title: Testis_microdeleted AZFc SCOS_P.ID.009

data_processing: The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction,  a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and  generate  log ratios of experimental vs. control signal.

label_protocol: To acquire the quantity of RNA needed for microarray analysis we amplified the RNA lineary using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (from Ambion Inc.). Reverse transcription uses an oligo(dT) primer bearing a T7 promoter using ArrayScript™, a reverse transcriptase (RT) engineered to produce higher yields of first strand cDNA than wild type enzymes . ArrayScript catalyzes the synthesis of virtually full-length cDNA, which is the best way to ensure production of reproducible microarray samples. The cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription (IVT) with T7 RNA Polymerase. The IVT is configured to incorporate the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) into the aRNA (the antisense amplified RNA is referred to as aRNA, in scientific literature it is also commonly called cRNA.)  during in vitro transcription. aaUTP contains a reactive primary amino group on the C5 position of uracil that can be chemically coupled to N-hydroxysuccinimidyl ester-derivatized reactive dyes (NHS ester dyes), such as Cy™3 and Cy5, in a simple, efficient reaction.


title: Testis_microdeleted AZFc oligozoo_P.ID.010

status: Public on Oct 04 2010

type: RNA

city: Chieti

first: Florina

last: Raicu

state: Abruzzo

address: Via Colle dell'Ara

department: Aging Research Center (CESI)

country: Italy

institute: G. d’Annunzio University Foundation Chieti

description: Both Cy3 and Cy5 lasers were balanced before performing the scanning using the calibration control spots with different concentration scattered on the array.

hyb_protocol: Cy3 or cy5 labelled targets were resuspended in 80 μl of hybridization cocktail and incubated at 95°C for 5 minutes. Samples were cooled for 15 minutes at room temperature. Hybridization cocktail contains the following reagents: 5xSSC, 0,1% SDS, 50% formamide, 1% ssDNA (Ambion, Austin, TX, USA). Samples were quick applied to our microarray (Microcribi Padova), covered with a cover slip, placed in moisturized hybridization chambers (MWG) and incubated overnight (14 - 16 hours) at 42 °C. Prior to hybridization we performed the prehybridization of microarray slides in order to wash unbound DNA from the slides after the addition of the probes. The prehybridization cocktail contains the flollowing reagents: 5xSSC, 0,1% SDS, 50% formamide, 1%ssDNA (Ambion, Austin, TX, USA), 10% Denhardt solution (Eurobio, France).After 16 hours hybridization of labeled aRNA sample mix at 42oC, the hybridization chamber was removed from the water bath, the arrays were washed with gentle stirring with the first wash buffer (1× SSC, 0,2% SDS) for 4 min. The array was washed in the next two wash buffers (0,1× SSC, 0,2 % SSC and two times with 0.2× SSC respectively) as before. The array was dried at room temperature in the dark and scanned.

scan_protocol: Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner "ScanArray Express" (Packard BioScience) and analysed using the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer) using a 5 micron resolution.

data_processing: The values of the median signal intensity from each spot were subtracted from the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for row data normalization to evaluate signal to noise ratio and generate log ratios of experimental vs. control signal.

molecule: total RNA

organism: Homo sapiens

source_name: biopsy normal testis obstructive azoospermia

label_protocol: To acquire the quantity of RNA needed for microarray analysis we amplified the RNA lineary using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (from Ambion Inc.). Reverse transcription uses an oligo(dT) primer bearing a T7 promoter using ArrayScript™, a reverse transcriptase (RT) engineered to produce higher yields of first strand cDNA than wild type enzymes . ArrayScript catalyzes the synthesis of virtually full-length cDNA, which is the best way to ensure production of reproducible microarray samples. The cDNA then undergoes second strand synthesis and clean-up to become a template for in vitro transcription (IVT) with T7 RNA Polymerase. The IVT is configured to incorporate the modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) into the aRNA (the antisense amplified RNA is referred to as aRNA, in scientific literature it is also commonly called cRNA.) during in vitro transcription. aaUTP contains a reactive primary amino group on the C5 position of uracil that can be chemically coupled to N-hydroxysuccinimidyl ester-derivatized reactive dyes (NHS ester dyes), such as Cy™3 and Cy5, in a simple, efficient reaction.

extract_protocol: Total RNA from the testicular tissue types biopsies was extracted according to SVtotal RNA Izolation System kit (Promega, Madison, WI, USA).

tag: 3-5 mm fragments per testis were excised, processed for histological analysis, and at least one sample per testis was submerged in 2 ml of RNAlater (Ambion, Austin, TX, USA) for RNA extraction. Y chromosome AZFc microdeleted.

source_name: testis biopsy microdeleted AZFc oligozoospermia


title: DAT_0.2µM_120h_Replicate1

status: Public on Oct 02 2010

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome - 430 2.0 arrays covering approximately 36,000 full-length mouse gene transcripts and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same (GCOS). The Scale factor (SF) was according to the Affymetrix recommended setting SF=1 and the TGT value was 500 and were used to generate a microarray quality control and data report. A T-test analysis was performed using Data Mining Tool (DMT) 3.0 from Affymetrix. A stringent comparison between normal and tumoral tissues was performed according to the consistency of gene expression changes. A t-test and a ranking analysis with up- and down-regulated genes were performed and only genes that exhibit a 100% concordance in the change direction with a p-value < 0.05 (t-test) and a fold change (FC) *2/FC*-2 were reported.

label: biotin

organism: Mus musculus

source_name: embryonic mouse fibroblasts Balb/c 3T3 cell line

label_protocol: Total RNA (5µg) was used to generate biotin-labeled cRNA (10 µg) by means of GeneChip® One-Cycle cDNA Synthesis Kit and GeneChip® IVT Labeling Kit (Affymetrix). Sample processing was performed exactly as described by the microarray manufacturer (Affymetrix). Quality control of cRNA was performed using a Bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

growth_protocol: The Balb/c 3T3 cell line was obtained from Cytotest Cell Research GmbH (RCC), Roßdorf, Germany. Cells were harvested and used within 9-10 passages to perform the experiments. Cells were cultured with M10F containing MEM (minimum essential medium) + 10% FBS and incubated at 37 °C and 5% CO2.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MidiKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Balb/c 3T3 cells were seeded at 200 cells in each 60 x 15 mm culture dish with 4 ml M10F, using six culture dishes for every treatment. When cells reached a confluence of 60-65%, the culture medium was removed and replaced with fresh medium containing all tested chemicals at a specific concentration and two time points (24 and 120h).   First we treated the cells both 24h and 120h with concentrations reported in the literature (0.5µM BaP, 50µM DAT, 25µM AAF and 2µM MCA). In a second approach IC20 concentrations were investigated for each chemical at both time points. The concentrations determined for IC20 ranged from 1.5 µM BaP to 700 µM DAT for 24h of treatment, and from 0.1 µM BaP or MCA to 10µM AAF for 120h of treatment. Balb/c 3T3 cells treated with 0.75% DMSO alone were kept as controls.

tag: strain

value: BALB/c

tag: cell line

value: 3T3 cell line

tag: treatment

value: 2, 4-diaminotoluene (DAT)

tag: dose

tag: time


title: DAT_700µM_24h_Replicate2


title: Control_DMSO_24h_E2_Replicate2

value: E2 = control of the second experimental approach


title: BaP_0.1µM_120h_Replicate1

value: benzo(a)pyrene (BaP)


title: MCA_20µM_24h_Replicate3

value: 3-methycholanthrene (MCA)


title: DAT_700µM_24h_Replicate3


title: DAT_0.2µM_120h_Replicate3


title: Control_DMSO_24h_E2_Replicate1


title: Control_DMSO_120h_E2_Replicate2


title: Control_DMSO_120h_E2_Replicate1


title: BaP_0.1µM_120h_Replicate3


title: BaP_1.5µM_24h_Replicate3


title: BaP_1.5µM_24h_Replicate1


title: DAT_700µM_24h_Replicate1


title: BaP_1.5µM_24h_Replicate2


title: Control_DMSO_24h_E2_Replicate3


title: MCA_2µM_24h_Replicate2


title: AAF_10µM_120h_Replicate3

value: 2-Acetylaminoflourene (AAF)


title: AAF_10µM_24h_Replicate2


title: MCA_2µM_24h_Replicate3


title: MCA_2µM_120h_Replicate2


title: AAF_10µM_120h_Replicate1


title: AAF_10µM_120h_Replicate2


title: MCA_2µM_120h_Replicate3


title: DAT_50µM_120h_Replicate2


title: MCA_2µM_24h_Replicate1


title: DAT_50µM_24h_Replicate2


title: MCA_20µM_24h_Replicate1


title: DAT_50µM_120h_Replicate1


title: DAT_50µM_24h_Replicate1


title: Control_DMSO_120h_Replicate1

value: control of the first experimental approach


title: Control_DMSO_120h_Replicate3


title: DAT_50µM_120h_Replicate3


title: MCA_2µM_120h_Replicate1


title: DAT_50µM_24h_Replicate3


title: Control_DMSO_24h_Replicate3


title: AAF_10µM_24h_Replicate1


title: Control_DMSO_120h_Replicate2


title: BaP_0.5µM_120h_Replicate2


title: Control_DMSO_24h_Replicate2


title: Control_DMSO_24h_Replicate1


title: BaP_0.5µM_120h_Replicate3


title: BaP_0.5µM_24h_Replicate3


title: AAF_10µM_24h_Replicate3


title: BaP_0.5µM_120h_Replicate1


title: AAF_25µM_120h_Replicate1


title: AAF_25µM_120h_Replicate3


title: BaP_0.5µM_24h_Replicate1


title: DAT_0.2µM_120h_Replicate2


title: AAF_25µM_120h_Replicate2


title: AAF_25µM_24h_Replicate1


title: thymus_XX_rep2

city: London

first: Patrick

middle: JEC

last: Wijchers

address: Imperial College London, Hammersmith Campus, Du Cane Road

department: Gene Control Mechanisms and Disease Group

country: United Kingdom

institute: MRC Clinical Sciences Centre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse genome 430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G scanner

data_processing: CEL files were imported into 'R', and processed using RMA bioconductor package with standard settings.

source_name: thymus, 8wk, XX female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were sacrificed when aged 7-8 weeks

extract_protocol: Thymus tissue was homogenised in LiCl/Urea, followed by sonication and overnight precipitation at 4 degrees. After centrifugation, pellets were washed once in LiCl/Urea, followed by Phenol-Chloroform (5:1) extraction and ethanol precipitation.

treatment_protocol: Mice were secrificed by cervical dislocation, and thymus was dissected, transferred into 1.5 ml eppendforf tube and snapfrozen in liquid nitrogen followed by storage at -80 degrees Celsius

tag: sex

value: female

tag: tissue

value: thymus

tag: sex chromosome complement

value: XX


title: AAF_25µM_24h_Replicate2


title: thymus_XY-sry_rep2

source_name: thymus, 8wk, XY-sry male

value: male

value: XY-sry


title: thymus_XY-sry_rep1


title: AAF_25µM_24h_Replicate3


title: M_I_C_5

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

hyb_protocol: Hybridization was performed for 17 h at 65°C using the In situ Hybridization Kit Plus (Agilent Technologies). All processing steps were performed in an ozone-controlled environment ([O3] <2 ppb).

scan_protocol: Slides were scanned at a 5 µm resolution with a G2505B DNA microarray scanner (Agilent Technologies). Image analysis and intra-array signal correction were performed using Agilent Feature Extractor Software A.9.1.3.

data_processing:
Data processing, analysis and visualizing were performed using R (version 2.9.2) and bioconductor (v.2.4.1). PCA analysis was conducted using the made4 library (v. 1.18.0). Data were normalized using quantile normalization (library limma, v.2.18.3). Supervised analysis was conducted using SAM multiclass algorithm (library siggenes, v.1.18.0). The normalized data matrix is missing 4 samples because they were excluded from analysis for technical reason (3 of them are highly divergent in the PCA analysis and quality assessement - One being obviously mislabelled for the sex (in regard to the label and expression data)). The samples were excluded before normalization. The normalized data matrix is also missing the rows for probes that had intensities bellow background levels for all samples.
Raw data and sample characteristics for the 4 samples excluded from normalization and downstream analysis are provided as supplementary files on the Series record.

label_protocol: Sample labeling and hybridization were performed according to protocols specified by the manufacturer (One-Color Microarray-Based Gene Expression Analysis). Briefly, 300 ng of total RNA and cyanine 3-labeled CTP (Cy-3) fluorescent dyes were used to generate fluorescent cRNA with Low RNA Input Fluorescent Amplification Kit (Agilent Technologies). All processing steps were performed in an ozone-controlled environment ([O3] <2 ppb).

growth_protocol: Forty C57BL/6 mice (20 males and 20 females) were obtained from Charles River Laboratories.

extract_protocol: Organs were aseptically extracted and stabilized in RNAlater. All specimens were stored at -80°C until use.Total RNA was extracted using the RNeasy minikit (Qiagen) and DNAse treatment. The quality and the quantity of RNA preparation were assessed using the 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Ten males and 10 females were sterilized at seven weeks of age. Ovaries were removed through bilateral incisions of the lumbar region and testes were removed through bilateral scrotum incision. After three weeks, five castrated and five intact animals of each gender were injected intraperitoneally with 10e5 C. burnetii organisms. Mice were sacrified at day one.

value: liver

value: Male

tag: infection status

value: Infected

tag: castration status

value: Castrated


title: thymus_XY-_rep1

source_name: thymus, 8wk, XY- female

value: XY-


title: thymus_XY-sry_rep3


title: thymus_XX_rep1


title: thymus_XY-_rep2


title: thymus_XXsry_rep2

source_name: thymus, 8wk, XXsry male

value: XXsry


title: thymus_XXsry_rep3


title: thymus_XXsry_rep1


title: thymus_XY-_rep3


title: thymus_XX_rep3


title: F_I_C_5

value: Female


title: M_UI_C_5

value: Uninfected


title: M_UI_I_5

value: Intact


title: F_I_C_4


title: F_I_I_5


title: M_UI_C_4


title: F_UI_C_5


title: F_I_I_4


title: M_I_I_4


title: F_UI_C_4


title: M_I_C_4


title: F_UI_I_4


title: F_I_C_3


title: M_I_C_3


title: M_UI_I_4


title: F_I_I_3


title: F_I_I_2


title: M_I_C_2


title: F_I_C_2


title: M_UI_C_3


title: M_UI_I_3


title: M_UI_C_2


title: F_UI_I_3


title: F_UI_C_3


title: M_I_I_2


title: F_I_C_1


title: F_UI_C_2


title: F_UI_I_2


title: MALTL 30

city: Zürich

first: Vanessa

middle: Jane

last: Craig

address: Winterthurerstrasse 190

country: Switzerland

institute: Institute of molecular cancer research

description: miRNA expression profile

hyb_protocol: All microarray experiments were performed using the Agilent Human miRNA Microarray Kit version 10.0. 100 ng total RNA were hybridized per sample and processed according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned with an Agilent Technology G2565B scanner. The scanned images were gridded and analyzed using Agilent Feature Extraction Software version 9.5. The 795 human mature miRNAs included on the array were represented by 2421 probes; the average intensity of all probes corresponding to one miRNA was calculated. Normalization was performed using quantile normalization implemented in the bioconductor package PreprocessCore. The false discovery rate was computed using the Benjamini-Hochberg algorithm.

data_processing:
The scanned images were gridded and analyzed using Agilent Feature Extraction Software version 9.5. The 795 human mature miRNAs included on the array were represented by 2421 probes; the average intensity of all probes corresponding to one miRNA was calculated.
The expression values were log-transformed, normalized, and subsequently scaled. The applied scaling is such that the average log expression value of a miRNA is set to 0. Normalization was performed using quantile normalization implemented in the bioconductor package PreprocessCore. The false discovery rate was computed using the Benjamini-Hochberg algorithm.

source_name: FFPE low grade MALT lymphoma sample

extract_protocol: Total RNA was extracted from three 20 μm slices per sample of formalin fixed, paraffin embedded material using the RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada). Total RNA concentrations were measured using an ND-1000 spectrophotometer (NanoDrop Technologies). RNA integrity was confirmed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: stomach

tag: disease status

value: low grade MALT lymphoma


title: MALTL 692

description: miRNA expression profile

label_protocol: All microarray experiments were performed using the Agilent Human miRNA Microarray Kit version 10.0. 100 ng total RNA were hybridized per sample and processed according to the manufacturer’s instructions.


title: MALTL 12

description: miRNA expression profile


title: MALTL 10

description: miRNA expression profile


title: MALTL 21

description: miRNA expression profile


title: MALTL 64

description: miRNA expression profile


title: M_I_C_1


title: F_UI_C_1


title: MALTL 652

description: miRNA expression profile


title: F_I_I_1


title: M_UI_I_1


title: M_UI_C_1


title: M_I_I_1


title: F_UI_I_1


title: Rumen_Low conc_pooled_rep4

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

country: Japan

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

description: Biological replicate 4 of 5. Pooled low concentrate fed Holstein

hyb_protocol: Hybridizations were carried out in a hybridization chamber (X2530, Genetix) at 42ºC overnight. Hybridized slides were washed with low stringency buffer (2 × standard sodium citrate (SSC) and 0.5% sodium dodecyl sulfate (SDS)), high stringency buffer.

scan_protocol: Hybridized slides were scanned with 5 micron resolution and their signal intensities were detected by Q-Scan (Genetix).

data_processing: Data analysis for the microarray was performed using GeneSifter software (VizX Labs, Seattle, WA, USA). Using GeneSifter, the background-corrected signal intensity for each spot was normalized by locally weighted scatter plot smoothing (LOWESS) method.

organism: Bos taurus

source_name: Pooled low concentrate reference

label_protocol: One microgram of total RNA was reverse-transcribed, amino-allyl coupled (Applied Biosystems) and labeled with Cy3 or Cy5 fluorescent dyes (GE Healthcare) according to the manufacturer’s instructions.

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

treatment_protocol: The dietary treatments were designated as low concentrate (LC; 8% concentrate) and high concentrate (HC; 64% concentrate).  Adaptation to the HC diet was carried out over 10 d, and cows received their respective treatment for at least 28 d before slaughter.

tag: diet condition

value: low concentrate

value: Holstein

source_name: High concentrate

value: high concentrate


title: Rumen_Low conc_pooled_rep2

description: Biological replicate 2 of 5. Pooled low concentrate fed Holstein


title: Rumen_Low conc_pooled_rep5

description: Biological replicate 5 of 5. Pooled low concentrate fed Holstein


title: Rumen_High conc_#9671

description: Biological replicate 5 of 5. High concentrate fed Holstein


title: Rumen_Low conc_pooled_rep1

description: Biological replicate 1 of 5. Pooled low concentrate fed Holstein


title: Rumen_Low conc_pooled_rep3

description: Biological replicate 3 of 5. Pooled low concentrate fed Holstein


title: MALTL 63

description: miRNA expression profile


title: Rumen_High conc_#9331

description: Biological replicate 4 of 5. High concentrate fed Holstein


title: highMALTL11B

description: miRNA expression profile

source_name: FFPE gDLBCL sample

value: gDLBCL


title: highMALTL210

description: miRNA expression profile


title: highMALTL 272

description: miRNA expression profile


title: gastritis 98

description: miRNA expression profile

source_name: FFPE gastritis sample

value: gastritis


title: highMALTL 32

description: miRNA expression profile


title: gastritis 93

description: miRNA expression profile


title: highMALTL1B

description: miRNA expression profile


title: gastritis 81

description: miRNA expression profile


title: highMALTL29

description: miRNA expression profile


title: HCC1 clone-1/8 replicate 3

city: milan

first: Federico

last: Colombo

address: via F. Sforza 35

institute: fondazione IRCCS Ca' Granda

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data signal was loaded into the R/Bioconductor software. Expression values were transformed to a log2 scale and the analysis pipeline lumi was then applied to correct background and normalize and summarize the probe level data into expression level data in order to build up a final ExpressionSet object. After the acquisition of the matrix of raw intensity data with the corresponding annotations, probes corresponding to predicted genes or not associated to a Entrez ID were discarded from the analysis; moreover, different probe signals corresponding to the same Entrez ID were converted into unique intensity signal, corresponding to the median of the values for each array, in order to obtain a single signal for each Entrez ID. After this process, we generated a boxplot of 16964 intensity signals whose values were log2-transformed and quantile normalized using the aroma.light package for Bioconductor.
Genes with a differential expression of at least 2 fold and with a corrected p value <0.01 were considered differentially expressed.

source_name: Human hepatocellular carcinoma cell clone-1/8

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cell suspensions obtained from tumor tissues were cultured onto collagen-coated Petri dishes at a density of 5 x 10^5 cells/cm2 with IMDM supplemented with 20% FBS, 1% non essential amino acids, 1% glutamine and 1% penicillin/streptomycin; cells were maintained at 37°C in a humidified 5% CO2 incubator. when cell colonies appeared in culture, they were removed and repalted in pastic flask coated with collagen. Once confluence war reached, cells were detached using trypsin/EDTA, counted and replated 1:3 at every split in order to determine their growth kinetic.

extract_protocol: Total RNA was extracted starting from 0.5-1 x 10^6 HCC cell lineages and clones by using the RNase Micro Kit (Qiagen, Crawley, UK) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: male

tag: hbv infection

tag: hcv infection

tag: cirrhosis


title: HCC1 clone-1/8 replicate 1

description: replicate 1

value: liver


title: HCC1 clone-1/7 replicate 1

description: replicate 1

source_name: Human hepatocellular carcinoma cell clone-1/7


title: BaP_0.5µM_24h_Replicate2

value: BALB/c

value: 3T3 cell line

value: benzo(a)pyrene (BaP)


title: HCC-3 replicate 3

description: replicate 3

source_name: Human hepatocellular carcinoma cell line 3


title: HCC1 clone-1/7 replicate 2

description: replicate 2


title: Rumen_High conc_#817

description: Biological replicate 2 of 5. High concentrate fed Holstein


title: highMALTL 25

description: miRNA expression profile


title: Rumen_High conc_#820

description: Biological replicate 3 of 5. High concentrate fed Holstein


title: Rumen_High conc_#780

description: Biological replicate 1 of 5. High concentrate fed Holstein


title: HCC1 clone-1/8 replicate 2

description: replicate 2


title: gastritis 3

description: miRNA expression profile


title: HCC-3 replicate 2

description: replicate 2


title: HCC-3 replicate 1

description: replicate 1


title: gastritis 2

description: miRNA expression profile


title: gastritis 4

description: miRNA expression profile


title: gastritis 9

description: miRNA expression profile


title: HCC-2 replicate 2

description: replicate 2

source_name: Human hepatocellular carcinoma cell line 2


title: HCC-2 replicate 1

description: replicate 1


title: HCC-1 replicate 3

description: replicate 3

source_name: Human hepatocellular carcinoma cell line 1


title: HCC-2 replicate 3

description: replicate 3


title: A262

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

country: USA

institute: Harvard University

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Drosophila melanogaster

source_name: Total RNA from Ycongo male genotype.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: genotype

value: Ycongo / 6175 back

tag: age

value: 2 days old

source_name: Total RNA from Yohio male genotype.

value: Yohio / 6175 back


title: HCC-1 replicate 2

description: replicate 2


title: A260

description: Biological replicate


title: A263

description: Biological replicate


title: A261

description: Biological replicate


title: A159

description: Biological replicate

source_name: Total RNA from XXYindia female genotype.

value: XXYindia

value: female (XXY)

value: 2 days old, unmated

source_name: Total RNA from XXYzimbabwe female genotype.

value: XXYzimbabwe


title: A158

description: Biological replicate


title: A259

description: Biological replicate


title: A157

description: Biological replicate

source_name: Total RNA from XXYcongo female genotype.

value: XXYcongo


title: A151_A

description: Biological replicate


title: HCC-1 replicate 1

description: replicate 1


title: A258

description: Biological replicate


title: A156_B

description: Biological replicate


title: duodenum knockout rep3C

city: Tampere

first: Pei-wen

last: Pan

address: Biokatu 6

country: Finland

institute: Institute of Medical Technology, University of Tampere

hyb_protocol: 750 ng of each sample was hybridized to Illumina´s Sentrix® MouseRef-8 v2 BeadChip, at 58 degree for 18 h

scan_protocol: Chips were scanned with Illumina BeadArray Reader v.3.5.49.29917 (Factor=1.52, PMT=552, Filter=100%)

data_processing: Array data were normalized with Chipster version 1.3.0 using the quantile normalization method

label: Biotin

source_name: mouse duodenum

label_protocol: Using Illumina TotalPrep RNA Amplification kit (#IL1791, Ambion), following the manufacturer's protocol. Input amount: 300ng of total RNA. Incubation of labeling reaction: 16h.

extract_protocol: Total RNAs were purified using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). On-column DNase digestion was performed during RNA purification process. RNA concentrations, A260/280, and A260/230 ratios were determined using the ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, USA).

tag: strain

value: female

value: 2 months

value: duodenum


title: RASSF1C_1

city: Los Angeles

first: xinmin

last: Li

state: CA

address: 1000 Veteran Ave

institute: UCLA

hyb_protocol: Affymetrix standard hyb protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Standard affy protocol on 2/21/2008 using Expression Console v.1.1.2800.19935 GeneChip.CallGEBaseCall.1 protocol

source_name: T47D human cell over-expression RASSF1C

label_protocol: Affymetrix standard labeling kit

growth_protocol: Cell culture was grown as recommended by the supplier

extract_protocol: Total RNA from human cell lines was isolated from confluent cultures using the Absolutely RNA Microprep Kit

treatment_protocol: over-expression techniques were used to modulate RASSF1C expression in human breast cancer cells

tag: cell line

value: T47D cell

tag: genotype/variation

value: over-expression RASSF1C


title: Control_3

source_name: T47D human cell control

value: control


title: Control_1


title: RASSF1C_3


title: duodenum knockout rep2C


title: duodenum knockout rep1C


title: duodenum wild type rep3C

value: wild type


title: RASSF1C_2


title: Control_2


title: duodenum wild type rep2C


title: A147

description: Biological replicate

source_name: Total RNA from XXYohio female genotype.

value: XXYohio


title: duodenum wild type rep1C


title: A148

description: Biological replicate


title: stomach knockout rep1B

source_name: mouse stomach

value: stomach


title: BM-MSC_rep 3

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: BM-MSC from patient

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA through R based affy module

source_name: BM-MSC from patient

label_protocol: standard Affymetrix procedures

extract_protocol:
All human MSCs used for experiment were cultured in the MesenCultTM medium in the presence of 5% CO2, or in Dulbecco's modified Eagle's medium DMEM supplemented with 10% fetal bovine serum . For BM-MSCs isolation, the mononuclear fraction of bone marrow was isolated by Histopaque-1077 gradient (1077-1; Sigma, USA), and plated in culture medium. Non-adherent cells were abandoned on next day
Total RNA were extracted by RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected into reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.

tag: cell type

value: BM-MSC


title: stomach wild type rep1B


title: A145

description: Biological replicate

tag: sex


title: A146

description: Biological replicate


title: A197

description: Biological replicate


title: A150

description: Biological replicate


title: stomach wild type rep2B

tag: tissue


title: stomach knockout rep3B


title: stomach wild type rep3B


title: BM-MSC_rep 2

description: BM-MSC from patient


title: BM-MSC_rep 4

description: BM-MSC from patient


title: Endometrium group B hCG not pregnant 5

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing: Affymetrix GeneChip Operating (GCOS) 1.4 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval, group B, not pregnant

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix)

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer' s protocol

tag: treatment

value: hCG

value: endometrium


title: Endometrium group B hCG not pregnant 4


title: submandibular gland wild type rep3A

source_name: mouse submandibular gland

value: submandibular gland


title: submandibular gland knockout rep2A


title: stomach knockout rep2B


title: A144

description: Biological replicate

value: female (XXY)


title: Sal1_2_REFERENCE

type: genomic

city: La Jolla

first: Neekesh

middle: V

last: Dharia

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

hyb_protocol: The samples were hybridized to the microarrays overnight at 45°C using Affymetrix kits following manufacturer’s instructions, washed, and scanned.

data_processing:
The Sample table contains microarray data for probes that uniquely map to the P. vivax genome.  The data has been normalized to a baseline synthetic array using the nonlinear piece-wise running median line for invariant probes (Dharia et al 2009).
The polymorphism detection was performed as previously described for P. falciparum (Dharia et al 2009). Briefly, using a sliding window of three overlapping probes we scanned for sets probes that had significantly lower hybridization in IQ07 when compared to the Sal1 references indicative of a polymorphism as determined by z-test using an empirically derived standard deviation. Combining the data from the sliding windows of three probes enabled us to establish the boundaries within which the polymorphisms were contained. To predict the precise position of SNPs, we used an empirically determined model of loss of hybridization based on the SNP position in probes. An F-test was then performed with the model, based on the null hypothesis of the mean equaling zero, in order to position the polymorphism prediction at the peak of the p-value.
additional results files: Sal1-vs-IQ07_p-values.txt
Sal1-vs-IQ07_p-values.txt contains the p-value that three consecutive overlapping probes contain a polymorphism in sample IQ07 when compared to the reference hybridizations of Sal1 using a z-test (Dharia et al 2009).

molecule: genomic DNA

organism: Plasmodium vivax

source_name: Genomic DNA from Sal1 reference

label_protocol: Twenty µg of genomic DNA from each amplification reaction (Sal1 in replicate and IQ07) and 2.5 ng each of Bio B, Bio C, Bio D and Cre Affymetrix control plasmids were fragmented with DNaseI and end-labeled with biotin.

growth_protocol: First, several hundred nanograms of pure P. vivax Sal1 DNA (the genome sequencing project reference strain) was obtained from John Barnwell at the Centers for Disease Control and Prevention. Secondly, we obtained P. vivax DNA isolated from a Peruvian patient known to have P. vivax malaria (IQ07). The material was derived from 5 ml of whole blood that had been obtained with informed consent. White blood cells were removed using a Whatman CF11 column (Whatman PLC, Kent, UK).

extract_protocol: The DNA extraction was performed using the Qiagen DNeasy Blood and Tissue Kit (#69504).

tag: reference

value: Genomic DNA hybridization of Sal1


title: Endometrium group B hCG not pregnant 3


title: submandibular gland knockout rep1A


title: Sal1_1_REFERENCE

scan_protocol: The samples were hybridized to the microarrays overnight at 45°C using Affymetrix kits following manufacturer’s instructions, washed, and scanned.


title: Control_1

first: Mark

middle: J

last: Arends

address: Hills Road

department: Pathology

institute: University of Cambridge

description:
replicate 1
M-Control-DMH_1

hyb_protocol: A total of 0.75 µg of biotin-labeled cRNA was hybridised at 58C for 16 h to Illumina’s Sentrix MouseRef-6 Expression Bead-Chips (Illumina, San Diego, CA). The arrays were washed, blocked and the labelled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: The arrays were scanned using an Illumina BeadStation 500× Genetic Analysis Systems scanner and the image data extracted using the Illumina BeadStudio software, Version 3.0.

data_processing: Data files generated from Illumina BeadStudio software were imported into Genespring GX version 10.0 (Agilent, Santa Clara, CA, USA). The raw signals were thresholded to 1.0 and normalisation was carried out using the percentile shift algorithm and this was followed by baseline transformation to the median of all the samples. Hierarchical clustering was carried out with in house clustering software using the Pearson uncentered similarity measure and Ward linkage algorithm. Pathway analysis of the up and down regulated genes between the Kras mutants and controls were carried out using Ingenuity Pathway analysis (Ingenuity Systems, CA, USA).

source_name: colorectal tissue

label_protocol: 0.5 µg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA isolation was carried out using the Qiagen RNeasy Mini Kit for animal tissues (Qiagen, Valencia, CA). The RNA quality and quantity was checked using an Agilent 2100 bio-analyzer and RNA 6000 nano-chips. Total RNA was used to generate biotin labeled cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX).

value: colorectal tissue


title: A22

description: Biological replicate

value: 2 days old, unmated

value: XXYcongo


title: IQ07

source_name: Genomic DNA from Peruvian patient isolate

tag: test

value: Genomic DNA hybridization of Peruvian isolate


title: Endometrium group B hCG not pregnant 2


title: Control_2

description:
replicate 2
M-Control-DMH_2


title: Control_3

description:
replicate 3
M-Control-DMH_3


title: A15

description: Biological replicate


title: Endometrium group B hCG not pregnant 1


title: BM-MSC_rep 1

description: BM-MSC from patient


title: Endometrium group A rFSH not pregnant 3

source_name: Endometrium on day of oocyte retrieval, group A, not pregnant

value: rFSH


title: Endometrium group A rFSH not pregnant 5


title: A01

description: Biological replicate


title: submandibular gland wild type rep1A

value: female

value: 2 months


title: LYVE-1 negative macrophages, rep 2

city: Adelaide

first: Emma

last: Gordon

state: South Australia

address: Frome Road

department: Haematology

country: Australia

institute: SA Pathology

description: Gene expression data from embryonic skin macrophages

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G and GCOS software v1.4

data_processing: The data were analyzed with Partek Genomics Suite v6.3 (RMA) using quantile normalization and median polish probeset summarization.

source_name: WT mouse skin LYVE-1 negative macrophages

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix Genearray protocol from 100ng total RNA (Affymetrix GeneChip Whole Transcript [WT] Sense Target Labeling Assay, rev 4, Affymetrix 2005-2007).

growth_protocol: Wild-type embryos were collected at embryonic day 15.5.

extract_protocol: Extraction of RNA was performed using RNAqueous (Ambion) according to manufacturer's instructions.

treatment_protocol: Embryonic skin was dissected in HHF (HBBS with HEPES and FBS) and digested in 5 ml of digestion buffer (DMEM with FBS with Collagenase II (Worthington), Collagenase IV (Worthington) and Deoxyribonuclease I (Worthington)) per 5-8 embryos. Digestion was performed at 37°C for 30 min. Macrophages were isolated on the basis of F4/80 expression using a magnetic cell separation procedure (MACS®) (Miltenyi Biotec) according to manufacturers instructions. F4/80-positive macrophages were separated on the basis of LYVE-1 expression using a MACS® procedure (Miltenyi Biotec) according to manufacturers instructions.

value: embryonic day 15.5


title: Kras_mut_3

description:
replicate 3
M-RMG_EGFP_Cre-DMH_3


title: LYVE-1 positive macrophages, rep 3

source_name: WT mouse skin LYVE-1 positive macrophages


title: A08

description: Biological replicate


title: A13

description: Biological replicate


title: LYVE-1 negative macrophages, rep 3


title: A11

description: Biological replicate


title: Kras_mut_4

description:
replicate 4
M-RMG_EGFP_Cre-DMH_4


title: submandibular gland wild type rep2A

value: wild type


title: A12

description: Biological replicate

value: XXYohio


title: Exp-6 M1-CdhA55(-)647-red vs M1-SF370-555-green

status: Public on Oct 01 2010

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

institute: Ohio State University

description: Comparison of gene expression in the M1-CdhA55(-) mutant vs the parental strain M1-SF370

hyb_protocol: The labeled cDNA-probes (wild-type and mutant strains) were combined and purified using QIAquickTM PCR spin columns (Qiagen). The labeled cDNA was hybridized with the array slide in the hybridization buffer (3xSSC, salmon testes (sonicated and denatured) DNA and 0.25% SDS) at 63C overnight using hybridization chamber (HybrChambTm, GeneMachines). The hybridized array slides were washed consecutively with 1 x SSC, 0.2 x SSC and 0.05 x SSC each with 0.03% SDS.

scan_protocol: Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro software (version 4.0, Axon instruments).

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as " "null". Accordingly, the value for that spot-cell was left empty. The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those showing log2 values > 1.0( up regualted) and Log2 values < 1 (down-regulated), Bioconductors Multtest package provided suitable method (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.

organism: Streptococcus pyogenes

source_name: M1-CdhA55(-) mutant

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

growth_protocol: Todd-Hewitt broth with 0.2% yeast extract

extract_protocol:
Washed mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer
Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes CdhA (SPy0019)(-)mutant expressing trauncated CdhA lacking C-terminal 55 amino acids that constitute a catalytic site/CHAP (Cysteine-histidine containing aminopetidase) domain was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain.

value: M1-CdhA55(-) mutant expressing CdhA lacking C-terminal 55 residues

value: mutant

source_name: M1-SF370 wild type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen).

growth_protocol: Todd-Hewitt broth_late log phase culture

extract_protocol:
Washed wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer
Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

treatment_protocol: Streptococcus pyogenes parent strain type M1 SF370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated from the wild-type strain.


title: submandibular gland knockout rep3A


title: Exp-7 M1-CdhA55(-)647-Red vs. M1-SF370-555-green


title: Exp-5 M1-CdhA55(-)555-green vs M1-SF370-647-red

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type  strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol:
Washed wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNAeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer
Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen).

treatment_protocol: Streptococus pyogenes CdhA (SPy0019)(-)mutant expressing CdhA lacking last 55 amino acids that constitute a catalytic site/CHAP (Cysteine-histidine containing aminopetidase) domain was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain.


title: LYVE-1 positive macrophages, rep 1


title: Endometrium group A rFSH not pregnant 4


title: LYVE-1 positive macrophages, rep 2


title: Exp-3 M1-CdhA55(-)555-green vs M1-SF370-647-red

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild  strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washed Wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNAeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  mutant strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen).

extract_protocol: Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).


title: Endometrium group A rFSH not pregnant 2


title: Exp-9 M1-CdhA(-) mutant vs. M1-SF370 wild-type

description: Comparison of gene expression in the M1-CdhA(-) mutant vs the parental strain M1-SF370

scan_protocol: Scan protocol Signals of the bound reagents on the microarray spots in terms of relative fluorescence values were measured and quantified by a laser scanner (GenePix 4100 ) at 10um/pixel resolution. The resulting images were processed using Gene Pix Pro software (version 4.0, Axon instruments).

data_processing: The web application CARMAweb (Comprehensive R based microarray analysis web service) was used for the normalization and analysis of microarray data. All raw data (in the form of *. GPR files) were uploaded to the web application in the data directory. Using appropriate navigation tree, background correction from the foreground signals was applied and within microarray normalization was achieved using the Lowess method. Genes flagged as bad spots by the scanning software were excluded from the analysis and all flagged spots were termed as "null". The normalized data were then subjected to fold-change analysis and t-statistics using Bioconductor multtest package. This package employs the moderated t-statistics from the LIMMA package (liner models for micro array data) based on bayesian Significantly differentially expressed genes were those showing log2 values > 1.0( up regualted) and Log2 values < 1 (down-regulated), Bioconductors Multtest package provided suitable method (e.g. Benjamini and Hochberg) adjust P values according to multiple hypothesis testing problems.

label: Alexafluor 555

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the   mutant strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washedmutant  streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes CdhA (SPy0019) deletion mutant was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain.

label: Alexafluor 647

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

extract_protocol: Washed wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).

treatment_protocol: Streptococcus pyogenes  wild-type strain M1SF370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated fronm the wild-type strain.

value: M1CdhA(-) mutant


title: Exp-8 M1-CdhA(-) mutant vs. M1-SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the   wild-type strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washed   wild-type  streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

source_name: M1-CdhA(-) mutant

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  mutant strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

extract_protocol: Washed    mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).


title: Exp-10 M1-CdhA(-) mutant vs. M1SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washed  wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

extract_protocol: Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).


title: Kras_mut_1

description:
replicate 1
M-RMG_EGFP_Cre-DMH_1


title: Exp-5 M1-CdhA(-) mutant vs. M1-SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  wild-type strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

treatment_protocol: Streptococcus pyogenes parent strain typeM1 SF370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated fronm the wild-type strain.

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the   mutant  strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,

extract_protocol: Washed  mutant  streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).


title: Endometrium group A rFSH not pregnant 1

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix)

value: endometrium


title: Exp-4 M1-CdhA55(-)647-red vs. M1-SF370-555-green

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant  strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol:
Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer
Washed  mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes CdhA (SPy0019)(-)mutant lacking last 55 amino acids that constitute a catalytic site/CHAP (Cysteine-histidine containing aminopetidase) domain was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain.

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen).

treatment_protocol: Streptococcus pyogenes parent strain type M1 SF370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated fronm the wild-type strain.


title: Exp-11 M1-CdhA(-) mutant vs. M1SF370 wild-type


title: Exp-1 M1-CdhA55(-)555-green vs M1-SF370-647-red

extract_protocol: Washed Wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen RNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

extract_protocol: Washed Mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNAeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).

treatment_protocol: Streptococus pyogenes CdhA55 (SPy0019)(-)mutant expressing CdhA  lacking last 55 amino acids that constitute a catalytic site/CHAP (Cysteine-histidine containing aminopetidase) domain was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain.


title: A04

description: Biological replicate

source_name: Total RNA from XXYcongo female genotype.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure


title: Exp-2 M1-CdhA55(-)647-red vs. M1-SF370-555-green

treatment_protocol: Streptococus pyogenes CdhA55 (SPy0019)(-)mutant expressing CdhA lacking last 55 amino acids that constitute a catalytic site/CHAP (Cysteine-histidine containing aminopetidase) domain was derived from the wild type strain M1SF370 using pFW5 suicide vector containing spectinimycin resistance marker the aad9 gene. Total RNA was isolated from this mutant strain

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen).


title: Exp-4 M1-CdhA(-) mutant vs. M1-SF370 wild-type

source_name: M1-Cdha(-) mutant


title: Kras_mut_2

description:
replicate 2
M-RMG_EGFP_Cre-DMH_2

label_protocol: 0.5 µg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA isolation was carried out using the Qiagen RNeasy Mini Kit for animal tissues (Qiagen, Valencia, CA). The RNA quality and quantity was checked using an Agilent 2100 bio-analyzer and RNA 6000 nano-chips. Total RNA was used to generate biotin labeled cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX).


title: Exp-6 M1-CdhA(-) mutant vs. M1-SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  mutant strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washed  mutant  streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

extract_protocol: Washed   wild-type streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).


title: LYVE-1 negative macrophages, rep 1

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix Genearray protocol from 100ng total RNA (Affymetrix GeneChip Whole Transcript [WT] Sense Target Labeling Assay, rev 4, Affymetrix 2005-2007).

extract_protocol: Extraction of RNA was performed using RNAqueous (Ambion) according to manufacturer's instructions.


title: Exp-7 M1-CdhA(-) mutant vs. M1-SF370 wild-type

source_name: M1CdhA(-) mutant


title: Exp-2 M1-CdhA(-) mutant vs. M1-SF370 wild-type

source_name: M1-SF370 wild-type

extract_protocol: Washed streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

treatment_protocol: Streptococcus pyogenes parent strain typeM1 SF370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated fronm the wild-type strain

extract_protocol: Washed Mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted using Qiagen RNeasy Mini kit ( cat# 74104). RNA was digested with RNAse-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using Nucleic acid Bioanalyzer (Agilent technologies).


title: Exp-3 M1-CdhA(-) mutant vs. M1-SF370 wild-type

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the mutant strain was labeled with Alexafluor-647 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen.

extract_protocol: Washed mutant streptococci were lysed with the amidase enzyme (lysin) and total RNA was extracted  using Qiagen TNAeasy minikit (cat #74104). RNA was digested with RNASe-free DNase-I (Invitrogen) and RNA quality and quantity was analyzed using nucleic acid bionalyzer (Agilent technologies).

label_protocol: From the total RNA, cDNA was synthesized using random hexamer, dNTPs (except that dTTP was replaced by the same amount of amino-allyl dUTP to incorporate dUTP into first-strand cDNA) and each reverse transcriptase reaction (Superscript II Reverse Transcriptase, Invitrogen). The amino allyl-modified cDNA was purified using QIAquick PCR spin columns (Qiagen). Purified cDNA from the  wild-type strain was labeled with Alexafluor-555 in 0.3M sodium carbonate (pH=9.0) for 1 h (dark) according to the manufacturer’s instructions (Molecular probes/Invitrogen,


title: activated murine splenic natural killer cells 3

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description:
2-NK IL15 24h 1e6 8/1/2007
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase

hyb_protocol: Labeled RNA was mixed into Hi-RPM Hyb Buffer (Agilent), applied to arrrays and inclubated at 55C for 20h

scan_protocol: Agilent DNA Micorarray Scanner

data_processing: Images were gridded and analyzed using Agilent feature extraction software version 9.5.3.1

source_name: murine splenic natural killer cells

label_protocol: Total RNA (100 ng) was  dephosphorylated with Calf Intestine Alkaline Phosphatase and then denatured in 100% DMSO.  Samples were labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase. Labeled RNAs were purified with Micro Bio-Spin 6 columns

growth_protocol: Spleens were harvested from 8-12 week old mice, single cell suspensions were generated by pressing through sterile 70 uM nylon mesh, and RBCs were lysed using ACK lysis buffer.  Viable splenocytes were stained with anti-mouse NK1.1 (PK136) and CD3 (145-2C11) mAbs and sorted by flow cytometry.

extract_protocol: Total RNA was extracted from NK cell lysates using the Trizol reagent according to the manufacturer’s instructions.

treatment_protocol: Purified NK cells were treated with 24 hour stimulation with recombinant murine IL-15 (100 ng/mL) or vehicle.

value: spleen

tag: developmental stage

value: adult

value: murine splenic natural killer cells


title: activated murine splenic natural killer cells 4

description:
4-NK IL15 24h 8/4/07
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: resting murine splenic natural killer cells 2

description:
516_2_0
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase

value: vehicle


title: resting murine splenic natural killer cells 4

description:
3-NK Rest 8/3/07
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: Exp-1 M1-CdhA(-) mutant vs. M1-SF370 wild-type

treatment_protocol: Streptococcus pyogenes parent strain typeM1 Sf370 was obtained from ATCC and grown to late logphase culture. Total RNA was isolated fronm the wild-type strain


title: activated murine splenic natural killer cells 2

description:
516_2_24
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: resting murine splenic natural killer cells 3

description:
1-NK Rest 1e6 7/31/2007
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: resting murine splenic natural killer cells 1

description:
516_1_0
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: activated murine splenic natural killer cells 1

description:
516_1_24
total RNA was labeled by ligation of one Cyanine 3-pCP molecule to the 3’ end by T4 RNA Ligase


title: DeltaADCR_vsWT_rep3

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate

hyb_protocol: Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer. Samples were heated for 3 min at 95C, chilled on ice for 3 min, and applied to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed for 5 min in prewarmed (30C) buffers. Buffer 1: 2X SSC, 0.1% SDS; Buffer 2: 1X SSC; Buffer 3: 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm. Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio ~ 1.0). Images were analyzed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Data were analyzed using software from the TM4 Microarray Software Suite (www.tm4.org). GenePix results files (.gpr) were converted to TIGR MultiExperiment Viewer file format (.mev) using ExpressConverter 2.1 software. Lowess (block) normalization was performed on non-background subtracted data using TIGR MIDAS 2.21 software. Spots flagged as bad (A=0 non-saturated pixels in spot; X= rejected due to spot shape and intensity relative to background) were removed from the analysis.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39 rpsL1 (Winkler lab strain IU1781)

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2

extract_protocol: Total RNA was extracted at OD620~0.2 using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: No treatment

value: virulent, capsule-producing serotype 2 strain D39 (NCTC 7466) transformed with rpsL1 allele

source_name: S. pneumoniae D39 rpsL1 delta adcR (Winkler lab strain IU2594)

value: adcR deletion mutant

value: virulent, capsule-producing serotype 2 strain IU1781 in which the adcR gene (spd2000) was deleted


title: DeltaADCR_vsWT_rep2

description: Independent biological replicate, dye swap


title: DeltaADCR_vsWT_rep1

description: Independent biological replicate


title: Embryonic Drosophila cells, Kc167 cells, DWG DamID, replicate 2 [DamID; reanalyzed for GSE22069]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Renormalized GSM509094
M2.DWG

hyb_protocol: Hybridizations were done using standard protocols (see http://microarrays.nki.nl/download/protocols.html).

scan_protocol: Microarrays were scanned in an Agilent scanner.

data_processing: Values of all reporters except NimbleGen control reporters were extracted from pair files, represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values from 2 replicates were median centered and averaged.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing DWG-Dam

label_protocol: 1 µg DamID DNA was directly labeled by Klenow random priming with Cy5/Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html) at NimbleGen, Reykjavik.

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWC-Dwg-MycDam (this study) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003).

treatment_protocol: Cells transfected with 20 μg DWG-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: embryo

tag: dam fusion

value: DWG

value: untreated

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: Dam only


title: Embryonic Drosophila cells, Kc167 cells, BEAF32B DamID, replicate 1 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509095
M1.BEAF32

source_name: Embryonic Drosophila cells, Kc167 cells, expressing BEAF32B-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWC-Beaf32B-MycDam (van Steensel B. et al., Genome Res. [Epub ahead of print]) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg BEAF32-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2.


title: Embryonic Drosophila cells, Kc167 cells, BEAF32B DamID, replicate 2 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509096
M2.BEAF32


title: Embryonic Drosophila cells, Kc167 cells, DWG DamID, replicate 1 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509093
M1.DWG


title: H3K9me2 ChIP replicate 1 [ChIP]

description: H3K9me2 ChIP untreated Kc167 cells

hyb_protocol: 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively.

scan_protocol: Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area.

data_processing: Scans were processed with NimbleScan 2.3 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios, normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate') and then median centered. All four scan intensities were processed in that way, and the highest intensity not suffering from overt saturation in either replicate was retained and used for further analyses.

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP fraction

label_protocol: 1 µg purified methyl-PCR or ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C.

extract_protocol: For DamID samples, sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003). All ChIP experiments and the subsequent linear amplification reactions were performed as described in Kind, J. et al., Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133, 813-828, 2008.

tag: chip antibody

value: anti-H3K9me2 (abcam 1220)

source_name: Embryonic Drosophila cells, Kc167 cells, input

value: none (input chromatin)


title: Embryonic Drosophila cells, Kc167 cells, CTCF DamID, replicate 2 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509088
M2.CTCF

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-CTCF

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWNDamMyc-CTCF (this study) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam-CTCF expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: CTCF


title: Embryonic Drosophila cells, Kc167 cells, SU(HW) DamID, replicate 1 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509089
M1.SU.HW.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SU(HW)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWNDamMyc-su(Hw) (van Steensel B. et al., Genome Res. [Epub ahead of print] ) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam-SU(HW) expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: SU(HW)


title: H3K27me3 ChIP replicate 2 [ChIP]

description: H3K27me3 ChIP untreated Kc167 cells

value: anti-H3K4me2 (upstate 07-449)


title: H3K27me3 ChIP replicate 1 [ChIP]

description: H3K27me3 ChIP untreated Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, GAF DamID, replicate 2 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509092
M2.GAF

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-GAF

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc-Gaf (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12027-32.) was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Dam-GAF expression plasmid/2*10e6 cells on day 1; harvested on day 2.

value: GAF


title: Embryonic Drosophila cells, Kc167 cells, GAF DamID, replicate 1 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509091
M1.GAF


title: Embryonic Drosophila cells, Kc167 cells, CTCF DamID, replicate 1 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509087
M1.CTCF


title: H3K9me2 ChIP replicate 2 [ChIP]

description: H3K9me2 ChIP untreated Kc167 cells


title: H3 ChIP replicate 1 [ChIP]

description: Histone H3 ChIP untreated Kc167 cells

value: anti-H3 (abcam 1791)


title: H1 ChIP replicate 2 [ChIP]

description: Histone H1 ChIP untreated Kc167 cells

value: anti-H1, affinity purified (Braunschweig et al., EMBO J 28, 3635-3645, 2009)


title: TOP1 replicate 2 [DamID]

description: TOP1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing TOP1-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWMycDam-TOP1 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg TOP1-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

tag: dam-fusion

treatment_protocol: Cells transfected with 20 μg Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Gal4-DBD replicate 1 [DamID]

description: Gal4-DBD DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-Gal4-DBD

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-Gal4-DBD was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg Gal4-DBD-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: H3 ChIP replicate 2 [ChIP]

description: Histone H3 ChIP untreated Kc167 cells


title: Gal4-DBD replicate 2 [DamID]

description: Gal4-DBD DamID untreated Kc167 cells


title: H1 ChIP replicate 1 [ChIP]

description: Histone H1 ChIP untreated Kc167 cells


title: H3K4me2 ChIP replicate 2 [ChIP]

description: H3K4me2 ChIP untreated Kc167 cells

value: anti-H3K4me2 (upstate 07-030)


title: H3K4me2 ChIP replicate 1 [ChIP]

description: H3K4me2 ChIP untreated Kc167 cells


title: TIP60 replicate 1 [DamID]

description: TIP60 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing TIP60-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWMycDam-TIP60 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg TIP60-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: Embryonic Drosophila cells, Kc167 cells, SU(HW) DamID, replicate 2 [DamID; reanalyzed for GSE22069]

description:
Renormalized GSM509090
M2.SU.HW.


title: TBP replicate 2 [DamID]

description: TBP DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-TBP

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-TBP was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg TBP-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-TBP


title: TOP1 replicate 1 [DamID]

description: TOP1 DamID untreated Kc167 cells


title: TBP replicate 1 [DamID]

description: TBP DamID untreated Kc167 cells


title: TIP60 replicate 2 [DamID]

description: TIP60 DamID untreated Kc167 cells


title: SU(VAR)3-9 replicate 2 [DamID]

description: SU(VAR)3-9 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SU(VAR)3-9-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-SU(VAR)3-9 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg (SU(VAR)3-9-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: SU(VAR)3-9 replicate 1 [DamID]

description: SU(VAR)3-9 DamID untreated Kc167 cells


title: SU(VAR)3-7 replicate 1 [DamID]

description: SU(VAR)3-7 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SU(VAR)3-7

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-SU(VAR)3-7 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg (SU(VAR)3-7-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: SUUR replicate 2 [DamID]

description: SUUR DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SUUR

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-SUUR was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SUUR-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-SUUR


title: SIR2 replicate 2 [DamID]

description: SIR2 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing SIR2-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-SIR2 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SIR2-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: SIN3A replicate 1 [DamID]

description: SIN3A DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SIN3A

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pDamMyc-SIN3A was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SIN3A-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: SUUR replicate 1 [DamID]

description: SUUR DamID untreated Kc167 cells


title: SU(VAR)2-10 replicate 1 [DamID]

description: SU(VAR)2-10 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-SU(VAR)2-10

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-SU(VAR)2-10 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg SU(VAR)2-10-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2


title: SU(VAR)3-7 replicate 2 [DamID]

description: SU(VAR)3-7 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-only


title: PHO replicate 1 [DamID]

description: PHO DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing PHO-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-PHO was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PHO-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: PHO-Dam


title: SIR2 replicate 1 [DamID]

description: SIR2 DamID untreated Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000)  was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: RPD3 replicate 2 [DamID]

description: RPD3 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RPD3-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pMycDam-RPD3 was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg RPD3-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 7


title: PCL replicate 2 [DamID]

description: PCL DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PCL

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pCreDamMyc-PCL was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PCL-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-PCL


title: PHO replicate 2 [DamID]

description: PHO DamID untreated Kc167 cells


title: PCAF replicate 2 [DamID]

description: PCAF DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-PCAF

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pGWDamMyc-PCAF was transfected into Kc cells as described (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

treatment_protocol: Cells transfected with 20 μg PCAF-Dam expression plasmid/2*10e6 Cells on day 1; harvested on day 2

value: Dam-PCAF


title: SU(VAR)2-10 replicate 2 [DamID]

description: SU(VAR)2-10 DamID untreated Kc167 cells