title: B_HCC_TLR4wt C3H/HeOuJ_22

source_name: HCC tissue of WT C3H/HeOuJ mice treated with DEN (100 mg/kg) at 12 weeks, CCl4 (0.5 ml/kg) at 13,15,17,19,21,23 weeks and sacrificed at 54 weeks


title: RiceShoot_VC56_2hr_nitrate_rep1

status: Public on Jan 03 2013

type: RNA

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Gene expression in a vector control transgenic rice (line #56) 2 hours after treatment with 10 mM nitrate

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60｡C for 30 minutes in a reaction volume of 55 ｵl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ｵl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Rice Gene Expression 4x44k Microarrays (G1529F015241) 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 Technologies) and 1 minute with 37｡C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (eXtended Dymanic range scan, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 015241_D_F_20110907) to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Oryza sativa

source_name: Vector control #56 2hr 10 mM KNO3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked using a Spectrophotometer and the Agilent 2100 Bioanalyzer.

growth_protocol: Rice T1 seeds were germinated on agar plates containing 50 ug/ml hygromycin B and grown for 5 days. Resistant seedlings were transferred to a hydroponic setting and grown with distilled water for 9 days in a growth chamber set to 16 hr Light/8 hr Dark conditions at 25｡C.

extract_protocol: Total RNA was isolated using TRIzol reagent and then treated with DNase I. After phenol and phenol:chloroform:isoamylalcohol extraction followed by ethanol precipitation, RNA was further purified using the RNeasy mini kit (QIAGEN). The quality of RNA was checked by measuring absorbance at 230, 260 and 280 nm using a spectrophotometer and also using the Agilent 2100 Bioanalyzer.

treatment_protocol: Rice seedlings were transferred to 10 mM potassium nitrate at 3 hours into the light period and incubated for 2 hours. Shoots were collected.

tag: organ

value: shoot

tag: genotype/variation

tag: treatment

value: 10 mM nitrate


title: B_HCC_TLR4wt C3H/HeOuJ_21

city: New York

first: Robert

middle: F

last: Schwabe

state: NY

address: Russ Berrie Pavilion, 1150 St. Nicholas Avenue

department: Medicine

country: USA

institute: Columbia University

hyb_protocol: 10 μg of aRNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

label: biotin

organism: Mus musculus

label_protocol: 100 ng RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by Trizol followed by column purification (Qiagen) and quantification by NanoDrop Spectrophotometer.

treatment_protocol: For all HCC mice, DEN (100 mg/kg) was administered by injection at 12 weeks. CCl4 (0.5 ml/kg) was administered by injection at weeks, 13,15,17.19,21,23. Antibotics (a combination of ampicillin (1 g/l), neomycin (1 g/l), metronidazole (1 g/l) and vancomycin (500 mg/l) were administered in drinking water for 2 weeks prior to the first DEN injection at continued up to week 54. After sacrifice, tissue from HCC lesions was dissected for the analysis. For control mice, normal liver tissue was used.

tag: gender

value: male

value: WT

tag: strain

tag: age

value: 54 weeks

tag: tissue

value: hepatocellular carcinoma


title: T87

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: DNAs were extracted using the QIAamp DNA mini kit (Qiagen, Courtaboeuf, France) from frozen tissue samples.

tag: sample id

tag: tissue type

value: Adenocarcinoma


title: T79


title: RiceShoot_VC60_0hr_rep1

description: Gene expression in a vector control transgenic rice (line #60) before treatment with 10 mM nitrate

source_name: Vector control #60 0hr


title: T97


title: RiceShoot_VC56_0hr_rep1

description: Gene expression in a vector control transgenic rice (line #56) before treatment with 10 mM nitrate

source_name: Vector control #56 0hr


title: T93


title: RiceShoot_NIGT1ox55_0hr_rep1

description: Gene expression in a NIGT1-overexpressing rice (line #55) before treatment with 10 mM nitrate

source_name: NIGT1 overexpressor #55 0hr

value: NIGT1-overexpressing rice (line #55)


title: B_HCC_TLR4wt C3H/HeOuJ_17


title: T68


title: T67


title: T69


title: RNF40 siRNA - 5 days adipocyte differentiation, rep2

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331).

scan_protocol: Illumina iScan Scanner.

data_processing: Log2 transformation of signal intensity, quantile normalization, R/Bioconductor, BeadStudio.

source_name: hMSC-Tert, RNF40 siRNA, 5 days adipocyte differentiation

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Cat # IL1791); 200ng total RNA input.

growth_protocol: hMSC-Tert cells were cultured in low glucose, phenol red-free MEM (Invitrogen, Carlsbad, CA), supplemented with 10% bovine growth serum (BGS; HyClone, USA) and 1X penicillin/streptomycin (Invitrogen).

extract_protocol: Total RNA was extracted using Qiazol (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For osteoblast differentiation, growth medium was supplemented with 10 mM β-glycerophosphate, 0.2 mM ascorbate, 10^-8 M calcitriol, and 10^-7 M dexamethasone. For adipocyte differentiation, normal growth medium containing 15% BGS was supplemented with 2 X 10^-6 M insulin, 0.45 mM isobutylmethyl-xanthine, 10-5 M troglitazone, and 10^-7 M dexamethasone.

tag: cell type

value: human immortalized mesenchymal stem cells

tag: sirna

tag: differentiation state

value: 5 days adipocyte differentiation


title: B_HCC_TLR4wt C3H/HeOuJ_19


title: B_HCC_TLR4wt C3H/HeOuJ_20


title: RNF40 siRNA - 5 days adipocyte differentiation, rep3


title: B_HCC_TLR4wt C3H/HeOuJ_18


title: A_Tlr4wtun3_H03

source_name: Livers of WT C3H/HeOuJ mice sacrificed at 15 weeks.

value: 15 weeks

value: liver


title: T80


title: RNF40 siRNA - 5 days adipocyte differentiation, rep1


title: T64


title: T58


title: A_Tlr4wtun2_H02


title: T62


title: RNF40 siRNA - 2 days adipocyte differentiation, rep3

source_name: hMSC-Tert, RNF40 siRNA, 2 days adipocyte differentiation

value: 2 days adipocyte differentiation


title: B_HCC_TLR4wt C3H/HeOuJ_16


title: T55

value: Bronchiolo-alveolar adenocarcinoma


title: RNF40 siRNA - 2 days adipocyte differentiation, rep2


title: RNF40 siRNA - 2 days adipocyte differentiation, rep1


title: T105


title: T54


title: T45


title: T53


title: 705N mRNA

city: shanghai

first: Jihong

last: Fu

state: shanghai

address: Kongjiang Road 1665, Shanghai, 200092, China

department: colorectal surgery department

country: China

institute: Xinhua Hospital

description: mRNA expression of normal colon mucosa

hyb_protocol: 2 ug of total RNA isolated from CRC tissues and corresponding normal tissues were reverse-transcribed into cDNA, and labeled with Cy3 or Cy5.  The labeled cDNA was then hybridized on a Whole Human Genome Agilent 4X44K Oligonucleotide Microarray (Agilent) according to the manufacture’s protocol using miRNA Complete Labeling and Hyb Kit. The chips were washed using Agilent Gene Expression Wash Buffer Kit (Agilent 5188-5327). Scanning of the microarrays was carried out immediately using the Agilent G2565BA Microarray Scanner System.Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version  9.5.3). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA,and the log 2 based data was then filtered on flags (IsFound, IsWellAboveBG, IsSaturated) to identify deifferentially expressed features between colorectal cancer sample and normal colon mucosa.T-test and Significant Analysis of Microarray analyses（SAM） were carried out to identify deregulated miRNAs.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version  9.5.3). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA,and the log 2 based data was then filtered on flags (IsFound, IsWellAboveBG, IsSaturated) to identify deifferentially expressed features between colorectal cancer sample and normal colon mucosa.T-test and Significant Analysis of Microarray analyses（SAM） were carried out to identify deregulated mNAs.

source_name: normal colon mucosa, patient 705

extract_protocol: Total RNA was extracted and isolated using mirVana TM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacture’s introduction. The concentration of RNA was measured by NanoDrop spectrophotometer. Total RNA concentration ranged form 100ng/ul to 1ug/ul. The RNA quality was evaluated by Agilent 2100 Bioanalyzer; RNAs with RIN>=7.0 and 28S/18S>0.7 were accepted for microarray analysis.

tag: age (yr)

value: Female

tag: location

value: Rectum

tag: t

tag: n

tag: m

tag: Stage

value: III

tag: differentiation

value: moderate

value: normal colorectal tissue

tag: individual

value: patient 705


title: RNF40 siRNA - 5 days osteoblast differentiation, rep1

source_name: hMSC-Tert, RNF40 siRNA, 5 days osteoblast differentiation

value: 5 days osteoblast differentiation


title: T49


title: RNF40 siRNA - 5 days osteoblast differentiation, rep2


title: RNF40 siRNA - 5 days osteoblast differentiation, rep3


title: RNF40 siRNA - 2 days osteoblast differentiation, rep3

source_name: hMSC-Tert, RNF40 siRNA, 2 days osteoblast differentiation

value: 2 days osteoblast differentiation


title: 702C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 702

label_protocol: 2 ug of total RNA isolated from CRC tissues and corresponding normal tissues were reverse-transcribed into cDNA, and labeled with Cy3 or Cy5.  The labeled cDNA was then hybridized on a Whole Human Genome Agilent 4X44K Oligonucleotide Microarray (Agilent) according to the manufacture’s protocol using miRNA Complete Labeling and Hyb Kit. The chips were washed using Agilent Gene Expression Wash Buffer Kit (Agilent 5188-5327). Scanning of the microarrays was carried out immediately using the Agilent G2565BA Microarray Scanner System.Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version  9.5.3). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA,and the log 2 based data was then filtered on flags (IsFound, IsWellAboveBG, IsSaturated) to identify deifferentially expressed features between colorectal cancer sample and normal colon mucosa.T-test and Significant Analysis of Microarray analyses（SAM） were carried out to identify deregulated miRNAs.

tag: gender

value: II

value: colorectal cancer tumor

value: patient 702


title: 702N mRNA

description: mRNA expression of normal colon mucosa

scan_protocol: canning of the microarrays was carried out immediately using the Agilent G2565BA Microarray Scanner System

source_name: normal colon mucosa, patient 702


title: 705C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 705


title: A_Tlr4wtun1_H01

value: male

tag: genotype/variation

value: WT

tag: strain


title: 698N mRNA

description: mRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 698

value: Male

value: Sigmoid colon

tag: tissue

value: patient 698


title: T43

tag: sample id

value: Adenocarcinoma


title: T39

tag: tissue type

value: Bronchiolo-alveolar adenocarcinoma


title: RNF40 siRNA - 2 days osteoblast differentiation, rep1

tag: cell type

value: human immortalized mesenchymal stem cells


title: RNF40 siRNA - Undifferentiated, rep3

source_name: hMSC-Tert, RNF40 siRNA, undifferentiated

tag: sirna

value: undifferentiated


title: T41


title: 667C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 667

value: Female

value: Transverse colon

value: moderate

value: patient 667


title: 667N mRNA

description: mRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 667

value: normal colorectal tissue


title: 698C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 698

value: II


title: FHL2-transfected_T4_rep2

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description:
F2_T4_2
FHL2-transfected (F2) VSa16 cells collected at T4_rep2

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Gene expression profiling was performed using the Agilent-016251 Sparus aurata Oligo Microarray platform  based on single-colour detection (Cyanine-3 only).

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.6 used XDR ID to link the pairs of scans together automatically when extracting data.

data_processing: Data processed with FeatureExtraction v9.5 and Cyclic lowess normalized using R2.6.1 statistical software.

organism: Sparus aurata

source_name: Sparus aurata pre-osteoblast cell line

label_protocol: Amplified and labeled with Cy3 according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: VSa16 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, antibiotics and antimycotics.

extract_protocol: Extracted according to Ambion TRI Reagent® protocol

treatment_protocol: F2 VSa16 cells were transfected with FHL2 gene as follows: coding sequence of gilthead seabream FHL2 cDNA was inserted into the expression vector pcDNA3.1 and FLAG epitope was added at its 5’ end. Construction was delivered into gilthead seabream pre-osteoblast VSa16 cells and then transfected cells were cultured for 3 weeks in medium supplemented with 300 µg/ml of geneticin.  Clones resistant to antibiotic were selected, transferred to new plates and further cultured.

tag: cell line

value: VSa16 pre-osteoblast cell line

tag: transfection

tag: time

value: T4 (4 weeks of cell confluency)


title: RNF40 siRNA - Undifferentiated, rep2

tag: differentiation state


title: FHL2-transfected_T4_rep4

description:
F2_T4_4
FHL2-transfected (F2) VSa16 cells collected at T4_rep4


title: 601N mRNA

description: mRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 601

tag: age (yr)

tag: location

value: Rectum

tag: t

tag: n

value: I

value: patient 601


title: FHL2-transfected_T4_rep1

description:
F2_T4_1
FHL2-transfected (F2) VSa16 cells collected at T4_rep1


title: RNF40 siRNA - 2 days osteoblast differentiation, rep2

value: 2 days osteoblast differentiation


title: Control siRNA - 5 days adipocyte differentiation, rep3

source_name: hMSC-Tert, control siRNA, 5 days adipocyte differentiation

value: control

value: 5 days adipocyte differentiation


title: T44

value: Large cell carcinoma


title: 601C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 601

tag: m

tag: Stage

tag: differentiation

value: colorectal cancer tumor

tag: individual


title: T32

value: Adenocarcinoma


title: FHL2-transfected_T0_rep4

description:
F2_T0_4
FHL2-transfected (F2) VSa16 cells collected at T0_rep4

value: T0 (initial confluent cultures)


title: T42


title: 705C microRNA

description: miRNA expression of colorectal cancer

hyb_protocol: 100ng of total RNA was reverse transcribed into cDNA and labeled with Cy3, and then hybridized on a miRNA array (Agilent-021827 Human miRNA Microarray (V3)) using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456).

scan_protocol: The slides were then scanned in microarray scanner by Agilent scan control software Version A7.0

data_processing: The data collection, background subtraction and with-in array normalization were carried out by Agilent Feature Extraction (FE) software version 9.5.3.

tag: gender

value: Female

value: III

tag: tissue

value: patient 705


title: 705N microRNA

description: miRNA expression of normal colon mucosa

label_protocol: 100ng of total RNA was reverse transcribed into cDNA and labeled with Cy3, and then hybridized on a miRNA array (Agilent-021827 Human miRNA Microarray (V3)) using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456).

value: moderate

value: normal colorectal tissue


title: Control siRNA - 5 days adipocyte differentiation, rep2

value: human immortalized mesenchymal stem cells


title: FHL2-transfected_T0_rep3

description:
F2_T0_3
FHL2-transfected (F2) VSa16 cells collected at T0_rep3

value: VSa16 pre-osteoblast cell line


title: T29

tag: sample id

tag: tissue type


title: 702N microRNA

description: miRNA expression of normal colon mucosa

value: Rectum

value: II

value: patient 702


title: FHL2-transfected_T0_rep2

description:
F2_T0_2
FHL2-transfected (F2) VSa16 cells collected at T0_rep2


title: T36


title: Control siRNA - 5 days adipocyte differentiation, rep1

tag: cell type

tag: sirna


title: Control siRNA - 2 days adipocyte differentiation, rep2

source_name: hMSC-Tert, control siRNA, 2 days adipocyte differentiation

value: 2 days adipocyte differentiation


title: RNF40 siRNA - Undifferentiated, rep1

value: undifferentiated


title: FHL2-transfected_T0_rep1

description:
F2_T0_1
FHL2-transfected (F2) VSa16 cells collected at T0_rep1

tag: cell line

tag: transfection


title: 590N mRNA

description: mRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 590

value: Sigmoid colon

value: patient 590


title: FHL2-transfected_T4_rep3

description:
F2_T4_3
FHL2-transfected (F2) VSa16 cells collected at T4_rep3

tag: time

value: T4 (4 weeks of cell confluency)


title: 590C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 590

tag: age (yr)

value: colorectal cancer tumor


title: Control siRNA - 2 days adipocyte differentiation, rep3

value: control

tag: differentiation state


title: 581C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 581

value: Male

tag: location

tag: t

value: patient 581


title: 702C microRNA

description: miRNA expression of colorectal cancer

value: Female

tag: n

tag: m


title: T22

value: Large cell carcinoma


title: Control_T4_rep4

description:
WT_T4_4
Control (WT) VSa16 cells collected at T4_rep4


title: T26

value: Adenocarcinoma


title: Control siRNA - 5 days osteoblast differentiation, rep3

source_name: hMSC-Tert, control siRNA, 5 days osteoblast differentiation

value: human immortalized mesenchymal stem cells

value: 5 days osteoblast differentiation


title: 667C microRNA

description: miRNA expression of colorectal cancer

value: Transverse colon

tag: Stage

tag: differentiation

value: moderate

value: patient 667


title: 698C microRNA

description: miRNA expression of colorectal cancer

tag: gender

value: II

tag: individual

value: patient 698


title: Control_T4_rep2

description:
WT_T4_2
Control (WT) VSa16 cells collected at T4_rep2

value: VSa16 pre-osteoblast cell line


title: 698N microRNA

description: miRNA expression of normal colon mucosa

value: Sigmoid colon

tag: tissue

value: normal colorectal tissue


title: Control_T4_rep3

description:
WT_T4_3
Control (WT) VSa16 cells collected at T4_rep3

value: T4 (4 weeks of cell confluency)


title: 577N mRNA

description: mRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 577

value: Rectum

value: patient 577


title: 667N microRNA

description: miRNA expression of normal colon mucosa


title: Control siRNA - 2 days osteoblast differentiation, rep2

source_name: hMSC-Tert, control siRNA, 2 days osteoblast differentiation

value: control

value: 2 days osteoblast differentiation


title: Control_T4_rep1

description:
WT_T4_1
Control (WT) VSa16 cells collected at T4_rep1


title: Control siRNA - 2 days adipocyte differentiation, rep1

value: 2 days adipocyte differentiation


title: Control_T0_rep4

description:
WT_T0_4
Control (WT) VSa16 cells collected at T0_rep4

value: T0 (initial confluent cultures)


title: Control siRNA - 5 days osteoblast differentiation, rep1

value: human immortalized mesenchymal stem cells


title: 601N microRNA

description: miRNA expression of normal colon mucosa

value: Female

value: I

value: patient 601


title: Control siRNA - 5 days osteoblast differentiation, rep2

value: 5 days osteoblast differentiation


title: 577C mRNA

description: mRNA expression of colorectal cancer

source_name: colorectal cancer sample, patient 577

value: Male

value: II

value: moderate

value: colorectal cancer tumor


title: Control_T0_rep3

description:
WT_T0_3
Control (WT) VSa16 cells collected at T0_rep3

value: VSa16 pre-osteoblast cell line


title: T18

tag: sample id

tag: tissue type

value: Bronchiolo-alveolar adenocarcinoma


title: 601C microRNA

description: miRNA expression of colorectal cancer

value: Rectum


title: Control siRNA - 2 days osteoblast differentiation, rep1

tag: cell type

tag: sirna


title: Control_T0_rep2

description:
WT_T0_2
Control (WT) VSa16 cells collected at T0_rep2

tag: cell line

tag: transfection


title: S.c. WT expression osmotic stress repl. 3

city: Burjassot

first: Paula

last: Alepuz

state: Valencia

address: Doctor Moliner, 50

department: Biochemistry and molecular biology

country: Spain

institute: University of Valencia

hyb_protocol: The hybridization of tiling array Affymetrix with cDNA produced from total RNA, was carried out according to the Affymetrix protocol and using GeneChip® Hybridization S. cerevisiae Tiling 1.0R Array, Wash and Stain Kit (P/N 900720).

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

data_processing:
High-density tiling arrays images were normalised and analysed using the Affymetrix Tiling Analysis Software; and were visualized by the Integrated Genome Browser (Affymetrix).
additional results files: Ratios between the average of WT osmotic stress (3 replicas) and WT non-stress (3 replicas) are in file t15vst0_signal.bar and t15vst0.TAG and t15vst0.txt
results file descriptions: t15vst0_signal.bar was generated using Affymetrix Tiling Analysis Software

organism: Saccharomyces cerevisiae

source_name: cDNA S.cerevisiae exponential grown  osmotic stress t=15 min NaCl 0.4M biolo. Replic. 3

label_protocol: Samples (7.5 μg of DNA) were enzymatically fragmented and labeled using the Gene Chip WT double strand DNA terminal labeling kit (Affymetrix)

growth_protocol: Yeast cells were grown at 30ºC in YPD media until exponential phase (OD600= 0.6).

extract_protocol: Total RNA was extracted from cell pellets using a FastPrep device (FastPrep 120, Bio101) in 0.5 ml of LETS buffer (0.1 M LiCl, 0.01 M EDTA, pH 8.0, 0.01 M Tris-HCl, pH 7.4, and 0.2% SDS [wt/vol]), 0.5 ml of phenol (pH 4.5):chloroform:isoamylic alcohol (25/24/1), and 0.3 ml of glass beads. Supernatants were extracted with phenol:chloroform:isoamylic alcohol (25/24/1) and chloroform:isoamylic alcohol (24/1). RNA was precipitated twice; first, by adding two volumes of 96% ethanol and 0.1 volumes of 5 M LiCl and then by incubating overnight at −20°C. Finally, the RNA was disolved in RNase-free water.

treatment_protocol: Then, NaCl was added to final concentration of 0.4 M and cells were incubated at 30ºC for 15 minutes.

tag: strain

tag: growth

value: exponential phase in YPD 0.4 M NaCl


title: S.c. WT expression osmotic stress repl. 2

source_name: cDNA S.cerevisiae exponential grown  osmotic stress t=15 min NaCl 0.4M biolo. Replic. 2


title: S.c. WT expression osmotic stress repl. 1

source_name: cDNA S.cerevisiae exponential grown  osmotic stress t=15 min NaCl 0.4M biolo. Replic. 1


title: 590N microRNA

description: miRNA expression of normal colon mucosa

tag: age (yr)

tag: location

value: Sigmoid colon

value: III

value: normal colorectal tissue

value: patient 590


title: Control_T0_rep1

description:
WT_T0_1
Control (WT) VSa16 cells collected at T0_rep1

value: control

tag: time

value: T0 (initial confluent cultures)


title: S.c. WT expression no-stress repl. 3

source_name: cDNA S.cerevisiae exponential grown  no stress t=0 biolo. Replic. 3

value: exponential phase in YPD


title: T4

value: Adenocarcinoma


title: S.c. WT expression no-stress repl. 1

source_name: cDNA S.cerevisiae exponential grown  no stress t=0 biolo. Replic. 1


title: T10


title: T2


title: S.c. WT expression no-stress repl. 2

source_name: cDNA S.cerevisiae exponential grown  no stress t=0 biolo. Replic. 2


title: T21


title: Control siRNA - Undifferentiated, rep2

source_name: hMSC-Tert, control siRNA, undifferentiated

value: human immortalized mesenchymal stem cells

tag: differentiation state

value: undifferentiated


title: 581N microRNA

description: miRNA expression of normal colon mucosa

source_name: normal colon mucosa, patient 581

value: Male

tag: t

tag: n

tag: m

tag: Stage

value: patient 581


title: 581C microRNA

description: miRNA expression of colorectal cancer

tag: gender

tag: differentiation

value: moderate

tag: tissue

value: colorectal cancer tumor

tag: individual


title: T6

tag: sample id

tag: tissue type

value: Large cell carcinoma


title: Control siRNA - Undifferentiated, rep3

tag: cell type

tag: sirna


title: 577C microRNA

description: miRNA expression of colorectal cancer

value: Rectum

value: II

value: patient 577


title: Control siRNA - Undifferentiated, rep1


title: 577N microRNA

description: miRNA expression of normal colon mucosa


title: 590C microRNA

description: miRNA expression of colorectal cancer

value: Female

value: Sigmoid colon

value: III


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 4

city: Rio de Janeiro

first: Anna Beatriz

middle: Robottom

last: Ferreira

state: Rio de Janeiro

address: Rua Adolfo Lutz 55 apt 201

country: Brazil

institute: Fundação Oswaldo Cruz

description: Biological replicate 4 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100

hyb_protocol: Samples were hybridized to HEEBO arrays under coverslips in 5X SSC and 0.1% SDS and incubated overnight at 60C in slide chambers placed in a water bath under agitation.

scan_protocol: Slides were hybridized at 100% laser power and PMT gain was set so that both channels of each slide were of similar overal intesity.

data_processing:
The hybridization signal values for the multiple probes for each mRNA were obtained with the use of GenePix Pro v.6.0 (Axon). The data were analyzed by R and limma packages. The the signal is background corrected by fitting a normal-exponential convolution model to a vector of observed intensities (offset = 50). The signal is normilized within arrays using the LOWESS correction. The signal is normalized between arrays using the quantile method.
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Schwann cell; non-infected control

label_protocol: RNA was amplified by the MessageAMP II aRNA kit (Ambion) after which 2ug were submitted to direct labeling of the second strand of cDNA. First strand of cDNA was made by reverse transcription with Superscript III. Remaining RNA was digested with Rnase One. cDNA was then purified in microcon 30 columns. Labelling occured by incorporation of Alexa 555 or 647-aha-dCTP during second strand cDNA synthesis using Bioprime DNA labeling kit (Invitrogen).

growth_protocol: Primary human Schwann cells were grown in human Schwann Cell Medium (ScienCell) containing 5% FCS and Pen/Strep and subcultured for no more than 5 passages by plating in culture flasks at 37C until monolayers were confluent.

extract_protocol: RNA was extracted from cells using RNAgents Total RNA Isolation System from Promega. RNA was DNAse treated and RNA integrity was analyzed on a Bioanalyzer and by agarose gel electrophoresis.

treatment_protocol: Cells were infected at a M.O.I of 100:1 with live M. leprae that had been passaged and purified from hind footpads of BALB/c athymic nude mice. Infected and non infected cells were incubated at 33C for 24 hours.

value: primary Schwann cells

tag: infection

value: non-infected control

source_name: Schwann cell; ML infected

value: M. leprae infected


title: 581N mRNA

description: mRNA expression of normal colon mucosa

tag: age (yr)

value: normal colorectal tissue


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 3

description: Biological replicate 3 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 5

description: Biological replicate 5 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 1

description: Biological replicate 1 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100


title: Resistant Infected 7

status: Public on Jan 02 2013

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

hyb_protocol: Hybridizations were performed in a rotisserie-style Micro-array Hybridization Oven (Agilent) overnight (18 h) at 65°C. Following hybridization, the slides were rinsed in gene expression wash buffers 1 and 2 (Agilent) following the manufacturer's instructions.

scan_protocol: The slides were scanned using an Agilent high-resolution micro-array scanner at a resolution of 5 μm. Images, saved as *.TIF files, were extracted, and initial analysis were performed with Feature Extraction software v9.5.3 (Agilent).

data_processing: Data has been normalized, sample per sample (within normalization), by subtracting the median to log2 transformed signal intensity.

organism: Oncorhynchus mykiss

source_name: Pronephros

label_protocol: The Cy3 was  incorporated by a T7 polymerase mediated transcription, and the excess of dye removed using the RNeasy kit (Quiagen). The level of dye incorporation was assessed by spectrophotometry (Nanodrop ND1000, LabTech).

extract_protocol: Trizol reagent was used for total RNA extraction. For micro-array analysis, we examined four RNA preparations from F. psychrophilum-infected fish and from control fish for each genetic background (biological replicates). Each sample comprised an equal quantity of RNA. RNA stability and integrity was assessed using Bioanalyzer (Agilent), and only RNA with RIN>8 were used. Each experimental sample was Cy3-labeled following the procedure recommended by Agilent, and was hybridized in one-color experiment. The RNA was first reverse transcribed, using a poly(dT)-T7 primer

tag: genetic line

value: Resistant

tag: treatment

value: Infected


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 6

description: Biological replicate 6 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100


title: T12

value: Bronchiolo-alveolar adenocarcinoma


title: Susceptible Infected 1

value: Susceptible


title: Resistant Control 16

value: Control


title: T8


title: Resistant Control 13


title: Resistant Control 12


title: Resistant Infected 4


title: Resistant Infected 6


title: Resistant Infected 8


title: Schwann cell primary culture infected with M. leprae MOI 1:100 replicate 2

description: Biological replicate 2 of 6. Schwann cell primary culture infected with M. leprae MOI 1:100


title: Susceptible Control 16


title: Resistant Infected 2


title: Susceptible Infected 2


title: Susceptible Control 12


title: Resistant Control 11


title: Resistant Control 10


title: Susceptible Infected 3


title: Resistant Infected 3


title: Susceptible Control 10


title: Susceptible Infected 7


title: Resistant Infected 5


title: Susceptible Control 13


title: Resistant Control 14


title: 126 (221), MUSCLE, Before

city: St. Louis

first: C. Charles

last: Gu

address: 660 S Euclid Ave

institute: Washington University

description: Gene expression data from human biopsy tissue samples

hyb_protocol: Prepare the hybridization cocktail containing fragmented and labeled aRNA. Heat the hybridization cocktail to 99 degree for 5 minutes. Incubate the probe array filled with Pre-hybridization mix at 45 degree for 10 minutes with rotation. Transfer the Hybridization Cocktail that has been heated at 99 degree to a 45 degree heat block for 5 minutes. Hybridize at 45 degree for 16 hours.

scan_protocol: Scanning of the arrays was done on an Affymetrix scanner 3000 and the Command Console Software was used to monitor scanning and to convert raw data into cell intensity files.

data_processing: Gene expression microarray data were analyzed by using using R/Bioconductor.  The quality of all expression microarray data were examined for comparable scale factor, similar average background and percent present calls, and RNA integrity using R package ‘simpleaffy’.

source_name: MUSCLE, RES, Before

label_protocol: Biotinylated cRNA were prepared according to 3`IVT Express Kit (Lot: 1004019).

growth_protocol: We assigned non-obese women with normal glucose tolerance to 1) the placebo, 2) the resveratrol supplementation, and 3) calorie restriction group.

extract_protocol: Total RNA was extracted from the frozen tissue samples (subcutaneous adipose tissue and skeletal muscle (vastus lateralis) biopsy samples) using Trizol.

treatment_protocol: Subjects were instructed to take one capsule (75 mg resveratrol or placebo) in the morning with breakfast for 12 weeks. Subjects randomized to the calorie restriction weight loss group participated in a lifestyle intervention calorie restriction program that included weekly ~1 h long dietary and behavioural education sessions led by an experienced weight management dietician.

value: muscle

tag: sample group

value: resveratrol

value: before


title: Resistant Control 15


title: 126 (221), ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, RES, After

value: adipose tissue

value: after


title: 219, MUSCLE, After

source_name: MUSCLE, PLC, After

value: placebo

value: Female


title: Susceptible Infected 8


title: 220, MUSCLE, After

source_name: MUSCLE, CR, After

value: calorie restrictive


title: 219, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, PLC, Before


title: 126 (221), MUSCLE, After

source_name: MUSCLE, RES, After


title: 126 (221), ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, RES, Before


title: 222, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, CR, Before


title: 222, MUSCLE, Before

source_name: MUSCLE, CR, Before


title: 222, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, CR, After


title: 220, ADIPOOSE TISSUE, After


title: 216, ADIPOOSE TISSUE, After


title: 217, MUSCLE, Before

source_name: MUSCLE, PLC, Before


title: 219, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, PLC, After


title: 218, ADIPOOSE TISSUE, Before


title: 218, ADIPOOSE TISSUE, After


title: 217, MUSCLE, After


title: 216, MUSCLE, After


title: 215, ADIPOOSE TISSUE, After


title: 215, MUSCLE, Before


title: 220, MUSCLE, Before


title: 222, MUSCLE, After


title: 219, MUSCLE, Before


title: 220, ADIPOOSE TISSUE, Before


title: 216, MUSCLE, Before


title: 216, ADIPOOSE TISSUE, Before


title: 215, MUSCLE, After


title: 214, MUSCLE, After


title: 214, MUSCLE, Before


title: 214, ADIPOOSE TISSUE, After


title: 213, MUSCLE, Before


title: 215, ADIPOOSE TISSUE, Before


title: 214, ADIPOOSE TISSUE, Before


title: 213, MUSCLE, After


title: 213, ADIPOOSE TISSUE, After


title: 211, MUSCLE, Before


title: 211, ADIPOOSE TISSUE, After


title: 211, MUSCLE, After


title: 212, MUSCLE, Before


title: 211, ADIPOOSE TISSUE, Before


title: 213, ADIPOOSE TISSUE, Before


title: 212, MUSCLE, After


title: 210, MUSCLE, Before


title: 208, ADIPOOSE TISSUE, Before


title: 210, ADIPOOSE TISSUE, After


title: 208, MUSCLE, Before


title: 209, ADIPOOSE TISSUE, After


title: 209, MUSCLE, Before


title: 206, ADIPOOSE TISSUE, After


title: 209, MUSCLE, After


title: 206, ADIPOOSE TISSUE, Before


title: 209, ADIPOOSE TISSUE, Before


title: 205, MUSCLE, After


title: 210, MUSCLE, After


title: 208, ADIPOOSE TISSUE, After


title: 208, MUSCLE, After


title: 206, MUSCLE, After


title: 205, ADIPOOSE TISSUE, After


title: 210, ADIPOOSE TISSUE, Before


title: 205, MUSCLE, Before


title: 203, ADIPOOSE TISSUE, Before


title: 205, ADIPOOSE TISSUE, Before


title: 203, MUSCLE, After


title: 201, MUSCLE, After


title: 202, ADIPOOSE TISSUE, After


title: 202, ADIPOOSE TISSUE, Before


title: 202, MUSCLE, After


title: 202, MUSCLE, Before


title: 203, ADIPOOSE TISSUE, After


title: 203, MUSCLE, Before


title: 206, MUSCLE, Before


title: 201, MUSCLE, Before


title: 125, ADIPOOSE TISSUE, After


title: 201, ADIPOOSE TISSUE, Before


title: 125, MUSCLE, Before


title: 120, ADIPOOSE TISSUE, Before


title: 125, ADIPOOSE TISSUE, Before


title: 121, MUSCLE, After


title: 118, ADIPOOSE TISSUE, After


title: 201, ADIPOOSE TISSUE, After


title: 121, ADIPOOSE TISSUE, Before


title: 121, MUSCLE, Before


title: 121, ADIPOOSE TISSUE, After


title: 125, MUSCLE, After


title: 119, MUSCLE, After


title: 120, ADIPOOSE TISSUE, After


title: 123, ADIPOOSE TISSUE, Before


title: 118, ADIPOOSE TISSUE, Before


title: 117, ADIPOOSE TISSUE, After


title: 123, ADIPOOSE TISSUE, After


title: 119, MUSCLE, Before


title: 117, ADIPOOSE TISSUE, Before


title: 117, MUSCLE, After


title: 117, MUSCLE, Before


title: 116, MUSCLE, After


title: prsW mutant_rep2

city: Coventry

first: Emma

middle: L

last: Denham

address: Gibbet Hill Road

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description:
growth in LB medium_O.D. 600nm 1.0
prsW_2

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

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

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: prsW mutant

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol:
B. subtilis 168 and respective mutants were grown in Luria Bertani broth O.D. 600nm 1.0
The complete description of the growth protocols can be found in Zweers et al., to be submitted.

extract_protocol: Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

tag: genotype/variation

value: prsW mutant


title: 114, MUSCLE, After


title: 115, MUSCLE, Before


title: 116, MUSCLE, Before


title: prsW mutant_rep1

description:
growth in LB medium_O.D. 600nm 1.0
prsW_1


title: 114, ADIPOOSE TISSUE, After


title: 115, MUSCLE, After


title: rasP mutant_rep1

description:
growth in LB medium_O.D. 600nm 1.0
rasP_1

source_name: rasP mutant

value: rasP mutant


title: rasP mutant_rep2

description:
growth in LB medium_O.D. 600nm 1.0
rasP_2


title: sigW mutant_rep3

description:
growth in LB medium_O.D. 600nm 1.0
sigW_3

source_name: sigW mutant

value: sigW mutant


title: 114, MUSCLE, Before


title: rasP mutant_rep3

description:
growth in LB medium_O.D. 600nm 1.0
rasP_3


title: Wild type parent strain_rep3

description:
growth in LB medium_O.D. 600nm 1.0
WT_3

source_name: Wild type parent strain

value: wild type


title: sigW mutant_rep2

description:
growth in LB medium_O.D. 600nm 1.0
sigW_2


title: sigW mutant_rep1

description:
growth in LB medium_O.D. 600nm 1.0
sigW_1


title: 113, MUSCLE, After


title: 113, MUSCLE, Before


title: 114, ADIPOOSE TISSUE, Before


title: 113, ADIPOOSE TISSUE, Before


title: 113, ADIPOOSE TISSUE, After


title: Carbon switch pho7+-dependency T=120 min replicate 2

city: Cambridge

first: Ian

middle: O'Brien

last: Carter-O'Connell

state: MA

address: 52 Oxford St. NW 440

department: MCB

institute: Harvard University

hyb_protocol: 300 ng of the Cy3 and 300 ng of the Cy5 labeled sample was competitively hybridized to the microarrays in 2xGEx Hybridization Buffer (Hi-RPM) (Agilent) for 17 hours at 60°C. Arrays were subsequently washed in 6.7X SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 minute, 0.67X SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1X SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were immediately scanned using an Axon 4000B scanner at 5 μm resolution.

data_processing: The average intensity of the Cy3 and Cy5 florescence at each spot was extracted using the GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Lowess and quantile normalization (time-course) were performed using the MATLAB bioinformatics toolbox.

organism: Schizosaccharomyces pombe 972h-

source_name: GE pho7+ T=120 min

label_protocol: Purified cDNA samples were labeled using N-hydroxyl succimamide esters of either Cy3 or Cy5 dyes (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 1.5 hours. Labeled cDNA was purified (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: S. pombe cells were maintained in previously described YES or EMM media. Prior to starvation, cells were grown at 30°C, 220RPM to mid-log phase (OD600~0.2) in 90%SD-10%EMM media supplemented with 10 mM KH2PO4 (high-Pi media).

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen). cDNA was generated in a reverse transcriptase reaction using 10 μg total RNA with a 1:1 mixture of oligo-dT and random hexamer primers (Operon) and a 2:3 ratio of amino-allyl-dUTP:dTTP (Sigma). Superscript II RT (Invitrogen) was added and the reaction mixture was incubated at 42°C for 2.5 hours. cDNA was purified using a PCR purification kit (Qiagen) after completing hydrolysis of remaining RNA.

treatment_protocol: Cells were collected via filtration, washed twice, transferred to fresh media lacking Pi (no-Pi), and grown at 30°C for up to 4 hours. Immediately prior to starvation (t=0), 20 mL of cells were added to 30 mL of methanol kept at -65°C to prevent further transcription or RNA degradation. At 30, 60, 120, and 240 minutes post-starvation this process was repeated. Cells were left in methanol for 10 minutes, pelleted, washed quickly in autoclaved water, re-suspended in 750 uL of RNAlater (Ambion), and snap-frozen in liquid nitrogen. To determine the extent of pho7+ and csk1+ regulation within the PHO response we grew the relevant strains (DP1, DP81, DP106, DP113) as described above, with the exception that cells were split into either high-Pi or no-Pi media and grown for 2 hours prior to RNA collection. For each individual stress response, initial cultures of DP1 and DP81 were grown in 90%SD-10%EMM media containing 10 mM KH2PO4 to early-log phase at 30°C. Cells were collected, washed twice with autoclaved water, and split into the following conditions (all modifications of the high-Pi media): +Pi – 10 mM KH2PO4, -Pi – 0 mM KH2PO4, +Fe – 100 uM Fe(III)Cl3, -Fe – 250 uM 2-2’-dipyridine (DIP) (Sigma), +Cu – 100 uM Cu(II)SO4, -Cu – 100 uM bathocuproine disulphonate (BCS) (Sigma), Osmotic Shift – 1.2 M NaCl instead of 0.1M NaCl, and Carbon Switch – 2% glycerol/1% ethanol (GE) instead of 2% glucose (G). Cells were grown for 2 hours and harvested as described above, except for the osmotic shift conditions which were performed 20 minutes post-shift.

tag: strain/genotype

value: strain DP1

source_name: GE pho7Δ T=120 min

value: pho7ΔKANMX6 strain DP81


title: Carbon switch pho7+-dependency T=120 min replicate 1


title: Wild type parent strain_rep1

description:
growth in LB medium_O.D. 600nm 1.0
WT_1


title: 112, ADIPOOSE TISSUE, After


title: Carbon switch T=120 min replicate 1

source_name: G pho7+ T=120 min


title: Carbon switch T=120 min replicate 2


title: Osmotic shift T=20 min replicate 2

source_name: 1.2M NaCl pho7+ T=20 min

source_name: 0.1M NaCl pho7+ T=20 min


title: 111, MUSCLE, Before


title: Osmotic shift pho7+-dependency T=20 min replicate 1

source_name: 1.2M NaCl pho7Δ T=20 min


title: 112, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, PLC, Before


title: Osmotic shift pho7+-dependency T=20 min replicate 2


title: Cu starvation pho7+-dependency T=120 min replicate 2

source_name: -Cu pho7+ T=120 min

source_name: -Cu pho7Δ T=120 min


title: 111, ADIPOOSE TISSUE, After


title: Cu starvation pho7+-dependency T=120 min replicate 1


title: Cu starvation T=120 min replicate 3

source_name: +Cu pho7+ T=120 min


title: Cu starvation T=120 min replicate 2


title: 111, MUSCLE, After

source_name: MUSCLE, CR, After


title: Cu starvation pho7+-dependency T=120 min replicate 3


title: Cu starvation T=120 min replicate 1


title: 110, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, RES, Before


title: 110, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, RES, After


title: Osmotic shift T=20 min replicate 1


title: Fe starvation pho7+-dependency T=120 min replicate 1

source_name: -Fe pho7+ T=120 min

source_name: -Fe pho7Δ T=120 min


title: Fe starvation pho7+-dependency T=120 min replicate 3


title: 111, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, CR, Before


title: Cilia-deleted 2

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

hyb_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day.

scan_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console).

data_processing: The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used. Baseline transformation to median was used.

source_name: Cilia mutant

label_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).  Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions.  After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed.  Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.

growth_protocol: Mouse, 7 day post-natal.

extract_protocol: Hindlimbs from postnatal day 7 mice were dissected and embedded in OCT, and stored at -80 ºC. 40 μm sections were cut and mounted on Superfrost Plus slides (Fischer). Sections were dehydrated immediately in 70 %, 90 %, 100 % EtOH, followed by xylene. The sections were air-dried. Proliferative zone chondrocytes were cut out from proximal tibia and distal femur using an 18 gauge needle, and collected in a tube containing 100 μl of lysis buffer from RNAqueous®-Micro Kit (Ambion, AM1931). The RNA isolation procedure was followed by the protocol for LCM (laser capture micro-dissection) samples in the manufacturer’s manual.

treatment_protocol: Comparison of control and Col2aCre;Ift88fl/fl proliferative zone chondrocytes.

tag: background strain

value: Proliferative zone chondrocytes


title: Fe starvation pho7+-dependency T=120 min replicate 2


title: Cilia-deleted 1


title: 109, MUSCLE, After


title: Fe starvation T=120 min replicate 2

source_name: +Fe pho7+ T=120 min


title: Fe starvation T=120 min replicate 3


title: Palmoplantar epidermis, biological rep2

first: Catherine

middle: P

last: Lu

address: 1230 York Ave

institute: Rockefeller University

description: Sweat gland _Palmoplantar epidermis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: Mouse paw pads

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

growth_protocol: RNA was extracted from FACS-purified cell populations

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

value: Palmoplantar epidermis

tag: genotype

value: wild-type

value: female

tag: genetic background


title: Control 2

source_name: Control


title: 109, MUSCLE, Before

source_name: MUSCLE, CR, Before

value: muscle

tag: gender


title: Fe starvation T=120 min replicate 1


title: 108, ADIPOOSE TISSUE, After

tag: tissue

value: resveratrol


title: Sweat gland luminal, biological rep2

description: Sweat gland _Coiled duct_luminal

value: Sweat gland luminal


title: no-Pi epistatic relationship T=120 min

source_name: no-Pi csk1Δ T=120 min

value: csk1ΔNATMX6 strain DP106

source_name: no-Pi pho7Δcsk1Δ T=120 min

value: pho7ΔKANMX6 csk1ΔNATMX6 strain DP113


title: Control 1


title: Sweat duct basal, biological rep2

description: Sweat gland _Straight duct_basal

value: Sweat duct basal


title: 108, ADIPOOSE TISSUE, Before

value: adipose tissue

value: before

value: Female


title: Female 3 aortic valve leaflet

city: Madison

first: Kristyn

middle: S.

last: Masters

email: kmasters@wisc.edu, cmccoy2@wisc.edu

state: WI

address: 1550 Engineering Drive, 2152 ECB

department: Biomedical Engineering

institute: UW-Madison

hyb_protocol: Following fragmentation, 10 ug of aRNA was applied to each AFX Porcine array.  The arrays were hybridized for 16 hours at 45°C in an AFX Hybridization Oven 640.  Post processing of the Porcine GeneChips was performed on the AFX 450 Fluidics Station according to all AFX protocols and procedures defined for the porcine array.

scan_protocol: GeneChips were scanned on a GC3000 G7 scanner. Data was extracted from images using the AFX Expression Console v1.1 software.

data_processing: The microarray data were processed using the open source statistical language R v2.12.0 and the libraries included in the Bioconductor Project 12.  Raw expression values from *.CEL files were background-corrected and normalized using the Robust Multi-array Analysis (RMA) method.

organism: Sus scrofa

source_name: aortic valve leaflet

label_protocol: 400 ng of total RNA was labeled using the Ambion MessageAmp Premier IVT kit following manufacturer's instructions.

extract_protocol: The leaflets were homogenized using sterile stainless steel beads and a BulletBlender tube agitator following manufacturer’s instructions.  RNA was isolated from the tissue using the RNeasy fibrous tissue spin-column kit according to the manufacturer’s instructions.

treatment_protocol: Aortic valve leaflets were surgically removed using sterile techniques from female and castrated male porcine hearts within 5 hours of death and the endothelial cells were manually denuded with a scalpel.  The leaflets were then rinsed twice in basal Medium 199 solution supplemented with 200 U/ml penicillin and 200 ug/ml streptomycin and stored in RNAlater until processing.

tag: breed

value: mixed

value: aortic valve leaflet

tag: Sex


title: high-Pi epistatic relationship T=120 min replicate 2

source_name: high-Pi pho7Δcsk1Δ T=120 min

source_name: high-Pi csk1Δ T=120 min


title: Sweat gland myoepithelial, biological rep2

description: Sweat gland _Coiled duct_myoepithelial

value: Sweat gland myoepithelial


title: Female 2 aortic valve leaflet


title: Sweat duct Suprabasal, biological rep2

description: Sweat gland _Straight duct_Suprabasal

value: Sweat duct Suprabasal


title: 107, MUSCLE, After

source_name: MUSCLE, PLC, After

value: placebo

value: after


title: Male 3 aortic valve leaflet

value: male


title: Palmoplantar epidermis, biological rep1

description: Sweat gland _Palmoplantar epidermis

value: Palmoplantar epidermis

value: wild-type

value: female


title: 107, MUSCLE, Before

source_name: MUSCLE, PLC, Before

value: muscle


title: Male 2 aortic valve leaflet


title: high-Pi epistatic relationship T=120 min replicate 1

value: csk1ΔNATMX6 strain DP106


title: Female 1 aortic valve leaflet


title: no-Pi pho7+csk1+-dependency T=120 min replicate 2

source_name: no-Pi pho7+csk1+ T=120 min

value: strain DP1

value: pho7ΔKANMX6 csk1ΔNATMX6 strain DP113


title: Male 1 aortic valve leaflet


title: 107, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, PLC, After

value: adipose tissue


title: high-Pi pho7+csk1+-dependency T=120 min replicate 1

source_name: high-Pi pho7+csk1+ T=120 min


title: no-Pi pho7+csk1+-dependency T=120 min replicate 1


title: high-Pi pho7+csk1+-dependency T=120 min replicate 2


title: 106, MUSCLE, Before

value: before


title: Sweat duct Suprabasal, biological rep1

description: Sweat gland _Straight duct_Suprabasal


title: 16- pig C - segment 4 - GIS26 STb LT

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridized on Affymetrix GeneChip ® Porcine Genome Arrays followed by staining and washing in a GeneChip ® fluidics station 450 (Affymetrix) according to the manufacturer's procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip ® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.26.1) of Bioconductor.

source_name: Mid-jejunum pig C, perfused with GIS26 STb LT mutant strain, 4h

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently, the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturer's protocol (Affymetrix).

growth_protocol: 5-week-old female piglets (Belgian Landrace), weaned on day 28, were purchased from a commercial piggery.

extract_protocol: Approximately 100 mg of frozen intestine was homogenized in 1 ml TRIzol ® Reagent (Invitrogen, Belgium) to extract total RNA. These homogenates were further purified using the RNeasy Mini Kit (Qiagen Benelux, The Netherlands) with an on column DNase treatment (RNase-free DNase set, Qiagen Benelux). Spectrophotometric RNA quality control was done using Nanodrop ® ND-1000 (Isogen Life Science, The Netherlands) using only samples with a 260/280 ratio between 1.8-2.1 and 260/230 ratio between 1.5-2.0. RNA integrity was assessed using a Bioanalyser 2100 (Agilent, California, USA).

treatment_protocol: The day before surgery, piglets were fasted. Premedication was administered by intramuscular injection of 40  mg/kg azaperon (Janssen Animal Health, Belgium) and 0.1 mg/kg morphine (Sterop, Belgium). Anesthesia was induced after 20 minutes by IV injection of 2-4 mg/kg propofol (AST Farma, The Netherlands). After endotracheal intubation, the piglets were kept under long-term anesthesia with a mixture of 1.5 % isoflurane (Ecuphar, Belgium) and 40% oxygen (Air Liquide, Belgium). Haematocrit values (Hct) were assessed at regular timepoints, and when the Hct values exceeded 35, piglets received 10-15 ml/kg/h ringer lactate (Baxter, Illinois, USA) via an infuse to prevent dehydration. Fentanyl (Janssen-Cilag, Belgium) at a rate of 5-10 mg/kg/h was given IV as an analgesic.

value: Belgian Landrace

value: jejunum

tag: pig

value: C

tag: segment

value: GIS26 STb LT mutant


title: 107, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, PLC, Before

value: Female


title: Sweat duct basal, biological rep1

description: Sweat gland _Straight duct_basal

value: Sweat duct basal


title: no-Pi csk1+-dependency T=120 min replicate 2

source_name: no-Pi csk1+ T=120 min


title: Sweat gland luminal, biological rep1

description: Sweat gland _Coiled duct_luminal

value: Sweat gland luminal


title: 18- pig C - segment 6 - GIS26 LT

source_name: Mid-jejunum pig C, perfused with GIS26 LT mutant strain, 4h

value: GIS26 LT mutant


title: Sweat gland myoepithelial, biological rep1

description: Sweat gland _Coiled duct_myoepithelial

source_name: Mouse paw pads

value: Sweat gland myoepithelial


title: 106, MUSCLE, After

value: placebo

value: after


title: 106, ADIPOOSE TISSUE, After


title: 17- pig C - segment 5 - GIS26 wild type

source_name: Mid-jejunum pig C, perfused with Escherichia coli (WT), 4h

value: female

value: GIS26 wild type


title: no-Pi csk1+-dependency T=120 min replicate 1

value: strain DP1

value: csk1ΔNATMX6 strain DP106


title: 15- pig C - segment 3 - PBS

source_name: Mid-jejunum pig C, perfused with PBS, 4h

value: PBS


title: 105, MUSCLE, After

source_name: MUSCLE, RES, After

value: muscle

value: resveratrol


title: Wild type parent strain_rep2

description:
growth in LB medium_O.D. 600nm 1.0
WT_2

source_name: Wild type parent strain

value: wild type


title: 106, ADIPOOSE TISSUE, Before

value: adipose tissue

value: before


title: B6 co-housed with Nod2 repl1 vs B6 repl3

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 3 as control sample for comparison to the Mus musculus strain C57Bl/6J co-housed with Mus musculus strain C57Bl/6J Nod2-/- replicat 3

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

scan_protocol: Arrays scanned using an Innoscan 700 scanner and Mapix version 4.2.1 software.

data_processing: Data analysis was carried out using R project version 2.13.1 with the limma package. The median values from each channel were log2 transformed, normalized within array using the LOWESS algorithm to remove intensity dependent effects within the calculated values and normalized between arrays using the quantile methods . Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from all the experimental plan.

source_name: Colonic biopsy of C57Bl6/J mice cohoused with Nod2-deficient mice (replicate 1)

label_protocol: Agilent's Quick Amp Labeling Kit generates fluorescent cRNA from 350ng of total RNA. After cDNA production using polyT-T7 promoter primer, the methods uses T7 RNA polymerase, with simultaneously amplifies target material and incorporates cyanine3 ou 5-labeled CTP.Samples purified using QIAGEN Rneasy kit before hybridization.

growth_protocol: Adult mice were housed in specific pathogen-free facility with unrestricted access to food and water

extract_protocol: The total RNA form colonic biopsy were isolate using QIAGEN RNEasy Mini kit with on column DNAse digestion. (respectively ref 74106 and 79254 QIAGEN)

treatment_protocol: C57Bl6J mice were cohoused or not 4 weeks with Nod2-deficient mice before necropsy.

value: colonic mucosa

value: cohoused with Nod2-deficient mice

tag: strain

source_name: Colonic biopsy of C57Bl6/J mice(sample 3)

value: control


title: high-Pi csk1+-dependency T=120 min replicate 1

source_name: high-Pi csk1Δ T=120 min

source_name: high-Pi csk1+ T=120 min


title: B6 co-housed with Nod2 repl1 vs B6 repl4

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 4 as control sample for comparison to the Mus musculus strain C57Bl/6J co-housed with Mus musculus strain C57Bl/6J Nod2-/- replicat 4

source_name: Colonic biopsy of C57Bl6/J mice(sample 4)


title: B6 co-housed with Nod2 repl1 vs B6 repl2

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 2 as control sample for comparison to the Mus musculus strain C57Bl/6J co-housed with Mus musculus strain C57Bl/6J Nod2-/- replicat 2

source_name: Colonic biopsy of C57Bl6/J mice(sample 2)


title: high-Pi csk1+-dependency T=120 min replicate 2


title: 14- pig C - segment 2 - GIS26 STa STb:KAN

source_name: Mid-jejunum pig C, perfused with GIS26 STa STb:KAN mutant strain, 4h

value: Belgian Landrace

value: jejunum

value: C

value: GIS26 STa STb:KAN mutant


title: no-Pi pho7+-dependency T=120 min replicate 2

source_name: no-Pi pho7+ T=120 min

source_name: no-Pi pho7Δ T=120 min

value: pho7ΔKANMX6 strain DP81


title: 13- pig C - segment 1 - GIS26 STa

source_name: Mid-jejunum pig C, perfused with GIS26 STa mutant strain, 4h

value: female

value: GIS26 STa mutant


title: 105, MUSCLE, Before

source_name: MUSCLE, RES, Before

value: Female


title: high-Pi pho7+-dependency T=120 min replicate 2

source_name: high-Pi pho7Δ T=120 min

source_name: high-Pi pho7+ T=120 min

value: strain DP1


title: 104, MUSCLE, After

source_name: MUSCLE, CR, After

value: muscle

value: calorie restrictive

value: after


title: no-Pi pho7+-dependency T=120 min replicate 1


title: NOD2_No_treatment_vs_NOD2_Metronidazole_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J Nod2-/- as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/-traited with metronidazole

scan_protocol: Arrays scanned using an Innoscan 700 scanner and Mapix version 3.2.1 software.

data_processing: Data analysis was carried out using R project version 2.11.1 with the limma package. The median values from each channel were log2 transformed, normalized within array using the LOWESS algorithm to remove intensity dependent effects within the calculated values and normalized between arrays using the quantile methods . Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from all the experimental plan.

source_name: Colonic biopsy of untreated mice in experimental model of CAC initiation (replicate 1), control samples

label_protocol: Agilent's Quick Amp Labeling Kit generates fluorescent cRNA from 1 µg of total RNA. After cDNA production using polyT-T7 promoter primer, the methods uses T7 RNA polymerase, with simultaneously amplifies target material and incorporates cyanine3 ou 5-labeled CTP.Samples purified using QIAGEN Rneasy kit before hybridization.

growth_protocol: Adult mice were housed in specific pathogen-free facility at with unrestricted access to food and water

treatment_protocol: Experimental models of CAC from C57Bl/6J strain and C57Bl/6J Nod2-/- strain were traited with Metronidazole (Panpharma; 1g/L) or a cocktail combining streptomycin (Panpharma; 2g/L), gentamicin (Panpharma; 200mg/L), ciprofloxacin (Panpharma; 125µg/L) and bacitracin (Acros organics; 1g/L) by supplementing drinking water.

tag: mouse strain

source_name: Colonic biopsie of experimental models of CAC initiation traited with a metronidazole


title: 105, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, RES, Before

value: adipose tissue

value: resveratrol


title: 10- pig B - segment 4 - PBS

source_name: Mid-jejunum pig B, perfused with PBS, 4h

value: B

value: PBS


title: B6 co-housed with Nod2 repl1 vs B6 repl1

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 1 as control sample for comparison to the Mus musculus strain C57Bl/6J co-housed with Mus musculus strain C57Bl/6J Nod2-/- replicat 1

source_name: Colonic biopsy of C57Bl6/J mice cohoused with Nod2-deficient mice (replicate 1)

value: colonic mucosa

value: cohoused with Nod2-deficient mice

source_name: Colonic biopsy of C57Bl6/J mice(sample 1)

value: control


title: 105, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, RES, After


title: 104, MUSCLE, Before

source_name: MUSCLE, CR, Before

value: before


title: 12- pig B - segment 6 - GIS26 wild type

source_name: Mid-jejunum pig B, perfused with Escherichia coli (WT), 4h

value: Belgian Landrace

value: jejunum

value: GIS26 wild type


title: NOD2_No_treatment_vs_NOD2_ATB_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J Nod2-/- as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/-traited with a cocktail of antibiotics

source_name: Colonic biopsie of experimental models of CAC initiation traited with a cocktail of several antibiotics


title: B6_No_treatment_vs_B6_Metronidazole_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J as control sample for comparison to the Mus musculus strain C57Bl/6J traited with metronidazole

value: wildtype


title: 11- pig B - segment 5 - GIS26 STb LT

source_name: Mid-jejunum pig B, perfused with GIS26 STb LT mutant strain, 4h

value: female

value: GIS26 STb LT mutant


title: Pi starvation T=120 min replicate 2

source_name: no-Pi T=120 min

value: strain DP1

source_name: high-Pi T=120 min


title: Pi starvation T=120 min replicate 1


title: 8- pig B - segment 2 - GIS26 STa

source_name: Mid-jejunum pig B, perfused with GIS26 STa mutant strain, 4h

value: GIS26 STa mutant


title: B6_Metronidazole_treatment_vs_NOD2_Metronidazole_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J traited metronidazole as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/- traited metronidazole

source_name: Colonic biopsy of metronidazole-treated mice in experimental model of CAC initiation (replicate 1), control samples


title: high-Pi pho7+-dependency T=120 min replicate 1

source_name: high-Pi pho7Δ T=120 min

value: pho7ΔKANMX6 strain DP81

source_name: high-Pi pho7+ T=120 min


title: 7- pig B - segment 1 - GIS26 STa STb:KAN

source_name: Mid-jejunum pig B, perfused with GIS26 STa STb:KAN mutant strain, 4h

value: GIS26 STa STb:KAN mutant


title: 9- pig B - segment 3 - GIS26 LT

source_name: Mid-jejunum pig B, perfused with GIS26 LT mutant strain, 4h

value: GIS26 LT mutant


title: 104, ADIPOOSE TISSUE, Before

description: Gene expression data from human biopsy tissue samples

source_name: ADIPOSE TISSUE, CR, Before

value: adipose tissue

value: calorie restrictive

value: Female


title: 104, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, CR, After

value: after


title: B6_ATB_treatment_vs_NOD2_ATB_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J traited with a cocktail of antibiotics as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/- traited with a cocktail of antibiotics

source_name: Colonic biopsy of antibiotics-treated mice in experimental model of CAC initiation (replicate 1), control samples


title: B6_No_treatment_vs_B6_ATB_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J as control sample for comparison to the Mus musculus strain C57Bl/6J traited with a cocktail of antibiotics

source_name: Colonic biopsy of untreated mice in experimental model of CAC initiation (replicate 1), control samples


title: 103, MUSCLE, After

source_name: MUSCLE, PLC, After

value: muscle

value: placebo


title: 103, MUSCLE, Before

source_name: MUSCLE, PLC, Before

value: before


title: Pi starvation T=240 min

source_name: no-Pi T=240 min

source_name: average of samples 1-5


title: 5- pig A - segment 5 - GIS26 STb LT

source_name: Mid-jejunum pig A, perfused with GIS26 STb LT mutant strain, 4h

value: Belgian Landrace

value: jejunum

value: A


title: 6- pig A - segment 6 - GIS26 STa STb:KAN

source_name: Mid-jejunum pig A, perfused with GIS26 STa STb:KAN mutant strain, 4h

value: female


title: AA (array)

city: Lisbon

first: Angela

last: Inácio

address: Campo Grande

country: Portugal

institute: centro de Biologia Ambiental

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Warm the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-warmed pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization. HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine labeled RNA with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature. Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

scan_protocol: Slides were scanned using the Agilent G2565AA DNA microarray scanner: Resolution: 10, Red laser PMT= 0, Green laser PMT= 100.

data_processing: Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer). Manually flagged bad spots were eliminated and the Cy3 median pixel intensity values were  background subtracted, followed by the averaging of quadruplicate features on the array. Data points were removed when intensity values were below 200% background. A global median normalization of miRNA microarray data was applied using BRB-ArrayTools v3.4.0 software. Cy3 intensities were obtained.

organism: Squalius alburnoides

source_name: AA liver, brain and muscle

label_protocol: Total RNA from all samples was labeled using the ULS microRNA labeling kit (Kreatech) according to the manufacturer’s instructions. Briefly, 2 ug of total RNA from each sample were incubated with Cy3-ULS for 15 min at 85ºC. The labeled RNAs were purified to remove non-reacted Cy-ULS to produce a fluorescently-labeled RNA sample for microarray analysis. Dye incorporation was monitored by UV-visible spectroscopy.

extract_protocol: Fishes were sacrificed by overdose on anaesthetic MS222, and the respective tissues/organs were dissected and preserved in RNAlatter® (Ambion) at -20ºC. Total RNA was extracted from liver, muscle and brain using the Tri-Reagent® (Ambion) following the supplier's instructions. Contaminant DNA was eliminated by the addition of TURBO™ DNase (Ambion) followed by purification with phenol/chloroform. Ethanol, Glycogen and Sodium Acetate (NaOAc) were used to achieve RNA precipitation. RNA quantity and quality was assessed using the Nanodrop and Agilent 2100 Bioanalyzer systems, respectively. Samples with a RIN number above 7 were used.

tag: genome composition

value: AA

value: liver, brain, muscle

tag: developmental stage

value: adult


title: PP (array)

organism: Squalius pyrenaicus

source_name: PP liver, brain and muscle

value: PP


title: B6_repl2_No_treatment_vs_NOD2_repl2_No_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 2 as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/- replicat 2

source_name: Colonic biopsy of untreated mice in experimental model of CAC initiation (replicate 2), control samples

value: wildtype

source_name: Colonic biopsie of experimental models of CAC initiation


title: Pi starvation T=120 min

source_name: no-Pi T=120 min

value: strain DP1


title: B6_repl1_No_treatment_vs_NOD2_repl1_No_treatment

description: Transcriptomic analysis used colonic biopsie from Mus musculus strain C57Bl/6J replicat 1 as control sample for comparison to the Mus musculus strain C57Bl/6J Nod2-/- replicat 1


title: 103, ADIPOOSE TISSUE, After

source_name: ADIPOSE TISSUE, PLC, After

value: adipose tissue

tag: treatment


title: PA (array)

source_name: PA liver, brain and muscle

value: PA


title: Pi starvation T=60 min

source_name: no-Pi T=60 min


title: Pi starvation T=0 min

source_name: no-Pi T=0 min


title: Pi starvation T=30 min

source_name: no-Pi T=30 min


title: 4- pig A - segment 4 - GIS26 LT

source_name: Mid-jejunum pig A, perfused with GIS26 LT mutant strain, 4h

value: GIS26 LT mutant


title: PAA (array)

source_name: PAA liver, brain and muscle

value: PAA


title: 2- pig A - segment 2 - GIS26 STa

source_name: Mid-jejunum pig A, perfused with GIS26 STa mutant strain, 4h

value: GIS26 STa mutant


title: 101, MUSCLE, Before

source_name: MUSCLE, CR, Before

value: muscle

tag: sample group

value: calorie restrictive

value: Female


title: 3- pig A - segment 3 - PBS

source_name: Mid-jejunum pig A, perfused with PBS, 4h

value: Belgian Landrace

value: jejunum

value: PBS


title: 103, ADIPOOSE TISSUE, Before

source_name: ADIPOSE TISSUE, PLC, Before

value: placebo

value: before


title: 101, MUSCLE, After

source_name: MUSCLE, CR, After

value: after


title: 1- pig A - segment 1 - GIS26 wild type

source_name: Mid-jejunum pig A, perfused with Escherichia coli (WT), 4h

value: female

value: A

value: GIS26 wild type


title: PNMYC_3 with array type Medicago from Affymetrix

status: Public on Jan 01 2013

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: Biological question (15 lines max): In natural ecosystems most vascular plants develop symbiosis with arbuscular mycorrhizal (AM) fungi which help them acquire nutrients such as phosphorus (P) and nitrogen (N). P has long been known to control AM symbiosis which takes place only when P is limiting. For N, however, its role in controlling mycorrhization is less clear. We have chosen the model plant Medicago truncatula to analyze the impact of P limitation and both P and N limitation on Medicago root transcriptome in response to the AM fungus Rhizophagus irregularis (formerly Glomus intraradices (BEG141)). These analyses may help us uncover signaling events involved in the interaction between these symbionts as well as genes encoding transporters potentially important for nutrient exchanges in these conditions. -

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), inoculated by R. irregularis, third replicate

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: roots - on sand - in chamber: 22°C light (380 µE m-2 s-1) for 16 h, 19°C dark for 8h -

treatment_protocol: Name:TRAITEMENT 1 - environmental treatment - abiotic stress,low p, normal n, non inoculated:quantity 130uM . Factor value : 130 µM P, 6 mM NH4NO3, non inoculated Medicago truncatula seedlings were transferred on sand (that was washed and baked at 180°C for 14 h) in the presence of non inoculated leek roots. Plants were cultivated for 4 weeks and watered 3 times a week with a modified Long Ashton solution containing 130 µM phosphate and full N (6 mM NH4NO3).

tag: cultivar

value: Jemalong

tag: age

value: 4 weeks


title: PNMYC_2 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), inoculated by R. irregularis, second replicate


title: PMYC_3 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM, inoculated by R. irregularis, third replicate


title: PN_2 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), not inoculated, second replicate


title: P_1 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM,not inoculated, first replicate


title: PMYC_2 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM, inoculated by R. irregularis, second replicate


title: PNMYC_1 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), inoculated by R. irregularis, first replicate


title: PMYC_1 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM, inoculated by R. irregularis, first replicate


title: P_3 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM,not inoculated, third replicate


title: PN_1 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), not inoculated, first replicate


title: P_2 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM,not inoculated, second replicate


title: PN_3 with array type Medicago from Affymetrix

source_name: low input of phosphate 130µM and low input of Nitrogen (0.6mM), not inoculated, third replicate


title: Root A24-39 water stress, biological rep3

city: Rehovot

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

country: Israel

institute: Hebrew University

description: Gene expression data from wheat roots RNA hybridized to Affymetrix wheat Genome Array

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using JMPGenomics (ver 3) with RMA and STD normalization and background correction feature.

organism: Triticum dicoccoides

source_name: Triticum turgidum subsp. Dicoccoides

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Y12-3 and A24-39 plants were grown in controled greenhouse and water stress treatment imposed at 4 leaf stage

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

treatment_protocol: Control plants (Well-watered conditions); water deficit (water stress was imposed at 4 leaf stage for 7 days)

value: Roots

value: 4  weeks

value: water stressed


title: Root Y12-3 water stress, biological rep2


title: Root A24-39 water stress, biological rep1


title: Root Y12-3 well-watered, control, biological rep3

value: well watered


title: Root A24-39 water stress, biological rep2


title: Root A24-39 well-watered, control, biological rep1


title: Root Y12-3 water stress, biological rep3


title: Root Y12-3 water stress, biological rep1


title: Root A24-39 well-watered, control, biological rep2


title: No.2 vs No.7 Tamoxifen-treated wild type prostaspheres versus Tamoxifen-treated Sox9 prostaspheres

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on Agilent Whole Mouse Genome G4122A Microarrays (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micometer resolutions. Data was extracted using Feature Extraction Software version 10.5.1.1 (Agilent Technologies).

data_processing: Within-array dye eﬀects were corrected by the 'loess' normalization method. No background subtraction was performed prior to normalization. Positive and negative microarray control features were not used to compute the 'loess' smoothing and were further excluded from subsequent analyses. Data pre-processing was performed using the R/Bioconductor package 'limma'.

source_name: No. 2 SOX9

label_protocol: 250 ng of total RNA input was reverse transcribed into by oligo dT primer incorporating a T7 promoter sequence, and labelled cRNA was obtained by T7 RNA polymerase transcription (Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies). cRNA was purified using RNeasy mini kit (Qiagen).

growth_protocol: C57/Bl6J, ERCre+/+Sox9flox/flox and ERCre+/+Sox9flox/+ urogenital sinus (UGS) were harvested at 16 days post conception.  UGS were collected, digested, washed.  Epithelial cells then were isolated, minced and incubated in collagenase (1mg/ml) and DNase (1mg/ml). Cells were washed, cultured overnight and isolated into single cells. Prostate epithelial cells were washed, cultured overnight, isolated into single cells, and passed in Matrigel to form prostaspheres.

extract_protocol: Total RNA was prepared from homogenized frozen tissue using the RNeasy system (Qiagen). RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: After 6 days in matrigel plus 10–8 millimolar Dihydrotestosterone, prostaspheres were exposed to Tamoxifen (5 micromolar) or vehicle for 6 additional days.  Prostaspheres were then snap frozen in liquid nitrogen.

value: prospheres from UGE

value: Tamoxifen

value: SOX9 wild type

source_name: No.7 Ctrl

value: Sox9 null


title: Root Y12-3 well-watered, control, biological rep2


title: Root A24-39 well-watered, control, biological rep3


title: Rest CKO E13.5 limb

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

description: E13.5 Rest CKO limb

hyb_protocol: A total of 1.5 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of Agilent 2x HI-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using the one color scan setting for 4x44k array slides (Scan Area 75x25 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 10-100% (XDR) ).

data_processing: The scanned images were analyzed with the Feature Extraction Software package v 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20101102) to obtain background-subtracted and spatially detrended Processed Signal intensities.  Data were analyzed by using the GeneSpring software program.

source_name: Rest CKO limb

label_protocol: Cy3 labeled cRNA was prepared using One-Color Low RNA Input Liner Amplification kit (Agilent)

growth_protocol: Rest conditional ablation was induced in Rest-floxed mice by doxycycline-inducible Cre alleles in utero.

extract_protocol: Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: Rest-floxed mice were treated with doxycycline (E8.5-E13.5) to induce Cre recombinase, and they were sacrificed at E13.5.

value: Rest conditional KO

value: limb


title: Rest WT E13.5 brain

description: E13.5 wild type brain

source_name: Wild type brain

value: wild type

value: brain


title: HGUPS_9

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

hyb_protocol: labeled and fragmented cRNA hybridized to MG_430 2.0 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit

growth_protocol: Tumors were explanted before compromising the life of the animals.

extract_protocol: Total RNA was extracted using Qiazol (Qiagen), purified using RNeasy columns according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. Quality and quantity were determined using a  Bioanalyzeand Nanodrop (Agilent Technologies).

treatment_protocol: Tumors explanted were frozen at -80C until processing.

tag: disease state

value: high-grade undifferentiated pleomorphic sarcoma (HGUP)

tag: genotype/variation


title: Rest CKO E13.5 brain

description: E13.5 Rest CKO brain

source_name: Rest CKO brain

tag: genotype

tag: genetic background


title: Rest WT E13.5 limb

description: E13.5 wild type limb

source_name: Wild type limb

tag: tissue


title: Root Y12-3 well-watered, control, biological rep1


title: HGUPS_7


title: HGUPS_6


title: HGUPS_4


title: HGUPS_8


title: HGUPS_3


title: HGUPS_5


title: HGUPS_1


title: No.6 vs No.9 Vehicle-treated Sox9 prostaspheres versus Tamoxifen-treated Sox9 prostaspheres

source_name: No. 6 SOX9

value: Vehicle

source_name: No. 9 Ctrl


title: HGUPS_2


title: Kit W/Wv mouse dura mater, naïve control, technical replicate 1

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from Kit W/Wv mouse dura mater treated as a naïve control

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/)  to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).

source_name: Kit W/Wv mouse, naïve control, dura mater

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University.  HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.

extract_protocol: RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).

treatment_protocol: Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.)  Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).

tag: background strain

value: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)

value: dura mater

tag: disease status

value: control


title: Kit W/Wv mouse dura mater, naïve control, technical replicate 3


title: WT mouse dura mater, EAE, technical replicate 3

description: Gene expression data from WT mouse dura mater with experimental autoimmune encephalomyelitis

source_name: WT mouse, experimental autoimmune encephalomyelitis, dura mater

value: day 6 experimental autoimmune encephalomyelitis


title: Kit W/Wv mouse dura mater, naïve control, technical replicate 2


title: Kit W/Wv mouse dura mater, EAE, technical replicate 2

description: Gene expression data from Kit W/Wv mouse dura mater with experimental autoimmune encephalomyelitis

source_name: Kit W/Wv mouse, experimental autoimmune encephalomyelitis, dura mater


title: Kit W/Wv mouse dura mater, EAE, technical replicate 3


title: WT mouse dura mater, naïve control, technical replicate 1

description: Gene expression data from WT mouse dura mater treated as a naïve control

source_name: WT mouse, naïve control, dura mater


title: WT mouse dura mater, EAE, technical replicate 1


title: Kit W/Wv mouse dura mater, EAE, technical replicate 1


title: WT mouse dura mater, naïve control, technical replicate 2


title: WT mouse dura mater, EAE, technical replicate 2


title: exp_c_WT

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

institute: Weizmann Institute of Science

description: SAMPLE 8

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

data_processing:
MAS5 using R microarray suite + lowess correction for each tissue, i.e. samples 1-2, samples 3-6, samples 7-8, using a MATLAB script.
values are in linear scale, p-values are for each probset as calculated by the MAS5 algorithm

molecule: polyA RNA

source_name: mouse embyro from implantation site

label_protocol: According to Affymetrix manual

extract_protocol: QIAGEN miniRNA extraction kit was used.  QIAGEN miniRNA extraction kit was used.

value: implantation site

value: WT


title: WT mouse dura mater, naïve control, technical replicate 3


title: exp_b_WT2

description: SAMPLE 6

source_name: mouse blastocyst

value: blastocyst


title: exp_a_WT

description: SAMPLE 2

source_name: mouse MII oocytes

value: MII oocyte


title: exp_c_KO

description: SAMPLE 7

value: KO


title: exp_b_KO1

description: SAMPLE 3


title: exp_b_KO2

description: SAMPLE 4


title: exp_b_WT1

description: SAMPLE 5


title: T-Cre conditional Tbx1 heterozygous control otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 1

city: Bronx

first: Tingwei

last: Guo

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

description:
Control1_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.

hyb_protocol: 10ug of cRNA was hybridized for 16hrs at 45C on Affymetrix Mouse 430_2 arrays.

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

data_processing: Data was analyzed using Affymetrix Expression Console software version 1.1 using Affymetrix default protocols.

source_name: E11.5 otic vesicle and periotic mesenchyme, T-Cre conditional Tbx1 heterozygous control

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 300ng of total RNA.

growth_protocol: Timed matings were dissected at embryonic day 11.5, and periotic tissue was isolated, including otic vesicle and perotic mesenchyme. RNA was isolated from the tissue immediately following dissection.

extract_protocol: Qiagen RNeasy Micro kit according to the manufacturer's protocol.

value: T-Cre conditional Tbx1 heterozygote

value: microdissected otic vesicle and periotic mesenchyme


title: T-Cre conditional Tbx1 heterozygous control otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 2

description:
Control2_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.


title: T-Cre conditional Tbx1 heterozygous control otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 3

description:
Control3_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.