title: Day14_YF1222; VaxDesign Mimic experiment


title: 34BM2523

status: Public on Dec 01 2008

type: RNA

city: Seattle

first: Derek

middle: L

last: Stirewalt

state: WA

address: 1100 Fairview Ave N, D5-112

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

description: For 34BM and T-cells, biotin-labeling of total RNA (5 µg) was performed as per standard Affymetrix protocol. For the 34P38NPBSC arrays, the single-stranded linear amplification protocol was used to process total RNA (100 nanograms) for the microarrays. Both protocols are described in detail in PMID14706461.

hyb_protocol: Hybridization was performed according to Affymetrix protocol.

scan_protocol: Arrays were scanned according to Affymetrix protocol.

data_processing: .DAT files were generated using GCOS 1.2.1 software (Affymetrix). CEL files were generated using MAS 5.0 softare (Affymetrix) with target signals for probe sets scaled to 500. Log2 expression values for individual probe sets were generated from .CEL files via robust multi-array average (gcRMA).

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD34 selected bone marrow

label_protocol: Target was labeled with Enzo BioArray High Yield RNA Trascript Labeling Kit (Enzo Life TEchnologies, Farmingdale, NY) according to manufacturer's protocol.

extract_protocol: Total RNA extracted using TRIzol reagent (Invitrogen, Carlsbad, CA)according to manufacturer's protocol.

tag: CD34 selected cells from cadaveric bone marrow of 16 yo Male.

tag: .CEL file is identical to GSM239341


title: Day7_YF1105; VaxDesign Mimic experiment

city: Montréal

first: Bastian

middle: Robert

last: Angermann

state: Quebec

address: 264 René-Lévesque Est

country: Canada

institute: Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR-CHUM) Saint-Luc

description: PBMCs used in the assays were acquired from normal healthy donors enrolled in a VaxDesign Corporation apheresis study program (protocol CRRI 0906009). Blood collections were performed at Florida’s Blood Centers (Olrando, FL) using standard techniques.  The enriched leukocytes were isolated and cryopreserved. Human DCs were prepared as described in Gaucher et al. “Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses , J. Exp. Med XXX. After 5 days of culture with IL-4 and GM-CSF, the DCs were infected with a 1:100 dilution of the live-attenuated YF-VAX® vaccine.  After 24 hrs, 5% human AB serum was added to the media to quench the infection. Alternatively, some of the DCs we not infected.  On the sixth day, all DCs were matured with an overnight treatment of 25 ng/mL TNF- (R&D Systems).

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Human RefSeq-8 BeadChips v2 at 58oC for 20 hours.

scan_protocol: Fluorescent array images were collected with Illumina BeadStation 500GX scanner fluorescent scanner and image intensity data were extracted using Illumina BeadStudio version 3 software.

data_processing: Illuma probe data were exported from BeadStudio as raw data and were screened for quality.  Samples failing chip visual inspection and control examination were removed. The R software was used to quantile normalize the probe intensities, and to minimum-replace (surrogate-replacement policy) values below background using the mean background vale of the probe controls rounded up to the rearest power of 2, determined from the microarray quality controls to reduce noise and reduce "over-inflated" expression ratios in subsequent steps.

label: biotin

source_name: Frozen stocks of autologous PBMCs were used as a source of lymphocytes.

label_protocol: Total RNA as amplified and labeled using the Illumina TotalPrep RNA Amplication kit which is based on the Eberwine amplification protocol. It involves a first cDNA synthesis step followed by in vitro transcription of cRNA.

extract_protocol: Total RNA was purified using RNA extraction kits from Qiagen.  Quantification was performed using NanoDrop Technologies spectrophotometer and RNA quality was assessed using the Experion automated electrophoresis system from Bio-Rad.

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for 7 days

tag: Yellow Fever unexposed volunteer


title: Day7_01105; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with untreatedDCs at a ratio of 60:1 for 7 days


title: Day14_01173; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with untreatedDCs at a ratio of 60:1 for 14 days


title: 34BM3077

tag: CD34 selected cells from cadaveric bone marrow of 32 yo Male.

tag: .CEL file is identical to GSM239344


title: Day7_YF1222; VaxDesign Mimic experiment


title: Day14_01222; VaxDesign Mimic experiment


title: Day3_01173; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with untreatedDCs at a ratio of 60:1 for 3 days


title: Day3_01222; VaxDesign Mimic experiment


title: Day7_01173; VaxDesign Mimic experiment


title: Day3_YF1173; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for3 days


title: Day7_YF1173; VaxDesign Mimic experiment


title: Day3_YF1222; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for 3 days


title: Day7_01222; VaxDesign Mimic experiment


title: Day3_01105; VaxDesign Mimic experiment


title: 34BM0030

tag: CD34 selected cells from cadaveric bone marrow of 18 yo Male

tag: Same .CEL file as GSM239170


title: 34BM0121

tag: CD34 selected cells from cadaveric bone marrow of 51 yo Male

tag: .CEL file is identical to GSM239338


title: CGCs_DIV5_ICRF

status: Public on Nov 30 2008

city: Okayama

first: Kuniaki

middle: Sano

state: Okayama

address: 2-5-1, Shikata-cho

department: Department of Neurogenomics

country: Japan

institute: Okayama Univsersity

description: Rat cerebellar granule cells cultured for 5 days in the presence of 10 µM ICRF-193

hyb_protocol: Biotinylated cRNAs were hybridized to GeneChip Rat Genome 230 2.0 for 16 h at 45°C in GeneChip Hybridization oven 640. After hybridization, arrays were washed and stained with Streptavidin-Phycoerythrin in GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. (MAS5.0 signal intensity)

label: phycoerythrin

organism: Rattus norvegicus

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol. One µg of total RNA was reverse-transcribed to cDNA by GeneChip One-Cycle cDNA Synthesis Kit. The cDNAs were transcribed to cRNAs in vitro with biotinylated nucleotides using GeneChip IVT Labeling Kit.

growth_protocol: Cerebellar tissue was isolated from the Wistar rat 8 days after birth. Minced tissue was treated briefly with trypsin-EDTA and DNase I in PBS. Dispersed cells were plated at 2.5x10^7 cells per 100 mm plastic dish pre-coated with poly-L-lysine. The cells were incubated at 37°C in DMEM containing 10% FCS, 25 mM KCl, and 60 μg/ml kanamycin sulfate.

extract_protocol: Total RNA was extracted by RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Dispersed cells were plated at 2.5x10^7 cells per 100 mm plastic dish pre-coated with poly-L-lysine. The cells were incubated at 37℃ in DMEM containing 10% FCS, 25 mM KCl, and 60 µg/ml kanamycin sulfate. After 15-16 h, medium was replaced with fresh medium supplemented with 10 µM cytosine arabinoside to suppress the glial growth. The medium change was repeated at 24 h and at every 48 h afterwards. It has been shown that under these conditions only precursor granule cells can survive after the final division in vitro. Topoisomerase IIbeta can be specifically inhibited throughout the culture period if 10 µM ICRF-193 was added dayly.

tag: Cerebellar granule cells prepared from P8 Wistar rats


title: 34BM2841

tag: CD34 selected cells from cadaveric bone marrow of 36 yo Male.

tag: .CEL file is identical to GSM239342


title: F9 cells Ezh2 chip on chip replicate 2

type: genomic

city: New York

first: Raphael

middle: F

last: Margueron

state: NY

address: 522 first Ave

department: Biochemistry

institute: NYU Langone medical center

description: Ezh2 genome-wide binding profiles in F9 cells by chip on chip

hyb_protocol: Hybridization onto the mouse promoter array, which includes 244K features distributed onto two slides (Agilent –G4490), washing and scanning were carried out according to the manufacturers instructions.

scan_protocol: According to Agilent Scanning Software

data_processing: Log ratios were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

molecule: genomic DNA

organism: Mus musculus

source_name: Input for mouse Ezh2 chromatin immunoprecipitation

label_protocol: Input samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy3 using Invitrogen CHG kit (18095-011). Labelling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).

growth_protocol: F9 cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: F9 cells were cross-linked by addition of formaldehyde (to 1% final concentration). Cross-linking was allowed to proceed at room temperature for 10 min and was terminated with glycine (final concentration 0.125 m). Cells were washed with PBS. Cells were collected by centrifugation and were rocked in buffer containing 50 mm HEPES (pH 7.5), 140 mm NaCl, 1 mm EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors (1 mm AEBSF, 10 μg/ml aprotinin, 1 μg/ml leupeptin, 1 μg/ml pepstatin A), at 4°C for 10 min. Cells were collected by centrifugation at 4K rpm for 10 min, and the resulting pellet was resuspended in 200 mm NaCl, 1 mm EDTA, 0.5 mm EGTA, 10 mm Tris (pH 8), and protease inhibitors and incubated 10 min at room temperature. Nuclei were collected by centrifugation at 4K rpm for 10 min, resuspended in sonication buffer (1 mm EDTA, 0.5 mm EGTA, 10 mm Tris at pH 8, and protease inhibitors), and sonicated on ice to an average length of 350 bp

tag: The F9 murine teratoma cell line (obtained from ATCC)

source_name: IP for mouse Ezh2 chromatin immunoprecipitation

label_protocol: IP samples were amplified by LMPCR and 1 microgram of LM-PCR product was labeled with Cy5 using Invitrogen CHG kit (18095-011). Labelling reaction were cleaned up by invitrogen bind and elute CGH columns (18095-011).


title: CGCs DIV5 (Cy5) vs DIV1 (Cy3)

description: DNA topoisomerase IIbeta (topo IIbeta) regulates  gene expression in developing cerebellar granule cells (CGC)

hyb_protocol: Labeled probes were hybridized to the array for 17 h at 60°C.

scan_protocol: Microarrays were imaged on an Agilent microarray scanner and expression data were obtained using the Agilent Feature Extraction software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Rat cerebellar granule cells cultured for 5 days

label_protocol: cDNA was reverse-transcribed to label with aminoallyl-dUTP. The cDNA was coupled with Cy5 dye

extract_protocol: Total RNA was extracted from the cultured cells using the RNeasy mini kit (Qiagen).

treatment_protocol: Dispersed cells were plated at 2.5x10^7 cells per 100 mm plastic dish pre-coated with poly-L-lysine. The cells were incubated at 37℃ in DMEM containing 10% FCS, 25 mM KCl, and 60 µg/ml kanamycin sulfate. After 15-16 h, medium was replaced with fresh medium supplemented with 10 µM cytosine arabinoside to suppress the glial growth. The medium change was repeated at 24 h and at every 48 h afterwards. It has been shown that under these conditions only precursor granule cells can survive after the final division in vitro.

tag: Cerebellar granule cells were prepared from P8 Wistar rats

source_name: Rat cerebellar granule cells cultured for one day

label_protocol: cDNA was reverse-transcribed to label with aminoallyl-dUTP. The cDNA was coupled with Cy3 dye


title: F9 cells Ezh1 chip on chip replicate 2

description: Ezh1 genome-wide binding profiles in F9 cells by chip on chip

source_name: Input for mouse Ezh1 chromatin immunoprecipitation

source_name: IP for mouse Ezh1 chromatin immunoprecipitation


title: Day14_YF1105; VaxDesign Mimic experiment

treatment_protocol: Purified CD4+ T cells were co-cultured  in the Mimic System with YF17D-pulsed DCs at a ratio of 60:1 for 14 days


title: CGCs_DIV5

description: Rat cerebellar granule cells cultured for 5 days

tag: Cerebellar granule cells were prepared from P8 Wistar rats.


title: CGCs DIV5 (Cy5) vs DIV5_ICRF (Cy3)

treatment_protocol: Dispersed cells were plated at 2.5x10^7 cells per 100 mm plastic dish pre-coated with poly-L-lysine. The cells were incubated at 37℃ in DMEM containing 10% FCS, 25 mM KCl, and 60 µg/ml kanamycin sulfate. After 15-16 h, medium was replaced with fresh medium supplemented with 10 µM cytosine arabinoside to suppress the glial growth. The medium change was repeated at 24 h and at every 48 h afterwards. It has been shown that under these conditions only precursor granule cells can survive after the final division in vitro. Topoisomerase IIbeta was specifically inhibited throughout the culture period by daily additions of 10 µM ICRF-193.

tag: Rat cerebellar granule cells cultured for 5 days in the presence of 10 µM ICRF-193


title: RGCC_016

status: Public on Nov 28 2008

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: 228 patients (included in clinical trial PACS01) + 24 patients (included based on the same inclusion criteria as those used for PACS01 trial).

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: Data were background noise subtracted (negative controls ± 6 SD), then normalized by original global intensity of hybridization. After expression data correction for the amount of PCR product spotted onto the membrane (testing probe data), data were log2-transformed and finally standardized. Only genes well measured for 70% of patients were retained.

source_name: Breast tumor tissue

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.

extract_protocol: All RNA was prepared on the same platform by the CsCl-cushion, as described (Chirgwin, 1979, Biochemistry, 18, 5294-5299.). The quality and the quantity of RNA samples were evaluated by Agilent 2100 Bioanalyser RNA LabChip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: Breast tumor tissue


title: RGCC_017


title: RGCC_024


title: RGCC_010


title: dmpARC_LDvsSD_rep4

status: Public on Nov 29 2008

city: Aberdeen

first: Gill

last: Campbell

address: Greenburn Road

department: Rowett Institute of  Nutrition and Health

country: United Kingdom

institute: University of Aberdeen

description: Each sample comes from one individual animal (no pools were used).

hyb_protocol: Hybridisation solution was prepared containing 130-160pmol of labelled RNA, 4ug of mouse Cot-1 DNA (Ambion, UK) and 3ul of 100x Denhardt’s solution made upto 130ul with Arrayhyb Microarray Hybridisation buffer (Sigma, UK). Prior to hybridisation, the microarray slides were prehybridised and placed in a GeneTAC hybridisation station (Genomic Solutions). The slides were heated to 55oC before addition of the hybridisation solution. The hybridisation was performed at 65oC for 16h, after which point the slides were washed with 0.5x SSC at 50oC for 3min, twice with 0.2x SSC/0.2% SDS at 50oC for 3min each and finally twice with 0.1x SSC at 20oC for 3min each.

scan_protocol: Slides were scanned in two channels using a GeneTAC LS IV hybridisation station (Genomic solution). The signal intensities were measured using the GeneTAC Integrator version 3.0.1 software (Genomic solution).

data_processing: Loess normalization was used to remove intensity depending dye-effects and also to transform intensities to the log2-scale.  As each clone was spotted in triplicates on the array, we averaged across the three replicates to obtain one log-ratio value per array/pair of samples. Spots that had been flagged during the image analysis process were omitted in this averaging process.

molecule: polyA RNA

organism: Phodopus sungorus

source_name: Cy3-Short Day Photoperiod

label_protocol: Using the regents in aminoallyl Message amplification kit and according to the instructions of the manufacturer (Ambion).

extract_protocol: Total RNA was extracted from the captured brain tissues. RNA was amplified using the reagents of aminoallyl Message amplification kit.

tag: 6 month old males were used for the study. The animals were maintained in short day photoperiod for 14 weeks before sacrifice. Brains were removed and sectioned. From the hypothalamic sections, dmpARC region was dissected using laser capture microdissection.

source_name: Cy5-LongDay Photoperiod

tag: 6 month old males were used for the study. The animals were maintained in long day photoperiod for 14 weeks before sacrifice. Brains were removed and sectioned. From the hypothalamic sections, dmpARC region was dissected using laser capture microdissection.


title: RGCC_022


title: RGCC_023


title: dmpARC_LDvsSD_rep2


title: RGCC_015


title: RGCC_011


title: RGCC_014


title: dmpARC_LDvsSD_rep3

tag: 6 month old males were used for the study. The animals were maintained in short day photoperiod for 14 weeks before sacrifice. Brains were removed and sectioned. From the hypothalamic sections, dmpARC region was dissected using laser capture microdissection..


title: RGCC_009


title: RGCC_008


title: dmpARC_LDvsSD_rep1


title: RGCC_020


title: RGCC_021


title: RGCC_019


title: RGCC_013


title: dmpARC_LDvsSD_rep5


title: RGCC_012


title: RGCC_007


title: RGCC_018


title: RGCC_006


title: CGCs_DIV1

description: Rat cerebellar granule cells cultured for one day


title: PACS01B_095


title: RGCC_004


title: RGCC_005


title: PACS01B_096


title: RGCC_001


title: RGCC_003


title: RGCC_002


title: PACS01B_100


title: PACS01B_097


title: PACS01B_092


title: PACS01B_091


title: PACS01B_094


title: PACS01B_099


title: PACS01B_098


title: PACS01B_083


title: PACS01B_090


title: PACS01B_093


title: PACS01B_087


title: PACS01B_088


title: U937 cells transfected with empty pSGMtNeo vector_ChIP with anti-HA antibody_replica2_array1

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

hyb_protocol: Hybridization is performed for  16 - 20 hours at 42°C.

scan_protocol: NimbleGen two-color arrays are scanned with a GenePix 4000B Scanner, to obtain images from for the 532nm and 635nm wavelengths.

data_processing: Data is pre-processed by NimbleGen Services using the NimbleGen NimbleScan software. Pair reports contain the raw data, listing the probe intensities of each array. Scaled Log2-Ratio Data is calculated for each sample from the experimental and reference conditions.

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HA antibody, pSGMtNeo

label_protocol: Experimental samples are labeled with Cy5, total DNA samples are labeled with Cy3 using 9mer primers that have Cy3 and Cy5 dyes attached and Klenow added.

growth_protocol: U937 cell lines were maintained in RPMI-1640 supplemented with 10% FCS and 2mM glutamine at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, harvested and washed twice with 1x PBS. Pellet was resuspended in ChIP lysis buffer (150mM NaCl, 1% Triton-X 100, 0,1% SDS, 500microM DTT, 10mM Tris-HCl, 5mM EDTA) and sonicated to obtain an average chromatin length of 500 bp. 5x106 cells were used for each IP and incubated at 4°C  overnight with immunopurified anti-HA antibody from clone 12CA5, previously coated on Dynabeads Protein A magnetic beads (Invitrogen, USA). Beads were then washed twice with each of the following buffers: Mixed Micelle Buffer (150mM NaCl, 1% Triton-X 100, 0,2% SDS, 20mM Tris-HCl, 5mM EDTA, 65% sucrose), LiCl/detergent wash (250mM LiCl, 0.5% Na deoxycholate, 0,5% NP-40, 10mM Tris-HCl, 1mM EDTA), Buffer 500 (500mM NaCl, % Triton-X 100, 0.1% Na deoxycholate, 25mM HEPES, 10mM Tris-HCl, 1mM EDTA) an a final wash was performed with 1x TE. Finally, beads were resuspended in 1x TE containing 1% SDS and incubated at 65°C for 10 minutes to elute immunocomplexes. Elution was repeated twice, and the samples were further incubated overnight at 65°C to reverse cross-linking, along with the untreated input (2,5% of the starting material).  After treatment with 0,5 mg/ml proteinase K for 3 hours, DNA was purified with Wizard SV Gel and PCR Clean-up system (Promega, USA) according to manufacturer’s protocol and eluted in nuclease-free water. ChIP products and input DNA were sent to NimbleGen Services (Madison, Wisconsin) for labeling, hybridization, scanning and preliminary data processing.

treatment_protocol: Cell lines were treated  for 8h with 100uM ZnSO4 prior to RNA extraction.

tag: product of ChIP with an anti-HA antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.

source_name: U937 myelomoncytic cells, total input DNA, pSGMtNeo

tag: total DNA from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: U937 cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_replica2_array1

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HA antibody, AML1/ETO

tag: product of ChIP with an anti-HA antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.

source_name: U937 myelomoncytic cells, total input DNA, AML1/ETO

tag: total DNA from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: U937 cells transfected with empty pSGMtNeo vector_ChIP with anti-HA antibody_replica1_array1


title: U937 cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_replica1_array1


title: PACS01B_085


title: PACS01B_089


title: PACS01B_084


title: PACS01B_082


title: PACS01B_080


title: PACS01B_081


title: PACS01B_079


title: PACS01B_078


title: PACS01B_077


title: PACS01B_076


title: PACS01B_066


title: PACS01B_074


title: PACS01B_069


title: PACS01B_072


title: PACS01B_073


title: PACS01B_068


title: PACS01B_067


title: PACS01B_071


title: PACS01B_070


title: 34BM2249

tag: CD34 selected cells from cadaveric bone marrow of 23 yo Female.

tag: .CEL file is identical to GSM239340


title: PACS01B_064


title: PACS01B_075


title: PACS01B_063


title: PACS01B_062


title: PACS01B_061


title: PACS01B_065


title: PACS01B_060


title: PACS01B_059


title: PACS01B_055


title: PACS01B_057


title: PACS01B_086


title: PACS01B_056


title: PACS01B_054


title: PACS01B_058


title: PACS01B_048


title: PACS01B_043


title: PACS01B_049


title: PACS01B_041


title: PACS01B_047


title: PACS01B_040


title: PACS01B_046


title: PACS01B_052


title: PACS01B_050


title: PACS01B_044


title: PACS01B_053


title: PACS01B_051


title: PACS01B_039


title: PACS01B_038


title: PACS01B_042


title: PACS01B_045


title: PACS01B_033


title: PACS01B_036


title: PACS01B_031


title: PACS01B_034


title: PACS01B_035


title: PACS01B_030


title: PACS01B_037


title: PACS01B_032


title: PACS01B_027


title: PACS01B_028


title: PACS01B_029


title: PACS01B_026


title: PACS01B_016


title: PACS01B_015


title: PACS01B_025


title: PACS01B_024


title: PACS01B_010


title: PACS01B_020


title: PACS01B_022


title: PACS01B_019


title: PACS01B_023


title: PACS01B_013


title: PACS01B_021


title: PACS01B_002


title: PACS01B_005


title: PACS01B_004


title: PACS01B_006


title: PACS01B_014


title: PACS01B_003


title: PACS01A_128


title: PACS01B_001


title: PACS01B_008


title: PACS01A_126


title: PACS01A_127


title: PACS01A_124


title: PACS01A_125


title: PACS01B_011


title: PACS01B_007


title: PACS01B_018


title: PACS01B_017


title: PACS01B_009


title: PACS01B_012


title: PACS01A_123


title: PACS01A_115


title: PACS01A_116


title: PACS01A_110


title: PACS01A_111


title: PACS01A_113


title: PACS01A_109


title: PACS01A_108


title: PACS01A_119


title: PACS01A_120


title: PACS01A_118


title: PACS01A_106


title: PACS01A_107


title: PACS01A_122


title: PACS01A_121


title: PACS01A_117


title: PACS01A_105


title: PACS01A_103


title: PACS01A_104


title: PACS01A_102


title: PACS01A_097


title: PACS01A_114


title: PACS01A_101


title: PACS01A_094


title: PACS01A_099


title: PACS01A_096


title: PACS01A_093


title: PACS01A_095


title: PACS01A_098


title: PACS01A_112


title: PACS01A_100


title: PACS01A_091


title: PACS01A_084


title: PACS01A_087


title: PACS01A_088


title: PACS01A_081


title: PACS01A_085


title: PACS01A_082


title: PACS01A_086


title: PACS01A_080


title: PACS01A_083


title: PACS01A_078


title: PACS01A_079


title: PACS01A_075


title: PACS01A_074


title: PACS01A_073


title: PACS01A_092


title: PACS01A_077


title: PACS01A_070


title: PACS01A_076


title: PACS01A_072


title: PACS01A_071


title: PACS01A_068


title: PACS01A_090


title: PACS01A_064


title: PACS01A_067


title: PACS01A_065


title: PACS01A_066


title: PACS01A_069


title: PACS01A_063


title: PACS01A_089


title: PACS01A_054


title: PACS01A_057


title: PACS01A_058


title: PACS01A_056


title: PACS01A_061


title: PACS01A_060


title: PACS01A_059


title: PACS01A_050


title: PACS01A_049


title: PACS01A_062


title: PACS01A_052


title: PACS01A_047


title: PACS01A_048


title: PACS01A_055


title: PACS01A_045


title: PACS01A_046


title: PACS01A_044


title: PACS01A_038


title: PACS01A_037


title: PACS01A_039


title: PACS01A_036


title: PACS01A_042


title: PACS01A_041


title: PACS01A_043


title: PACS01A_051


title: PACS01A_033


title: PACS01A_053


title: PACS01A_035


title: PACS01A_034


title: PACS01A_040


title: PACS01A_032


title: PACS01A_028


title: PACS01A_029


title: PACS01A_031


title: PACS01A_027


title: PACS01A_025


title: PACS01A_023


title: PACS01A_030


title: PACS01A_019


title: PACS01A_020


title: PACS01A_022


title: PACS01A_021


title: PACS01A_024


title: PACS01A_018


title: PACS01A_015


title: PACS01A_016


title: PACS01A_017


title: PACS01A_013


title: PACS01A_010


title: PACS01A_012


title: PACS01A_011


title: PACS01A_014


title: PACS01A_026


title: PACS01A_009


title: Magnifica_hyb_2

city: Cambridge

first: Irene

last: Newton

state: MA

address: 16 Divinity Ave

department: OEB

institute: Harvard University

description: comparative genomic hybridization

scan_protocol: Gene chips were scanned using the GeneChip Scanner 3000

data_processing: GCOS affymetrix processing

organism: Calyptogena magnifica symbiont

source_name: Clam gill tissue containing symbionts

label_protocol: Enzo bioarray kit

extract_protocol: Qiagen genomic tip extraction protocol

treatment_protocol: dilute DNAse treatment to remove much of host genomic DNA contamination

tag: Calyptogena magnifica symbiont


title: PACS01A_008


title: Pacifica_hyb_1

description: comparative genomic hybridization

organism: Calyptogena pacifica gill symbiont

tag: Calytptogena pacifica symbiont


title: PACS01A_005


title: Pacifica_hyb_3

description: comparative genomic hybridization


title: PACS01A_006


title: PACS01A_004


title: PACS01A_007


title: Magnifica_hyb_1

description: comparative genomic hybridization


title: Pacifica_hyb_2

description: comparative genomic hybridization


title: Kilmeri_hyb_3

description: comparative genomic hybridization

organism: Calyptogena kilmeri gill symbiont

tag: Calyptogena kilmeri symbiont


title: PACS01A_002


title: Kilmeri_hyb_2

description: comparative genomic hybridization


title: PACS01A_003


title: PACS01A_001


title: Kilmeri_hyb_1

description: comparative genomic hybridization


title: U937 cells transfected with empty pSGMtNeo vector - Replica 1

hyb_protocol: Hybridization is performed for 16 - 20 hours at 42°C.

scan_protocol: NimbleGen arrays are scanned with a GenePix 4000B Scanner.

source_name: U937 myelomoncytic cell line, transfected with pSGMtNeo vector

label_protocol: Doublestranded cDNA was random-prime labeled with Cy3-nonamers.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. First strand cDNA synthesis was performed on 15ugr of total RNA with Superscript III (Invitrogen, USA) using Oligo(dT)12–18 Primer according to manufacturer’s protocol. Complementary second strand was then synthesized and 4ug of doublestranded cDNAs were shipped to NimbleGen Services for labeling, hybridization, and scanning.

tag: U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: ct28dv53d, p1s21t.gpr

status: Public on Nov 27 2008

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
Cane toad 28 days vs 53 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

hyb_protocol: Prehybridization of slides, application of the probe to the microarray slides, hybridisation, and subsequent washing steps were performed according to manufacturer's instructions (Corning Microarray Technology).

scan_protocol: Slides were scanned and analysed with a GenePix 4000B laser scanner and GenePix 3.0 and 4.0 software (Axon Instruments).

data_processing:
Normalization Method: Limma PrintTipLoess Normalisation within arrays, Limma Quantile Normalisation between arrays. Ref: Smyth, G.K. 2004. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments. Statistical Applications in Genetics and Molecular Biology. Vol. 3: Iss. 1, Article 3.

Sample data table VALUE column reports log2 (pre-metamorph/post-metamorph) ratios

organism: Rhinella marina

label_protocol: Total RNA (100 mg) was reverse transcribed (Qiagen) and labelled cDNA probes were generated using the fluorophores, Cy3 and Cy5 (Amersham Pharmacia Biotech).

extract_protocol: Samples were harvested at 9, 18, 28 (pre-metamorph), 30 and 53 (post-metamorph) days of age and RNA extracted using Trizol Reagent (Invitrogen).

tag: 28d, Biological Repl

value: 1, Technical repl:1

tag: 53d, Biological Repl


title: U937 cells transfected with empty pSGMtNeo vector - Replica 2


title: U937 cells expressing AML1/ETO - Replica 1

source_name: U937 myelomoncytic cell line, transfected with HA-tagged AML1/ETO

tag: U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: ct28dv53d, p1s21b.gpr

description:
Cane toad 28 days vs 53 days
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: false

value: 1, Technical repl:2


title: ct28dv30d, p1s17t.gpr

description:
Cane toad 28 days vs 30 days
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: false

value: 1, Technical repl:3

tag: 30d, Biological Repl


title: ct28dv30d, p1s15b.gpr

description:
Cane toad 28 days vs 30 days
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: ct18dv30d, p1s24b.gpr

description:
Cane toad 18 days vs 30 days
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

tag: 18d, Biological Repl

value: 2, Technical repl:1


title: ct28dv53d, p1s22t.gpr

description:
Cane toad 28 days vs 53 days
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: true


title: U937 cells transfected with empty pSGMtNeo vector - ChIP with anti-HEB antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HEB antibody, transfected with pSGMtNeo vector

label_protocol: Experimental samples are labeled with Cy5, total DNA samples used as reference are labeled with Cy3 using 9mer primers that have Cy3 and Cy5 dyes attached and Klenow added.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature, harvested and washed twice with 1x PBS. Pellet was resuspended in ChIP lysis buffer (150mM NaCl, 1% Triton-X 100, 0,1% SDS, 500microM DTT, 10mM Tris-HCl, 5mM EDTA) and sonicated to obtain an average chromatin length of 500 bp. 5x106 cells were used for each IP and incubated at 4°C  overnight with immunopurified anti-HA antibody from clone 12CA5,  or commercially available antibodies against ETO (Santa Cruz sc-9737), AML1/RUNX1 (Abcam ab23980), HEB (Santa Cruz sc-357), or trimethylated H3K4 (Abcam ab8580),previously coated on Dynabeads Protein A magnetic beads (Invitrogen, USA). Beads were then washed twice with each of the following buffers: Mixed Micelle Buffer (150mM NaCl, 1% Triton-X 100, 0,2% SDS, 20mM Tris-HCl, 5mM EDTA, 65% sucrose), LiCl/detergent wash (250mM LiCl, 0.5% Na deoxycholate, 0,5% NP-40, 10mM Tris-HCl, 1mM EDTA), Buffer 500 (500mM NaCl, % Triton-X 100, 0.1% Na deoxycholate, 25mM HEPES, 10mM Tris-HCl, 1mM EDTA) an a final wash was performed with 1x TE. Finally, beads were resuspended in 1x TE containing 1% SDS and incubated at 65°C for 10 minutes to elute immunocomplexes. Elution was repeated twice, and the samples were further incubated overnight at 65°C to reverse cross-linking, along with the untreated input (2,5% of the starting material).  After treatment with 0,5 mg/ml proteinase K for 3 hours, DNA was purified with Wizard SV Gel and PCR Clean-up system (Promega, USA) according to manufacturer’s protocol and eluted in nuclease-free water. ChIP products and input DNA were sent to NimbleGen Services (Madison, Wisconsin) for labeling, hybridization, scanning and preliminary data processing.

tag: product of ChIP with an anti-HEB antibody from U937  cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.

source_name: U937 myelomoncytic cells, total input DNA, transfected with pSGMtNeo vector


title: U937 cells expressing AML1/ETO-HA - ChIP with anti-3MetK4 antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-3MetK4 antibody, transfected with HA-tagged AML1/ETO

tag: product of ChIP with an anti-3MetK4 antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.

source_name: U937 myelomoncytic cells, total input DNA, transfected with HA-tagged AML1/ETO


title: ct28dv53d, p1s14b2.gpr

description:
Cane toad 28 days vs 53 days
Biological Replicate: 2, Technical Replicate: 3, Dye Swapped: true

value: 2, Technical repl:3


title: ct18dv30d, p1s11b2.gpr

description:
Cane toad 18 days vs 30 days
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: true


title: ct18dv30d, p1s11t2.gpr

description:
Cane toad 18 days vs 30 days
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: false


title: ct28dv30d, p1s15t2.gpr

description:
Cane toad 28 days vs 30 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: ct18dv30d, p1s9b2.gpr

description:
Cane toad 18 days vs 30 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: U937 cells expressing AML1/ETO - Replica 2


title: U937 cells expressing AML1/ETO-HA - ChIP with anti-HEB antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HEB antibody, transfected with HA-tagged AML1/ETO

tag: product of ChIP with an anti-HEB antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: ct9dv30d, p1s24t2.gpr

description:
Cane toad 9 days vs 30 days
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false

tag: 9d, Biological Repl


title: ct9dv30d, p1s23b2.gpr

description:
Cane toad 9 days vs 30 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true


title: ct28dv53d, p1s14t2.gpr

description:
Cane toad 28 days vs 53 days
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: ct9dv30d, p1s23t.gpr

description:
Cane toad 9 days vs 30 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: U937 cells transfected with empty pSGMtNeo vector_ChIP with anti-HA antibody_replica2_array2

tag: product of ChIP with an anti-HA antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.

tag: total DNA from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: U937 cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_replica1_array2

tag: product of ChIP with an anti-HA antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.

tag: total DNA from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: U937 cells expressing AML1/ETO-HA_ChIP with anti-HA antibody_replica2_array2


title: ct9dv53d, p1s19t.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 2, Technical Replicate: 3, Dye Swapped: true


title: ct18dv53d, p1s9t.gpr

description:
Cane toad 18 days vs 53 days
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: true


title: ct9dv30d, p1s13t.gpr


title: ct18dv53d, p1s7t.gpr

description:
Cane toad 18 days vs 53 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false


title: Bacteria_XDM2_BCYE_Rep3

city: Berlin

first: Tiago

last: Lopes

address: Robert Rossle Strasse, 10

country: Germany

institute: Max-Delbruck Center for Molecular Medicine

description: It is worth mentioning that the chips were spotted within the lab. For the complete procedure, please refer to the manuscript.

hyb_protocol: The hybridization and washing conditions were carried out in a GeneTac Hybridization (Genetic MicroSystems) device. Initially, the slides containing the microarrays were denaturalized at 65 degreesC for 5 min. A solution containing 8 ?L of blocking liquid (Amersham Biosciences RPN 3601), 19 ?L of SSC 20×, 5.5 ?L SDS 2% w/v, 100 pmol of cDNA marked with fluorescent dyes Cy3 and Cy5, totaling 110 ?L, was denaturalized at 95 °C for 2 min, deposited on the slide and kept for 12 h at 42 degreesC. After hybridization, the slides were washed at 25 degreesC in the following solution: 2× SSC/SDS 0.5% w/w, 0.5× SSC and 0.05× SSC. All of the washing steps consisted of 10 cycles with 10 s of solution flux and 20 s of incubation. The slides were dried for 15 min and submitted to fluorescence detection.

data_processing: The slides were submitted to fluorescence reading in a model GMSTM 418 Arrayer Scanner (Affymetrix Inc.) under different wavelengths: 550 nm (Cy3) and 650 nm (Cy5). The location and identity of each gene in the slide was defined in a text file, created with the aid of the CloneTracker2 program (BioDiscovery). The signal was quantified through ImaGene software (v. 4.1, BioDiscovery) in which two images from the Cy3 and Cy5 fluorescent dyes were overlapped and the spots classified according to morphology and intensity. For transformation of data, the background signal was discounted from the signal of each spot using the local background obtained by the GeneSight (BioDiscovery) program and the data obtained from the intensity ratio of the signal measured by the Cy5 (experiment) over the Cy3 (control) were normalized using the Lowess method (Cleveland, 1979). The replicas inside each slide were combined by the median of their values and the statistical analysis was carried out using the SAM (Significance Analysis of Microarrays) program (Tusher et al., 2001).

organism: Xylella fastidiosa

source_name: Total RNA from Xylella fastidiosa Grown Under XDM2 Medium, labeled with Cyanine-5.

label_protocol: The construction of fluorescent cDNA for hybridization reactions used a CyScribe cDNA Post Labeling kit (Amersham Biosciences) with 30 ?g of RNA and 15 microgram of random primers (Amersham Bioscience). The reverse transcriptase reaction occurred at 37 degrees C for 3 h in a programmable thermocycler (PTC-100 Programmable Thermal Controller - MJ Research, Inc.). As the control of the transcriptase reaction, 1 microliter of the synthetic RNA from the Lucidea Universal ScoreCard kit (Amersham Biosciences) was used. The reaction was neutralized with 20 microliter of 2 M of HEPES and the cDNAs were purified through precipitation with 3 M of sodium acetate, 75 microliter of 100% v/v ethanol and kept at – 20 degrees C for the whole night. After centrifuging and washing with 70% ethanol the cDNA was resuspended in 30 microliter of the CyDye diluted in 0.1 M of bicarbonate of soda, pH 9.0. The sample was kept at 25 degrees C, in the dark for 1 h and the labeling reactions were stopped by the addition of 15 microliter of 4 M of hydroxylamine for 15 min at 25 degreesC. The sample was resuspended in 400 microliter of TE buffer (10 mM of Tris-HCl pH 8.0, 1 mM of EDTA) and concentrated in a Microcon-type column - YM30 (Millipore). The efficiency of the reading was monitored by  measuring absorption at 650 nm.

growth_protocol: The bacteria were cultivated for four days at 30 degree C in Erlenmeyer of 250 mL 108 containing 30 mL of the XDM2 medium (Lemos et al., 2003) under shaking conditions (140 rpm).

extract_protocol: The methodology used for the RNA extraction (Chomczynski and 114 Sacchi, 1987) involved a monophasic solution of phenol and guanidine isothiocyanate (Trizol 115 – Invitrogen). The RNA samples treated with DNAse I were purified through the 116 NucleoSpin® RNA II BD Bioscience kit (Clontech), resuspended in H2ODEPC and stored at – 117 80 degreesC.

tag: Strain

tag: Source

value: Isolated from citrus

source_name: Total RNA from Xylella fastidiosa Grown Under BCYE Medium, labeled with Cyanine-3.

label_protocol: The construction of fluorescent cDNA for hybridization reactions used a CyScribe cDNA Post Labeling kit (Amersham Biosciences) with 30 ?g of RNA and 15 microgram of random primers (Amersham Bioscience). The reverse transcriptase reaction occurred at 37 degrees C for 3 h in a programmable thermocycler (PTC-100 Programmable Thermal Controller - MJ Research, Inc.). As the control of the transcriptase reaction, 1 microliter of the synthetic RNA from the Lucidea Universal ScoreCard kit (Amersham Biosciences) was used. The reaction was neutralized with 20 microliter of 2 M of HEPES and the cDNAs were purified through precipitation with 3 M of sodium acetate, 75 microliter of 100% v/v ethanol and kept at -20 degrees C for the whole night. After centrifuging and washing with 70% ethanol the cDNA was resuspended in 30 microliter of the CyDye diluted in 0.1 M of bicarbonate of soda, pH 9.0. The sample was kept at 25 degreesC, in the dark for 1 h and the labeling reactions were stopped by the addition of 15 microliter of 4 M of hydroxylamine for 15 min at 25 degreesC. The sample was resuspended in 400 microliter of TE buffer (10 mM of Tris-HCl pH 8.0, 1 mM of EDTA) and concentrated in a Microcon-type column - YM30 (Millipore). The efficiency of the reading was monitored by  measuring absorption at 550 nm.

growth_protocol: The bacteria were cultivated for four days at 30 degrees C in Erlenmeyer of 250 mL 108 containing 30 mL of the modified BCYE (Campanharo et al., 2003) under shaking conditions (140 rpm).

extract_protocol: The methodology used for the RNA extraction (Chomczynski and 114 Sacchi, 1987) involved a monophasic solution of phenol and guanidine isothiocyanate (Trizol 115 – Invitrogen). The RNA samples treated with DNAse I were purified through the 116 NucleoSpin® RNA II BD Bioscience kit (Clontech), resuspended in H2ODEPC and stored at – 117 80 degrees C.


title: U937 cells expressing AML1/ETO-HA - ChIP with anti-AML1 antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-AML1 antibody, transfected with HA-tagged AML1/ETO

tag: product of ChIP with an anti-AML1 antibody from U937cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: U937 cells transfected with empty pSGMtNeo vector_ChIP with anti-HA antibody_replica1_array2


title: ct9dv53d, p1s18t.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false


title: U937 cells expressing AML1/ETO-HA - ChIP with anti-ETO antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-ETO antibody, transfected with HA-tagged AML1/ETO

tag: product of ChIP with an anti-ETO antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: Bacteria_XDM2_BCYE_Rep2

scan_protocol: The slides were submitted to fluorescence reading in a model GMSTM 418 Arrayer Scanner (Affymetrix Inc.) under different wavelengths: 550 nm (Cy3) and 650 nm (Cy5).


title: ct9dv53d, p1s18b.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 2, Technical Replicate: 2, Dye Swapped: false

value: 2, Technical repl:2


title: U937 cells expressing AML1/ETO-HA - ChIP with anti-HA antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HA antibody, transfected with HA-tagged AML1/ETO


title: Bacteria_XDM2_BCYE_Rep1


title: ct9dv53d, p1s5t.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 1, Technical Replicate: 2, Dye Swapped: false


title: ct9dv53d, p1s5b.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 1, Technical Replicate: 3, Dye Swapped: true


title: U937 cells transfected with empty pSGMtNeo vector - ChIP with anti-ETO antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-ETO antibody, transfected with pSGMtNeo vector

tag: product of ChIP with an anti-ETO antibody from U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: U937 cells transfected with empty pSGMtNeo vector - ChIP with anti-AML1 antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-AML1 antibody, transfected with pSGMtNeo vector

tag: product of ChIP with an anti-AML1 antibody from U937  cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: WBC Brahman 3

status: Public on Nov 26 2008

city: Brisbane

first: Emily

middle: Kate

last: Piper

address: Seddon Buildings (Bldg 82)

department: School of Veterinary Science

institute: University of Queensland

hyb_protocol: As per GeneChip expression manual, performed by the Australian Genome Research Facility

scan_protocol: Agilent Microarray Scanner (Agilent Technologies) as per Affymetrix GeneChip manual

data_processing: The data were analyzed with R/Bioconductor using RMA normalization. Additional parameters: background correction was convolution, quantile normalization and summarization with median polish.

organism: Bos indicus

source_name: White blood cell, peripheral circulation

growth_protocol: White blood cells obtained via jugular venipuncture were collected into an EDTA vacuntainer; no growth or culture protocol was performed.

extract_protocol: 5 ml whole blood collected into EDTA vacutained was combined with 45 ml red blood cell lysis buffer and allowed to stand at room temperature for 10 min. Sample was spun at 250 g for 10 min to pellet cells and supernatant removed. The cell pellet containing a whole white blood cell extract was resuspended in 4 ml Trizol reagent (Invitrogen) and total RNA isolation carried out according to the manufacturer's instructions. DNase treatment was carried out with Turbo DNase (Ambion) according to the manufacturer's instructions.

tag: Gender

value: female; Age:6 months; Tissue:white blood cells; Disease state:heavy challenge with R.microplus


title: WBC Brahman 1

label_protocol: As per GeneChip expression manual, performed by the Australian Genome Research Facility


title: WBC Brahman 2


title: U937 cells transfected with empty pSGMtNeo vector - ChIP with anti-HA antibody

source_name: U937 myelomoncytic cells, product of ChIP with an anti-HA antibody, transfected with pSGMtNeo vector

tag: product of ChIP with an anti-HA antibody from U937  cell line (human cell line established from a diffuse histiocytic lymphoma and displaying  monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: WBC Holstein 3

organism: Bos taurus


title: WBC Holstein 2


title: WBC Holstein 1


title: NTHi 4h; 1740174049_F

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

institute: University of Texas-M.D. Anderson Cancer Center

description: Gene expression in C57BL/6 mouse lungs after exposure to aerosolized NTHi lysate

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3.  Data generated both with rank invariant normalization, using sham group as the reference group.

source_name: Lung homogenate, 4h NTHi treatment

label_protocol: labeling with Cy3-Streptavidin per Illumina instructions.

growth_protocol: Frozen stock (1 x 107 CFU/ml) of non-typeable Haemophilus influenzae (NTHi) was grown on chocolate agar at 300 ul per 10 cm plate (Remel) for 24 h at 37ºC in 5% CO2, then harvested and incubated for 16 h in 1 l brain-heart infusion broth (Acumedia) supplemented with 3.5 ug/ml NAD (Sigma-Adrich).

extract_protocol: total RNA extracted using Qiagen Rneasy per manufacturers instructions.  cRNA amplification using Ambion total prep kit per manufacturers instructions.

treatment_protocol: The NTHi cell pellet was washed and resuspended in 20 ml 0.9% sodium chloride solution.  This suspension was passed three times through an EmulsiFlex C5 cell disruptor (Avestin) at greater then 10,000 psi, then diluted to 4-5 mg/ml in 0.9% sodium chloride solution by bicinchoninic assay (Pierce) and centrifuged at 15,000 x g for 10 min.  The supernatant was collected, the protein concentration was adjusted to 2.5 mg/ml, and the lysate was sterilized by passage through a 0.2 µm filter and frozen in 8 ml aliquots at -80ºC.  For treatment, a thawed aliquot was placed in an AeroMist CA-209 nebulizer driven by 10 l/min 5% CO2 in air for 20 min, resulting in aerosolization of 4 ml of lysate, with the protein concentration in residual lysate


title: NTHi 2h; 1740174013_B

source_name: Lung homogenate, 2h NTHi treatment


title: Sham; 1740174049_A

source_name: Lung homogenate, 2h Sham treatment


title: ct9dv53d, p1s4t.gpr

description:
Cane toad 9 days vs 53 days
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false

tag: 53d, Biological Repl


title: NTHi 2h; 1740174047_B


title: NTHi 4h; 1740174047_F


title: ES cells_H2O2_SIRT1-IP

city: Boston

first: Philipp

last: Oberdoerffer

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: no additional information

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in a total volume of 35 ul using 2X Hybridization Buffer (composition is proprietary) and hybridization component A (composition is priorietary). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegens standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: mouse embryonic stem (ES) cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming per manufacturer's protocol. Input DNA was labeled with Cy3, IP DNA was labeled with Cy5 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: standard growth conditions

extract_protocol: Mouse embryonic stem (ES) cells were fixed in 1% formaldehyde for 20 min at 37 degree Celsius, cells were than lysed and processed using the Upstate Chromatin IP Kit following the manufacturer's instructions. Samples were sonicated 5 times for 10 s and subjected to 1h preclear and o/n IP using Rabbit anti Sir2 (Upstate), Rabbit Ig (Upstate) or Rabbit anti-acetyl H1K26 (Vaquero et al., Mol Cell 2004). Input and IP samples were amplified using LM-PCR following the NImblegen protocol.

treatment_protocol: 1h with 2 mM H2O2

tag: Input fraction

tag: IP fraction


title: NTHi 4h; 1740174047_C


title: NTHi 2h; 1740174013_E


title: NTHi 2h; 1740174049_B


title: ES cells_H2O2_H1AcK26-IP

description: no additional information


title: NTHi 4h; 1740174013_C


title: ES cells_untreated_SIRT1-IP

description: no additional information

treatment_protocol: no treatment


title: Sham; 1740174047_D


title: ES cells_untreated_H1AcK26-IP

description: no additional information


title: NTHi 4h; 1740174049_C


title: Sham; 1740174013_D


title: Salt-resistant fraction (P1) vs Input

first: Mary Miyaji-Yamaguchi

address: 2-5-1 Shikata-cho

institute: Okayama University

description: DNA fragments from the salt-resistant fraction (P1) vs Input

hyb_protocol: Performed by NimbleGen following company specifications.

data_processing: modified ACME, which calculates the probability values based on hypergeometric distribution instead of chi-square distribution.

label_protocol: Labeled using random 9mer primers according to NimbleGen protocol.

extract_protocol: The VP16-treated cells were lysed with a buffer containing 1% Sarkosyl, 10 mM Tris-HCl (pH7.5), 10 mM EDTA, and protease inhibitor mixture. Concentrated CsCl was added to a final concentration of 0.5 M. To fragment DNA, the lysates were sonicated. Before immunoprecipitation (IP), 3 volumes of a buffer containing 10 mM Tris-HCl (pH7.5), 10 mM EDTA, 100 mM NaCl, and protease inhibitor mixture was added to 1 volume of lysates and the diluted lysates were centrifuged for 15 min at 15000 rpm at 4˚C. The supernatant was pre-cleared for 2 h at 4°C and IP reaction was initiated by the addition of Dynabeads protein G, which had been pre-incubated with 5 µg of specific antibody (3B6) or control antibody (mouse IgG). The beads suspension was incubated overnight at 4°C and the IP fraction was recovered by magnetic separation followed by washing 3 times with TEST-150 (10 mM Tris-HCl: pH7.5, 10 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, protease inhibitor). The IP-beads were then eluted 3 times with 500 µl of TEST-500 (10 mM Tris-HCl: pH7.5, 10 mM EDTA, 500 mM NaCl, 0.1% Triton X-100, protease inhibitor) by magnetic searation each time and the eluates were pooled (designated as P2 fraction). DNA fragments still bound on the beads (designated as P1 fraction) were treated with RNase A at 55˚C for 30 min, Proteinase K at 55˚C overnight, and purified by phenol/chloroform extractions followed by ethanol-precipitation with 10 µg of glycogen.

treatment_protocol: Primary cultures of rat cerebellar granule cells at day 2 were treated with 0.5 mM Etoposide (VP-16) in serum-free medium for 15 min.

source_name: Input

extract_protocol: The VP16-treated cells were lysed with a buffer containing 1% Sarkosyl, 10 mM Tris-HCl (pH7.5), 10 mM EDTA, and protease inhibitor mixture. Concentrated CsCl was added to a final concentration of 0.5 M. To fragment DNA, the lysates were sonicated. Before immunoprecipitation (IP), 3 volumes of a buffer containing 10 mM Tris-HCl (pH7.5), 10 mM EDTA, 100 mM NaCl, and protease inhibitor mixture was added to 1 volume of lysates and the diluted lysates were centrifuged for 15 min at 15000 rpm at 4˚C. The supernatant was pre-cleared for 2 h at 4°C and DNA fragments were treated with RNase A at 55˚C for 30 min, Proteinase K at 55˚C overnight, and purified by phenol/chloroform extractions followed by ethanol-precipitation with 10 µg of glycogen and digested with a restriction enzyme MboI.

tag: DNA fragments from eTIP input.


title: NTHi 2h; 1740174049_E


title: Sham; 1740174047_A


title: Sham; 1740174013_A


title: NTHi 4h; 1740174013_F


title: Sham; 1740174049_D


title: Salt-released fraction (P2) vs Input

description: DNA fragments from the salt-released fraction (P2) vs Input

scan_protocol: Performed by NimbleGen following company specifications.

tag: DNA fragments from salt-released fraction (P2).

tag: DNA fragments from eTIP input


title: ES cells_untreated_Rabbit-Ig-IP

description: no additional information


title: Patient2_339_GH_Day1_GH0_8AM

status: Public on Nov 25 2008

first: Patricia

last: Maningat

address: 1100 Bates St

department: CNRC

institute: Baylor College of Medicine

hyb_protocol: 750 ng of labeled cRNAs were hybridized to the Human Ref 8 V2 Beadchip arrays (Illumina  Inc., San Diego, CA) at 55oC overnight (16h) following the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Doc. # 111226048 Rev. B, Illumina Inc)  and stained with 1 g/ml streptavidin-Cy3 (Amersham Biosciences, Piscataway, NJ) for visualization

scan_protocol: Probe arrays were scanned using the BeadArray reader (Factor 1)

data_processing: Gene expression analysis was performed using the Sentrix BeadChip and BeadStation system from Illumina, Inc

label_protocol: 440 ng total RNA was used for in vitro transcription, overnight for 14h using biotin-11-dUTP for labeling of the cRNA product using the Illumina®TotalPrep RNA amplification kit (Ambion, Inc., Austin, TX)

extract_protocol: RNA was isolated from the milk fat globule using Trizol following the manufacturer's protocol

tag: Milk Fat Globule


title: Patient2_339_GH_Day1_GH0_2AM


title: Patient2_339_GH_Day1_GH0_5AM


title: Patient2_339_GH_Day1_GH0_11PM


title: NTHi 2h; 1740174047_E


title: Patient2_339_GH_Day1_GH0_8PM


title: Patient2_339_GH_Day1_GH0_2PM


title: Patient3_339_GH_Day1_GH0_5AM


title: Patient2_339_GH_Day1_GH0_11AM


title: Patient2_339_GH_Day1_GH0_5PM


title: Patient3_339_GH_Day1_GH0_11PM


title: Patient3_339_GH_Day1_GH0_2AM


title: CD4-CD8-_DN_Thymocytes_TCDD_1

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

department: Immunology

institute: Institute for Environmental Research

description: Female, 6-8 week old C57BL/6 mice were i.p. injected with corn oil alone. 5 days after the injection thymocytes were labled by in vivo FITC injection. 24h after injection thymi and spleen were surgically removed and CD4-CD8- cells from thymus (thymocytes) or spleen (thymus emigrants) directly FACS sorted into TRIzol.

hyb_protocol: Affymetrix standard protocols

scan_protocol: Affymetrix standard protocols

data_processing: Cel files were processed using RMA (affy-package, R2.0)

label: PE

label_protocol: Affymetrix standard protocols

extract_protocol: RNA was extracted using linear poly acrylamide as precipitation aid. Extracted RNA was amplified using Ambions message Amp kit and checked for purity and integrity. The following steps were done according to Affymetrix standard protocols.

treatment_protocol: Female, 6-8 week old C57BL/6 mice were i.p. injected with 10Âµg/kg TCDD in corn oil or corn oil alone. 5 days after the injection thymocytes were labled by in vivo FITC injection. 24h after injection thymi and spleen were surgically removed and CD4-CD8- cells from thymus (thymocytes) or spleen (thymus emigrants) directly FACS sorted into TRIzol.

tag: Tissue

value: Thymus

tag: Cell Type

value: CD4-CD8- Thymocytes

tag: Age

value: 6-8 weeks

tag: Treatment

tag: Replicate


title: Patient3_339_GH_Day1_GH0_5PM


title: Patient3_339_GH_Day1_GH0_8PM


title: Patient3_339_GH_Day1_GH0_8AM


title: CD4-CD8-_DN_Thymocytes_TCDD_2

tag: Strain


title: Patient3_339_GH_Day1_GH0_2PM


title: CD4-CD8-_DN_thymus emigrants_TCDD_1

description: Female, 6-8 week old C57BL/6 mice were i.p. injected with 10µg/kg TCDD in corn oil or corn oil alone. 5 days after the injection thymocytes were labled by in vivo FITC injection. 24h after injection thymi and spleen were surgically removed and CD4-CD8- cells from thymus (thymocytes) or spleen (thymus emigrants) directly FACS sorted into TRIzol.

source_name: CD4-CD8-_DN_thymus emigrants


title: Patient3_339_GH_Day1_GH0_11AM


title: Patient5_339_GH_Day1_GH0_5AM


title: Patient5_339_GH_Day1_GH0_2AM


title: CD4-CD8-_DN_thymus emigrants_TCDD_2

treatment_protocol: Female, 6-8 week old C57BL/6 mice were i.p. injected with 10µg/kg TCDD in corn oil or corn oil alone. 5 days after the injection thymocytes were labled by in vivo FITC injection. 24h after injection thymi and spleen were surgically removed and CD4-CD8- cells from thymus (thymocytes) or spleen (thymus emigrants) directly FACS sorted into TRIzol.

value: Thymus Emigrants


title: CD4-CD8-_DN_fetal_thymus_emigrants_TCDD_2

description: C57BL/6 dams were terminally mated and fetuses surgically removed at dpc 15. Fetal thymus organ culture were performed as described before. Briefly 5-6 fetal thymus lobes were cultured on culture inlays for 6 days. Medium (RPMI 1640, with 10nM TCDD or solvent control) was excanged every 2 days. At day six thymus lobes were flushed 2x with 200µl  ice cold PBS, which was recovered for cell isolation. Thymus emigrants were transfered to single cell suspensions by gently grinding. CD4-CD8- were subsequently sorted with anti CD4 and anti CD8 MACS beads to a purity >95% which was routinely checked by FACS analysis.

source_name: CD4-CD8-_DN_fetal_thymus emigrants

extract_protocol: RNA was extracted from pooled DN thymocytes using TRIzol. After checking RNA purity and integrity RNA was amplified using Ambions Message Amp kit. Further lableling reactions and hybridization were performed according to Affymetrix standard protocols.

treatment_protocol: C57BL/6 dams were terminally mated and fetuses surgically removed at dpc 15. Fetal thymus organ culture were performed as described before. Briefly 5-6 fetal thymus lobes were cultured on culture inlays for 6 days. Medium (RPMI 1640, with 10nM TCDD or solvent control) was excanged every 2 days. At day six thymus lobes were flushed 2x with 200µl  ice cold PBS which was recovered for cell isolation. Thymus emigrants were transfered to single cell suspensions by gently grinding. CD4-CD8- were subsequently sorted with anti CD4 and anti CD8 MACS beads to a purity >95% which was routinely checked by FACS analysis.

value: Thymusemigrants

value: dpc 21


title: CD4-CD8-_DN_thymus emigrants_corn_oil_1

value: Thymus emigrants


title: CD4-CD8-_DN_fetal_thymus_emigrants_TCDD_1


title: CD4-CD8-_DN_Thymocytes_Oil_2

value: Corn oil


title: Patient5_339_GH_Day1_GH0_8AM


title: CD4-CD8-_DN_thymus emigrants_corn_oil_2

value: Dioxane 2


title: CD4-CD8-_DN_fetal_thymus_emigrants_Dioxane_2


title: Liver 5d vehicle 4

city: Groton

first: James

last: Fischer

state: CT

department: Exploratory Medicinal Sciences

institute: Pfizer, Inc

description: vechicle treatment

hyb_protocol: 10 ug of biotinylated cRNA were hybridized to MG_U74Av2 GeneChips for 16 hours at 45oC.  Washing and staining was done using GeneChip Fluidics Station 450 EukGE-WS2v3.

scan_protocol: The GeneChips were scanned with the Agilent GeneArray Scanner

data_processing: MAS5 scaled to 300.  To calculate fold change values, intensity values less then 50 were adjusted to 50.

source_name: liver

label_protocol: 5 ug total RNA was used as a template for ds cDNA synthesis using Life /Technologies Superscript II cDNA synthesis kit.  All of the ds cDNA was used for the labeling reaction using the ENZO Bioarray HighYield RNA Transcript Labeling Kit (T7) (42655)

extract_protocol: frozen liver samples (~100 mg) were homogenized with a Polytron homogenizer in 4mls RLT buffer (RNAeasy/Qiagen) with 10 ul/ml BME; 600 ul processed with Qiagen Rneasy mini columns

treatment_protocol: liver samples were dissected then flash frozen with liquid nitrogen

tag: Male B6/CBF1J


title: Patient5_339_GH_Day1_GH0_8PM


title: Liver 5d vehicle 3

description: vechicle treatment


title: Liver 5d vehicle 2

description: vechicle treatment


title: CD4-CD8-_DN_fetal_thymus_emigrants_Dioxane

value: Dioxane


title: Liver 5d vehicle 1

description: vechicle treatment


title: Liver 5d CP-865520 3

description: CP-865520 treatment


title: CD4-CD8-_DN_Thymocytes_Oil_1

value: Corn Oil


title: Liver 5d CP-865520 4

description: CP-865520 treatment


title: CD4-CD8-_DN_fetal_thymocytes_Dioxane

description: C57BL/6 dams were terminally mated and fetuses surgically removed at dpc 15. Fetal thymus organ culture were performed as described before. Briefly 5-6 fetal thymus lobes were cultured on culture inlays for 6 days. Medium (RPMI 1640, with 10nM TCDD or solvent control) was excanged every 2 days. At day six thymus lobes were washed 2x with ice cold PBS and transfered to single cell suspensions by gently grinding. CD4-CD8- were subsequently sorted with anti CD4 and anti CD8 MACS beads to a purity >95% which was routinely checked by FACS analysis.

value: 0.1%V Dioxane


title: CD4-CD8-_DN_fetal_thymocytes_TCDD

treatment_protocol: C57BL/6 dams were terminally mated and fetuses surgically removed at dpc 15. Fetal thymus organ culture were performed as described before. Briefly 5-6 fetal thymus lobes were cultured on culture inlays for 6 days. Medium (RPMI 1640, with 10nM TCDD or solvent control) was excanged every 2 days. At day six thymus lobes were washed 2x with ice cold PBS and transfered to single cell suspensions by gently grinding. CD4-CD8- were subsequently sorted with anti CD4 and anti CD8 MACS beads to a purity >95% which was routinely checked by FACS analysis.


title: DC_TCDD_2

description: MACS purified primary DCs after 24h in vivo treatment with TCDD.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data was processed using RMA (affy-package, R 2.2)

source_name: MACS purified DCs from spleen

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA was isolated from MACS purified DCs (purity >90%) using TRIzol and after insuring integrity amplified with the Ambion Message amp kit. Amplified RNA was processed according to Affymetrix standard protocols

treatment_protocol:
For each group 3 female C57BL/6 mice (age 8-12 weeks) were i.p. injected
with 10 µg/kg TCDD or DMSO solvent control. After 24 h mice were sacrificed
and spleens removed under sterile conditions. Samples were pooled and homogenized by
pressing through a nylon mesh. Erytrocytes were lysed with ACT buffer and
DCs enriched by BSA density gradient centrifugation. DCs were MACS
sorted to a purity >90% (controlled routinely by FACS staining)
RNA was isolated using TRIzol, checked for purity and integrity and amplified
with the Ambion Message AMP amplification kit. Further steps were
performed according to the Affymetrix standard protocol

value: female

value: 8-12 weeks

value: 10 µg/kgTCDD in corn oil i.p. injected 24h before DC isolation

tag: Biological replicate


title: DC_TCDD_1

tag: Gender

value: 10 µg/kg TCDD in corn oil i.p. injected 24h before DC isolation


title: Liver 5d CP-868388 4

description: CP-868388 treatment


title: Patient5_339_GH_Day1_GH0_5PM


title: Liver 5d CP-865520 2

description: CP-865520 treatment


title: Liver 5d CP-865520 1

description: CP-865520 treatment


title: Liver 5d CP-775146 2

description: CP-775146 treatment


title: Patient5_339_GH_Day1_GH0_11PM


title: Liver 5d CP-775146 1

description: CP-775146 treatment


title: Liver 5d CP-868388 3

description: CP-868388 treatment


title: Liver 5d CP-868388 2

description: CP-868388 treatment


title: Patient5_339_GH_Day1_GH0_11AM


title: Patient5_339_GH_Day1_GH0_2PM


title: Liver 5d CP-868388 1

description: CP-868388 treatment


title: Patient4_339_GH_Day1_GH0_8AM


title: Patient4_339_GH_Day1_GH0_2AM


title: Patient4_339_GH_Day1_GH0_11PM


title: Patient4_339_GH_Day1_GH0_5AM


title: Liver 24hr vehicle 2

description: vechicle treatment


title: Liver 24hr vehicle 4

description: vechicle treatment


title: Liver 24hr vehicle 3

description: vechicle treatment


title: DC_DMSO_2

description: MACS purified primary DCs after 24h in vivo treatment with DMSO.

value: DMSO in corn oil i.p. injected 24h before DC isolation


title: Patient4_339_GH_Day1_GH0_8PM


title: DC_DMSO_1


title: Patient4_339_GH_Day1_GH0_5PM


title: Liver 24hr CP-865520 3

description: CP-865520 treatment


title: Liver 24hr CP-865520 4

description: CP-865520 treatment


title: Spleen CD8 T cells DMSO2

description: Female, 8-12 week old C57BL/6 mice were i.p. injected with DMSOand sacrificed after 24h. Single cell suspensions from spleen were FACS sorted for CD8 T cells (purity>99%). Cells were sorted into ice cold 10%FCS supplemented PBS and RNA isolated using the TRIzol protocol. RNA was amplified using the Ambion message AMP amplification kit and amplified RNA further processed using Affymetrix standard  procedures

hyb_protocol: Affymetrix standard  procedures

scan_protocol: Affymetrix standard  procedures

data_processing: .Cel files were processed using RMA (R2.2, affy-package) and are represented as log2 intensities

label: Affymetrix standard  procedures

source_name: Spleen T cells isolated from C57BL/6 mice treated for 24h with DMSO

label_protocol: Affymetrix standard  procedures

treatment_protocol: Female, 8-12 week old C57BL/6 mice were i.p. injected with DMSO and sacrificed after 24h. Single cell suspensions from spleen were FACS sorted for CD8 T cells (purity>99%).

tag: Mice

value: DMSO i.p. injected


title: Liver 24hr vehicle 1

description: vechicle treatment


title: Liver 24hr CP-868388 3

description: CP-868388 treatment


title: Liver 24hr CP-868388 4

description: CP-868388 treatment


title: Liver 24hr CP-865520 2

description: CP-865520 treatment


title: Liver 24hr CP-868388 2

description: CP-868388 treatment


title: Liver 24hr CP-868388 1

description: CP-868388 treatment


title: Liver 24hr CP-775146 4

description: CP-775146 treatment


title: Liver 24hr CP-865520 1

description: CP-865520 treatment


title: WT_CD4_T_cells_TCDD_2

description: 8-12 week old, female wt mice were i.p. injected with TCDD in corn oil and sacrificed after 24 h. Spleenic CD4 T cells were FACS sorted and RNA extracted using TRIzol.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed using the RMA algorithm from the Bioconductor affy package based on R2.2

label: standard Affymetrix protocol

source_name: Spleenic CD4 cells, from WT mice treated for 24h with 10µg/kg TCDD

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were FACS sorted in ice cold PBS, supplemented with 10% FCS and RNA isolated using TRIZOL. Target RNA amplification was done using the Ambion message AMP kit and the amplified RNA further processed using the Affymetrix standard protocol.

treatment_protocol: Mice were i.p. injected with 10 µg/kg in corn oil and sacrificed after 24h.

tag: Source

value: FACS sorted spleenic CD4 T cells

value: i.p. 10 µg/kg TCDD 24h prior to sacrifice


title: Spleen CD8 T cells DMSO1

description: Female, 8-12 week old C57BL/6 mice were i.p. injected with DMSO and sacrificed after 24h. Single cell suspensions from spleen were FACS sorted for CD8 T cells (purity>99%). Cells were sorted into ice cold 10%FCS supplemented PBS and RNA isolated using the TRIzol protocol. RNA was amplified using the Ambion message AMP amplification kit and amplified RNA further processed using Affymetrix standard  procedures


title: Patient6_339_GH_Day1_GH0_8AM


title: Spleen CD8 T cells TCDD1

description: Female, 8-12 week old C57BL/6 mice were i.p. injected with 10 µg/kg TCDD and sacrificed after 24h. Single cell suspensions from spleen were FACS sorted for CD8 T cells (purity>99%). Cells were sorted into ice cold 10%FCS supplemented PBS and RNA isolated using the TRIzol protocol. RNA was amplified using the Ambion message AMP amplification kit and amplified RNA further processed using Affymetrix standard  procedures

source_name: Spleen T cells isolated from C57BL/6 mice treated for 24h with 10µg/kg TCDD

value: TCDD 10µg/kg i.p. injected


title: Patient4_339_GH_Day1_GH0_11AM


title: Spleen CD8 T cells TCDD2

extract_protocol: Cells were sorted into ice cold 10%FCS supplemented PBS and RNA isolated using the TRIzol protocol. RNA was amplified using the Ambion message AMP amplification kit and amplified RNA further processed using Affymetrix standard  procedures

treatment_protocol: Female, 8-12 week old C57BL/6 mice were i.p. injected with 10 µg/kg TCDD and sacrificed after 24h. Single cell suspensions from spleen were FACS sorted for CD8 T cells (purity>99%).


title: Patient4_339_GH_Day1_GH0_2PM


title: WT_CD4_T_cells_DMSO_1

description: 8-12 week old, female wt mice were i.p. injected with DMSO in corn oil and sacrificed after 24 h. Spleenic CD4 T cells were FACS sorted and RNA extracted using TRIzol.

source_name: Spleenic CD4 cells, from WT mice treated for 24h with DMSO

treatment_protocol: Mice were i.p. injected with DMSO in corn oil and sacrificed after 24h.

value: i.p. DMSO 24h prior to sacrifice


title: Liver 24hr CP-775146 1

description: CP-775146 treatment


title: Liver 24hr CP-775146 3

description: CP-775146 treatment


title: Patient6_339_GH_Day1_GH0_5AM


title: Liver 24hr CP-775146 2

description: CP-775146 treatment


title: Patient6_339_GH_Day1_GH0_2AM


title: WT_CD4_T_cells_TCDD_1

description: 8-12 week old, female AhR KO mice were i.p. injected with TCDD in corn oil and sacrificed after 24 h. Spleenic CD4 T cells were FACS sorted and RNA extracted using TRIzol.

treatment_protocol: Mice were i.p. injected with 10µg/kg TCDD in corn oil and sacrificed after 24h.


title: Patient6_339_GH_Day1_GH0_11PM


title: AhR_KO_CD4_T_cells_DMSO_2

description: 8-12 week old, female AhR KO mice were i.p. injected with DMSO in corn oil and sacrificed after 24 h. Spleenic CD4 T cells were FACS sorted and RNA extracted using TRIzol.

source_name: Spleenic CD4 cells, from AhR KO mice treated for 24h DMSO

value: AHR ko backcrossed to C57BL/6


title: rat embryonic fibroblast cells sample3

city: Los Angeles

first: Qilong

last: Ying

state: CA

address: 1501 San Pablo St, ZNI 507

department: Broad Center for Regenerative Medicine and Stem Cell Research

institute: USC

description: rat embryonic fibroblast cell sample3

hyb_protocol: Hybridization to the Affymetrix GeneChip Gene 1.0 ST Array is performed according to standard Affymetrix protocols. 5.5μg of fragmented and labeled DNA is added to 3.7μl of control oligonucleotide B2 (3nM), 11μl of 20x eukaryotic hybridization controls (bioB, bioC, bioD, and cre), 15.4μl of DMSO, 110μl of 2x hybridization buffer, and H2O to a final volume of 220μl. The hybridization cocktail is heated to 99oC for 5 min. An Affymetrix Gene 1.0 ST array is prepared by wetting for 10 min at 45oC with 1x hybridization buffer. The hybridization cocktail is transferred to a 45oC heat block for 5 min, and is clarified by centrifugation. The buffer solution is removed from the array and the clarified hybridization cocktail is added to the array cartridge.4 The array is hybridized for 16 hours in a 45oC rotisserie oven (60 rpm).

scan_protocol: The hybridized array is washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR), scanned in the Affymetrix scanner signal detected and registered by Expression Console software (Affymetrix).

data_processing: Extracted the expression data, performed normalization and transformation (Threshold all values to 5, Median Shift normalization to the 75 percentile, Baseline transformation using the median of all Samples) and Found Significant Differentially Expressed Genes. Unpaired t-test and Benjamini-Hochberg Correction were performed to produce table consisting of Probe Names, p-values, corrected p-values, Fold change (Absolute) and regulation. Fold change gives the absolute ratio of normalized intensities (no log scale) between the average intensities of the samples grouped.

source_name: rat embryonic fibroblast cells

label_protocol: Prior to hybridization, 5.5μg of ssDNA is fragmented by incubation for 1hr at 37oC, follows by 2 min at 93oC. The 45μl mixture is added with 12μl of 5X TdT buffer, 2μl of TdT, 1μl of 5mM DNA labeling reagent, and is incubated at 37oC for 1hr, and follows by 70oC for 10 min.

extract_protocol: Total RNA isolation from tissue: Cell culture is treated with 500μl of TriZol (Invitrogen,Carlsbad, CA) in a 1.5ml eppendorf and centrifuged for 20 min (4oC) at 12,000 x g. The supernatant is transferred to a fresh eppendorf and precipitated by the addition of 100ul chloroform and vortexed vigorously for 15 seconds. The sample is incubated for 3 minutes at room temperature and centrifuged for 15 minutes (4oC) at 10,000 x g. The aqueous phase is transferred to a fresh eppendorf and precipitated by the addition of 250μl isopropanol. The precipitate is incubated for 10 minutes at room temperature and centrifuged for 20 minutes (4oC) at 10,000 x g. The sample is washed once with 70% ethanol and allowed the pellet to air dry prior to resuspension in 100μl of DEPC treated water. The RNA is purified by Rneasy Clean up column (Qiagen, Valencia, CA).

tag: strain

value: DA

tag: rat embryonic fibroblast cells

tag: 14.5 rat embryos


title: rat embryonic fibroblast cells sample2

description: rat embryonic fibroblast cell sample2


title: mouse embryonic stem cells sample3

description: Mouse ES cells sample3

source_name: mouse embryonic stem cells

tag: mouse ES cells


title: Patient6_339_GH_Day1_GH0_8PM


title: AhR_KO_CD4_T_cells_TCDD_2

source_name: Spleenic CD4 cells, from AhR KO mice treated for 24h with 10µg/kg TCDD

treatment_protocol: Mice were i.p. injected with TCDD in corn oil and sacrificed after 24h.


title: Patient6_339_GH_Day1_GH0_5PM


title: rat embryonic stem cells sample3

description: rat embryonic stem cells cultured in 3I sample3

source_name: rat embryonic stem cells

tag: rat ES cells cultured in 3I medium


title: WT_CD4_T_cells_DMSO_2

source_name: Splenic CD4 cells, from WT mice treated for 24h with DMSO


title: AhR_KO_CD4_T_cells_TCDD_1

description: 8-12 week old, female AhR KO mice were i.p. injected with 10 µg/kg TCDD in corn oil and sacrificed after 24 h. Spleenic CD4 T cells were FACS sorted and RNA extracted using TRIzol.


title: rat embryonic stem cells sample2

description: rat embryonic stem cells cultured in 3I sample2


title: rat embryonic fibroblast cells sample1

description: rat embryonic fibroblast cell sample1


title: Patient6_339_GH_Day1_GH0_2PM

tag: Milk Fat Globule


title: AhR_KO_CD4_T_cells_DMSO_1

source_name: Spleenic CD4 cells, from AhR KO mice treated for 24h with DMSO


title: mouse embryonic stem cells sample1

description: Mouse ES cells sample1


title: mouse embryonic stem cells sample2

description: Mouse ES cells sample2


title: Patient6_339_GH_Day1_GH0_11AM


title: KJ_Pup#135_PND35_Testis_DBP-DBP

status: Public on Nov 24 2008

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

description: KJ_Pup#135_PND35_Testis_DBP-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

source_name: testis exposed to DBP-DBP

extract_protocol: Extraction Method: RNAlater follwed by Qiagen AllPrep DNA/RNA Mini Kit

treatment_protocol: in vivo Treatment: Daily 50 mg/kg dibutyl phthalate from GD12-20 via dam and single 500 mg/kg DBP at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35, Dose or Concentration: 50  and 500, Units of Dose or Concentration: mg/kg

tag: Sample Type

value: Tissue, Tissue:none, Tissue Harvest Methods:Tissue was excised from animal, detunicated, and snap frozen prior to RNA isolation.

tag: Array Type

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: good

tag: Sample Preservation

value: Snap Frozen

tag: Strain or Line

value: Fisher 344

tag: NCBI Taxonomy ID

tag: Developmental State

value: Peripubertal

tag: Sacrifice Method

value: carbon dioxide

tag: Sex

value: male

tag: Units of Age

value: Postnatal Day

tag: Genetic Modifications

tag: Disease State


title: KJ_Pup#133_PND35_Testis_DBP-DBP

description: KJ_Pup#133_PND35_Testis_DBP-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: Age


title: KJ_Pup#134_PND35_Testis_DBP-Oil

description: KJ_Pup#134_PND35_Testis_DBP-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to DBP-oil

treatment_protocol: in vivo Treatment: Daily dibutyl phthalate from GD12-20 via dam and single corn oil exposure at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35, Dose or Concentration: 50, Units of Dose or Concentration: mg/kg


title: KJ_Pup#132_PND35_Testis_DBP-Oil

description: KJ_Pup#132_PND35_Testis_DBP-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).


title: rat embryonic stem cells sample1

description: rat embryonic stem cells cultured in 3I sample1

tag: strain

tag: rat ES cells cultured in 3I medium


title: KJ_Pup#124_PND35_Testis_DBP-DBP

description: KJ_Pup#124_PND35_Testis_DBP-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: Sample Type


title: KJ_Pup#128_PND35_Testis_DBP-DBP

description: KJ_Pup#128_PND35_Testis_DBP-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: Array Type


title: KJ_Pup#120_PND35_Testis_Oil-Oil

description: KJ_Pup#120_PND35_Testis_Oil-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to oil-oil

treatment_protocol: in vivo Treatment: Daily Corn Oil from GD12-20 via dam and single corn oil gavage at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35

tag: Ratio


title: KJ_Pup#123_PND35_Testis_DBP-Oil

description: KJ_Pup#123_PND35_Testis_DBP-Oil_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

tag: RNA Integrity Number


title: KJ_Pup#115_PND35_Testis_Oil-DBP

description: KJ_Pup#115_PND35_Testis_Oil-DBP_Rat230_2_KJ_CIIT06012: Pregnant Fisher 344 rats will be purchased from Charles River Laboratories, Inc. and delivered to CIIT on gestational day (GD) 7 (GD0 = day first vaginal plug positive).  At gestational day 12 (GD12), the dams will be exposed once/day until GD20 to 50 mg/kg dibutyl phthalate (DBP) in corn oil vehicle via oral gavage.  Each dose group will contain 4-6 vehicle control or phthalate treated dams.   Groups of animals will be sacrificed at GD20, postnatal day (PND) 35, and PND90 for endpoint analysis. At GD20, treated and control animals will be examined for various endpoints including body weight, testicular histopathology, gene expression profile via microarray analysis, and anogenital distance (AGD).  AGD (at parturition; PND1) and nipple number/location (at PND14 and day of sacrifice) will be determined on animals in the postnatal groups.  At PND35 or 90, one male from each in utero corn oil vehicle or DBP exposed group will receive a second gavage of either corn oil or 500 mg/kg DBP.  6 hours after the second gavage, the following endpoints will be examined: 1) testis histopathology; 2) spermatid head quantification (PND90 only); 3) testis and body weights; 5) genome-wide gene expression (via microarray); and 6) germ cell apoptosis (TUNEL assay).

source_name: testis exposed to oil-DBP

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Clean up

treatment_protocol: in vivo Treatment: Daily corn oil from GD12-20 via dam and single 500 mg/kg dibutyl phthalate exposure at PND35, Treatment Duration: GD12-20 and PND35, Treatment Time: sacrificed 6 hr after last exposure, Vehicle for Chemical: Corn Oil, Route of Exposure: Oral Gavage of Dam during Gestation and Oral Gavage at PND35, Dose or Concentration: 500 , Units of Dose or Concentration: mg/kg

tag: Bioanalyzer Results