title: wild-type-control, biological rep3

description: Gene expression data from wild-type control(RNAi)

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: wild-type worms on control(RNAi)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Wild-type and atfs-1(tm4525) worms were synchronized by bleaching and raised in liquid culture.

extract_protocol: Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.

treatment_protocol: Worms were fed either control (RNAi) and spg-7 (RNAi) and harvested at L4 stage

value: whole organism

tag: genotype

value: wild-type

tag: knockdown

value: control RNAi

tag: genetic background


title: atfs-1(tm4525)-control, biological rep3

status: Public on Jul 12 2012

type: RNA

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from atfs-1(tm4525) on control(RNAi)

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: atfs-1(tm4525) worms on control(RNAi)

tag: tissue

tag: age


title: Nurr_2minus

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse WG-6 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing:
The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed.
1. Illumina data are loaded into GenomeStudio and produced the raw data automatically. There is no normalization and background correction applied during this process. The data will be automatically normalized in Partek. To avoid shifting the data, Partek doesn't recommend to use background correction. Otherwise the negative intensities in the data will create problems for the following analysis.
2. Data from GenomeStudio is exported in a custom Partek report file for seamless importation into Partek. Gene level option is chosen and the probe intensities are summarized and averaged for the same genes. The intensity is log2 transformed at the same time.
3. After the Partek version data is imported into Partek, there are options for normalization to be chosen. But it is not necessary to use normalization according to Partek. So there is no further background correction and normalization. The user assigned the factor (sample attributes) before ANOVA analysis and did one factor analysis.

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

tag: strain

tag: cell type

value: mESC

tag: genotype/variation


title: wild-type-treated, biological rep3

description: Gene expression data from wild-type spg-7(RNAi)

source_name: wild-type worms on spg-7(RNAi)

value: spg-7 RNAi


title: atfs-1(tm4525)-treated, biological rep3

description: Gene expression data from atfs-1(tm4525) on spg-7(RNAi)

source_name: atfs-1(tm4525) worms on spg-7l(RNAi)


title: Nurr_2plus


title: Smo-deficient OP9 cells, rep3

city: Baltimore

first: Stephen

last: Desiderio

state: MD

address: 733 N. Broadway

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: Gene expression data from Smo-deficient cells

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix Scanner 3000 with 7G upgrade

data_processing:
Affymetrix Expression Suite 1.1
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-algorithm-param-quantification-name = med-polish
affymetrix-algorithm-param-quantification-scale = log2

label: Biotin

source_name: Smo-deficient OP9 cells

label_protocol: Affymetrix standard

growth_protocol: Maintained in ATCC-recommended medium at sub-confluency

extract_protocol: Qiagen RNA easy kit

tag: cell line


title: Control OP9 cells, rep2

description: Gene expression data from control cells

source_name: Control OP9 cells


title: Control OP9 cells, rep1

description: Gene expression data from control cells


title: Control OP9 cells, rep3

description: Gene expression data from control cells


title: Mouse T cells exposed to retinal pigment epithelium (RPE)

city: Tokyo

first: Sunao

last: Sugita

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

department: Ophthalmology

country: Japan

institute: Tokyo Medical and Dental Univ.

description: Strain: C57 BL/6 background; Gender: male; Age: 6-week-old; Tissue: primary cultured retinal pigment epithelium (RPE)

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45 degree Celsius, 16 hours). Hybridization was controled by adding cRNA cocktail (BioC, BioD, Cre) mixed as described in previous versions of the Expression Analysis Technical Manual.  Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Chip analysis was performed using the Affymetrix GeneChip Operating Software v1.3.

label_protocol: 5 micrograms of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix).  Double-stranded cDNA was cleaned up by using Phase Lock Gels (Eppendorf)-Phenol/Chloroform Extraction (Ambion). In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNA of these T cells (RPE-exposed T cells and control T cells) was isolated with Trizol reagent (Invitrogen-Life Technologies).  RNA was further purified using an RNeasy Mini Kit (Qiagen).

value: C57 BL/6 background

tag: gender

value: male


title: Mouse CD4 T cells

description: Strain: C57 BL/6 background; Gender: male; Age: 6-week-old; Tissue: T cells

source_name: Mouse control T cells

value: T cells


title: msh1,stunt,biological rep 1

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

description:
Gene expression data from stunted msh1 transgenic line
msh1_stunt-1

hyb_protocol: RNA was hybridized to individual Affymetrix GeneChip oligonucleotide ATH1 array using manufacturers instructions

scan_protocol: According to Affymetrix instructions

data_processing: Expression data from Affymetrix genechips were normalized using the Robust Multichip Average (RMA) method using bioconductor’s affy package in the R language

organism: Arabidopsis thaliana

source_name: msh1 stunted line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: green house grown at 12/12 day and night cycle.

extract_protocol: total RNA was extracted from each plant using TRIzol (Invitrogen) extraction procedure followed by purification on RNeasy columns (Qiagen).

treatment_protocol: 8 weeks old plants

value: above ground part of plant

value: 8-week-old old plant

value: stunted msh1 RNAi transgenic line


title: msh1,stunt,biological rep 3

description:
Gene expression data from stunted msh1 transgenic line
msh1_stunt-3


title: msh1,variegation, Col-0, biological rep 3

description:
Gene expression data from variegation msh1 transgenic line
msh1_var-3

source_name: msh1 variegated line

value: variegation msh1 RNAi transgenic line


title: msh1,stunt,biological rep 2

description:
Gene expression data from stunted msh1 transgenic line
msh1_stunt-2


title: Nurr_1plus


title: wild-type-treated, biological rep2


title: atfs-1(tm4525)-treated, biological rep2


title: wild-type-control, biological rep2


title: atfs-1(tm4525)-control, biological rep2


title: Hes_2minus


title: Nurr_1minus


title: wild-type-treated, biological rep1


title: wild-type-control, biological rep1


title: atfs-1(tm4525)-treated, biological rep1


title: Hes_1plus


title: atfs-1(tm4525)-control, biological rep1


title: ID patient 19

type: genomic

city: Amsterdam

first: Els

last: Voorhoeve

address: De Boelelaan 1117

department: Clinical Genetics

country: Netherlands

institute: VU medical center

hyb_protocol: Following standard manufacturer's procedures

scan_protocol: Scanned on scanner following the manufacturer's procedures

data_processing: The CNV-calling was performed using Bluefuse Multi v2.2 (8114), algorithm Cytochip v2. Smoothing: backbone=1, Disease=1, no minimal deletion of duplication size was used.

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA patient 19

label_protocol: As per manufacturer

extract_protocol: Genomic DNA was extracted from  peripheral blood using chemagen. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: lymfocytes

tag: disease

value: intellectual disability/autism

value: child

source_name: sex matched DNA control pool of at least 10 different healthy individuals

tag: reference


title: Hes_1minus


title: Panc1 DMSO 1

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: LCCC, 450 West Drive

department: Surgical Oncology

institute: University of North Carolina at Chapel Hill

description: Panc1 DMSO1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference

tag: sample type

value: whole human total RNA

source_name: Panc1 DMSO1

extract_protocol: Qiagen All-prep Kit

tag: media

value: DMSO


title: Hes_2plus


title: SW620

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: HT29 DMSO 4

description: HT29 DMSO#4

source_name: HT29 DMSO#4


title: HT29 DMSO 2

description: HT29 DMSO#2

source_name: HT29 DMSO#2


title: MiaPaca2 DMSO 2

description: MiaPaca2 DMSO2

source_name: MiaPaca2 DMSO2


title: MiaPaca2


title: Panc1 DMSO 4

description: Panc1 DMSO4

source_name: Panc1 DMSO4


title: msh1,variegation, Col-0, biological rep 2

description:
Gene expression data from variegation msh1 transgenic line
msh1_var-2


title: MiaPaca2 DMSO 1

description: MiaPaca2 DMSO1

source_name: MiaPaca2 DMSO1


title: HPAFII

description: HPAFII

source_name: HPAFII

value: HPAFII


title: HPAC

description: HPAC

source_name: HPAC

value: HPAC


title: wild type, Col-0, biological rep 2

description:
Gene expression data from wild type
Col0-2

source_name: wild type

value: wild type


title: colon conventionalized t=8d_rep1

status: Public on Jul 11 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 144 arrays that were used in this experiment were provided as 1x 96 array plate and 3x 24 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0). The SI samples were normalzed together, separately from the colon samples.

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 1

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: Germ free (GF) mice (male, C57 BL/6) were purchased from the Centre de Recherché, Institute National de la Recherche Agronomique (Jouy-en-Josas, France). Mice were maintained under sterile conditions. Mice had ad libitum access to sterilized water and were maintained on a commercial laboratory chow diet (UAR 1016C Laboratory Chow, UAR, Villemoisson sur Orge, France) that was sterilized by gamma irradiation (45KGy).

extract_protocol: Total mouse RNA was obtained from a 2-cm segment of jejunum, ileum and colon by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by DNAse treatment and column purification using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.

treatment_protocol: After 2 weeks of acclimatization and diet adaptation, a subset of GF mice were randomly assigned to sacrifice by oral anesthesia using isoflurane (t=d0, GF). The remaining GF mice were conventionalized by oral gavage with 0.5ml of mixed fecal suspension derived from 0.2g of freshly obtained fecal material of conventionally raised  mice (C57 BL/6) diluted 100-folds in Brain Heart infusion (BHI) broth. Conventionalized mice were sacrificed at days (d) d1, d2, d4, d8, d16 and d30 after conventionalization. Small intestine (SI; jejunum, and ileum), and large intestine (LI; colon) from each mouse were removed. The 2 segments of the SI and the entire colon were then divided into 2-cm segments that were immediately stored in RNA-later at room temperature for 1 hour prior to subsequent storage at -80°C for RNA isolation.

value: colon

tag: days of conventionalized

tag: age at start of experiment

value: 8 wks


title: colon conventionalized t=2d_rep6

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 6

value: 10 wks


title: colon conventionalized t=2d_rep4

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 4

value: male


title: colon conventionalized t=8d_rep6

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 6


title: HCT-116


title: colon conventionalized t=8d_rep3

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 3


title: colon germ-free t=0d_rep10

source_name: colon from germ-free mouse (day 0), replicate 10


title: colon conventionalized t=4d_rep11

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 11


title: colon conventionalized t=16_rep6

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 6


title: colon conventionalized t=8d_rep2

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 2


title: colon germ-free t=0d_rep11

source_name: colon from germ-free mouse (day 0), replicate 11


title: colon conventionalized t=2d_rep5

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 5


title: wild type, Col-0, biological rep 3

description:
Gene expression data from wild type
Col0-3


title: colon conventionalized t=16_rep5

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 5


title: colon conventionalized t=8d_rep5

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 5


title: Capan2

source_name: Human Reference


title: colon conventionalized t=4d_rep10

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 10


title: colon conventionalized t=8d_rep4

source_name: colon from mouse 8 days after conventionalization (day 8), replicate 4


title: colon conventionalized t=16_rep4

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 4


title: colon conventionalized t=2d_rep3

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 3


title: msh1,variegation, Col-0, biological rep 1

description:
Gene expression data from variegation msh1 transgenic line
msh1_var-1

source_name: msh1 variegated line


title: wild type, Col-0, biological rep 1

description:
Gene expression data from wild type
Col0-1

source_name: wild type


title: colon conventionalized t=16_rep1

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 1


title: colon conventionalized t=16_rep3

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 3


title: colon conventionalized t=2d_rep1

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 1


title: colon conventionalized t=16_rep2

source_name: colon from mouse 16 days after conventionalization (day 16), replicate 2


title: colon conventionalized t=2d_rep2

source_name: colon from mouse 2 days after conventionalization (day 2), replicate 2


title: colon conventionalized t=1d_rep5

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 5


title: colon conventionalized t=4d_rep6

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 6


title: colon conventionalized t=4d_rep7

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 7


title: colon conventionalized t=4d_rep8

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 8


title: colon conventionalized t=4d_rep1

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 1


title: colon conventionalized t=30d_rep2

source_name: colon from mouse 30 days after conventionalization (day 30), replicate 2


title: colon conventionalized t=4d_rep3

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 3


title: colon conventionalized t=30d_rep1

source_name: colon from mouse 30 days after conventionalization (day 30), replicate 1


title: colon conventionalized t=4d_rep2

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 2


title: colon conventionalized t=30d_rep3

source_name: colon from mouse 30 days after conventionalization (day 30), replicate 3


title: colon conventionalized t=1d_rep2

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 2


title: colon germ-free t=0d_rep7

source_name: colon from germ-free mouse (day 0), replicate 7


title: colon conventionalized t=4d_rep4

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 4


title: colon germ-free t=0d_rep9

source_name: colon from germ-free mouse (day 0), replicate 9


title: colon conventionalized t=1d_rep6

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 6


title: colon conventionalized t=1d_rep1

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 1


title: colon germ-free t=0d_rep5

source_name: colon from germ-free mouse (day 0), replicate 5


title: colon germ-free t=0d_rep6

source_name: colon from germ-free mouse (day 0), replicate 6


title: colon conventionalized t=4d_rep9

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 9


title: colon germ-free t=0d_rep4

source_name: colon from germ-free mouse (day 0), replicate 4


title: colon germ-free t=0d_rep8

source_name: colon from germ-free mouse (day 0), replicate 8


title: colon conventionalized t=4d_rep5

source_name: colon from mouse 4 days after conventionalization (day 4), replicate 5


title: colon conventionalized t=1d_rep3

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 3


title: colon conventionalized t=1d_rep4

source_name: colon from mouse 1 day after conventionalization (day 1), replicate 4


title: colon conventionalized t=30d_rep4

source_name: colon from mouse 30 days after conventionalization (day 30), replicate 4


title: colon germ-free t=0d_rep3

source_name: colon from germ-free mouse (day 0), replicate 3


title: colon germ-free t=0d_rep2

source_name: colon from germ-free mouse (day 0), replicate 2


title: colon germ-free t=0d_rep1

source_name: colon from germ-free mouse (day 0), replicate 1


title: ileum conventionalized t=16d_rep4

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 4

value: ileum


title: ileum conventionalized t=16d_rep6

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 6


title: ileum conventionalized t=16d_rep5

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 5


title: ileum conventionalized t=16d_rep3

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 3


title: ileum conventionalized t=8d_rep6

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 6


title: ileum conventionalized t=8d_rep2

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 2


title: ileum conventionalized t=8d_rep5

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 5


title: ileum conventionalized t=4d_rep9

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 9


title: ileum conventionalized t=16d_rep1

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 1


title: ileum conventionalized t=2d_rep4

source_name: ileum from mouse 2 days after conventionalization (day 2), replicate 4


title: ileum conventionalized t=8d_rep3

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 3


title: ileum conventionalized t=4d_rep7

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 7


title: ileum conventionalized t=4d_rep11

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 11


title: ileum conventionalized t=1d_rep1

source_name: ileum from mouse 1 day after conventionalization (day 1), replicate 1


title: ileum conventionalized t=4d_rep8

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 8


title: ileum conventionalized t=2d_rep3

source_name: ileum from mouse 2 days after conventionalization (day 2), replicate 3


title: ileum conventionalized t=8d_rep1

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 1


title: ileum conventionalized t=8d_rep4

source_name: ileum from mouse 8 days after conventionalization (day 8), replicate 4


title: ileum conventionalized t=1d_rep4

source_name: ileum from mouse 1 day after conventionalization (day 1), replicate 4


title: ileum conventionalized t=2d_rep2

source_name: ileum from mouse 2 days after conventionalization (day 2), replicate 2


title: ileum conventionalized t=4d_rep10

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 10


title: ileum germ-free t=0d_rep11

source_name: ileum from germ-free mouse (day 0), replicate 11


title: ileum germ-free t=0d_rep10

source_name: ileum from germ-free mouse (day 0), replicate 10


title: ileum conventionalized t=4d_rep6

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 6


title: ileum conventionalized t=1d_rep3

source_name: ileum from mouse 1 day after conventionalization (day 1), replicate 3


title: ileum conventionalized t=2d_rep1

source_name: ileum from mouse 2 days after conventionalization (day 2), replicate 1


title: ileum conventionalized t=1d_rep5

source_name: ileum from mouse 1 day after conventionalization (day 1), replicate 5


title: ileum conventionalized t=1d_rep2

source_name: ileum from mouse 1 day after conventionalization (day 1), replicate 2


title: ileum germ-free t=0d_rep9

source_name: ileum from germ-free mouse (day 0), replicate 9


title: ileum germ-free t=0d_rep8

source_name: ileum from germ-free mouse (day 0), replicate 8


title: ileum conventionalized t=16d_rep2

source_name: ileum from mouse 16 days after conventionalization (day 16), replicate 2


title: ileum germ-free t=0d_rep6

source_name: ileum from germ-free mouse (day 0), replicate 6


title: ileum germ-free t=0d_rep7

source_name: ileum from germ-free mouse (day 0), replicate 7


title: jejunum conventionalized t=8d_rep5

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 5

value: jejunum


title: jejunum conventionalized t=16d_rep3

source_name: jejunum from mouse 16 days after conventionalization (day 16), replicate 3


title: jejunum conventionalized t=16d_rep5

source_name: jejunum from mouse 16 days after conventionalization (day 16), replicate 5


title: jejunum conventionalized t=16d_rep1

source_name: jejunum from mouse 16 days after conventionalization (day 16), replicate 1


title: jejunum conventionalized t=16d_rep2

source_name: jejunum from mouse 16 days after conventionalization (day 16), replicate 2


title: jejunum conventionalized t=4d_rep8

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 8


title: jejunum conventionalized t=16d_rep4

source_name: jejunum from mouse 16 days after conventionalization (day 16), replicate 4


title: jejunum conventionalized t=8d_rep1

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 1


title: jejunum conventionalized t=2d_rep4

source_name: jejunum from mouse 2 days after conventionalization (day 2), replicate 4


title: jejunum conventionalized t=8d_rep4

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 4


title: jejunum conventionalized t=4d_rep11

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 11


title: jejunum conventionalized t=2d_rep3

source_name: jejunum from mouse 2 days after conventionalization (day 2), replicate 3


title: jejunum conventionalized t=4d_rep7

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 7


title: jejunum conventionalized t=8d_rep3

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 3


title: jejunum conventionalized t=4d_rep10

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 10


title: jejunum conventionalized t=4d_rep6

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 6


title: jejunum conventionalized t=4d_rep9

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 9


title: jejunum conventionalized t=1d_rep2

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 2


title: jejunum conventionalized t=8d_rep2

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 2


title: jejunum conventionalized t=8d_rep6

source_name: jejunum from mouse 8 days after conventionalization (day 8), replicate 6


title: jejunum conventionalized t=2d_rep2

source_name: jejunum from mouse 2 days after conventionalization (day 2), replicate 2


title: jejunum conventionalized t=1d_rep4

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 4


title: jejunum conventionalized t=2d_rep5

source_name: jejunum from mouse 2 days after conventionalization (day 2), replicate 5


title: jejunum conventionalized t=1d_rep1

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 1


title: jejunum conventionalized t=1d_rep5

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 5


title: jejunum conventionalized t=2d_rep1

source_name: jejunum from mouse 2 days after conventionalization (day 2), replicate 1


title: jejunum conventionalized t=1d_rep3

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 3


title: jejunum germ-free t=0d_rep9

source_name: jejunum from germ-free mouse (day 0), replicate 9


title: jejunum conventionalized t=1d_rep6

source_name: jejunum from mouse 1 day after conventionalization (day 1), replicate 6


title: jejunum germ-free t=0d_rep8

source_name: jejunum from germ-free mouse (day 0), replicate 8


title: jejunum germ-free t=0d_rep7

source_name: jejunum from germ-free mouse (day 0), replicate 7


title: jejunum conventionalized t=30d_rep4

source_name: jejunum from mouse 30 days after conventionalization (day 30), replicate 4


title: jejunum conventionalized t=4d_rep1

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 1


title: jejunum conventionalized t=4d_rep5

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 5


title: jejunum conventionalized t=4d_rep4

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 4


title: ileum conventionalized t=30d_rep2

source_name: ileum from mouse 30 days after conventionalization (day 30), replicate 2


title: ileum conventionalized t=4d_rep4

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 4


title: ileum conventionalized t=4d_rep1

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 1


title: jejunum germ-free t=0d_rep10

source_name: jejunum from germ-free mouse (day 0), replicate 10


title: jejunum germ-free t=0d_rep6

source_name: jejunum from germ-free mouse (day 0), replicate 6


title: ileum conventionalized t=30d_rep1

source_name: ileum from mouse 30 days after conventionalization (day 30), replicate 1


title: jejunum germ-free t=0d_rep1

source_name: jejunum from germ-free mouse (day 0), replicate 1


title: jejunum conventionalized t=30d_rep1

source_name: jejunum from mouse 30 days after conventionalization (day 30), replicate 1


title: jejunum conventionalized t=30d_rep3

source_name: jejunum from mouse 30 days after conventionalization (day 30), replicate 3


title: jejunum conventionalized t=30d_rep2

source_name: jejunum from mouse 30 days after conventionalization (day 30), replicate 2


title: ileum conventionalized t=30d_rep3

source_name: ileum from mouse 30 days after conventionalization (day 30), replicate 3


title: ileum germ-free t=0d_rep2

source_name: ileum from germ-free mouse (day 0), replicate 2


title: jejunum conventionalized t=4d_rep3

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 3


title: ileum conventionalized t=30d_rep4

source_name: ileum from mouse 30 days after conventionalization (day 30), replicate 4


title: ileum conventionalized t=4d_rep5

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 5


title: ileum germ-free t=0d_rep1

source_name: ileum from germ-free mouse (day 0), replicate 1


title: ileum germ-free t=0d_rep3

source_name: ileum from germ-free mouse (day 0), replicate 3


title: ileum germ-free t=0d_rep5

source_name: ileum from germ-free mouse (day 0), replicate 5


title: ileum conventionalized t=4d_rep2

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 2


title: jejunum germ-free t=0d_rep4

source_name: jejunum from germ-free mouse (day 0), replicate 4


title: jejunum germ-free t=0d_rep2

source_name: jejunum from germ-free mouse (day 0), replicate 2


title: ileum conventionalized t=4d_rep3

source_name: ileum from mouse 4 days after conventionalization (day 4), replicate 3


title: jejunum germ-free t=0d_rep5

source_name: jejunum from germ-free mouse (day 0), replicate 5


title: ileum germ-free t=0d_rep4

source_name: ileum from germ-free mouse (day 0), replicate 4


title: jejunum conventionalized t=4d_rep2

source_name: jejunum from mouse 4 days after conventionalization (day 4), replicate 2


title: jejunum germ-free t=0d_rep3

source_name: jejunum from germ-free mouse (day 0), replicate 3


title: Me23682_Apollon siRNA_32hrs_rep3

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

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

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

tag: disease state

value: Melanoma

tag: treatment

value: Apollon siRNA

tag: drug concentration

value: 75 nM

tag: time exposure


title: Me23682_control siRNA_32hrs_rep2

value: control siRNA


title: Me23682_control siRNA + PLX4720_24+8hrs_rep2

value: control siRNA + PLX4720


title: Me23682_Apollon siRNA + PD0325901_24+8hrs_rep1

value: Apollon siRNA + PD0325901

value: 75 nM + 5 nM


title: Me23682_Apollon siRNA + PLX4720_24+8hrs_rep3

value: Apollon siRNA + PLX4720


title: Me23682_control siRNA + PD0325901_24+8hrs_rep3

value: control siRNA + PD0325901


title: sample 132_se/ARDS Day 7

city: Boston

first: Judie

middle: Ann

last: Howrylak

state: MA

address: 75 Francis Street

department: Pulmonary and Critical Care Medicine

institute: Brigham and Women's Hospital

description:
sample 132
170372_DO011140202DR_5388500004_D

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: se/ARDS Day 7

label_protocol: Biotinylated cRNA were prepared with the Ambion Total RNA Amplification  kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen's PAXgene Blood RNA Kit

tag: subject id

tag: tissue

value: whole blood


title: Me23682_Apollon siRNA + fotemustine_24+6hrs_rep1

value: Apollon siRNA + fotemustine


title: Me23682_Apollon siRNA + PD0325901_24+8hrs_rep2


title: Me23682_Apollon siRNA + fotemustine_24+6hrs_rep2


title: Me23682_Apollon siRNA + PLX4720_24+8hrs_rep1


title: Me23682_Apollon siRNA + fotemustine_24+6hrs_rep3


title: Me23682_Apollon siRNA + PD0325901_24+8hrs_rep3


title: Me23682_Apollon siRNA + PLX4720_24+8hrs_rep2


title: Me23682_control siRNA + fotemustine_24+6hrs_rep3

value: control siRNA + fotemustine


title: Me23682_control siRNA + PD0325901_24+8hrs_rep1


title: Me23682_control siRNA + PD0325901_24+8hrs_rep2


title: sample 125_se/ARDS Day 0

description:
sample 125
170370_DO011140168DR_5388500011_C

source_name: se/ARDS Day 0


title: sample 129_se/ARDS Day 0

description:
sample 129
170374_DO011140249DR_5388500010_G


title: Me23682_Apollon siRNA_32hrs_rep2


title: Me23682_control siRNA + fotemustine_24+6hrs_rep2


title: Me23682_control siRNA_32hrs_rep1


title: Me23682_control siRNA + PLX4720_24+8hrs_rep3


title: Me23682_Apollon siRNA_32hrs_rep1


title: sample 131_se/ARDS Day 0

description:
sample 131
170376_DO011140285DR_5388500004_C


title: sample 126_se/ARDS Day 7

description:
sample 126
170369_DO01114014XDR_5388500011_D


title: sample 130_se/ARDS Day 7

description:
sample 130
170377_DO011140301DR_5388500010_H


title: Me23682_control siRNA + PLX4720_24+8hrs_rep1


title: Me23682_control siRNA_32hrs_rep3


title: Me23682_control siRNA + fotemustine_24+6hrs_rep1


title: sample 121_Sepsis Day 0

description:
sample 121
170379_DO011140348DR_5388500009_G

source_name: Sepsis Day 0


title: sample 118_Sepsis Day 0

description:
sample 118
170436_DO011145253DR_5388500008_G


title: sample 106_Sepsis Day 0

description:
sample 106
170378_DO01114032XDR_5388500003_E


title: sample 115_SIRS Day 0

description:
sample 115
169983_DO011140717DR_5388500003_J

source_name: SIRS Day 0


title: sample 124_se/ARDS Day 7

description:
sample 124
170240_DO011139972DR_5388500009_D


title: sample 119_Sepsis Day 7

description:
sample 119
170429_DO011145154DR_5388500008_H

source_name: Sepsis Day 7


title: sample 110_Sepsis Day 0

description:
sample 110
170371_DO011140186DR_5388500006_H


title: sample 108_Sepsis Day 0

description:
sample 108
170437_DO011145271DR_5388500004_E


title: sample 114_SIRS Day 0

description:
sample 114
169959_DO011140492DR_5388500002_J


title: sample 111_Sepsis Day 7

description:
sample 111
170197_DO011145334DR_5388500006_I


title: sample 103_Sepsis Day 7

description:
sample 103
170189_DO011143282DR_5388500004_B


title: sample 117_Sepsis Day 7

description:
sample 117
170431_DO011145235DR_5388500007_H


title: sample 104_Sepsis Day 0

description:
sample 104
170375_DO011140267DR_5388500002_F


title: sample 101_SIRS Day 0

description:
sample 101
169984_DO011140735DR_5388500017_J


title: sample 122_Sepsis Day 7

description:
sample 122
170430_DO011145172DR_5388500009_H


title: sample 123_se/ARDS Day 0

description:
sample 123
169794_DO011139639DR_5388500009_C


title: sample 99_se/ARDS Day 0

description:
sample 99
169728_DO011139340DR_5388500007_C


title: sample 98_se/ARDS Day 7

description:
sample 98
169765_DO011139387DR_5388500003_D


title: sample 96_Sepsis Day 7

description:
sample 96
170192_DO011143345DR_5388500003_B


title: sample 112_SIRS Day 0

description:
sample 112
169961_DO011140519DR_5388500001_J


title: sample 93_Sepsis Day 7

description:
sample 93
170198_DO011145352DR_5388500002_D


title: sample 100_se/ARDS Day 7

description:
sample 100
169771_DO011139468DR_5388500007_D


title: sample 95_Sepsis Day 0

description:
sample 95
169892_DO01114230XDR_5388500003_A


title: sample 107_Sepsis Day 7

description:
sample 107
170241_DO011145451DR_5388500003_F


title: sample 113_se/ARDS Day 0

description:
sample 113
169768_DO011139421DR_5388500002_K


title: sample 109_Sepsis Day 7

description:
sample 109
170432_DO011145190DR_5388500004_F


title: sample 102_Sepsis Day 0

description:
sample 102
169893_DO011142328DR_5388500004_A


title: sample 105_Sepsis Day 7

description:
sample 105
170236_DO011145370DR_5388500002_E


title: sample 97_se/ARDS Day 0

description:
sample 97
169770_DO01113944XDR_5388500003_C


title: sample 86_se/ARDS Day 7

description:
sample 86
169764_DO011139369DR_5388500002_B


title: sample 73_Sepsis Day 0

description:
sample 73
169888_DO011142229DR_5388500017_A


title: sample 92_Sepsis Day 0

description:
sample 92
169891_DO011142283DR_5388500002_C


title: sapmle 74_Sepsis Day 7

description:
sapmle 74
170190_DO011143309DR_5388500017_B


title: sample 89_Sepsis Day 7

description:
sample 89
170242_DO01114547XDR_5388500001_F


title: sample 76_se/ARDS Day 7

description:
sample 76
169840_DO011139918DR_5388500017_D


title: sample 77_SIRS Day 0

description:
sample 77
169956_DO011140456DR_5388500011_J


title: sample 88_Sepsis Day 0

description:
sample 88
169890_DO011142265DR_5388500001_E


title: sample 78_se/ARDS Day 0

description:
sample 78
169833_DO011139837DR_5388500001_A


title: sample 84_Sepsis Day 7

description:
sample 84
170237_DO011145399DR_5388500001_D


title: sample 71_SIRS Day 0

description:
sample 71
169934_DO011140393DR_5388500009_K


title: sample 87_se/ARDS Day 0

description:
sample 87
169772_DO011139486DR_5388500001_K


title: sample 83_Sepsis Day 0

description:
sample 83
169889_DO011142247DR_5388500001_C


title: sample 79_se/ARDS Day 7

description:
sample 79
169799_DO011139738DR_5388500001_B


title: sample 72_SIRS Day 0

description:
sample 72
169985_DO011140753DR_5388500010_K


title: sample 70_se/ARDS Day 7

description:
sample 70
169798_DO01113971XDR_5388500012_D


title: sample 85_se/ARDS Day 0

description:
sample 85
169835_DO011139873DR_5388500002_A


title: sample 90_SIRS Day 0

description:
sample 90
169971_DO011140654DR_5388500012_J


title: sample 66_Sepsis Day 0

description:
sample 66
169887_DO011142200DR_5388500012_A


title: sample 67_Sepsis Day 7

description:
sample 67
170193_DO011143363DR_5388500012_B


title: sample 69_se/ARDS Day 0

description:
sample 69
169797_DO011139693DR_5388500012_C


title: sample 75_se/ARDS Day 0

description:
sample 75
169830_DO011139774DR_5388500017_C


title: sample 65_se/ARDS Day 0

description:
sample 65
169841_DO011139936DR_5388500017_K


title: sample 58_SIRS Day 0

description:
sample 58
169972_DO011140672DR_5388500002_H


title: sample 63_Sepsis Day 0

description:
sample 63
169886_DO011142184DR_5388500017_E


title: sample 60_SIRS Day 0

description:
sample 60
169969_DO011140618DR_5388500003_H


title: sample 64_Sepsis Day 7

description:
sample 64
170195_DO011143408DR_5388500017_F


title: sample 61_SIRS Day 0

description:
sample 61
169967_DO011140573DR_5388500004_H


title: sample 57_Sepsis Day 7

description:
sample 57
170243_DO011145498DR_5388500012_E


title: sample 56_Sepsis Day 0

description:
sample 56
170380_DO011140366DR_5388500012_F


title: sample 49_SIRS Day 0

description:
sample 49
169968_DO011140591DR_5388500017_H


title: sample 50_SIRS Day 0

description:
sample 50
169970_DO011140636DR_5388500001_H


title: sample 55_Sepsis Day 7

description:
sample 55
170238_DO011145415DR_5388500011_F


title: sample 52_Sepsis Day 0

description:
sample 52
169914_DO011142463DR_5388500010_E


title: sample 53_Sepsis Day 7

description:
sample 53
170191_DO011143327DR_5388500010_F


title: sample 41_Sepsis Day 0

description:
sample 41
169898_DO011142409DR_5388500011_A


title: sample 54_Sepsis Day 0

description:
sample 54
169915_DO011142481DR_5388500011_E


title: sample 46_Sepsis Day 7

description:
sample 46
170194_DO011143381DR_5388500009_F


title: sample 44_Sepsis Day 7

description:
sample 44
170196_DO011145316DR_5388500008_F


title: sample 34_Sepsis Day 0

description:
sample 34
169925_DO011143100DR_5388500009_A


title: sample 36_SIRS Day 0

description:
sample 36
169957_DO011140474DR_5388500012_H


title: sample 37_Sepsis Day 0

description:
sample 37
169897_DO011142382DR_5388500010_A


title: sample 40_se/ARDS Day 7

description:
sample 40
169775_DO01113953XDR_5388500010_D


title: sample 48_SIRS Day 0

description:
sample 48
169968_DO011140591DR_5388500004_K


title: sample 45_Sepsis Day 0

description:
sample 45
169913_DO011142445DR_5388500009_E


title: sample 39_se/ARDS Day 0

description:
sample 39
169791_DO011139576DR_5388500010_C


title: sample 31_Sepsis Day 7

description:
sample 31
170373_DO011140220DR_5388500007_F


title: sample 43_Sepsis Day 0

description:
sample 43
169899_DO011142427DR_5388500008_E


title: sample 29_SIRS Day 0

description:
sample 29
169935_DO01114041XDR_5388500009_J


title: sample 42_Sepsis Day 7

description:
sample 42
170244_DO011145514DR_5388500011_B


title: sample 32_SIRS Day 0

description:
sample 32
169987_DO011140771DR_5388500010_J


title: sample 38_Sepsis Day 7

description:
sample 38
170239_DO011145433DR_5388500010_B


title: sample 28_SIRS Day 0

description:
sample 28
169982_DO011140690DR_5388500008_J


title: sample 27_Sepsis Day 7

description:
sample 27
169923_DO011143066DR_5388500006_G


title: sample 116_Sepsis Day 0

description:
sample 116
170434_DO011145217DR_5388500007_G


title: sample 30_Sepsis Day 0

description:
sample 30
169929_DO011143183DR_5388500007_E


title: sample 35_Sepsis Day 7

description:
sample 35
169896_DO011142364DR_5388500009_B


title: sample 33_SIRS Day 0

description:
sample 33
169965_DO011140555DR_5388500011_H


title: sample 26_Sepsis Day 0

description:
sample 26
169853_DO011142166DR_5388500006_F


city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
Sample name: condKO.TH2.a
Raw data file: Ansel miRNA_252073610011_S01_miRNA-v1_95_May07_1_3.txt
Hybridized to custom array based on  miRBase v11

hyb_protocol: Cy3-labelled RNA) was fragmented at 60Â°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters

source_name: Eri1 fl/fl CD4-cre conditional knockout Th2 Rep2 (40 hr activated CD4+ T cells grown in Th2 conditions)

label_protocol: Total RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol

extract_protocol: miRNeasy kit (Qiagen)

treatment_protocol: purified CD4+ T cells were activated with hamster anti-mouse CD3 (2C11, 0.25 µg/ml) and anti-mouse CD28 (37.51, 1 µg/ml) antibodies crosslinked on goat-anti-hamster IgG-coated plates (0.3 mg/ml in PBS for 1 h at 37°C; MP Biomedicals) in Th2 conditions (500 U/ml IL4, 5 µg/ml anti-IFN-γ). At 40 hours of activation, total RNA was isolated using the miRNeasy kit (Qiagen).

value: CD4 T cells from Spleen and Lymph Nodes

tag: strain

tag: age

value: 6-8 weeks


title: Eri1 knockout Th2 Rep1

description:
Sample name: totKO.TH2
Raw data file: miRNA Ansel _252073610007_S01_GE1-v5_95_Feb07_1_3.txt
Hybridized to custom array based on  miRBase v11

source_name: Eri1 knockout Th2 Rep1 (40 hr activated CD4+ T cells grown in Th2 conditions)

value: ICR and C57BL/6 mix


title: Eri1 fl/fl wildtype Th2 Rep2

description:
Sample name: WT.FlFl.TH2
Raw data file: Ansel miRNA_252073610010_S01_miRNA-v1_95_May07_2_4.txt
Hybridized to custom array based on  miRBase v11

source_name: Eri1 fl/fl wildtype Th2 Rep2 (40 hr activated CD4+ T cells grown in Th2 conditions)


title: sample 24_se/ARDS Day 7

description:
sample 24
169831_DO011139792DR_5388500008_D


title: sample 23_se/ARDS Day 0

description:
sample 23
169774_DO011139511DR_5388500008_C


title: sample 22_Sepsis Day 7

description:
sample 22
169932_DO011143246DR_5388500008_B


title: sample 10_se/ARDS Day 0

description:
sample 10
169790_DO011139558DR_5388500012_K


title: sample 15_Sepsis Day 7

description:
sample 15
169922_DO011143048DR_5388500007_B


title: sample  21_Sepsis Day 0

description:
sample  21
169894_DO011142346DR_5388500008_A


title: sample 8_se/ARDS Day 0

description:
sample 8
169792_DO011139594DR_5388500006_D


title: sample 14_Sepsis Day 0

description:
sample 14
169926_DO011143129DR_5388500007_A


title: sample 2_Sepsis Day 7

description:
sample 2
169921_DO01114302XDR_5388500006_B


title: sample 9_se/ARDS Day 7

description:
sample 9
170235_DO011139954DR_5388500006_E


title: sample 18_SIRS Day 0

description:
sample 18
169936_DO011140438DR_5388500006_J


title: Eri1 wildtype Th2 Rep1

description:
Sample name: totWT.TH2
Raw data file: miRNA Ansel _252073610007_S01_GE1-v5_95_Feb07_2_2.txt
Hybridized to custom array based on  miRBase v11

source_name: Eri1 wildtype Th2 Rep1 (40 hr activated CD4+ T cells grown in Th2 conditions)


title: human duct cell, 14 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133A]

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

country: Belgium

institute: Vrije Universiteit Brussel

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d14-133A-a1

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40mM Tris, 30mM magnesium acetate, 10mM potassium acetate), the labelled cRNA was hybridized for 16h to the Affymetrix HG133A

scan_protocol: Arrays were stained with phycoerythrin-streptavidin with the Affymetrix Fluidics Station 400, and scanned in the Affymetrix GeneArray2500scanner.

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity. Using the PM-MM model with mismatch correction, a 90% confidence interval was calculated for the fold change in gene expression in each comparison, and the lower limit of this interval (LCB) was used as a measure of differential gene expression.   Transcripts were considered as differentially regulated by Ngn3 when 1.5 fold (LCB, unpaired P < 0.05) up- or down-regulated in AdGFP-Ngn3 versus AdGFP controls, at 3 and/or 14 dpi. Transcripts that showed differential expression between day 3 and day 14 in AdGFP-Ngn3 duct cells but not in AdGFP control cells, were also considered Ngn3-regulated. Data from day 14 and 20 were pooled and treated as biological replicates.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Adult human duct cells were composed of >90% Cytokeratin19+ cells and <5% Synaptophysin+ cells. On day 4 after isolation, the duct cell-enriched fraction was tansduced and further cultured in suspension as described by Heimberg H et al ( Diabetes 2001,49: 571-579)

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

treatment_protocol: Transfection with recombinant, replication-deficient adenoviruses expressing GFP (AdGFP) as compared to Ngn3 in combination with GFP (AdGFP-Ngn3)

tag: cell type

value: pancreatic duct cells

tag: genotype/variation

value: Transfected with recombinant, replication-deficient adenoviruses expressing GFP-Ngn3 (AdGFP-Ngn3)

tag: control/ngn3 transfection stage

value: 14 days after Ad-Ngn3-GFP transduction


title: human duct cell, 14 days after transduction with Ad-Ngn3-GFP vector, biological rep3 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d14-133A-b2


title: human duct cell, 20 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d20-133A-c1

value: 20 days after Ad-Ngn3-GFP transduction


title: human duct cell, 14 days after transduction with Ad-Ngn3-GFP vector, biological rep2 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d14-133A-b1


title: human duct cell, 14 days after transduction with AdGFP control vector, biological rep1 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d14-133A-a1

value: Transfected with recombinant, replication-deficient adenoviruses expressing GFP (AdGFP)

value: 14 days after AdGFP control transduction


title: sample 25_Sepsis Day 0

description:
sample 25
169928_DO011143165DR_5388500004_J


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep3 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133A-c1

value: 3 days after Ad-Ngn3-GFP transduction


title: sample 20_SIRS Day 0

description:
sample 20
169963_DO011140537DR_5388500007_J


title: sample 6_Sepsis Day 0

description:
sample 6
169930_DO01114320XDR_5388500003_K


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep2 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133A-b1


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133A-a1


title: sample 1_Sepsis Day 0

description:
sample 1
170433_DO011142508DR_5388500006_A


title: human duct cell, 14 days after transduction with AdGFP control vector, biological rep2 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d14-133A-b1


title: human duct cell, 14 days after transduction with Ad-Ngn3-GFP vector, biological rep2 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d14-133B-b1

data_processing: Scanned arrays were analyzed with dChip model-based expression analysis to the array with the median intensity. Using the PM-MM model with mismatch correction, a 90% confidence interval was calculated for the fold change in gene expression in each comparison, and the lower limit of this interval (LCB) was used as a measure of differential gene expression. Transcripts were considered as differentially regulated by Ngn3 when 1.5 fold (LCB, unpaired P < 0.05) up- or down-regulated in AdGFP-Ngn3 versus AdGFP controls, at 3 and/or 14 dpi. Transcripts that showed differential expression between day 3 and day 14 in AdGFP-Ngn3 duct cells but not in AdGFP control cells, were also considered Ngn3-regulated. Data from day 14 and 20 were pooled and treated as biological replicates.


title: sample 7_se/ARDS Day 0

description:
sample 7
169832_DO011139819DR_5388500011_K


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133B-a1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep4 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133A-c1

value: 3 days after AdGFP control transduction


title: M21_2d_2

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: GCRMA

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard Affymetrix protocol

tag: cell line

tag: integrin

value: high

tag: growth condition


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep3 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133A-b2


title: human duct cell, 14 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d14-133B-a1


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep2 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133B-b1


title: human duct cell, 3 days after transduction with Ad-Ngn3-GFP vector, biological rep3 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d3-133B-c1


title: human duct cell, 14 days after transduction with AdGFP control vector, biological rep2 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d14-133B-b1


title: human duct cell, 20 days after transduction with AdGFP control vector, biological rep3 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d20-133A-c1

value: 20 days after AdGFP control transduction


title: human duct cell, 14 days after transduction with AdGFP control vector, biological rep1 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d14-133B-a1


title: human duct cell, 20 days after transduction with AdGFP control vector, biological rep3 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d20-133B-c1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep2 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133B-b1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep2 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133A-b1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep1 [HG133A]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133A-a1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep4 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133B-c1


title: human duct cell, 3 days after transduction with AdGFP control vector, biological rep1 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-GFP-d3-133B-a1


title: human duct cell, 20 days after transduction with Ad-Ngn3-GFP vector, biological rep1 [HG133B]

description:
each biological replicate obtained from pooled cultures of 3 human organs, 9 donor organs in total
HHei-Diab-Ngn3-GFP-d20-133B-c1


title: M21_2d_3


title: M21_3d_2


title: M21L_3d_3

value: low


title: M21L_3d_2


title: M21_3d_3


title: M21_2d_1


title: M21_3d_1


title: M21L_3d_1


title: M21L_2d_3


title: M21L_2d_2


title: M21L_2d_1


title: XHF2381

city: Phoenix

first: Brock

last: Armstrong

state: AZ

address: 445 N. 5th Street

department: Cancer and Cell Biology

institute: TGen

description: Reference

hyb_protocol: Hyb done as described by Agilent SOP

scan_protocol: Scan Done according to Agielnt SOP

data_processing:
Feature extrated as described by Agilent SOP
Log10 ratio of sample to reference

label_protocol: Samples labeled according to Agilent SOP

extract_protocol: DNA isloated according to Qiagen DNA easy SOP

treatment_protocol: Selection: Xenograft tumors minced and flow sorted for anueplid cells with Dapi stined nuclei

value: Glioblastoma

source_name: Female Reference Genome

tag: reference

value: Female Reference Genome


title: oxLDL-15

city: Los Angeles

first: Ayca

last: Erbilgin

address: 675 Charles E Young Dr South

department: Medicine/Cardiology

institute: University of California, Los Angeles

description: Gene expression data from amplified RNA isolated directly from the intima of mouse aortas.

hyb_protocol: Entire sample was hybridized for 40 hr on a 96 well HTA plate according to manufacturer protocol.

scan_protocol: GeneChips were processed using GCOS.

data_processing: Microarray results were normalized using RMA in the “affy” package

source_name: MAECs isolated from aortas treated with media + oxLDL for 4 hours

label_protocol: The products of RNA amplification were treated with the NuGEN Encore Biotin Module prior to hybridization according to manufacturer’s protocol

growth_protocol: Mice were maintained in the UCLA barrier facility on chow diet prior to euthanization

extract_protocol: RNA was extracted using the RNAqueous®-Micro Kit by Ambion. The buffer and collagenase solution containing scraped endothelial cells was pipetted directly into 100 uL of Lysis buffer in a 200 uL PCR tube, vortexed, then incubated at 42 C for 30 minutes on a PCR thermalcycler. RNA isolation continued following the manufacturer’s protocol, including suggestions to pre-wet the filter assembly with 30 uL Lysis buffer prior to isolation and to preheat elution solution to 95 C. RNA was stored at -80 C after isolation.

treatment_protocol: DMEM with 1% FBS was used as the cell culture medium; vessels were incubated for 4 hours in a cell culture incubator at 37 C, 5% CO2. 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (OxPAPC) and oxLDL were prepared as previously described 28, 29 Lipopolysaccharide (LPS) was purchased from List Biological Laboratories. OxPAPC and oxLDL were added to DMEM for a final concentration of 50 ug/mL, LPS was formulated for a final concentration of 4 ng/mL. After aortas were opened en face, each was placed in one well of a 12-well cell culture plate along with 1 mL of the appropriate DMEM formulation pre-warmed to 37C. After the 4 hour treatment, aortas were removed from media and placed lumen side up on a glass slide; isolation continued as described above, beginning with hematoxylin treatment.

tag: genotype

value: wild-type

value: aortic endothelial cells

value: DMEM + oxLDL, 4 hrs

value: atherosclerotic treatment


title: oxLDL-16


title: SF7227

description: Reference


title: SF7796

description: Reference


title: XHF2609

description: Reference


title: oxPAPC-11

source_name: MAECs isolated from aortas treated with media + oxPAPC for 4 hours

value: DMEM + oxPAPC, 4 hrs


title: MDAGSC13

description: Reference


title: LPS-3

source_name: MAECs isolated from aortas treated with media + LPS for 4 hours

value: DMEM + LPS, 4 hrs


title: X1066

description: Reference


title: oxPAPC-13


title: LPS-4


title: LPS-10


title: DMEM-11

source_name: MAECs isolated from aortas treated with media for 4 hours

value: DMEM cell media, 4 hrs

value: control


title: oxLDL-14


title: DMEM-9


title: oxPAPC-12


title: MDAGSC2

description: Reference


title: MDAGSC11

description: Reference


title: DMEM-10


title: BL6_wt_4 wk-15

source_name: MAECs isolated from 4 week wild-type mice

value: no treatment

value: control normal-lipidemic


title: GS2

description: Reference


title: HF2355

description: Reference


title: HF2597

description: Reference


title: BL6_wt_4 wk-14


title: MDAGSC17

description: Reference


title: GBM85

description: Reference


title: HF2587

description: Reference


title: HF2354

description: Reference


title: HF2562

description: Reference


title: GBM59

description: Reference


title: GBM84

description: Reference


title: BL6_wt_4 wk-8


title: BL6_apoe_4 wk-3

source_name: MAECs isolated from 4 week ApoE -/- mice

value: ApoE -/-

value: pre-lesioned hyperlipidemic


title: BL6_apoe_4 wk-6


title: BL6_wt_4 wk-12


title: BL6_wt_4 wk-13


title: BL6_wt_4 wk-7


title: GBM Xenograft[X1016p16]

description: Reference

hyb_protocol: 40 hour hyb as Agilent protocol describes

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version  10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) No background, linear Lowess

source_name: GBM Xenograft[X1016p16]

label_protocol: Followed protocal as suggested by agilent

growth_protocol: Xenograft cell lines were injected intracranially to generate orothotopic tumors.  Mice were sacificed when moribound then brains were collected after cold perfusion of PBS.  Brains were flash frozen and kept frozen until RNA isolation.

extract_protocol: Followed manufactors directions for the GE Healthcare RNA Illustra minspin kit

tag: gender

value: male

tag: treatment status

source_name: Reference RNA from pooled cellines

value: Reference RNA from pooled cellines


title: BL6_apoe_4 wk-5

tag: treatment

tag: disease state


title: BL6_apoe_4 wk-4


title: GBM55

description: Reference


title: GBM38

description: Reference


title: GBM26

description: Reference


title: GBM Xenograft[SF7796]

description: Reference

source_name: GBM Xenograft[SF7796]

value: unknown

value: UNTREATED


title: GBM43

description: Reference

value: Glioblastoma

value: Female Reference Genome


title: GBM Xenograft[SF7300]

description: Reference

source_name: GBM Xenograft[SF7300]


title: GBM08

description: Reference


title: GBM12

description: Reference


title: GBM05

description: Reference


title: GBM Xenograft[S2381]

description: Reference

source_name: GBM Xenograft[S2381]


title: GBM64

description: Reference


title: GBM46

description: Reference


title: GBM15

description: Reference


title: GBM Xenograft[S2414]

description: Reference

source_name: GBM Xenograft[S2414]

value: female


title: GBM Xenograft[S2355]

description: Reference

source_name: GBM Xenograft[S2355]


title: GBM Xenograft[NS2]

description: Reference

source_name: GBM Xenograft[NS2]


title: GBM14

description: Reference


title: GBM Xenograft[S2354]

description: Reference

source_name: GBM Xenograft[S2354]


title: GBM28

description: Reference


title: GBM Xenograft[GS-2]

description: Reference

source_name: GBM Xenograft[GS-2]


title: GBM Xenograft[S2303]

description: Reference

source_name: GBM Xenograft[S2303]


title: High Cholesterol Diet, c-Met KO mice, rep2

city: Bethesda

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description:
SAMPLE 14
Replicate 2 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from Illumina, Inc. The background noise was subtracted and quantile normalization was applied.

source_name: liver, c-Met KO, high cholesterol diet

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Kit. Quality control and measurement were performed using a NanoDrop and Agilent Bioanalyser.

treatment_protocol: Mice were fed a high cholesterol diet (2% cholesterol and 0.5 % sodium cholate ) or a Chow regular diet (Chow) as control.

tag: background strain

value: c-Met knockout

value: liver

value: high cholesterol diet

tag: treatment duration

value: 30 days


title: GBM Xenograft[N30]

description: Reference

source_name: GBM Xenograft[N30]


title: High Cholesterol Diet, c-Met KO mice, rep1

description:
SAMPLE 13
Replicate 1 of 4.

tag: tissue


title: High Cholesterol Diet, WT mice, rep4

description:
SAMPLE 12
Replicate 4 of 4.

source_name: liver, WT, high cholesterol diet

value: wild type


title: GBM Xenograft[MDAGSC17]

description: Reference

source_name: GBM Xenograft[MDAGSC17]


title: High Cholesterol Diet, c-Met KO mice, rep3

description:
SAMPLE 15
Replicate 3 of 4.


title: High Cholesterol Diet, WT mice, rep3

description:
SAMPLE 11
Replicate 3 of 4.


title: High Cholesterol Diet, WT mice, rep1

description:
SAMPLE 9
Replicate 1 of 4.


title: GBM Xenograft[GBM 66]

description: Reference

source_name: GBM Xenograft[GBM 66]


title: Chow Diet, c-Met KO mice, rep4

description:
SAMPLE 8
Replicate 4 of 4.

source_name: liver, c-Met KO, control diet

value: regular chow diet


title: GBM Xenograft[GBM 59]

description: Reference

source_name: GBM Xenograft[GBM 59]


title: High Cholesterol Diet, WT mice, rep2

description:
SAMPLE 10
Replicate 2 of 4.


title: High Cholesterol Diet, c-Met KO mice, rep4

description:
SAMPLE 16
Replicate 4 of 4.


title: GBM Xenograft[GBM 44]

description: Reference

source_name: GBM Xenograft[GBM 44]

source_name: Reference RNA from pooled cellines


title: G16

description: Reference

source_name: Female Reference Genome


title: CW421

description: Reference


title: Chow Diet, c-Met KO mice, rep3

description:
SAMPLE 7
Replicate 3 of 4.


title: GBM Xenograft[G85]

description: Reference

source_name: GBM Xenograft[G85]


title: Chow Diet, c-Met KO mice, rep1

description:
SAMPLE 5
Replicate 1 of 4.


title: GBM Xenograft[G84]

description: Reference

source_name: GBM Xenograft[G84]


title: GBM Xenograft[G76]

description: Reference

source_name: GBM Xenograft[G76]


title: Chow Diet, c-Met KO mice, rep2

description:
SAMPLE 6
Replicate 2 of 4.


title: Chow Diet, WT mice, rep4

description:
SAMPLE 4
Replicate 4 of 4.

source_name: liver, WT, control diet


title: Chow Diet, WT mice, rep1

description:
SAMPLE 1
Replicate 1 of 4.


title: GBM Xenograft[G61]

description: Reference

source_name: GBM Xenograft[G61]


title: GBM Xenograft[G91]

description: Reference

source_name: GBM Xenograft[G91]


title: GBM Xenograft[GBM 14]

description: Reference

source_name: GBM Xenograft[GBM 14]


title: Chow Diet, WT mice, rep3

description:
SAMPLE 3
Replicate 3 of 4.


title: GBM Xenograft[G43]

description: Reference

source_name: GBM Xenograft[G43]


title: GBM Xenograft[G79]

description: Reference

source_name: GBM Xenograft[G79]


title: GBM Xenograft[G36]

description: Reference

source_name: GBM Xenograft[G36]


title: GBM Xenograft[G6]

description: Reference

source_name: GBM Xenograft[G6]


title: GBM Xenograft[G80]

description: Reference

source_name: GBM Xenograft[G80]


title: Chow Diet, WT mice, rep2

description:
SAMPLE 2
Replicate 2 of 4.


title: GBM Xenograft[GBM 39]

description: Reference

source_name: GBM Xenograft[GBM 39]


title: GBM Xenograft[G5]

description: Reference

source_name: GBM Xenograft[G5]


title: GBM Xenograft[G55]

description: Reference

source_name: GBM Xenograft[G55]


title: GBM Xenograft[G64]

description: Reference

source_name: GBM Xenograft[G64]

source_name: Reference RNA from pooled cellines


title: GBM Xenograft[G46]

description: Reference

source_name: GBM Xenograft[G46]


title: GBM Xenograft[G38]

description: Reference

source_name: GBM Xenograft[G38]

value: 2 cycles of TMZ adjuvant - 2/13/04 recurrent dz by biopsy - then 4 cycles of CCI-779 then BCNU then hospice


title: GBM Xenograft[G22]

description: Reference

source_name: GBM Xenograft[G22]


title: H3R2me2 vs Input at t=60

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: Hebrew University

description: MNase-ChIP vs input

hyb_protocol: Labeled probes (a mixture of Cy5-labeled input and Cy3-labeled ChIP-ed material) were hybridized onto an Agilent yeast tiled oligonucleotide microarray (G4495A) at 65°C for 16 h and washed as described on http://www.microarrays.org

scan_protocol: The arrays were scanned at 5 μ resolution with an Agilent scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

source_name: yeast cells

label_protocol: ChIP material was amplified using the DNA linear amplification method described previously (Liu et al., 2005; Liu et al., 2003). 3ug of the amplified ChIP products was labeled via the amino-allyl methods as described on http://www.microarrays.org.

growth_protocol: Yeast cells By4741 were grown to mid-log on YPD and At “time zero” cells were treated with 1.5mM diamide (D3648, Sigma).

extract_protocol: At t = 0, 4, 8, 15, 30, and 60 minutes, cells were fixed by 1% formaldehyde, followed after 15 minutes by quenching with 125 mM glycine. Cells were then pelleted, washed with water, and subjected to MNase digestion as previously described (Kaplan et al., Plos Genetics 2008; Radman-Livaja et al., PLoS Genetics, 2010) and immunoprecipitation.

tag: strain

tag: sample type

value: Input

tag: time

value: 60 minutes

tag: antibody

tag: vendor/catalog/lot


title: H3S10p vs Input at t=4

description: MNase-ChIP vs input

value: 4 minutes


title: H3S10p vs Input at t=60

description: MNase-ChIP vs input


title: GBM Xenograft[G16]

description: Reference

source_name: GBM Xenograft[G16]

tag: age


title: H3R2me2 vs Input at t=30

description: MNase-ChIP vs input

value: 30 minutes


title: GBM Xenograft[G116]

description: Reference

source_name: GBM Xenograft[G116]

value: Reference RNA from pooled cellines


title: H3S10p vs Input at t=0

description: MNase-ChIP vs input

value: 0 minutes


title: H3R2me2 vs Input at t=15

description: MNase-ChIP vs input

value: 15 minutes


title: H3S10p vs Input at t=30

description: MNase-ChIP vs input


title: H3R2me2 vs Input at t=4

description: MNase-ChIP vs input


title: GBM Xenograft[G117]

description: Reference

source_name: GBM Xenograft[G117]

value: unknown

value: Glioblastoma


title: H3R2me2 vs Input at t=8

description: MNase-ChIP vs input

value: 8 minutes


title: H3S10p vs Input at t=8

description: MNase-ChIP vs input


title: H3S10p vs Input at t=15

description: MNase-ChIP vs input


title: H3K4me3 vs Input at t=30

description: MNase-ChIP vs input


title: GBM Xenograft[G12]

description: Reference

source_name: GBM Xenograft[G12]


title: H3K4me3 vs Input at t=15

description: MNase-ChIP vs input


title: GBM Xenograft[G102]

description: Reference

source_name: GBM Xenograft[G102]


title: GBM Xenograft[G10]

description: Reference

source_name: GBM Xenograft[G10]


title: 2 hour Anti-IgM Treated replicate 2

city: Umeå

first: Thomas

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

institute: Umeå University

description: Anti-IgM Treated

hyb_protocol: Labeled cRNA (1.5 ug) were hybridized to the Sentrix MouseRef-6 Expression Beadchip for 16-18 h at 58 °C, according to the manufacturer's instructions (Illumina).

scan_protocol: Following attachment of Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences), arrays were scanned with an Illumina bead array reader.

data_processing: Signal intensities of genes were normalized by cubic spline method.

source_name: Spleen

label_protocol: Total RNA was amplified and purified to yield biotinylated cRNA using an Ambion Illumina RNA amplification kit (Ambion).

growth_protocol: Mice were maintained for 8 weeks in a controlled environment with a 12 h dark/light cycle.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) and further purified using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Spleen of 8 weeks old mice was isolated and B cells were purified and stimulated with IL-4 (Pepro-Tech) and CD40L (R&D Systems) as indicated at 5 ng/ml and 200 ng/ml, respectively. The BCR of stimulated cells was activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 2.5 μg/ml for 1 and 2 hours.

value: 8 weeks

value: Spleen

tag: cell type

value: Primary B-lymphocytes

value: 2 hour Anti-IgM Treated


title: 2 hour Anti-IgM Treated replicate 3

description: Anti-IgM Treated


title: H3K4me3 vs Input at t=4

description: MNase-ChIP vs input


title: H3K4me3 vs Input at t=8

description: MNase-ChIP vs input


title: H3K36me3 vs Input at t=15

description: MNase-ChIP vs input


title: H3K4me3 vs Input at t=0

description: MNase-ChIP vs input


title: H3K4me3 vs Input at t=60

description: MNase-ChIP vs input


title: H3K36me3 vs Input at t=30

description: MNase-ChIP vs input


title: H3R2me2 vs Input at t=0

description: MNase-ChIP vs input


title: 2 hour Anti-IgM Treated replicate 1

description: Anti-IgM Treated


title: Evolved Strain3, Biological Rep2

city: Albuquerque

first: Anthony

last: Aragon

state: NM

address: Castetter Hall Room 214

institute: University of New Mexico

description: Gene expression data from evolved strain

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0004.

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

data_processing: Affymetrix .cel files were analyzed using GeneSpring 11.5.1.  Raw files were summerized using RMA and the resulting files were quantile normalized with all 8 files compared to the two control replicates

source_name: Evolved strain 3

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix 3' IVT Express protocol from 100ng of total RNA .

growth_protocol: Cultures of parental strain BY4742 were grown in 100 ml of CM Broth with Glucose (2% glucose, 0.5% Ammonium Sulfate) at 30°C with aeration. Every day for a month 10μl of the culture was transferred to a flask with fresh medium.

extract_protocol: Total RNA was isolated using RiboPure™ yeast kit (Life Technologies) as per manufacture instructions.

treatment_protocol: Contiuned exposure to high levels of glucose

value: Evolved strain 3


title: 1 hour Anti-IgM Treated replicate 2

description: Anti-IgM Treated

value: 1 hour Anti-IgM Treated


title: H3K36me3 vs Input at t=8

description: MNase-ChIP vs input


title: Untreated rep 2

description: control

value: control


title: H3K36me3 vs Input at t=60

description: MNase-ChIP vs input

value: Input


title: Evolved Strain3, Biological Rep1


title: Evolved Strain2, Biological Rep2

source_name: Evolved strain 2

value: Evolved strain 2


title: H3K36me3 vs Input at t=4

description: MNase-ChIP vs input

value: 4 minutes


title: 1 hour Anti-IgM Treated replicate 3

description: Anti-IgM Treated


title: 1 hour Anti-IgM Treated replicate 1

description: Anti-IgM Treated


title: H3K36me3 vs Input at t=0

description: MNase-ChIP vs input


title: H3K14ac vs Input at t=60 rep

description: MNase-ChIP vs input

value: 60 minutes


title: H3K14ac vs Input at t=30 rep

description: MNase-ChIP vs input

value: 30 minutes


title: Untreated rep 1

description: control


title: Anti-IgM Treated mutant E12 replicate 2

description: Anti-IgM Treated

treatment_protocol: Spleen of 8 weeks old mice heterozygous for deletion of E2A gene was isolated and B cells were purified and stimulated with IL-4 and CD40L at 5 ng/ml and 200 ng/ml, respectively for 14 hours followed by infection with retroviruses expressing either wildtype or mutant E12. After 12 h incubation, the infection was repeated for 12 h, followed by incubation for a further 22 h post-infection in fresh complete medium with the stimulants to allow for expression of GFP and E12. In addition to CD40L plus IL-4, the medium was supplemented with LPS (200 ng/ml) during retroviral infection incubations to improve infection efficiency. After 22 hour post-infection these BCR of stimulated cells was activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 2.5 μg/ml for 3 hour.

tag: genotype/variation

value: mutant E12

value: Anti-IgM Treated


title: H3K14ac vs Input at t=8 rep

description: MNase-ChIP vs input


title: H3K14ac vs Input at t=4 rep

description: MNase-ChIP vs input


title: Evolved Strain1, Biological Rep2

source_name: Evolved strain 1

value: Evolved strain 1


title: Untreated rep 3

description: control


title: Anti-IgM Treated mutant E12 replicate 1

description: Anti-IgM Treated


title: Evolved Strain2, Biological Rep1


title: H3K14ac vs Input at t=60

description: MNase-ChIP vs input


title: H3K14ac vs Input at t=15 rep

description: MNase-ChIP vs input

value: 15 minutes


title: Anti-IgM Treated mutant E12 replicate 3

description: Anti-IgM Treated


title: Untreated mutant E12 replicate 3

description: control


title: H3K14ac vs Input at t=30

description: MNase-ChIP vs input


title: H3K14ac vs Input at t=8

description: MNase-ChIP vs input

value: 8 minutes


title: H3K14ac vs Input at t=15

description: MNase-ChIP vs input


title: H3K14ac vs Input at t=0 rep

description: MNase-ChIP vs input

value: 0 minutes


title: Evolved Strain1, Biological Rep1


title: Parental, Biological Rep1

description: Gene expression data from parental strain

source_name: Parental

value: Parental BY4742


title: Untreated mutant E12 replicate 2

description: control

value: 8 weeks

value: Spleen


title: Parental, Biological Rep2


title: Anti-IgM Treated wt replicate 1

description: Anti-IgM Treated

value: wildtype


title: H3K14ac vs Input at t=4

description: MNase-ChIP vs input


title: Untreated mutant E12 replicate 1

description: control


title: H3K14ac vs Input at t=0

description: MNase-ChIP vs input


title: Anti-IgM Treated wt replicate 2

description: Anti-IgM Treated


title: Untreated wt replicate 3

description: control


title: Untreated wt replicate 1

description: control


title: Anti-IgM Treated wt replicate 3

description: Anti-IgM Treated


title: Muscle KO Aged 1027

city: La Jolla

first: Gretchen

last: Meyer

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Mouse Genome 430A 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 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Tibialis Anterior Muscle, Desmin Knockout, Aged

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

extract_protocol: Rneasy Kit (Qaigen) extraction of total RNA was performed

tag: genetic background

value: tibialis anterior


title: NK1.1pos_IL18_rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: Samples were hybridized using Hybridization Kit materials (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix); Fluidics Protocol FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data processing was done using GeneSpring GX 11 software (Agilent). ExonRMA16 summarization was applied to core probe set intensities.
probe_group_file: MoGene-1_0-st-v1.r4.pgf
meta-probeset_file: MoGene-1_0-st-v1.r4.mps

source_name: NK cells, NK1.1 positive, IL18 stimulated

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix)

growth_protocol: NK1.1 isolated NK cells (NK1.1 isolation Kit, Miltenyi) were cultured in RPMI + GlutaMax (Invitrogen) with 10% FCS (Sigma-Aldrich), 1% Pen/Strep (Invitrogen), 1% Pyruvate (PAA), 1% NEAA (PAA), 300 IU IL-2 (R&D), and 25 ng/ml IL-18 (MBL) over night.

extract_protocol: Column based (Qiagen)

treatment_protocol: Unstimulated as well as IL-18 generated NK cells were sorted by FACS (FACSAria). Unstimulated NK cells were sorted for NK1.1 positive, CD3 negative, CD11b positive and c-kit negative, alive cells. IL-18 cultured NK cells were sorted for NK1.1 positive, CD3 negative, CD11b negative and c-kit positive, alive cells.

value: NK1.1 positive

value: IL-18 generated


title: NK1.1pos_unst_rep2

source_name: NK cells, NK1.1 positive, unstimulated

value: unstimulated


title: Untreated wt replicate 2

description: control

value: control


title: NK1.1pos_unst_rep3


title: NK1.1pos_IL18_rep3


title: Muscle KO Aged 1217


title: Muscle KO Aged 1215


title: Muscle KO Aged 1106


title: NK1.1pos_IL18_rep1


title: GLI2 ChIP, Biol Rep 1

city: Houston

first: Pawel

last: Stankiewicz

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

hyb_protocol: Hybridization was performed at 65°C fro 24 hrs on custom-designed 16q24.1 region-specific 4x44K oligonucleotide microarray

scan_protocol: Scanning was performed using Agilent DNA microarray scanner

data_processing: Data were analyzed usuing Agilent Genomic Workbench software

source_name: GLI2 transfected HPMECs immunoprecipitated with anti-GLI2 Anitbody

label_protocol: Immunoprecipitated DNA was amplified using GenomePlex Complete Whole genome Amplification kit (Sigma-Aldrich). Amplified samples were labeled with Cyanine dUTP using Agilent genomic DNA enzymatic labeling kit

growth_protocol: HPMEC were cultured to confluence in EMS medium supplemented with 10% FBS, ECGS and 1% penicillin-streptomycin at 37°C with 5% CO2. Fibroblasts were cultured in DMEM medium, supplemented with 10% FBS and 1% penicillin-streptomycin, at 37°C with 10% CO2.

extract_protocol: MinElute PCR purification kit (Qiagen) was used to purify and concentrate DNA to final volume of 10ul.

treatment_protocol: Cells were transfected 24 hrs before assay with GLI2 expressing plasmid pCS2Gli2 using Lipofectamine LTX and Plus Reagent (Invitrogen). Cells were incubated with 1% formaldehyde for 10 mins at room temperature followed by lysis in SDS lysis buffer and sonicated. 5ul of anti-GLI2 antibody was added to 1ml of sample and GLI2-DNA complex was immunoprecipitated overnight at 4°C.

value: Human pulmonary microvascular endothelial cells (HPMEC)

source_name: skin fibroblasts

value: fibroblasts


description:
Sample name: condKO.TH2_b
Raw data file: miRNA_252154210013_S01_miRNA-v1_95_May07_1_4.txt
Hybridized to custom array based on  miRBase v12

source_name: Eri1 fl/fl CD4-cre conditional knockout Th2 Rep3 (40 hr activated CD4+ T cells grown in Th2 conditions)

value: CD4 T cells from Spleen and Lymph Nodes

value: 6-8 weeks


title: OLD21

city: L'Hospitalet de Llobregat

first: Antonio

last: Gómez

state: Barcelona

address: Av. Gran Vía s/n km. 2,7.

department: Epigenetics and Biology of Cancer Program

country: Spain

institute: IDIBELL

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

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

data_processing:
Genomic DNA was genotyped using Illumina HumanOmni5-Quad BeadChip Genotyping BeadChips (Illumina).
Image data was analyzed using GenomeStudio2011.1 with GT module 1.9.4 (Illumina).

label: C-Bio and A-DNP

source_name: Whole blood

label_protocol: 400ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-AMM) and random primer mix (WG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cord-blood (newborns) and whole-blood (centenarian) was performed using proteinase K and repeated phenol-chloroform extraction.

value: Whole blood

value: naive cells

tag: cell subtype

value: PBMNC

tag: developmental stage

value: centenarian


title: OLD19

description: Genomic DNA was genotyped using Illumina HumanOmni5-Quad BeadChip Genotyping BeadChips (Illumina).


title: OLD18


title: Eri1 +/+ CD4-cre wildtype Th2 Rep3

description:
Sample name: WT.Cre.TH2
Raw data file: miRNA_252154210013_S01_miRNA-v1_95_May07_2_1.txt
Hybridized to custom array based on  miRBase v12

source_name: Eri1 +/+ CD4-cre wildtype Th2 Rep3 (40 hr activated CD4+ T cells grown in Th2 conditions)


title: OLD17


title: ACD lung_gDNA3 (sample 81.3)

hyb_protocol: Hybridization was performed at 65°C on custom-designed 16q24.1 region-specific 4x44K oligonucleotide agilent microarray

scan_protocol: 4x44 microarrays were scanned using Agilent DNA Microarray Scanner

source_name: Genomic DNA from frozen/FFPE lung tissue of ACD/MPV patient

label_protocol: Samples were labeled with Cyanine dUTP using agilent genomic DNA enzymatic labeling kit

growth_protocol: Lungs were either frozen or formalin fixed paraffin embedded (FFPE) prior to DNA extraction. Peripheral blood was stored at +4°C prior to DNA extraction.

extract_protocol: Peripheral blood DNA was extracted using Gentra Puregene Blood Kit (Qiagen). DNA from frozen lung tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen). DNA from FFPE lung tissues was isolated following manufacturer's protocol (Agilent technologies).

tag: diagnosis

value: Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV)

value: lung

source_name: Peripheral blood genomic DNA  from normal control

value: healthy

value: peripheral blood


title: NK1.1pos_unst_rep1

tag: treatment


title: CB40

source_name: Cord blood

value: Cord blood

value: newborn


title: Muscle KO Adult 01271

source_name: Tibialis Anterior Muscle, Desmin Knockout, Adult

value: tibialis anterior


title: GLI2 ChIP, Biol Rep 2


title: HPMECs histone positive control

source_name: HPMECs immunoprecipitated with anti-mono/di/tri methyl-histone H3 (lys4) clone AW304,  rabbit monoclonal IgG (Upstate#05-791)


title: Muscle KO Adult 01031


title: Muscle KO Adult 0713


title: Muscle KO Adult 0706


title: NB

value: CD4+ cells


title: CB36


title: Muscle WT Aged 12172

source_name: Tibialis Anterior Muscle, Wildtype, Aged

value: wt


title: CB20


title: Muscle WT Aged 12171


title: Mtb infected-12wks-2

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: Public Health Research Institute at UMDNJ

description:
Biological replicate
Mtb infected-12w-2

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for applied genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing:
Microarray data from the scanned images were extracted using feature extraction software from Agilent technologies and downstream analysis was performed using commercial software.
Lowess-error-normalised log2 ratio (Red vs Green Channel) for significant difference in fold change in gene expression was calculated and represented as Mtb infected at Tx/uninfected

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

growth_protocol: New Zealand White rabbits were infected aerogenically with MtbCDC1551 at 3.5log10 (on day 0).  Lung tissues from rabbits were isolated from uninfected and at Day 2,4, 8 and 12 weeks post infection and used for total RNA isolation.

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Uninfected

tag: time point

value: 12 wks post infection


title: Muscle KO Adult 01032


title: Mtb infected-12wks-3

description:
Biological replicate
Mtb infected-12w-3


title: CB12


title: ACD lung_gDNA2 (sample 77.3)


title: Mtb infected-8wks-2

description:
Biological replicate
Mtb infected-8w-2

value: 8 wks post infection


title: ACD lung_gDNA1 (sample 64.5)


title: Muscle WT Aged 0123


title: Muscle WT Aged 0106


title: Mtb infected-12wks-1

description:
Biological replicate
Mtb infected-12w-1


title: Mtb infected-4wks-2

description:
Biological replicate
Mtb infected-4w-2

value: 4 wks post infection


title: Muscle WT Aged 0121


title: Mtb infected-8wks-1

description:
Biological replicate
Mtb infected-8w-1


title: CB13


title: CB37


title: A31NEW

value: Whole blood


title: A38NEW

value: naive cells


title: 103


title: Mtb infected-4wks-1

description:
Biological replicate
Mtb infected-4w-1


title: Mtb infected-4wks-3

description:
Biological replicate
Mtb infected-4w-3


title: Muscle WT Adult 07272

source_name: Tibialis Anterior Muscle, Wildtype, Adult


title: Gal11 Knockout Replicate 2

status: Public on Jul 10 2012

city: Pittsburgh

last: Gitter

state: PA

address: 5000 Forbes Ave

department: Computer Science Department

institute: Carnegie Mellon University

description: WIS_251632210283_pmt10_GE2_107_Sep09_1_4.txt

hyb_protocol: The samples were hybridized to yeast dual color expression microarrays (8x15K, G2509F) using standard Agilent protocols, reagents, and instruments.

scan_protocol: The scanned images were analyzed using Agilent's Feature Extraction software.

data_processing: After background subtraction, probe location normalization based on a Gaussian image filtering technique was applied.  This was followed by quantile normalization. The software we used included Agilent Feature Extraction Software version 10.7.3.1 for scanning, the MATLAB Bioinformatics Toolbox version 3.4 (R2009b) for quantile normalization, and a custom script from a colleague for the probe location normalization.

source_name: Gal11 Knockout Replicate 2

label_protocol: The samples were amplified, labeled, using standard Agilent protocols, reagents, and instruments.

growth_protocol: Cells were grown to logarithmic phase in SC medium (OD=0.5). The cells were harvested, pelleted and frozen for further analysis.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

treatment_protocol: Soribitol experiments were similarly performed by growing to logarithmic phase in SC medium and then washing and resuspending in SC medium with 1M sorbitol for 30 minutes.

value: Gal11 Knockout

tag: medium

value: sorbitol


title: Muscle WT Adult 0629

tag: tissue


title: Rvs167 Knockout Replicate 2

description: WIS_251632210283_pmt10_GE2_107_Sep09_2_3.txt

source_name: Rvs167 Knockout Replicate 2

value: Rvs167 Knockout


title: Pcl2 Knockout Replicate 2

source_name: Pcl2 Knockout Replicate 2

value: Pcl2 Knockout


title: Mtb infected-2wks-2

description:
Biological replicate
Mtb infected-2w-2

value: 2 wks post infection


title: Wild Type Sorbitol Replicate 2

description:
WIS_251632210283_pmt10_GE2_107_Sep09_2_2.txt
Control

source_name: Control Replicate 2

value: wild type


title: Wild Type Sorbitol Replicate 3

description:
WIS_251632210283_pmt10_GE2_107_Sep09_2_3.txt
Control

source_name: Control Replicate 3


title: Wild Type Sorbitol Replicate 4

description:
WIS_251632210283_pmt10_GE2_107_Sep09_2_4.txt
Control

source_name: Control Replicate 4


title: Wild Type Sorbitol Replicate 1

description:
WIS_251632210283_pmt10_GE2_107_Sep09_2_1.txt
Control

source_name: Control Replicate 1


title: Mtb infected-2wks-3

description:
Biological replicate
Mtb infected-2w-3


title: Muscle WT Adult 07273

tag: strain


title: Muscle WT Adult 0701


title: Gal11 Knockout Replicate 1

description: WIS_251632210283_pmt10_GE2_107_Sep09_1_3.txt

source_name: Gal11 Knockout Replicate 1


title: Fus3 Knockout Replicate 1

description: WIS_251632210283_pmt10_GE2_107_Sep09_1_2.txt

source_name: Fus3 Knockout Replicate 1

value: Fus3 Knockout


title: Fus3 Knockout Replicate 2

description: WIS_251632210283_pmt10_GE2_107_Sep09_2_2.txt

source_name: Fus3 Knockout Replicate 2


title: Bem1 Knockout Replicate 2

description: WIS_251632210283_pmt10_GE2_107_Sep09_2_1.txt

source_name: Bem1 Knockout Replicate 2

value: Bem1 Knockout


title: Muscle WT Adult 07271

value: tibialis anterior


title: Pcl2 Knockout Replicate 1

source_name: Pcl2 Knockout Replicate 1


title: Rvs167 Knockout Replicate 1

description: WIS_251632210283_pmt10_GE2_107_Sep09_1_1.txt

source_name: Rvs167 Knockout Replicate 1


title: Mtb infected-2wks-1

description:
Biological replicate
Mtb infected-2w-1


title: Asf1 Knockout Replicate 2

description: WIS_251632210283_pmt10_GE2_107_Sep09_2_4.txt

source_name: Asf1 Knockout Replicate 2

value: Asf1 Knockout


title: ACD lung_gDNA1 (sample 57.3)

hyb_protocol: Labeled samples were hybridized to 4.2M whole genome arrays at 42°C for 60-72 hrs,followed by disassembling of slides from hybridization apparatus at 42° in the wash buffer containing DTT followed by three washes at room temperature in the same buffer for 2mins, 1min and 15secs respectively. The slides were dried in a microarray dryer for 1 min.

scan_protocol: 4.2M microarrays were scanned on a Roche-NimbleGen MS 200 Microaarray scanner

data_processing: Scanned images were processed using NumbleScan v2.5 (Roche Nimblegen) and analyzed using Signalmap v1.9 (rocheNimbleGen)

source_name: Genomic DNA from frozen/FFPE lung tissue of ACD/MPV patient

label_protocol: 0.5ug of genomic DNA was labeled using the NimbleGen Dual-color DNA labeling kit according to manufacturer's instructions.

extract_protocol: Peripheral blood DNA was extracted using Gentra Puregene Blood Kit (Qiagen), DNA from frozen lung tissues was extracted using Dneast Blood & Tissue kit(Qiagen), DNA from FFPE lung tissues was isolated following manufacturer's protocol ( Agilent technologies)

value: Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV)

value: lung

source_name: Peripheral blood genomic DNA from normal control

value: healthy

value: peripheral blood


title: Asf1 Knockout Replicate 1

source_name: Asf1 Knockout Replicate 1


title: KOVB3_134

city: Kyoto

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were analyzed with Affymetrix microarray scanner using AGCC software.

data_processing: The data were analyzed with R.

source_name: ovarian cancer, ascites1

label_protocol: Labeling was performed according to Affymetrix GeneChip 3' IVT Express Kit protocol.

extract_protocol: Total RNA was extracted using Qiagen RNA easy.

value: ovarian cancer

value: positive

tag: Stage

tag: histology

value: endometrioid


title: KOVB3_138

value: serous


title: KOVB4_3

value: clear


title: KOVB3_139


title: KOVB4_2


title: KOVB3_133


title: KOVB4_13


title: KOVB3_132


title: ACD lung_gDNA2 (sample 59.4)