title: RPE , replicate 1

description:
(7) (RPE 1)
Slide 7
present call rate per slide: 0.599664991624791
Hy3 raw: 1_Exiqon_13973496_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973496_S01_Cropped.txt

source_name: Total RNA from RPE of adult mice (RPE 1)


title: infected vs uninfected late time point 2, dye swap

status: Public on Nov 22 2010

type: RNA

city: Pretoria

first: Dave

middle: K

last: Berger

state: Gauteng

address: Room 6-26, Agricultural Sciences Building, University of Pretoria, Lunnon Rd

department: Plant Science, Forestry & Agricultural Biotech. Instit. (FABI)

country: South Africa

institute: University of Pretoria

hyb_protocol: Probes were prepared by combining selected Cy3 and Cy5 labelled samples, which were then dried in a vacuum desiccator, and resuspended in 45 µl hybridisation buffer [50% formamide, 25% hybridisation buffer (Amersham Biosciences), 25% deionised water].  Probes were denatured at 92ºC for 5 min.The glass slide was initially incubated in pretreatment solution (3.5X SSC; 0.2% SDS; 1% bovine serum albumin) without probe at 60ºC for 20 min.  Thereafter, the slide was placed in a HybUP hybridisation chamber (NB Engineering, Pretoria, South Africa) with the denatured probe solution at 42ºC for 16 h.  After hybridisation, slides were washed for 4 min at 42ºC with 1 X SSC/0.2% SDS, 0.1 X SSC/0.2% SDS (twice) followed by three washes in 0.1 X SSC for 1 min at room temperature.  Slides were rinsed with distilled water, and dried by centrifugation (2000Xg for 2 min).

scan_protocol: Washed slides were scanned with a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA, USA).  Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: Scanned images (tiff images) were imported into GenePix Pro 5.0 (Axon Instruments), and fluorescence intensity in both red (CyanineTM-5 dye) and green (CyanineTM-3 dye) channels for each spot was quantified.  Grids were predefined and manually adjusted to ensure optimal spot recognition, and spots with dust or locally high background were flagged as bad.  Fluorescence data from a total of 12 slides were imported into limmaGUI (linear models for microarray data Graphical User Interface) (Wettenhall and Smyth, 2004) in the R computing environment where data was normalised (within array global loess normalisation and between array quantile normalisation), and linear models were fitted in order to contrast post treatment expression values with the non-treated sample (time = 0 h). Differentially expressed genes for each treatment were defined as those with a fold-change (expression ratio) greater than or equal to two between a particular time point and t=0, and were significant at P ≤ 0.05 (moderated t test as implemented in limmaGUI with Bonferonni correction for multiple testing (Wettenhall and Smyth 2004).

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Uninfected leaf, wilt symptom 3-4

label_protocol: 500ng mRNA was used per labelling reaction using the Amersham indirect labeling kit according to manufacturer's protocol. The samples were purified using the Qiagen PCR purification kit.

growth_protocol: Arabidopsis Col-5 seeds were sterilised in 1.5% sodium hypochlorite and 70% ethanol and germinated on MS media for two weeks before planting into Jiffy pots. Plants were maintained in control conditions and grown for four weeks under 16hr light, 25-26 deg C, 50% relative humidity and 300-350lum/sqf. Plants were watered with Feedall fertiliser once a week.

extract_protocol: Total RNA was isolated from leaves using TriReagent (Sigma, Aldrich) according to the manufacturer's instructions.  mRNA was isolated using the OligoTex mRNA isolation Kit (Qiagen).

treatment_protocol: Infections were preformed according to Deslandes et al. 1998. Jiffy pots were cut in half to expose the roots and soaked in a 1E08 cfu/ml of R. solanacearum BCCF401. Control plants were treated with media only. Plants were maintained on vermiculite and disease symproms post inoculation were recorded.

tag: infection

tag: ecotype

source_name: Infected leaf, wilt symptom 3-4

value: Ralstonia solanacearum isolate BCCF401


title: RETINA, replicate 1

city: Naples

first: Marianthi

last: Karali

address: Via Pietro Castellino, 111

country: Italy

institute: Telethon Institute for Genetics & Medicine (TIGEM)

description:
(1) (RETINA 1)
Slide 1
present call rate per slide: 0.624790619765494
Hy3 raw: 1_Exiqon_13973490_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973490_S01_Cropped.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Project_Summary Report version 3.5 results presented in Sample data tables.
When calling of a particular miRNA failed on an array this is indicated by the acronym null. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software. Further, all capture probes with Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide is indicated by the acronym null.

organism: Mus musculus

source_name: Total RNA from retinas of adult mice (RETINA 1)

label_protocol: One µg total RNA from sample and reference (Eye sample) was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: not applicable

extract_protocol: Total RNA extracted with the miRNeasy kit (Qiagen)

treatment_protocol: not applicable

tag: tissue

value: Retina

tag: strain

source_name: Total RNA from entire eyeballs from adult mice

value: Entire Eyeball


title: RETINA, replicate 2

description:
(2) (RETINA 2)
Slide 2
present call rate per slide: 0.638190954773869
Hy3 raw: 1_Exiqon_13973491_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973491_S01_Cropped.txt

source_name: Total RNA from retinas of adult mice (RETINA 2)


title: CORNEA, replicate 1

description:
(5) (CORNEA 1)
Slide 5
present call rate per slide: 0.611390284757119
Hy3 raw: 1_Exiqon_13973494_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973494_S01_Cropped.txt

source_name: Total RNA from corneas of adult mice (CORNEA 1)

value: Cornea


title: LENS, replicate 2

description:
(4) (LENS 2)
Slide 4
present call rate per slide: 0.644891122278057
Hy3 raw: 1_Exiqon_13973493_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973493_S01_Cropped.txt

source_name: Total RNA from lenses of adult mice (LENS 2)

value: Lens


title: CORNEA, replicate 2

description:
(6) (CORNEA 2)
Slide 6
present call rate per slide: 0.574539363484087
Hy3 raw: 1_Exiqon_13973495_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973495_S01_Cropped.txt

source_name: Total RNA from corneas of adult mice (CORNEA 2)


title: infected vs uninfected early time point 1

source_name: Uninfected leaf, wilt symptom 1-2

source_name: Infected leaf, wilt symptom 1-2


title: CD8 KLF13 KO 1

status: Public on Nov 23 2010

city: Bethesda

first: Dazhi

last: Lai

state: MD

address: 10 Center Dr, 7B20A

department: NHLBI

country: USA

institute: NIH

hyb_protocol: Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse Gene ST 1.0 GeneChip

scan_protocol: scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix GCOS software.

data_processing: Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.  Significant genes were analyzed for enrichment for pathways using DAVID bioinformatics database (http://david.abcc.ncifcrf.gov/) and Ingenuity Pathway Analysis software.

label: biotin

source_name: CD8 KLF13 KO

label_protocol: 200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer's protocol.

extract_protocol: Total RNA was isolated with RNAeasy kit from Qiagen RNeasy. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

value: BALB/c

tag: cell type

value: CD8 T

tag: genotype/variation

value: KLF13 KO


title: LENS, replicate 1

description:
(3) (LENS 1)
Slide 3
present call rate per slide: 0.611390284757119
Hy3 raw: 1_Exiqon_13973492_S01_Cropped.txt
Hy5 raw: 0_Exiqon_13973492_S01_Cropped.txt

source_name: Total RNA from lenses of adult mice (LENS 1)


title: CD8 KLF13 KO 2


title: ApoB, 17063  B6-Ldlr(tm1)Tg(APOA1-CETP)#18

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: C57Bl6 or B6-Ldlr(tm1)Tg(APOA1-CETP) treated with control PBS or two oligoes against apoB, 17063 or 17068

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: Liver

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cDNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: sample type

value: liver

tag: treatment

tag: genotype


title: Cells treated with BSA

type: other

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

hyb_protocol: The hybridization is performed under LifterSlipTM(Erie Company).The hybridization is performed at 42C overnight.

scan_protocol: Array scanning is performed with a confocal LuxScanTM scanner(CapitalBio Corp).

data_processing: Data analysis from the obtained TIFF images is performed using SpotDataTM Pro software (CapitalBio Corp). Hybridization intensity values from individual samples were then filtered and normalized to per-chip mean values. We considered candidate miRNAs with a signal above 500 to be positive.

molecule: other

organism: Homo sapiens

source_name: THP-1 Cell

label_protocol: The T4 RNA ligase labeling method of Thomson was used.

growth_protocol: THP-1 cells were  grown in RPMI1640 supplemented with fetal bovine serum,penicillin (100 U/ml), and streptomycin (100 mg/ml) at 37 ◦C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: 50μg total RNA purified using the mirVANA miRNA Isolation Kit (Applied Biosystems, Foster City, CA) was labeled with fluorescein and hybridization was carried out on miRNA microarray chips.

treatment_protocol: THP-1 cells were treated with AGEs-BSA (AGEs) at 2mg/ml for 6h . Cells treated with BSA of the same concentration and time served as controls.

tag: stimulation

value: BSA


title: PBS, C57B6L6#25

value: PBS


title: ApoB, 17063  B6-Ldlr(tm1)Tg(APOA1-CETP)#16


title: ApoB, 17068  C57BL6#35


title: Cells Treated with AGE-BSA

value: AGE-BSA


title: HTHY5 (sham/saline)

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Sham Surgery (control animals)

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 followed by purification of mRNA using Qiagen purification kit.

treatment_protocol: Female mice were anesthetized with 200 mg/kg ketamine (Ketalean, 100mg/ml, Bimeda-MTC Animal Health Inc., Cambridge, Ontario, Canada) and 10 mg/kg xylazine hydrochloride (Rompun 20mg/ml, Bayer Inc. Toronto, Ontario, Canada) by intraperitoneal injection (i.p.).  The mice were positioned in dorsal recumbency, and the ventrums were shaved and prepared with 70% ethanol.  A ventral midline incision (~1 cm) was made to allow exteriorization of the cecum.  The cecum was ligated 1 cm from the apex with 3-0 silk suture, and penetrated through-and-through with a 22-gauge needle.  The abdominal incision was then closed in two layers with 4**â?¬â?*0 nylon suture. Injection of saline or MSCs was administrated 6 hours after animals had undergone the CLP procedure to induce sepsis.  Mice were anaesthetized by induction of xylazine and ketamine through intraperitoneal injection.  The jugular vein of each mouse was exposed by blunt dissection followed by insertion of a small canula (PE10) into the vein.  Saline or cultured male MSCs (at 2.5 x 105 cells, 100 mL total volume) was slowly infused via the inserted canula 6 hours following sham-operation or CLP.  Sham surgery, in which the cecum was exteriorized and manipulated as described but not ligated or punctured, was performed in control animals.

value: Spleen

tag: gender

value: female


title: BME_Stat_rep4

type: mixed

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

description: Biological replicate 4 of 4. Total RNA from BME at stationary phase co-hybridized against BME gDNA.

hyb_protocol: Prior to hybridization, oligo-arrays were pretreated by washing in 0.2% SDS, followed by 3 washes in distilled water and immersed in pre-hybridization buffer [5X SSC, 0.1% SDS; 1% BSA in 100ml of water] at 45ºC for at least 45 min. Immediately before hybridization, the slides were washed 4 times in distilled water, dipped in 100% isopropanol for 10 sec and dried by centrifugation at 1,000X g for 2 min.  Dried, labeled cDNA samples were re-suspended in nuclease–free water and mixed with 0.5 μg of labeled gDNA to the final volume of 35 µl. Samples were heated at 95ºC for 5 min and then kept at 45ºC until hybridization. Following incubation at 45ºC, 35 μl of 2X formamide-based hybridization buffer [50% formamide; 10X SSC; 0.2% SDS] was added to each sample, well mixed and applied to a custom 3.2K B. melitensis oligo-arrays. Four slides for each condition (i.e. late-log and stationary growth phase) were hybridized at 45ºC for ~20 h in a dark, humid chamber (Corning) and then washed for 10 min at 45ºC with low stringency buffer [1X SSC, 0.2% SDS] followed by two 5-min washes in a higher stringency buffer [0.1X SSC, 0.2% SDS and 0.1X SSC] at room temperature with agitation. Slides were dried by centrifugation at 800X g for 2 min and immediately scanned.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). The genes represented on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePixPro 4.0; Axon Instruments Inc.).

data_processing: Genes with fluorescent signal values below background were disregarded in all analyses. Data were analyzed using GeneSpring 7.0 (Silicon Genetics, Redwood City, CA), Significance Analysis of Microarrays (SAM) (Stanford University, Stanford, CA) and Spotfire DecisionSite 8.2 (Spotfire, Inc., Somerville, MA). Computational hierarchical cluster analysis and analysis of variance (ANOVA) were performed using Spotfire DecisionSite 8.2. ANOVA was also performed, as an additional filtering aid, using GeneSpring. For each software program used, data were first normalized by either mean (for Spotfire pairwise comparisons and SAM two-class comparisons) or percentile value (for GeneSpring analyses). Normalizations against genomic DNA were performed as described by Talaat et al. (2002).

organism: Brucella melitensis

source_name: Total RNA from Brucella melitensis 16M at stationary phase of growth labeled with Cyanine-3 (green).

label_protocol: Ten μg of B. melitensis 16M total RNA were reverse transcribed overnight to amino-allyl cDNA using 6 mg of random hexamer primers (Invitrogen), 0.6 μl 50X dNTPs (Invitrogen) / aa-dUTP (Ambion) mix (2:3 aa-dUTP:dTTP) and 400U Superscript III (Invitrogen). The reaction was stopped by incubating the samples with 1M NaOH at 65ºC for 15 min and neutralized by adding 1M HCl. Unincorparated aa-dUTPs and free amines were removed by column passage. Speedvac-dried samples were rehydrated in 0.1M Na2CO3 buffer (pH 9.0) and labeled with Cy3-ester (Amersham Pharmacia Biosciences). After one hour incubation in the dark, uncoupled dye was removed using columns (Qiagen) and Cy3 incorporation calculated by NanoDrop® ND-1000 (NanoDrop). B. melitensis genomic DNA was labeled overnight by directed incorporation of Cy5-dCTP (Amersham Pharmacia Biosciences, Piscataway, NJ) during reverse transcription using random primers solution and Klenow fragment from BioPrime DNA labeling system kit (Invitrogen) and 50X dNTPs (1:2 dCTP) (Invitrogen). The reaction was stopped by adding 5 μl of stop buffer from the BioPrime kit and unincorporated Cy dye was removed using PCR purification kit (Qiagen), eluted in 1mM Tris pH 8.0 and kept in the dark at 4ºC until used.

growth_protocol: Smooth virulent Brucella melitensis 16M Biotype 1 (ATCC 23456) (American Type Culture Collection, Manassas, VA), re-isolated from an aborted goat fetus and its derivatives were maintained as frozen glycerol stocks.  Individual 50 ml conical tubes were filled with 10 ml of cell culture media [F12K medium (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (ATCC)], inoculated with 0.25 ml (1:40 for late-log cultures) and 1 ml (1:10 for stationary cultures) of a saturated culture of B. melitensis 16M and incubated at 37ºC with 5% CO2 overnight with loose lids and 200 rpm shaking. Growth curves of cultures were determined by comparing the optical density (OD) of the culture at 600nm with bacterial colony forming units (CFU). Bacterial numbers were assessed by plating a serial dilution on tryptic soy agar (TSA) (BD, Franklin Lakes, NJ) and incubating at 37ºC with 5% CO2 for 4 days.

extract_protocol: Total RNA was isolated by adding ice-cold ethanol/phenol solution to the B. melitensis culture and the bacteria recovered by centrifugation. The media was then removed and the pellet suspended in TE buffer–lysozyme solution containing 10% SDS. After 2 min of incubation, acid water-saturated phenol was added to the lysate and mixed, and the sample incubated for 6 min at 64ºC. Tubes were kept on ice for at least 2 min and then centrifuged at maximum speed. The upper layer, containing the RNA, was transferred to a new tube, mixed with an equal volume of chloroform and then separated by centrifugation. The aqueous phase was mixed with 100% cold ethanol and stored at -20ºC. After at least one hour of incubation, RNA was pelleted by centrifugation, washed in 80% ethanol and suspended in DEPC-treated water with 2% DTT and 1% RNase inhibitor. Contaminant genomic DNA was removed by RNase-free DNase I treatment and samples were stored at -80ºC until used.  Genomic DNA was isolated from a pellet from a saturated culture of B. melitensis 16M grown on tryptic soy broth (TSB), washed with 25 ml of J-buffer [0.1M Tris pH 8.0; 0.1M EDTA; 0.15M NaCl] and then lysed in 1 ml of J-buffer containing 10% lysozyme solution (10mg/ml in 0.25M Tris, pH 8.0). After 10 min of incubation, DNA was released from the cells by sodium salt of N-lauroyl sarcosine followed by degradation of RNA by DNase-free RNase, and digestion of proteins with proteinase K. The resulting solution was transferred to a dialysis bag and dialyzed against TE [10mM Tris, pH 8.0 and 1mM EDTA] overnight at 37ºC. DNA was subsequently extracted twice using neutral water-saturated phenol first and then twice with ether before dialyzing overnight against TE. Genomic DNA was stored at 4ºC until used.

tag: Strain

value: 16M Biotype 1 (ATCC 23456)

tag: Stationary growth phase

molecule: genomic DNA

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cyanine-5 (red).


title: ApoB, 17063  C57BL6#37


title: BME_Stat_rep2

description: Biological replicate 2 of 4. Total RNA from BME at stationary phase co-hybridized against BME gDNA.


title: BME_Stat_rep3

description: Biological replicate 3 of 4. Total RNA from BME at stationary phase co-hybridized against BME gDNA.


title: BME_Stat_rep1

description: Biological replicate 1 of 4. Total RNA from BME at stationary phase co-hybridized against BME gDNA.


title: BME_Log_rep4

description: Biological replicate 4 of 4. Total RNA from BME at late log phase co-hybridized against BME gDNA.

source_name: Total RNA from Brucella melitensis 16M at late log phase of growth labeled with Cyanine-3 (green).

tag: Late log growth phase


title: HTHY4 (sham/saline)


title: ApoB, 17068  B6-Ldlr(tm1)Tg(APOA1-CETP)#11


title: ApoB, 17068  C57BL6#33


title: MSC8 (CLP/MSC)

source_name: Cecal-Ligation-and-Puncture (CLP) Model of Sepsis + MSC administration


title: heat stressed caryopses at T 5:00 PM, biological rep1

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

country: Germany

institute: University of Tuebingen

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 5:00 PM; 3 h after start of experiment, 11 h after onset of light; continuously heat treated

hyb_protocol: After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 13.5µg of cRNA was hybridized to Affymetrix Barley1 GeneChips (GEO accsession GPL1340) according to manufacturers manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturers manual.

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 200.

organism: Hordeum vulgare

source_name: Barley caryopses

label_protocol: 1µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Amplification Kit; Ambion).

growth_protocol: Barley plants were grown in the green house in 10 cm pots in soil with additional lighting from Xenon light bulbs (15h light [6:00 AM - 9:00 PM], 9h dark [9:00 PM - 6:00 AM]; ~24°C; 40% rel. Humidity, October 2006)

extract_protocol: 100mg of pooled homogenized plant material was mixed with 900µl of sarcosyl buffer (1% sodium lauryl sarcosinate, 0.1M Tris-HCl pH 7.5, 0.1M NaCl, 20mM EDTA, 50mM beta-mercaptoethanol) and purification of nucleic acids was done by three steps of phenol-chloroform-isoamylalcohol (25:24:1) extractions. Precipitation of nucleic acids was performed with sodium acetate (pH 5.2) and 1 volume isopropanol. After centrifugation, sediment was washed with ethanol and purified RNA was dissolved in DEPC treated water. Incubation at 65°C for 5min, followed by centrifugation at 4°C was performed to remove residual high molecular weight polysaccharides. The obtained RNA solution was purified following the RNeasy (Quiagen) clean up protocol. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).

treatment_protocol: For heat exposure, half of the plants were moved into a custom-made acrylic (perspex) glass cabinet with a constantly elevated temperature of 42°C, whereas the control plants were kept at normal temperature. To avoid an interference with drought stress, both control and heat stressed plants were sufficiently watered prior to the experiment. For both control and heat-treated samples, pooled caryopses (form 3 plants) from the respective time points were used for RNA extraction and hybridization on Affymetrix microarrays (Barley1 GeneChip; GEO accsession GPL1340). Biological replicates were performed.

value: whole carypses from the mid region of the spike, awns removed

value: Hordeum vulgare cultivar 'Golden Promise'

tag: age

value: 11 to 12 days after anthesis


title: MSC7 (CLP/MSC)


title: heat stressed caryopses at T 2:00 PM, biological rep2

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 2:00 PM; 0.5 h after start of experiment, 8 h after onset of light; continuously heat treated


title: heat stressed caryopses at T 8:00 PM, biological rep2

description: Gene expression data from developing Barley caryopses 12 days after anthesis, at 8:00 PM; 6 h after start of experiment, 1 hr before turn off the light; continuously heat treated


title: CLP10 (CLP/saline)

source_name: Cecal-Ligation-and-Puncture (CLP) Model of Sepsis + saline administration


title: PBS, C57B6L6#21


title: heat stressed caryopses at T 8:00 PM, biological rep1


title: CLP8 (CLP/saline)


title: HTHY3 (sham/saline)


title: BME_Log_rep3

description: Biological replicate 3 of 4. Total RNA from BME at late log phase co-hybridized against BME gDNA.


title: PBS, C57B6L6#24


title: BME_Log_rep2

description: Biological replicate 2 of 4. Total RNA from BME at late log phase co-hybridized against BME gDNA.


title: HTHY1 (sham/saline)


title: ApoB, 17063  B6-Ldlr(tm1)Tg(APOA1-CETP)#19


title: ApoB, 17068  C57BL6#32


title: MSC5 (CLP/MSC)


title: heat stressed caryopses at T 5:00 PM, biological rep2


title: BME_Log_rep1

description: Biological replicate 1 of 4. Total RNA from BME at late log phase co-hybridized against BME gDNA.


title: ApoB, 17063  C57BL6#39


title: heat stressed caryopses at T 2:00 PM, biological rep1


title: ApoB, 17063  C57BL6#40


title: PBS, B6-Ldlr(tm1)Tg(APOA1-CETP)#5

value: PBS, B6-Ldlr(tm1)Tg(APOA1-CETP)#5


title: MSC4 (CLP/MSC)


title: CLP3 (CLP/saline)


title: lung 20.10

status: Public on Nov 21 2010

city: Cambridge

first: sarah

middle: louise

last: kempster

state: Cambridgeshire

address: Rosie Hospital, Robinson Way

department: obstetrics and gynaecology

country: United Kingdom

institute: university of cambrige

description: lung 20.10

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16hr at 45C on GeneChip Rat Genome 230 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: Data was analysed using RMA from R/Bioconductor, both lung and intestine array data was analysed together.

organism: Rattus norvegicus

source_name: whole lung embryo E20

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

growth_protocol: Timed mated wistar rats were euthanized by CO2 overdose. Pups were delivered by caesarean section, euthanized by cervical dislocation, and tissue removed under a dissecting microscope. Tissue from multiple siblings was snap frozen in liquid nitrogen prior to storage at -80ºC for subsequent RNA analysis.

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

tag: gestational age

value: lung

value: wistar


title: lung 20.2

description: lung 20.2


title: PBS, B6-Ldlr(tm1)Tg(APOA1-CETP)#3

value: PBS, B6-Ldlr(tm1)Tg(APOA1-CETP)#3


title: CLP2 (CLP/saline)


title: lung 20.6

description: lung 20.6


title: lung 20.4

description: lung 20.4


title: lung 20.9

description: lung 20.9


title: lung 20.8

description: lung 20.8


title: lung 20.7

description: lung 20.7


title: lung 16.9

description: lung 16.9

source_name: whole lung embryo E16


title: root_Fe_def_5d_2_2

type: genomic

city: Durham

first: Wolfgang

last: Busch

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

description: Wildtype control (no GFP) ChIP sample v PYE:GFP transcription factor ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis

hyb_protocol: Hybridization was performed according to the  Agilent Mammalian ChIP-on-chip Kit protocol

scan_protocol: Scanner G2565BA with protocoll CGH-v4_95_Feb07

data_processing: Signal extraction and initial data processing were done using the Agilent feature extraction software. Additional analysis as described in Long et al., 2010

label_protocol: DNA from the pye-1 / ProPYE:PYE:GFP and wildtype ChIPs were blunted using T4 DNA polymerase, cleaned up with the Qiagen Reaction Cleanup Kit, amplified with 22 PCR cycles, and subsequently cleaned up according to the Agilent Mammalian ChIP-on-chip Kit protocol. 2ug of DNA was fragmented, and labeled with Cyanine 3-dUTP, and Cyanine 5-dUTP according to the Agilent Mammalian ChIP-on-chip Kit protocol.

growth_protocol: pye-1 / ProPYE:PYE:GFP and wildtype lines were germinated and grown on iron deficient media for 5 days  as described in Long et. al. 2010

extract_protocol: Chromatin Immunoprecipitation as described in Long et. al. 2010

treatment_protocol: Whole root tissue was fixed as described in Long et. al. 2010

value: whole roots

tag: growth protocol

value: 5d on -Fe media grown seedlings

tag: antibody

value: anti-GFP

tag: antibody manufacturer

value: ABCAM

tag: antibody catalog #

tag: lot #

source_name: wt

value: wild type


title: lung 16.10

description: lung 16.10

tag: tissue

tag: strain


title: lung 16.7

description: lung 16.7


title: lung 16.2

description: lung 16.2


title: lung 16.5

description: lung 16.5


title: lung 20.5

description: lung 20.5


title: ApoB, 17068  B6-Ldlr(tm1)Tg(APOA1-CETP)#12

tag: sample type

value: liver


title: lung 20.3

description: lung 20.3


title: lung 16.1

description: lung 16.1


title: lung 16.6

description: lung 16.6


title: root_Fe_def_5d_2_1

description: PYE:GFP transcription factor ChIP sample v wildtype control (no GFP) ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis


title: lung 20.1

description: lung 20.1


title: ApoB, 17068  B6-Ldlr(tm1)Tg(APOA1-CETP)#13

tag: treatment


title: root_Fe_def_5d_1_2

tag: genotype


title: lung 16.8

description: lung 16.8


title: root_Fe_def_5d_1_1


title: lung 16.4

description: lung 16.4


title: intestine 16.10

description: intestine 16.10

source_name: whole intestine embryo E16

label_protocol: Biotinylated cRNA were prepared according to the standard One-Cycle Affymetrix protocol from 1ug of total RNA (GeneChip Expression Analysis Technical Manual 701021 Rev. 5 Affymetrix).

value: intestine


title: intestine 20.2

description: intestine 20.2

source_name: whole intestine embryo E20


title: intestine 20.3

description: intestine 20.3


title: intestine 20.9

description: intestine 20.9


title: lung 16.3

description: lung 16.3


title: intestine 16.9

description: intestine 16.9


title: intestine 20.4

description: intestine 20.4


title: a2NTD 24hr C

status: Public on Nov 20 2010

city: North Chicago

first: Kenneth

last: Beaman

state: IL

address: 3333 Green Bay Rd

department: Microbiology and Immunology

institute: Rosalind Franklin University of Medicine and Science

data_processing: The 2-ΔΔCt method was used calculate fold differences in gene expression in cells cultured with media versus cells cultured with a2NTD after normalization to five housekeeping genes.

source_name: THP-1 cells

growth_protocol: THP-1 cells were maintained at 2.0 - 7.5 x10E5 cells/ml in RPMI/10%FCS/1x antibiotic,antimycotic (Invitrogen) at 37°C with 5% CO2.

extract_protocol:
GenElute Mammalian Total RNA miniprep kit (RTN70) from Sigma. See manufacturer's website for protocol. http://www.sigmaaldrich.com/etc/medialib/docs/Sigma/Bulletin/1/rtn70bul.Par.0001.File.tmp/rtn70bul.pdf
cDNA protocol: Reverse transcription and cDNA synthesis was prepared via the RT2 first strand kit (SA Biosciences, Frederick, MD).
real-time PCR protocol: Equal concentrations of cDNA were loaded onto PCR arrays using SYBR green chemistry from SA Biosciences.  Arrays were run on an Applied Biosystems 7500 real-time PCR system (Foster City, CA).

treatment_protocol: THP-1 cells (0.5x10E6) were stimulated in media or with a2NTD (0.1ug/ml) for 2, 6, 12, and 24hr at 37°C.  At each time point, cells were washed twice in ice-cold PBS.  The cell pellet samples were flash frozen in a propanol/dry ice slurry.  Samples were saved at -80°C until time of RNA isolation.  Each experiment was done on three separate occcasions.

value: monocytic leukemia

tag: time

value: 24 hr


title: intestine 20.6

description: intestine 20.6


title: intestine 16.8

description: intestine 16.8


title: intestine 16.4

description: intestine 16.4


title: intestine 16.5

description: intestine 16.5


title: a2NTD 24hr B


title: intestine 20.8

description: intestine 20.8


title: intestine 20.10

description: intestine 20.10


title: Media 24hr A

value: media


title: Media 24hr B


title: Media 24hr C


title: a2NTD 24hr A


title: intestine 16.3

description: intestine 16.3


title: intestine 16.7

description: intestine 16.7


title: intestine 20.1

description: intestine 20.1


title: intestine 16.1

description: intestine 16.1


title: intestine 16.6

description: intestine 16.6


title: a2NTD 12hr C

value: 12 hr


title: intestine 20.5

description: intestine 20.5


title: a2NTD 12hr B


title: intestine 16.2

description: intestine 16.2


title: a2NTD 12hr A


title: Media 12hr A


title: Media 12hr B


title: Media 12hr C


title: a2NTD 6hr C

value: 6 hr


title: a2NTD 6hr B


title: Media 6hr B


title: Media 6hr A


title: Media 2hr A

value: 2 hr


title: Media 2hr B


title: Media 6hr C


title: a2NTD 6hr A


title: intestine 20.7

description: intestine 20.7


title: a2NTD 2hr A


title: Media 2hr C


title: a2NTD 2hr B


title: a2NTD 2hr C


title: WT1-Sox10_24h_rep2

city: SEOUL

first: IK JOO

last: SEONG

address: Seodeamungu Deahyundong

department: Life Science

country: South Korea

institute: Ewha woman university

label: Biotin

source_name: B16F10  cells

extract_protocol: RNA was extracted and 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.

value: melanoma

tag: cell line

tag: genotype/variation


title: MT1-Sox10_24h_ rep2


title: MT1-Sox10_24h_ rep3


title: WT1-Sox10_24h_rep3


title: MT1-Sox10_24h_ rep1


title: WT1-Sox10_24h_rep1


title: Transverse_Colon_3_09

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

hyb_protocol: Labeled samples were hybridized to the HEEBO array in 3x SSC at 65C 16 hours.

scan_protocol: HEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the Spotreader program (Niles Scientific, Portola Valley, CA. USA)

data_processing: Spot analysis was performed with Spotreader and stored in a relational database (Acuity).

source_name: Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Trizol reagent and Invitrogen Purelink RNA purification system

value: transverse colon biopsy

tag: disease state

source_name: Reference RNA from a pool of all 12 amplified RNA samples

label_protocol: RNA extracted from the 12 samples was amplified separately using Amino Allyl MessageAmp II aRNA kit from Ambion and then pooled. The pooled amplified material was then coupled to Cy3.

value: reference

value: colon biopsies


title: Sigmoid_Colon_3_09

source_name: Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

value: sigmoid colon biopsy


title: Ascending_Colon_2_09

source_name: Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

value: ascending colon biopsy


title: Sigmoid_Colon_2_09

value: ulcerative colitis patient infected with Trichuris trichiura


title: Ascending_Colon_1_09


title: Transverse_Colon_2_09


title: Ascending_Colon_4_09


title: Transverse_Colon_1_09


title: Terminal_Ileum_2_09

source_name: Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

value: terminal ileum biopsy


title: Ascending_Colon_3_09


title: Rectosigmoid_Colon_2_08

source_name: Amplified RNA from rectosigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

value: rectosigmoid colon biopsy


title: Sigmoid_Colon_1_09


title: RectoSigmoid_Colon_4_08


title: Transverse_Colon_3_08


title: Ascending_Colon_2_08


title: Rectosigmoid_Colon_1_08


title: Rectosigmoid_Colon_3_08


title: Transverse_Colon_2_08


title: Transverse_Colon_4_08


title: Ascending_Colon_1_08


title: Terminal_Ileum_1_09


title: Terminal_Ileum_1_07

source_name: Reference RNA from a pool of all 14 amplified RNA samples

label_protocol: RNA extracted from the 14 samples was amplified separately using Amino Allyl MessageAmp II aRNA kit from Ambion and then pooled. The pooled amplified material was then coupled to Cy3.


title: Sigmoid_Colon_2_07


title: Ascending_Colon_3_08


title: Sigmoid_Colon_4_07


title: Ascending_Colon_4_08


title: Terminal_Ileum_2_07


title: Transverse_Colon_1_08


title: Sigmoid_Colon_1_07


title: Rectum_2_07

source_name: Amplified RNA from rectum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura

value: rectum biopsy


title: Transverse_Colon_2_07


title: Transverse_Colon_1_07


title: Ascending_Colon_2_07


title: Sigmoid_Colon_3_07


title: Rectum_3_07


title: Ascending_Colon_3_07


title: DSS_14

source_name: Amplified RNA from whole blood from DSS individual

extract_protocol: PAXgene tubes and Qiagen PAXgene Blood RNA Kit.

value: whole blood

value: dengue shock syndrome

source_name: Amplified reference RNA from a pool of PBMCs of 5 healthy individuals

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy3.

value: blood

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

value: healthy


title: DSS_23


title: DHF_15

source_name: Amplified RNA from whole blood from DHF individual

value: dengue hemorrhagic fever


title: DSS_20


title: DSS_51


title: DSS_48


title: DHF_18


title: DSS_22


title: Rectum_1_07


title: Ascending_Colon_1_07


title: DHF_53


title: DSS_7


title: DHF_5


title: DHF_55


title: DF_49

source_name: Amplified RNA from whole blood from DF individual

value: dengue fever


title: DF_54


title: DHF_124


title: DSS_134


title: DF_261


title: DF_47


title: DF_263


title: DF_52


title: DF_257


title: DF_252


title: DF_17


title: DF_56


title: DF_126


title: DF_120


title: DF_117


title: DF_60


title: crh-1 null (3)

city: La Jolla

first: Ana

middle: PC

last: Rodrigues

address: 10010 North Torrey Pines Road

institute: Salk Institute for Biological Studies

scan_protocol: Scanner: GeneChip scanner 3000 7G as described in the Affymetrix GeneChip Expression Analysis Technical Manual

data_processing: Software used to generate the CEL files: GCOS v1.4. Data were processed using Biocondutor. Standard data quality validation as suggested by Affymetrix was carried out with the 'simpleaffy' package followed by 'affyPLM', which identified no problematic chips. The raw data were preprocessed according to the GC-RMA method (implemented in 'gcrma').

organism: Caenorhabditis elegans

source_name: C. elegans L4 crh-1 null

label_protocol: Labeling kit: 3' IVT kit for expression array from Affymetrix as described in the Affymetrix GeneChip Expression Analysis Technical Manual

growth_protocol: Egg preps were made using standard bleaching techniques and L1 larvae were synchronized by hatching eggs O/N in M9 buffer. 750 L1s were seeded per 12cm Lg NG plate seeded with OP50. All L1s were seeded at the same time. Biological replicates for each strain were prepared on separate days.

extract_protocol: Worms were harvested for RNA extraction when they reached L4 larval stage by snap freezing in liquid nitrogen in Trizol. Samples were frozen at times that account for variation in development time between groups. 3000 worms were used for each sample. RNA preps were carried out at the same time (12 hours prior to array) using trizol/chloroform extraction and then run through RNeasy cleanup column.

tag: developmental stage


title: DF_116


title: DF_128


title: aak-2 o/e (1)

hyb_protocol: as described in the Affymetrix GeneChip Expression Analysis Technical Manual

source_name: C. elegans L4 aak-2 null

value: AGD383 - N2; uthIs202 [Paak-2c::aak2 (aa1-321)::Tomato::unc-54 3'UTR, rol6]


title: DF_57


title: Normal_4

source_name: Amplified RNA from whole blood from normal individual


title: tax-6 null (1)

source_name: C. elegans L4 tax-6 null


title: DF_127


title: aak-2 o/e (3)


title: DF_125


title: DF_114


title: tax-6 null (2)


title: tax-6 null (3)


title: Normal_2


title: Normal_1


title: Normal_3


title: aak-2 o/e (2)


title: Convalescent_6

source_name: Amplified RNA from whole blood from convalescent individual

value: convalescent


title: Convalescent_3

value: reference


title: Convalescent_5


title: Convalescent_4


title: crh-1 null (2)


title: WT (3)

source_name: C. elegans L4 N2


title: WT (2)


title: WT (1)


title: Convalescent_1


title: The control brain RNA

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software version 1.1 (Affymetrix).

source_name: The normal human frontal lobe RNA

label_protocol: One hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

extract_protocol: The standard protocol for total RNA isolation was used. The quality of total RNA was evaluated on 2100 Bioanalyzer (Agilent Technologies).

value: brain frontal lobe

tag: ethnic group

value: four Caucasians

tag: gender

value: male and female

tag: age

value: 32-61 years

tag: cause of death

value: sudden death


title: [2000050406] Control Cy5 v Trypsin Cy3

status: Public on Nov 19 2010

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: Biological replicate 3 of 3, HEK293 cells vs treated with trypsin for 6 hr, harvested after treatments

hyb_protocol: Follwed protocol described in PMID: 15998744

scan_protocol: Cy3 and Cy5 hybridization signals were collected using the Agilent 600B Array Scanner.

data_processing: Intensity and background data for each element were calculated using Imagene 5.5 (BioDiscovery Inc., Australia). The data were further normalized with Agilent Genespring 7.3.

source_name: Total RNA extracted from HEK293 control (without treatment)

label_protocol: For each comparison, 2 µg of amplified RNA was labelled with Cy3-dUTP or Cy5-dUTP (Amersham Biosciences, Australia).

growth_protocol: HEK293 cells were maintained in DMEM with 10% fetal bovine serum, penicillin /streptomycin (5000 units/mL; 5000 μg/mL), Non-Essential Amino Acid, and L-glutamine in 95% air/5% CO2 at 37 ºC. The cells were seeded at 100,000 cells/mL and subcultured after detachment with 0.05% trypsin/0.5 mM EDTA.

extract_protocol: Total RNA was extracted following RNeasy mini kit from Qiagen, USA.

treatment_protocol: Cells were grown to 90% confluence, switched to serum free medium containing 0.03% bovine serum albumin (BSA), and incubated for 3 h. Cells were then treated with either 50nM trypsin (Invitrogen, USA), 1μM PAR2 agonist peptide (2f-LIGRLO-NH2; synthesized in-house) or vehicles (phosphate buffered saline, pH 7.4) and incubated for additional 90 min, 3, 6 or 12 hours.

tag: passage

value: Human embryonic kidney

source_name: Total RNA extracted from HEK293 treated with Trypsin for 6 hour

tag: treating agent

value: Trypsin

tag: treatment duration


title: The Nasu-Hakola disease brain RNA

source_name: The Nasu-Hakola disease frontal lobe RNA of autopsized frozen sample

tag: tissue

value: one Japanese patient

value: male

value: 39 year old

value: decubital infection


title: [2000050391] Control Cy5 v Control Cy3

description: Biological replicate 1 of 3, Untreated control HEK293 cells, harvested after treatments

source_name: Total RNA extracted from HEK293 control (no treatment)


title: [2000050399] Control Cy5 v 1.5hr Cy3

description: Biological replicate 1 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 1.5 hr, harvested after treatments

source_name: Total RNA extracted from HEK293 treated with 2f-LIGRLO-NH2 for 1.5 hour


title: [2000050403] Control Cy5 v 3hr Cy3

description: Biological replicate 2 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 3 hr, harvested after treatments

source_name: Total RNA extracted from HEK293 treated with 2f-LIGRLO-NH2 for 3 hour


title: [2000050398] Control Cy5 v 3hr Cy3

description: Biological replicate 3 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 3 hr, harvested after treatments


title: crh-1 null (1)

tag: strain


title: [2000050404] Control Cy5 v Trypsin Cy3

description: Biological replicate 1 of 3, HEK293 cells vs treated with trypsin for 6 hr, harvested after treatments


title: Testis_KO_rep4

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

description: Expression profiling of mouse ing2 -/- testis vs WT reveals gene expression differences consistent with spermatogenic arrest and infertility

hyb_protocol: RNA was hybridized to GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: GeneChips were scanned using a high-resolution microarray scanner 3000, and GeneChip Operating Software workstation version 1.3.

data_processing: The .CEL files were imported into Affymetrix Expression Console software and gene-level data was generated after robust multiarray analysis (RMA) background correction.

source_name: Whole testis from Ing2 -/- littermate

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

extract_protocol: Trizol

value: testis

value: 2-3 months

value: Ing2 KO


title: [2000050392] Control Cy5 v Control Cy3

description: Biological replicate 2 of 3, Untreated control HEK293 cells, harvested after treatments


title: Testis_KO_rep3


title: [2000050405] Control Cy5 v Trypsin Cy3

description: Biological replicate 2 of 3, HEK293 cells vs treated with trypsin for 6 hr, harvested after treatments


title: [2000050400] Control Cy5 v 1.5hr Cy3

description: Biological replicate 2 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 1.5 hr, harvested after treatments


title: [2000050401] Control Cy5 v 1.5hr Cy3

description: Biological replicate 3 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 1.5 hr, harvested after treatments


title: [2000050402] Control Cy5 v 3hr Cy3

description: Biological replicate 1 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 3 hr, harvested after treatments


title: [2000050397] Control Cy5 v Control Cy3

description: Biological replicate 3 of 3, Untreated control HEK293 cells, harvested after treatments


title: [2000050390] Control Cy5 v 12hr Cy3

description: Biological replicate 3 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 12 hr, harvested after treatments

source_name: Total RNA extracted from HEK293 treated with 2f-LIGRLO-NH2 for 12 hour


title: Testis_WT_rep2

source_name: Whole testis from Ing2 WT littermate

value: wild-type


title: [2000050394] Control Cy5 v 12hr Cy3

description: Biological replicate 2 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 12 hr, harvested after treatments


title: Testis_KO_rep1


title: [2000050395] Control Cy5 v 12hr Cy3

description: Biological replicate 1 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 12 hr, harvested after treatments


title: Testis_KO_rep5


title: Testis_WT_rep3


title: Testis_WT_rep1


title: Testis_KO_rep2


title: water treated plant vs BABA treated plant replicate 3

city: Lausanne

first: Johann

last: Weber

state: VD

address: Genopode Building

department: Center for integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
water_BABA3
CA679

hyb_protocol: Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC,  1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.

scan_protocol: Agilent microarray scanner, 10 μm resolution

data_processing: GenePix Pro 6.0 was used to analyse the images and  generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values. LimmaGui software package (Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics, 20:3705-3706) was used for data analysis.

source_name: rosette leaves from BABA treated plants

label_protocol: Total RNA from leaves was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, U.S.A.). 5 microgram of amplified RNA were reverse transcribed into cyanin3 or cyanin 5 labeled cDNA, purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6147)

extract_protocol: Total RNA extracted using lithium chloride 6M overnight at 4C

tag: ecotype

tag: treatment

value: BABA

source_name: rosette leaves from water treated plants


title: water treated plant vs BABA treated plant replicate 2

description:
water_BABA2
CA641


title: control plant vs BABA treated plant infected with Pst DC3000 replicate 2

description:
ctr_BABA_Pst2
CA680

source_name: rosette leaves from BABA treated plants infected with Pst

tag: pre-treatment

tag: infection

value: Pst DC3000

source_name: rosette leaves from control plants infected with Pst


title: [2000050393] Control Cy5 v 6hr Cy3

description: Biological replicate 3 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 6 hr, harvested after treatments

tag: cell line

source_name: Total RNA extracted from HEK293 treated with 2f-LIGRLO-NH2 for 6 hour


title: water treated plant vs BABA treated plant replicate 1

description:
water_BABA1
CA 790


title: [2000050396] Control Cy5 v 6hr Cy3

description: Biological replicate 2 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 6 hr, harvested after treatments


title: 66 mt E11.5 heart

first: Chong

middle: Yon

last: Park

address: 1650 Owens St.

department: Cardiovascular Diseases

institute: Gladstone Institute

description: Targeted deletion of skNAC in mice rsulted in embryonic lethality with cardiac defects by E12.5.  In order to investigate the molecular mechanism of the cardiac defect, we compared gene expression profiles of the knockout heart and wild type heart.

hyb_protocol: Generic Affymetrix Eukaryotic Array

scan_protocol: Generic Affymetrix Eukaryotic Array

data_processing: GCOS (MAS5)

source_name: skNAC knockout heart

label_protocol: 500ng of total RNA was amplified by using MessageAmpTM-Biotin Enhanced Kit from Ambion

value: ventricle


title: [2000050388] Control Cy5 v 6hr Cy3

description: Biological replicate 1 of 3, HEK293 cells vs treated with 2f-LIGRLO-NH2 for 6 hr, harvested after treatments


title: control plant vs BABA treated plant infected with Pst DC3000 replicate 3

description:
ctr_BABA_Pst3
CA793


title: control plant vs BABA treated plant infected with Pst DC3000 replicate 1

description:
ctr_BABA_Pst1
CA643


title: SSEA1+ c-kit+ day 4 RA  Pten-/-  mESC, biological rep2

city: Los Angeles

first: Anne

last: Lindgren

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

hyb_protocol: Affymetrix Mouse Genome 430 2.0 Array

scan_protocol: Chips were scanned using the Affymatrix GeneChip Scanner 3000 7G

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

source_name: SSEA1+ c-kit+ RA differentiated Pten-/- mouse ESC, biological rep2

label_protocol: FL-Ovation® cDNA Biotin Module V2

growth_protocol: Cells were grown in 6 well plates at a starting number of 50,000 for 4 days in mESC media without LIF with 10uM Ratinoic acid without media changes

extract_protocol: QIAGEN Rneasy Micro kit and Nu-GEN WT-Ovation® FFPE RNA Amplification System

treatment_protocol: Cells were differentiated for 4 days on mouse ES media without LIF and with 10uM Retinoic acid. Cells were stained and sorted for SSEA1 and c-kit on a BD FACS ARIA.

value: SSEA1 c-kit positive differentiated cells

tag: genotype

value: Pten-/-

value: 129 background


title: 1 mt E11.5 heart


title: 13 wt E11.5 heart

source_name: wild-type heart


title: SSEA1+ c-kit+ day 4 RA  wt mESC, biological rep1

source_name: SSEA1+ c-kit+ RA differentiated wild type mouse ESC, biological rep1

value: wild type


title: 23 wt E11.5 heart


title: 57 wt E11.5 heart


title: SSEA1+ c-kit+ day 4 RA  wt mESC, biological rep2

source_name: SSEA1+ c-kit+RA differentiated wild type mouse ESC, biological rep2


title: SSEA1+ c-kit+ day 4 RA  Pten-/-  mESC, biological rep1

source_name: SSEA1+ c-kit+RA differentiated Pten-/- mouse ESC, biological rep1


title: healthy pbmc rep1

status: Public on Nov 18 2010

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

description: gene expression of the Peripheral Blood Mononuclear Cells from the 4 completely healthy volunteers with equal quantity

hyb_protocol: The Cy3-labled RNA was dried for 1-2h at 55°C. then assembled the hybridization mixture  and hybridize for 20h at 55°C. Finally the hibridized slides were washed for scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides [Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (XDR Hi) and 5%(XDR Lo)].

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent G4450AA) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood Mononuclear Cells from completely healthy subjects

label_protocol: the microRNAs were labled by Cy3 using theAgilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456). Details were that 100ng total RNA was treated with phosphatase at 37 °C for 30min. The dephosphorylated RNA was labled as the kit instruction .

extract_protocol: RNA was prepared using the mirVana™ RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PBMC were prepared by the Ficoll-Paque PREMIUM (GE) following the manufacture instruction. The purified PBMCs were washed twice with PBS.

value: 2 males and 2 females

value: 22 to 29 years old

tag: cell type

value: Peripheral Blood Mononuclear Cells

tag: disease state

value: healthy


title: latent pbmc rep3

source_name: Peripheral Blood Mononuclear Cells from latent infected subjects

value: latent tuberculosis


title: healthy pbmc rep2


title: healthy pbmc rep3


title: latent pbmc rep2

description: gene expression of the Peripheral Blood Mononuclear Cells from the 4 latent-infected volunteers with equal quantity


title: latent pbmc rep1


title: PIWI-Q2569.Clone_8 extraction4_array1

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

organism: Drosophila melanogaster

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage

tag: Sex

value: Male


description: channel ch1 is input DNA;

source_name: PIWI-Q2569.D.mel 3rd Instar Larvae Nuclei extraction4_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Growth conditions and collection protocol to harvest third instar larvae from bottles.
Drosophila tissues were homogenized, and treated with formaldehyde.  Nuclei were lysed with SDS and sonication in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Oregon-R

value: 3rd Instar Larvae


title: Psc.BG3 extraction4_array1

description: channel ch1 is input DNA;

source_name: Psc.BG3 extraction4_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: Psc.S2 extraction2_array1

description: channel ch1 is input DNA;

source_name: Psc.S2 extraction2_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: Psc.BG3 extraction2_array1

description: channel ch1 is input DNA;

source_name: Psc.BG3 extraction2_array1 channel_1


title: H3K36me1.S2 extraction2_array1

description: channel ch1 is input DNA;


title: ZW5.BG3 extraction4_array1

description: channel ch1 is input DNA;

source_name: ZW5.BG3 extraction4_array1 channel_1


title: H3K36me1.S2 extraction4_array1

description: channel ch1 is input DNA;


description: channel ch1 is input DNA;

source_name: PIWI-Q2569.D.mel 3rd Instar Larvae Nuclei extraction2_array1 channel_1


title: patients pbmc rep3

description: gene expression of the Peripheral Blood Mononuclear Cells from the 4 volunteer patients with equal quantity

source_name: Peripheral Blood Mononuclear Cells from patients

tag: gender

tag: age

value: tuberculosis


title: patients pbmc rep2


title: 26 mt E11.5 heart

value: ventricle


title: ZW5.BG3 extraction2_array1

description: channel ch1 is input DNA;

source_name: ZW5.BG3 extraction2_array1 channel_1


title: SPT16_Q2583.S2 extraction4_array1

description: channel ch1 is input DNA;


title: PIWI-Q2569.Clone_8 extraction2_array1

description: channel ch1 is input DNA;


title: MRG15_Q2481.S2 extraction2_array1

description: channel ch1 is input DNA;


title: Psc.S2 extraction4_array1

description: channel ch1 is input DNA;

source_name: Psc.S2 extraction4_array1 channel_1


title: patients pbmc rep1

value: 2 males and 2 females


title: MRG15_Q2481.Kc extraction4_array1

description: channel ch1 is input DNA;

value: se/e

value: Female


title: SPT16_Q2583.S2 extraction2_array1

description: channel ch1 is input DNA;


title: MRG15_Q2481.S2 extraction4_array1

description: channel ch1 is input DNA;


title: MRG15_Q2481.BG3 extraction2_array1

description: channel ch1 is input DNA;


title: MRG15_Q2481.Kc extraction2_array1

description: channel ch1 is input DNA;


title: MRG15_Q2481.BG3 extraction4_array1

description: channel ch1 is input DNA;


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new lot).Clone_8 extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new abcam lot).Kc extraction4_array1 channel_1


title: ASH1 Q4177.S2 extraction2_array1

description: channel ch1 is input DNA;

source_name: ASH1 Q4177.S2 extraction2_array1 channel_1


title: ASH1 Q4177.S2 extraction4_array1

description: channel ch1 is input DNA;

source_name: ASH1 Q4177.S2 extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9me2-Ab2 (new lot).2-4 hr OR embryo extraction2_array1 channel_1

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

value: Embryo 2-4hr OR

value: wild type


description: channel ch1 is input DNA;

source_name: H3K9me2 antibody2.D.mel 3rd Instar Larvae Nuclei extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9me2 antibody2.D.mel 3rd Instar Larvae Nuclei extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new lot).Clone_8 extraction4_array1 channel_1

value: dorsal mesothoracic disc


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new abcam lot).D.mel 3rd Instar Larvae Nuclei extraction2_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new abcam lot).D.mel 3rd Instar Larvae Nuclei extraction4_array1 channel_1


description: channel ch1 is input DNA;

source_name: H3K9acS10P (new abcam lot).Kc extraction2_array1 channel_1


title: Convalescent_2

source_name: Amplified RNA from whole blood from convalescent individual

value: whole blood

value: convalescent

source_name: Amplified reference RNA from a pool of PBMCs of 5 healthy individuals

tag: sample type

value: reference

value: blood

value: peripheral blood mononuclear cells (PBMCs)

value: healthy


description: channel ch1 is input DNA;

source_name: H3K9me2-Ab2 (new lot).2-4 hr OR embryo extraction4_array1 channel_1

value: Oregon-R


title: PBL 6069

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2. The analysis was carried out after removing probes for genes on the X and Y chromosomes.

source_name: PBL normal

label_protocol: Infinium Assay for Methylation

growth_protocol: The samples were primary (non-transformed) cells from peripheral blood.  PBL indicates total leukocytes.  T-cells (not further fractionated by sub-type) were prepared using RosetteSep kits.

extract_protocol: Qiagen DNeasy Kit

value: normal


title: PBL 5194


title: PBL 5617


title: PBL 6070


title: PBL 5559


title: PBL 5790


title: PBL 5431


title: PBL 5090


title: PBL 5616


title: PBL 5560


title: PBL 5455


title: PBL 5188


title: PBL 5615


title: PBL 5638


title: PBL DS 817

source_name: PBL DS

value: Trisomy 21


title: PBL 6067


title: PBL 5190


title: PBL DS 809


title: PBL 5457


title: PBL 5791


title: PBL 5189


title: PBL 5441


title: PBL 5191


title: PBL DS 808


title: NE Treated BMDC_6 hr rep1

city: Ann Arbor

first: Paul

middle: Edward

last: Makidon

state: MI

address: 9340 MSRB III, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

description: Gene expression data 6 hours following exposure to NE

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 Array. GeneChips were washed and stained in the Affymetrix Fluidics station 450

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-Statistical language.  RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Bone Marrow Derived Denndritic Cells 6 hours following 0.001% NE exposure

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit rotocol from 50 ng total RNA (Ovation RN Amplfication System V2 Manual, 2007, NuGen)

growth_protocol: A single cell suspension of bone marrow cells were obtained frm BALB/c mouse tiba and were cultured at 1 x 10^6 cells/ml in 10 ml of RPMI, 10% FBS and supplemented with 20 ng/ml of GM-CSF and 10 ng/ml of IL-4.

extract_protocol: Total RNA was extracted per sample using RNA easy (Qiagen)

treatment_protocol: NE (W805EC) was added to the media to a final concentration of 0.001% and inucubated for 6 hours. Conrol cells were incubated with media only for 6 hours.

value: female

value: Bone Marrow Derived Dendritic Cells (BMDC)

value: BALB/c

value: 8 weeks

tag: agent

value: naomeulsion (W805EC)

tag: time point

value: 6 hrs


title: NE Treated BMDC_6 hr rep2

description: Gene expression data 6 hours following exposure to PBS

source_name: Bone Marrow Derived Dendritic Cells 6 hours following media incubation

tag: tissue


title: Control BMDC-6 hr rep2

tag: strain

value: PBS


title: PBL DS 806


title: Control BMDC-6 hr rep1


title: Lung_MMP3_rep3

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data from mouse lung homogenate

hyb_protocol: 4.5 micrograms of fragmented cDNA (NuGen uses cDNA, not cRNA) were hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX 7.3.1 using Affymetrix default analysis settings and standard Genespring normalizations (per chip normalize to 50th percentile, per gene normalize to median)

source_name: lung; MMP3

label_protocol: This project used the Affymetrix Mouse 430 2.0 GeneChip 100 ng of total RNA was used as input into the NuGen WT-Ovation FFPE System v.2 (amplification kit); samples were labeled by FL-Ovation cDNA biotin module v2.  according to manufacturer's protocols.

growth_protocol: Mice received 1st injection of urethane at 6 weeks of age, and all were harvested 14 weeks later.

extract_protocol: RNA samples were prepared using Qiagen Rneasy FFPE kit.

treatment_protocol: Mice received an initial urethane injection of 25 mg urethane in 300 ul saline.  Mice received 4 more urethane injections at weekly intervals of 20 mg urethane in 300 ul saline.  All mice were fed 200 mg/kg doxycycline feed.

tag: transgene

tag: genetic background

value: lung


title: PBL DS 805


title: TOSE4

city: London

first: Hagen

last: Kulbe

address: Charterhouse Square

department: Centre for Cancer and Inflammation

institute: Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry

description: Spontaneously transformed ovarian surface epithelium cell line 4.

hyb_protocol: Standard Affymetrix protocol.

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

data_processing: Affymetrix GCOS 1.4 and GTYPE 4.0. CHP files were generated using the Birdseed v2 algorithm.

source_name: spontaneously transformed ovarian surface epithelium cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Cells were extracted from soft agar colonies grown on plastic.

extract_protocol: Genomic DNA was extracted from cell pellets using Qiagen DNAeasy.

treatment_protocol: No treatment.

value: spontaneously transformed hTERT-immortalized ovarian surface epithelium cells


title: Lung_MMP3_rep1


title: Lung_non-MMP3_rep1

source_name: lung; non-MMP3

value: CCSP


title: Lung_non-MMP3_rep3


title: PBL DS 801


title: PBL DS 803


title: NE Treated Epithelium_24 hr

description: Gene expression data 24 hours following exposure to NE

source_name: Nasal Epithelium from CD-1 Mice 24 hours following 20% NE exposure

growth_protocol: Mice were maintained in standard conditions for 6 or 24 hours following nasal adminsistration of either PBS or NE.

treatment_protocol: 5 microliters per nare of either sterile PBS (control) or 20% v/v NE (W805EC) was administered via pipette.  Nasal epithelium was harvested immediatley post-mortem either 6 or 24 hours and cryopreseved in OTC via immersion in liquid nitrogen.

value: nasal epithelium

value: 20% (v/v) naomeulsion (W805EC)

value: 24 hours


title: Lung_MMP3_rep2


title: T-cells DS 799

source_name: T-cells DS


title: PBL DS 792


title: PBL DS 800


title: PBL DS 798


title: TOSE1

description: Spontaneously transformed ovarian surface epithelium cell line 1.


title: T-cells DS 798


title: T-cells DS 792


title: T-cells DS 790


title: NE Treated Epithelium_6 hr

source_name: Nasal Epithelium from CD-1 Mice 6 hours following 20% NE exposure

value: 6 hours


title: Lung_non-MMP3_rep2


title: PBL DS 802


title: T-cells DS 791


title: PBL DS 791


title: Control Epithelium-6 hr

source_name: Nasal Epithelium from CD-1 Mice 6 hours following PBS exposure


title: 6 PPARg fl/-LysCre IL-4 macrophage+RSG

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
24_(Mouse430_2).CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Mouse Genome 430 2.0  Affymetrix microarrays according to Affymetric standardized protocol.

scan_protocol: Microarrays were scanned canned according to Affymetric standardized protocol.

data_processing: The data were generated with GCOS, and txt files were analyzed in GeneSpring 7.3.

source_name: PPARg fl/-LysCre bone marrow-derived macrophage treated with IL-4+RSG

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

growth_protocol: Bone marrow cells were isolated from the femur, washed twice with PBS and cultured in RPMI+10% FCS supplemented with glutamine, penicillin and streptomycin and 20 ng/ml M-CSF. Fresh media and cytokines were added every other day for 10 days.

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

treatment_protocol: Cell were treated after plating into 6-well cell culture plates with the indicated cytokines (20 ng/ml M-CSF. 20 ng/ml IL-4 and vehicle (DMSO:ethanol) or 1 uM Rosiglitazone.

tag: mouse

tag: genotype/variation

value: PPARg fl/-LysCre

value: bone marrow-derived macrophage

tag: activation

tag: treatment

value: Rosiglitazone

tag: time

value: 10 days


title: PBL DS 797

tag: disease state

value: Trisomy 21


title: PBL DS 788


title: 6 PPARg fl/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
22_(Mouse430_2).CEL

source_name: PPARg fl/-LysCre bone marrow-derived macrophage treated with RSG

tag: cell type

value: Control


title: 5 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
19_(Mouse430_2).CEL

source_name: PPARg fl/-LysCre bone marrow-derived macrophage treated with IL-4


title: 5 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
20_(Mouse430_2).CEL


title: 5 PPARg fl/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
17_(Mouse430_2).CEL

source_name: PPARg fl/-LysCre bone marrow-derived macrophage


title: T-cells DS 789


title: 6 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
23_(Mouse430_2).CEL


title: PBL DS 772


title: 4 PPARg fl/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
16_(Mouse430_2).CEL


title: 4 PPARg fl/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
14_(Mouse430_2).CEL


title: PBL DS 784


title: 6 PPARg fl/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
21_(Mouse430_2).CEL


title: PBL DS 741


title: 5 PPARg fl/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
18_(Mouse430_2).CEL


title: PBL DS 774


title: PBL DS 771


title: PBL DS 740


title: 4 PPARg fl/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg fl/-LysCre mouse
13_(Mouse430_2).CEL


title: PBL DS 718


title: PBL DS 785


title: 4 PPARg fl/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg fl/- LysCre mouse
15_(Mouse430_2).CEL


title: 3 PPARg +/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
10_(Mouse430_2).CEL

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with RSG

value: PPARg +/-LysCre


title: 3 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
12_(Mouse430_2).CEL

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with IL-4+RSG


title: PBL DS 745


title: 3 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
11_(Mouse430_2).CEL

source_name: PPARg +/-LysCre bone marrow-derived macrophage treated with IL-4


title: PBL DS 706

source_name: PBL DS


title: PBL DS 701


title: PBL DS 702


title: 2 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
8_(Mouse430_2).CEL


title: 3 PPARg +/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
9_(Mouse430_2).CEL

source_name: PPARg +/-LysCre bone marrow-derived macrophage


title: 2 PPARg +/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
6_(Mouse430_2).CEL


title: PBL DS 267


title: PBL DS 442


title: T-cells 5803

source_name: T-cells normal

value: normal


title: 2 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
7_(Mouse430_2).CEL


title: 2 PPARg +/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
5_(Mouse430_2).CEL


title: 1 PPARg +/-LysCre IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
4_(Mouse430_2).CEL


title: T-cells 5804


title: PBL DS 511


title: T-cells 5802


title: T-cells 5801


title: 1 PPARg +/-LysCre control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
2_(Mouse430_2).CEL


title: Control Epithelium_24 hr

description: Gene expression data 24 hours following exposure to PBS

source_name: Nasal Epithelium from CD-1 Mice 24 hours following PBS exposure

value: female

value: 8 weeks


title: 1 PPARg +/-LysCre IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
3_(Mouse430_2).CEL


title: 1 PPARg +/-LysCre control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from PPARg +/-LysCre mouse
1_(Mouse430_2).CEL


title: 5 STAT6KO IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
20_(Mouse430_2).CEL

data_processing: The data were generated with GCOS, and cel files were analyzed in GeneSpring 7.3 using GC-RMA.

source_name: STAT6 KO bone marrow-derived macrophage treated with IL-4+RSG

value: STAT6 KO


title: 6 STAT6KO control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from STAT6KO mouse
21_(Mouse430_2).CEL

source_name: STAT6 KO bone marrow-derived macrophage


title: 6 STAT6KO IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
24_(Mouse430_2).CEL


title: 5 STAT6KO control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
18_(Mouse430_2).CEL

source_name: STAT6 KO bone marrow-derived macrophage treated with RSG


title: 3 Wild-type IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
11_(Mouse430_2).CEL

source_name: Wild-type bone marrow-derived macrophage treated with IL-4

value: Wild-type


title: 4 STAT6KO IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from STAT6KO mouse
15_(Mouse430_2).CEL

source_name: STAT6 KO bone marrow-derived macrophage treated with IL-4


title: 2 Wild-type IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
7_(Mouse430_2).CEL


title: 6 STAT6KO IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from STAT6KO mouse
23_(Mouse430_2).CEL


title: 4 STAT6KO control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from STAT6KO mouse
13_(Mouse430_2).CEL


title: 1 Wild-type IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
3_(Mouse430_2).CEL


title: 1 Wild-type control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
1_(Mouse430_2).CEL

source_name: Wild-type bone marrow-derived macrophage


title: 4 STAT6KO control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
14_(Mouse430_2).CEL


title: 3 Wild-type control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
10_(Mouse430_2).CEL

source_name: Wild-type bone marrow-derived macrophage treated with RSG


title: 1 Wild-type IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild type mouse
4_(Mouse430_2).CEL

source_name: Wild-type bone marrow-derived macrophage treated with IL-4+RSG


title: 6 STAT6KO control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
22_(Mouse430_2).CEL


title: 2 Wild-type IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild type mouse
8_(Mouse430_2).CEL


title: 4 STAT6KO IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
16_(Mouse430_2).CEL


title: 5 STAT6KO IL-4 macrophage

description:
Gene expression data of IL-4-treated bone marrow-derived macrophages derived from STAT6KO mouse
19_(Mouse430_2).CEL


title: 1 Wild-type control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
2_(Mouse430_2).CEL


title: 3 Wild-type IL-4 macrophage+RSG

description:
Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild type mouse
12_(Mouse430_2).CEL


title: 3 Wild-type control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
9_(Mouse430_2).CEL


title: 2 Wild-type control macrophage

description:
Gene expression data of bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
5_(Mouse430_2).CEL


title: Cell-line, MIN6, biological replicate 3

city: Leuven

first: Katleen

last: Lemaire

address: Herestraat 49, bus 901

country: Belgium

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16h at 45C.

scan_protocol: The arrays were washed and stained in a fluidics station (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All images were analyzed using GCOS version 1.4 with the MAS5 algorithm

source_name: Mouse insulinoma

label_protocol: Cellular mRNA was reverse transcribed into cDNA (SuperScript Choice System Invitrogen, Carlsbad, CA using oligo-dT primers and a T7 RNA polymerase promoter site). Two ug of total RNA was used to prepare biotinylated cRNA with IVT labeling kit (Affymetrix, Santa Clara, CA) according to the Genechip expression analysis technical manual 701025 Rev.5. The concentration of labelled cRNA was measured using the NanoDrop ND-1000 spectrophotometer. Labeled cRNA was fragmented in a fragmentation buffer during 35 min at 94C. The quality of labelled and fragmented cRNA was analysed using the Agilent bioanalyzer 2100.

extract_protocol: Total RNA from mouse tussues was extracted using Trizol reagent according to the manufacturer's protocol (Invitrogen), followed by a cleanup procedure with Rneasy colmuns (Qiagen). RNA from mouse islets as well as mouse pituitary and adrenal gland was extracted using the absolutely RNA microprep (Stratagene). For MIN6 cells we used the PureLink micro-to-midi RNA kit (INvitrogen)

value: Cell-line, MIN6

value: insulinoma


title: 2 Wild-type control macrophage+RSG

description:
Gene expression data of RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
6_(Mouse430_2).CEL


title: Cell-line, MIN6, biological replicate 1


title: Cell-line, MIN6, biological replicate 2