title: colon VC 2 day DSS rep4

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 2 day of DSS treatment, replicate 4


title: Oregon Rhesus Macaque Embryonic Stem9 (ORMES9),biological rep A

status: Public on Jun 21 2010

type: RNA

city: Beaverton

first: Hathaitip

last: Sritanaudomchai

state: OR

country: USA

institute: OHSU

description: Gene expression profile of ORMES9A is homozygous parthenote profile, only one allele inherited from the mother, in biological replicate A.

hyb_protocol: Labeled target is fragmented at 95C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files).  Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

label: Biotin

molecule: total RNA

organism: Macaca mulatta

source_name: ORMES9A were embryonic stem cells which dereived from IVF blastocyst.

label_protocol: Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

growth_protocol: ORMES9A were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol: ORMES9A established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.13.

tag: gender

value: female

tag: embryo

value: Blastocyst

tag: cell type

value: embryonic stem cell


title: C2C12 NegControl IgG, rep 1

city: Newark

first: Ju Youn

last: Lee

state: NJ

address: 185 South Orange Ave. MSB-E501

department: Biochemistry

institute: UMDNJ-New Jersey Medical School

description: This sample was negative IP

hyb_protocol: 100ng of total RNA for immunoprecipitation arrays were used to generate labeled cDNA fragments for hybridization to Mouse Affymetrix Gene 1.0 ST Arrays following the manufacturer’s protocol (GeneChipTM WT cDNA Synthesis Kit #900652 and #900720).

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000G

data_processing: Transcripts whose probe sets with detection above background (DABG) P-value < 0.05 in at least 2 out of 3 replicates at the 0 min time point were considered expressed and used for subsequent analyses. All probe set values were normalized to the 5th percentile value of all probe sets on the same array.

label: biotin

organism: Mus musculus

source_name: C2C12 Negative IP(IgG)

label_protocol: Biotinylated DNA probes were prepared according to Whole Transcript Sense Target Labeling Manual (Affymetrix)

growth_protocol: C2C12 cells were obtained from ATCC (CRL-1772). These cell lines were cultured in DMEM with 10% FBS, 10 U/ml penicillin, 10 µg/ml streptomycin, and 1g/ml puromycin.  The cells were maintained below 70% confluency to prevent differentiation.

extract_protocol: Cells were collected in Trizol™ (Invitrogen) at the indicated time points following the incubation and total RNA was prepared according to the manufacturers instructions.  RNA concentration, purity, and quality were determined via Bioanalyzer (Agilent).

treatment_protocol: Immunoprecipitates were isolated by incubating 100µl of cleared lysate with 7µl of normal IgG (Santa Cruz sc-3877) or αCUGBP1 antibody (monoclonal 3B1) for 1 hour on ice. Following brief centrifugation at 4°C, the reaction was transferred to 100µl of a 10% slurry of Protein-G sepharose beads (Sigma) in NT-2 buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2, 0.05% Nonidet P-40) and rocked for 1 hour at 4˚C. Beads were washed twice with 250µl of NT-2 buffer, transferred to a micro-spin column (Pierce) and washed four more times with 200L of NT-2 buffer.

tag: antibody

value: normal IgG

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

value: proliferating C2C12 (LKO-1) cells (<70% confluency)


title: colon VC 2 day DSS rep1

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

hyb_protocol: The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

scan_protocol: The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were normalized using GC-RMA algorithm in R statistical environment (version 2.10.1). Linear modeling was performed using the bioconductor package 'limma'.

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 2 day of DSS treatment, replicate 1

label_protocol: RNA was processed and labeled according to the standard target labeling protocols.

growth_protocol: Intestine tissue and intestinal epithelial cells were obtained from tissue-specific PPARγ fl/fl; Villin Cre+ (VC+) and Villin Cre- control mice (WT). Duodenum, jejunum, ileum, cecum and colon were excised. For cell isolation, the different parts of the intestine were washed with PBS, minced and digested twice in CMF/FBS/EDTA media at 37oC for 15 minutes. The digest was passed through a nylon mesh and supernatants were collected and centrifuged. Cells were washed and resuspended in lysis buffer. DNA was extracted by using the QIAamp DNA Mini Kit, Blood and Body Fluid Spin Protocol (Qiagen). For whole tissue DNA isolation, each part of the intestine was collected and homogenized and then genomic DNA was extracted by QIAamp DNA Mini Kit, Tissue Protocol (Qiagen).  And PCR was performed as previously described [Adachi2006] and PCR amplifications were resolved through ethidium bromide staining on a 2% agarose gel and run at 120 V for 30 minutes.

extract_protocol: After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

treatment_protocol: PPAR g flfl; Villin Cre+ (VC+, n=45) and control PPAR g flfl; Villin Cre- (WT, n=42) mice were used for these experiments. These mice express a transgenic recombinase under the control of the Villin-Cre promoter .  The mice were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 750 F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.  Mice were challenged with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 molecular weight (ICN Biomedicals, Aurora, OH) in the drinking water.  After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection).  For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score . Briefly, disease activity index consisted of a scoring for diarrhea and lethargy (0–3), whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area (0–4).  Mice in the DSS study were euthanized on days 0, 2, and 7 of the DSS challenge by carbon dioxide narcosis followed by secondary thoracotomy and blood was withdrawn from the heart.  Spleen and mesenteric lymph nodes (MLN) were scored based on size and macroscopic inflammatory lesions (0-3), excised, and single-cell suspensions were prepared as previously described  for flow cytometry.

tag: genotype

value: Villin-CRE+ (PPAR g null epithelial cell)

tag: day of dss treatment

tag: tissue

value: colonic mucosa


title: C2C12 CUGBP1 IP, rep 2

description: This sample was CUGBP1 IP

source_name: C2C12 CUGBP1 IP

value: CUG-BP1 (3B1)


title: soybean seed 72h rep1

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

description: Gene expression data from 5WAF seeds free-running in continuous light at 72h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with fluidics protocol EukGE_WS2v5 and user prepared solutions. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning.

data_processing: Data tables report only soybean probe set data, as discussed in publication.  Signal intensity data were normalized using the threestep method from Bioconductor: GCRMA background correction, scaling normalization, and median polish for summarization, for all probes on the array.

organism: Glycine max

source_name: entrained soybean seed 72h light

label_protocol: Biotinylated cRNA were prepared from 2.5 ug total RNA according to the BioArray Single Round RNA Amplification and Labeling System ver. 2.1 (Enzo Life Sciences).

growth_protocol: Plants were grown in soil under 12h light (350micromoles m-2 s-1):12 h dark cycles at 25C, 75% relative humidity in a growth chamber with fluorescent and incandescent lighting. Seeds staged at 5 weeks after flowering (WAF) were collected at times specified after lights were switched to constant 350 micromoles m-2 s-1.

extract_protocol: Seeds (with seed coats) were flash frozen in liquid nitrogen, total RNA was extracted by the CTAB method.

treatment_protocol: Plants were introduced to free-running constant light at subjective dawn, humidity and temperature remained constant.

value: seed

value: Williams 82

tag: time


title: soybean seed 60h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 60h

source_name: entrained soybean seed 60h light


title: soybean seed 64h rep1

description: Gene expression data from 5WAF seeds free-running in continuous light at 64h

source_name: entrained soybean seed 64h light


title: rhesus Parthenogenetic Embryonic Stem Cell2 (rPESC2), biological rep C

description: Gene expression profile of rPESC2C is heterozygous parthenote profile, ie, contains two different forms, one for each allele present, in biological replicate C.

source_name: rPESC2C were embryonic stem cells which derived from parthenogenetic blastocyst.

growth_protocol: rPESC2C were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: rPESC2C established from rhesus monkey parthenogenetic blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage 16.


title: soybean seed 64h rep2


title: Oregon Rhesus Macaque Embryonic Stem22 (ORMES22),biological rep C

description: Gene expression profile of ORMES22C is biparental controls profile in biological replicate C.

source_name: ORMES22C were embryonic stem cells which dereived from IVF blastocyst.

growth_protocol: ORMES22C were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: ORMES22C established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.19.


title: colon VC 0 day DSS rep3

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 0 day of DSS treatment, replicate 3


title: rhesus Parthenogenetic Embryonic Stem Cell2 (rPESC2), biological rep B

description: Gene expression profile of rPESC2B is heterozygous parthenote profile, ie, contains two different forms, one for each allele present, in biological replicate B.

source_name: rPESC2B were embryonic stem cells which derived from parthenogenetic blastocyst.

growth_protocol: rPESC2B were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: rPESC2B established from rhesus monkey parthenogenetic blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.10.


title: colon VC 0 day DSS rep2

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 0 day of DSS treatment, replicate 2


title: Oregon Rhesus Macaque Embryonic Stem22 (ORMES22),biological rep B

description: Gene expression profile of ORMES22B is biparental controls profile in biological replicate B.

source_name: ORMES22B were embryonic stem cells which dereived from IVF blastocyst.

growth_protocol: ORMES22B were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: ORMES22B established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.21.


title: rhesus Parthenogenetic Embryonic Stem Cell2 (rPESC2), biological rep A

description: Gene expression profile of rPESC2A is heterozygous parthenote profile, ie, contains two different forms, one for each allele present, in biological replicate A.

source_name: rPESC2A were embryonic stem cells which derived from parthenogenetic blastocyst.

growth_protocol: rPESC2A were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: rPESC2A established from rhesus monkey parthenogenetic blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.16.


title: soybean seed 68h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 68h

source_name: entrained soybean seed 68h light


title: colon VC 7 day DSS rep1

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 7 day of DSS treatment, replicate 1


title: colon VC 0 day DSS rep1

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 0 day of DSS treatment, replicate 1


title: soybean seed 72h rep2


title: C2C12 with actinomycin D, time 110 min, rep 3

description: This sample was collected at 110 min after actinomycin D treatment

hyb_protocol: 300ng of total RNA for half life arrays were used to generate labeled cDNA fragments for hybridization to Mouse Affymetrix Gene 1.0 ST Arrays following the manufacturer’s protocol (GeneChipTM WT cDNA Synthesis Kit #900652 and #900720).

source_name: C2C12 with actinomycin D, time 110 min

treatment_protocol: Transcription was inhibited by addition of Actinomycin-D (8μg/mL Sigma) for a period of 30 min.

tag: cell line

value: CRL-1772 (ATCC)


title: soybean seed 68h rep1


title: Skin fibroblasts, biological rep A

description: Gene expression of fibroblastsA is somatic cells control profile in biological replicate A.

source_name: Somatic fibroblastsA were derived from a skin biopsy from a nine year old adult rhesus monkey.

growth_protocol: FibroblastsA were grown at 37oC, 3% CO2, 5%O2 and 92% N2 in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 10% fetal bovine serum (FBS), with the pH adjusted to 7.2 with NaOH. Medium was changed every other day.

treatment_protocol: FibroblastsA were isolated from back skin tissues with 0.1 mg/ml collagenase. The fibroblast cells have been stored at -80°C until total RNA was extracted.

value: male

value: Skin

value: fibroblasts


title: soybean seed 56h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 56h

source_name: entrained soybean seed 56h light


title: C2C12 with actinomycin D, time 230 min, rep 3

description: This sample was collected at 230 min after actinomycin D treatment

source_name: C2C12 with actinomycin D, time 230 min


title: C2C12 with actinomycin D, time 230 min, rep 2


title: C2C12 CUGBP1 IP, rep 1

description: This sample was CUGBP1 IP

source_name: C2C12 CUGBP1 IP


title: soybean seed 60h rep1

source_name: entrained soybean seed 60h light


title: soybean seed 56h rep1


title: soybean seed 52h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 52h

source_name: entrained soybean seed 52h light


title: Oregon Rhesus Macaque Embryonic Stem22 (ORMES22),biological rep A

description: Gene expression profile of ORMES22A is biparental controls profile in biological replicate A.

source_name: ORMES22A were embryonic stem cells which dereived from IVF blastocyst.

growth_protocol: ORMES22A were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: ORMES22A established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.18.


title: C2C12 with actinomycin D, time 230 min, rep 1


title: Skin fibroblasts, biological rep B

description: Gene expression of fibroblastsB is somatic cells control profile in biological replicate B.

source_name: Somatic fibroblastsB were derived from a skin biopsy from a nine year old adult rhesus monkey.

growth_protocol: FibroblastsB were grown at 37oC, 3% CO2, 5%O2 and 92% N2 in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 10% fetal bovine serum (FBS), with the pH adjusted to 7.2 with NaOH. Medium was changed every other day.

treatment_protocol: FibroblastsB were isolated from back skin tissues with 0.1 mg/ml collagenase. The fibroblast cells have been stored at -80°C until total RNA was extracted.


title: soybean seed 48h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 48h

source_name: entrained soybean seed 48h light


title: C2C12 with actinomycin D, time 110 min, rep 1


title: C2C12 with actinomycin D, time 110 min, rep 2


title: colon_WT_7dayDSS_rep2

data_processing: The data were normalized using GC-RMA algorithm in R statistical environment (version 2.9.0). Linear modeling was performed using the bioconductor package 'limma'.

source_name: colonic mucosa, wild-type CD4+ T cells, 7 day of DSS treatment, replicate 2

growth_protocol: PPAR g flfl; CD4Cre+ (CD4cre, n=34) and wild-type mice (WT, n=34) in C57BL/6J background were used for these experiments. The CD4cre mice (kindly provided by Dr. R.B. Clark, University of Connecticut) express a transgenic recombinase under the control of the CD4-Cre promoter. Since all T cells express CD4 at the thymic level (during the double-positive stage) the PPAR g gene is deleted from both CD4+ and CD8+ T cells. The mice were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 deg F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.

treatment_protocol: Mice were challenged with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water and euthanized on days 0, 2, and 7 of the DSS challenge by carbon dioxide narcosis.

tag: genotype/variation

value: Wild-type

tag: agent

value: DSS

tag: time (days of dss treatment)


title: colon_WT_7dayDSS_rep1

source_name: colonic mucosa, wild-type CD4+ T cells, 7 day of DSS treatment, replicate 1


title: C2C12 with actinomycin D, time 50 min, rep 3

description: This sample was collected at 50 min after actinomycin D treatment

source_name: C2C12 with actinomycin D, time 50 min


title: 10A Cell Line Radiation-treated

city: Baltimore

first: Venu

last: Raman

state: MD

address: 733 North Broadway

department: Rad MR Research

institute: The Johns Hopkins University School of Medicine

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

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

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.

organism: Homo sapiens

source_name: Breast epithelial cells - Radiation

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 (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: The immortalized non-tumorigenic human mammary epithelial cell line, MCF 10A, was maintained in Growth Medium composed of DMEM/F12 (Mediatech, Inc., Herndon, VA) supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor (EGF), 10 μg/ml insulin, 0.5 μg/ml hydrocortisone (Sigma, St. Louis, MO), and 100 ng/ml cholera toxin (Cambrex, Westborough, MA).

extract_protocol: RNeasy Kit (QIAGEN)

treatment_protocol: Immortalized non-tumorigenic human mammary epithelial cell line, MCF 10A was exposed to radiation, then incubated for 72 hr.

value: MCF 10A human breast epithelial cell line

tag: protocol

value: radiation treated


title: soybean seed 52h rep1


title: 10A Cell Line Smoke- and Radiation-treated

source_name: Breast epithelial cells - Smoke and Radiation

treatment_protocol: Immortalized non-tumorigenic human mammary epithelial cell line, MCF 10A was exposed to cigarette smoke extract AND radiation, then incubated for 72 hr.

value: cigarette smoke extract and radiation treated


title: colon_WT_2dayDSS_rep3

source_name: colonic mucosa, wild-type CD4+ T cells, 2 day of DSS treatment, replicate 3


title: colon_WT_2dayDSS_rep2

source_name: colonic mucosa, wild-type CD4+ T cells, 2 day of DSS treatment, replicate 2


title: soybean seed 44h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 44h

source_name: entrained soybean seed 44h light


title: C2C12 with actinomycin D, time 50 min, rep 2


title: soybean seed 48h rep1


title: colon_WT_0dayDSS_rep3

source_name: colonic mucosa, wild-type CD4+ T cells, 0 day of DSS treatment, replicate 3

value: no DSS


title: Mycelium_AonBon_rep4

city: Bloomington

first: Claire

last: Burns

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description: Biological replicate 4 of 4

hyb_protocol: Microarray slides were blocked prior to hybridization with 5xSSC, 0.1%SDS, 0.1mg.ml-1 BSA at 42oC for 45 min, after which slides were rinsed twice in room temperature 0.1xSSC for 5 min each, followed by a final 10s rinse in water.  Slides were dried by centrifugation for 1min in a Labnet C1303 slide spinner. Arrays were placed in Corning hybridization chambers and mSeries Lifterslips (Erie Scientific) placed over the array grids.  Labelled cDNAs were combined in 50μl with 30% deionized formamide (Ambion), 5xSSPE, 0.2% SDS, 1μg.μl-1 tRNA (Invitrogen), 40ng.μl-1 oligo dA (Invitrogen).  The hybridization mixture was heated at 100oC for 2min, cooled to 25oC, and applied to the microarray slide.  Slides were hybridized for 16 hours at 42oC, and then washed at ambient temperature for 5 min each in 1xSSC, 0.03%SDS , then 0.2xSSC, and finally 0.1xSSC. Slides were dried by centrifugation, as previously, and scanned immediately.

scan_protocol: Microarray slides were scanned using a GenePix 4000B scanner (Molecular Devices).  PMT settings were adjusted so the dye channels were balanced, with a few saturated spots, to maximize data capture.  Spots were identified using GenePix Pro software (Molecular Devices) and manual inspection. Spots were manually flagged to be excluded from analysis if there were areas of poor quality such as scratches or dust.  Spots were also flagged for omission, using GenePix software, if they fulfilled any of the following criteria: manually flagged, spots not found, sum of medians (experimental/control) < 200, spot pixels < 40.  Flagged data was not included in the statistical analysis.

data_processing: Data normalization and filtering were performed using the Bioconductor package (http://www.bioconductor.org/) within the R statistical framework (http://www.r-project.org/).  OLIN was used for intra-slide normalization and log2 transformation.  For statistical analysis, data for a given oligonucleotide were included if two out of four biological replicates for each experimental strain contained data for both probes.  Ratio values were exported for further analysis, with individual flagged ratio values omitted. Ratio values were z-adjusted. Statistical significance of differential expression was assessed using the one class function in Significance Analysis of Microarrays (SAM) software.

label: Alexa fluor 647

organism: Coprinopsis cinerea

source_name: C. cinerea AmutBmut # 425 mycelium (experimental)

label_protocol: Total RNA (20 ug) was reverse transcribed and labelled with Alexa fluor using the Invitrogen Superscript Indirect labeling kit.

growth_protocol: For each biological replicate, C.cinerea dikaryon strains AmutB43 (422), A43Bmut (423), A43B43 (424), and AmutBmut (425) were incubated 3 days at 37°C on YMGt media with cellophane membranes.

extract_protocol: Five colonies were harvested for each sample after 3 days of growth, and immediately frozen in liquid nitrogen. RNA was extracted from all the tissue collected using RNeasy Plant mini-prep kit.

tag: strain

value: AmutBmut # 425

value: mycelium

label: Alexa fluor 555

source_name: C. cinerea A43B43 # 424 mycelium (control)

value: A43B43 # 424, unmated monokaryotic strain


title: Mycelium_AonBon_rep2

description: Biological replicate 2 of 4


title: 10A Cell Line Control

source_name: Breast epithelial cells - Control

treatment_protocol: Immortalized non-tumorigenic human mammary epithelial cell line, MCF 10A was NOT exposed to radiation or cigarette smoke condensate, then  incubated for 72 hr.

value: untreated control


title: colon_WT_2dayDSS_rep1

source_name: colonic mucosa, wild-type CD4+ T cells, 2 day of DSS treatment, replicate 1


title: C2C12 with actinomycin D, time 10 min, rep 2

description: This sample was collected at 10 min after actinomycin D treatment

source_name: C2C12 with actinomycin D, time 10 min

value: proliferating C2C12 (LKO-1) cells (<70% confluency)


title: Mycelium_AonBon_rep3

description: Biological replicate 3 of 4


title: C2C12 with actinomycin D, time 10 min, rep 3


title: C2C12 with actinomycin D, time 10 min, rep 1


title: colon_WT_0dayDSS_rep1

source_name: colonic mucosa, wild-type CD4+ T cells, 0 day of DSS treatment, replicate 1


title: C2C12 with actinomycin D, time 50 min, rep 1


title: soybean seed 40h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 40h

source_name: entrained soybean seed 40h light

value: seed


title: C2C12 with actinomycin D, time 0 min, rep 2

description: This sample was collected at 0 min after actinomycin D treatment

source_name: C2C12 with actinomycin D, time 0 min


title: colon_CD4cre_7dayDSS_rep3

source_name: colonic mucosa, PPARg null CD4+ T cells, 7 day of DSS treatment, replicate 3

value: CD4-CRE+ (PPAR g null)


title: C2C12 with actinomycin D, time 0 min, rep 3

value: CRL-1772 (ATCC)


title: soybean seed 36h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 36h

source_name: entrained soybean seed 36h light

value: Williams 82


title: Mycelium_Bon_rep3

description: Biological replicate 3 of 4

source_name: C. cinerea A43Bmut # 423 mycelium (experimental)


title: Mycelium_Bon_rep2

description: Biological replicate 2 of 4


title: soybean seed 44h rep1


title: colon_CD4cre_7dayDSS_rep1

source_name: colonic mucosa, PPARg null CD4+ T cells, 7 day of DSS treatment, replicate 1


title: colon_CD4cre_7dayDSS_rep2

source_name: colonic mucosa, PPARg null CD4+ T cells, 7 day of DSS treatment, replicate 2


title: Mycelium_Bon_rep4

description: Biological replicate 4 of 4


title: soybean seed 36h rep1


title: soybean seed 40h rep1


title: soybean seed 32h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 32h

source_name: entrained soybean seed 32h light


title: colon_WT_0dayDSS_rep2

source_name: colonic mucosa, wild-type CD4+ T cells, 0 day of DSS treatment, replicate 2


title: Mycelium_AonBon_rep1

description: Biological replicate 1 of 4


title: colon_CD4cre_2dayDSS_rep3

source_name: colonic mucosa, PPARg null CD4+ T cells, 2 day of DSS treatment, replicate 3


title: C2C12 with actinomycin D, time 0 min, rep 1


title: soybean seed 32h rep1


title: Mycelium_Bon_rep1

description: Biological replicate 1 of 4


title: Mycelium_Aon_rep4

description: Biological replicate 4 of 4

source_name: C. cinerea AmutB43 # 422 mycelium (experimental)


title: colon_CD4cre_2dayDSS_rep2

source_name: colonic mucosa, PPARg null CD4+ T cells, 2 day of DSS treatment, replicate 2


title: soybean seed 28h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 28h

source_name: entrained soybean seed 28h light


title: Mycelium_Aon_rep1

description: Biological replicate 1 of 4

source_name: C. cinerea A43B43 # 424 mycelium (control)


title: Mycelium_Aon_rep3

description: Biological replicate 3 of 4


title: soybean seed 28h rep1


title: Mycelium_Aon_rep2

description: Biological replicate 2 of 4


title: soybean seed 24h rep2

description: Gene expression data from 5WAF seeds free-running in continuous light at 24h

source_name: entrained soybean seed 24h light


title: soybean seed 24h rep1


title: colon_CD4cre_0dayDSS_rep3

source_name: colonic mucosa, PPARg null CD4+ T cells, 0 day of DSS treatment, replicate 3


title: A8 PBMC T6 rep 8

status: Public on Jun 20 2010

city: Singapore

first: Lim

last: Chee Seng

address: Singapore

country: Singapore

institute: National University of Singapore

description: Gene Expression Data 6 hour

hyb_protocol: Following fragmentation, 10 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 400.

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

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

source_name: PBMC 6 hour

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

growth_protocol: PBMC cells were harvested in the morning from healthy human subject.

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

treatment_protocol: PBMC cells were maintained in the RPMI 1640 medium and induced with H2O2 after 24 hour harvesting from whole blood.

value: PBMC

tag: sex

value: female


title: A7 PBMC T3 rep 7

description: Gene Expression Data 3 hour

source_name: PBMC 3 hour


title: A6 PBMC T3 rep 6

description: Gene Expression Data 3 hour


title: A1 PBMC T6 rep 1

description: Gene Expression Data 6 hour


title: colon_CD4cre_0dayDSS_rep1

source_name: colonic mucosa, PPARg null CD4+ T cells, 0 day of DSS treatment, replicate 1


title: A8 PBMC T3 rep 8

description: Gene Expression Data 3 hour


title: A7 PBMC T6 rep 7

description: Gene Expression Data 6 hour


title: A6 PBMC T6 rep 6

description: Gene Expression Data 6 hour


title: A4 PBMC T6 rep 4

description: Gene Expression Data 6 hour


title: A5 PBMC T6 rep 5

description: Gene Expression Data 6 hour


title: colon_CD4cre_2dayDSS_rep1

source_name: colonic mucosa, PPARg null CD4+ T cells, 2 day of DSS treatment, replicate 1


title: GIST sample 24

type: genomic

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

hyb_protocol: Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: Human GIST tissue 24

label_protocol: Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.

growth_protocol: A total of 25 GIST specimens were obtained from surgical resection.

extract_protocol: Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.

treatment_protocol: No treatment was carried out.

tag: gender

value: male

source_name: Human Genomic DNA (Promega)

extract_protocol: not applicable


title: GIST sample 16

source_name: Human GIST tissue 16


title: GIST sample 22

source_name: Human GIST tissue 22


title: GIST sample 18

source_name: Human GIST tissue 18


title: A2 PBMC T6 rep 2

description: Gene Expression Data 6 hour


title: GIST sample 21

source_name: Human GIST tissue 21


title: 10A Cell Line Smoke-treated

source_name: Breast epithelial cells - cigarette smoke treated

treatment_protocol: Immortalized non-tumorigenic human mammary epithelial cell line, MCF 10A was exposed to cigarette smoke extract, then incubated for 72 hr.

value: cigarette smoke extract treated


title: A3 PBMC T6 rep 3

description: Gene Expression Data 6 hour


title: colon_CD4cre_0dayDSS_rep2

source_name: colonic mucosa, PPARg null CD4+ T cells, 0 day of DSS treatment, replicate 2


title: GIST sample 14

source_name: Human GIST tissue 14


title: GIST sample 23

source_name: Human GIST tissue 23


title: GIST sample 19

source_name: Human GIST tissue 19


title: GIST sample 25

source_name: Human GIST tissue 25


title: A5 PBMC T3 rep 5

description: Gene Expression Data 3 hour


title: GIST sample 17

source_name: Human GIST tissue 17


title: GIST sample 13

source_name: Human GIST tissue 13


title: GIST sample 15

source_name: Human GIST tissue 15


title: GIST sample 20

source_name: Human GIST tissue 20


title: A4 PBMC T3 rep 4

description: Gene Expression Data 3 hour

source_name: PBMC 3 hour


title: A7 PBMC T0 rep 7

description: Gene Expression Data Baseline

source_name: PBMC 0 hour


title: GIST sample 11

source_name: Human GIST tissue 11

source_name: Human Genomic DNA (Promega)


title: A6 PBMC T0 rep 6

description: Gene Expression Data Baseline


title: A1 PBMC T0 rep 1

description: Gene Expression Data Baseline


title: GIST sample 9

source_name: Human GIST tissue 9


title: A2 PBMC T0 rep 2

description: Gene Expression Data Baseline


title: GIST sample 10

source_name: Human GIST tissue 10


title: GIST sample 7

source_name: Human GIST tissue 7


title: GIST sample 4

source_name: Human GIST tissue 4


title: GIST sample 3

source_name: Human GIST tissue 3


title: A3 PBMC T0 rep 3

description: Gene Expression Data Baseline


title: GIST sample 2

source_name: Human GIST tissue 2


title: A4 PBMC T0 rep 4

description: Gene Expression Data Baseline


title: A5 PBMC T0 rep 5

description: Gene Expression Data Baseline


title: GIST sample 1

source_name: Human GIST tissue 1


title: GIST sample 6

source_name: Human GIST tissue 6


title: GIST sample 5

source_name: Human GIST tissue 5


title: A3 PBMC T3 rep 3

description: Gene Expression Data 3 hour


title: A2 PBMC T3 rep 2

description: Gene Expression Data 3 hour


title: GM12878 +VITD 8hr BR1 15.11.2009

status: Public on Jun 19 2010

city: Aarhus N

first: Thomas

last: Thykjaer

address: IncubaSciencePark Skejby

country: Denmark

institute: AROS Applied Biotechnology

description: 8 hour calcitriol stimulated

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console ver. 1.0. using Affymetrix default analysis settings and RMA normalisation.

source_name: hapmap cell line GM12878

label_protocol: Biotinylated cDNA were prepared according to the WT Affymetrix protocol from 100 ng total RNA.

extract_protocol: Exiqon RNA extraction kit according to manufacturers instructions

tag: time point

value: 8 hr

value: calcitriol


title: GIST sample 12

source_name: Human GIST tissue 12


title: GM12878 +VITD 36hr BR1 15.11.2009

description: 36 hour calcitriol stimulated

value: 36 hr


title: GM12878 +VITD 36hr BR2 15.11.2009

description: 36 hour calcitriol stimulated


title: GM12878 +VITD 8hr BR2 15.11.2009

description: 8 hour calcitriol stimulated


title: AG09319 +VITD 8hr BR2 15.11.2009

description: 8 hour calcitriol stimulated

source_name: cell line Ag09319


title: HEP-G2 +VITD 36hr BR1 15.11.2009

description: 36 hour calcitriol stimulated

source_name: cell line HEP-G2


title: GM12878 Unstim BR2 15.11.2009


title: AG09319 Unstim BR2 15.11.2009


title: GM12878 Unstim BR1 15.11.2009


title: AG09319 +VITD 36hr BR2 15.11.2009

description: 36 hour calcitriol stimulated


title: AG09319 +VITD 8hr BR1 15.11.2009

description: 8 hour calcitriol stimulated


title: S.R. K562, BR1, 36hr

description: 36 hour calcitriol stimulated

source_name: cell line K562


title: HEP-G2 +VITD 8hr BR2 15.11.2009

description: 8 hour calcitriol stimulated


title: HEP-G2 +VITD 8hr BR1 15.11.2009

description: 8 hour calcitriol stimulated


title: AG09319 +VITD 36hr BR1 15.11.2009

description: 36 hour calcitriol stimulated


title: S.R. K562, BR2, 36hr

description: 36 hour calcitriol stimulated


title: AG09319 Unstim BR1 15.11.2009


title: HEP-G2 +VITD 36hr BR2 15.11.2009

description: 36 hour calcitriol stimulated


title: HEP-G2 Unstim BR1 15.11.2009


title: HEP-G2 Unstim BR2 15.11.2009


title: S.R. K562, BR2, 8hr

description: 8 hour calcitriol stimulated


title: S.R. K562, BR2, 0hr


title: S.R. K562, BR1, 8hr

description: 8 hour calcitriol stimulated


title: S.R. HL60, BR2, 8hr

description: 8 hour calcitriol stimulated

source_name: cell line HL60


title: S.R. HL60, BR2, 36hr

description: 36 hour calcitriol stimulated


title: S.R. HL60, BR1, 36hr

description: 36 hour calcitriol stimulated


title: S.R. HL60, BR1, 8hr

description: 8 hour calcitriol stimulated


title: S.R. K562, BR1, 0hr


title: S.R. Ag09309, BR2, 36hr

description: 36 hour calcitriol stimulated

source_name: cell line Ag09309


title: S.R. HL60, BR2, 0hr


title: S.R. Ag09309, BR2, 8hr

description: 8 hour calcitriol stimulated


title: S.R. Ag09309, BR1, 36hr

description: 36 hour calcitriol stimulated


title: S.R. Ag09309, BR1, 0hr


title: S.R. GM18054, BR2, 36hr

description: 36 hour calcitriol stimulated

source_name: hapmap cell line GM10854


title: S.R. GM18054, BR2, 8hr

description: 8 hour calcitriol stimulated


title: A8 PBMC T0 rep 8

description: Gene Expression Data Baseline

source_name: PBMC 0 hour

tag: cell type


title: S.R. HL60, BR1, 0hr


title: A1 PBMC T3 rep 1

description: Gene Expression Data 3 hour

source_name: PBMC 3 hour


title: S.R. Ag09309, BR2, 0hr


title: GIST sample 8

source_name: Human GIST tissue 8

source_name: Human Genomic DNA (Promega)


title: S.R. GM18054, BR1, 8hr

description: 8 hour calcitriol stimulated


title: S.R. GM18054, BR1, 36hr

description: 36 hour calcitriol stimulated


title: S.R. GM18054, BR1, 0hr


title: S.R. Ag09309, BR1, 8hr

description: 8 hour calcitriol stimulated


title: S.R. GMO7348, BR2, 8hr

description: 8 hour calcitriol stimulated

source_name: hapmap cell line GM07348


title: S.R. GMO7348, BR2, 0hr


title: S.R. GMO7348, BR1, 0hr


title: S.R. GMO7348, BR1, 8hr

description: 8 hour calcitriol stimulated


title: S.R. GMO7348, BR1, 36hr

description: 36 hour calcitriol stimulated


title: S.R. GMO7348, BR2, 36hr

description: 36 hour calcitriol stimulated


title: S.R. GM18054, BR2, 0hr


title: S.R. GMO7019, BR2, 8hr

description: 8 hour calcitriol stimulated

source_name: hapmap cell line GM07019


title: S.R. GMO7019, BR1, 36hr

description: 36 hour calcitriol stimulated


title: S.R. GMO7019, BR2, 36hr

description: 36 hour calcitriol stimulated


title: S.R. GMO7019, BR2, 0hr


title: S.R. GMO7019, BR1, 8hr

description: 8 hour calcitriol stimulated


title: mid2 mutant 4 hours exposure to Congo Red 1

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: For each condition tested, comparison of treated and non-treated samples, the total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.

hyb_protocol: Slides were prehybridized in prehybridization solution (6 x SSC, 0.5% SDS, 1% bovine serum albumin (A-7906, Sigma) for 1 h and were then hybridized overnight in a LucideaTM SlidePro Automated Hybridization Station (Amersham Biosciences). Before scanning, the chips were washed and dried in a same LucideaTM SlidePro Automated Hybridization

scan_protocol: Microarrays were scanned with aGenePix 4000B scanner (Axon Instruments, Union City, CA) at a resolution of 5 μm (PMT values ranging from 550 to 700 and laser power 100%). GenePix Pro 4.0 analysis software (Axon Instruments, Union City, CA) was used to locate spots in the microarray with the appropriate grid and to obtain the two Cy3/Cy5 image TIFF files. All images were further processed using GenePix 4.0 software according to the manufacturer’s instructions.

data_processing: Flagged spots and spots with an average intensity minus background below the mean of the background (considering this as the median of the local background for each spot) for all the non-flagged spots in any of the channels (Cy3 or Cy5) were not retained for further analysis. Within this group, the spots showing in one channel a value of intensity minus background higher than 5 times the mean of the background for all spots in the microarray for that channel were recovered. The reproducibility of replicates in each microarray (two spots per ORF) was analyzed by creating a normal distribution log2 (RA _ 1/RB), where RA and RB are the ratios of replicated spots after background subtraction and normalization. Replicates that exceeded the average by more than _3 S.D. were discarded. Data analysis was accomplished using the GeneSight 4.0 software package (BioDiscovery Inc, El Segundo, CA). Locally weighed linear regression (lowess) analysis was performed as a normalization method to remove the intensity-dependent deviation in the log2(ratio) values. Significance analysis of the results was conducted using a Student’s t test (GeneSight). Genes with p values of less than 0.05 were considered to be significantly differentially expressed with respect to the treatment condition.

organism: Saccharomyces cerevisiae

source_name: total RNA Saccharomyces cereviase mid2 mutant, without Congo Red

label_protocol: cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy5- dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20 μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)

extract_protocol: Total RNA was isolated from exponentially growing cells (5 x 108) by the “mechanical disruption protocol” using the RNeasy MIDI kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

tag: genetic background

value: mid2 mutant

tag: treatment

value: without Congo Red

tag: comment

value: S. cerevisiae (mid2 mutant strain BY4741) was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 ug/ml. Cells were collected at 4 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase mid2 mutant, 4 hours exposure to Congo Red

value: 4 hours exposure to Congo Red


title: WSC1extMID2cyt strain 2 hours exposure to caspofungin 4

source_name: total RNA Saccharomyces cereviase WSC1extMID2cyt strain, 2 hours exposure to caspofungin

label_protocol:
cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy5-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20
μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)

tag: genotype

value: WSC1extMID2cyt strain

value: 2 hours exposure to caspofungin

value: S. cerevisiae (WSC1extMID2cyt strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase WSC1extMID2cyt strain, without caspofungin

value: without caspofungin


title: mid2 mutant 4 hours exposure to Congo Red 2


title: SR21

description: 36hr estrogen stimulated

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix ScanArray 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console ver. 1.0.1. using Affymetrix default analysis settings and RMA as normalization method.

source_name: GM10861 HapMap Cell line

label_protocol: Biotinylated cDNA were prepared according to the WT Affymetrix protocol from 300 ng total RNA.

value: estrogen


title: wsc1 mutant 4 hours exposure to Congo Red 2

source_name: total RNA Saccharomyces cereviase wsc1 mutant, 4 hours exposure to Congo Red

value: wsc1 mutant

value: S. cerevisiae (wsc1 mutant strain BY4741) was grown on YEPD. For Congo Red experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Congo Red to a final concentration of 30 ug/ml. Cells were collected at 4 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wsc1 mutant, without Congo Red


title: S.R. GMO7019, BR1, 0hr


title: wsc1 mutant 4 hours exposure to Congo Red 3

source_name: otal RNA Saccharomyces cereviase wsc1 mutant, 4 hours exposure to Congo Red


title: wsc1 mutant 4 hours exposure to Congo Red 1


title: SR23

description: 36hr calcitriol and estrogen stimulated

value: calcitriol and estrogen


title: WSC1extMID2cyt strain 2 hours exposure to caspofungin 2


title: SR19

description: 36hr estrogen stimulated


title: wsc1 mutant 4 hours exposure to Congo Red 4


title: SR24

description: 36hr calcitriol and estrogen stimulated


title: SR15


title: WSC1extMID2cyt strain 2 hours exposure to caspofungin 1


title: SR22

description: 36hr calcitriol and estrogen stimulated


title: SR14


title: SR17

description: 36hr calcitriol stimulated


title: SR18

description: 36hr calcitriol stimulated


title: SR20

description: 36hr estrogen stimulated


title: SR13


title: MID2extWSC1cyt strain 2 hours exposure to caspofungin 1

source_name: total RNA Saccharomyces cereviase MID2extWSC1cyt strain, without caspofungin

value: MID2extWSC1cyt strain

value: S. cerevisiae (MID2extWSC1cyt strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase MID2extWSC1cyt strain, 2 hours exposure to caspofungin


title: MID2extWSC1cyt strain 2 hours exposure to caspofungin 4


title: MID2extWSC1cyt strain 2 hours exposure to caspofungin 2


title: SR16

description: 36hr calcitriol stimulated


title: mid2 mutant 2 hours exposure to caspofungin 4

source_name: total RNA Saccharomyces cereviase mid2 mutant, 2 hours exposure to caspofungin

value: S. cerevisiae (mid2 mutant strain BY4741) was grown on YEPD. For caspofunginexperiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase mid2 mutant, without caspofungin


title: mid2 mutant 2 hours exposure to caspofungin 1

value: S. cerevisiae (mid2 mutant strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.


title: SR10

description: 36hr calcitriol and estrogen stimulated

source_name: GM10855 HapMap Cell line


title: Wild type 2 hours exposure to caspofungin 4

source_name: total RNA Saccharomyces cereviase wild type, 3 hours exposure to caspofungin

value: wild type

value: 3 hours exposure to caspofungin

value: S. cerevisiae (strain BY4741) was grown on YEPD. For caspofunginexperiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wild type, without caspofungin

label_protocol:
cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy3-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20
μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)


title: wsc1 mutant 2 hours exposure to caspofungin 2

source_name: total RNA Saccharomyces cereviase wsc1 mutant, 2 hours exposure to caspofungin

value: S. cerevisiae (wsc1 mutant strain BY4741) was grown on YEPD. For caspofunginexperiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wsc1 mutant, without caspofungin


title: mid2 mutant 2 hours exposure to caspofungin 2

value: mid2 mutant


title: SR08

description: 36hr estrogen stimulated


title: SR09

description: 36hr estrogen stimulated


title: wsc1 mutant 2 hours exposure to caspofungin 1

value: S. cerevisiae (wsc1 mutant strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.


title: SR11

description: 36hr calcitriol and estrogen stimulated


title: SR12

description: 36hr calcitriol and estrogen stimulated


title: mid2 mutant 2 hours exposure to caspofungin 3

value: 2 hours exposure to caspofungin


title: SR07

description: 36hr estrogen stimulated


title: sho1 mutant 3 hours exposure to zymolyase 2

source_name: total RNA Saccharomyces cereviase sho1 mutant, 3 hours exposure to zymolyase

value: sho1 mutant

value: 3 hours exposure to zymolyase

value: S. cerevisiae (sho1 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase sho1 mutant, without zymolyase

label_protocol: cDNA was synthesized from 25–30 μg of total RNA by reverse transcription, using the CyScribeTM First-Strand cDNA Labeling Kit, incorporating Cy3-dUTP (Amersham Biosciences) into the cDNA corresponding to each sample to be compared. Labeled cDNA was dried in a vacuum trap and used as a hybridization probe after resuspension in 45 μl of hybridization solution (50% Formamide, 6 x SSC, 0.5% SDS, 5 x Denhardt’s, 20 μg of poly(A) (P-9403, Sigma) and salmon sperm (Invitrogen, 100 μg/ml)

value: without zymolyase

value: S. cerevisiae (hog1 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 C and processed for RNA extraction.


title: Wild type 2 hours exposure to caspofungin 3

value: without caspofungin

value: S. cerevisiae (strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wild type, 2 hours exposure to caspofungin


title: SR06

description: 36hr calcitriol stimulated

value: calcitriol


title: Wild type 2 hours exposure to caspofungin 2


title: mid2 mutant 3 hours exposure to zymolyase 2

source_name: total RNA Saccharomyces cereviase mid2 mutant, 3 hours exposure to zymolyase

value: S. cerevisiae (mid2 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase mid2 mutant, without zymolyase


title: SR04

description: 36hr calcitriol stimulated


title: SR05

description: 36hr calcitriol stimulated


title: mid2 mutant 3 hours exposure to zymolyase 3


title: Wild type 2 hours exposure to caspofungin 1

value: S. cerevisiae (strain BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with caspofungin  to a final concentration of 15ng/ml. Cells were collected at 2 hours of growth, frozen at -80 C and processed for RNA extraction.


title: sho1 mutant 3 hours exposure to zymolyase 1


title: mid2 mutant 3 hours exposure to zymolyase 4


title: Skin fibroblasts, biological rep C

description: Gene expression of fibroblastsC is somatic cells control profile in biological replicate C.

source_name: Somatic fibroblastsC were derived from a skin biopsy from a nine year old adult rhesus monkey.

growth_protocol: FibroblastsC were grown at 37oC, 3% CO2, 5%O2 and 92% N2 in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 10% fetal bovine serum (FBS), with the pH adjusted to 7.2 with NaOH. Medium was changed every other day.

treatment_protocol: FibroblastsC were isolated from back skin tissues with 0.1 mg/ml collagenase. The fibroblast cells have been stored at -80°C until total RNA was extracted.

value: male

value: Skin

value: fibroblasts


title: mid2 mutant 3 hours exposure to zymolyase 1


title: wsc1 mutant 3 hours exposure to zymolyase 4

source_name: total RNA Saccharomyces cereviase wsc1 mutant, 3 hours exposure to zymolyase

value: wsc1 mutant

value: S. cerevisiae (wsc1 mutant strain BY4741) was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 C for 2h. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with Zymolyase to a final concentration of 0,8U/ml. Cells were collected at 3 hours of growth, frozen at -80 C and processed for RNA extraction.

source_name: total RNA Saccharomyces cereviase wsc1 mutant, without zymolyase


title: M12.52 pancreas

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

description: M12.52 pancreas

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

scan_protocol: Agilent Scanner protocol for a full slide

data_processing: Agilent Feature Extraction Software (v 9.1.1) was used for background subtraction and LOWESS normalization.

source_name: Secondary derived from mouse 12

label_protocol: Agilent label protocol

growth_protocol: BM transplant

extract_protocol: the DNA was extracted with the Maxwell 16 Cell DNA Purificiation Kit on the automated Maxwell 16 system. (http://www.promega.com/maxwell16/default.htm)

value: T-lymphoblastic lymphoma

value: Balb/c

source_name: Normal wildtype Balb/c mouse

tag: gentype/variation

value: wildtype


title: M12.53 pancreas

description: M12.53 pancreas


title: wsc1 mutant 3 hours exposure to zymolyase 3

value: 3 hours exposure to zymolyase


title: wsc1 mutant 3 hours exposure to zymolyase 2

source_name: total RNA Saccharomyces cereviase hog1 mutant, without zymolyase

value: hog1 mutant


title: SR03


title: M12 LN neck

description: M12 LN neck

source_name: Primary transplant


title: M12.50 LN neck

description: M12.50 LN neck


title: M12.49 pancreas

description: M12.49 pancreas


title: SR01

source_name: GM10855 HapMap Cell line


title: ADSC-vector_adipogenic induction media-treated_rep1

status: Public on Jun 18 2010

city: SUita

first: Masaki

last: Mori

state: Osaka

address: 2-2 Yamada-oka

department: Graduate School of Medicine

institute: Osaka University

description:
ADSC-EGFP adipogenesis.
Image_Name: 220444A03

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented by NimbleScan software (Roche NimbleGen, Inc.). Students’ two-tail t-tests were conducted among the samples for each transcript and fold-change was determined. Transcripts whose abundance was significantly altered (P < 0.05) and an absolute fold change greater than 2 were defined as differentially regulated.

source_name: ADSC-vector, adipogenic induction media-treated

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Adipose-derived stem cells (ADSCs) were isolated from human flank lipoaspirate obtained in elective liposuction surgery procedures (Lonza, Switzerland) and maintained in Mesenchymal Stem Cell Growth Medium (Lonza).

extract_protocol: Total RNA was extracted from ADSCs using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Quality and yield were verified by NimbleGen.

treatment_protocol: For adipocyte differentiation, 2 day post-confluent cells were treated with differentiation-inducing medium containing 0.5 mM 3 isobutyl-1-methylxanthine (IBMX), 10 µg/ml insulin, 1 µM dexamethasone, and 10% FBS in DMEM for 14 days. The induction medium was changed every two days.

tag: tissue

value: adipose

value: adipose-derived stem cells (ADSCs)

tag: transduced gene

value: control vector

value: adipogenic-induction media


title: 280-A

city: Durham

first: Janet

middle: Y.

last: Leung

state: NC

address: 101 Science Dr.

institute: Duke University

description: gene expression data from MTB/TOM mouse mammary

hyb_protocol: (following Affymetrix guidelines)

scan_protocol: (following Affymetrix guidelines)

data_processing: RMA normalization using Affymetrix Expression Console version 1.1

source_name: Mus Musculus-recurrent

label_protocol: (following Affymetrix guidelines)

growth_protocol: Mice were administered 2mg/ml doxycycline in their drinking water at age 6 wks.  Doxycycline was removed post surgery.

extract_protocol: RNA was extracted using Qiagen RNA purification columns.

value: mammary tissue

value: FVB

value: MTB/TOM

tag: age


title: 308-2-A


title: 243-A


title: SR02

tag: cell line


title: 308-1-A


title: 308-3-A


title: wsc1 mutant 3 hours exposure to zymolyase 1

value: without zymolyase


title: 251-A


title: 267-1-A


title: 276-A


title: ADSCs_untreated_rep1

description:
ADSC No induction.
Image_Name: 220444A01

source_name: ADSCs, untreated

value: untreated


title: ADSCs_adipogenic induction media-treated_rep1

description:
ADSC adipogenesis.
Image_Name: 220444A02

source_name: ADSCs, adipogenic induction media-treated


title: 270-A


title: M10 BM

description: M10 BM

value: Myeloid hyperplasia

tag: genotype/variation


title: 279-A


title: 239-3-A


title: 239-1-A


title: 239-2-A


title: ADSC-Hoxc8_adipogenic induction media-treated_rep1

description:
ADSC-HOXC8 adipogenesis.
Image_Name: 220444A04

source_name: ADSC-Hoxc8, adipogenic induction media-treated

value: human Hoxc8


title: 238-A


title: M9 spleen

description: M9 spleen


title: 233-A


title: 235-A


title: M7 spleen

description: M7 spleen


title: 169-1-A


title: 207-3-A


title: 53tumor1-A


title: 226-A


title: 53tumor2-A


title: 169-3-A


title: 6-A


title: 82-A


title: 114-4-A


title: 9-A


title: 114-1-A


title: 88-A


title: 4-A


title: 36-2-A


title: 55-A


title: 207-2-A


title: 61-A


title: 67-A


title: B308-4

source_name: Mus Musculus-primary


title: B308-2


title: 165-A


title: B280


title: 236-A


title: B308-1


title: 169-2-A


title: 13-R-A


title: B272


title: B276


title: B239


title: B82


title: B114-3


title: B233


title: B114-4


title: B279


title: B270


title: B207-2


title: B179


title: B53bottom


title: B243


title: B55


title: B226


title: B165


title: B236


title: B163


title: B175-2


title: B172


title: B67


title: B53top


title: B176


title: O 043

city: Grand Rapids

first: Min-Han

last: Tan

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

description: mRNA profiling

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Statistical analyses were performed in the statistical environment R 2.6.0, utilizing packages from the Bioconductor project.10  The robust multichip average (RMA) algorithm was used to perform pre-processing of the CEL files, including background adjustment, quartile normalization and summarization.

source_name: Oncocytoma tissue

tag: disease state

value: Renal oncocytoma


title: B207-3


title: B61


title: O 16

description: mRNA profiling


title: B169


title: B267-1


title: B13R


title: B36tumor2


title: B9


title: B6


title: B4


title: O 99

description: mRNA profiling


title: O 110

description: mRNA profiling


title: Evi1-4

city: Tokyo

first: Akihide

last: Yoshimi

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

department: Department of Hematology & Oncology

institute: Tokyo University

description: gene expression data from Evi1-transduced bone marrow

hyb_protocol: Biotin-labeled cDNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer.

scan_protocol: Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

data_processing:
Expression  data  were  extracted  from  image  files produced  on  Affymetrix®  GeneChip  Operating  Software  1.0®  (GCOS®).
Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).

source_name: 5-FU-primed bone marrow mononuclear cells, Evi1-transduction

label_protocol: Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.

growth_protocol: 5-FU-primed mononuclear bone marrow cells harvested from C57/B6 mice were retrovirally transduced with Evi1-GFP or GFP and cultured in Methocult 3434 for 48 hrs. GFP positive cells were sorted and subjected to the analysis.

extract_protocol: Total RNA was isolated using the Qiagen RNease mini kit.

value: mononuclear bone marrow cells

tag: treatment protocol

value: Evi1 retroviral transduction


title: O 14

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep16

city: Burjassot

first: Julian

last: Carretero

state: Valencia

address: Ave. Vicent Andres Estelles s/n

department: Physiology

institute: University of Valencia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A2 Array. GeneChips were washed and stained in the Affymetrix FS-4500 fluidics station

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 .

data_processing: The data were analyzed with RMA normalization method.

source_name: Metastasis attached to adrenal gland

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Transgenes were induced by adeno-Cre treatment of mice at 5-6 weeks of age

extract_protocol: Trizol extraction of total RNA and Qiagen Rneasy clean-up were performed according to the manufacturer's instructions.

treatment_protocol: Primary lung adenocarcinomas and metastases were macrodissected and frozen in liquid nitrogen and stored at 80° until use

value: Metastasis

value: LSL-Kras, Lkb1L/L

value: adeno-Cre treatment at 5-6 weeks of age


title: O 20

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep17

source_name: Lymph node metastasis


title: Evi1-3

tag: strain


title: O 19

description: mRNA profiling


title: Evi1-2


title: Evi1-1


title: Kras/Lkb1 metastasis, biological rep15

source_name: Metastasis met outside of thoracic cavity


title: O 15

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep12


title: Kras/Lkb1 metastasis, biological rep14


title: O 13

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep11

source_name: Metastasis attached to rib cage


title: Kras/Lkb1 metastasis, biological rep10


title: mock-3

description: gene expression data from mock-transduced bone marrow

source_name: 5-FU-primed bone marrow mononuclear cells, control transduction

value: mock retroviral transduction


title: mock-4


title: O 11

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep9


title: Kras/Lkb1 metastasis, biological rep13


title: Kras/Lkb1 metastasis, biological rep8


title: 325.5wt_071906

city: Kansas City

first: Jay

last: Vivian

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

description: Expression analysis of yolk sac from wild-type E9.5 mouse.

hyb_protocol: Per standard Affymetrix protocol.

scan_protocol: Automated process conducted using the Agilent GeneArray Scanner.

data_processing: Bioconductor package in R; MAS5.0 normalization.

source_name: Mouse yolk sac tissues at E9.5, wild type

label_protocol: Oligo-dT first-strand synthesis, biotin labelled via in vitro transcription.

growth_protocol: A male Tie2 Tg/0 mouse was mated with a female ROSA +/N1ICD and the presence of a vaginal plug was taken as 0.5dpc.

extract_protocol: Qiagen Rneasy RNA purification.

treatment_protocol: Embryos were dissected from the decidual tissue at E9.5.  The yolk sac was separated from the embryo and the embryo was used for genotyping.  Total RNA was isolated from the yolk sac.

value: yolk sac

value: embryonic day 9.5


title: B251


title: mock-1


title: Kras/Lkb1 metastasis, biological rep3


title: Kras/Lkb1 metastasis, biological rep6


title: 325.7wt_071906


title: Kras/Lkb1 metastasis, biological rep4


title: 325.6trans_071906

description: Expression analysis of yolk sac from Notch1-activated E9.5 mouse.

source_name: Mouse yolk sac tissues at E9.5, Notch1 activated

value: Tie2 Tg/0; ROSA +/N1ICD


title: Kras/Lkb1 metastasis, biological rep5


title: O 07

description: mRNA profiling


title: O 05

description: mRNA profiling


title: mock-2


title: Kras/Lkb1 metastasis, biological rep1


title: Kras/Lkb1 metastasis, biological rep7


title: O 04

description: mRNA profiling


title: Kras/Lkb1 metastasis, biological rep2


title: O 09

description: mRNA profiling


title: Kras/Lkb1 primary tumor, biological rep9

source_name: Primary tumor

value: Lung tumor


title: 314.6trans_071906


title: C 002

description: mRNA profiling

source_name: Chromophobe RCC tumor tissue

value: Chromophobe renal cell carcinoma


title: C 028

description: mRNA profiling


title: Kras/Lkb1 primary tumor, biological rep3


title: Kras/Lkb1 primary tumor, biological rep7


title: Kras/Lkb1 primary tumor, biological rep2


title: Kras/Lkb1 primary tumor, biological rep8


title: Kras/Lkb1 primary tumor, biological rep6


title: Kras/Lkb1 primary tumor, biological rep5


title: O B01

description: mRNA profiling


title: C 141

description: mRNA profiling


title: C 16

description: mRNA profiling


title: Kras/Lkb1 primary tumor, biological rep4


title: C 144

description: mRNA profiling


title: mouse heart overexpressing the mineralocorticoid receptor, pool 1c

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

country: France

institute: L'institut du thorax

hyb_protocol: Pre-incubation of hybridization mixture with human Cot-I DNA, yeast tRNA and polyA RNA at 37°C for 30 minutes. Overnight hybridization at 42°C

scan_protocol: Scanned on Scanarray 4000XL, GSI-Lumonics, signal quantification using GenePix Pro 5.0

data_processing: A Lowess normalization procedure was applied channel-by-channel. For each microarray, Cy3- and Cy5-signal intensities were individually normalized to a prototype defined as the median profile of all Cy3- or Cy-5 signal intensities

label_protocol: CyScribe cDNA Post Labelling Kit (Amersham Pharmacia Biotech) (1 µg mRNA per labeling reaction)

extract_protocol: Total RNA extraction using TRIZOL (Invitrogen), mRNA isolation using the Oligotex mRNA kit (Qiagen).

value: heart

tag: protocol

tag: sample type

value: test

source_name: heart tissue, control

value: control


title: Mouse Skin 6 Adam17 KO

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mouse skin Adam17 knockout

hyb_protocol: hybridization was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays, using the AGCC (Affymetrix) software.

scan_protocol: image aquisition was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays using the AGCC (Affymetrix) software.

data_processing:
data was processed using the AGCC (Affymetrix) software and normalized using the RMA method. Signals, that were not stronger than the 95th percentile of all intron probes on the array were excluded from further analysis.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Adam17 knockout mouse

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays.

growth_protocol: All experiments were carried out in accordance with the animal care guidelines of the University of Kiel (acceptance no.: V 742-72 241.121-3 (20-2/04) and (76-7/00)). Mice were maintained in a 12-h light-dark cycle under standard conditions and were provided with food and water ad libitum. Procedures involving animals and their care were conducted in conformance with national and international laws and policies. Blood was drawn from the mice by cardiac puncture under general anesthesia.

extract_protocol: Quiagen RNA extraction (Rneasy) according to the manufacturers guidelines

value: skin

value: Adam17 knockout


title: mouse heart overexpressing the mineralocorticoid receptor, pool 1b


title: Kras primary tumor, biological rep9

value: LSL-Kras


title: Kras/Lkb1 primary tumor, biological rep1


title: STAT4-wild type T cells, cultured 7 days in Th1 condition

city: Bethesda

first: Golnaz

last: Vahedi

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Gene expression data from wild type CD4+ T cells cultured for 7 days in Th1 condition

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing: Data processing were done using Affymetrix Power Tool (APT) v. 1.10.2, quantile normalization RMA

source_name: primary CD4+ T cells from spleen and lymph nodes

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

growth_protocol: Control and STAT-deficient naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-12 (20 ng/ml) and anti-IL-4 (10 mg/ml) for 3 days, followed by IL-2 (50 U/ml) and IL-12 (10 ng/ml) for 4 days (Th1 conditions), or anti-CD3, anti-CD28 (10 mg/ml each), IL-4 (10 ng/ml) and anti-IFN-g (10 mg/ml) for 3 days, followed by IL-2 (50 U/ml) and IL-4 (10 ng/ml) for 4 days (Th2 conditions).

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: After 7 day culture in vitro, cells were restimulated for 2hr with plate-bound anti-CD3, anti-CD28 (10 mg each) and IL-12 (20 ng/ml) for Th1 condition or IL-4 (10 ng/ml) for Th2 condition.

tag: cell

value: CD4+ T cell

value: C57BL/6J (wild type)


title: C 086

description: mRNA profiling

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


title: STAT6-deficient T cells, cultured 7 days in Th2 condition

description: Gene expression data from STAT6-deficient CD4+ T cells cultured  for 7 days in Th2 condition

value: B6.129S2©-STAT6<tm1Gru>/J (STAT6KO)


title: C 14

description: mRNA profiling


title: C 15

description: mRNA profiling


title: STAT4-deficient T cells, cultured 7 days in Th1 condition

description: Gene expression data from STAT4-deficient CD4+ T cells cultured for 7 days in Th1 condition

value: C57BL6-STAT4<tm1> (STAT4KO)


title: Mouse Skin 5 WT

description: mouse skin Adam17 wildype

source_name: Adam17 wildtype mouse

value: Adam17 wild type


title: mouse heart overexpressing the mineralocorticoid receptor, pool 1a


title: Mouse Colon 6 Adam17 KO

description: mouse colon Adam17 knockout

value: colon


title: mouse heart overexpressing the glucocorticoid receptor, sample 5 pool 3

value: glucocorticoid receptor overexpression


title: Kras primary tumor, biological rep6

value: adeno-Cre treatment at 5-6 weeks of age


title: Mouse Skin 4 Adam17 KO

description: mouse skin Adam17 knockout


title: mouse heart overexpressing the glucocorticoid receptor, sample 4 pool 2


title: Kras primary tumor, biological rep5


title: STAT6-wild type T cells, cultured 7 days in Th2 condition

description: Gene expression data from wild type CD4+ T cells cultured for 7 days in Th2 condition


title: Mouse Skin 3 WT

description: mouse skin Adam17 wildype


title: Mouse Skin 2 Adam17 KO

description: mouse skin Adam17 knockout


title: C 13

description: mRNA profiling


title: Mouse Skin 1 WT

description: mouse skin Adam17 wildype


title: Kras primary tumor, biological rep4


title: Mouse Colon 5 WT

description: mouse colon Adam17 wildype


title: C 09

description: mRNA profiling


title: C 11

description: mRNA profiling


title: mouse heart overexpressing the glucocorticoid receptor, sample 3 pool 2


title: C 12

description: mRNA profiling


title: mouse heart overexpressing the glucocorticoid receptor, sample 6 pool 3


title: Kras primary tumor, biological rep8


title: Kras primary tumor, biological rep7


title: Kras primary tumor, biological rep3


title: mouse heart overexpressing the glucocorticoid receptor, sample 2 pool 1


title: C 05

description: mRNA profiling


title: Kras primary tumor, biological rep2


title: Mouse Colon 4 Adam17 KO

description: mouse colon Adam17 knockout


title: Mouse Colon 2 Adam17 KO

description: mouse colon Adam17 knockout


title: Mouse Colon 3 WT

description: mouse colon Adam17 wildype


title: C 04

description: mRNA profiling


title: mouse heart overexpressing the glucocorticoid receptor, sample 1 pool 1


title: C 01

description: mRNA profiling


title: deletion mutant 1 grown for 96 hours

status: Public on Jun 17 2010

city: Bochum

first: Jens

last: Kamerewerd

address: Universitätsstrasse 150

department: General and Molecular Botany

institute: Ruhr-University Bochum

description: whole genome expression data

hyb_protocol: EukGE-WS2v4_450 (Affymetrix)

scan_protocol: GCS3000-Scanner (Affymetrix). Hybridized arrays were scanned and analysed using the Affymetrix GeneChip® Operating Software.

data_processing: Data was analyzed with R-package affylmGUI using RMA algorithm

organism: Penicillium chrysogenum

source_name: mycelium from deletion mutant 1 grown for 96 hours

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer protocol

growth_protocol: solid production medium at 25 °C, 48, 60 and 96 hours

extract_protocol: Mycelia were ground to a fine powder under liquid nitrogen and total RNA was purified using Trizol reagent followed by an RNeasy® clean-up (Qiagen, Hilden, Germany) and DNAseI digestion. RNA quality was determined using an Agilent 2100 Bioanalyzer.

value: vegetative mycelium

value: deltaPcvelA


title: deletion mutant 2 grown for 48 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 48 hours

value: deltaPclaeA


title: deletion mutant 2 grown for 60 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 60 hours


title: Mouse Colon 1 WT

description: mouse colon Adam17 wildype


title: deletion mutant 2 grown for 96 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 96 hours


title: Kras primary tumor, biological rep1

value: Lung tumor


title: recipient strain grown for 48 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 48 hours


title: deletion mutant 1 grown for 60 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 60 hours


title: recipient strain grown for 60 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 60 hours


title: recipient strain grown for 96 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 96 hours


title: deletion mutant 1 grown for 48 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 48 hours


title: reference strain grown for 60 hours

description: whole genome expression data

source_name: mycelium from reference strain grown for 60 hours


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group3

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: The control RNAi is ‘empty’ vector L4440 RNAi feeding vector plasmid (1999 Firelab vector kit) transformed HT115(DE3).  The empty vector RNAi was used as the food source for our array experiment.

hyb_protocol: Hybridization was carried out using a Lucidea Slide Pro machine. All wash solutions were made using Ambion Pre-Made Solutions (Nuclease-free Water, 20% SDS and 20XSSC) and filtered sterilized with a 500ml, 0.22uM filter unit. All C. elegans arrays from the Washington University in St. Louis Genomic Sequencing Center arrive pretreated; no blocking step was necessary. To prepare the aRNA sample for hybridization, the labeled aRNA sample was brought up to a volume with Nuclease-free water and Dextran Sulfate/ Hybe Buffer mix was added to the aRNA sample. The mixture was warmed to 50oC. Using a Hamilton syringe the labeled sample was loaded into the Lucidea chamber. The hybridization program was run for 16hrs at 42oC with a cycling speed of 10µl/sec every 30 minutes. The array was then washed at a speed of 50ul/sec with the following wash buffers in succession: 2X SSC +0.1% SDS (warmed to 42oC for 1st wash solution), 2X SSC, 0.2XSSC, and a 95% ethanol drying step.

scan_protocol: The array slide was loaded into a Perkin Elmer Scan Array Express 2-Laser Scanner. A QuickScan was performed, which scans the first 3-4 rows of the array. A surface calibration was then performed using the Spot Report control spots on the array. After surface calibration, the PMT and POW settings were adjusted to have the control spots match in intensity. The array was then scanned. Images were quantitated using GenePix 5.0 software package which overlays the GAL file (provided by the Washington University in St. Louis Genomic Sequencing Center) on the two array TIFF images (Cy3 and Cy5).  Pixels per spot, per channel were counted by the software and a gpr file was generated.

data_processing: Arrays were normalized using LIMMA (Smyth & Speed 2003)

organism: Caenorhabditis elegans

source_name: Wild type (N2)_pooled mix

label_protocol: Each sample, including the reference pool, was subjected to two rounds of linear amplification using the MessageAmp kit from Ambion for the first round and the Amino Allyl Message Amplification II kit from Ambion for the second round. After amplification, each sample was assessed for yield and overall quality via Bioanlayzer (Agilent) and Nanodrop. Samples that did not pass QC were discarded, and not used in the final analysis. Post Labeling Reactive Dyes (Cy3 and Cy5) from Amersham were used in conjunction with the reagents and protocol from the Ambion Amino Allyl Message Amplification II Kit to label the aRNA.  5ug of aRNA plus aRNA spike were labeled (aRNA Spike: equal amounts of the 10 Stratagene Spot Repot Spikes were combined and then amplified 1 round, to make an aRNA Spot Report Spike mix). All controls were labeled with the Cy3 dye and all experimental samples were labeled with the Cy5 dye. The Cy3 and Cy5 sample pairs were combined and purified.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: whole organism

source_name: daf16(M26); daf-2(e1370) Heat Shocked on Control RNAi

tag: fraction

value: Fraction 3 - heavy polysomes

tag: group

value: Group 3

value: Heat Shocked


title: reference strain grown for 96 hours

description: whole genome expression data

source_name: mycelium from reference strain grown for 96 hours


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction3_group4

source_name: daf16(M26); daf-2(e1370) on Control RNAi

value: Group 4


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group4

value: Fraction 2 - light polysomes

tag: treatment


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction1_group4

value: Fraction 1 - ribosomal and free RNA


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group4


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction2_group4


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group4


title: small RNA_chip_F7_flower2

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

description:
small RNA
A total of 12 hybridization intensities in three biological replicates per a species were obtained, and log values of hybridization intensities were used for normalization and statistical analysis.

hyb_protocol: After prehybridization, the chip was hybridized to small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C. Posthybridization washes were done sequentially once each with 6XSSPET and 3XSSPET and twice with 0.5XSSPET.

scan_protocol: Hybridized chip was scanned using a Genepix 4000B (Molecular Devices, Sunnyvale, CA), and data were extracted using software provided by CombiMatrix (Mukilteo, WA).

data_processing: If the hybridization intensities of a miRNA were not significantly higher than the background signals, the miRNA was considered to be not expressed.

organism: Arabidopsis arenosa x Arabidopsis thaliana

source_name: flower buds

label_protocol: Small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C.

extract_protocol: Small RNAs were enriched from total RNA using mirRVana isolation kit (Ambion, Austin, TX).

value: F7 progeny of A. thaliana and A. arenosa hybrid

value: flower buds


title: small RNA_chip_A_suecica_flower2

organism: Arabidopsis suecica

value: Arabidopsis suecica


title: small RNA_chip_F7_flower1


title: small RNA_chip_A_suecica_flower3


title: small RNA_chip_F7_flower3


title: small RNA_chip_A_suecica_flower1


title: small RNA_chip_A_arenoa_flower3

organism: Arabidopsis thaliana

value: Arabidopsis arenosa


title: small RNA_chip_A_arenoa_flower2


title: reference strain grown for 48 hours

description: whole genome expression data

source_name: mycelium from reference strain grown for 48 hours


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group3


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group3


title: small RNA_chip_A_suecica_leaf5

source_name: Young Leaf

value: Young Leaf


title: small RNA_chip_A_suecica_leaf6


title: small RNA_chip_A_suecica_leaf9


title: small RNA_chip_A_suecica_leaf7


title: small RNA_chip_A_thaliana_flower2

value: Arabidopsis thaliana 4x


title: small RNA_chip_A_thaliana_flower3


title: small RNA_chip_A_arenoa_flower1


title: small RNA_chip_A_thaliana_flower1


title: small RNA_chip_A_suecica_leaf8


title: small RNA_chip_A_suecica_leaf4


title: small RNA_chip_A_suecica_leaf1


title: small RNA_chip_A_suecica_leaf2


title: small RNA_chip_A_suecica_leaf3


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group2

value: Group 2


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction3_group2


title: small RNA_chip_F7_leaf9


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction2_group3


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction1_group3


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction3_group3


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group1

value: Group 1


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group2


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group2


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group1


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction1_group2


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction1_group1


title: daf16(M26); daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group4

source_name: daf-2(e1370) Heat Shocked on Control RNAi


title: small RNA_chip_F7_leaf6


title: small RNA_chip_F7_leaf7


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction2_group1


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction2_group4


title: daf-2(e1370)_on Control RNAi_Fraction3_group4

source_name: daf-2(e1370) on Control RNAi


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction3_group1


title: small RNA_chip_F7_leaf8


title: daf16(M26); daf-2(e1370)_on Control RNAi_Fraction2_group2


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction3_group3


title: small RNA_chip_F7_leaf5


title: daf-2(e1370)_Heat Shocked_on Control RNAi_Fraction1_group4


title: small RNA_chip_F7_leaf4


title: T7-SAGE transcriptome of end bud epithelial cells of embryonic mouse salivary glands

type: SAGE

anchor: NlaIII

city: Suita

first: Takayoshi

last: Sakai

address: 1-8 Yamadaoka

department: Oral-Facial Disorders

institute: Osaka Univ Grad Sch Dent

description: Mus musculus embryonic submandibular salivary glands from embryonic day 12.5 embryos were laser microdissected to isolate epithelial cells from regions adjacent to forming clefts or from the peripheral end bud region.  The isolated region-specific samples were then subjected to T7-SAGE transcriptome analysis.

data_processing: SAGE 2000 software from http://www.sagenet.org

source_name: Embryonic submandibular salivary gland

extract_protocol: Protocol as published in: Sakai T, Larsen M, Yamada KM. Microanalysis of gene expression in tissues using T7-SAGE: serial analysis of gene expression after high-fidelity T7-based RNA amplification. Curr Protoc Cell Biol. 2002 Nov;Chapter 19:Unit 19.3.

tag: cell type

value: laser microdissected epithelial cells from end bud of embryonic salivary gland


title: small RNA_chip_F7_leaf3