1_Cells_rep1

description: Biological replicate 1 of 3. RWPE-1 cells harvested after 24 h incubation in the absense of bovine pituitary extract.


title: PC-3_Exosomes_rep3

description: Biological replicate 3 of 3. Exosomes isolated from cell culture media from PC-3 cells after 24 h incubation using ultracentrifugation.


title: PC-3_Cells_rep2

description: Biological replicate 2 of 3. PC-3 cells harvested after 24 h incubation under serum free conditions.


title: PC-3_Cells_rep1

description: Biological replicate 1 of 3. PC-3 cells harvested after 24 h incubation under serum free conditions.


title: CHC1474T

data_processing: The data were normalised using the signal intensities by BeadStudio software (Illumina)

label: Biotin

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

extract_protocol: RNA extracted from FFPE blocks using Qiagen Rneasy kit according to company protocol

value: FLC liver tissue


title: CHC1471T


title: 70Z/3 miR27a clone 2

city: South Bend

first: Richard

last: Dahl

state: IN

address: Harper Hall 227, 1234 Notre Dame Ave.

department: Microbiology and Immunology

institute: Indiana University School of Medicine, South Bend

description: Hematopoietic cells transduced with retrovirus expressing single pre-miRNA gene

hyb_protocol: Following fragmentation 10ug of cRNA was hybridized to a Affymetrix Mouse430_2 GeneChip.

scan_protocol: The hybridized GeneChips were washed and processed for analysis using the automated Affymetrix stations, and then scanned using the high resolution Affymetrix GeneChip scanner 3000 as recommended by Affymetrix.

data_processing:
The Affymetrix Expression Console Software Version 1.4.0 was used to create summarized expression values (CHP-files) from expression array feature intensities (CEL-files).
Raw data were normalized with robust multichip analysis (RMA) with Affymetrix transcriptome analysis console (TAC) software.

source_name: 70Z/3 stably expressing exogenous miRNA_miR27_2

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: 70Z/3 cells were maintained at 37C and 5% CO2

extract_protocol: Trizol extraxtion of total RNA was performed according to manufacturers instructions.

treatment_protocol: Cells were infected with retroviral supernatant for 48h, and grown an additional 24h before sorting for GFP+ cells.  Infected cells were expanded and used for total RNA extraction.

tag: cell type

value: pre-B cell


title: CHC1475T


title: CHC1465T


title: 70Z/3 miR24-2 clone 2

source_name: 70Z/3 stably expressing exogenous miRNA_miR24_2


title: 70Z/3 MSCV clone 2 replicate

source_name: 70Z/3 stably expressing exogenous miRNA_MSCV_2


title: 70Z/3 MSCV clone 1 replicate

source_name: 70Z/3 stably expressing exogenous miRNA_MSCV_1


title: CHC1464T


title: Abeta at T20, biological repeat 1

city: Milwaukee

first: Wail

middle: Mostafa

last: Hassan

address: 2400 E. Hartford Ave.

department: Biomedical Sciences

institute: University of Wisconsin

description: Gene expression data from Abeta-expressing worms 20 hours after temperature upshift

hyb_protocol: Standard Affymetrix protocol. This was done at core facility at University fo Colorado Boulder many years ago.

data_processing: CEL files were created using Expression Console version 1.1 and were analyzed using GeneSpringGX. Sample 2179-8-3 was excluded due to low array quality.

organism: Caenorhabditis elegans

source_name: 20 hours postupshift

label_protocol: Biotinylated cRNA was synthesized using an Affymetrix kit (Affymetrix, Inc., Santa Clara, CA) using manufacturer's standard protocols. Briefly, 5 ug of total RNA from each sample were used to prepare cDNA by reverse transcription. Next, single stranded cDNA was converted into double stranded cDNA by second strand synthesis. The resulting double stranded cDNA was used as a template for in vitro transcription in the presence of biotinylated UTP and CTP to produce biotinylated cRNA.

growth_protocol: Worms were grown on NGM with OP50 lawn

extract_protocol: RNA was extracted using Rneasy Kit (Qiagen)

tag: time point

tag: genotype/variation

value: Abeta


title: Abeta at T16, biological repeat 1

description: Gene expression data from Abeta-expressing worms 16 hours after temperature upshift

scan_protocol: Standard Affymetrix protocol. This was done at core facility at University fo Colorado Boulder many years ago.

source_name: 16 hours postupshift


title: 70Z/3 miR24-2 clone 1

source_name: 70Z/3 stably expressing exogenous miRNA_miR24_1


title: Abeta at T16, biological repeat 4


title: CHC1473T

tag: tissue


title: Abeta at T12, biological repeat 3

description: Gene expression data from Abeta-expressing worms 12 hours after temperature upshift

source_name: 12 hours postupshift


title: Abeta at T16, biological repeat 2


title: 70Z/3 miR27a clone 1

source_name: 70Z/3 stably expressing exogenous miRNA_miR27_1


title: Abeta at T12, biological repeat 4


title: 70Z/3 miR23a clone 1

source_name: 70Z/3 stably expressing exogenous miRNA_miR23_1


title: 70Z/3 miR23a clone 2

source_name: 70Z/3 stably expressing exogenous miRNA_miR23_2


title: CHC1468T


title: Abeta at T12, biological repeat 2


title: GFP::degron at T16, biological repeat 4

description: Gene expression data from GFP::degron-expressing worms 16 hours after temperature upshift


title: CHC1310T


title: CHC442T


title: Abeta at T8, biological repeat 2

description: Gene expression data from Abeta-expressing worms 8 hours after temperature upshift

source_name: 8 hours postupshift


title: 70Z/3 MSCV clone 1


title: CHC1462T


title: RWPE-1_Cells_rep2

description: Biological replicate 2 of 3. RWPE-1 cells harvested after 24 h incubation in the absense of bovine pituitary extract.


title: Control1 [set 2]

description: non-heart failure subject

value: control (no past history of heart failure/disease)

value: peripheral blood


title: GFP::degron at T16, biological repeat 2


title: CHC412T


title: Abeta at T4, biological repeat 1

description: Gene expression data from Abeta-expressing worms 4 hours after temperature upshift

source_name: 4 hours postupshift


title: Abeta at T16, biological repeat 3


title: CHC906T


title: GFP::degron at T16, biological repeat 3


title: CHC1463T


title: GFP::degron at T20, biological repeat 1

description: Gene expression data from GFP::degron-expressing worms 20 hours after temperature upshift


title: GFP::degron at T12, biological repeat 4

description: Gene expression data from GFP::degron-expressing worms 12 hours after temperature upshift


title: GFP::degron at T16, biological repeat 1


title: Abeta at T12, biological repeat 1


title: Abeta at T8, biological repeat 1


title: CHC410T


title: Abeta at T8, biological repeat 4


title: CH406T


title: CHC407T


title: Abeta at T0, biological repeat 1

description: Gene expression data from Abeta-expressing worms at the time of temperature upshift

source_name: At temperature upshift


title: CHC408T


title: CHC411T


title: PC-GF-C3

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description:
PA181_GF-PC-3-Crypt_FS324-64_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

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

data_processing: The data was processed with quantile normlaization, pm-only for background coreection, iterative PLIER algorithm for expresion index calculation.  The analysis was performed by expression console software

source_name: LCM Crypt fraction of Proximal colon of Germ-free mouse

label_protocol: 1000 picograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA from the entire expressed transcriptome according to the Nugen Technologies, Inc. protocols Ovation® Pico WTA System V2 (M01224v2) and Encore Biotine Module (M01111v5).

growth_protocol: Germ-free C57Bl/6 mice were maintained in standard makrolon cages according to standard protocols inside sterile flexible film isolators. Conventionally raised C57Bl/6 mice were kept in sterilized, filter-topped IVC cages under specific pathogen-free conditions. All animals were housed with wood shavings and wooden wool and had free access to standard autoclaved chow diet (Labdiet, USA) and water. Mice were kept with 12 hours light/dark cycle at 18-22°C temperature and 35-65% relative humidity which was continuously and automatically registered and regulated. A maximum of 5 mice were kept in one cage. Germ-free mice were colonized by oral gavage of pooled caecal content of conventionally raised age and sex matched mice. Animals used for experiments were females and 10-12 weeks of age at harvest.

extract_protocol: RNA was isolated from the lysates of the LCM harvested fractions using RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA concentration and quality were evaluated using capillary electrophoresis on a 2100 Bioanalyzer with RNA 6000 Pico kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: 10-12 weeks old mice were sacrificed before and during the time course of colonization with a normal microbiota (on days 1, 3, 5 and 7) by cervical dislocation and the intestine removed. The distal part of the small intestine (ileum) and the proximal part of the colon were excised, flushed with PBS and finally flushed and embedded with OCT freezing medium. The complete procedure from sacrificing the mouse until the frozen tissue blocks took less than five minutes to preserve RNA integrity. All material and solutions used further were RNase-free. 8 µm thick cryosections were cut from the OCT blocks at -20°C using a microtome (Leica), placed onto PEN membrane slides (ZEISS) and immediately stained for LCM. Briefly, slides were dehydrated in absolute and 70% ethanol for 30s each, dipped into RNase-free water to remove excessive OCT and then incubated in 1% cresyl violet in 50% ethanol step for another 30s. Slides were partially destained by dipping in 70% and absolute ethanol before air-drying. Slides were stored in airtight containers at -80°C until laser capture microdissection (LCM). Airtight containers were equilibrated to ambient temperature before opening. LCM was performed using PALM Microbeam Microdissection microscope (ZEISS) and fractions were collected dry. The harvested fractions were immediately lyzed in RLT containing 1% β-mercaptoethanol and stored at -80°C.

value: female

value: 10-12 weeks

tag: bacterial status

value: Germ-free

value: Proximal colon

tag: fraction

value: Crypt

tag: replicate


title: PC-GF-T3

description:
PA181_GF-PC-3-Tip_FS324-59_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

source_name: LCM Tip fraction of Proximal colon of Germ-free mouse

value: Tip


title: PC-GF-C1

description:
PA181_GF-PC-1-Crypt_FS324-56_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: GFP::degron at T8, biological repeat 4

description: Gene expression data from GFP::degron-expressing worms 8 hours after temperature upshift


title: GFP::degron at T8, biological repeat 2


title: GFP::degron at T12, biological repeat 5


title: 70Z/3 MSCV clone 2

tag: cell line


title: GFP at T16, biological repeat 4

description: Gene expression data from GFP-expressing worms 16 hours after temperature upshift

value: GFP


title: GFP at T16, biological repeat 3


title: GFP::degron at T8, biological repeat 3


title: GFP::degron at T12, biological repeat 3


title: GFP::degron at T8, biological repeat 1


title: PC-GF-T2

description:
PA181_GF-PC-2-Tip_FS324-66_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: CHC232T


title: GFP::degron at T12, biological repeat 2


title: Abeta at T8, biological repeat 3


title: CHC255T


title: Ile-GF-C3

description:
PA181_GF-Ile-3-Crypt_FS324-54_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

source_name: LCM Crypt fraction of Ileum of Germ-free mouse

value: Ileum


title: GFP::degron at T4, biological repeat 1

description: Gene expression data from GFP::degron-expressing worms 4 hours after temperature upshift


title: GFP::degron at T0, biological repeat 1

description: Gene expression data from GFP::degron-expressing worms at the time of temperature upshift


title: GFP at T20, biological repeat 1

description: Gene expression data from GFP-expressing worms 20 hours after temperature upshift


title: GFP::degron at T12, biological repeat 1


title: GFP at T12, biological repeat 5

description: Gene expression data from GFP-expressing worms 12 hours after temperature upshift


title: CHC093T


title: GFP at T16, biological repeat 1


title: PC-GF-T1

description:
PA181_GF-PC-1-TipFS324-65_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: GFP at T12, biological repeat 4


title: Ile-GF-T2

description:
PA181_GF-Ile-2-Tip_FS324-51_130417.CEL
Gene expression data from LCM Tip fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

source_name: LCM Tip fraction of Ileum of Germ-free mouse


title: GFP at T16, biological repeat 2


title: FLC_61

value: Normal liver tissue


title: Ile-GF-T3

description:
PA181_GF-Ile-3-Tip_FS324-53_130417.CEL
Gene expression data from LCM Tip fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: Ile-GF-C2

description:
PA181_GF-Ile-2-Crypt_FS324-52_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: CHC187T


title: PC-7d-C3

description:
PA181_7d-PC-3-Crypt_FS324-48_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: CONV-D day 7


title: GFP at T12, biological repeat 3


title: Ile-GF-T1

description:
PA181_GF-Ile-1-Tip_FS324-49_130417.CEL
Gene expression data from LCM Tip fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: CHC026T


title: PC-7d-T3

description:
PA181_7d-PC-3-Tip_FS324-47_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: FLC_09


title: GFP at T8, biological repeat 4

description: Gene expression data from GFP-expressing worms 8 hours after temperature upshift


title: GFP at T12, biological repeat 2


title: GFP at T12, biological repeat 1


title: GFP at T8, biological repeat 3


title: FLC_33


title: FLC_52


title: FLC_53


title: FLC_59


title: FLC_58


title: FLC_56


title: PC-7d-C1

description:
PA181_7d-PC-1-Crypt_FS324-44_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: AJ 7 days post-infection [AJ7094]

city: Montreal

first: Sean

last: Beatty

state: Quebec

address: 3649 Promenade Sir-William-Osler

department: Human Genetics

country: Canada

institute: McGill University

description: biological replicate 1

data_processing: Variance Stabilizing Transformation (VST) (Lin, S.M., Du, P., Kibbe, W.A., (2008), Robust-Spline Normalization (RSN), and Force-positive background correction were applied to the array data using the Lumi package for R (Lumi - Du, P., Kibbe, W.A. and Lin, S.M. 2008, R-  R Core Team 2013).

source_name: AJ 7 days post-infection

extract_protocol: Total spleen RNA was extracted from AcB60, and A/J with TriZol reagent (InVitrogen, Burlington ON) and purified using a Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: Infected samples were taken from mice infected with 1000 CFUs of Salmonella Typhimurium strain Keller

value: AJ

value: 13 weeks

tag: Sex

tag: infected with

value: 1000 CFUs of S. Typhimuirum

value: 7 days post-infection

value: spleen homogenate


title: PC-GF-C2

description:
PA181_GF-PC-2-Crypt_FS324-58_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: Ile-7d-C2

description:
PA181_7d-Ile-2-Crypt_FS324-34_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: Ile-7d-T2

description:
PA181_7d-Ile-2-Tip_FS324-33_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: AJ 7 days post-infection [AJ7098]

description: biological replicate 2


title: FLC_55

value: FLC liver tissue


title: FLC_60


title: Ile-GF-C1

description:
PA181_GF-Ile-1-Crypt_FS324-50_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum of Germ-free 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: PC-7d-C2

description:
PA181_7d-PC-2-Crypt_FS324-46_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: FLC_49


title: FLC_54


title: GFP at T4, biological repeat 1

description: Gene expression data from GFP-expressing worms 4 hours after temperature upshift


title: PC-7d-T1

description:
PA181_7d-PC-1-Tip_FS324-43_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: PC-7d-T2

description:
PA181_7d-PC-2-Tip_FS324-69_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: GFP at T8, biological repeat 2


title: Ile-7d-T3

description:
PA181_7d-Ile-3-Tip_FS324-35_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: Ile-7d-T1

description:
PA181_7d-Ile-1-Tip_FS324-68_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: GFP at T0, biological repeat 1

description: Gene expression data from GFP-expressing worms at the time of temperature upshift


title: PC-5d-C3

description:
PA181_5d-PC-3-Crypt_FS324-42_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: CONV-D day 5


title: AJ 7 days post-infection [AJ7109]

description: biological replicate 3

value: female


title: PC-5d-T3

description:
PA181_5d-PC-3-Tip_FS324-41_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: 10-12 weeks


title: FLC_50


title: Ile-7d-C3

description:
PA181_7d-Ile-3-Crypt_FS324-36_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: AJ 5 days post-infection [AJ5103]

description: biological replicate 2

source_name: AJ 5 days post-infection

value: 5 days post-infection


title: AJ 5 days post-infection [AJ5091]

description: biological replicate 1


title: Ile-7d-C1

description:
PA181_7d-Ile-1-Crypt_FS324-32_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 7 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: AJ 5 days post-infection [AJ5108]

description: biological replicate 3


title: AJ 3 days post-infection [AJ3096]

description: biological replicate 1

source_name: AJ 3 days post-infection

value: 3 days post-infection


title: AJ 3 days post-infection [AJ3110]

description: biological replicate 3


title: FLC_47


title: FLC_43


title: AJ uninfected [AJ0132]

description: biological replicate 2

source_name: AJ uninfected

value: none (naïve control)


title: PC-5d-T2

description:
PA181_5d-PC-2-Tip_FS324-39_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

value: Proximal colon

value: Tip


title: PC-5d-C1

description:
PA181_5d-PC-1-Crypt_FS324-38_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: Crypt


title: AcB60 7 days post-infection [ACB607105]

description: biological replicate 2

source_name: AcB60 7 days post-infection

value: 16 weeks


title: FLC_39


title: FLC_37


title: PC-5d-T1

description:
PA181_5d-PC-1-Tip_FS324-37_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: AcB60 7 days post-infection [ACB607092]

description: biological replicate 1


title: Ile-5d-T3

description:
PA181_5d-Ile-3-Tip_FS324-63_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: Ileum


title: Ile-5d-T2

description:
PA181_5d-Ile-2-Tip_FS324-27_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: AcB60 7 days post-infection [ACB607107]

description: biological replicate 3


title: AcB60 3 days post-infection [ACB603131]

description: biological replicate 3

source_name: AcB60 3 days post-infection


title: FLC_31


title: Ile-5d-C2

description:
PA181_5d-Ile-2-Crypt_FS324-28_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: GFP at T8, biological repeat 1

description: Gene expression data from GFP-expressing worms 8 hours after temperature upshift

value: GFP


title: AJ uninfected [AJ0122]

description: biological replicate 1

value: AJ

value: 13 weeks


title: FLC_26


title: FLC_30


title: FLC_35


title: AJ uninfected [AJ0133]

description: biological replicate 3


title: FLC_22


title: FLC_23


title: PC-3d-T3

description:
PA181_3d-PC-3-Tip_FS324-23_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: CONV-D day 3


title: FLC_41


title: FLC_32


title: PC-5d-C2

description:
PA181_5d-PC-2-Crypt_FS324-40_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: AcB60 3 days post-infection [ACB603112]

description: biological replicate 2

value: 1000 CFUs of S. Typhimuirum

value: spleen homogenate


title: Ile-5d-C3

description:
PA181_5d-Ile-3-Crypt_FS324-30_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: CONV-D day 5


title: AcB60 3 days post-infection [ACB603100]

description: biological replicate 1

value: female


title: Ile-5d-C1

description:
PA181_5d-Ile-1-Crypt_FS324-26_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: 10-12 weeks


title: FLC_20

value: FLC liver tissue


title: Ile-5d-T1

description:
PA181_5d-Ile-1-Tip_FS324-25_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 5 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: FLC_18


title: AcB60 uninfected [ACB600136]

description: biological replicate 3

source_name: AcB60 uninfected


title: PC-3d-C3

description:
PA181_3d-PC-3-Crypt_FS324-24_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: PC-3d-T1

description:
PA181_3d-PC-1-Tip_FS324-19_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: FLC_17


title: hfREF24 [set 1]

description: reduced ejection fraction

tag: sample group

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)

value: peripheral blood

tag: molecule subtype

value: microRNA


title: hfPEF3 [set 1]

description: preserved ejection fraction

value: patients with heart ailment (hfPEF)

tag: % of left ventricular ejection fraction

value: preserved left ventricular ejection fraction (hfPEF)


title: Control13 [set 1]

description: non-heart failure subject

value: control (no past history of heart failure/disease)


title: Control14 [set 1]

description: non-heart failure subject


title: PC-3d-C2

description:
PA181_3d-PC-2-Crypt_FS324-22_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

tag: strain

tag: age

value: Proximal colon

value: Crypt


title: hfREF23 [set 1]

description: reduced ejection fraction


title: AcB60 uninfected [ACB600119]

description: biological replicate 1

value: 16 weeks

value: none (naïve control)


title: hfPEF2 [set 1]

description: preserved ejection fraction


title: FLC_13

value: Normal liver tissue


title: FLC_12


title: FLC_08


title: FLC_14


title: AcB60 uninfected [ACB600127]

description: biological replicate 2

value: spleen homogenate


title: FLC_15


title: FLC_19


title: AJ 3 days post-infection [AJ3102]

description: biological replicate 2

value: AJ

value: 13 weeks

value: 1000 CFUs of S. Typhimuirum

value: 3 days post-infection


title: hfREF22 [set 1]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)


title: Control12 [set 1]

description: non-heart failure subject


title: Control11 [set 1]

description: non-heart failure subject


title: E10.5 Mouse Otic Vesicles _ 3

city: Stanford

first: Byron

middle: H

last: Hartman

state: CA

address: 300 Pasteur Drive Edwards R219

department: Otolaryngology - Head and Neck Surgery

institute: Stanford University School of Medicine

description: Sample OV_3.AVG_Signal

data_processing: The data were normalized using quantile normalization in R

source_name: mouse otic vesicle

extract_protocol: RNA was extracted with Machery Nagel RNA XS kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: dissected pooled otic vesicles


title: E10.5 Mouse Embryo Minus Otic Region _ 3

description: Sample Embryo_3.AVG_Signal

source_name: mouse embryo sans otic

value: whole embryos minus the otic regions


title: hfREF21 [set 1]

description: reduced ejection fraction

value: reduced left ventricular ejection fraction (hfREF)

value: peripheral blood

value: microRNA


title: E10.5 Mouse Periotic Tissues _ 3

description: Sample Periotic_3.AVG_Signal

source_name: mouse periotic tissue

value: dissected periotic tissues


title: FLC_02 N

source_name: FLC_02 N


title: FLC_05

value: FLC liver tissue


title: Ile-3d-C3

description:
PA181_3d-Ile-3-Crypt_FS324-12_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

tag: gender

value: female

value: 10-12 weeks

value: CONV-D day 3

value: Ileum

value: Crypt


title: E10.5 Mouse Otic Vesicles _ 1

description: Sample OV_1.AVG_Signal


title: Control10 [set 1]

description: non-heart failure subject

value: control (no past history of heart failure/disease)


title: FLC_02


title: E10.5 Mouse Otic Vesicles _ 2

description: Sample OV_2.AVG_Signal


title: hfREF20 [set 1]

description: reduced ejection fraction


title: PC-3d-C1

description:
PA181_3d-PC-1-Crypt_FS324-20_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: Proximal colon


title: NAC RNAi replicate 4

city: Konstanz

first: Tancred

last: Frickey

state: BW

address: Universitaetsstr. 10

department: Biology

country: Germany

institute: University of Konstanz

description: Biological replicate 4 of 4. NAC RNAi

hyb_protocol: hybridization was performed by Oaklabs according to their standard protocol

scan_protocol: scanning was performed by Oaklabs according to their standard protocol

data_processing: Create two files specifying what experimental samples are to be found in what data-file CYT refers to the measured cytosolic fraction, ER refers to the measured membrane-associated fraction (predominantly Endoplasmic Reticulum) Empty_vector (ev) is the control experiment, RNAi_vector (RNAi) is the experiments in which the genes of interest were knocked down by RNAi. Read the data into 'R' using read.maimages ('limma' package) commands: RAWev <- read.maimages(targetsev, path="./", source="agilent.median") RAWrnai <- read.maimages(targetsrnai, path="./", source="agilent.median"). Normalize this data within each array using the 'loess' normalization implemented in the 'limma' package commands: LOESSev <- normalizeWithinArrays(RAWev, method="loess") LOESSrnai <- normalizeWithinArrays(RAWrnai, method="loess"). Lastly write the data to the files 'MAev.Rfile' (normalized empty_vector experiment data) and 'MArnai.Rfile' (normalized RNAi-experiment data).

source_name: cytosolic ribosomes

label_protocol: 50 ng RNA were labelled according to Oaklabs standard protocol

growth_protocol: Worms were grown at 25°C (non-permissive temperature) in liquid culture

extract_protocol: RNA was extracted with Qiagen RNeasy Mini Kit according to manufacturer's instructions

treatment_protocol: RNAi was performed by feeding bacteria producing dsRNA, start of RNAi treatment was in the L2/L3 larval stage

value: SS104, sterile mutant

value: day 3 adult

tag: vector

value: NAC RNAi

source_name: ER-attached ribosomes


title: E10.5 Mouse Periotic Tissues _ 2

description: Sample Periotic_2.AVG_Signal


title: E10.5 Mouse Periotic Tissues _ 1

description: Sample Periotic_1.AVG_Signal


title: Ile-3d-T2

description:
PA181_3d-Ile-2-Tip_FS324-67_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

value: Tip


title: Ile-3d-C2

description:
PA181_3d-Ile-2-Crypt_FS324-10_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: FLC_01 N

source_name: FLC_01 N

value: Normal liver tissue


title: PC-1d-T3

description:
PA181_1d-PC-3-Tip_FS324-17_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: CONV-D day 1


title: PC-1d-C3

description:
PA181_1d-PC-3-Crypt_FS324-18_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: PC-3d-T2

description:
PA181_3d-PC-2-Tip_FS324-21_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: Control replicate 4

description: Biological replicate 4 of 4. Control

value: empty


title: PC-1d-T1

description:
PA181_1d-PC-1-Tip_FS324-13_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: E10.5 Mouse Embryo Minus Otic Region _ 2

description: Sample Embryo_2.AVG_Signal

value: whole embryos minus the otic regions


title: PC-1d-C2

description:
PA181_1d-PC-2-Crypt_FS324-16_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: Ile-3d-T3

description:
PA181_3d-Ile-3-Tip_FS324-11_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3


title: Ile-3d-C1

description:
PA181_3d-Ile-1-Crypt_FS324-8_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: Ile-3d-T1

description:
PA181_3d-Ile-1-Tip_FS324-7_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 3 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1


title: Control9 [set 1]

description: non-heart failure subject

value: peripheral blood

value: microRNA


title: hfREF19 [set 1]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)


title: PC-1d-T2

description:
PA181_1d-PC-2-Tip_FS324-15_130418.CEL
Gene expression data from LCM Tip fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

value: female

value: 10-12 weeks


title: Control8 [set 1]

description: non-heart failure subject


title: Control6 [set 1]

description: non-heart failure subject


title: Control7 [set 1]

description: non-heart failure subject


title: E10.5 Mouse Embryo Minus Otic Region _ 1

description: Sample Embryo_1.AVG_Signal


title: NAC RNAi replicate 3

description: Biological replicate 3 of 4. NAC RNAi


title: PC-1d-C1

description:
PA181_1d-PC-1-Crypt_FS324-14_130418.CEL
Gene expression data from LCM Crypt fraction of Proximal colon after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: Crypt


title: hfREF16 [set 1]

description: reduced ejection fraction


title: hfREF17 [set 1]

description: reduced ejection fraction


title: Control5 [set 1]

description: non-heart failure subject

value: control (no past history of heart failure/disease)


title: hfREF18 [set 1]

description: reduced ejection fraction


title: FLC_01

value: FLC liver tissue


title: Control4 [set 1]

description: non-heart failure subject


title: NAC RNAi replicate 2

description: Biological replicate 2 of 4. NAC RNAi

value: SS104, sterile mutant


title: Control3 [set 1]

description: non-heart failure subject


title: Control2 [set 1]

description: non-heart failure subject


title: Ile-1d-T3

description:
PA181_1d-Ile-3-Tip_FS324-5_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: Ileum


title: Ile-1d-C2

description:
PA181_1d-Ile-2-Crypt_FS324-4_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2


title: Control replicate 1

description: Biological replicate 1 of 4. Control

value: day 3 adult


title: GF_PC_C4

description: PA181_GF-PC-5-Crypt_FS291-16_130115_(MoGene-2_0-st).CEL

data_processing: The data was processed with quantile normalization, pm-only for background coreection, iterative PLIER algorithm for expresion index calculation.  The analysis was performed by expression console software

source_name: LCM Crypt fraction of Proximal colon_Germ-free mouse

growth_protocol: Germ-free C57Bl/6 mice were maintained in standard makrolon cages according to standard protocols inside sterile flexible film isolators. Conventionally-raised C57Bl/6 mice were kept in sterilized, filter-topped IVC cages under specific pathogen-free conditions. All animals were housed with wood shavings and wooden wool and had free access to standard autoclaved chow diet (Labdiet, USA) and water. Mice were kept with 12 hours light/dark cycle at 18-22°C temperature and 35-65% relative humidity which was continuously and automatically registered and regulated. A maximum of 5 mice were kept in one cage. Animals used for experiments were females and 10-12 weeks of age at harvest.

treatment_protocol: 10-12 weeks old mice were sacrificed by cervical dislocation and the intestine removed. The distal part of the small intestine (ileum) and the proximal part of the colon were excised, flushed with PBS and finally flushed and embedded with OCT freezing medium. The complete procedure from sacrificing the mouse until the frozen tissue blocks took less than five minutes to preserve RNA integrity. All material and solutions used further were RNase-free. 8 µm thick cryosections were cut from the OCT blocks at -20°C using a microtome (Leica), placed onto PEN membrane slides (ZEISS) and immediately stained for LCM. Briefly, slides were dehydrated in absolute and 70% ethanol for 30s each, dipped into RNase-free water to remove excessive OCT and then incubated in 1% cresyl violet in 50% ethanol step for another 30s. Slides were partially destained by dipping in 70% and absolute ethanol before air-drying. Slides were stored in airtight containers at -80°C until laser capture microdissection (LCM). Airtight containers were equilibrated to ambient temperature before opening. LCM was performed using PALM Microbeam Microdissection microscope (ZEISS) and fractions were collected dry. The harvested fractions were immediately lyzed in RLT containing 1% β-mercaptoethanol and stored at -80°C.

value: Germ-free

value: Proximal colon


title: Control replicate 3

description: Biological replicate 3 of 4. Control


title: Ile-1d-T1

description:
PA181_1d-Ile-1-Tip_FS324-61_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: CONV-D day 1

value: Tip


title: GF_PC_T3

description: PA181_GF-PC-4-Tip_FS291-13_130115_(MoGene-2_0-st).CEL

source_name: LCM Tip fraction of Proximal colon_Germ-free mouse


title: GF_PC_T4

description: PA181_GF-PC-2-Tip_FS291-9_130118_(MoGene-2_0-st).CEL


title: hfREF13 [set 1]

description: reduced ejection fraction


title: hfREF14 [set 1]

description: reduced ejection fraction


title: hfPEF1 [set 1]

description: preserved ejection fraction

value: patients with heart ailment (hfPEF)

value: preserved left ventricular ejection fraction (hfPEF)


title: hfREF15 [set 1]

description: reduced ejection fraction

value: peripheral blood

value: microRNA


title: hfREF12 [set 1]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)


title: NAC RNAi replicate 1

description: Biological replicate 1 of 4. NAC RNAi

value: NAC RNAi


title: Ile-1d-C3

description:
PA181_1d-Ile-3-Crypt_FS324-6_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #3

value: female

value: 10-12 weeks

value: Crypt


title: HCC827 control, biological rep1

city: Shanghai

first: Meiyu

last: Geng

address: 555 Zuchongzhi Road

country: China

institute: Shanghai Institute of Material Medica

description: Gene expression data from HCC827 treated with DMSO

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix)in Hybridization Oven 645 (Affymetrix)and Fluidics Station 450 (Affymetrix) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies).

source_name: HCC827 treated with DMSO

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Affymetrix) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were routinely cultured in air incubator at 37°C with 5% CO2

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit (QIAGEN) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: Cells were treated with DMSO or SGX-523 at 1uM for 24 and 48 hours.

tag: sample type

value: Non-small cell lung cancer

tag: treatment

value: HCC827 treated with DMSO


title: HCC827 SGX-523 48h, biological rep3

description: Gene expression data from HCC827 treated with SGX-523 at 1uM for 48h


title: Ile-1d-C1

description:
PA181_1d-Ile-1-Crypt_FS324-2_130417.CEL
Gene expression data from LCM Crypt fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #1

value: Ileum


title: HCC827 SGX-523 24h, biological rep3

description: Gene expression data from HCC827 treated with SGX-523 at 1uM for 24h


title: HCC827 SGX-523 48h, biological rep1

source_name: HCC827 treated with SGX-523 at 1uM for 48h


title: GF_PC_C5

description: PA181_GF-PC-3-Crypt_FS291-12_130118_(MoGene-2_0-st).CEL

value: Germ-free


title: GF_PC_C2

description: PA181_GF-PC-4-Crypt_FS291-14_130115_(MoGene-2_0-st).CEL

value: Proximal colon


title: hfREF11 [set 1]

description: reduced ejection fraction


title: GF_PC_T2

description: PA181_GF-PC-1-Tip_FS291-7_130118_(MoGene-2_0-st).CEL


title: HCC827 SGX-523 24h, biological rep1

source_name: HCC827 treated with SGX-523 at 1uM for 24h


title: GF_PC_C1

description: PA181_GF-PC-1-Crypt_FS292-1_130118_(MoGene-2_0-st).CEL


title: Ile-1d-T2

description:
PA181_1d-Ile-2-Tip_FS324-3_130417.CEL
Gene expression data from LCM Tip fraction of Ileum after CONV-D day 1 of 10-12 weeks old female C57Bl/6 mouse, biological replicate #2

value: CONV-D day 1


title: HCC827 control, biological rep2

source_name: HCC828 treated with DMSO


title: HCC827 control, biological rep3

source_name: HCC829 treated with DMSO


title: MKN-45 SGX-523 48h, biological rep2

description: Gene expression data from MKN-45 treated with SGX-523 at 1uM for 48h

value: Gastric cancer


title: Control replicate 2

description: Biological replicate 2 of 4. Control

value: SS104, sterile mutant

value: day 3 adult

value: empty


title: MKN-45 SGX-523 24h, biological rep2

description: Gene expression data from MKN-45 treated with SGX-523 at 1uM for 24h


title: HCC827 SGX-523 48h, biological rep2

value: HCC827 treated with SGX-523 at 1uM for 48h


title: GF_PC_T1

description: PA181_GF-PC-3-Tip_FS292-2_130118_(MoGene-2_0-st).CEL

value: Tip


title: HCC827 SGX-523 24h, biological rep2

value: HCC827 treated with SGX-523 at 1uM for 24h


title: GF_PC_T5

description: PA181_GF-PC-5-Tip_FS291-15_130115_(MoGene-2_0-st).CEL


title: hfREF10 [set 1]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)

value: peripheral blood

value: microRNA


title: GF_IL_T5

description: PA181_GF-Ile-5-Tip_FS292-11_130115_(MoGene-2_0-st).CEL

source_name: LCM Tip fraction of Ileum_Germ-free mouse

value: female

value: 10-12 weeks


title: hfREF9 [set 1]

description: reduced ejection fraction


title: MKN-45 SGX-523 24h, biological rep3

source_name: MKN-45 treated with SGX-523 at 1uM for 24h


title: MKN-45 SGX-523 48h, biological rep1

source_name: MKN-45 treated with SGX-523 at 1uM for 48h


title: GF_PC_C3

description: PA181_GF-PC-2-Crypt_FS291-10_130118_(MoGene-2_0-st).CEL

value: Crypt


title: GF_IL_C4

description: PA181_GF-Ile-5-Crypt_FS292-12_130115_(MoGene-2_0-st).CEL

source_name: LCM Crypt fraction of Ileum_Germ-free mouse

value: Germ-free

value: Ileum


title: hfREF7 [set 1]

description: reduced ejection fraction


title: hfREF6 [set 1]

description: reduced ejection fraction


title: hfREF8 [set 1]

description: reduced ejection fraction


title: MKN-45 SGX-523 48h, biological rep3

value: MKN-45 treated with SGX-523 at 1uM for 48h


title: hfREF3 [set 1]

description: reduced ejection fraction


title: hfREF4 [set 1]

description: reduced ejection fraction


title: hfREF5 [set 1]

description: reduced ejection fraction


title: GF_IL_T3

description: PA181_GF-Ile-4-Tip_FS293-3_130115_(MoGene-2_0-st).CEL


title: GF_IL_T1

description: PA181_GF-Ile-3-Tip_FS293-1_130118_(MoGene-2_0-st).CEL


title: MKN-45 control, biological rep1

description: Gene expression data from MKN-45 treated with DMSO

source_name: MKN-45 treated with DMSO

value: Gastric cancer

value: MKN-45 treated with DMSO


title: EBC-1 SGX-523 48h, biological rep3

description: Gene expression data from EBC-1 treated with SGX-523 at 1uM for 48h

value: Non-small cell lung cancer


title: MKN-45 control, biological rep2

source_name: MKN-46 treated with DMSO


title: MKN-45 SGX-523 24h, biological rep1

value: MKN-45 treated with SGX-523 at 1uM for 24h


title: GF_IL_T4

description: PA181_GF-Ile-2-Tip_FS292-5_130118_(MoGene-2_0-st).CEL


title: EBC-1 SGX-523 48h, biological rep1

source_name: EBC-1 treated with SGX-523 at 1uM for 48h


title: GF_IL_C2

description: PA181_GF-Ile-4-Crypt_FS292-10_130115_(MoGene-2_0-st).CEL


title: GF_IL_C3

description: PA181_GF-Ile-2-Crypt_FS292-6_130118_(MoGene-2_0-st).CEL


title: hfREF2 [set 1]

description: reduced ejection fraction


title: GF_IL_C5

description: PA181_GF-Ile-3-Crypt_FS292-8_130118_(MoGene-2_0-st).CEL


title: MKN-45 control, biological rep3

source_name: MKN-47 treated with DMSO


title: GF_IL_C1

description: PA181_GF-Ile-1-Crypt_FS292-4_130118_(MoGene-2_0-st).CEL


title: hfREF1 [set 1]

description: reduced ejection fraction


title: Control1 [set 1]

description: non-heart failure subject

value: control (no past history of heart failure/disease)


title: EBC-1 SGX-523 48h, biological rep2

value: EBC-1 treated with SGX-523 at 1uM for 48h


title: CR_PC_T3

description: PA181_CR-PC-4-Tip_FS289-9_130118_(MoGene-2_0-st).CEL

source_name: LCM Tip fraction of Proximal colon_Conventionally-raised mouse

value: Conventionally-raised

value: Proximal colon

value: Tip


title: EBC-1 SGX-523 24h, biological rep3

description: Gene expression data from EBC-1 treated with SGX-523 at 1uM for 24h


title: EBC-1 SGX-523 24h, biological rep2

source_name: EBC-1 treated with SGX-523 at 1uM for 24h


title: CR_PC_T5

description: PA181_CR-PC-5-Tip_FS291-5_130118_(MoGene-2_0-st).CEL


title: CR_PC_C4

description: PA181_CR-PC-5-Crypt_FS291-6_130118_(MoGene-2_0-st).CEL

source_name: LCM Crypt fraction of Proximal colon_Conventionally-raised mouse


title: GF_IL_T2

description: PA181_GF-Ile-1-Tip_FS292-3_130118_(MoGene-2_0-st).CEL


title: EBC-1 SGX-523 24h, biological rep1

value: EBC-1 treated with SGX-523 at 1uM for 24h


title: EBC-1 control, biological rep2

description: Gene expression data from EBC-1 treated with DMSO

source_name: EBC-1 treated with DMSO

value: EBC-1 treated with DMSO


title: EBC-1 control, biological rep3


title: CR_PC_C2

description: PA181_CR-PC-4-Crypt_FS289-10_130118_(MoGene-2_0-st).CEL

value: female


title: CR_PC_T1

description: PA181_CR-PC-3-Tip_FS289-7_130115_(MoGene-2_0-st).CEL

value: 10-12 weeks


title: EBC-1 control, biological rep1


title: hfPEF10 [set 3]

description: preserved ejection fraction

value: patients with heart ailment (hfPEF)

value: preserved left ventricular ejection fraction (hfPEF)

value: peripheral blood

value: microRNA


title: hfPEF9 [set 3]

description: preserved ejection fraction


title: hfPEF8 [set 3]

description: preserved ejection fraction


title: CR_PC_C5

description: PA181_CR-PC-3-Crypt_FS289-8_130115_(MoGene-2_0-st).CEL

value: Crypt


title: CR_PC_T4

description: PA181_CR-PC-2-Tip_FS289-1_130115_(MoGene-2_0-st).CEL


title: hfREF2 [set 3]

description: reduced ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)


title: Control4 [set 3]

description: non-heart failure subject


title: CR_PC_C3

description: PA181_CR-PC-2-Crypt_FS291-2_130115_(MoGene-2_0-st).CEL


title: Control3 [set 3]

description: non-heart failure subject


title: CR_PC_C1

description: PA181_CR-PC-1-Crypt_FS286-11_130115_(MoGene-2_0-st).CEL


title: Control2 [set 3]

description: non-heart failure subject


title: CR_PC_T2

description: PA181_CR-PC-1-Tip_FS286-10_130115_(MoGene-2_0-st).CEL


title: CR_IL_T5

description: PA181_CR-Ile-5-Tip_FS286-6_130118_(MoGene-2_0-st).CEL

source_name: LCM Tip fraction of Ileum_Conventionally-raised mouse

value: Ileum


title: Control1 [set 3]

description: non-heart failure subject

value: control (no past history of heart failure/disease)


title: CHC1310T

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

description: Genomic DNA extracted from liver tumors was genotyped using Infinium HumanHap370-v1 Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
standard Illumina protocol
Log_R_Ratio (exported from Beadstudio , GC_SCORE (exported from Beadstudio software); Theta (exported from Beadstudio software); R (exported from Beadstudio software); B_Allele_Freq (exported from Beadstudio software)software)

label: C-Bio and A-DNP

source_name: Fibrolamellar carcinoma

label_protocol: standard Illumina protocol

extract_protocol: DNA and RNA samples were extracted from frozen tissues, in accordance with standard procedures, as previously described [Rebouissou et al. J Biol Chem 2007]

value: Female

value: liver

tag: disease state

value: Fibrolamellar carcinoma

tag: patient number


title: CR_IL_C4

description: PA181_CR-Ile-5-Crypt_FS286-7_130118_(MoGene-2_0-st).CEL

source_name: LCM Crypt fraction of Ileum_Conventionally-raised mouse

tag: bacterial status

value: Conventionally-raised

tag: tissue


title: hfREF1 [set 3]

description: reduced ejection fraction


title: CR_IL_T3

description: PA181_CR-Ile-4-Tip_FS285-2_130118_(MoGene-2_0-st).CEL

tag: fraction

value: Tip

tag: replicate


title: hfPEF7 [set 3]

description: preserved ejection fraction


title: CHC906T


title: CR_IL_C2

description: PA181_CR-Ile-4-Crypt_FS284-8_130118_(MoGene-2_0-st).CEL