title: CAI4 vs Control

status: Public on May 20 2008

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

country: Germany

institute: Hans Knoell Institute

description: The Hyphal Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin (CAI4)

hyb_protocol: For transcriptional profiling, we used C. albicans microarrays (Eurogentec, http://www.eurogentec.com) as described (Fradin et al., 2005, Mol Microbiol). Sample RNA (from C. albicans strains incubated with ferritin) was cohybridized with a ‘common reference’ (RNA from SC5314 grown in YPD, mid-log phase, 37°C). Slides were hybridized, washed and scanned as described (Fradin et al., 2005, Mol Microbiol).

data_processing: Data normalization (LOWESS) and analysis were performed in Gene-Spring 7.2 software (Agilent Technologies). Reliable expression of genes was defined as normalized expression of present genes that did not vary more than 1.5 standard deviations within replicate arrays. Using Student’s t-test, a P-value < 0.05 was considered as significant. Microarray data from four independent experiments (including two dye swaps) were used.

organism: Candida albicans

label_protocol: Total RNA was linearly amplified and labelled using the ‘Low RNA Input Fluorescent Linear amplification Kit’ (Agilent Technologies, http://www.agilent.de).

extract_protocol:
C. albicans cells growing under iron limitation were washed and enumerated. Approximately 2 x 10E6 cells were add per well in a 24 well plate containing Poly-L-Lysin -coated 12-mm diamenter glass coverslips in 1ml RPMI 1640 with 100 µg/ml ferritin. After 1.5 h incubation at 37°C under 5% CO2, the medium was removed and 100 µl peqGOLD RNAPure (PeqLab, http://www.peqlab.de) was added per well. The cells were immediately removed from the cover slips using a pipette point. For each strain, cells from 12 wells were pooled in a microcentrifuge tube and immediately shock frozen in liquid nitrogen.
Frozen cells were lysed and homogenized (Precellys 24, PeqLab) with glass beads (0.5 mm, Roth). Total RNA was extracted as described (Fradin et al., 2005, Mol Microbiol).

tag: C. albicans strain CAI4+CIp10 (Murad et al., 2000)

source_name: Common control

extract_protocol: Strain SC5314 was grown to mid-log phase in YPD at 37°C. Cells were pelletet and immediatly frozen in liquid nitrogen. Total RNA was extracted as described (Fradin et al., 2005, Mol Microbiol).

tag: C. albicans strain SC5314 grown to mid-log phase in YPD at 37°C


title: deltaRAS1 vs Control

type: RNA

description: The Hyphal Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin (RAS1)

scan_protocol: Slides were hybridized, washed and scanned as described (Fradin et al., 2005, Mol Microbiol).

molecule: total RNA

extract_protocol:
C. albicans cells growing under iron limitation were washed and enumerated. Approximately 2 x 10E6 cells were add per well in a 24 well plate containing Poly-L-Lysin -coated 12-mm diamenter glass coverslips in 1ml RPMI 1640 with 100 µg/ml ferritin. After 1.5 h incubation at 37°C under 5% CO2, the medium was removed and 100 µl peqGOLD RNAPure (PeqLab, http://www.peqlab.de) was added per well. The cells were immediately removed from the cover slips using a pipette point. For each strain, cells from 12 wells were pooled in a microcentrifuge tube and immediately shock frozen in liquid nitrogen.
Frozen cells were lysed and homogenized (Precellys 24, PeqLab) with glass beads (0.5 mm, Roth). Total RNA was extracted as described (Fradin et al., 2005, Mol Microbiol)

tag: C. albicans deltaRAS1 strain (Feng et al., 1999)


title: deltaHGC1 vs Control

description: The Hyphal Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin (HGC1)

tag: C. albicans deltaHGC1 mutant (Zheng et al., 2004)


title: Normal Thymus-female (probe set)

status: Public on Jul 03 2008

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

description: probe set (exon) summary data generated from A13Exon.CEL

hyb_protocol: Each sample was hybridized to a GeneChip® Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA) according to manufacturer's instructions

scan_protocol: Affymetrix GCS 3000 7G scanner

data_processing: scanning through GeneChip® Operating Software  (GCOS)

label: biotin

organism: Homo sapiens

source_name: Normal Thymus

label_protocol: Whole transcripts sense targeting labeling assay

extract_protocol: RNeasy lipid tissue kit (Qiagen, Valencia, CA)

tag: Thymus

tag: Gender

value: Female, age:46


title: MG-thymoma-male (transcript)

description: transcript cluster id summary data generated from A11Exon.CEL

source_name: MG-thymoma

value: Male, age:44


title: H3K4me2 normalized to H3

status: Public on Feb 12 2008

type: genomic

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

description: This single channel data is submitted as 2 channel in order to represent the ChIP-chip nature of the experiment. Analysis was performed using Hs_PromPR_v02-3_NCBIv34.bpmap, but probe coordinates were mapped to NCBIv35 (hg17) using the LiftOver tool (UCSC). Subsequent analysis was done relative to hg17.

hyb_protocol: Array hybridization was carried out using the Affymetrix Chromatin Immunoprecipitation (ChIP) Assay kit according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G per manufacturer's protocol.

data_processing: Processed values (normalized log-ratios) for ChIP-chip "Samples" were calculated by (1) taking logs of raw intensities, (2) scaling probes with the same G/C content in each array to have a median zero, (3) and taking the difference between the H2B (or H3K4me2) and a specific control (one of H3/Control-Input/Control-Ab). Probe locations refer to the hg17 version of the human genome (UCSC).

molecule: genomic DNA

source_name: H3K4me2 ChIP DNA from HCT116

label_protocol: DNA amplification and labeling were carried out using the Affymetrix Chromatin Immunoprecipitation (ChIP) Assay kit according to the manufacturer’s instructions.

growth_protocol: HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FCS and antibiotics

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of Cell lysis buffer (5mM PIPES, pH=8, 85mM KCL, 0.5% NP-40). Nuclei were pelleted (4000rpm, 5min) and resuspended in Nuclei Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0). The crosslinked chromatin was then sheared to an average size of 500 bp. The lysate was then centrifuged to remove cell debris. The chromatin was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with the antibody and with protein A sepharose beads (30 µl) at 4C. The immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; Dilution buffer (see above), dialysis buffer (2mM EDTA. 50mM TRIS pH=8) LiCl buffer (500 mM LiCl, 100 mM Tris pH=8.0, 1% Na deoxycholate, 1% NP40) and TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in elution buffer (1% SDS, 100 mM NaHCO3) followed by the addition of RNAse A (37C 1hr) and proteinaseK to 500 µg/ml (45C 3hr). Samples were then subjected to overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by the PCR product purification kit (QIAGEN). RNA was extracted using the QIAGEN RNeasy kit according to the manufacturer's protocol.

treatment_protocol: Treatment: no treatment

tag: Age

value: cell line

tag: Human colorectal cancer

tag: Antibody

source_name: H3 ChIP DNA from HCT116


title: UbH2B normalized to non-specific antibody

source_name: UbH2B ChIP DNA from HCT116

source_name: Control antibody ChIP DNA from HCT116

value: Control antibody


title: Stomach - Wildtype - 1

status: Public on Feb 14 2008

city: Baton Rouge

first: Brenda

last: Richards

state: LA

address: 6400 Perkins Rd.

department: Basic Science

institute: Pennington Biomedical Research Center

description: Two strains were used – B6.CAST-17 congenic and WT for this study. Each strain was represented by two pools for a total of four samples from each strain.  Thus, two biological replicates were analyzed for each strain.

hyb_protocol: Fifteen microgram of DIG labeled fragmented cRNA was used for microarray hybridization and performed according to the Applied Biosystems protocols

scan_protocol: Chemiluminescence detection, imaging, auto girding, and image analysis was done according to the Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v1.0.3

data_processing: Signal intensities across microarrays were normalized using quantile-quantile normalization method (www.bioconductor.org)

label: DIG-UTP

organism: Mus musculus

source_name: Stomach tissue

label_protocol: 1 microgram of total RNA was used to transcribe DIG labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0

extract_protocol: Mice were food deprived beginning at 1300 (during the light period) and euthanized 4 h later with an overdose of isoflurane inhalation followed by decapitation.  The stomach was quickly removed, rinsed with cold PBS, frozen in liquid nitrogen, and stored at –80 deg. C.  RNA was isolated using TRIzol extraction protocol.  Quality and quantity was assesed by Agilent bioanalyzer  (Agilent Technologies, Palo Alto, CA)

tag: STRAIN

tag: GENDER

value: MALE

tag: TISSUE

value: STOMACH

tag: DIET

value: CHOW


title: Normal Thymus-male (probe set)

description: probe set (exon) summary data generated from A14Exon.CEL

value: Male, age:43


title: MG-thymoma-female (probe set)

description: probe set (exon) summary data generated from A12Exon.CEL

value: Female, age:53


title: Stomach - Congenics - 2


title: UbH2B normalized to Input DNA

source_name: Input DNA from HCT116

tag: no antibody


title: Stomach - Wildtype - 2

source_name: Stomach RNA


title: Brenda_Richards_Liver_2choice diet_B6.CAST-17 congenics

status: Public on Dec 11 2007

description: Pooled hypothalamus samples from 6 B6.CAST-17 congenic mice fed with 2-choice diet paradigm (carbohydrate/protein and fat/protein diet).

source_name: Liver

extract_protocol: The tissues were removed quickly, frozen in liquid nitrogen and stored at -80 oC. Total RNA was isolated from harvested tissue using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio), and purified using Qiagen RNAeasy columns (Qiagen, Valencia, CA). RNA was stored at -80oC in RNAse free water. Quality and quantity of RNA was determined using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA

value: B6.CAST-17 congenic mice strain

value: LIVER

value: 2-choice diet fed (Carbohydrate/protein and Fat/protein diet) for 24 hours


title: BG3 Nipped-B

status: Public on Oct 18 2007

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

description: Nipped-B genome localization in ML-DmBG3 cells

hyb_protocol: The microarrays were hybridized, washed and stained according to the procedures in the Affymetrix Chromatin Immunoprecipitation Assay Protocol.

scan_protocol: The microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to the manual.

data_processing: The processed sgr data files were generated from the Affymetrix cel files using the TiMAT programs developed by the Berkeley Drosophila Transcription Network Project (http://bdtnp.lbl.gov/TiMAT/TiMAT2/index.html). The probe intensities for all immunoprecipitation and control (input and/or mock) cel files in each hybridization set (each sample is a hybridization set) were normalized using median scaling and assigned to a genome position using a tpmap file based on the April 2004 release of the Drosophila melangaster genome sequence (Berkeley Drosophila Genome Project). The relative immunoprecipitation and control sample normalized intensities were used to generate scores for the microarray features. 675 bp windows were used to generate trimmed mean log2 immunoprecipitation/control ratios for microarray features to produce the sgr files. The sgr files don't line up precisely with the oligos because they were produced using a windowing algorithm in the TiMAT  programs. A sliding 675 bp window was used to generate trimmed means. Each window had to contain at least 10 statistically validated oligos, and the high and low values are tossed, and the midpoint of the window is assigned the mean of the remaining oligos in the window. While the TiMAT programs produce multiple outputs, including sgr files of the raw oligo scores, and predicted peaks at 1% false discovery rates, etc, the sgr files showing the trimmed mean window scores provide the most user accessible and useful way of viewing the data. Almost all the data shown in the paper describing this work is the trimmed mean scores generated using windows. The windowing method is briefly described in Schwartz et al. 2006 Nat Genet 38:700.

organism: Drosophila melanogaster

source_name: ML-DmBG3 cultured cells

label_protocol: Multiple aliquots of each immunoprecipitation sample (6 to 8 microliters), mock immunoprecipition sample, or input chromatin sample (crosslinks reversed and purified as for immunoprecipitation) were amplified sequentially by Sequenase using primer A (GTTTCCCAGTCACGGTC(N)9) and Taq polymerase using primer B (GTTTCCCAGTCACGGTC) according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/downloads/manuals/chromatin_immun_ChIP.pdf, P/N 702238 Rev. 3). The amplified DNA was fragmented with DNaseI (Epicentre) to a size of 25 to 200 bp, and end-labeled with biotin-ddATP using terminal transferase according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol.

growth_protocol: Kc, Sg4 and ML-DmB3 cells were grown to approximately 5 million cells per ml in Schneider's media with appropropriate supplements: Kc, 5% FCS; Sg4, 10% FCS; ML-DmBG3, 10% FCS and 10 micrograms per ml insulin.

extract_protocol: Fixed cells (approximately 500 million) were washed once in 200 ml PBS, once in buffer A [10 mM Hepes (pH 7.9), 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100] and once in buffer B [10 mM Hepes (pH 7.9), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100]. The cells were sonicated in the presence of glass beads (400 to 600 microns) in buffer [10 mM Hepes (pH 7.9), 1 mM EDTA, 0.5 mM EGTA]. Sarkosyl was added to 0.5%, followed by centrifugation in an Eppendorf microfuge at top speed for 10 minutes at 4°C. The supernatant was stored at –80°C. For immunoprecipitation, a 500 microliter chromatin aliquot was adjusted to a total volume of 500 microliters in immunoprecipitation buffer [10 mM Hepes (pH 7.9), 140 mM NaCl, 1 mM EDTA (pH 8.0), 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate, 0.2% (w/v) SDS], and pre-cleared by incubation with 30 microliters of protein A agarose beads (Pierce) for 3 hours at 4°C, followed by centrifugation to remove the beads. Each aliquot was incubated with 30 microliters of the appropriate pre-immune or immune serum overnight at 4°C. Immunocomplexes were bound to 30 microliters of protein A beads at 4°C for 4 hours. Beads were collected by centrifugation for 15 seconds at top speed in an Eppendorf microfuge, washed 5 times with 1 ml of immunoprecipitation buffer, once with 1 ml of LiCl buffer [250 mM LiCl, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate], and twice with 1 ml of TE at 4°C. Beads were suspended in 100 microliters of TE, and crosslinks reversed by RNase A and proteinase K treatment at 68 degrees. DNA was recovered by purification on Qiagen minielute columns in approximately 30 microliters of water. The antibodies used are described in Misulovin et al. Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma, in press. Two independent chromatin preparations were made for each cell type, and at least one immunoprecipitation sample and one control sample (mock immunoprecipitation or input) was prepared from each biological replicate.

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min, and fixation was stopped with 0.125 M glycine (pH 7.0).

tag: Two biological replicate chromatin preparations immunoprecipitated with anti-Nipped-B antiserum

tag: Two input samples from two biological replicate chromatin preparations


title: BG3 PolII

description: RNA polymerase II genome localization in ML-DmBG3 cells

tag: Two biological replicate chromatin preparations immunoprecipitated with anti-RNA polymerase II antiserum


title: Brenda_Richards_Hypothalamus_C57BL/6J_2 choice diet

description: Pooled hypothalamus samples from 6 C57BL/6J mice fed with 2-choice diet paradigm (carbohydrate/protein and fat/protein diet).

source_name: Hypothalamus

value: HYPOTHALAMUS


title: UbH2B normalized to H3


title: Sg4 PolII

description: RNA polymerase II genome localization in Sg4 cells

source_name: Sg4 cultured cells, S2 subline


title: BG3 Smc1

description: Smc1 genome localization in ML-DmBG3 cells

tag: Two biological replicate chromatin preparations immunoprecipitated with anti-Smc1 antiserum


title: Brenda_Richards_Liver_Chow_C57BL/6J

extract_protocol: The tissues were removed quickly, frozen in liquid nitrogen and stored at -80 oC. Total RNA was isolated from harvested tissue using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio), and purified using Qiagen RNAeasy columns (Qiagen, Valencia, CA). RNA was stored at -80oC in RNAse free water. Quality and quantity of RNA was determined using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA)


title: Brenda_Richards_ABI_Hypothalamus_B6.CAST-17-congenics_Chow

description: Pooled hypothalamus samples from 6 C57BL/6J mice fed with chow

value: CHOW FED


title: Sg4 SA

description: Stromalin genome localization in Sg4 cells

tag: Two biological replicate chromatin preparations immunoprecipitated with anti-SA antiserum


title: Sg4 Nipped-B

description: Nipped-B genome localization in Sg4 cells


title: Brenda_Richards_Hypothalamus_2choice diet_B6.CAST-17 congenics


title: Kc Smc1

description: Smc1 genome localization in Kc cells

source_name: Kc cultured cells

tag: One mock immunoprecipitation and one input chromatin sample from two biological replicate chromatin preparations


title: Brenda_Richards_ABI_Hypothalamus_C57BL/6J_Chow

description: Pooled hypothalamus samples from 6 C57BL/6J mice fed with chow.

extract_protocol: The hypothalamus was removed quickly, frozen in liquid nitrogen and stored at -80 oC. Total RNA was isolated from harvested tissue using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio), and purified using Qiagen RNAeasy columns (Qiagen, Valencia, CA). RNA was stored at -80oC in RNAse free water. Quality and quantity of RNA was determined using Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA)


title: Brenda_Richards_Liver_B6.CAST-17congenics_Chow

value: B6.CAST-17 congenic


title: Brenda_Richards_Liver_2choice diet_C57BL/6J


title: Sg4 Smc1

description: Smc1 genome localization in Sg4 cells

tag: Two mock immunprecipitation and one input chromatin sample rrom two biological replicate chromatin preparations


title: Zebrafish-PGRP-SC

status: Public on Aug 13 2007

city: Wuhan

first: M

middle: X

last: Chang

address: Luojiaashan

country: China

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Gene expression data from the embryos injected with zfPGRP-SC

hyb_protocol: Fifteen microgram aliquants of the fragmented cRNA were hybridized with the D. rerio Genome AFF-F0027 GeneChip® microarray (Affymetrix, CA) in hybridization cocktail. Hybridization was allowed to proceed overnight (16 h) at 45 °C

scan_protocol: The distribution of fluorescent material on the array was obtained using GeneChip® Scanner 3000 (Affymetrix, CA)

data_processing: The scanned images were firstly assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling factor of 500 was used to normalize the different arrays. The differentially expressed genes were judged according to change p-value calculated by GCOS 1.4, and 2-fold change as an empirical criterion.

organism: Danio rerio

source_name: 24 hours post-fertilization embryos

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

growth_protocol: Zebrafish embryos were maintained at 28 ± 0.5 °C

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

treatment_protocol: Selected embryos were transferred to 2 mL Eppendorf tube, rinsed with DEPC-treated water. After discarding water, the Trizol solution (GibcoBRL) was added to Eppendorf tube containing embryos.

tag: the embryos injected with zfPGRP-SC


title: Zebrafish-control siRNA

description: Gene expression data from the embryos injected with the control siRNA


title: norm_exp_set_NK

status: Public on Jun 06 2008

city: Chicago

last: Emerson

state: IL

address: 1101 East 57th Street

institute: University of Chicago

description: Normalization and subsequent analysis was conducted independently on 9 arrays: 6 lab strains and the three replicates from the natural isolate.

hyb_protocol: Following labeling, 25ml of the terminal labeled solution were hybridized according to standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Affymetrix GeneChip Scanner 3000.

data_processing: The data was independently processed for each analysis group of 9 arrays (3 replicates for each of: natural isolate and two lab strains) using R and Bioconductor. The data was first quantile normalized, and then the natural logarithm was recorded as “LNNORMINTENSITY” (see supplementary norm*.txt files). Following initial processing, the probes representing the 5% most variable probes among the three natural isolate replicates or the reference genome replicates were discarded.  These probes are included in the sample data table, though with "NULL" to indicate their removal from the dataset.  The data was then subjected to analysis using an HMM, details of which are in the Supporting Online Material with the original publication. Results of the HMM analysis are included in the GEO Sample table.

source_name: natural isolate NK (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)

label_protocol:
Labeling was conducted following Affymetrix oligoarray target pre-processing as described bellow. There are two main steps: 1- Genomic DNA fragmentation and 2- Terminal labeling.

1- Genomic DNA fragmentation:
1.1- The following reaction mix was prepared:
6 ul 10x One-Phor-All buffer (1x)
25 ul of Genomic DNA
0.5 ul DNase I (0.168u/ul)
28.5 ul Nuclease-free ddH2O
1.2- The reaction was incubated at 37ºC for 10 minutes.
1.3- DNase I was inactivated at 100ºC for 10 minutes.
2- Terminal labeling was done using the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix P/N 900181) to label 3' termini of the fragmentation products. The details of the protocol are described below.
2.1 The following reaction mix was prepared:
20 ul of reaction buffer (5x)
10 ul CoCl2 (10x)
4 ul Biotin-ddUTP (100x)
8 ul Terminal Deoxyribonucleotide transferase (50x)
54 ul of the fragmentation product (from the Genomic DNA fragmentation step)

2.2- The reaction was incubated at 37ºC for 60 minutes.
2.3- The reaction was stopped by adding 4 ul of 0.25M EDTA.
2.4- The target was then ready to be hybridized onto Tiling arrays.

growth_protocol: Flies were kept at room temperature in standard cornmeal-molasses-yeast medium. DNA was extracted from female virgins.

extract_protocol: Genomic DNA was extracted following the DNA purification protocol for 20-30 flies from PUREGENE with an added phenol-chloroform extraction step. DNA was extracted from 30 female virgin flies. After the protein precipitation step (and before the DNA precipitation step) a phenol-chloroform step was performed as follows: 1- an equal volume of pheno:chloroform:isoamyl:alcohol (25:24:1) was added to the solution containing DNA and mixed by inverting gently (50 times); 2- the solution was centrifuged at 14000rpm for two minutes; 3- the top aqueous layer was transferred to a new tube; 4- an equal volume of chloroform:isoamyl-alcohol (24:1) was added to the solution and mixed by inverting gently; 4- the solution was centrifuged at 14000rpm for two minutes; and 5- the top aqueous layer was transferred to a new tube. The PUREGENE DNA purification protocol was resumed starting in the DNA precipitation step. DNA was rehydrated using 50ml of DNA Hydration solution yielding a concentration of 400mg/ml.

treatment_protocol: No treatments were applied to the flies before DNA extraction.

tag: natural isolate from sub-Saharan Africa


title: norm_exp_set_La79

source_name: natural isolate La79 (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: PU.1 ChIP versus IgG ChIP

status: Public on Oct 11 2007

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

description: 3 biological replicates of PU.1 and IgG Immunoprecipitation were performed each

hyb_protocol: Affymetrix Chromatin Immunoprecipitation Assay Protocol

data_processing: Affymetrix GCOS processed image files to generate CEL files. The Affymetrix CEL files were analyzed with Genomatix Chipinspector using SAM analysis with multiple T-test and FDR to retrieve signficantly enriched promoters.

source_name: PU.1 ChIP from RAW264.7 macrophages

growth_protocol: RAW264.7 cells were cultured in DMEM /10% FCS

extract_protocol: Chromatin was prepared as described in Weigelt et al. 2007, Journal of Leukocyte Biology doi:10.1189/jlb.0707447

treatment_protocol: ChIP analysis was performed as described in Weigelt et al. 2007, Journal of Leukocyte Biology doi:10.1189/jlb.0707447

tag: RAW264.7 macrophages

tag: PU.1 ChIP from RAW264.7 macrophages

source_name: IgG ChIP from RAW264.7 macrophages

tag: IgG ChIP from RAW264.7 macrophages


title: norm_exp_set_ZH1

source_name: natural isolate ZH1; 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_OK17

source_name: natural isolate OK17; 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_MW6

source_name: natural isolate MW6 (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_Nr

source_name: natural isolate Nr; 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_NM

source_name: natural isolate NM (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_KM

source_name: natural isolate KM (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_KK

source_name: natural isolate KK (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_MD

source_name: natural isolate MD (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_ZS5

source_name: natural isolate ZS5; 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_Co

source_name: natural isolate Co (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_Ken48

source_name: natural isolate Ken48 (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: Stomach - Congenics - 1

description: Two strains were used – B6.CAST-17 congenic and WT for this study. Each strain was represented by two pools for a total of four samples from each strain.  Thus, two biological replicates were analyzed for each strain.

source_name: Stomach

tag: STRAIN


title: norm_exp_set_Ga

source_name: natural isolate Ga (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)


title: norm_exp_set_ML

source_name: natural isolate ML (3 reps); 'ref' lab strain (3 reps); 'train' lab strain (3 reps)