title: left ventricle, aorta banding, wildtype, rep4

source_name: left ventricle, aorta banding, wildtype


title: left ventricle, aorta banding, wildtype, rep3

status: Public on Oct 01 2010

type: RNA

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 450C in the hybridization oven at 60 rpm, as described by manufacturer (Affymetrix).

scan_protocol: Gene Chips were scanned using the Hewlett Packard GeneArray Scanner 3000 7G.

data_processing: The data were preprocessed using the robust multi-array average (RMA) package in R with default settings, i.e. quantile normalization and RMA background correction

label: phycoerythrin

molecule: total RNA

organism: Mus musculus

label_protocol: According to standard Affymetrix protocol (FS450_00007).

extract_protocol: Total RNA was isolated with an RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized with isoflurane and sacrificed by cervical dislocation. Left ventricle was quickly excised and immediately frozen in liquid nitrogen.

tag: gender

value: male

tag: genotype

value: Wildtype C57BL/6

tag: tissue

value: left ventricle myocardium


title: left ventricle, aorta banding, cxcr5 knockout, rep3

value: CXCR5 -/-, C57BL/6 background


title: 6hpi_cbp1_(D7_190)

city: San Francisco

first: Sajeev

last: Batra

state: CA

country: USA

institute: UCSF

hyb_protocol: Cy5 labeled sample was hybridized to the MEEBO array in 3x SSC at 65C 36 hours.

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using Spotreader (Niles Scientific) and GenePix 6.0 (Molecular Devices).

data_processing: Spot analysis was performed with GenePix v6.0 and normalization performed in Nomad 2.0. Data table contains log2 of the Nomad-normalized Ratio Of Medians (635/532) with flag values < 0 removed.

source_name: Amplified RNA from bone marrow-derived macrophages

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

extract_protocol: Qiagen RNeasy Mini kit

tag: treatment

value: test sample 6hpi_cbp1_(D7_190)

tag: strain

tag: age

value: 8 w

value: bone marrow derived macrophages

source_name: pooled amplified sample RNA

label_protocol: RNA extracted from the pooled RNA reference sample was coupled to Cy3.

extract_protocol: Qiagen RNeasy RNA Isolation kit

value: reference sample


title: left ventricle, aorta banding, cxcr5 knockout, rep4


title: 3hpi_cbp1_(D7_189)

value: test sample 3hpi_cbp1_(D7_189)


title: 12hpi_cbp1_(D7_191)

value: test sample 12hpi_cbp1_(D7_191)


title: 12hpi_ura+ura_(D7_198)

value: test sample 12hpi_ura+ura_(D7_198)


title: left ventricle, aorta banding, wildtype, rep1


title: 6hpi_ura+ura_(D7_197)

value: test sample 6hpi_ura+ura_(D7_197)


title: left ventricle, aorta banding, wildtype, rep2


title: 3hpi_ura+ura_(D7_196)

value: test sample 3hpi_ura+ura_(D7_196)


title: 3hpi_mock_(D7_182)

value: test sample 3hpi_mock_(D7_182)


title: 12hpi_mock_(D7_195)

value: test sample 12hpi_mock_(D7_195)


title: left ventricle, aorta banding, cxcr5 knockout, rep1


title: 6hpi_mock_(D7_183)

value: test sample 6hpi_mock_(D7_183)


title: left ventricle, aorta banding, cxcr5 knockout, rep2


title: 24hpi_mock_(D5_134)

value: test sample 24hpi_mock_(D5_134)


title: 6hpi_mock_(D5_130)

value: test sample 6hpi_mock_(D5_130)


title: IL1b MF, rep3

city: New York

first: Michael

last: Quante

state: NY

address: 1130 St. Nicholas Av

department: Digestive and Liver Disease

institute: Columbia University Medical Center

description: Biological replicate 3 of 3.

hyb_protocol: Expression profiling is accomplished using the MouseWG-6 v2 whole-genome gene expression array and direct hybridization assay (Illumina, Inc.).  Initially, 500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.  1500ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the MouseWG-6 BeadChips.  Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

scan_protocol: Illumina BeadArray Reader

data_processing: Illumina’s GenomeStudio (v2010.1) gene expression module (v1.6.0) to report both un-normalized and quantile-normalized, background-corrected gene expression signal levels. Expression intensities were obtained from the Illumina arrays using the standard Illumina algorithm and software (Kuhn et al., 2004). Differential expression was obtained using Limma (Smyth, 2004) as implemented in oneChannelGUI (Sanges et al., 2007) operating as part of the Bioconductor Suite (Gentleman et al., 2004)  in the R statistical computing environment (Ihaka and Gentleman, 1996). A significance cutoff of the Benjamini-Hochberg False Discovery Rate <0.05 was used (Benjamini and Hochberg, 1995).

label: biotin

source_name: stomach, BM-derived CAFs

growth_protocol: Helicobacter felis-infected or IL-1ß transgenic mice were transplanted with EGFP-labeled bone marrow, and at the age of 15-18 months, bone marrow-derived gastric GFP-positive CAFs were isolated by FACS. For whole gastric CAF isolation, aSMA-RFP reporter mice were infected with H. felis, and after 18 months, CAFs were isolated by FACS.

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

treatment_protocol: To isolate WT (WT-MF), bone marrow-derived (BM-MF) and αSMA-RFP MF (RFP-MF) from the stomach, antrum and corpus of the stomach from C57BL/6, IL-1β/αSMA-RFP and αSMA-RFP reporter mice were isolated (McKaig et al., 1999). After washing 3 times in HBSS, the stomach was cut into small pieces (10-15 pieces). The pieces were incubated with collagenase I at 37ºC for 1 hour. After that the cell suspension was filtered with a cell strainer to remove large stomach pieces and the filtrate was washed with PBS twice. Harvested cells were cultured in RPMI medium supplemented with 10% FBS (Hyclone) and penicillin-streptomycin at 37ºC in 5% CO2. Characteristic features of MF (abundant myofibrils with dense bodies, indented nucleus, basal lamina-like structure, capacity to express alpha smooth muscular action, vimentin and laminin) were demonstrated in both primary and secondary cultures.

value: IL-1ß transgenic

tag: infection

value: non-infected

value: 15-18 months

value: stomach

tag: cell type

value: bone marrow-derived GFP-positive cancer-associated fibroblasts


title: 8hpi_mock_(D5_131)

value: test sample 8hpi_mock_(D5_131)

value: 8 w

value: bone marrow derived macrophages


title: 4hpi_mock_(D5_129)

value: test sample 4hpi_mock_(D5_129)

value: reference sample


title: IL1b MF, rep2

description: Biological replicate 2 of 3.

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer’s instructions.


title: HF MF, rep1

description: Biological replicate 1 of 2.

source_name: stomach, total CAFs

value: Helicobacter felis

value: 18 months

value: whole gastric cancer-associated fibroblasts


title: 2hpi_mock_(D5_127)

value: test sample 2hpi_mock_(D5_127)

label_protocol: RNA extracted from the pooled RNA reference sample was coupled to Cy3


title: 12hpi_mock_(D5_132)

value: test sample 12hpi_mock_(D5_132)


title: HF MF, rep2

description: Biological replicate 2 of 2.


title: 2hpi_mock_(D5_128)

value: test sample 2hpi_mock_(D5_128)


title: IL1b MF, rep1

description: Biological replicate 1 of 3.


title: JIA PBMC Pre treatment A235_L221

status: Public on Sep 27 2010

city: London

first: Lucy

middle: R

last: Wedderburn

address: 30 Guilford Street

department: Rheumatology

country: United Kingdom

institute: Institute of Child Health, UCL

description: JIA PBMC Pre treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Human U133 2.0 array. GeneChips were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: RMA

organism: Homo sapiens

source_name: PBMC

label_protocol: RNA was coverted to cDNA (Roche) using an oligod(T) primer and converted to cRNA using In Vitro Triscription labelling kit (Affymetrix

extract_protocol: Total RNA was extracted from 3x10e6 PBMC using TRIzol reagent (Invitrogen, UK)

treatment_protocol: This was a non-interventional study. Juvenile idiopathic arthritis patients were treated with methotrexate and samples collected prior to treatment and after 6 months on therapy.

value: PBMC

tag: responder

value: Methotrexate pre-treatment

tag: subject


title: 12hpi_cbp1+CBP1_(D3_093)

value: test sample 12hpi_cbp1+CBP1_(D3_093)


title: JIA PBMC Post treatment A235_L027(2)

description: JIA PBMC Post treatment

value: Not ACR70

value: Methotrexate post-treatment


title: JIA PBMC Post treatment A235_L221(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_287

description: JIA PBMC Pre treatment


title: JIA PBMC Pre treatment A235_L016

description: JIA PBMC Pre treatment


title: JIA PBMC Pre treatment A235_L027

description: JIA PBMC Pre treatment


title: JIA PBMC Post treatment A235_L014(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_L017

description: JIA PBMC Pre treatment


title: JIA PBMC Post treatment A235_L112(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_L112

description: JIA PBMC Pre treatment


title: JIA PBMC Post treatment A235_L017(2)

description: JIA PBMC Post treatment


title: JIA PBMC Post treatment A235_287(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_L015

description: JIA PBMC Pre treatment


title: JIA PBMC Pre treatment A235_L010

description: JIA PBMC Pre treatment


title: JIA PBMC Pre treatment A235_L014

description: JIA PBMC Pre treatment


title: Nhp6A_M29A_1_and_2_anti-Nhp6

status: Public on Sep 15 2010

type: genomic

city: Los Angeles

first: Noah

middle: L.

last: Dowell

address: 615 Charles E. Young Drive South, BSRB 357

department: Biological Chemistry

institute: UCLA

description:
Input_1_111897-111895.CEL
Input_2_116092-116087.CEL

hyb_protocol: These samples were hybridized by the UCLA Clinical Microarray Core according to Affymetrix protocol.

scan_protocol: These samples were scanned by the UCLA Clinical Microarray Core according to Affymetrix protocol.

data_processing: Nhp6A (and Nhp6A point mutants) ChIP samples and associated Input samples were loaded into Affymetrix Tiling Array Software and quantile normalized with a max gap of 80, min run of 40 and across a bandwith of 30 to create the BAR files. A custom Python script extracted and averaged probe intensities from the BAR file, over defined intervals (100 bp) flanking TSSs of protein coding genes and is provided as a TXT file. This data was clustered (K-means) using CLUSTER (Eisen et al. 1998) and visualized with Java Treeview (Saldanha 2004). Nhp6A and histone H3 raw Affymetrix data was also processed, loess normalized to sonicated input DNA, and analyzed in R using the Starr package (www.bioconductor.org). Nhp6A and histone H3 probe intensities were smoothed with a sliding median window of 150 and 75 bp, respectively. Smoothed normalized histone H3 and Nhp6A intensity data was plotted along yeast chromosome 3 using GenomeGraphs package (www.bioconductor.org). The raw loess normalized and smoothed data files are provided as TXT files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: anti-Nhp6A ChIP DNA from asynchronously dividing yeast.

label_protocol: ChIP DNA was linearly amplified according to the Affymetrix provided protocol (http://www.affymetrix.com/support/downloads/manuals/chromatin_immun_ChIP.pdf).  The GeneChip WT Double-stranded DNA Terminal Labeling Kit (Affymetrix, #900812) was used to fragment the DNA to appropriate hybridization length and to biotin label with terminal deoxynucleotidyl transferase.

growth_protocol: Asynchronously dividing cells were grown at 30C in rich media (YPD,  2% glucose) to OD 0.8-1.0.

extract_protocol: Crosslinked chromatin was extracted by shearing the cell membranes with glass beads.  After addition of beads and lysis buffer to cell pellet, tubes were vortexed for 10 x 1min with recovery periods on ice. Samples were soft spun and the soluble chromatin was removed for ChIP.

treatment_protocol: Cells were treated with formaldehyde (1% final) for 15min.  Crosslinking was quenched with glycine (~250mM).  Cells were spun down and stored at -80ºC until chromatin extraction.

tag: genotype/variation

tag: od

tag: antibody

value: anti-Nhp6A, custom polyclonal antibody

tag: fraction

value: ChIP

source_name: Input DNA from cells at 0.8-1.0 OD

value: Input


title: JIA PBMC Post treatment A235_L015(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_L009

description: JIA PBMC Pre treatment


title: Nhp6A_F48A_1_and_2_anti-Nhp6


title: Nhp6A_WT_anti_H3_4_and_5

source_name: anti-Histone H3 ChIP DNA from asynchronously dividing yeast.

value: WT

value: anti-Histone H3

tag: antibody manufacturer

value: Abcam

tag: antibody cat #

tag: antibody lot #


title: del_nhp6_anti_H3_3_and_4


title: Nhp6A_F48A_1_and_2_anti_H3


title: Nhp6A_P18A_1_and_2_anti-Nhp6


title: JIA PBMC Post treatment A235_L016(2)

description: JIA PBMC Post treatment


title: JIA PBMC Post treatment A235_L003(2)

description: JIA PBMC Post treatment


title: JIA PBMC Pre treatment A235_L003

description: JIA PBMC Pre treatment


title: JIA PBMC Post treatment A235_L010(2)

description: JIA PBMC Post treatment


title: JIA PBMC Post treatment A235_L009(2)

description: JIA PBMC Post treatment


title: Nhp6A_WT_1_and_2_anti-Nhp6


title: 6hpi_G217B_(D1_181)

value: test sample 6hpi_G217B_(D1_181)

value: 8 w

value: bone marrow derived macrophages

value: reference sample


title: YFPGNL_rep2

city: Freising-Weihenstephan

first: Claus

last: Schwechheimer

address: WZW - Lehrstuhl Systembiologie der Pflanzen, Am Hochanger 4

country: Germany

institute: Claus Schwechheimer

description: Gene expression of whole seedlings at day 5

hyb_protocol: The probes were hybridized in rotating hybridization chambers (Agilent Technologies) and incubated at 65 °C for 17 h overnight in a hybridization oven. Subsequently, the arrays were washed according to manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1. (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 021169_D_F_20090824) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: 5 days-old seedlings, replicate 2

label_protocol: Cy3-labeled cRNA was prepared from 0.5 µg total RNA

growth_protocol: Seedlings were grown in 100 µE continuous white light on 1X MS medium supplemented with 1% sucrose for 5 days.

extract_protocol: RNA was prepared using the Machery-Nagel Nucleo Spin RNA Plant Kit.

value: YFPGNL transgenic


title: ga1 (Col)_rep2

value: ga1 mutant


title: pif1345_rep2

value: pif1 pif3 pif4 pif5 (pif1345 mutant)


title: GNCGFP_rep3

source_name: 5 days-old seedlings, replicate 3

value: GNCGFP transgenic


title: YFPGNL_rep3


title: ga1 (Col)_rep3


title: pif1345_rep1

source_name: 5 days-old seedlings, replicate 1


title: wild type (Col)_rep3

value: wild type


title: wild type (Col)_rep2


title: GNCGFP_rep2


title: pif1345_rep3


title: ga1 (Col)_rep1


title: Epidermis from Wild type skin rep1

city: Durham

first: Carrie

middle: A

last: Ambler

state: Durham

address: South Road

department: School of Biological and Biomedical Sciences

institute: Durham University

hyb_protocol: NuGEN Hybridisation v1.0

scan_protocol: PICR Scanner 3000

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

source_name: Epidermis from Wild type  controls; female; treated with 4OHT for 14 days

label_protocol: WT Ovation Pico target prep v1.0

growth_protocol: Mice were housed in a pathogen-free animal facility

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: 7 week old  mice were treated with 4OHT for 14 days.  Skin was collected and stored in RNAlater for 24 hours before RNA was collected from epidermis, dermis, or Whole Skin.

value: 7 weeks at start of treatment

tag: genetic background

value: C57Bl6xCBA F1

value: Epidermis

value: Wild type


title: Whole Skin from Wild type rep2

source_name: Whole Skin from Wild type controls; female; treated with 4OHT for 14 days

value: Whole Skin

tag: genotype


title: Whole Skin from Wild type rep1

tag: tissue


title: Dermis from Transgenic skin rep1

source_name: Dermis from K14NICDER Transgenic  female; treated with 4OHT for 14 days

value: Dermis

value: K14NICDER transgenic


title: Dermis from Transgenic skin rep2


title: Epidermis from Transgenic skin rep2

source_name: Epidermis from  K14NICDER Transgenic  female; treated with 4OHT for 14 days


title: Whole Skin from Transgenic rep2

source_name: Whole Skin from  K14NICDER Transgenic  female; treated with 4OHT for 14 days


title: GNCGFP_rep1


title: Epidermis from Wild type skin rep2


title: wild type (Col)_rep1


title: Dermis from Transgenic skin rep3


title: Whole Skin from Transgenic rep3


title: Epidermis from Wild type skin rep3


title: Epidermis from Transgenic skin rep3


title: Whole Skin from Wild type rep3


title: Whole Skin from Transgenic rep1


title: Dermis from Wild type skin rep2

source_name: Dermis from Wild type  controls; female; treated with 4OHT for 14 days


title: nhp6A-F48A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 1

hyb_protocol: The Agilent protocol (chem.agilent.com) was followed for labeling and hybridizing the cDNA to the 4 x 44K (V1) S. cerevisiae gene expression arrays.

scan_protocol: The arrays were scanned on the Agilent G2565BA fluorescent scanner.

data_processing: Data extraction and quality assessment was performed with Agilent Feature Extraction Software (version 10.5.1.1).  Log ratio values are present in the Agilent Feature Extraction files provided.  Identification of genes differentially expressed between wild-type and mutant strains was done in R using the limma package (Smyth et al. 2005).   All data (minimum of two biological replicates) was loess normalized and background subtracted within each array and fit to a linear model with a simple design matrix comparing mutant signals to wild-type signals (Smyth and Speed 2003; Smyth 2004; Ritchie et al. 2007).  An empirical Bayes method was used to calculate a moderated t-statistic and the associated P-values (Smyth 2004).  The Benjamini and Hochberg method was used to control the false discovery rate, and differentially expressed genes were analyzed using the S. cerevisiae Genome Database for Gene Ontology enrichment (Hochberg and Benjamini 1990; Dwight et al. 2002).

source_name: Saccharomyces cerevisiae

label_protocol: The Agilent Quick Amp Two-color Labeling Kit (# 5190-0444) was used to fluorescently label the RNA.

growth_protocol: Asynchronously dividing cells  (OD ~ 1.0) growing at 30ºC  in rich media (YP with 2% glucose).

extract_protocol: RNA was isolated from cells using the hot phenol method (Köhrer and Domdey 1991). Total RNA was further isolated from genomic DNA using the Qiagen Rneasy Plus Mini Kit (# 74134).

value: NHP6A ∆nhp6B

value: nhp6A-F48A ∆nhp6B


title: Dermis from Wild type skin rep3


title: nhp6A-P18A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 2

description: Asynchronously dividing cells  (OD ~ 1.0) growing at 30ºC

value: nhp6A-P18A ∆nhp6B


title: ∆nhp6A ∆nhp6B vs Nhp6A ∆nhp6B, replicate 2

value: ∆nhp6A ∆nhp6B


title: nhp6A-M29A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 1

value: nhp6A-M29A ∆nhp6B


title: Epidermis from Transgenic skin rep1


title: nhp6A-M29A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 2


title: Dermis from Wild type skin rep1


title: APEC wild type, strain 362, 0R:H10

status: Public on Sep 10 2010

city: Campinas

first: Fernanda

last: Pace

address: Av. Marechal Cândido Rondom

country: Brazil

institute: Universidade Estadual de Campinas

hyb_protocol: RNA hybridization were performed as described in the Affymetrix Gene Expression Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Data of Affymetrix GeneChip E.coli genome 2.0 were acquired by GeneChip Scanner 3000 using the software GCOS v 1.4, by selecting wild type strain (SEPT362) as the baseline for comparison.

data_processing: Data were analyzed with DChip and Microarray Suite Version (MAS 5.0).  The DChip comparison (mt/wt) results are provided in supplementary txt files.

organism: Escherichia coli

source_name: APEC Wild Type (0R:H10)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol - Expression analyzes technical manual, 2001 - from 6ug of total RNA.

growth_protocol: Bacteria were grown at 37°C, in DMEM media, until reach OD 600 = 0.8

extract_protocol: RNA from each strains was extracted using the RiboPure bacterial RNA isolation kit (Ambion), following the manufacturer´s guidelines. Total RNA concentration was determined by a NanoDrop ND-100.

value: 0R:H10, avian septicemic escherichia coli

value: Wild Type


title: nhp6A-P18A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 1


title: ∆nhp6A ∆nhp6B vs Nhp6A ∆nhp6B, replicate 1


title: APEC hcp deleted mutant compared to APEC wild type

source_name: APEC hcp deleted mutant, compared to wild type strain, grown at 37°C, OD=0.8

value: hcp deleted mutant


title: APEC icmF deleted mutant compared to APEC wild type

source_name: APEC icmF deleted mutant, compared to wild type strain, grown at 37°C, OD=0.8

value: icmF deleted mutant


title: APEC clpV deleted mutant compared to APEC wild type

source_name: APEC clpV deleted mutant, compared to wild type strain, grown at 37°C, OD=0.8

value: clpV deleted mutant


title: 06-S

status: Public on Sep 09 2010

first: Dan

last: Littman

address: 540 1st ave

institute: NYU Medical Center

description: Donor 2

hyb_protocol: According to Affymetrix protocols

scan_protocol: According to Affymetrix protocols

data_processing: Data was analyzed using R version 2.6.0 (r43408) and Bioconductor packages "simpleaffy" (version 2.14.05) and "hgu133plus2" (version 2.0.1) with the MAS 5.0 algorithm.

source_name: Monocyte-derived dendritic cells

label_protocol: According to Affymetrix protocols

growth_protocol: Human CD14+ monocytes were isolated from buffy coats of adult peripheral blood using a Ficoll gradient and two sequential purifications with anti-CD14 magnetic beads (Miltenyi). Purified monocytes were cultured in the presence of GM-CSF and IL-4 for 4 days in RPMI media containing 10% fetal bovine serum and antibiotics.

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

treatment_protocol: 100,000 MDDC were plated in 96 well U bottom plate in the presence of 5 micrograms/ml of polybrene. MDDC were infected with HIVGFP(G) and SIVVLP(G) supernatants that were generated by transient transfection of 293T cells. Celles were harvested 48 hours after infection.

value: Monocyte-derived dendritic cells

tag: virus

value: SIVVLP(G)


title: 07-HS

description: Donor 1

value: HIVGFP(G) + SIVVLP(G)


title: nhp6A-F48A ∆nhp6B  vs Nhp6A ∆nhp6B, replicate 2


title: 08-HS

description: Donor 2


title: 03-H

description: Donor 1

value: HIVGFP(G)


title: FoxQ1 siRNA 48hrs TGF-b1 40hrs 2

status: Public on Sep 01 2010

city: Heidelberg

first: Alexander

last: Feuerborn

state: BW

address: Im Neuenheimer Feld 280

department: Department of cellular and molecular pathology

institute: DKFZ

hyb_protocol: Following fragmentation, 6.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430A_2.0 mouse arrays

scan_protocol: GeneChips were scanned using the using a GeneChip™ scanner 3000.

data_processing: CEL files were imported to R statistical package version 2.7.1 using R Affy package version 1.18.2. Microarray data was subjected to VSN normalization. Significance analysis was performed using the bioconductor package SAMR, which implements SAM statistics in R.

source_name: cell culture

label_protocol: Synthesis of cDNA and generation of cRNA was done with the GeneChip® 3’ IVT Express Kit according to the supplier's instructions (Affymetrix)

growth_protocol: Cells were grown under standard growth conditions (37°C, 5%CO2).

extract_protocol: RNA was extracted using Qiagen RNAeasy Mini Kit according to the manufacturer's instruction.

treatment_protocol: Cells were revere transfected with 25nM siRNA for eight hours and subsequently treated with 5ng/ml TGF-b1 for additional 40hrs

tag: treatment

value: FoxQ1 siRNA 48hrs TGF-b1 40hrs


title: YFPGNL_rep1

value: YFPGNL transgenic


title: FoxQ1 siRNA 48hrs TGF-b1 40hrs 1

description: NM18 cells were reverse transfected with 25nM ns-siRNA or FoxQ1 for eight hours. Cells were subsequently treated with 5ng/ml TGF-b1 for additional 40 hours.


title: 05-S

description: Donor 1


title: ns-siRNA 48hrs TGF-b1 40hrs 2

value: ns-siRNA 48hrs TGF-b1 40hrs


title: ns-siRNA 48hrs TGF-b1 40hrs 1


title: ns-siRNA 48hrs TGF-b1 40hrs 3


title: FoxQ1 siRNA 48hrs TGF-b1 40hrs 3


title: ns-siRNA 48hrs 3

value: ns-siRNA 48hrs


title: ns-siRNA 48hrs 1


title: ns-siRNA 48hrs 2


title: child trio id 9 9593

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington School of Medicine

hyb_protocol: The labeled genomic DNA was precipitated with ~0.1 volume 5M NaCl and ~1 volume isopropanol. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html), but with the following modifications: 9 ug each of test and reference labeled DNA was resuspended in 3.3 uL VWR water with 8.7 uL hybe solution and arrays were hybridized in Maui hybridization stations for 72 h at 42C.

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 Nimblegen's standard protocol for Nimblescan 2.5 CGH data extraction.

source_name: 593 genomic DNA from whole blood

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers (for test and control samples, respectively) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html) but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occuring overnight.

extract_protocol: In test samples, DNA was isolated from whole blood using Gentra Puergene kits. For NA15510, genomic DNA was previously extracted from LCLs by Coriell cell repositories.

tag: trio id

tag: member

value: child

value: whole blood

tag: gender

value: female

source_name: NA15510 genomic DNA from LCLs

tag: sample source

value: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories

tag: cell line


title: 04-H

description: Donor 2

tag: cell type


title: child trio id 8 8723

source_name: 723 genomic DNA from whole blood

value: male


title: mother trio id 7 710847

source_name: 10847 genomic DNA from whole blood

value: mother


title: child trio id 7 710846

source_name: 10846 genomic DNA from whole blood


title: father trio id 9 9214

source_name: 214 genomic DNA from whole blood

value: father


title: mother trio id 9 9470

source_name: 470 genomic DNA from whole blood


title: mother trio id 3 311063

source_name: 11063 genomic DNA from whole blood


title: father trio id 6 61858

source_name: 1858 genomic DNA from whole blood


title: child trio id 6 62648

source_name: 2648 genomic DNA from whole blood


title: father trio id 4 410655

source_name: 10655 genomic DNA from whole blood


title: child trio id 2 210942

source_name: 10942 genomic DNA from whole blood


title: mother trio id 4 410654

source_name: 10654 genomic DNA from whole blood


title: mother trio id 1 110872

source_name: 10872 genomic DNA from whole blood


title: mother trio id 8 8846

source_name: 846 genomic DNA from whole blood


title: 73-67

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: Afferent Lymph was collected from up to 5 pen raised, nematode naïve, outbreed Romney sheep (Tag No’s 1001, 1002, 1003, 1004, 1006). During this time a Pre-Infection sample was collected, the sheep were immunised by 3 truncated (2 week) T. colubiformis infections (40,000 Tc) followed by a Challenge Infection with 40,000 T. colubiformis L3 (Challenge Infection weeks 1-3). The Challenge Infection will enable us to determine changes in gene expression when the sheep gut rejects the parasitic nematodes.

hyb_protocol: Micro array slides were prehybridized in a preheated (42oC) 0.22 µm filtered solution of 5 x SSC, 0.1% SDS and 0.25% BSA (A-788; Sigma Chemical company, St. Louis, MO, USA) for 20 min at 42oC. Slides were rinsed in deionised water then isopropanol and air dried before hybridization. cDNA labeled samples were heat-denatured (95oC for 5 min) and mixed with 60 µL of pre-warmed (68oC) SlideHyb No1 (Ambion, Austin, TX, USA) added. The final cDNA labeled solution was loaded onto the slides with lifter coverslips (Erie Scientific, Portsmouth, NH, USA). Hybridizations were conducted for 20 h at 52oC in sealed humidified chambers (CMT Hybridization Chambers, Corning, NY, USA). Following hybridization, slides were washed for 5 min each in (1) 2 x SSC, 0.1% SDS, (2) 1 x SSC and (3) 0.1 x SSC then centrifuged at 1000 g for 5 min

scan_protocol: The slides were stored in the dark to minimize photo bleaching, and scanned for both dye channels at 532 and 635 nm within two days using an GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with a 10-μm resolution. The photomultiplier tube voltage was adjusted to obtain an equal global intensity in both channels.

data_processing: The normalization method used as in PubMed ID 15231532 [Bioinformatics. 2004 Nov 22;20(17):3196-205].

organism: Ovis aries

source_name: Challenge Infection week 1 Pool

label_protocol: Fluorescent-labeling reactions used the SuperScript Indirect cDNA Labeling System (Invitrogen, Auckland, NZ). cDNA synthesised from 20µg total appropriately pooled RNA was labeled in the presence of either mono-functional N-hydroxysuccinimide (NHS)-ester Cy5 or Cy3 dyes (Amersham Biosciences, Piscataway, NJ, USA). Labeled cDNAs were purified to remove unincorporated dyes using the supplied SNAP columns, combined and concentrated to 10 µL by ethanol precipitation.

growth_protocol: Lymph cells were collected daily, RNA extracted and pooled for each weekly period for all sheep

extract_protocol: Total RNA was extracted using Trizol® Reagent (Invitrogen Auckland, NZ), a modification of the acid guanidinium thiocyanate-phenol-chloroform extraction method according to the manufacturers’ protocol and incorporated the optional step (for tissues with high content of protein, fat, polysaccharides) during sample homogenization. The appropriate RNA samples were pooled and further purified using an RNeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: Challenge Infection week 1 Pool

value: Afferent Lymph collected over a 12 week period from sheep 1001-6

tag: strain

source_name: Challenge Infection week 3 Pool

treatment_protocol: Challenge Infection week 3 Pool


title: child trio id 4 410653

source_name: 10653 genomic DNA from whole blood


title: mother trio id 6 61806

source_name: 1806 genomic DNA from whole blood

source_name: NA15510 genomic DNA from LCLs


title: 73-70

source_name: Challenge Infection week 2 Pool

treatment_protocol: Challenge Infection week 2 Pool

value: up to 5 pen raised, nematode naïve, outbreed Romney sheep


title: child trio id 1 110871

source_name: 10871 genomic DNA from whole blood


title: father trio id 5 510458

source_name: 10458 genomic DNA from whole blood


title: father trio id 8 8403

source_name: 403 genomic DNA from whole blood


title: AE16T

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by Trizol

hyb_protocol: Total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the R function rma() in the Bioconductor package affy

label: Biotin

source_name: tumor tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Total RNA was extracted and purified by standard Trizol method and followed with qualification check by Agilent 2100.

tag: tissue type

value: esophageal squamous cell carcinoma (ESCC)


title: 73-66


title: AE13T

description: frozen tissue extracted by Trizol


title: child trio id 3 311020

source_name: 11020 genomic DNA from whole blood


title: mother trio id 2 210943

source_name: 10943 genomic DNA from whole blood


title: mother trio id 5 510422

source_name: 10422 genomic DNA from whole blood


title: father trio id 1 110873

source_name: 10873 genomic DNA from whole blood


title: child trio id 5 510421

source_name: 10421 genomic DNA from whole blood


title: MCF7 extracellular/cellular

city: North Chicago

first: Dominik

middle: M

last: Duelli

state: IL

address: 3333 Green Bay Road

department: Pathology

institute: Rosalind Franklin University of Medicine and Science

description: RNA extracted from the cells or from a pellet of the spent media

hyb_protocol: using µParaflo® Microfluidic Biochip Technology

scan_protocol: GenePix™ 4000B Array Scanner software system from Axon Instruments

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

source_name: MCF7 cells

label_protocol: Scanned on an Axon GenePix 4000B Microarray Scanner

growth_protocol: Cells were grown according to ATCC instructions.

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

value: cellular

source_name: MCF7 exosomes

value: extracellular


title: AE06T

description: frozen tissue extracted by Trizol


title: AE15T

description: frozen tissue extracted by Trizol


title: AE48T

description: frozen tissue extracted by Trizol


title: AE07T

description: frozen tissue extracted by Trizol


title: AE04T

description: frozen tissue extracted by Trizol


title: AE11T

description: frozen tissue extracted by Trizol


title: AE33T

description: frozen tissue extracted by Trizol


title: AE02T

description: frozen tissue extracted by Trizol


title: AE32T

description: frozen tissue extracted by Trizol


title: AE03T

description: frozen tissue extracted by Trizol


title: AE08T

description: frozen tissue extracted by Trizol


title: AE01T

description: frozen tissue extracted by Trizol


title: AE35T

description: frozen tissue extracted by Trizol


title: AE52T

description: frozen tissue extracted by Trizol


title: AE36T

description: frozen tissue extracted by Trizol


title: AE12T

description: frozen tissue extracted by Trizol


title: AE05T

description: frozen tissue extracted by Trizol


title: AE14T

description: frozen tissue extracted by Trizol


title: AE51T

description: frozen tissue extracted by Trizol


title: AE50T

description: frozen tissue extracted by Trizol


title: AE47T

description: frozen tissue extracted by Trizol


title: AE09T

description: frozen tissue extracted by Trizol


title: AE49T

description: frozen tissue extracted by Trizol


title: AE34T

description: frozen tissue extracted by Trizol


title: AE46T

description: frozen tissue extracted by Trizol


title: AE42T

description: frozen tissue extracted by Trizol


title: AE53T

description: frozen tissue extracted by Trizol


title: AE41T

description: frozen tissue extracted by Trizol


title: 73-68

source_name: Challenge Infection week 1 Pool


title: AE40T

description: frozen tissue extracted by Trizol


title: AE39T

description: frozen tissue extracted by Trizol


title: AE38T

description: frozen tissue extracted by Trizol


title: AE29T

description: frozen tissue extracted by Trizol


title: AE26T

description: frozen tissue extracted by Trizol


title: AE31T

description: frozen tissue extracted by Trizol


title: AE23T

description: frozen tissue extracted by Trizol


title: AE27T

description: frozen tissue extracted by Trizol


title: AE22T

description: frozen tissue extracted by Trizol


title: AE44T

description: frozen tissue extracted by Trizol


title: AE37T

description: frozen tissue extracted by Trizol


title: AE30T

description: frozen tissue extracted by Trizol


title: AE16N

description: frozen tissue extracted by Trizol

source_name: adjacent normal tissue


title: AE24T

description: frozen tissue extracted by Trizol


title: AE13N

description: frozen tissue extracted by Trizol


title: AE17T

description: frozen tissue extracted by Trizol


title: AE21T

description: frozen tissue extracted by Trizol


title: AE25T

description: frozen tissue extracted by Trizol


title: AE10N

description: frozen tissue extracted by Trizol


title: AE18T

description: frozen tissue extracted by Trizol


title: AE11N

description: frozen tissue extracted by Trizol


title: AE15N

description: frozen tissue extracted by Trizol


title: AE19T

description: frozen tissue extracted by Trizol


title: AE20T

description: frozen tissue extracted by Trizol


title: AE06N

description: frozen tissue extracted by Trizol


title: AE48N

description: frozen tissue extracted by Trizol


title: AE07N

description: frozen tissue extracted by Trizol


title: AE04N

description: frozen tissue extracted by Trizol


title: AE03N

description: frozen tissue extracted by Trizol


title: AE01N

description: frozen tissue extracted by Trizol


title: AE09N

description: frozen tissue extracted by Trizol


title: AE32N

description: frozen tissue extracted by Trizol


title: AE02N

description: frozen tissue extracted by Trizol


title: AE08N

description: frozen tissue extracted by Trizol


title: AE12N

description: frozen tissue extracted by Trizol


title: AE33N

description: frozen tissue extracted by Trizol


title: AE05N

description: frozen tissue extracted by Trizol


title: AE49N

description: frozen tissue extracted by Trizol


title: AE46N

description: frozen tissue extracted by Trizol


title: AE35N

description: frozen tissue extracted by Trizol


title: AE53N

description: frozen tissue extracted by Trizol


title: AE41N

description: frozen tissue extracted by Trizol


title: AE50N

description: frozen tissue extracted by Trizol


title: AE47N

description: frozen tissue extracted by Trizol


title: AE44N

description: frozen tissue extracted by Trizol


title: AE14N

description: frozen tissue extracted by Trizol


title: AE34N

description: frozen tissue extracted by Trizol


title: AE42N

description: frozen tissue extracted by Trizol


title: AE52N

description: frozen tissue extracted by Trizol


title: AE40N

description: frozen tissue extracted by Trizol


title: AE51N

description: frozen tissue extracted by Trizol


title: AE36N

description: frozen tissue extracted by Trizol


title: AE31N

description: frozen tissue extracted by Trizol


title: AE38N

description: frozen tissue extracted by Trizol


title: AE10T

description: frozen tissue extracted by Trizol


title: AE39N

description: frozen tissue extracted by Trizol


title: AE37N

description: frozen tissue extracted by Trizol


title: AE30N

description: frozen tissue extracted by Trizol


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayC_081210

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

source_name: Sample Type: Cells, Cell Type: CH12.LX

label_protocol: standard Affymetrix protocol

growth_protocol: Growth Media: RPMISAdvance, HIFBS, HEPES, Pen/Strepp, L Glutamine, Mercaptoethanol, Amount of Media: 25, Units of Media: ml

extract_protocol: Extraction Method:  Addition of lysis buffer followed by disruption with a Dounce homogenizer. Lysates sonicated and DNA sheared to an average length of 300-500bp

treatment_protocol: in vitro Treatment: DMSO, Units of Treatment Repeat: nM, Treatment Duration: 1, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: Media

tag: array type

tag: pooled from multiple samples

value: No

tag: number of cells seeded

value: 1X10^5 cells/ml, 25ml in P150s

tag: units of harvest time point

value: hr

tag: antibody name

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

tag: sample type

value: ChIP


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayC_081210

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

treatment_protocol: in vitro Treatment: TCDD, Units of Treatment Repeat: nM, Treatment Duration: 1, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: Media, Dose or Concentration: 10, Units of Dose or Concentration: nM


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayC_081210

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayC_081210

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayC_081210

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: AE24N

description: frozen tissue extracted by Trizol


title: AE28N

description: frozen tissue extracted by Trizol


title: AE21N

description: frozen tissue extracted by Trizol


title: AE29N

description: frozen tissue extracted by Trizol


title: AE17N

description: frozen tissue extracted by Trizol


title: AE25N

description: frozen tissue extracted by Trizol


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayC_081210

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayC_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: AE27N

description: frozen tissue extracted by Trizol


title: AE23N

description: frozen tissue extracted by Trizol


title: AE26N

description: frozen tissue extracted by Trizol


title: AE22N

description: frozen tissue extracted by Trizol


title: AE18N

description: frozen tissue extracted by Trizol


title: AE19N

description: frozen tissue extracted by Trizol


title: Adult at T34 in CC, time-series experiment 6

city: Reno

middle: Martinus

last: van der Linden

state: NV

address: 1664 N. Virginia St.

department: Biology

institute: University of Nevada

description:
C. elegans_CC34_6
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Whole Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

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

data_processing: The GeneChip Robust Multiarray Averaging (GC-RMA) method in the R v2.7.1 software package was used to derive log2 expression values for each probe set from Affymetrix generated .CEL files. Expression values were normalized and standardized as described Keegan et al. 2007. Briefly, for each time-point in a time-series experiment, the expression level relative to the mean (in log2 expression values) over that experiment was calculated. This normalization was performed separately for each independent time-series experiment. Arrays in the independent time-course experiments were standardized by setting the mean expression of each array to 0 and the variance to 1. For samples with biological replicates, the log2 expression values for each biological replicate were averaged, and the averaged log2 value was further processed with GC-RMA, standardized and normalized.

organism: Caenorhabditis elegans

source_name: C. elegans adults 34 hr time-point during CC free-running

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (GeneChip Expression Analysis Technical Manual, 701025 Rev.6, 2004, Affymetrix).

growth_protocol: Growth-synchronized populations of wild-type Bristol N2 late L1 larvae were transferred to plates seeded with E. coli HB101 bacteria. Two populations of worms were entrained to opposing light/dark or temperature cycles in two different incubators: 12 hr at 25ºC (W) followed by 12 hr at 15ºC (C), or 12 hr of light (L) followed by 12 hr of dark (D). After reaching adulthood, the two populations of worms were transferred to the same incubator and allowed to free-run at constant 15ºC (CC) or in constant darkness (DD). Non-entrained control experiments for light/dark were performed in parallel in the same incubator in complete darkness. Temperature cycling experiments were conducted in constant darkness in temperature programmable incubators (Tritech Research). Light/dark cycling experiments were conducted at 18ºC in programmable incubators (Precision Scientific; cold white light (light source F20T12/CW) at about 500-1000 lux). To inhibit progeny production during entrainment, L4 larvae were quickly transferred to plates containing bacteria and 25 μM FUDR.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Trizol-extracted total RNA was treated with DNAase (New England Biolabs) as described (www.wormbook.org).

treatment_protocol: Adults were harvested and washed at least twice in cold 1x M9 buffer (<15 min) every 4 hrs during the last day of entrainment and subsequent free-running days. Trizol Reagent (Invitrogen) was added to harvested worm samples and pellets were immediately frozen in liquid nitrogen.

value: Bristol N2

tag: genotype

value: wild-type

tag: developmental stage

value: adult

tag: tissue

value: whole body

tag: conditions

value: constant cold (CC)

tag: time

value: 34 hr

tag: experiment


title: Adult at T38 in CC, time-series experiment 6

description:
C. elegans_CC38_6
This Sample represents 2 biological replicates.
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 38 hr time-point during CC free-running

value: 38 hr


title: Adult at T14 in WC, time-series experiment 6

description:
C. elegans_WC14_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 14 hr time-point during WC entrainment

value: 12:12 hr warm/cold (WC) cycles

value: 14 hr


title: Adult at T30 in CC, time-series experiment 6

description:
C. elegans_CC30_6
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 30 hr time-point during CC free-running

value: 30 hr


title: Adult at T26 in CC, time-series experiment 6

description:
C. elegans_CC26_6
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 26 hr time-point during CC free-running

value: 26 hr


title: Adult at T18 in WC, time-series experiment 6

description:
C. elegans_WC18_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 18 hr time-point during WC entrainment

value: 18 hr


title: Adult at T42 in CC, time-series experiment 6

description:
C. elegans_CC42_6
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 42 hr time-point during CC free-running

value: 42 hr


title: Adult at T22 in WC, time-series experiment 6

description:
C. elegans_WC22_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 22 hr time-point during WC entrainment

value: 22 hr


title: Adult at T46 in CC, time-series experiment 6

description:
C. elegans_CC46_6
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 46 hr time-point during CC free-running

value: 46 hr


title: AE20N

description: frozen tissue extracted by Trizol

value: esophageal squamous cell carcinoma (ESCC)


title: Adult at T46 in CC, time-series experiment 4

description:
C. elegans_CC46_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.


title: Adult at T10 in WC, time-series experiment 6

description:
C. elegans_WC10_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 10 hr time-point during WC entrainment

value: 10 hr


title: Adult at T38 in CC, time-series experiment 4

description:
C. elegans_CC38_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: Bristol N2


title: Adult at T6 in WC, time-series experiment 6

description:
C. elegans_WC6_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 6 hr time-point during WC entrainment

value: wild-type

value: 6 hr


title: Adult at T2 in WC, time-series experiment 6

description:
C. elegans_WC2_6
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

source_name: C. elegans adults 2 hr time-point during WC entrainment

value: adult

value: whole body

value: 2 hr


title: Adult at T34 in CC, time-series experiment 4

description:
C. elegans_CC34_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: constant cold (CC)

value: 34 hr


title: Adult at T26 in CC, time-series experiment 4

description:
C. elegans_CC26_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.


title: Adult at T30 in CC, time-series experiment 4

description:
C. elegans_CC30_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD2_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_TCDD2_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

value: No

value: 1X10^5 cells/ml, 25ml in P150s

value: hr

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

value: ChIP


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: AE28T

description: frozen tissue extracted by Trizol

source_name: tumor tissue


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Adult at T6 in WC, time-series experiment 4

description:
C. elegans_WC6_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 12:12 hr warm/cold (WC) cycles


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Adult at T10 in WC, time-series experiment 4

description:
C. elegans_WC10_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T18 in WC, time-series experiment 4

description:
C. elegans_WC18_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 18 hr


title: Adult at T22 in WC, time-series experiment 4

description:
C. elegans_WC22_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 22 hr


title: Adult at T2 in WC, time-series experiment 4

description:
C. elegans_WC2_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T34 in CC, time-series experiment 3

description:
C. elegans_CC34_3
This Sample represents 2 biological replicates.
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.


title: Adult at T38 in CC, time-series experiment 3

description:
C. elegans_CC38_3
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: 38 hr


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Adult at T14 in WC, time-series experiment 4

description:
C. elegans_WC14_4
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: Bristol N2

value: 14 hr


title: Adult at T46 in CC, time-series experiment 3

description:
C. elegans_CC46_3
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: wild-type

value: 46 hr


title: Adult at T42 in CC, time-series experiment 3

description:
C. elegans_CC42_3
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: adult

value: whole body

value: 42 hr


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayA_081209

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayA_081209: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Adult at T14 in WC, time-series experiment 3

description:
C. elegans_WC14_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T26 in CC, time-series experiment 3

description:
C. elegans_CC26_3
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: constant cold (CC)

value: 26 hr


title: Adult at T30 in CC, time-series experiment 3

description:
C. elegans_CC30_3
This Sample represents 2 biological replicates.
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

value: 30 hr


title: Adult at T18 in WC, time-series experiment 3

description:
C. elegans_WC18_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T10 in WC, time-series experiment 3

description:
C. elegans_WC10_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 10 hr


title: Adult at T2 in WC, time-series experiment 3

description:
C. elegans_WC2_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 2 hr


title: Adult at T6 in WC, time-series experiment 3

description:
C. elegans_WC6_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 6 hr


title: Adult at T22 in WC, time-series experiment 2

description:
C. elegans_WC22_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 12:12 hr warm/cold (WC) cycles


title: Adult at T22 in WC, time-series experiment 3

description:
C. elegans_WC22_3
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T10 in WC, time-series experiment 2

description:
C. elegans_WC10_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T6 in WC, time-series experiment 2

description:
C. elegans_WC6_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T10 in WC, time-series experiment 1

description:
C. elegans_WC10_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T14 in WC, time-series experiment 1

description:
C. elegans_WC14_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T14, non-entrained control time-series experiment 6

description:
C. elegans_C14_6
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 14 hr time-point during non-entrained DD

value: non-entrained constant darkness (DD)

value: control 6


title: Adult at T22 in WC, time-series experiment 1

description:
C. elegans_WC22_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 22 hr


title: Adult at T18 in WC, time-series experiment 2

description:
C. elegans_WC18_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: Bristol N2

value: 18 hr


title: child 1358 NA12710

description: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories

hyb_protocol: The labeled genomic DNA was precipitated with ~0.1 volume 5M NaCl and ~1 volume isopropanol. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html), but with the following modifications: 9 ug each of test and reference labeled DNA was resuspended in 2.5 uL VWR water with 6.5 uL hybe solution and arrays were hybridized in Maui hybridization stations for 72 h at 42C.

source_name: NA12710 genomic DNA from lymphoblastoid cell lines

extract_protocol: genomic DNA was previously extracted from LCLs by Coriell cell repositories

tag: pedigree

tag: gender

value: male

tag: pedigree member

value: child

source_name: NA15510 genomic DNA from LCLs

value: female


title: child 1358 NA12712

source_name: NA12712 genomic DNA from lymphoblastoid cell lines

growth_protocol: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories

tag: cell line


title: child 1358 NA12719

source_name: NA12719 genomic DNA from lymphoblastoid cell lines

treatment_protocol: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories


title: Adult at T14 in WC, time-series experiment 2

description:
C. elegans_WC14_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

tag: strain

value: wild-type

value: adult

value: whole body

value: 14 hr


title: Adult at T2, non-entrained control time-series experiment 6

description:
C. elegans_C2_6
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 2 hr time-point during non-entrained DD


title: Adult at T6 in WC, time-series experiment 1

description:
C. elegans_WC6_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: Adult at T22, non-entrained control time-series experiment 6

description:
C. elegans_C22_6
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 22 hr time-point during non-entrained DD


title: Adult at T18 in WC, time-series experiment 1

description:
C. elegans_WC18_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.


title: paternal grandfather 1358 NA12716

source_name: NA12716 genomic DNA from lymphoblastoid cell lines

value: paternal grandfather

value: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories


title: Adult at T2 in WC, time-series experiment 1

description:
C. elegans_WC2_1
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: 2 hr


title: child 1358 NA12709

source_name: NA12709 genomic DNA from lymphoblastoid cell lines


title: Adult at T18, non-entrained control time-series experiment 6

description:
C. elegans_C18_6
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 18 hr time-point during non-entrained DD


title: mother 1358 NA12708

source_name: NA12708 genomic DNA from lymphoblastoid cell lines

value: mother


title: Adult at T10, non-entrained control time-series experiment 6

description:
C. elegans_C10_6
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 10 hr time-point during non-entrained DD

value: 10 hr


title: paternal grandmother 1358 NA12717

source_name: NA12717 genomic DNA from lymphoblastoid cell lines

value: paternal grandmother


title: Adult at T22, non-entrained control time-series experiment 4

description:
C. elegans_C22_4
Gene expression data from adult worms during complete darkness.

value: non-entrained constant darkness (DD)

value: control 4


title: Adult at T2 in WC, time-series experiment 2

description:
C. elegans_WC2_2
Gene expression data from adult worms during 12:12 hr warm/cold (WC) entrainment cycles.

value: Bristol N2

value: 12:12 hr warm/cold (WC) cycles


title: child 1358 NA12714

source_name: NA12714 genomic DNA from lymphoblastoid cell lines


title: child 1358 NA12713

source_name: NA12713 genomic DNA from lymphoblastoid cell lines

value: male


title: child 1358 NA12711

source_name: NA12711 genomic DNA from lymphoblastoid cell lines

value: child


title: child 1459 NA12876

source_name: NA12876 genomic DNA from lymphoblastoid cell lines

value: female


title: father 1358 NA12707

source_name: NA12707 genomic DNA from lymphoblastoid cell lines

value: father


title: child 1358 NA12715

source_name: NA12715 genomic DNA from lymphoblastoid cell lines


title: Adult at T18, non-entrained control time-series experiment 4

description:
C. elegans_C18_4
Gene expression data from adult worms during complete darkness.

value: wild-type

value: adult

value: 18 hr


title: maternal grandmother 1459 NA12875

source_name: NA12875 genomic DNA from lymphoblastoid cell lines

value: maternal grandmother

source_name: NA15510 genomic DNA from LCLs


title: Adult at T14, non-entrained control time-series experiment 4

description:
C. elegans_C14_4
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 14 hr time-point during non-entrained DD

value: whole body

value: 14 hr


title: Adult at T46 in DD, time-series experiment 6

description:
C. elegans_DD46_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 46 hr time-point during DD free-running

value: constant darkness (DD)

value: 46 hr


title: child 1459 NA12870

source_name: NA12870 genomic DNA from lymphoblastoid cell lines

value: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories


title: Adult at T6, non-entrained control time-series experiment 4

description:
C. elegans_C6_4
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 6 hr time-point during non-entrained DD

value: non-entrained constant darkness (DD)

value: 6 hr


title: paternal grandmother 1459 NA12873

source_name: NA12873 genomic DNA from lymphoblastoid cell lines

value: paternal grandmother


title: Adult at T2, non-entrained control time-series experiment 4

description:
C. elegans_C2_4
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 2 hr time-point during non-entrained DD

value: Bristol N2

value: 2 hr

value: control 4


title: child 1459 NA12869

source_name: NA12869 genomic DNA from lymphoblastoid cell lines

value: female

value: child


title: Adult at T42 in DD, time-series experiment 6

description:
C. elegans_DD42_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 42 hr time-point during DD free-running

value: wild-type

value: 42 hr


title: mother 1459 NA12865

description: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories

source_name: NA12865 genomic DNA from lymphoblastoid cell lines

value: mother


title: child 1459 NA12871

source_name: NA12871 genomic DNA from lymphoblastoid cell lines

value: male


title: child 1459 NA12868

source_name: NA12868 genomic DNA from lymphoblastoid cell lines


title: Adult at T10, non-entrained control time-series experiment 4

description:
C. elegans_C10_4
Gene expression data from adult worms during complete darkness.

source_name: C. elegans adults 10 hr time-point during non-entrained DD

value: adult

value: whole body

value: 10 hr


title: maternal grandfather 1459 NA12874

source_name: NA12874 genomic DNA from lymphoblastoid cell lines

value: maternal grandfather


title: child 1408 NA12152

source_name: NA12152 genomic DNA from lymphoblastoid cell lines

value: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories


title: Adult at T42 in CC, time-series experiment 4

description:
C. elegans_CC42_4
Gene expression data from adult worms during 12:12 hr cold/cold (CC) free-running cycles.

source_name: C. elegans adults 42 hr time-point during CC free-running

value: constant cold (CC)


title: Adult at T34 in DD, time-series experiment 6

description:
C. elegans_DD34_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 34 hr time-point during DD free-running

value: constant darkness (DD)

value: 34 hr


title: father 1459 NA12864

source_name: NA12864 genomic DNA from lymphoblastoid cell lines

value: father

source_name: NA15510 genomic DNA from LCLs


title: child 1459 NA12866

source_name: NA12866 genomic DNA from lymphoblastoid cell lines


title: child 1408 NA12148

source_name: NA12148 genomic DNA from lymphoblastoid cell lines


title: child 1408 NA12149

source_name: NA12149 genomic DNA from lymphoblastoid cell lines


title: child 1408 NA12151

source_name: NA12151 genomic DNA from lymphoblastoid cell lines


title: maternal grandmother 1408 NA12156

source_name: NA12156 genomic DNA from lymphoblastoid cell lines

value: maternal grandmother


title: child 1459 NA12867

source_name: NA12867 genomic DNA from lymphoblastoid cell lines


title: child 1408 NA12150

source_name: NA12150 genomic DNA from lymphoblastoid cell lines


title: Adult at T38 in DD, time-series experiment 6

description:
C. elegans_DD38_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 38 hr time-point during DD free-running

value: Bristol N2

value: 38 hr


title: child 1408 NA12157

source_name: NA12157 genomic DNA from lymphoblastoid cell lines

value: female

value: child


title: maternal grandfather 1408 NA12155

source_name: NA12155 genomic DNA from lymphoblastoid cell lines


title: Adult at T30 in DD, time-series experiment 6

description:
C. elegans_DD30_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 30 hr time-point during DD free-running

value: wild-type

value: 30 hr


title: child 1408 NA12153

source_name: NA12153 genomic DNA from lymphoblastoid cell lines

value: male


title: Adult at T26 in DD, time-series experiment 6

description:
C. elegans_DD26_6
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 26 hr time-point during DD free-running

value: adult

value: 26 hr


title: Adult at T18 in LD, time-series experiment 6

description:
C. elegans_LD18_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 18 hr time-point during LD entrainment

value: whole body

value: 12:12 hr light/dark (LD) cycles

value: 18 hr


title: AE53T

description: frozen tissue extracted by Trizol

source_name: tumor tissue

tag: tissue type

value: esophageal squamous cell carcinoma (ESCC)


title: Adult at T14 in LD, time-series experiment 6

description:
C. elegans_LD14_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 14 hr time-point during LD entrainment

value: 14 hr


title: mother 1408 NA10831

source_name: NA10831 genomic DNA from lymphoblastoid cell lines

value: mother

source_name: NA15510 genomic DNA from LCLs

value: Lymphoblastoid cell lines were established and maintained by Coriell Cell repositories


title: Adult at T2 in LD, time-series experiment 6

description:
C. elegans_LD2_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 2 hr time-point during LD entrainment

value: 2 hr


title: Adult at T46 in DD, time-series experiment 4

description:
C. elegans_DD46_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 46 hr time-point during DD free-running

value: Bristol N2

value: constant darkness (DD)

value: 46 hr


title: AE48T

description: frozen tissue extracted by Trizol


title: child 1408 NA12147

source_name: NA12147 genomic DNA from lymphoblastoid cell lines

value: female

value: child


title: AE51T

description: frozen tissue extracted by Trizol


title: AE49T

description: frozen tissue extracted by Trizol


title: Adult at T10 in LD, time-series experiment 6

description:
C. elegans_LD10_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 10 hr time-point during LD entrainment

value: wild-type

value: 10 hr


title: Adult at T6 in LD, time-series experiment 6

description:
C. elegans_LD6_6
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 6 hr time-point during LD entrainment

value: adult

value: 6 hr


title: Adult at T42 in DD, time-series experiment 4

description:
C. elegans_DD42_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 42 hr time-point during DD free-running

value: whole body

value: 42 hr


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD3_Mouse_ArrayB_090108

description: 0412HI_AhR_IP_TCDD3_Mouse_ArrayB_090108: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

source_name: Sample Type: Cells, Cell Type: CH12.LX

tag: array type

tag: pooled from multiple samples

value: No

value: 1X10^5 cells/ml, 25ml in P150s

value: hr

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

value: ChIP


title: Adult at T38 in DD, time-series experiment 4

description:
C. elegans_DD38_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 38 hr time-point during DD free-running

value: 38 hr


title: father 1408 NA10830

description: Lymphoblastoid cell lines were established using EBV and phytohemagluttinin as a mitogen by Coriell cell repositories

source_name: NA10830 genomic DNA from lymphoblastoid cell lines

value: male

value: father


title: AE47T

description: frozen tissue extracted by Trizol

value: esophageal squamous cell carcinoma (ESCC)


title: Adult at T30 in DD, time-series experiment 4

description:
C. elegans_DD30_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 30 hr time-point during DD free-running

value: Bristol N2

value: constant darkness (DD)

value: 30 hr


title: AE42T

description: frozen tissue extracted by Trizol


title: AE43T

description: frozen tissue extracted by Trizol


title: AE46T

description: frozen tissue extracted by Trizol


title: AE45T

description: frozen tissue extracted by Trizol


title: Adult at T22 in LD, time-series experiment 4

description:
C. elegans_LD22_4
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 22 hr time-point during LD entrainment

value: wild-type

value: 12:12 hr light/dark (LD) cycles

value: 22 hr


title: Adult at T26 in DD, time-series experiment 4

description:
C. elegans_DD26_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 26 hr time-point during DD free-running

value: adult

value: whole body

value: 26 hr


title: AE44T

description: frozen tissue extracted by Trizol


title: AE50T

description: frozen tissue extracted by Trizol


title: AE52T

description: frozen tissue extracted by Trizol


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO3_Mouse_ArrayB_081210

description: 0412HI_AhR_IP_DMSO3_Mouse_ArrayB_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

value: No

tag: number of cells seeded

value: 1X10^5 cells/ml, 25ml in P150s

tag: units of harvest time point


title: Adult at T18 in LD, time-series experiment 4

description:
C. elegans_LD18_4
This Sample represents 2 biological replicates.
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 18 hr time-point during LD entrainment

value: 18 hr


title: Adult at T34 in DD, time-series experiment 4

description:
C. elegans_DD34_4
Gene expression data from adult worms during 12:12 hr dark/dark (DD) free-running cycles.

source_name: C. elegans adults 34 hr time-point during DD free-running

value: 34 hr


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO2_Mouse_ArrayB_081210

description: 0412HI_AhR_IP_DMSO2_Mouse_ArrayB_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.

value: hr

tag: antibody name

value: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor:Biomol (Plymouth Meeting, PA); Catalog #:SA210-0100

tag: sample type

value: ChIP


title: AE41T

description: frozen tissue extracted by Trizol

source_name: tumor tissue

value: esophageal squamous cell carcinoma (ESCC)


title: Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayB_081210

description: 0412HI_AhR_IP_DMSO1_Mouse_ArrayB_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Cells_CH12.LX_0412HI_AhR_IP_TCDD1_Mouse_ArrayB_081210

description: 0412HI_AhR_IP_TCDD1_Mouse_ArrayB_081210: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.


title: Adult at T14 in LD, time-series experiment 4

description:
C. elegans_LD14_4
Gene expression data from adult worms during 12:12 hr light/dark (LD) entrainment cycles.

source_name: C. elegans adults 14 hr time-point during LD entrainment

value: Bristol N2

tag: genotype

tag: developmental stage

value: 14 hr