title: EMP3_spleen_rep3

city: Neuherberg

first: Martin

last: Irmler

address: Ingolstaedter Landstrasse 1

institute: Helmholtz Zentrum München GmbH

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: EMP3 mutant (spleen)

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: mouse id

tag: sex

value: male

tag: age

value: 17 weeks

value: spleen

source_name: EMP3 wild type pool


title: patient 422,post

status: Public on Jan 01 2011

type: RNA

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

country: USA

institute: Duke University Medical Center

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair and normalized by MAS5.0 algorithm using the Affymetrix Expression Console software (v1.0).  A present/absent call is included.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of 1µg total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with DNase to minimize genomic DNA.

treatment_protocol: 4mm punch biopsies were obtained prior to ADH-1 and again prior to isolated-limb-infusion with melphalan following a protocol approved by the Duke University institutional review board.  Biopsies were snap frozen and stored at -130.

tag: disease

value: in-transit disease

tag: stage

tag: disease state

value: PD

tag: treatment

value: previous ILI


title: d3 -LIF replicate 2

city: Shanghai

first: Xiang

last: Li

state: Shanghai

address: 225 South Chongqing Road

country: China

institute: Institute of Health Sciences

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline with IlluminaGUI in R

organism: Mus musculus

source_name: CGR8 ES cells

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

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

tag: strain

tag: cell line

tag: protocol

value: d3 -LIF


title: patient 420-B,post

value: SD

value: no previous ILI/ILP


title: Mouse melanocytes 01d after UVB treatment, rep1

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

hyb_protocol: Per manufacturer recommendation.

scan_protocol: Per manufacturer recommendation.

data_processing: A variance stabilization transformation followed by quantile normalization and quality assessment were performed using the lumi bioconductor package.

source_name: Flow-sorted melanocytes, UVB, 1 day

label_protocol: Per manufacturer recommendation.

growth_protocol: A double homozygous Dct-rtTA/TRE-H2BGFP transgenic mouse line (Dct-GFP) was established in the albino FVB/N background, and males were crossed with wildtype FVB/N females to produce litters that were 100% Dct-GFP double heterozygous.

extract_protocol: Melanocytes were isolated from the dorsal skin of Dct-GFP mouse pups irradiated at P1 with either UVB or UVA. Doxycycline-induced GFP-labeled melanocytes were isolated via fluorescence-activated cell sorting (FACS) at 1 day, 6 days, and 21 days post irradiation. Following FACS collection of cells into PBS+1% BSA solution, the cells were centrifuged at 4C. Total RNA was isolated from the pelleted cells by Trizol (Invitrogen) organic extraction, followed by the RNeasy Micro Kit (Qiagen Sciences, MD, USA) procedure.

treatment_protocol: Precisely defined wideband wavelengths and physiologically relevant doses of UVB (output peak = 308 nm; total dose = 6 kJ/m2; equivalent to 15 times the Standard Erythemal Dose) and UVA (output peak = 375 nm; total dose = 150 kJ/m2) were used to irradiate Dct-GFP neonatal mice at postnatal day 1 (P1). To avoid potential complications of GFP expression, including toxicity associated with chronic expression and UV absorption, GFP was routinely induced by doxycycline administration only after UV irradiation, 24 hours prior to skin harvest.

tag: strain/background

value: FVB/N

tag: genotype

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

tag: developmental stage

value: postnatal

tag: tissue

value: dorsal skin

tag: cell type

value: melanocytes

tag: uv treatment

value: UVB

tag: days to harvest of cells

tag: group


title: d0 -LIF replicate 2

description: replicate 2

value: d0 -LIF


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 1

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description: L. pneumophila infection of human macrophages (THP-1) at time 6h.

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded.

label: AlexaFluor 546

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: 3XSCOTS cDNA obtained from JR32 infecting THP-1 macrophages at time 6h

label_protocol: 2 µg of cDNA was labeled using amino-allyl dUTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.). Subsequently, the resulting cDNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 546.

extract_protocol: TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase I (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 rounds of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122).

tag: condition

value: L pneumophila inside human THP-1 macrophages

label: AlexaFluor 647

molecule: genomic DNA

source_name: Genomic DNA used as reference channel

label_protocol: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

extract_protocol: Wizard Genomic Purification Kit (Promega).

tag: reference

value: genomic DNA


title: liver_old_PPB_3

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

description: Gene expression data from liver tissue of 12-yr-old dogs after 1 yr on PPB diet.

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine Genome Array (version 1) using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages.

organism: Canis lupus familiaris

source_name: Liver tissue at 12 yrs, after 1 year on PPB diet

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Young dogs (mean age = 8 wk at baseline) were fed ad libitum throughout the study to allow for adequate growth; old dogs (mean age = 11.1 yr at baseline) were fed to maintain baseline BW.

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were allotted to 1 of 2 diets and fed for 12 months: 1) animal-protein based (APB) diet primarily composed of highly digestible, animal-derived ingredients and formulated to exceed protein and fat recommendations provided by the Association of American Feed Control Officials (AAFCO) for growth and reproduction; or 2) plant-protein based (PPB) diet primarily composed of moderately digestible, plant-derived ingredients and formulated to meet protein and fat recommendations for growth and reproduction by AAFCO.  The exception was 10% meat and bone meal in the diet.  All samples were collected after an overnight food-restricted period.

value: liver

tag: age

value: 12 yrs

tag: diet

value: plant-protein based

tag: breed

value: beagle

tag: gender

value: female


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 5

description: L. pneumophila infection of human macrophages (THP-1) at time 0.

source_name: 3XSCOTS cDNA obtained from JR32 infecting THP-1 macrophages at time 0


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 3


title: patient 418-B,post

tag: disease

value: in-transit disease

tag: stage

tag: disease state

value: CR

tag: treatment


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 6


title: d0 -LIF replicate 1

description: replicate 1

tag: strain

tag: cell line

tag: protocol


title: liver_young_PPB_3

description: Gene expression data from liver tissue of 1-yr-old dogs after 1 yr on PPB diet.

source_name: Liver tissue at 1 yr, after 1 year on PPB diet

tag: tissue

value: 1 yr


title: Rm8530 mucR biological replicate 3

city: Richardson

first: Juan

last: González

state: TX

address: 800 West Campbell Rd. RL 11

department: Molecular and Cell Biology

institute: University of Texas at Dallas

description: Gene expression data from Rm8530 mucR

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Medicago 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 with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
In order to determine fold changes in gene expression as a result of the disruption of mucR, signals were further analyzed by GeneSifter Microarray Analysis Online.  Biological replicates of Rm8530 were organized into Group 1 and Rm8530 mucR into group 2.  T-test comparison of these two groups was normalized to the median of the data set and log transformed.  Observed fold changes required the presence of signal in at least one group and a p-value < 0.05.

organism: Sinorhizobium meliloti

source_name: S. meliloti with a disrupted mucR

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: S. meliloti strains were grown to  OD600 = 1.2 in minimal low-phosphate media with streptomycin 500 ug ml-1 and constant shaking at 30°C.

extract_protocol: Extraction of total RNA was performed using a QIAGEN RNeasy kit according to manufacturer's instructions.

treatment_protocol: Cultures were centrifuged, supernatants were removed, and pellets were frozen in liquid nitrogen followed by storage at -80°C.

tag: bacterial stage

value: planktonic

value: Rm8530 mucR

tag: genotype/variation

value: mucR disrupted with mTn5

tag: growth condition

value: minimal low phosphate to OD600 = 1.2


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 4

tag: condition


title: patient 416-B,post

value: SD

value: no previous ILI/ILP


title: patient 420-A,pre


title: patient 418-A,pre


title: patient 416-A,pre


title: liver_old_PPB_2


title: Rm8530 mucR biological replicate 2

description: Gene expression data from Rm8530 mucR


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 3

tag: reference


title: liver_old_APB_3

description: Gene expression data from liver tissue of 12-yr-old dogs after 1 yr on APB diet.

source_name: Liver tissue at 12 yrs, after 1 year on APB diet

tag: age

value: animal-protein based


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 2

value: L pneumophila inside human THP-1 macrophages


title: liver_young_PPB_2

tag: diet


title: liver_young_APB_3

description: Gene expression data from liver tissue of 1-yr-old dogs after 1 yr on APB diet.

source_name: Liver tissue at 1 yr, after 1 year on APB diet

tag: breed


title: liver_young_APB_2

tag: gender


title: patient 415-B,post

tag: disease

value: PD

value: previous vaccine tx


title: Rm8530 biological replicate 2

description: Gene expression data from Rm8530

source_name: S. meliloti with an intact mucR

value: mucR intact


title: Rm8530 mucR biological replicate 1

description: Gene expression data from Rm8530 mucR


title: patient 407-C,2nd

tag: stage


title: Rm8530 biological replicate 1

description: Gene expression data from Rm8530


title: patient 415-A,pre

tag: disease state


title: Rm8530 biological replicate 3

description: Gene expression data from Rm8530


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 6

description: L. pneumophila was grown to post-exponential phase in rich AYE broth.

source_name: 3XSCOTS cDNA obtained from JR32 grown to post-exponential phase

tag: media

value: AYE broth, 37C

value: genomic DNA


title: patient 407-B,post

tag: treatment


title: liver_young_PPB_1

value: liver

value: plant-protein based

value: beagle

value: female


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 4


title: liver_young_APB_1

value: 1 yr


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 5


title: JR32 infection of THP-1 macrophage time 0 (SCOTS treated), replicate 1


title: patient 407-A,pre

value: in-transit disease

value: CR


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 3


title: liver_old_APB_2

value: 12 yrs


title: E13 Atoh1 cells at E14, rep3

city: New York

first: Rob

last: Machold

state: NY

address: 522 First Avenue

department: Otolaryngology

institute: NYU School of Medicine

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E13.5
Atoh1_E13C

hyb_protocol: Hybridization was performed on Affymetrix 430_2 GeneChip arrays at the Genomics Core Laboratory (Memorial Sloan-Kettering Cancer Center)

scan_protocol: GeneChips were scanned at the Genomics Core Laboratory (Memorial Sloan-Kettering Cancer Center)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: r1/isthmus cells expressing Atoh1 at E13.5, purified at E14.5

label_protocol: Labeling of total RNA for analysis on Affymetrix 430_2 microarrays was performed at the Genomics Core Laboratory (Memorial Sloan-Kettering Cancer Center)

growth_protocol: Embryos transgenic for Atoh1-CreER; EGFP reporter (RCE) were generated by breeding Atoh1-CreER males with RCE homozygous females. The day of the observed plug was considered day 0.5.

extract_protocol: Extraction of total RNA was performed from frozen cell pellets at the Genomics Core Laboratory (Memorial Sloan-Kettering Cancer Center)

treatment_protocol: To obtain selective labeling of E10.5 or E13.5 Atoh1 expressing cells, tamoxifen (4 mg/35 g pregnant dam) was administered at either E10.5 or E13.5 by oral gavage. Transgenic E14.5 embryos were identified by EGFP fluorescence prior to dissection of the r1/isthmus region of the neural tube. Tissue was dissociated using papain/DNAse treatment in HBSS and trituration with glass polished pipets prior to FACS purification of EGFP+ cells.

tag: strain

value: Swiss Webster

value: brain (r1/isthmic region only)

tag: cell type

value: r1/isthmus cells

tag: genotype

value: Atoh1-CreER; EGFP reporter

tag: time of atoh1 expression


title: E13 Atoh1 cells at E14, rep1

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E13.5
Atoh1_E13A

tag: tissue


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 2


title: E13 Atoh1 cells at E14, rep2

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E13.5
Atoh1_E13B


title: JR32 strain grown to post-exponential phase (SCOTS treated), replicate 1


title: liver_old_PPB_1


title: E10 Atoh1 cells at E14, rep2

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E10.5
Atoh1_E10B

source_name: r1/isthmus cells expressing Atoh1 at E10.5, purified at E14.5


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 6

description: L. pneumophila was grown to exponential phase in rich AYE broth. This is the control condition to identify L. pneumophila genes differentially expressed during intracellular multiplication.

source_name: 3XSCOTS cDNA obtained from JR32 grown to exponential phase


title: E10 Atoh1 cells at E14, rep3

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E10.5
Atoh1_E10C


title: patient 403-C,2nd

value: PD

value: previous ILI


title: mouse jejunum_hnf1alphacontrol_rep3

city: Sherbrooke

first: Francois

last: Boudreau

state: Quebec

address: 3001 12e ave Nord

department: Anatomy and Cell Biology

institute: University of Sherbrooke

description: Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

hyb_protocol: The hybridization mixture was prepared by mixing 15 ug biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours). After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

scan_protocol: Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody (Vector Laboratories).

data_processing: The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the RMA algorithm.

source_name: adult mouse jejunum, hnf1alpha control

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

growth_protocol: Mice were maintained in a pathogen-free environnment.

extract_protocol: Extraction with the Ambion Totally RNA kit.

treatment_protocol: Injection of ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice.

value: mixed background

value: 4 months

value: wildtype

value: jejunum

tag: sample type

value: control littermate


title: E10 Atoh1 cells at E14, rep1

description:
Gene expression data from E14.5 r1/isthmus cells that expressed Atoh1 at E10.5
Atoh1_E10A


title: patient 412-A,pre

source_name: melanoma

value: PR

value: no previous ILI/ILP


title: liver_old_APB_1

value: liver

value: animal-protein based

value: beagle

value: female


title: patient 403-A,post

value: in-transit disease


title: patient 412-B,pre


title: Day 112 Mouse inguinal fat over nutrition 2

city: Baton Rouge

first: Robert

middle: A.

last: Koza

state: LA

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

hyb_protocol: Microarray hybridization 3 technical replicates of each sample (using ten micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

scan_protocol: Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

data_processing: Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

label: Dig-UTP

source_name: Mouse age 112 days inguinal fat overnutrition diet

label_protocol: 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

growth_protocol: At birth, litter sizes were adjusted to 8 pups per litter for control and lactation under-nutrition and 4 pups per litter for lactation over-nutrition with both male and female pups; however, only male pups (12 pups per sample) were sacrificed to form the pools for each time point.

extract_protocol: Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

treatment_protocol: See Samples Section for protocol during pregnancy and lactation. After weaning the offspring from the 3 nutritional conditions were treated the same; from weaning until 8 wk of age mice were fed a low fat chow diet (LabDiets 5053 11 Kcal % fat) ad libitum. At 8 wk of age mice were fed ad libitum a high saturated fat diet D12331 (Research Diets,) for 8 weeks. From weaning until 7 wk of age male mice were group housed (3–5 mice per pen) until 7 wk of age, at which time they were singly housed for the remainder of the experiment.

value: male

value: inguinal fat

value: 112 days

value: Lactation over-nutrition condition (LON)- mother was fed a high fat 58 Kcal % fat diet (Research Diet 12331, New Brunswick, New Jersey, United States) ad libitum.

tag: litter size

value: reduced to 4 pups


title: patient 403-B,pre

value: PD

value: previous ILI


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 5

value: AYE broth, 37C

tag: reference

value: genomic DNA


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 4


title: mouse jejunum_hnf1alphacontrol_rep2

value: mixed background

tag: age

value: 4 months

value: wildtype

value: jejunum

value: control littermate


title: Day 112 Mouse inguinal fat over nutrition 3

tag: diet


title: patient 427,post

value: PR

value: no previous ILI/ILP


title: patient 402-A,pre

value: in-transit disease


title: mouse jejunum_hnf1alphacontrol_rep1


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 1


title: rb-smyd, 5

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: SAOS cells transiently transfected with human RB and mouse SMYD2.

hyb_protocol: As recommended by the manufacturer (Affymetrix, Santa Clara).

scan_protocol: Gene Chip Scanner 3000.

data_processing: RMA

source_name: osteosarcoma cell line SAOS, RB and SMYD2

extract_protocol: RNA was extracted with Trizol (Invitrogen) and cleaned using the Qiagen RNeasy kit.

tag: cell line

value: SAOS

value: osteosarcoma

tag: transient transfection

value: human RB1 and mouse SMYD2


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 2


title: JR32 strain grown to exponential phase (SCOTS treated), replicate 3


title: DMSO_1h

city: Atlanta

first: Michael

last: Zilliox

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

description: S. cerevisiae, strain BY4742, treated with DMSO for 1 hour

hyb_protocol: 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip mouse 430 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA.  The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.1 (GCOS) software from Affymetrix, using the standard default settings.

data_processing: MAS 5.0 and PLIER

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: RNA was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).

extract_protocol: Hot acidic phenol extraction

value: with DMSO for 1 hour


title: Day 112 Mouse inguinal fat over nutrition 1

tag: gender

value: male

value: inguinal fat

value: 112 days

value: Lactation over-nutrition condition (LON)- mother was fed a high fat 58 Kcal % fat diet (Research Diet 12331, New Brunswick, New Jersey, United States) ad libitum.

value: reduced to 4 pups


title: Day 56 Mouse inguinal fat over nutrition 3

source_name: Mouse age 56 days inguinal fat overnutrition diet

value: 56 days


title: rb-smyd, 4

label_protocol: As recommended by the manufacturer (Affymetrix, Santa Clara).


title: patient 402-B,post

tag: disease

tag: stage

value: PD

value: previous ILI


title: rb-smyd, 3


title: Day 56 Mouse inguinal fat over nutrition 2


title: rb, 4

description: SAOS cells transiently transfected with human RB.

source_name: osteosarcoma cell line SAOS, RB

value: human RB1


title: Cnb1

description: S. cerevisiae, cnb1 knock-out isogenic to strain BY4742, treated with amiodarone for 6 hours

tag: genotype/variation

value: cnb1 knock-out

value: with amiodarone for 6 hours


title: rb, 5


title: Day 56 Mouse inguinal fat over nutrition 1


title: mouse jejunum_hnf1alphamutant_rep2

source_name: adult mouse jejunum, hnf1alpha mutant

value: mixed background

value: 4 months

value: hnf1alpha KO

value: jejunum

value: mutant


title: Day 21 Mouse inguinal fat over nutrition 2

source_name: Mouse age 21 days inguinal fat overnutrition diet

value: 21 days


title: AMD_EGTA_Ca_10min

description: S. cerevisiae, strain BY4742, treated with amiodarone, EGTA and calcium for 10 minutes.

tag: treatment


title: mouse jejunum_hnf1alphamutant_rep1

tag: strain


title: mouse jejunum_hnf1alphamutant_rep3


title: rb, 3

value: SAOS

tag: cell type

value: osteosarcoma


title: Day 21 Mouse inguinal fat over nutrition 3

value: male

value: inguinal fat


title: Day 10 Mouse inguinal fat over nutrition 3

source_name: Mouse age 10 days inguinal fat overnutrition diet

value: 10 days

value: Lactation over-nutrition condition (LON)- mother was fed a high fat 58 Kcal % fat diet (Research Diet 12331, New Brunswick, New Jersey, United States) ad libitum.

value: reduced to 4 pups


title: Day 21 Mouse inguinal fat over nutrition 1


title: AMD_1h

description: S. cerevisiae, strain BY4742, treated with amiodarone for 1 hour

value: with amiodarone for 1 hour


title: 195627

type: genomic

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: aCGH analysis

hyb_protocol: Labelled DNAs were hybridized to whole-genome oligonucleotide 1x244K microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNAs (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 1x244k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies) applying Z-Score algorithm.

source_name: tumor sample

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2,5 ug of test and reference genomic DNAs were separately digested with AluI/RsaI restriction enzyme mix (Promega). After purification with QIAprep MiniPrep kit (Qiagen), fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (Thermo) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was extracted overnight with lysis buffer containing K proteinase (0.2 mg/ml) followed by standard phenol/chloroform extraction. DNA content and quality were measured by Biophotometer (Eppendorf)

value: cerebellum

tag: histology

value: classic medulloblastoma

source_name: Human Genomic DNA: female Cat G1521,Promega, Madison, WI

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: Day 10 Mouse inguinal fat over nutrition 2


title: 154904

description: aCGH analysis


title: smyd, 5

description: SAOS cells transiently transfected with mouse SMYD2.

source_name: osteosarcoma cell line SAOS, SMYD2

value: mouse SMYD2


title: Day 10 Mouse inguinal fat over nutrition 1


title: AMD_6h

description: S. cerevisiae, strain BY4742, treated with amiodarone for 6 hours

value: with amiodarone for 6 hours


title: control, 5

description: Non-transformed SAOS cells.

source_name: osteosarcoma cell line SAOS, wild type

tag: genotype

value: wild type


title: smyd, 3


title: smyd, 4


title: Wild type retina adult, mouse 763

city: Davis

first: Carol

middle: Marie

last: Rubin

address: One Shields Avenue

department: Neurobiology Physiology and Behavior

institute: University of California, Davis

description:
WT Adult 763 retina
C57BL/6J

hyb_protocol: 10 ug of fragmented LGN aRNA or 20 ug of retinal RNA were hybridized on the Affymetrix Fluidics Station 450 following the protocol in the GeneChip Expression Analysis Technical Manual

scan_protocol: GeneChips were scanned with the 3000 GeneChip Scanner

data_processing: dCHIP, quantile normalization, PM/MM difference model

source_name: Adult wild type (C57BL/6J) male mus musculus  left and right total retinas

label_protocol: Samples were labeled using the Ambion MessageAmp II-Biotin Enhanced kit and protocols

extract_protocol: RNA was extracted using Qiagen RNeasy Micro Kit reagents and protocols

tag: developmental stage

value: Adult (after retinal ganglion cell segregation in lateral geniculate nucleus is complete)

tag: tissue

value: left and right total retinas

tag: mouse


title: Day 5 Mouse inguinal fat over nutrition 3

source_name: Mouse age 5 days inguinal fat overnutrition diet

value: 5 days

tag: litter size


title: Day 5 Mouse inguinal fat over nutrition 2

tag: age


title: Wild type retina adult, mouse 748

description:
WT Adult 748 retina
C57BL/6J


title: Xu b2 -/- retina adult, mouse 78

description:
Xu Adult 78 retina
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

source_name: Adult Chrnb2 mutant male mus musculus (Xu) left and right total retinas.  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

value: Chrnb2-/- (verified by PCR from tail snip, parents are Xu mutant)

tag: mutant allele

value: Xu


title: Day 112 Mouse inguinal fat under nutrition 3

source_name: Mouse age 112 days inguinal fat undernutrition diet

value: male

value: inguinal fat

value: 112 days

tag: diet

value: Lactation under-nutrition condition-mother was only fed 50% of the food (LabDiet 5015) consumed by the control mice the previous 24 hr.

value: 8 pups


title: 196684

description: aCGH analysis

value: cerebellum

tag: reference


title: Xu b2 -/- retina adult, mouse 77

description:
Xu Adult 77 retina
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

tag: gender


title: Day 5 Mouse inguinal fat over nutrition 1

value: Lactation over-nutrition condition (LON)- mother was fed a high fat 58 Kcal % fat diet (Research Diet 12331, New Brunswick, New Jersey, United States) ad libitum.

value: reduced to 4 pups


title: control, 3

description: Non-transformed SAOS cells.

tag: cell line

value: SAOS

value: osteosarcoma

tag: transient transfection


title: 181900

description: aCGH analysis

value: classic medulloblastoma

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: 182059

description: aCGH analysis


title: control, 4

description: Non-transformed SAOS cells.

value: wild type


title: Day 112 Mouse inguinal fat under nutrition 2


title: 153342

description: aCGH analysis


title: Day 112 Mouse inguinal fat under nutrition 1


title: Picciotto b2 -/- retina adult, mouse 1543

description:
Pic Adult 1543 retina
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

source_name: Adult Chrnb2 mutant male mus musculus (Picciotto) left and right total retinas.  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

value: Adult (after retinal ganglion cell segregation in lateral geniculate nucleus is complete)

tag: genotype/variation

value: Chrnb2-/- (verified by PCR from tail snip, parents are Picciotto mutant)

value: Picciotto

value: left and right total retinas


title: 193263

description: aCGH analysis

value: male


title: smyd, 1

value: mouse SMYD2


title: Day 56 Mouse inguinal fat under nutrition 2

source_name: Mouse age 56 days inguinal fat undernutrition diet

value: inguinal fat

value: 56 days

value: Lactation under-nutrition condition-mother was only fed 50% of the food (LabDiet 5015) consumed by the control mice the previous 24 hr.


title: rb-smyd, 1

source_name: osteosarcoma cell line SAOS, RB and SMYD2

value: human RB1 and mouse SMYD2


title: 195589

description: aCGH analysis

value: cerebellum


title: Xu b2 -/- LGN P4, mouse C

description:
Xu P4 C LGN
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

source_name: Postnatal day 4 Chrnb2 mutant male mus musculus (Xu) left and right total lateral geniculate nucleus (LGN).  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Xu mutant)

value: Xu

value: C


title: Day 56 Mouse inguinal fat under nutrition 3

value: 8 pups


title: Wild type LGN P4, mouse D

description:
WT P4 D LGN
C57BL/6J

source_name: Postnatal day 4 wild type (C57BL/6J) male mus musculus  left and right total lateral geniculate nucleus (LGN)

value: wild type

value: D


title: Day 56 Mouse inguinal fat under nutrition 1


title: Wild type LGN P4, mouse A

description:
WT P4 A LGN
C57BL/6J

value: left and right total lateral geniculate nucleus (LGN)

value: A


title: Wild type LGN P4, mouse E

description:
WT P4 E LGN
C57BL/6J

value: E


title: Day 21 Mouse inguinal fat under nutrition 3

source_name: Mouse age 21 days inguinal fat undernutrition diet

value: male

value: 21 days


title: control, 1

description: Non-transformed SAOS cells.

value: SAOS

value: osteosarcoma


title: Picciotto b2 -/- retina adult, mouse 1542

description:
Pic Adult 1542 retina
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

value: Adult (after retinal ganglion cell segregation in lateral geniculate nucleus is complete)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Picciotto mutant)

value: Picciotto

value: left and right total retinas


title: 195615

description: aCGH analysis

value: cerebellum

value: classic medulloblastoma

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: #169

description: aCGH analysis


title: Xu b2 -/- LGN P4, mouse A

description:
Xu P4 A LGN
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Xu mutant)

value: Xu


title: #165

description: aCGH analysis


title: Day 21 Mouse inguinal fat under nutrition 1

value: inguinal fat

value: Lactation under-nutrition condition-mother was only fed 50% of the food (LabDiet 5015) consumed by the control mice the previous 24 hr.

value: 8 pups


title: AML sample #96

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

description: AML samples investigated according to WHO 2008 classification

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.22.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64).

label: Biotin

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Samples are from untreated AML patients.

tag: sample id

tag: analysis i

value: AML-NOS

tag: analysis ii

value: AML-NOS plus AML-MLD-sole


title: AML sample #94


title: #106

description: aCGH analysis

tag: histology


title: #160

description: aCGH analysis

value: male


title: Xu b2 -/- LGN P4, mouse B

description:
Xu P4 B LGN
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

tag: strain

value: left and right total lateral geniculate nucleus (LGN)

value: B


title: Day 21 Mouse inguinal fat under nutrition 2

value: 21 days


title: #93

description: aCGH analysis


title: Day 10 Mouse inguinal fat under nutrition 3

source_name: Mouse age 10 days inguinal fat undernutrition diet

value: 10 days


title: AML sample #95

value: AML-MLD-sole


title: rb, 1

source_name: osteosarcoma cell line SAOS, RB

value: SAOS

tag: cell type

value: osteosarcoma

value: human RB1


title: AML sample #92


title: Day 10 Mouse inguinal fat under nutrition 2

tag: tissue


title: Day 10 Mouse inguinal fat under nutrition 1


title: Picciotto b2 -/- LGN P4, mouse C

description:
Pic P4 C LGN
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

source_name: Postnatal day 4 Chrnb2 mutant male mus musculus (Picciotto) left and right total lateral geniculate nucleus (LGN).  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

tag: developmental stage

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Picciotto mutant)

value: Picciotto

tag: mouse

value: C


title: 188181

description: aCGH analysis

source_name: tumor sample

value: cerebellum

value: classic medulloblastoma

source_name: Human Genomic DNA: female Cat G1521,Promega, Madison, WI

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: Picciotto b2 -/-LGN P4, mouse B

description:
Pic P4 B LGN
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

value: male


title: AML sample #90

value: AML-NOS plus AML-MLD-sole


title: AML sample #91

value: AML-NOS


title: Day 5 Mouse inguinal fat under nutrition 3

source_name: Mouse age 5 days inguinal fat undernutrition diet

value: inguinal fat

tag: age

value: 5 days

value: Lactation under-nutrition condition-mother was only fed 50% of the food (LabDiet 5015) consumed by the control mice the previous 24 hr.

tag: litter size

value: 8 pups


title: Day 5 Mouse inguinal fat under nutrition 2

tag: diet


title: Wild type retina P4, mouse B

description:
WT P4 B retina
C57BL/6J

source_name: Postnatal day 4 wild type (C57BL/6J) male mus musculus  left and right total retinas

value: wild type

value: left and right total retinas

value: B


title: Picciotto b2 -/- LGN P4, mouse D

description:
Pic P4 D LGN
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Picciotto mutant)

tag: mutant allele

value: left and right total lateral geniculate nucleus (LGN)

value: D


title: #29

description: aCGH analysis

value: cerebellum

value: classic medulloblastoma

tag: gender

tag: reference


title: AML sample #88


title: AML sample #89


title: #45

description: aCGH analysis

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: #32

description: aCGH analysis

value: male


title: Wild type retina P4, mouse A

description:
WT P4 A retina
C57BL/6J

value: A


title: AML sample #93

value: AML-MLD-sole

value: AML-NOS plus AML-MLD-sole


title: AML sample #87

value: AML-NOS


title: 37472

description: aCGH analysis


title: Wild type retina P4, mouse C

description:
WT P4 C retina
C57BL/6J

value: C


title: Day 5 Mouse inguinal fat under nutrition 1

value: inguinal fat

value: 5 days

value: Lactation under-nutrition condition-mother was only fed 50% of the food (LabDiet 5015) consumed by the control mice the previous 24 hr.

value: 8 pups


title: 35867

description: aCGH analysis


title: Day 112 Mouse inguinal fat control 3

source_name: Mouse 112 days inguinal fat chow diet

value: 112 days

value: control condition-mother was fed the breeder diet 5015 (22 kcal % fat) ad libitum


title: AML sample #86


title: Day 112 Mouse inguinal fat control 2


title: AML sample #85


title: 37974

description: aCGH analysis


title: 2667-I-01

description: aCGH analysis


title: Xu b2 -/- retina P4, mouse A

description:
Xu P4 A retina
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

source_name: Postnatal day 4 Chrnb2 mutant male mus musculus (Xu) left and right total retinas.  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: Chrnb2-/- (verified by PCR from tail snip, parents are Xu mutant)

value: Xu

value: left and right total retinas


title: Xu b2 -/- retina P4, mouse B

description:
Xu P4 B retina
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

value: B


title: AML sample #84


title: AML sample #83


title: MB_Cl_TO

description: aCGH analysis

value: cerebellum

value: classic medulloblastoma

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: Picciotto b2 -/- retina P4, mouse C

description:
Pic P4 C retina
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

source_name: Postnatal day 4 Chrnb2 mutant male mus musculus (Picciotto) left and right total retinas.  C57BL/6J mice mutated in the Chrnb2 gene, see reference under Description field

value: Chrnb2-/- (verified by PCR from tail snip, parents are Picciotto mutant)

value: Picciotto

value: male


title: Day 112 Mouse inguinal fat control 1

value: inguinal fat


title: MB011

description: aCGH analysis


title: Picciotto b2 -/- retina P4, mouse A

description:
Pic P4 A retina
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

value: A


title: Xu b2 -/- retina P4, mouse C

description:
Xu P4 C retina
Xu, W., A. Orr-Urtreger, et al. (1999). Multiorgan autonomic dysfunction in mice lacking the beta2 and the beta4 subunits of neuronal nicotinic acetylcholine receptors. J Neurosci 19(21): 9298-305.

value: C


title: AML sample #82

value: AML-NOS

value: AML-NOS plus AML-MLD-sole


title: MB009

description: aCGH analysis


title: Day 56 Mouse inguinal fat control 2

source_name: Mouse age 56 days inguinal fat chow diet

value: 56 days

value: control condition-mother was fed the breeder diet 5015 (22 kcal % fat) ad libitum

value: 8 pups


title: Picciotto b2 -/- retina P4, mouse B

description:
Pic P4 B retina
Picciotto, M. R., M. Zoli, et al. (1995). Abnormal avoidance learning in mice lacking functional high-affinity nicotine receptor in the brain. Nature 374(6517): 65-7.

value: Postnatal day 4 (before retinal ganglion cell segregation in lateral geniculate nucleus)

value: left and right total retinas


title: Day 56 Mouse inguinal fat control 3


title: Day 21 Mouse inguinal fat control 3

source_name: Mouse age 21 days inguinal fat chow diet

value: 21 days


title: Vehicle- treated rep4

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by Affymetrix

scan_protocol: As suggested by Affymetrix using the Affymetrix scanner

data_processing: Data less than  0.01 set to 0.01. Per chip, Normalized to 50th Percentile, Per Gene Normalized to Median.

label: streptavidin Cy3

source_name: mammary tissue from transgenic mouse line

label_protocol: As recommended by Affymetrix

growth_protocol: Tumors were detected in female mice by manual palpation and measured with the use of calipers.

extract_protocol: Total RNA was isolated by using the mirVana miRNA Isolation Kit (Ambion/Invitrogen) according to the manufacturer’s instructions.  8 ng of total RNA from each mouse was reverse transcribed into cDNA by using iSCRIPT cDNA Synthesis kit (Bio-Rad Laboratories) on a Peltier Thermal Cycler (MJ Research).

tag: genotype

value: MMTV-PyMT

value: mammary


title: SKI606-treated rep3

treatment_protocol: SKI-606 was formulated in 0.5% methocellulose and 0.4% Tween 80 and administered by oral gavage at 100 mg/kg.


title: AML sample #78

value: AML-MLD-sole


title: SKI606-treated rep1


title: MB008

description: aCGH analysis

value: cerebellum

value: classic medulloblastoma

value: female

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: SKI606-treated rep4


title: DE5_rep3

first: Elizabeth

last: Thomas

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

data_processing: Slides were scanned using Illumina BeadStation and signal extracted using Illumina BeadStudio software.  Raw data is the output of the BeadStudio software and was analyzed using Bioconductor packages.  Data was normalized using the LIMMA package.

source_name: striatum

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

tag: genotype/variation

value: striatum

value: 14 months


title: Day 21 Mouse inguinal fat control 2

value: male

value: inguinal fat


title: Day 10 Mouse inguinal fat control 2

source_name: Mouse age 10 days inguinal fat chow diet

value: 10 days


title: Day 10 Mouse inguinal fat control 1

value: control condition-mother was fed the breeder diet 5015 (22 kcal % fat) ad libitum


title: AML sample #81

tag: sample id

value: AML-NOS plus AML-MLD-sole


title: AML sample #77

tag: analysis i

value: AML-NOS


title: Day 10 Mouse inguinal fat control 3

value: 8 pups


title: DE5_rep2


title: AML sample #76

tag: analysis ii


title: Day 56 Mouse inguinal fat control 1

value: 56 days


title: Day 21 Mouse inguinal fat control 1

value: 21 days


title: AML sample #79


title: Vehicle- treated rep3

value: MMTV-PyMT

value: mammary


title: AML sample #80


title: SKI606-treated rep2


title: DE5_rep4


title: MB005

description: aCGH analysis

value: cerebellum

tag: histology


title: MB007

description: aCGH analysis

value: classic medulloblastoma


title: DE5_rep1

tag: strain


title: MB002

description: aCGH analysis

value: unknown

value: female


title: MB004

description: aCGH analysis

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: AML sample #74


title: MB001

description: aCGH analysis


title: AML sample #73


title: wt_rep3

value: wild type

value: striatum

value: 14 months


title: Day 5 Mouse inguinal fat control 3

source_name: Mouse age 5 days inguinal fat chow diet

value: male

value: inguinal fat

value: 5 days


title: Vehicle- treated rep1


title: AML sample #75

source_name: mononuclear cells after Ficoll purification

value: AML-MLD-sole

value: AML-NOS plus AML-MLD-sole


title: Vehicle- treated rep2


title: wt_rep2


title: Day 5 Mouse inguinal fat control 1

value: control condition-mother was fed the breeder diet 5015 (22 kcal % fat) ad libitum

value: 8 pups


title: AML sample #72

value: AML-NOS


title: Day 5 Mouse inguinal fat control 2


title: MG1655 lacIq pBRplac #3

first: Chase

middle: Lawrence

last: Beisel

address: 18 Library Dr. MSC 5430

department: CBMP

institute: NICHD

hyb_protocol: Following fragmentation, 6 µg of cDNA was hybridized for 16 hr at 45˚C on GeneChip E.coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip operating software (1.4.0.036) using the following expression analysis settings: 1. Scaling: All probe set with target intensity of each array arbitrarily set to 500 2. Normalization: All probe set

organism: Escherichia coli str. K-12 substr. MG1655

source_name: MG1655 lacIq harboring pBRplac, experiment #3

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 6 µg total RNA (Section 3 Prokaryotic sample and array processing).

growth_protocol: M6155 lacIq cells were grown overnight in LB with Amplicillin at 37°C. Overnight cultures were diluted into the same type of media to an ABS600 of 0.01 and shaken at 37°C.

extract_protocol: After treatment with IPTG for 7 min, total RNA was isolated using the hot phenol extraction procedure.

treatment_protocol: At an ABS600 of 0.4, IPTG was added to the cultures to a final concentration of 1 mM.

value: K12 substr. MG1655

tag: cell type

value: MG1655 lacIq

tag: vector

value: pBRplac


title: wt_rep1

tag: tissue


title: HNF4fxVilCRE_MUT2

hyb_protocol: The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours). After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

scan_protocol: Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody Vector Laboratories). The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples.

data_processing: FlexArray 1.3 was used for data analysis (www.genomequebec.mcgill.ca)

label_protocol: Total RNA has been isolated by Ambion ToTALLY RNA kit from total jejunum biopsies

growth_protocol: Mice were maintained in pathogen free environnement.

extract_protocol: Total RNA with Ambion Totally RNA

treatment_protocol: Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice

value: adult

value: jejunum


title: AML sample #70


title: HNF4fxVilCRE_MUT3


title: MG1655 lacIq pSpot42 #1

source_name: MG1655 lacIq harboring pSpot42 experiment #1


title: MG1655 lacIq pBRplac #2

source_name: MG1655 lacIq harboring pBRplac, experiment #2


title: AML sample #71


title: HNF4fxVilCRE_MUT1


title: MG1655 lacIq pSpot42 #2

source_name: MG1655 lacIq harboring pSpot42 experiment #2


title: HNF4fxVilCRE_CTRL3


title: MG1655 lacIq pSpot42 #3

source_name: MG1655 lacIq harboring pSpot42 experiment #3


title: AML sample #69


title: Emphysema #442

city: Houston

first: Farrah

last: Kheradmand

address: One Baylor Plaza

institute: Baylor College of Medicine

description: patient 2

data_processing: Data were processed by variance stabilizing transform and quantile normalization

source_name: Lung myeloid dendritic cells

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

extract_protocol: RNA was extracted with Trizol reagent

value: Female

tag: age (y)

tag: disease state

value: Emphysema

value: lung myeloid dendritic cells


title: MG1655 lacIq pBRplac #1

source_name: MG1655 lacIq harboring pBRplac, experiment #1


title: Control #195

description: healthy control 1

value: Male

value: Control


title: AML sample #66


title: Emphysema #440

description: patient 1


title: AML sample #65


title: Control #450

description: healthy control 3


title: Emphysema #445

description: patient 3


title: HNF4fxVilCRE_CTRL2

tag: age


title: Control #444

description: healthy control 2


title: AML sample #68


title: AML sample #64


title: H2-2

city: Sendai

first: Yoshihiko

last: Uehara

state: Miyagi

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

department: Cell Biology

country: Japan

institute: Tohoku Univ. Sch. Med.

description: Gene exrpression data from one irradiated mouse

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

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

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

source_name: irradiated mouse liver at 20.0 mGy/day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Specific Pathogen Free

extract_protocol: ISOGEN (Nippon Gene, Tokyo) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Irradiation with 137Cs γ-rays was carried out for 485 days (22 h/day) at dose-rates of 16.6 mGy/day (H1), 0.858 mGy/day (M1) or 0.042 mGy/day (L1) in the first experiment. Irradiation was carried out for 401 days at dose-rates of 20.0 mGy/day (H2), 1.00 mGy/day (M2) or 0.05 mGy/day (L2) in the second experiment. Mice were sacrificed immediately after the termination of irradiation, and liver was dissected and stored at -20°C in RNAlater (Ambion).

tag: sex

value: male

value: liver


title: Muscle_3030_HRT_user

city: Jyväskylä

first: Paula

last: Ronkainen

address: PO Box 35

country: Finland

institute: University of Jyväskylä

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised using the affy package for R.

source_name: Human skeletal muscle

label_protocol: IVT reaction overnight (14h), during which cRNA was biotinylated (Ambion's Illumina RNA TotalPrep Amplification kit).

extract_protocol: RNA was extracted with Trizol reagent. The RNA/cRNA concentrations were checked with Nanodrop ND-1000 (Thermo Fisher Scientific Inc.) and RNA/cRNA quality using Experion electrophoresis station (Bio-Rad Laboratories).

value: female

value: Vastus lateralis muscle

tag: hrt status

value: user of postmenopausal, estrogen-based HRT


title: H2-3


title: HNF4fxVilCRE_CTRL1


title: FL_021

city: Southport

middle: Richard

last: Green

state: Queensland

address: 58 Parklands Drive

department: Griffith Insitute for Health & Medical Research

country: Australia

institute: Griffith University

description: As per manufacturer's instructions

hyb_protocol: As per manufacturer's instructions

scan_protocol: As per manufacturer's instructions

data_processing: Data extracted with GCOS (Affymetrix) and copy number called by CNAT 4.0 (Affymetrix)

source_name: Tumor tissue

label_protocol: As per manufacturer's instructions

extract_protocol: Refer to Green et al. (2009) Leuk. Res., 33:731-734

tag: diagnosis

value: Follicular Lymphoma


title: AML sample #61

value: not included

value: AML-MRC


title: H2-1


title: AML sample #67

value: AML-NOS

value: AML-NOS plus AML-MLD-sole


title: Muscle_3029_non_HRT

description: replicate 1

tag: gender

value: never-user


title: Muscle_3027_HRT_user

description: replicate 1


title: AML sample #62


title: Muscle_3026_HRT_user

description: replicate 1


title: M2-1

source_name: irradiated mouse liver at 1.00 mGy/day


title: FL_020

description: As per manufacturer's instructions


title: FL_017

description: As per manufacturer's instructions


title: M2-2


title: M2-3


title: Muscle_3028_non_HRT

description: replicate 1


title: L2-3

source_name: irradiated mouse liver at 0.05 mGy/day


title: FL_018

description: As per manufacturer's instructions


title: FL_016

description: As per manufacturer's instructions


title: AML sample #60


title: AML sample #59


title: AML sample #58

value: AML-MLD-sole


title: L2-2


title: Muscle_3025_non_HRT

description: replicate 1


title: FL_014

description: As per manufacturer's instructions


title: Muscle_3024_non_HRT

description: replicate 1


title: FL_015

description: As per manufacturer's instructions


title: C2

description: Gene exrpression data from pooled RNA from 6 unirradiated control mice

source_name: unirradiated mouse liver


title: Muscle_3023_HRT_user

description: replicate 1


title: FL_012

description: As per manufacturer's instructions


title: L2-1


title: H1-3

source_name: irradiated mouse liver at 16.6 mGy/day


title: Muscle_3015_HRT_user

description: replicate 1


title: AML sample #55


title: Muscle_3016_non_HRT

description: replicate 1


title: Muscle_3021_HRT_user

description: replicate 1


title: AML sample #56


title: H1-1


title: H1-2


title: AML sample #57


title: Muscle_3022_non_HRT

description: replicate 1


title: M1-3

source_name: irradiated mouse liver at 0.858 mGy/day


title: FL_013

description: As per manufacturer's instructions


title: FL_010

description: As per manufacturer's instructions


title: FL_011

description: As per manufacturer's instructions


title: FL_009

description: As per manufacturer's instructions


title: AML sample #54


title: AML sample #53


title: Muscle_3010_non_HRT

description: replicate 1


title: AML sample #52


title: L1-1

source_name: irradiated mouse liver at 0.042 mGy/day


title: FL_008

description: As per manufacturer's instructions


title: Muscle_3012_non_HRT

description: replicate 1


title: FL_007

description: As per manufacturer's instructions


title: Muscle_3009_HRT_user

description: replicate 1


title: C1

description: Gene exrpression data from pooled RNA from 3 unirradiated control mice


title: L1-3


title: M1-1


title: L1-2


title: Muscle_3013_HRT_user

description: replicate 1


title: FL_005

description: As per manufacturer's instructions


title: FL_003

description: As per manufacturer's instructions


title: AML sample #50

source_name: mononuclear cells after Ficoll purification


title: Muscle_3008_non_HRT

description: replicate 1


title: FL_002

description: As per manufacturer's instructions


title: AML sample #49


title: M1-2


title: Muscle_3014_non_HRT

description: replicate 1


title: FL_004

description: As per manufacturer's instructions


title: FL_006

description: As per manufacturer's instructions


title: AML sample #63


title: alpha7-/-, Aged_a7_764

city: Tel Aviv

first: Merav

last: Kedmi

address: 6 Weizmann street

country: Israel

institute: Tel Aviv Sourasky Medical Center

description: alpha7-/-, Aged_a7_764

hyb_protocol: According to the manufacturer's (Affymetrix) instructions

scan_protocol: Affymetrix Gene-Array Scanner

data_processing: data from each array was scaled using MAS5 software, and the mean intensity for each array was adjusted by a scaling factor to a set target intensity of 150.

source_name: whole brain

extract_protocol: Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

value: 2 years


title: AML sample #48


title: AML sample #51


title: Muscle_3011_HRT_user

description: replicate 1


title: AML sample #46


title: FL_001

description: As per manufacturer's instructions


title: AML sample #47


title: IgE-crosslinked BMMC_rep4

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: microRNA profiling of activated mast cells obtained by presensitization of BMMCs with anti-DNP IgE followed by IgE-crosslinking by DNP-antigen challenge for 2 hours

hyb_protocol: Standard Agilent labeling protocol: the labeled samples were hybridized for 20 hours at 55°C.

scan_protocol: Standard Agilent labeling protocol: the arrays were scanned with an Agilent DNA Microarray Scanner BA. The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and grid: 019119_D_20080215).

data_processing: Extracted data were analyzed by Genespring GX10.0. Raw data were normalized to the 75th percentile signal intensity and entities showing present call in all samples of a condition were filtered out. Differentially expressed genes were selected when passing the signal intensity filter (entities where at least 100 percent of samples in any 1 out of 4 conditions have values within cut-off) and showing at least 2-fold statistically significant change (ANOVA and Tukey HSD post-hoc test, with Benjamini-Hochberg Multiple Testing Correction p-value<0,05) between BMMC and any other groups.

source_name: activated BMMCs

label_protocol: Standard Agilent labeling protocol with 100 ng quality-checked total RNA.

growth_protocol: Culture of bone marrow cells in complete RPMI 1640 supplemented with IL3 (5ng/ml) and SCF (20ng/ml) for 4 weeks.

extract_protocol: RNAs from cell samples was extracted by miRNeasy Mini Kit, the quantity and quality of total RNA was assessed by NanoDrop ND-1000 spectrophotometer and Agilent 2100 Bioanalyzer, respectively. Only those samples were used for microarray experiments that gave >8.0 for RNA integrity number, showed a clear gel image and no DNA contamination was observed on the histogram.

treatment_protocol: Bone marrow-derived mouse mast cells (BMMCs) were cultured for 4 weeks in the presence of SCF and IL-3. On the 6th day, CD117+ cells (putative committed immature progenitors) were magnetically separated. In order to differentiate the 4 weeks old BMMCs toward mucosal-type mast cells the medium was supplemented with IL-9+TGF-beta for 5 additional days. BMMCs were activated by IgE-crosslinking.

value: Balb/c

tag: group

value: IgE-crosslinked BMMC


title: DLBCL_021

description: As per manufacturer's instructions

value: Diffuse Large B-cell Lymphoma


title: Muscle_3007_HRT_user

description: replicate 1


title: AML sample #44


title: alpha7-/-, Aged_a7_751

description: alpha7-/-, Aged_a7_751

label_protocol: According to the manufacturer's (Affymetrix) instructions

tag: genotype/variation


title: AML sample #45

tag: sample id


title: DLBCL_020

description: As per manufacturer's instructions


title: Muscle_3001_HRT_user

description: replicate 1


title: alpha7-/-, Aged_a7_52

description: alpha7-/-, Aged_a7_52


title: AML sample #42

tag: analysis i


title: alpha7-/-, Aged_a7_752

description: alpha7-/-, Aged_a7_752


title: IgE-crosslinked BMMC_rep2


title: Muscle_3002_non_HRT

description: replicate 1


title: alpha7-/-, Aged_a7_53

description: alpha7-/-, Aged_a7_53


title: DLBCL_019

description: As per manufacturer's instructions


title: DLBCL_018

description: As per manufacturer's instructions


title: MMC_rep4

description: microRNA profiling of mucosal-type mast cells generated by additional differentiation of immature BMMCs for 5 days by supplementation of IL9 and TGFbeta.

source_name: mucosal-type mast cells

value: MMC


title: IgE-crosslinked BMMC_rep1


title: IgE-crosslinked BMMC_rep3


title: AML sample #41

tag: analysis ii


title: MMC_rep3


title: BMMC_rep4

description: microRNA profiling of immature BMMCs obtained by cultivation of bone marrow cells in the presence of IL3 and SCF for 4 weeks

source_name: immature BMMCs

value: BMMC


title: alpha7-/-, Young_a7_1069

description: alpha7-/-, Young_a7_1069

value: 8 weeks


title: DLBCL_016

description: As per manufacturer's instructions


title: AML sample #40

description: AML samples investigated according to WHO 2008 classification


title: AML sample #39


title: AML sample #43


title: DLBCL_017

description: As per manufacturer's instructions


title: alpha7-/-, Young_a7_1073

description: alpha7-/-, Young_a7_1073


title: alpha7-/-, Young_a7_1067

description: alpha7-/-, Young_a7_1067


title: BMMC_rep3


title: DLBCL_015

description: As per manufacturer's instructions


title: alpha7-/-, Young_a7_1066

description: alpha7-/-, Young_a7_1066


title: AML sample #35


title: AML sample #34


title: DLBCL_014

description: As per manufacturer's instructions


title: AML sample #38


title: alpha7-/-, Young_a7_1062

description: alpha7-/-, Young_a7_1062


title: DLBCL_011

description: As per manufacturer's instructions


title: BMMC_rep1


title: Wild-Type, Aged_a7_759

description: Wild-Type, Aged_a7_759

value: Wild-Type


title: MMC_rep2


title: AML sample #33


title: AML sample #37


title: AML sample #31


title: Wild-Type, Aged_a7_708

description: Wild-Type, Aged_a7_708


title: Wild-Type, Aged_a7_765

description: Wild-Type, Aged_a7_765


title: Wild-Type, Young_a7_556

description: Wild-Type, Young_a7_556


title: AML sample #30


title: DLBCL009

description: No additional information

data_processing: DNA copy number was called using the CNAT 4.0 algorithm (Affymetrix) with reference to genomic DNA obtained from peripheral blood lymphocytes of healthy donors.

extract_protocol: As described in Green et al. (2009) Leuk. Res., 33: 731-734


title: DLBCL_013

description: As per manufacturer's instructions


title: c-kit positive mast cell progenitors_rep3

description: microRNA profiling of magnetically separated c-kit-positive cells derived from bone marrow cell culture at day 6 in the presence of IL3 and SCF

source_name: separated c-kit+ cells from in vitro differentiating culture

value: c-kit+ mast cell progenitors


title: DLBCL006

description: No additional information


title: DLBCL008

description: No additional information


title: DLBCL005

description: No additional information


title: MMC_rep1


title: Wild-Type, Young_a7_1072

description: Wild-Type, Young_a7_1072


title: Wild-Type, Young_a7_1070

description: Wild-Type, Young_a7_1070


title: Wild-Type, Young_a7_1068

description: Wild-Type, Young_a7_1068


title: AML sample #36


title: AML sample #29


title: c-kit positive mast cell progenitors_rep1


title: DLBCL004

description: No additional information


title: AML sample #27


title: DLBCL003

description: No additional information


title: AML sample #25


title: Whole-genome transcriptional profile in Streptococcus mutans strain UA159 (covR mutant, sample #1)

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

description:
covR mutant of Streptococcus mutans strain UA159
The whole procedure of RNA labeling, hybridization and detection has been previously published in NimbleGen Arrays User’s Guide

hyb_protocol: Hybridization protocol was done according to the NimbleGen Arrays User's Guide

scan_protocol: Scan protocol was done according to the NimbleGen Arrays User's Guide

data_processing: Data processing was done according to the NimbleGen Arrays User's Guide

organism: Streptococcus mutans

source_name: Streptococcus mutans strain UA159 (covR mutant)

label_protocol: The probe was labeled according to the NimbleGen Arrays User's Guide

growth_protocol: The Streptococcus mutans was grown in Todd-Hewitt medium (BBL, Becton Dickinson) supplemented with 0.2% yeast extract (THY)

extract_protocol: RNA extraction was performed as described by Biswas et al. 2007. Regulation of gbpC expression in Streptococcus mutans. J. Bacteriol. 189:6521-6531

tag: genotype

value: covR mutant


title: adult 10 week old, biological rep 1, WT

city: Berlin

first: Thomas

middle: E

last: Willnow

state: Berlin

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

description: gene expression profile from adult kidney

hyb_protocol: Following fragmentation the Eukaryotic Target Hybridization protocol from Affymetrix was used.

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

data_processing: The data were analysed using R/Bioconductor and normalized using the RMA function with the “fast” option disabled.

source_name: adult kidney

label_protocol: Biotinylated cRNA were prepared according to the standart protocol from Affymetrix (1999-2004) Synthesis of Biotin-labeled cRNA for both the One-Cycle and Two-Cycle Targeting labeling assay.

extract_protocol: Trizol extraction of total RNA followewd by Proteinase K digestion and purification using the RNeasy-Mini-Kit from Qiagen.

value: kidney

tag: developmental stage

value: adult

value: 10 weeks

value: male

tag: genome/variation

value: wild type


title: adult 10 week old, biological rep 3, WT


title: adult 10 week old, biological rep 2, WT


title: DLBCL002

description: No additional information


title: Whole-genome transcriptional profile in Streptococcus mutans strain UA159 (sample #1)

description:
The human pathogen Streptococcus mutans is a gram-positive bacterium that residues in the oral cavity and is considered to be the primary etiological agent in the formation of dental caries
The whole procedure of RNA labelling, hybridization and detection has been previously published in NimbleGen Arrays User's Guide

source_name: Streptococcus mutans strain UA159

growth_protocol: The Streptococcus mutans was grown in Todd-Hewitt medium (BBL; Becton Dickinson) supplemented with 0.2% yeast extract (THY)

value: wildtype


title: DLBCL_012

description: As per manufacturer's instructions


title: DLBCL010

description: No additional information


title: Wild-Type, Aged_a7_744

description: Wild-Type, Aged_a7_744

tag: strain


title: CLL011

description: No additional information.

hyb_protocol: According to manufacturer's protocol.

scan_protocol: According to manufacturer's protocol.

data_processing: DNA copy number was calculated using GeneChip Genotype Analysis Software (Affymetrix) and the associated Copy Number Analysis Tool (CNAT Version 4.0).

source_name: Peripheral Blood B-cell

label_protocol: According to manufacturer's protocol.

extract_protocol: Lymphocytes were enriched from whole-blood by density-gradient centrifugation using ACCUSPIN™ system HISTOPAQUE®-1077 columns (Sigma-Aldrich) according to the manufacturer’s protocol. B-cells were isolated from lymphocyte enrichments using Dynabeads® CD19 (Invitrogen) and a magnetic particle concentrator according to the manufacturer’s protocol. Extractions were performed as in Green et al. (Leuk. Res. 2009;33:731-734)

value: Chronic Lymphocytic Leukemia


title: adult 10 week old, biological rep 3, TG

tag: tissue

value: expressing the intracellular domain of megalin


title: adult 10 week old, biological rep 2, TG


title: BMMC_rep2

value: Balb/c


title: adult 10 week old, biological rep 1, TG

value: expressing the soluble intracellular domain of megalin


title: Macrophage Kdo2 for 6h with siMLL Expression

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Macrophage Expression in response to Kdo2 for 6 hours and to siRNA against MLL

data_processing: quantile normalized using Illumina Inc. BeadStudio version 1.5.1.3

extract_protocol: Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer .

tag: cell type

tag: treatment


title: CLL010

description: No additional information.


title: AML sample #21

value: AML-NOS

value: AML-NOS plus AML-MLD-sole


title: BT15337

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on custom Affymetrix GeneChip GPL11169. 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 with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Bacteroides thetaiotaomicron

source_name: chuR mutant bacteria from C57BL/6 mouse cecum fed plant-rich diet

label_protocol: Biotin-UDP end labeling.

extract_protocol: Phenol/chloroform bead-beating on cecal contents, Qiagen RNAEasy extraction, Ambicon DNAEasy treatment; Final Qiagen RNAEasy cleanup.

treatment_protocol: Total RNA was extracted directly from cecal contents that contained only wild-type or mutant B. thetaiotaomicron.

value: chuR mutant

tag: isolation source

value: cecum of C57BL/6 mouse fed plant-rich diet


title: Macrophage Kdo2 for 6h with siCtrl Expression

description: Macrophage Expression in response to Kdo2 for 6 hours and to scrambled siRNA

value: Kdo2 for 6 hours and to scrambled siRNA


title: c-kit positive mast cell progenitors_rep2

value: c-kit+ mast cell progenitors


title: AML sample #20

city: New York

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.22.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.


title: AML sample #28

value: not included

value: AML-MRC


title: CLL008

description: No additional information.


title: CLL007

description: No additional information.


title: Wild-Type, Young_a7_1058

description: Wild-Type, Young_a7_1058

value: Wild-Type

tag: age

value: 8 weeks


title: Macrophage Ctrl with siCtrl Expression

description: Macrophage Expression in response to scrambled siRNA

value: scrambled siRNA


title: AML sample #26


title: BT15335


title: Whole-genome transcriptional profile in Streptococcus mutans strain UA159 (covR mutant, sample #2)

value: covR mutant


title: AML sample #18


title: AML sample #19


title: CLL005

description: No additional information.


title: CLL003

description: No additional information.


title: Whole-genome transcriptional profile in Streptococcus mutans strain UA159 (sample #2)

description:
The human pathogen Streptococcus mutans is a gram-positive bacterium that residues in the oral cavity and is considered to be the primary etiological agent in the formation of dental caries
The whole procedure of RNA labeling, hybridization and detection has been previously published in NimbleGen Arrays User’s Guide

value: wildtype


title: BT15333

source_name: wild-type bacteria from C57BL/6 mouse cecum fed plant-rich diet

value: wild-type


title: AML sample #17


title: BT15332


title: AML sample #24


title: Macrophage Ctrl with siMLL Expression rep1

description: Macrophage Expression in response to siRNA against MLL

value: siRNA against MLL


title: Wild-Type, Aged_a7_758

description: Wild-Type, Aged_a7_758

value: 2 years


title: CLL002

description: No additional information.

value: Chronic Lymphocytic Leukemia


title: CLL012

description: No additional information.


title: DLBCL001

description: No additional information

source_name: Tumor tissue

value: Diffuse Large B-cell Lymphoma


title: AML sample #23

value: AML-MLD-sole

value: AML-NOS plus AML-MLD-sole


title: AML sample #22


title: BT15331

source_name: chuR mutant bacteria from C57BL/6 mouse cecum fed simple sugar diet

value: chuR mutant

value: cecum of C57BL/6 mouse fed simple sugar diet


title: c-kit positive mast cell progenitors_rep4

value: Balb/c

value: c-kit+ mast cell progenitors


title: CLL009

description: No additional information.


title: Mulberry-5

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

description: gene expression data from liver of rat fed a high-fat diet with mulberry leaves

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using statistical language R and MAS 5.0 software in Affy package.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual) from 2 ug total RNA.

extract_protocol: RNAiso extraction (Takara Bio) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rats fed a high-fat diet were orally administrated dried mulberry leaf powder suspended in 0.5% carboxymethylcellulose at 0 or 500 mg/kg body weight/day. The administration was performed on a 6 weekly basis by gastric probe after fasting overnight. After 7 weeks, rats were anesthetized and killed by exsanguination. Parts of liver of each rat was taken and immediately immersed in RNAlater (Applied Biosystems).

value: Wistar/ST


title: BT15336

value: cecum of C57BL/6 mouse fed plant-rich diet


title: CLL001

first: Michael

description: No additional information.


title: Macrophage Ctrl with siGABP Expression

description: Macrophage Expression in response to siRNA against GABP

value: siRNA against GABP


title: myocyte_serum containing media_adeno-bGal_sample1

city: cincinnati

first: izhak

last: kehat

state: OH

address: 3333 burnet ave

institute: CCHMC

description: Gene expression data from cardiomyocytes in 10% serum containing media, infected with adeno-beta-galactosidase

hyb_protocol: Hybridization cocktail for a single probe array contained 2.5 ?g of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer.  GeneChip Rat Gene 1.0 ST Array– Affymetrix was hybridized at 45?C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix)

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

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

source_name: Primary culture of neonatal rat ventricular cardiomyocytes, serum containing media

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum.  Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with culture media containing 10% fetal calf serum, infected with adenovirus encoding for beta-Galactosidase and grown for 48 hrs.

value: Neonatal cardiomyocytes


title: Macrophage Kdo2 for 6h with siGABP Expression

description: Macrophage Expression in response to Kdo2 for 6 hours and to siRNA against GABP


title: BT15330


title: myocyte_serum containing media_adeno-HD4_sample1

description: Gene expression data from cardiomyocytes in 10% serum containing media, infected with adeno-HDAC4

treatment_protocol: Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum.  Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with culture media containing 10% fetal calf serum, infected with adenovirus encoding for HDAC4 and grown for 48 hrs.


title: Mulberry-4

source_name: liver of rat fed a high-fat diet with mulberry leaves


title: BT15334


title: Mulberry-1


title: myocyte_serum containing media_adeno-bGal_sample2


title: myocyte_serum free media_adeno-HD4_sample1

description: Gene expression data from cardiomyocytes in serum free media, infected with adeno-HDAC4

source_name: Primary culture of neonatal rat ventricular cardiomyocytes, serum free media

treatment_protocol: Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum.  Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with serum free culture media, infected with adenovirus encoding for HDAC4 and grown for 48 hrs.


title: BT15329


title: Macrophage Ctrl with siMLL Expression rep2


title: AML sample #16

source_name: mononuclear cells after Ficoll purification

value: not included

value: AML-MRC


title: CLL006

description: No additional information.


title: myocyte_serum free media_adeno-HD4_sample2


title: BT15326

source_name: wild-type bacteria from C57BL/6 mouse cecum fed simple sugar diet

value: wild-type


title: Macrophage Ctrl with siMLL Expression rep3

value: siRNA against MLL


title: AML sample #32


title: myocyte_serum free media_adeno-bGal_sample2

description: Gene expression data from cardiomyocytes in serum free media, infected with adeno-beta-galactosidase

treatment_protocol: Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum.  Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with serum free culture media, infected with adenovirus encoding for beta galactosidase and grown for 48 hrs.


title: myocyte_serum containing media_adeno-HD4_sample2


title: cell25_not stim._90min_rep3

city: Munich

first: Wolfgang

last: Hammerschmidt

address: Marchioninistr. 25

department: Gene Vectors

institute: Helmholtz Zentrum München

description: This sample is of the lymphoblastoid cell line 2525. It is the third of three technical replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

scan_protocol: Scanning was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

data_processing: The raw .call data was subjected to Multi-Lowess normalization.

source_name: human lymphoblastoid cell line 2525 BCR not stimulated

label_protocol: Labeling was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

growth_protocol: LCLs 2525 and 3696.10 were cultivated in RPMI-1640 media supplemented with 10% fetal bovine serum, penicillin (100U/ml), streptomycin (100μg/ml), sodium selenit (100nM), sodium pyruvate (1mM), bathocuproinedisulfonic acid (40nM) and 0.87‰ α-thioglycerol

extract_protocol: Total RNA was extracted, using the RNeasy mini Kit (Qiagen), followed by DNase digest for 90min at 37°C; mRNA was transcribed into cDNA by NimbleGen

treatment_protocol: Cells were seeded at 10^7 per 3ml and left untreated or stimulated for 90 min; BCR stimulation: 25ug/ml goat-anti-human IgG/M (dianova); LMP2A:mCD69 stimulation: 1ug/ml armenian hamster-anti-murineCD69 + 5ug/ml goat-anti-armenian hamster IgG (dianova)

value: primary human b cells infected with EBV mutant 2525

value: wtLMP2A knockout


title: BT15327


title: cell25_stimulated_90min_rep3

source_name: human lymphoblastoid cell line 2525 BCR stimulated for 90 min


title: Control-3

description: gene expression data from liver of rat fed a high-fat diet without mulberry leaves


title: Control-1

source_name: liver of rat fed a high-fat diet without mulberry leaves


title: Mulberry-3


title: BT15328


title: Control-5


title: 900_24_3

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the University Hospital Muenster IFG Microarray Core Facility.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G was used.

data_processing: Data were processed using XRAY software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized and log transformed.

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.9

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Rat primary cultured inner medullary collecting duct cells cultivated at different osmolalities

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Treated with 5 µM Cyclosporin A for 24h as indicated.

value: Renal inner medulla

value: collecting duct cells

tag: culture condition

value: 600 mosmol/kg

tag: treatment group

value: challenged for 24h with 900 mosmol/kg


title: Mulberry-2