title: Estrogen sample 2

city: blacksburg

first: rujuan

last: dai

state: VA

address: 1410 price fork RD

department: CMMID

institute: virginia Tech

description: Estrogen treated mouse sample2

hyb_protocol: Hybridization is performed using a micro-circulation pump (Atactic Technologies).  The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: Hybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device).  Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing: normalized by limma package in R using VSN method

label: LC Mir-Label Prtl-060518

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining; two different tags are used for the two RNA samples in dual-sample experiments.

growth_protocol: All animals were housed in the animal facility at the Center for Molecular Medicine and Infectious Diseases (CMMID). The Animal Care Committee at Virginia Polytechnic Institute and State University approved all animal procedures. Mice were euthanized 7-8 wks after implantation, and splenic lymphocytes were isolated and cultured using procedures described in detail 21,29.  In brief, spleens from individual mice were dissociated in phenol red free RPMI-1640 incomplete medium (CellGro).  Splenic lymphocytes were isolated with ACK-Tris-NH4Cl lysis buffer per our previous studies, and washed with complete RPMI-1640 that was supplemented with steroid-free 10% charcoal-stripped fetal bovine serum (Atlanta Biologicals), 2 mM L-glutamine (Mediatech), 100 IU/ml penicillin (Mediatech), 100 ug/ml streptomycin (Mediatech), and 1% non-essential amino acids (Mediatech).  Splenic lymphocytes were resuspended in complete medium and adjusted to 5x1000000/ml before plating the cells.

extract_protocol: Total RNAs were isolated from freshly-isolated splenic lymphocytes from 2 pairs of placebo-and estrogen-treated mice as described above.  Small RNA enrichment and miRNA microarray assays were performed by LC Sciences

treatment_protocol: Wildtype C57BL/6 male mice (Charles River Laboratories) were orchiectomized and surgically implanted with 17B-estradiol (Sigma-Aldrich) or empty (placebo control) silastic implants as extensively described in our previous studies

tag: estrogen treated sample2


title: adult_vs_postsettlement

status: Public on Dec 05 2008

type: RNA

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

country: Australia

institute: Australian National University

description: The VALUE in the sample data table incorporates the data for 4 replicates of direct comparisons; two in one dye orientation and two in the other and also indirect comparisons from other hybridisations in the experiment

scan_protocol: Slides were scanned using a GenePix 4200A scanner, and data extracted using Spot [http://www.csiro.au/products/ps1ry.html].

data_processing: All further analyses were carried out using the limma package for the R system [http://www.r-project.org/].  Print-tip loess normalisation was performed on each slide. Quantile normalisation was applied to mean log-intensities in order to make the distributions essentially the same across arrays.

label: Cy3, Cy5

molecule: total RNA

organism: Acropora millepora

source_name: adult

label_protocol:
cDNA for probing arrays was produced from unamplified total RNA.
For each of the above stages, total RNA (80ug) was reverse transcribed, labelled and hybridised using standard protocols [http://www.microarray.adelaide.edu.au/].

extract_protocol: extracted using RNAWiz (Ambion) as per manufacturers' instructions

tag: adult developmental stage

source_name: postsettlement

tag: postsettlement larva developmental stage


title: proximal colon AOM rat 1

city: Sydney

first: Caroline

middle: Audrey

last: Kerr

state: NSW

address: 11 Julius Ave North Ryde

department: Moelcular health Technologies

institute: CSIRO

description: Gene expression data from azoxymethane treated rat colonic epithelium.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

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

label: biotin

organism: Rattus norvegicus

source_name: Rat scraped colonic epithelium (proximal)

label_protocol: Approximately 4.5 µg of total RNA was processed to produce biotinylated cRNA targets according to the standard Affymetrix protocol.

growth_protocol: Animals were housed in wire-bottomed caging in a temperature controlled room (22-24°C) with a 12 h light/dark cycle. They were randomly allocated into two groups (n=20) with approximately equal body weights. They were given free access to water and modified AIN-93G diet.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by QIAGEN RNAeasy column cleanup.

treatment_protocol: Rats were injected with azoxymethane (AOM; 15 mg/kg subcutaneously).  Six hours after injection the rats were anaesthetised with isoflurane and killed by exsanguination. The large bowel (excluding the rectum) was removed, opened longitudinally along the mesenteric border and digesta removed. The colon was rinsed clean with PBS and transferred to a chilled ceramic plate for dissection and the distal and proximal sections scraped off with a microscope slide and placed in RNAlater solution then stored at -80oC

tag: Dawley rats weighing approximately 176 +- 2.4g


title: postsettlement_vs_presettlement

description: The VALUE in the sample data table incorporates the data for 4 replicates of direct comparisons; two in one dye orientation and two in the other, and also from indirect comparisons through other hybridisations in the experiment

hyb_protocol: hybridised using standard protocols [http://www.microarray.adelaide.edu.au/].

source_name: presettlement

tag: presettlement larva developmental stage


title: Estrogen sample 1

country: USA

description: microRNA extraction and hybridization

data_processing: normalized by LIMMA in R using vsn method

organism: Mus musculus

treatment_protocol: Wildtype C57BL/6 male mice (Charles River Laboratories) were orchiectomized and surgically implanted with 17B-estradiol (Sigma-Aldrich) or empty (placebo control) silastic implants

tag: Estrogen treated sample1


title: Placebo sample 2

description: microRNA extraction and hybridization

tag: placebo control_sample2


title: Placebo sample 1

description: microRNA extraction and hybridization

tag: placebo control sample1


title: MvsF(H48)_bioRep5

status: Public on Dec 04 2008

city: Baltimore

first: Luigi

last: Marchionni

state: MD

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

department: Oncology

institute: Johns Hopkins University

description: Hybridizations on January 31, 2005.

hyb_protocol: 1.5 microgram of each of fragmented labeled sample was incubated at 65 Celsius in hybridization chambers for 17 hours. Slides were washed and dried according to the Agilent microarray processing protocols.

scan_protocol: Images were obtained using the Agilen scanner (Version A.7.5.1, Jun  1 2004). Data were extracted with  Agilent Feature Extraction software (version 9.5.3.1).

data_processing:
Within-array ”loess” normalization and beetwen-arrays ”scale” normalization were applied. No background subtraction was performed. Positive and negative controls features were not used to compute the ”loess” smoothing and in subsequent analyses. For each individual array M-values corresponding to sequence-identical features were averaged after preprocessing.
Data table VALUE column represents log2 (drug/no drug) ratios or log2 (male/female) ratios.

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

growth_protocol: C57/Bl6J (Jackson) pregnancies were timed according to scheduled 4-hour male-female pairings. Embryos were dissected at specified time points with the sex determined by inspection of gonads under a dissecting microscope. UGS tissue was carefully dissected to remove accessory ducts and immediately snap frozen

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

treatment_protocol: Paired pregnant females were pulsed with 50mg/kg dihydrotestosterone at 16.0 days post conceptionand; urogenital sinus tissue from female embryos were compaired to vehicle  after 6 and 12 hr. For the 48 hr (MvsF) time point tissue from unmanipulated male and female littermates were harvested at 17.5 dpc

tag: C57/Bl6J, male embryo, urogenital sinus harvested after 17.5 days post conception.

tag: C57/Bl6J, female embryo, urogenital sinus harvested after 17.5 days post conception.


title: H12_bioRep3_dyeSwap

description: Hybridizations on October 25 2005.

tag: C57/Bl6J, female embryo, urogenital sinus harvested after 6 hours from  vehicle (Triolein) pulse in the pregnant mother at 16.0 days post conception.

tag: C57/Bl6J, female embryo, urogenital sinus harvested after 6 hours from  50mg/kg dihydrotestosterone pulse in the pregnant mother at 16.0 days post conception.


title: MvsF(H48)_bioRep1

description: Hybridizations on January 31, 2005.


title: proximal colon AOM rat 4

treatment_protocol: Rats were injected with azoxymethane (AOM; 15 mg/kg subcutaneously).  Six hours after injection the rats were anaesthetised with isoflurane and killed by exsanguination. The large bowel (excluding the rectum) was removed, opened longitudinally along the mesenteric border and digesta removed. The colon was rinsed clean with PBS and transferred to a chilled ceramic plate for dissection and the distal and proximal sections scraped off with a microscope slide and placed in RNAlater solution then stored at -80oC!Sample_growth_protocol = Animals were housed in wire-bottomed caging in a temperature controlled room (22-24°C) with a 12 h light/dark cycle.


title: MvsF(H48)_bioRep2_dyeSwap

description: Hybridizations on January 31, 2005.


title: MvsF(H48)_bioRep2

description: Hybridizations on January 31, 2005.


title: MvsF(H48)_bioRep5_dyeSwap

description: Hybridizations on January 31, 2005.


title: MvsF(H48)_bioRep1_dyeSwap

description: Hybridizations on January 31, 2005.


title: MvsF(H48)_bioRep3_dyeSwap

description: Hybridizations on January 31, 2005.


title: MvsF(H48)_bioRep3

description: Hybridizations on January 31, 2005.


title: presettlement_vs_prawnchip

description: The VALUE in the sample data table incorporates the data for 4 replicates of the direct comparison; two in one dye orientation and two in the other and also indirect comparisons via other hybridisations in the experiment.

source_name: prawnchip

tag: prawnchip developmental stage


title: MvsF(H48)_bioRep4

description: Hybridizations on January 31, 2005.


title: H12_bioRep2_dyeSwap

description: Hybridizations on October 25 2005.


title: MvsF(H48)_bioRep4_dyeSwap

description: Hybridizations on January 31, 2005.


title: H12_bioRep1_dyeSwap

description: Hybridizations on October 25 2005.


title: H6_bioRep4_dyeSwap

description: Hybridizations on August 16, 2005.


title: HEK293_MUT-FOXP3_rep6

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: cDNA was added to hybridization buffer containing Cot-1 DNA (0.5 mg/ml final concentration), yeast tRNA (0.2 mg/ml), and poly(dA)40-60 (0.4 mg/ml). Hybridization was performed on a Ventana Discovery (Tucson, AZ) system for 6 hr at 42°C. Microarrays were washed to a final stringency of 0.1X SSC.

scan_protocol: Agilent DNA Microarray Scanner Model G2505B, 5 micron resolution. Fluorescence intensity was determined using Imagene™ software (BioDiscovery, El Segundo, CA).

data_processing: Net signal intensities were obtained following local background subtraction from each spot. Normalization for differences among experiments was conducted as previously described in Mech Ageing Dev 126:1135 (2005) and Bioinformatics 19:204 (2003).

organism: Homo sapiens

source_name: HEK293 cell line transfected with inducible mutated FOXP3

label_protocol: cDNA was synthesized with direct incorporation of Cy3-dUTP from 2 μg of total RNA using Endo-Free reverse transcriptase (Ambion, Austin, TX). RNA was mixed with 500 ng of anchored oligo-dT primer, brought to 20 μl volume with DEPC water, heated to 70°C for 10 min, and then transferred to 50°C for 10 minutes. To this was added a solution containing 2 μl of 10x RT buffer (Ambion), 0.5 nmole Cy3-dUTP, 2.5 mM each of dATP, dCTP, and dGTP, 1.5 mM TTP, 40 units of RNAse inhibitor, and 1 μl reverse transcriptase. cDNA was synthesized at 50°C for 2 hours using a Gene Amp PCR System 9700 (Perkin-Elmer Applied Biosystems, Foster City, CA, USA). Reactions were terminated by adding 5 μl 0.5 M EDTA and 10 μl of 1.0 N NaOH and heating to 60°C for 60 min. The final cDNA solution was neutralized with 25 μl of 1.0 M Tris-HCl. pH 8.0. cDNA was purified with a Montage 96-well format vacuum system (Millipore, Billerica, MA).

extract_protocol: Total RNA was isolated from 293 cell lines expressing WT or mutant (ΔFKH) FOXP3 24 hours after the addition of Doxycycline (1μg/ml) to induce expression of the FOXP3 protein. RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) per the manufacturer’s protocol.

treatment_protocol: Doxycycline 1 micro/ml induction of FOXP3. See J Immunol 177:3133 (2006)

tag: Stable tetracycline-inducible HEK293 cell Lines that express amino-terminal V5-tagged wild-type (amino acids 2-431) or mutant (amino acids 2-334, lacking the forkhead domain) FOXP3 in response to tetracycline as previously described in J Immunol 177:3133 (2006).


title: H12_bioRep3

description: Hybridizations on October 25 2005.


title: H12_bioRep1

description: Hybridizations on October 25 2005.


title: H6_bioRep3_dyeSwap

description: Hybridizations on August 16, 2005.


title: H12_bioRep2

description: Hybridizations on October 25 2005.


title: HEK293_MUT-FOXP3_rep4


title: HEK293_MUT-FOXP3_rep1


title: HEK293_MUT-FOXP3_rep5


title: HEK293_MUT-FOXP3_rep2


title: HEK293_MUT-FOXP3_rep3


title: WT_1a

first: Ivana

last: Celic

address: 725 N Wolfe Street

institute: JHSOM

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45°C with rotation (60rpm).

scan_protocol: Using Affymetrix’ GeneChip Scanner and default parameters described by the manufacturer.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: wild-type

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit.

growth_protocol: Saccharomyces cerevisiae were grown in YPD media.

extract_protocol: Hot acid phenol extraction following purification using RNeasy kit (Qiagen).

tag: Strain

value: YCB617 (FY background)


title: WT_2a


title: HEK293_WT-FOXP3_rep6

source_name: HEK293 cell line transfected with inducible wild-type FOXP3


title: H6_bioRep1_dyeSwap

description: Hybridizations on August 16, 2005.


title: H6_bioRep4

description: Hybridizations on August 16, 2005.


title: H6_bioRep2_dyeSwap

description: Hybridizations on August 16, 2005.


title: HEK293_WT-FOXP3_rep2

tag: Stable tetracycline-inducible HEK293 cell Lines that express

tag: amino-terminal V5-tagged wild-type (amino acids 2-431) or mutant (amino acids 2-334, lacking the forkhead domain) FOXP3 in

tag: response to tetracycline as previously described in J Immunol 177:3133 (2006).


title: HEK293_WT-FOXP3_rep4


title: HEK293_WT-FOXP3_rep3


title: HEK293_WT-FOXP3_rep5


title: H6_bioRep1

description: Hybridizations on August 16, 2005.


title: H6_bioRep2

description: Hybridizations on August 16, 2005.


title: hst3hst4_2a

source_name: hst3hst4 mutant

value: YCB600 (FY background)

tag: HST3 and HST4 genes, which encode putative NAD-dependent deacetylases that regulate histone 3 K56 acetylation, are deleted.


title: hst3hst4_1a


title: proximal colon AOM rat 2


title: HEK293_WT-FOXP3_rep1

tag: amino-terminal V5-tagged wild-type (amino acids 2-431) FOXP3 in


title: Mutant hypothyroid MH_5

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: affymetrix

hyb_protocol: affymetrix

scan_protocol: affymetrix

data_processing: RMA signal intensity calculation

source_name: Mutant hypothyroid

label_protocol: WT labeling kit (www.affymetrix.com)

extract_protocol: Total RNA from was isolated using Trizol as described above and  further purified with RNeasy Mini kit per manufacturer’s instructions (Qiagen, Valencia, CA). 200 ng total RNA was then used for GeneChip analysis. Preparation of terminal-labeled cDNA, hybridization to genome-wide murine Gene Level 1.0 ST GeneChips (Affymetrix, Santa Clara, CA, USA) and scanning of the arrays were carried out according to manufacturer’s protocols (https://www.affymetrix.com).

tag: Mouse liver total RNA; mixed strain background (B6;129S); NCoRloxP/loxP-AlbuminCre;

tag: mice were put on a low iodine diet supplemented with 0.15% PTU (LoI/PTU-Harlan Teklad TD.95125) for 3 weeks.


title: Control hypothyroid CH_20

description: affymetrix

source_name: control hypothyroid

tag: Mouse liver total RNA; mixed strain background (B6;129S); NCoRloxP/loxP ; mice were put on a low iodine diet supplemented with 0.15% PTU (LoI/PTU-Harlan Teklad TD.95125) for 3 weeks.


title: Mutant euthyroid MN_2

description: affymetrix

source_name: Mutant euthyroid

tag: Mouse liver total RNA; mixed strain background (B6;129S); NCoRloxP/loxP-AlbuminCre; standard chow (Harlan Teklad F6 Rodent Diet 8664)


title: Control euthyroid CN_14

description: affymetrix

source_name: Control euthyroid

tag: Mouse liver total RNA; mixed strain background (B6;129S); NCoRloxP/loxP; standard chow (Harlan Teklad F6 Rodent Diet 8664)


title: Mutant euthyroid MN_3

description: affymetrix


title: Control euthyroid CN_15

description: affymetrix

tag: Mouse liver total RNA; mixed strain background (B6;129S); NCoRloxP/loxP; standard chow (Harlan Teklad F6 Rodent Diet 8664


title: Kidney_Lmx1b null mouse_rep2

city: Regensburg

first: Anne

last: Rascle

address: Universitaetsstrasse

country: Germany

institute: University of Regensburg

description: Test sample for the microarray analysis (Lmx1b null mouse), replicate 2.

hyb_protocol: Labeled cRNA (1.5 µg) from each sample was hybridized onto Agilent Whole Mouse Genome 4x44K Expression Arrays and washed according to manufacturer’s instructions.

scan_protocol: Fluorescent signals were measured using an Agilent DNA Microarray Scanner according to manufacturer’s instructions. Microarray data was extracted using Agilent Feature Extraction Software.

data_processing: Significance analysis was performed with ArrayAssist Software (Agilent). Transcripts showing a fold change above 2-fold and a p-value below 0.05 were considered as significantly regulated.

source_name: Kidney from Lmx1b conventional knockout mouse

label_protocol: DNase-treated total RNA (1 µg) was synthesized into Cyanine 3 labeled cRNA (One-Color Microarray-Based Gene Expression Analysis Protocol, version 1.0.1, Agilent Technologies).

growth_protocol: On the day of birth, offspring was killed, kidneys were removed and snap-frozen in liquid nitrogen. Total RNA was isolated from a half kidney of three wild-type homozygous and three Lmx1b-/- homozygous mice for microarray analyses.

extract_protocol: Total RNAs were isolated using the Nucleospin RNA II kit (Macherey-Nagel), including an on-column DNase I treatment to eliminate genomic DNA contamination, following the manufacturer's recommendations.

tag: Kidney isolated from wild type and Lmx1b conventional knock-out newborn mice (Rohr et al. 2002. J Clin Invest 109:1073-82).


title: Kidney_Lmx1b null mouse_rep1

description: Test sample for the microarray analysis (Lmx1b null mouse), replicate 1.

treatment_protocol: On the day of birth, offspring was killed, kidneys were removed and snap-frozen in liquid nitrogen. Total RNA was isolated from a half kidney of three wild-type homozygous and three Lmx1b-/- homozygous mice for microarray analyses.


title: Mutant hypothyroid MH_6

description: affymetrix


title: Mutant hypothyroid MH_7

description: affymetrix


title: Control hypothyroid CH_17

description: affymetrix


title: Mutant euthyroid MN_4

description: affymetrix


title: H6_bioRep3

description: Hybridizations on August 16, 2005.

tag: C57/Bl6J, female embryo, urogenital sinus harvested after 6 hours from  vehicle (Triolein) pulse in the pregnant mother at 16.0 days post conception.


title: Kidney_wild type mouse_rep3

description: Reference sample for the microarray analysis (wild type mouse), replicate 3.

source_name: Kidney from wild type mouse


title: Kidney_wild type mouse_rep1

description: Reference sample for the microarray analysis (wild type mouse), replicate 1.


title: Kidney_Lmx1b null mouse_rep3

description: Test sample for the microarray analysis (Lmx1b null mouse), replicate 3.


title: Control hypothyroid CH_18

description: affymetrix


title: HtTA_LMX1B_Expt1_d4

description: Induced sample for the microarray analysis (expressing cells), replicate 1.

hyb_protocol: Following fragmentation and terminal labeling, ssDNA products (5.5 µg) were hybridized to the array for 16 h at 45 °C at 60 rpm in a rotating chamber. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChipTM Scanner 3000-7G. Signal intensity calculation was performed using the RMA algorithm as implemented in the Affymetrix Expression Console 1.1 software.

source_name: HtTA-LMX1B cells grown in the absence of doxycycline (induced cells)

label_protocol: Sample preparation was carried out in accordance with the Affymetrix GeneChipTM Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 2). Three-hundred nanograms of DNase-treated total RNA were used to generate Biotin-Labeled sense strand (ss) DNA.

growth_protocol: HtTA-LMX1B cells were grown in Dulbecco’s modified Eagle’s medium (DMEM high glucose with L-Glutamine) containing 10% FBS, 200 µg/ml Geneticin, no doxycycline, and 300 µg/ml Hygromycin B. Medium was changed every 2 days. The absence of doxycycline induces expression of human LMX1B. These cells thus represent the induced sample for the microarray analysis.

tag: Tet-off inducible HeLa cell line (HtTA) expressing human LMX1B protein upon doxycycline removal


title: Kidney_wild type mouse_rep2

description: Reference sample for the microarray analysis (wild type mouse), replicate 2.


title: Control euthyroid CN_13

description: affymetrix


title: HtTA_LMX1B_Expt2_d4

description: Induced sample for the microarray analysis (expressing cells), replicate 2.

treatment_protocol: HtTA-LMX1B cells were grown in Dulbecco’s modified Eagle’s medium (DMEM high glucose with L-Glutamine) containing 10% FBS, 200 µg/ml Geneticin, no doxycycline, and 300 µg/ml Hygromycin B. Medium was changed every 2 days. The absence of doxycycline induces expression of human LMX1B. These cells thus represent the induced sample for the microarray analysis.


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 12 h after A-factor addition 3rd

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

description: To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.

hyb_protocol: Microarray hybridization was carried out at 42°C for 18 h with mixing by using 120 μl per slide of SlideHyb#1 hybridization solution (Ambion) in a GeneTac HybStation (Genomic Solution). The posthybridization washing consisted of three cycles of 20-second incubations with each of the following solutions: 2× SSC plus 0.1% SDS (medium stringency) at 42°C, 0.1× SSC plus 0.05% SDS (high stringency) at 25°C, and 0.1× SSC (low stringency) at 25°C. After being washed, the slides were dried by centrifugation for 5 min at 350 × g at room temperature.

scan_protocol: The slides scanned with with a 428 array scanner (Affymetrix). The spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using the Limma loess method by ArrayPipe 2.0. Average normalized expression ratios (experiment/control) were calculated for each gene and tested for significance (p < 0.05). Ratio of experiment compared with control were further screened for difference from control, which was defined as having an expression ratio of either >2.0 or <0.5.

organism: Streptomyces griseus subsp. griseus NBRC 13350

source_name: control

label_protocol: Cy3 labeled cDNA were prepared by indirect labeling.

extract_protocol: Total RNA was isolated by RNAqueous mini kit (Ambion) and carried out DNaseI treatment to remove contaminated genomic DNA.

source_name: experiment

label_protocol: Cy5 labeled cDNA were prepared by indirect labeling.

tag: S. griseus IFO13350 afsA deficient mutant 12 h after A-factor addition


title: HtTA-LMX1B_Expt1_d0

description: Reference sample for the microarray analysis (non-expressing cells), replicate 1.

source_name: HtTA-LMX1B cells grown in the presence of doxycycline (non-induced cells)

growth_protocol: HtTA-LMX1B cells were grown in Dulbecco’s modified Eagle’s medium (DMEM high glucose with L-Glutamine) containing 10% FBS, 200 µg/ml Geneticin, 30 ng/ml doxycycline, and 300 µg/ml Hygromycin B. Medium was changed every 2 days. The presence of doxycycline prevents expression of human LMX1B. These cells thus represent the non-induced reference sample for the microarray analysis.


title: HtTA-LMX1B_Expt2_d0

description: Reference sample for the microarray analysis (non-expressing cells), replicate 2.

treatment_protocol: HtTA-LMX1B cells were grown in Dulbecco’s modified Eagle’s medium (DMEM high glucose with L-Glutamine) containing 10% FBS, 200 µg/ml Geneticin, 30 ng/ml doxycycline, and 300 µg/ml Hygromycin B. Medium was changed every 2 days. The presence of doxycycline prevents expression of human LMX1B. These cells thus represent the non-induced reference sample for the microarray analysis.


title: 42MGBA

type: protein

city: Cambridge

first: Jinyan

last: Du

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Institute

description:
antibodies against the analytes were coupled to beads of corresponding color; total mouse, rat or rabbit IgG were used as negative controls; a phospho-tyrosine peptide was coupled to beads as a positive control
raw data: C10 of Output 050307-3.csv

hyb_protocol: antibody coupled beads were incubated with total protein lysates to capture targeted analytes; the beads were then labelled with biotinylated phospho-tyrosine antibodies and streptavidin, R-phycoerythrin conjugates

scan_protocol: The data were collected with a Luminex 100 instrument

data_processing: The background readings for each capture antibody were obtained using microspheres incubated with 1x cell lysis buffer (Cell Signaling Technology). Values were considered positive if they were 3-fold over the background and represented by log2-transformation of the folds over background. Negative values were threshold to -5.

molecule: protein

source_name: glioma

label_protocol: According to manufacturer's protocol

growth_protocol: Cells from each cell line were grown on a 100mm dish to about 80% confluency.

extract_protocol: Media were removed and ice-cold 1x cell lysis buffer were added (2ml per 100mm dish); lysates were collected by scrapping and then incubated on ice for 30min; after centrifuging at 13000rpm on a desktop centrifuge for 10min; supernatant was collected; the

tag: glioma


title: 2X density sample 5 vs 1X density sample 5

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

hyb_protocol: Hybridization protocol was as designated by the chip manufacturer referenced in Horvath, D.P., Gulden, R., and Clay, S.A. Microarray analysis of late-season velvetleaf (Abutilon theophrasti) effect on corn. Weed Sci. 54: 983-994. 2006.

scan_protocol: Intensities based on fluorescence for each probe were visualized and quantified with a GenePix scanner (MDS Analytical Technologies) and GenePix Pro software.

data_processing: GeneMaths XT software (Applied Maths Inc.) was used to log transform (log 2) the intensity readings and normalize the arrays against each other. Probes that had hybridization intensity less than 2 times the standard deviation plus the average of the negative controls were deleted and technical replicates for each probe were averaged.

organism: Zea mays

source_name: Maize 2X density plot # 5

label_protocol: two-step labeling with alexafluor amino labeling kit from invitrogen as suggested by manufacturer.

growth_protocol: Corn was planted during the 1st week in May 2006, in Aurora South Dakota. The longitude and latitude at the site was 96 degrees 40’ west and 44 degrees 18’ north, respectively.  The soil parent materials were loess over glacial outwash, and the soil series was a Brandt silty clay loam (fine-silty, mixed, superactive, frigid Calcic Hapludolls). The surface horizon contained 110 g sand, 580 g silt, and 310 g clay kg-1. Total nitrogen in the 0-15 and 15-60 cm depths were 5.1 and 10.2 Mg N ha-1, respectively. Total C in the 0-15 and 15-60 cm depths were approximately 44.6 and 78.5 Mg C ha-1, respectively. The slope at the site was between 0 to 2%.  Plants recieved ample rainfall supplemented by irrigation and were fertilized with 228 kg N ha-1.

extract_protocol: Chang, S., J. Puryear, and J. Cairney. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113-116.

treatment_protocol: Corn was planted at a density of 149,000 plant ha-1, with 38 cm corn rows.

tag: The top 150-200 mm of the tip of the uppermost fully expanded leaf from maize variety DKC46-22 collected at V12 on July 10 and 11 from 12:00 to 2:00 PM. Weather was sunny and breezy 32-36 C.

source_name: Maize 1X density plot # 5

treatment_protocol: Corn was planted at a density of 74,500 plant ha-1, with 76 cm corn rows.


title: 2X density sample 8 vs 1X density sample 8

source_name: Maize 2X density plot # 8


title: 2X density sample 6 vs 1X density sample 6

source_name: Maize 2X density plot # 6

source_name: Maize 1X density plot # 6


title: 1X density sample 5 vs 60% shade sample 8

source_name: 1X density plot # 5

source_name: Maize 60% shade plot # 8

treatment_protocol: Corn was planted at a density of 74,500 plant ha-1, with 76 cm corn rows. 60% shade cloths were applied over the plots when plants were at the V5 stage and remained over the plots until harvest.


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 8 h after A-factor addition 2nd

tag: S. griseus IFO13350 afsA deficient mutant 8 h after A-factor addition


title: 1X density sample 6 vs 60% shade sample 5

source_name: 1X density plot # 6

source_name: Maize 60% shade plot # 5


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 12 h after A-factor addition 2nd


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 8 h after A-factor addition 1st


title: 1X density sample 8 vs 60% shade sample 6

source_name: 1X density plot # 8

source_name: Maize 60% shade plot # 6


title: 60% shade sample 8 vs 2X density sample 8

source_name: 2X density plot # 8


title: RPMI-8402_CompE_72hs

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: This sample was used as experimental sample in an experiment testing the effects of inhibition of NOTCH1 signaling using a gamma-secretase inhibitor (CompE)

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

source_name: RPMI-8402 T-ALL cell line

label_protocol: Affymetrix standard procedures

growth_protocol: Cells were cultured in RPMI 1640 media with 10% FBS, supplemented with pen/strep

extract_protocol: Ambion RNAqueous miniquit following standard procedures

tag: RPMI-8402 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 12 h after A-factor addition 1st

source_name: control


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 8 h after A-factor addition 3rd

source_name: experiment


title: P12-ICHIKAWA_CompE_72hs

source_name: P12-ICHIKAWA T-ALL cell line

treatment_protocol: This sample was used as experimental sample in an experiment testing the effects of inhibition of NOTCH1 signaling using a gamma-secretase inhibitor (CompE)

tag: P12-ICHIKAWA T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 4 h after A-factor addition 2nd

tag: S. griseus IFO13350 afsA deficient mutant 4 h after A-factor addition


title: PF-382_CompE_72hs

source_name: PF-382 T-ALL cell line

tag: PF-382 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 4 h after A-factor addition 3rd


title: 60% shade sample 5 vs 2X density sample 5

source_name: Maize 60% shade

source_name: 2X density


title: MOLT3_CompE_72hs

source_name: MOLT3 T-ALL cell line

tag: MOLT3 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 4 h after A-factor addition 1st


title: 60% shade sample 6 vs 2X density sample 6

source_name: Maize 60% shade plot #6

source_name: 2X density plot # 6


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 2 h after A-factor addition 3rd

tag: S. griseus IFO13350 afsA deficient mutant 2 h after A-factor addition


title: HPB-ALL_CompE_72hs

source_name: HPB-ALL cell line

tag: HPB-ALL T-ALL cell line


title: KOPTK1_CompE_72hs

source_name: KOPTK1 T-ALL cell line

tag: KOPTK1 T-ALL cell line


title: CUTLL1_CompE_72hs

source_name: CUTLL1 cell line

treatment_protocol: Cells were treated with a gamma-secretase inhibitor, CompE 100nM, for 72 hs

tag: CUTLL1 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 2 h after A-factor addition 1st


title: DND41_CompE_72hs

source_name: DND41 cell line

tag: DND41 T-ALL cell line


title: RPMI8402_DMSO_72hs

description: This sample was used as control sample in an experiment testing the effects of inhibition of NOTCH1 signaling using a gamma-secretase inhibitor (CompE)

source_name: RPMI8402 T-ALL cell line

treatment_protocol: Cells were treated with vehicle only (DMSO)for 72 hs

tag: RPMI8402 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 2 h after A-factor addition 2nd


title: PF382_DMSO_72hs

source_name: PF382 T-ALL cell line

tag: PF382 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 1 h after A-factor addition 3rd

tag: S. griseus IFO13350 afsA deficient mutant 1 h after A-factor addition


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 1 h after A-factor addition 2nd


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 30 min after A-factor addition 3rd

tag: S. griseus IFO13350 afsA deficient mutant 30 min after A-factor addition


title: P12-ICHIKAWA_DMSO_72hs

growth_protocol: Cells were cultured in RPMI 8402 media with 10% FBS, supplemented with pen/strep


title: CCRF-CEM_CompE_72hs

source_name: CCRF-CEM T-ALL cell line

tag: CCRF-CEM T-ALL cell line


title: HPB-ALL_DMSO_72hs

source_name: HPB-ALL T-ALL cell line


title: KOPTK1_DMSO_72hs


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 1 h after A-factor addition 1st

source_name: control


title: MOLT3_DMSO_72hs


title: DND41_DMSO_72hs

source_name: DND41 T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 30 min after A-factor addition 2nd

source_name: experiment


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 15 min after A-factor addition 3rd

tag: S. griseus IFO13350 afsA deficient mutant 15 min after A-factor addition


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 15 min after A-factor addition 2nd


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 30 min after A-factor addition 1st


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 5 min after A-factor addition 3rd

tag: S. griseus IFO13350 afsA deficient mutant 5 min after A-factor addition


title: CUTLL1_DMSO_72hs

source_name: CUTLL1 T-ALL cell line


title: ALL-SIL_CompE_72hs

source_name: ALL-SIL T-ALL cell line

treatment_protocol: Cells were treated with CompE 100nM for 72 hs

tag: ALL-SIL T-ALL cell line


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 15 min after A-factor addition 1st


title: CCRF-CEM_DMSO_72hs


title: Rox1 40nM DIP-chip Replicate B

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Biology

institute: University of North Carolina at Chapel Hill

description:
DIP-chip done using MBPRox1DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

hyb_protocol: Competitively hybed ~10ug channel 1 and 2 DNA on NimbleGen 385k whole genome arrays using Maui SL mixers in Maui hybridization chamber.  Washed as per NimbleGen hybridization protocol.

scan_protocol: Scanned on GenePix 4000B scanner as per NimbleGen protocol

data_processing: Raw log2 ratio for experiments (obtained from GFF output file from NimbleScan) was median-center z-scored.

molecule: genomic DNA

source_name: MBP-Rox1DBD DIP DNA

label_protocol: NimbleGen amplification and labeling

extract_protocol:
Cold Spring Harb. Protoc.; 2008; doi:10.1101/pdb.prot4972
Amplified by Invitrogen WGA protocol

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPRox1DBD purified from E. coli.

source_name: S288C Genomic DNA

extract_protocol: CsCl Prep

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared by sonication to avg size of 600bp


title: CC-P71_tumor

status: Public on Dec 03 2008

city: Durham

first: Chaitanya

middle: R

last: Acharya

address: 203 Research Drive,Medical Sciences Research Building, Suite 433

department: Dept. of Surgery

institute: Duke University

description: Array Print: Hs-OperonV2-vB2.2

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42Ã¸C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100Ã¸C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42Ã¸C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42Ã¸C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Slides were scanned on an Axon scanner using GenePixPro (3.0) software. Spot quality was assessed according to criteria in GenePixPro (3.0) software. Background subtraction and normalization was performed upon data extraction from the CIT/NIH-microarray database, mAdb (http://nciarray.nci.nih.gov/).

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

label_protocol: Cy3 and Cy5 Labeling protocols - generic

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

tag: Tissue

value: Colon

tag: age

tag: no recurrence

source_name: Control


title: CC-P8_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P9_tumor

description: Array Print: Hs-OperonV2-vB2.2

tag: recurrence


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 5 min after A-factor addition 2nd


title: CC-P7_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P72_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: S. griseus IFO13350 afsA deficient mutant vs afsA deficient mutant 5 min after A-factor addition 1st


title: CC-P73_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Rox1 40nM DIP-chip Replicate A


title: Rap1 40nM DIP-chip Replicate B

description:
DIP-chip done using MBPRap1DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Rap1DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPRap1DBD purified from E. coli.


title: ALL-SIL_DMSO_72hs

description: This sample was used as reference in an experiment testing the effects of inhibition of NOTCH1 signaling using a gamma-secretase inhibitor (CompE)

source_name: ALL-SIL cell line

treatment_protocol: Cells were treated with vehicle only (DMSO) for 72 hs


title: CC-P69_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P66_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P67_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P63_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P65_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P61_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P60_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Pho4 40nM DIP-chip Replicate A

description:
DIP-chip done using MBPPho4DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Pho4DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPPho4DBD purified from E. coli.


title: CC-P64_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P62_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P70_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Pho2 40nM DIP-chip Replicate B

description:
DIP-chip done using MBPPho2DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Pho2DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPPho2DBD purified from E. coli.


title: CC-P58_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P59_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Pho4 40nM DIP-chip Replicate B


title: CC-P57_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P6_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P54_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P56_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P53_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Cbf1 40nM DIP-chip Replicate B

description:
DIP-chip done using MBPCbf1DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Cbf1DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPCbf1DBD purified from E. coli.


title: CC-P55_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P52_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_17

city: Barcelona

first: Ramón

last: Bataller

address: C/Casanova, 143

department: Liver Unit

country: Spain

institute: Hospital Clínic, IDIBAPS

description: RNA was isolated from rat livers using the QIAGEN RNeasy kit (Qiagen). RNA integrity was checked with the Agilent 2100 Bioanalyser (Agilent Technologies) and only high quality RNA samples were hybridized to Rat Genome 230 2.0 GeneChips (Affymetrix). Briefly, 2 µg of total RNA were used to generate double strand cDNA using an oligo dT- primer containing the T7 RNA polymerase promoter site and the SuperScript Choice System kit (Invitrogen).

hyb_protocol: The resulting cRNA was purified and fragmented and 15 µg were hybridized to RAT Genome 230 2.0 GeneChips for 16 hours , at 45ºC and 60 rpm

scan_protocol: The labelled arrays were scanned with a Gene chip scanner 3000.

data_processing: Data processing cel files were normalized with 'gcrma' function of the Bioconductor package 'gcrma' in R.

source_name: Liver from rats submitted to Bile Duct Ligation for two weeks and infused with ghrelin throughout these two weeks.

label_protocol: cDNA was purified by the GeneChip Sample Clean Up Module, followed by in vitro synthesis of biotinylated cRNA using the BioArray High Yield RNA transcription kit (Affymetrix). The arrays were then washed and labelled with streptavidin-phycoerythrin (SAPE), and the signal was amplified with an anti-streptavidin biotinylated antibody followed by a second round of staining with SAPE using an Affymetrix fluidics station 450.

extract_protocol: QIAGEN RNeasy kit

treatment_protocol: Ghrelin infused by sub-cutaneous osmotic mini-pump. Bile Duct Ligation was performed at week 7. At week 9 rat was sacrificed.

tag: Liver of male wistar rats, 9 weeks.


title: DAL82_4561.2_ArrayA

status: Public on Dec 26 2008

city: Toronto

first: Lourdes

last: Pena-Castillo

state: Ontario

address: 160 College St. Room 1350

department: Banting and Best Department of Medical Research

country: Canada

institute: University of Toronto

description: Yeast DAL82_4561.2_ArrayA

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) under LifterSlip cover slips (Erie Scientific) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 100 nM (unless otherwise specified) in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at 20°C. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. Slides were spun dry by centrifugation at 40 g for 5 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars at 20°C on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa488-conjugated antibody (488 nm ex, 522 nm em). Separately, slides were scanned after primer extension to quantify the amount of incorporated Cy3-conjugated dUTP (543 nm ex, 570 nm em). Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices)

data_processing: Every non-palindromic 8-mer occurs on at least 32 spots in each chamber of our universal PBM and we provide several scores for each 8-mer in each experiment: (1) Median Intensity, (2) Z-Score, and (3) Enrichment Score (E-Score). E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots.

source_name: Baker's yeast DAL82

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: Protein open reading frames, consisting of the pfam-defined DNA-binding domain and 15 amino acids of flanking sequence (or to the end of the full open reading frame) were cloned into pMAGIC1  by either RT-PCR from pooled yeast mRNA or by gene synthesis (DNA 2.0).  We transferred the inserts into a T7-GST-tagged variant of pML280 following.  We expressed proteins by either (i) purification from E. coli C41 DE3 cells (Lucigen), or (ii) in vitro translation reactions (Ambion ActivePro Kit) without purification.

tag: Yeast DAL82


title: Leu3 40nM DIP-chip Replicate B

description:
DIP-chip done using MBPLeu3DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Leu3DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPLeu3DBD purified from E. coli.


title: CC-P5_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_16


title: CC-P50_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_13


title: Liver_Bile_Duct_Ligation_15


title: Rap1 40nM DIP-chip Replicate A


title: Liver_Bile_Duct_Ligation_14


title: V1038_Patient with Amyotrophic Lateral Sclerosis

status: Public on Dec 25 2008

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Array CGH analysis of a patient with ALS

hyb_protocol: Hybridisation was done overnight at 42C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

scan_protocol: Slides were scanned using an Axon4000B.

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalised by subgrid LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Mar. 2007)

source_name: DNA isolated from EBV-transformed lymphoblastoid cell line

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics, http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH2006.html)

extract_protocol: DNA was extracted from patient cell line using the QIAamp Blood DNA Midi Kit

tag: male ALS patient

source_name: DNA isolated from EBV-transformed cell line (reference)

extract_protocol: DNA was extracted from EBV-transformed lymphoblastoid cell line using standard phenol-chloroform extraction procedures

tag: healthy male donor


title: CC-P48_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Leu3 40nM DIP-chip Replicate A


title: Pho2 40nM DIP-chip Replicate A


title: Swi5 40nM DIP-chip Replicate B

description:
DIP-chip done using MBPSwi5DBD competitively hybridized against whole genome S288C DNA on NimbleGen 385k feature arrays.
As in DIP-chip: rapid and accurate determination of DNA-binding specificity. Liu X, Noll DM, Lieb JD, Clarke ND. Genome Res. 2005. 15: 421-427

source_name: MBP-Swi5DBD DIP DNA

tag: Genomic DNA isolated by CsCl prep from S288C strain, sheared to avg size of 600bp, and then used for DIP-chip with 40nM MBPSwi5DBD purified from E. coli.


title: CC-P45_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P47_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P49_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_9

source_name: Liver from rats submitted to Bile Duct Ligation for two weeks.

treatment_protocol: Saline infused by sub-cutaneous osmotic mini-pump. Bile Duct Ligation was performed at week 7. At week 9 rat was sacrificed.


title: Liver_Bile_Duct_Ligation_12


title: Liver_Bile_Duct_Ligation_11


title: CC-P46_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_8


title: Liver_Bile_Duct_Ligation_10


title: Swi5 40nM DIP-chip Replicate A


title: CC-P43_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_6

source_name: Control liver

treatment_protocol: Saline infused by sub-cutaneous osmotic mini-pump. Abdominal incision as a sham operation at week 7. At week 9 rat was sacrificed.


title: CC-P44_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P42_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_7


title: CC-P41_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Liver_Bile_Duct_Ligation_5


title: CC-P51_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Cbf1 40nM DIP-chip Replicate A


title: C.j. 11168 versus NW Dye Swap of DNA comparison #2

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

description: Biological replicate 4 of 4: genomic DNA content comparison, dye swap.

hyb_protocol: Ambion SlideHyb solution was added to the denatured, labeled and combined samples.  Hybridized in cassettes in 54 degree water bath overnight

scan_protocol: Affymetrix 428 scanner was used for each channel separately, maximizing gains for sample clarity

data_processing: After GenePix was used for spot sizing and evaluation, gpr files were generated for each test/sample.  GACK analysis was then performed to evaluate presence/absence of each ORF

organism: Campylobacter jejuni

source_name: C.j. NW genomic DNA

label_protocol: DNA was labeled with aminoallyl-dUTP using the BioPrime random priming DNA labeling kit (Invitrogen, Carlsbad, CA).

growth_protocol: Each strain was streaked from frozen stock on two tryptose soya agar plates containing 5% defibrinated sheeps’ blood; plates were incubated for 48 hours at 37 C in 5% CO2.  A single isolated colony from each plate was chosen and streaked onto another plate (biological replicates).

extract_protocol: Genomic DNA was isolated using the CTAB protocol described in Ausbel, et.al. 1 mg. Of DNA was sheared with sonication to 0.52.0 kbp prior to labeling

treatment_protocol: Growth from each of the second plates was harvested separately.

tag: Campylobacter jejuni strain NW

tag: Non-disease causing Cj

source_name: C.j. 11168 genomic DNA

tag: Campylobacter jejuni strain 11168

tag: Disease causing Cj


title: C.j. 11168 versus NW Dye Swap of DNA comparison #1

description: Biological replicate 3 of 4: genomic DNA content comparison, dye swap.


title: C.j. 11168 versus NW DNA comparison #2

description: Biological replicate 2 of 4: genomic DNA content comparison.


title: C.j. 11168 versus NW DNA comparison #1

description: Biological replicate 1 of 4: genomic DNA content comparison.


title: CC-P4_tumor

description: Array Print: Hs-OperonV2-vB2.2

tag: Tissue

tag: age


title: CC-P68_tumor

description: Array Print: Hs-OperonV2-vB2.2

tag: no recurrence


title: CC-P39_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P37_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: bodies_sechellia_C_Cy5_1

first: Ian

last: Dworkin

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

description: dye swap

hyb_protocol: Hybridizations were performed using printed slides treated with 5× SSC, 0.1% SDS, and 1% BSA for 45 min to block non-specific binding. Hybridization reactions containing labeled cDNA, 5× SSC, poly-adenine oligo, 5× Denhardt's solution, 50% formamide, 0.5% SDS, and calf thymus DNA were placed onto the prepared slides and incubated for 20 h at 42 °C.

scan_protocol: ScanArray 4000 (Packard Biochip) with Scanarray express (Perkin Elmer)

data_processing: Raw fluorescence intensities (background subtracted) using connected-component spot segmentation algorithms were exported from UCSF SPOT. Normalization used a global linear normalization (mixed model) step for dye (fixed), array (random) and their interaction (random). The residuals from the normalization step represent the relative fluorescence intensity (log2 RFI) for each feature as the fold change in expression intensity relative to the sample mean conditioned on array and dye.

organism: Drosophila sechellia

source_name: bodies sechellia CHOICE

label_protocol: mRNA (500 ng total RNA starting material from each sample) was amplified using the Low RNA input fluorescent linear amplification kit, according to manufacturer’s specifications (Agilent technologies). cRNA products were pooled, and for each sample to be hybridized 4 microG of cRNA was indirectly labeled with aminoallyl during cDNA synthesis (Promega ImProm II enzyme), linked to Cy3 or Cy5 esters and hybridized overnight following the standard operating procedure #M004 from The Institute for Genomic Research .To reduce technical variation, samples were pooled and then split following both the amino-allyl and dye incorporation.

growth_protocol: reared at 25° C on agar-yeast-cornmeal medium with constant humidity in an environmental chamber

extract_protocol: Total RNA from heads or bodies was extracted using TRIzol reagent as per manufacturer instructions. RNA was further purified using a Qiagen RNeasy Mini Kit per the manufacturer’s protocol

tag: Female adult, 3 to 6 days old, bodies


title: Liver_Bile_Duct_Ligation_4


title: CC-P38_tumor

description: Array Print: Hs-OperonV2-vB2.2

source_name: Control


title: bodies_sechellia_C_Cy5_3

description: dye swap


title: bodies_simulans_NC_Cy5_3

description: dye swap

organism: Drosophila simulans

source_name: bodies simulans NO CHOICE


title: bodies_simulans_C_Cy5_1

description: dye swap

source_name: bodies simulans CHOICE


title: Liver_Bile_Duct_Ligation_3

treatment_protocol: aline infused by sub-cutaneous osmotic mini-pump. Abdominal incision as a sham operation at week 7. At week 9 rat was sacrificed.


title: bodies_simulans_C_Cy5_2

description: dye swap


title: bodies_sechellia_NC_Cy5_2

description: dye swap

source_name: bodies sechellia NO CHOICE


title: Liver_Bile_Duct_Ligation_1

description: RNA was isolated from rat livers using the QIAGEN RNeasy kit (Qiagen). RNA integrity was checked with the Agilent 2100 Bioanalyser  (Agilent Technologies) and only high quality RNA samples were hybridized to Rat Genome 230 2.0 GeneChips (Affymetrix). Briefly, 2 µg of total RNA were used to generate double strand cDNA using an oligo dT- primer containing the T7 RNA polymerase promoter site and the SuperScript Choice System kit (Invitrogen).

label_protocol: cDNA was purified by the GeneChip  Sample Clean Up Module, followed by in vitro synthesis of biotinylated cRNA using the BioArray High Yield RNA transcription kit (Affymetrix). The arrays were then washed and labelled with streptavidin-phycoerythrin (SAPE), and the signal was amplified with an anti-streptavidin biotinylated antibody followed by a second round of staining with SAPE using an Affymetrix fluidics station 450.


title: bodies_simulans_C_Cy5_3

description: dye swap


title: bodies_simulans_NC_Cy5_1

description: dye swap


title: Liver_Bile_Duct_Ligation_2


title: CC-P40_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P34_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P35_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: bodies_sechellia_C_Cy5_2

description: dye swap


title: bodies_simulans_NC_Cy5_2

description: dye swap


title: bodies_sechellia_NC_Cy3_1

description: dye swap


title: CC-P36_tumor

description: Array Print: Hs-OperonV2-vB2.2

tag: recurrence


title: CC-P33_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: bodies_sechellia_C_Cy3_3

description: dye swap


title: bodies_sechellia_C_Cy3_2

description: dye swap


title: bodies_simulans_NC_Cy3_1

description: dye swap


title: bodies_sechellia_NC_Cy3_3

description: dye swap


title: bodies_simulans_C_Cy3_1

description: dye swap


title: bodies_simulans_NC_Cy3_2

description: dye swap


title: bodies_simulans_C_Cy3_3

description: dye swap


title: bodies_sechellia_NC_Cy3_2

description: dye swap


title: CC-P32_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: bodies_simulans_C_Cy3_2

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy5_rep_3

description: dye swap

hyb_protocol: Hybridizations were performed using printed slides treated with 5× SSC, 0.1% SDS, and 1% BSA for 45 min to block non-specific binding. Hybridization reactions containing labeled cDNA, 5× SSC, poly-adenine oligo, 5× Denhardt's solution, 50% formamide, 0.5% SDS, and calf thymus DNA were placed onto the prepared slides and incubated for 16 h at 42 °C using a MAUI Mixed (BioMicro Systems).

organism: Drosophila melanogaster

source_name: 3rd instar wing imaginal discs_genotype_wt_strain_Ore

growth_protocol: larvae were reared at 25° C on agar-yeast-cornmeal medium with constant humidity in an environmental chamber

extract_protocol: Total RNA from wing imaginal discs from wandering third instar larvae was extracted and purified using a Qiagen RNeasy Mini Kit per the manufacturer’s protocol, with DNase1 digestion.

tag: wing imaginal disc, 3rd instar


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy5_rep_3

description: dye swap

source_name: 3rd instar wing imaginal discs_genotype_sd_strain_Ore


title: heads_simulans_C_Cy5_3

description: dye swap

source_name: simulans CHOICE

tag: Female adult, 3 to 6 days old


title: CC-P30_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy3_rep_3

description: dye swap

source_name: 3rd instar wing imaginal discs_genotype_wt_strain_Sam


title: CC-P31_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy5_rep_3

description: dye swap

source_name: 3rd instar wing imaginal discs_genotype_sd_strain_Sam


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy5_rep_2

description: dye swap


title: CC-P3_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy3_rep_3

description: dye swap


title: heads_simulans_C_Cy5_2

description: dye swap


title: heads_sechellia_NC_Cy5_3

description: dye swap

source_name: sechellia NO CHOICE


title: heads_sechellia_C_Cy5_3

description: dye swap

source_name: sechellia CHOICE


title: CC-P29_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy3_rep_3

description: dye swap


title: CC-P28_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy3_rep_2

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy5_rep_1

description: dye swap


title: heads_simulans_NC_Cy5_3

description: dye swap

source_name: simulans NO CHOICE


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy3_rep_2

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy5_rep_3

description: dye swap


title: heads_simulans_NC_Cy5_2

description: dye swap


title: CC-P26_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_NC_Cy5_2

description: dye swap


title: CC-P27_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy3_rep_3

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy5_rep_2

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy3_rep_2

description: dye swap


title: heads_sechellia_C_Cy5_2

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy5_rep_2

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy5_rep_1

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy3_rep_1

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Ore_Cy3_rep_2

description: dye swap


title: CC-P25_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_simulans_NC_Cy5_1

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy3_rep_1

description: dye swap


title: heads_simulans_C_Cy5_1

description: dye swap


title: CC-P23_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_C_Cy5_1

description: dye swap


title: CC-P24_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_sd_Sam_Cy5_rep_1

description: dye swap


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy5_rep_1

description: dye swap


title: CC-P22_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: wing_imaginal_disc_Drosophila_wt_Sam_Cy3_rep_1

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy3_rep_1

description: dye swap


title: CC-P21_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_simulans_C_Cy3_2

description: dye swap


title: wing_imaginal_disc_Drosophila_sd_Ore_Cy5_rep_2

description: dye swap


title: CC-P2_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_NC_Cy_5_1

description: dye swap


title: heads_simulans_C_Cy3_3

description: dye swap


title: CC-P19_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P18_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_NC_Cy3_3

description: dye swap


title: heads_simulans_NC_Cy3_3

description: dye swap


title: CC-P17_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_NC_Cy3_2

description: dye swap


title: heads_sechellia_C_Cy3_3

description: dye swap


title: CC-P14_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P15_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_C_Cy3_1

description: dye swap


title: heads_simulans_C_Cy3_1

description: dye swap


title: heads_sechellia_NC_Cy3_1

description: dye swap


title: heads_simulans_NC_Cy3_2

description: dye swap


title: CC-P13_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_simulans_NC_Cy3_1

description: dye swap


title: CC-P11_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P10_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: heads_sechellia_C_Cy3_2

description: dye swap


title: CC-P1_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: CC-P16_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Smad3 KO Primary, 48 hr TGFbeta1, rep1 - mAdbID:50982

status: Public on Dec 02 2008

city: Washington

first: DONG-SOON

last: BAE

state: DC

address: 2300 I Street, NW

department: Pharmacology & Physiology

institute: George Washinton Uni.

description: mAdb experiment ID: 50982

hyb_protocol: protocol_name: NCI cDNA Microarray Hybridization other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual": http://nciarray.nci.nih.gov/reference/nciarrayspacket01-04A.pdf)

source_name: Smad3 KO Primary, untreated, Cy3

label_protocol: protocol_name: Cy3 Labeling Protocol

growth_protocol:
protocol_name: Cell Line Growth Protocol
other: Primary keratinocytes were isolated from newborn mice strains and cultured as described (Hennings, 1980; Vijayachandra et al., 2003).

extract_protocol:
protocol_name: RNA Extraction with TRIZOL
extraction_method: TRIZOL
other: Total RNA was isolated from keratinocytes using TRIzol extraction reagent (Gibco BRL) and samples were further purified using the QIAGEN RNeasy Midi Kit (Qiagen) according to the manufacturers' protocols. A column DNase digestion was carried out to remove genomic DNA contamination.

tag: strain

value: skin

value: keratinocytes

value: gene knock out

source_name: Smad3 KO Primary, 48 hour, Cy5

label_protocol: protocol_name: Cy5 Labeling Protocol

treatment_protocol:
treatment_type: compound
compound: TGFbeta1
treatment_dose: 1 ng/ml
treatment_time: 48 hrs


title: Smad3 KO Ras, 48hr TGFbeta1,(rev.fluor.),rep2 - mAdbID:51091

description: mAdb experiment ID: 51091

source_name: Smad3 KO Ras, untreated, Cy5 (rev.fl.)

growth_protocol:
protocol_name: Cell Line Growth Protocol with Ha-ras
other: Primary keratinocytes were isolated from newborn mice strains and cultured as described (Hennings, 1980; Vijayachandra et al., 2003). On day 3 of culture, the keratinocytes were transduced with a replication-defective retrovirus containing the Ha-ras gene. After 4 days of Ha-ras infection, cells underwent subsequent experimental treatments. Cell culture medium was changed 24 hours before the chemical treatment.

value: keratinocytes plus Ha-ras

source_name: Smad3 KO Ras, 48 hour, Cy3 (rev.fl.)


title: CC-P12_tumor

description: Array Print: Hs-OperonV2-vB2.2


title: Balb/c Primary, 48 hr TGFbeta1 (rev.fluor.), rep3 - mAdbID:40785

description: mAdb experiment ID: 40785

source_name: Balb/c Primary, untreated, Cy5(rev.fl.)

value: Balb/c

source_name: Balb/c Primary, 48 hour, Cy3(rev.fl.)


title: Balb/c Ras, 48 hr TGFbeta1, rep4 - mAdbID:46777

description: mAdb experiment ID: 46777

source_name: Balb/c Ras, untreated, Cy3

source_name: Balb/c Ras, 48 hour, Cy5


title: Balb/c Primary, 48 hr TGFbeta1, rep5 - mAdbID:46774

description: mAdb experiment ID: 46774

source_name: Balb/c Primary, untreated, Cy3

source_name: Balb/c Primary, 48 hour, Cy5


title: Smad3 KO Ras, 48 hr TGFbeta1, rep1 - mAdbID:50983

description: mAdb experiment ID: 50983

source_name: Smad3 KO Ras, untreated, Cy3

source_name: Smad3 KO Ras, 48 hour, Cy5


title: Smad3 WT Ras, 48 hr TGFbeta1 - mAdbID:50981

description: mAdb experiment ID: 50981

source_name: Smad3 WT Ras, untreated, Cy3

source_name: Smad3 WT Ras, 48 hour, Cy5


title: Smad3 WT Primary, 48 hr TGFbeta1 - mAdbID:50980

description: mAdb experiment ID: 50980

source_name: Smad3 WT Primary, untreated, Cy3

source_name: Smad3 WT Primary, 48 hour, Cy5


title: Balb/c Ras, 6 hr TGFbeta1, rep8 - mAdbID:40742

description: mAdb experiment ID: 40742

source_name: Balb/c Ras, 6 hour, Cy5

treatment_protocol:
treatment_type: compound
compound: TGFbeta1
treatment_dose: 1 ng/ml
treatment_time: 6 hrs


title: Balb/c Ras, 48 hr TGFbeta1, (rev.fluor), rep5 - mAdbID:46778

description: mAdb experiment ID: 46778

source_name: Balb/c Ras, untreated, Cy5 (rev.fl.)

source_name: Balb/c Ras, 48 hour, Cy3 (rev.fl.)


title: Balb/c Primary, 48 hr TGFbeta1 (rev.fluor.), rep4 - mAdbID:46776

description: mAdb experiment ID: 46776


title: Balb/c Primary, 1 hr TGFbeta1, rep6 - mAdbID:40775

description: mAdb experiment ID: 40775

source_name: Balb/c Primary, 1 hour, Cy5

treatment_protocol:
treatment_type: compound
compound: TGFbeta1
treatment_dose: 1 ng/ml
treatment_time: 1 hrs


title: Balb/c Ras, 48 hr TGFbeta1, rep2 - mAdbID:39690

description: mAdb experiment ID: 39690


title: Balb/c Primary, 48 hr TGFbeta1, rep2 - mAdbID:40784

description: mAdb experiment ID: 40784


title: Balb/c Primary, 1 hr TGFbeta1, rep5 - mAdbID:39689

description: mAdb experiment ID: 39689


title: Balb/c Primary, 6 hr TGFbeta1, rep7 - mAdbID:40777

description: mAdb experiment ID: 40777

source_name: Balb/c Primary, 6 hour, Cy5


title: Balb/c Ras, 24 hr TGFbeta1, rep7 - mAdbID:40779

description: mAdb experiment ID: 40779

source_name: Balb/c Ras, 24 hour, Cy5

treatment_protocol:
treatment_type: compound
compound: TGFbeta1
treatment_dose: 1 ng/ml
treatment_time: 24 hrs


title: Balb/c Ras, 48 hr TGFbeta1, rep3 - mAdbID:40783

description: mAdb experiment ID: 40783


title: Balb/c Ras, 1 hr TGFbeta1, rep6 - mAdbID:40741

description: mAdb experiment ID: 40741

source_name: Balb/c Ras, 1 hour, Cy5


title: Smad3 KO Primary, 48hr TGFbeta1,(rev.fluor.),rep2 - mAdbID:51090

description: mAdb experiment ID: 51090

source_name: Smad3 KO Primary, untreated,Cy5(rev.fl.)

source_name: Smad3 KO Primary, 48 hour, Cy3 (rev.fl.)


title: Balb/c Ras, 1 hr TGFbeta1, rep5 - mAdbID:39688

description: mAdb experiment ID: 39688

source_name: Balb/c Ras, untreated, Cy3


title: Balb/c Ras, 48 hr TGFbeta1, rep1 - mAdbID:39553

description: mAdb experiment ID: 39553

source_name: Balb/c Ras, 48 hour, Cy5


title: Balb/c Primary, 24 hr TGFbeta1, rep5 - mAdbID:39552

description: mAdb experiment ID: 39552

source_name: Balb/c Primary, untreated, Cy3

source_name: Balb/c Primary, 24 hour, Cy5


title: Balb/c Primary, 24 hr TGFbeta1, rep6 - mAdbID:40782

description: mAdb experiment ID: 40782


title: Balb/c Primary, 48 hr TGFbeta1, rep1 - mAdbID:39554

description: mAdb experiment ID: 39554

source_name: Balb/c Primary, 48 hour, Cy5


title: Balb/c Primary, 6 hr TGFbeta1, rep5 - mAdbID:36598

description: mAdb experiment ID: 36598


title: Balb/c Primary, 6 hr TGFbeta1, rep6 - mAdbID:39320

description: mAdb experiment ID: 39320


title: Balb/c Ras, 6 hr TGFbeta1, rep7 - mAdbID:39332

description: mAdb experiment ID: 39332


title: Balb/c Ras, 24 hr TGFbeta1, rep6 - mAdbID:39551

description: mAdb experiment ID: 39551


title: Balb/c Ras, 24 hr TGFbeta1, (rev.fluor.), rep4 - mAdbID:36575

description: mAdb experiment ID: 36575

source_name: Balb/c Ras, 24 hour, Cy3 (rev.fl.)


title: Balb/c Ras, 1 hr TGFbeta1, rep4 - mAdbID:36568

description: mAdb experiment ID: 36568


title: Balb/c Primary, 6 hr TGFbeta1, rep3 - mAdbID:36324

description: mAdb experiment ID: 36324


title: Balb/c Primary, 24 hr TGFbeta1, rep2 - mAdbID:36326

description: mAdb experiment ID: 36326


title: Balb/c Ras, 24 hr TGFbeta1, rep5 - mAdbID:36574

description: mAdb experiment ID: 36574


title: Balb/c Primary, 24 hr TGFbeta1, rep4 - mAdbID:36597

description: mAdb experiment ID: 36597


title: Balb/c Primary, 6 hr TGFbeta1, rep4 - mAdbID:36325

description: mAdb experiment ID: 36325


title: Balb/c Ras, 6 hr TGFbeta1 (rev.fluor.), rep5 - mAdbID:36303

description: mAdb experiment ID: 36303

source_name: Balb/c Ras, 6 hour, Cy3 (rev.fl.)


title: Balb/c Ras, 24 hr TGFbeta1, rep2 - mAdbID:36308

description: mAdb experiment ID: 36308


title: Balb/c Primary, 1 hr TGFbeta1, rep2 - mAdbID:36306

description: mAdb experiment ID: 36306


title: Balb/c Ras, 6 hr TGFbeta1, rep6 - mAdbID:36569

description: mAdb experiment ID: 36569


title: Balb/c Ras, 6 hr TGFbeta1, rep4 - mAdbID:36302

description: mAdb experiment ID: 36302


title: Balb/c Primary, 24 hr TGFbeta1, rep1 - mAdbID:35968

description: mAdb experiment ID: 35968


title: Loucy day 3 100nM MRK-003

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: T-ALL cell line

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: T-ALL

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Loucy day 3 DMSO

tag: Loucy day 3 100nM MRK-003


title: Be13 day 3  100nM MRK-003

description: T-ALL cell line

tag: Be13 day 3  DMSO

tag: Be13 day 3  100nM MRK-003


title: SUPT 11 day 3 100nM MRK-003

description: T-ALL cell line

tag: SUPT 11 day 3 DMSO

tag: SUPT 11 day 3 100nM MRK-003


title: Balb/c Ras, 1 hr TGFbeta1, rep2 - mAdbID:36301

description: mAdb experiment ID: 36301


title: Balb/c Primary, 1 hr TGFbeta1, rep1 - mAdbID:35966

description: mAdb experiment ID: 35966


title: Supt13 day 3 100nM MRK-003

description: T-ALL cell line

tag: Supt13 day 3 DMSO

tag: Supt13 day 3 100nM MRK-003


title: HBP ALL day 3 100nM MRK-003

description: T-ALL cell line

tag: HBP ALL day 3 DMSO

tag: HBP ALL day 3 100nM MRK-003


title: SKW3 day 3 100nM MRK-003

description: T-ALL cell line

tag: SKW3 day 3 DMSO

tag: SKW3 day 3 100nM MRK-003


title: CEM day 3 100nM MRK-003

description: T-ALL cell line

tag: CEM day 3 DMSO

tag: CEM day 3 100nM MRK-003


title: RPMI 8402 day 3 100nM MRK-003

description: T-ALL cell line

tag: RPMI 8402 day 3 DMSO

tag: RPMI 8402 day 3 100nM MRK-003


title: DND41 day 3 100nM MRK-003

description: T-ALL cell line

tag: DND41 day 3 DMSO

tag: DND41 day 3 100nM MRK-003


title: Hsb2 day 3 100nM MRK-003

description: T-ALL cell line

tag: Hsb2 day 3 DMSO

tag: Hsb2 day 3 100nM MRK-003


title: Balb/c Ras, 24 hr TGFbeta1, rep3 - mAdbID:35751

description: mAdb experiment ID: 35751

tag: strain


title: Tall1 day 3 100nM MRK-003

description: T-ALL cell line

tag: Tall1 day 3 DMSO

tag: Tall1 day 3 100nM MRK-003


title: Molt16 day 3 100nM MRK-003

description: T-ALL cell line

tag: Molt16 day 3 DMSO

tag: Molt16 day 3 100nM MRK-003


title: Balb/c Primary, 1 hr TGFbeta1, rep3 - mAdbID:35749

description: mAdb experiment ID: 35749


title: C57 ES cell(2)

city: Seoul

first: Hyun-Jai

last: Cho

address: 28 Yongon-Dong, Jongno-gu

department: Division of Cardiology, Department of Internal Medicine

country: South Korea

institute: Seoul National University Hospital

description: C57 ES cell replicate 2

hyb_protocol: Hybridization to the Affymetrix GeneChip Gene 1.0 ST Array is performed according to standard Affymetrix protocols.

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: The scanned data was processed using Affymetrix Expression Console version1.1 RMA Normalization and the further analysis was performed using Multi-Experiment Viewer(MEV) version 4.0

source_name: C57 ES cell

label_protocol: Labeling was performed following the standard Affymetrix protocol

extract_protocol: Total RNA was extracted by RNeasy  Mini kit(Qiagen)

value: C57BL/6 mouse


title: PF382 day 3 100nM MRK-003

description: T-ALL cell line

tag: PF382 day 3 DMSO


title: Molt13 day 3 100nM MRK-003

description: T-ALL cell line

tag: Molt13 day 3 DMSO

tag: Molt13 day 3 100nM MRK-003


title: MOLT 4 day 3 100nM MRK-003

description: T-ALL cell line

tag: MOLT 4 day 3 DMSO

tag: MOLT 4 day 3 100nM MRK-003


title: Supt7 day 3 100nM MRK-003

description: T-ALL cell line

tag: Supt7 day 3 DMSO

tag: Supt7 day 3 100nM MRK-003


title: Jurkat day 3 100nM MRK-003

description: T-ALL cell line

tag: Jurkat day 3 DMSO

tag: Jurkat day 3 100nM MRK-003


title: C57 ES cell(3)

description: C57 ES cell replicate 3


title: dedifferentiated mouse cardiac fibroblast(2)

description: dedifferentiated mouse cardiac fibroblast replicate 2


title: dedifferentiated mouse cardiac fibroblast(1)

description: dedifferentiated mouse cardiac fibroblast replicate 1


title: mouse cardiac fibroblast(3)

description: mouse cardiac fibroblast cell replicate 3

source_name: C57 ES cell adult mouse cardiac fibroblast


title: Balb/c Primary, 6 hr TGFbeta1, rep1 - mAdbID:34742

description: mAdb experiment ID: 34742


title: koptk1 day 3 100nM MRK-003

description: T-ALL cell line

tag: koptk1 day 3 DMSO

tag: koptk1 day 3 100nM MRK-003


title: Balb/c Primary, 6 hr TGFbeta1, rep2 - mAdbID:35617

description: mAdb experiment ID: 35617


title: dedifferentiated mouse cardiac fibroblast(3)

description: dedifferentiated mouse cardiac fibroblast replicate 3


title: Balb/c Ras, 6 hr TGFbeta1, rep3 - mAdbID:35616

description: mAdb experiment ID: 35616

source_name: Balb/c Ras, 6 hour, Cy5


title: Balb/c Ras, 1 hr TGFbeta1, rep3 - mAdbID:35693

description: mAdb experiment ID: 35693


title: C57 ES cell(1)

description: C57 ES cell replicate 1


title: Balb/c Ras, 1 hr TGFbeta1, rep1 - mAdbID:34692

description: mAdb experiment ID: 34692


title: mouse cardiac fibroblast(2)

description: mouse cardiac fibroblast cell replicate2


title: Balb/c Ras, 24 hr TGFbeta1, rep1 - mAdbID:34789

description: mAdb experiment ID: 34789


title: mouse cardiac fibroblast(1)

description: mouse cardiac fibroblast cell replicate 1


title: Balb/c Ras, 6 hr TGFbeta1, rep2 - mAdbID:34257

description: mAdb experiment ID: 34257


title: Balb/c Primary, 24 hr TGFbeta1, rep3 - mAdbID:35694

description: mAdb experiment ID: 35694


title: Balb/c Ras, 6 hr TGFbeta1, rep1 - mAdbID:34256

description: mAdb experiment ID: 34256


title: A20_20h_P

status: Public on Dec 01 2008

city: Amsterdam

first: Stephan

middle: Henrik

last: Schirmer

address: Meibergdreef 9

department: Cardiology

country: Netherlands

institute: Academic Medical Center

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted using Illumina's BeadStudio software. From 13 controls and 18 patients we analyzed CD14+ monocyte, CD4+ T-cell, LPS-stimulated monocytes and macrophage samples, in total 130 arrays (including 6 technical replicates). From the CD34+ cell samples, only 23 passed quality control and were analyzed by array, giving a grand total of 153 arrays. Normalization and statistical analysis of the bead summary data from the arrays was carried out using the limma package14 and in-house scripts in R/Bioconductor. Bead summary intensities were log2-transformed and then normalized using quantile normalization. To find differentially expressed genes, we performed a linear model analysis. Technical replicates were handled by estimating a common value for the intra-replicate correlation and including it in the linear model. Differential expression between the treatments of interest was assessed using a moderated t-test. This test is similar to a standard t-test for each probe except that the standard errors are moderated across genes to ensure more stable inference for each gene. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

source_name: macrophages

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Using immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA), CD14+ monocytes, CD4+ T-cells and CD34+ stem cells were positively isolated for direct cell lysis, while negatively isolated monocytes were split into two fractions for stimulation with 10 ng/ml lipopolysaccharide (LPS) for 3h, or for 20h cell culture towards macrophages.

extract_protocol: Positively isolated monocytes, T-cells and stem cells as well as cultured stimulated monocytes and macrophages were lysed and total RNA was isolated (Absolutely RNA Microprep Kit, Stratagene, La Jolla, CA).

tag: patient

tag: patient ID_REF


title: A2_CD34_C

scan_protocol: According to beadchip array manufacturer's protocol

source_name: stem cells

tag: control


title: A11_T_P

source_name: T cells


title: A8_CD34_C


title: A19_T_P


title: A4_20h_C


title: A10_T_P


title: A35_CD34_P


title: A13_T_C


title: A36_3h_P

source_name: stimulated monocyes


title: Balb/c Primary, 1 hr TGFbeta1, rep4 - mAdbID:36576

description: mAdb experiment ID: 36576

tag: strain

source_name: Balb/c Primary, 1 hour, Cy5


title: A35_CD14_P

source_name: resting monocyes


title: A12_T_C


title: A5_T_C


title: A24_T_P


title: A1_20h_C


title: A27_CD14_P


title: A35_T_P


title: A6_T_P


title: A1_T_C


title: A27_T_P


title: A9_CD34_C


title: A13_3h_C


title: A22_3h_P


title: A19_CD34_P


title: A3_3h_C


title: A33_3h_P


title: A20_CD34_P


title: A15_3h_P


title: A24_20h_P


title: A24_3h_P


title: A5_3h_C


title: A9_T_C


title: A13_20h_C


title: A22_20h_P


title: A10_3h_P


title: A30_3h_C


title: A8_20h_C


title: A20_T_P


title: A11_3h_P


title: A37_3h_P


title: A8_3h_C


title: A27_20h_P


title: A4_3h_C


title: A24_CD14_P


title: A36_CD34_P


title: A4_T_C


title: A27_CD34_P


title: A34_T_P


title: A34_3h_P


title: A11_20h_P


title: A27_3h_P


title: A38_CD34_P


title: A34_CD14_P


title: A39_20h_C


title: A39_CD34_C


title: A7_CD34_P


title: A41_CD34_C


title: A36_20h_P


title: A4_CD14_C


title: A1_20h_C_rep2


title: A38_20h_P


title: A6_20h_P


title: A35_3h_P


title: A8_CD14_C


title: A15_20h_P


title: A11_CD14_P


title: A19_3h_P


title: A7_CD14_P


title: A2_CD14_C


title: A19_CD14_P


title: A12_CD14_C


title: A3_CD14_C


title: A12_3h_C


title: A35_T_P_rep2


title: A11_T_P_rep2


title: A7_3h_P


title: A33_T_P


title: A15_T_P


title: A33_CD14_P


title: A2_3h_C


title: A32_3h_C


title: A3_T_C


title: A4_CD34_C


title: A39_T_C


title: A9_20h_C


title: A3_CD34_C


title: A34_CD34_P


title: A8_T_C


title: A7_T_P


title: A37_20h_P


title: A20_20h_P_rep2


title: A2_T_C


title: A38_T_P


title: A31_3h_P


title: A6_CD14_P


title: A30_20h_C


title: A33_CD34_P


title: A1_CD14_C


title: A1_3h_C


title: wt de novo strain N3369 MeDIP

city: Eugene

first: Zachary

last: Lewis

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

description: ChIP-chip experiment

hyb_protocol: See Lee et al. (2006) Nature Protocols

scan_protocol: Arrays were scanned using the Genepix 4000 scanner. Data was aquired using Genepix pro software (Axon).

data_processing: The Value column was determined by creating a log2 value from the median normalized log2 value from the .gpr file

organism: Neurospora crassa

source_name: wild type strain N3369

label_protocol: See Lee et al. (2006) Nature Protocols

growth_protocol: See Tamaru et al. (2003) Nature Genetics for procedure

tag: total input

tag: methylated DNA immunoprecipitated fraction


title: A7_20h_P


title: A31_CD34_P


title: de novo 5mC strain N3368 MeDIP

description: ChIP-chip experiment

source_name: wild type strain 3369

extract_protocol: See Tamaru et al. (2003) Nature Genetics for procedure

tag: total input DNA

source_name: wild type strain N3368

tag: methylated DNA immunoprecipitate fraction


title: double argonaute mutant strain N3406 MeDIP

description: ChIP-chip experiment

source_name: double argonaute mutant strain N3406

treatment_protocol: See Tamaru et al. (2003) Nature Genetics for procedure


title: A6_3h_P


title: A31_T_P


title: A32_CD34_C


title: A32_T_C


title: hpo mutant strain N2556 H3K9me3 ChIP-chip

description: ChIP-chip experiment

source_name: hpo mutant strain N2556 standard growth conditions

growth_protocol: See Tamaru et al. (2003) Nature Genetics

tag: H3K9me3 immunoprecipitated fraction


title: A2_20h_C


title: wt H3K4me2

description: ChIP-chip experiment

source_name: wt strain N150 standard growth conditions

tag: total genomic DNA

source_name: wild type strain N150 standard growth conditions

extract_protocol: See Tamaru et al. (2003) Nature Genetics

tag: histone H3K4me2 immunoprecipitated fraction


title: HP1-GFP ChIP-chip

description: Chip-chip experiment

scan_protocol: Arrays were scanned using the Genepix 4000 scanner.  Data was aquired using Genepix pro software (Axon).

source_name: standard growth conditions strain N3415

growth_protocol: see Tamaru et al. (2003) Nature Genetics for procedure

treatment_protocol: See Tamaru et al. (2003) Nature Genetics

tag: anti HP1-GFP immunoprecipitate fraction


title: HP1-FLAG ChIP-chip

description: Chip-chip experiment

source_name: standard growth conditions strain N3320

tag: total input fraction

tag: anti-FLAG immunoprecipitate fraction


title: A32_CD14_C


title: dim-2 mutant strain N1850 H3K9me2 ChIP-chip

description: ChIP-chip experiment

source_name: dim-2 mutant strain N1850 standard growth conditions


title: wt strain N150 MeDIP rep 2

description: Chip-chip experiment

tag: Methylated DNA immunoprecipitated fraction


title: wt H3K9me3 rep 2

description: Chip-chip experiment

source_name: standard growth conditions

source_name: K9me3 immunoprecipitate fraction from standard growth conditions

tag: immunoprecipitate fraction


title: wt H3K9me3 rep 1

description: Chip-chip experiment

source_name: input stantard growth conditions

tag: H3K9me3 immunoprecipitate fraction


title: wt strain N150 MeDIP rep 1

description: Chip-chip experiment

source_name: wt strain N150

source_name: wild type strain N150

tag: Methylated DNA immunoprecipitate fraction


title: A22_T_P

source_name: T cells

tag: patient

tag: patient ID_REF


title: A1_CD34_C

source_name: stem cells

tag: control


title: A35_20h_P

source_name: macrophages


title: A34_20h_P


title: A41_20h_C


title: A4_20h_C_rep2


title: A30_T_C


title: A41_3h_C

source_name: stimulated monocyes


title: A10_CD14_P

source_name: resting monocyes


title: A6_CD34_P


title: A15_CD14_P


title: A31_CD14_P


title: A5_CD14_C


title: A25_20h_P


title: A25_3h_P


title: A13_T_C_rep2


title: A39_CD14_C


title: A37_T_P


title: A38_CD14_P


title: A39_3h_C


title: A38_3h_P


title: A36_CD14_P


title: A33_20h_P


title: A37_CD14_P


title: A25_T_P


title: A25_CD14_P


title: A19_20h_P


title: A3_20h_C


title: A20_CD14_P


title: A9_3h_C


title: A41_CD14_C


title: A9_CD14_C


title: A41_T_C


title: A32_20h_C


title: A13_CD14_C


title: A12_20h_C


title: A13_CD34_C


title: A30_CD14_C


title: A31_20h_P


title: A22_CD14_P


title: A10_20h_P


title: A5_20h_C


title: A20_3h_P


title: rde-4 mutant, biological rep 3

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

description:
Gene expression data from stage L1-L2 rde-4 mutant nematodes
A7037_rde-4_3

hyb_protocol: Following fragmentation, 18 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 7G.

data_processing: Raw data (CEL files) processing and normalization was performed using the Bioconductor (http://www.bioconductor.org/ ) packages ‘affy’ and ‘gcrma’ to generate the dataset of GC-RMA expression measures.

organism: Caenorhabditis elegans

source_name: L1-L2 stage nematodes, rde-4 mutant

label_protocol: Biotinylated cRNA was prepared according to the standard (one-cycle) Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix, P/N 702232 Rev. 2).

growth_protocol: Worms were maintained on nematode growth medium plates seeded with OP50 bacteria.

extract_protocol: Tri Reagent (MRC) was used for total RNA preparation from frozen worms resulting in 5-30 microgram RNA per sample. The quality of RNA samples was confirmed by BioRad Bioanalyzer.

treatment_protocol: Nematodes were synchronized at L1 stage by hypochlorite treatment of gravid hermaphrodites and hatching their eggs overnight in liquid culture without food. Resulting populations were cultured on OP50 bacteria for 6-7h and collected for RNA preparations.

tag: strain


title: lin-35 mutant, biological rep 1

description:
Gene expression data from stage L1-L2 lin-35 unc-13 double mutant nematodes
A7038_lin-35_1

source_name: L1-L2 stage nematodes, lin-35 mutant


title: lin-35 mutant, biological rep 2, technical rep 2

description:
Gene expression data from stage L1-L2 lin-35 unc-13 double mutant nematodes
A7040_lin-35_3


title: lin-35 mutant, biological rep 2, technical rep 1

description:
Gene expression data from stage L1-L2 lin-35 unc-13 double mutant nematodes
A7039_lin-35_2


title: A10_CD34_P


title: rde-4 mutant, biological rep 2

description:
Gene expression data from stage L1-L2 rde-4 mutant nematodes
A7036_rde-4_2