title: beta-cells_non-diabetic condition_surgical specimen4

description:
Gene expression data from surgical samples
Surgical-795


title: Testis, WT, biological replicate 1

status: Public on Jun 02 2010

type: RNA

city: Oslo

first: Anja

last: Nilsen

address: Sognsvannsveien 20

country: Norway

institute: University of Oslo

description: Gene expression data

hyb_protocol: 15 ug of biotinylated and fragmented cRNA samples were hybridized on to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix) according to manufacturers protocols (Affymetrix)

scan_protocol: GeneChip® Scanner 3000 (GCS 3000)

data_processing: QCs including scale factor, background, noise, spikes and RNA degradation were checked and validated using the yaqcaffy library (http://www.bioconductor.org/packages/2.3/ bioc/ vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf). Affymetrix raw data was generated with GCOS 1.4 (GeneChip operating  software, Affymetrix)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse testis from wild type with C57/BL6 genetic background

label_protocol: Biotinylated cRNA was synthesized using the One-Cycle Target labelling and Control kit (Affymetrix)

growth_protocol: Mouse testes were dissected from 12 week old mice

extract_protocol: Whole testes were snap frozen in liquid nitrogen. Total RNA was prepared using Trizol. RNA quality was checked on the Bioanalyser Agilent 2100. All the RNA samples had RIN values between 9.8 and 10.

tag: tissue

value: testis

tag: genotype

tag: age

value: 12 weeks


title: Testis, WT, biological replicate 2

description: Gene expression data


title: HeLa_Control (Cy5)_HeLa_MALAT-1 (Cy3)_Replication 1

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description:
Mammalian non-coding transcript
Hela Malat 100-2

hyb_protocol: Hybridization_Kit: Agilent in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Agilent Feature Extraction ver 9.5, normalized (lowess and rank consistency)

organism: Homo sapiens

source_name: HeLa MALAT-1 Cy3

label_protocol: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Cells were grown at 37°C, 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% fetal calf serum and penicillin/streptomycin

extract_protocol: Invitrogen Trizol reagent

treatment_protocol: To carry out RNA interference, siRNA duplexes, synthesized by SIGMA or Invitrogen were transfected into cells using Lipofectamine RNAi MAX (Invitrogen) according to the manufacturer's guidelines

tag: cell line

value: HeLa TO cells

tag: protocol

value: MALAT-1 knockdown

tag: sirna

source_name: HeLa Control-1 Cy5

treatment_protocol: Control

value: control


title: Caseum 2-C

city: Ithaca

first: Mi-Jeong

last: Kim

state: NY

address: C5 104 VMC Cornell University

department: Microbiology and Immunology

country: USA

institute: Cornell University

description: Gene expression data from caseous human pulmonary TB granuloma

hyb_protocol: Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C.  Genechips were washed and stained in Affymetrix Fluidics Station FS450.

scan_protocol: Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays.  The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program.  MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.

source_name: Caseous human pulmonary TB granuloma

label_protocol: Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).

growth_protocol: Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.

extract_protocol: Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).

treatment_protocol: Cryosections were made from human lung tissues.  After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection.  The dissected materials were stored at -80°C until further processing.

value: caseous granuloma


title: Oligodendrocytes_R4 vs. Astrocytes_R4

status: Public on Jun 01 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Oligodendrocytes_R4 vs. Astrocytes_R4

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). Images were quantified using the software 'Automic Imageprocessing for Microarrays'[Katzer, Mathias (2004) Automatisches Segmentieren von Microarraybildern. Dissertation, Faculty of Technology, Bielefeld University]

data_processing: Log2-ratios between the Hy3/Hy5 have been provided. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm using R 2.5 (limma package).

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit

growth_protocol: Preparation of mouse oligodendrocyte primary cultures was performed as described previously (Trajkovic et al., 2006). After 10 to 14 days, oligodendrocytes were shaken off the mixed glial cultures. Afterwards the cultures without oligodendrocytes, but containing astrocytes and microglia, were maintained in DMEM with 10% FCS. 7-10 days after shaking of oligodendrocytes another shaking of the culture released the microglia from the astrocyte layer. Microglia were harvested at this point. Primary astrocytes were harvested by trypsination after oligodendrocytes and microglia were shaken off.

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

treatment_protocol: No treatment but different cell types were analysed.

tag: strain

tag: cell type

value: Oligodendrocytes

value: Astrocytes


title: Caseum 2-A


title: HeLa_Control (Cy3)_HeLa_MALAT-1 (Cy5)_Replication 1

description:
Mammalian non-coding transcript
Hela Malat 100-1

source_name: HeLa Control Cy3

source_name: HeLa MALAT Cy5


title: HeLa_Control (Cy3)_HeLa_MALAT-1 (Cy5)_Replication 2

description:
Mammalian non-coding transcript
Hela Malat 126-3

value: stealth MALAT483


title: Testis, WT, biological replicate 3

description: Gene expression data


title: Testis, Alkbh1 KO, biological replicate 2

description: Gene expression data

source_name: Mouse testis from Alkbh1 knock-out with C57/BL6 genetic background


title: Normal-B

description: Gene expression data from human normal lung parenchyma

source_name: Normal lung parenchyma

value: normal lung parenchyma


title: beta-cells_non-diabetic condition_surgical specimen3

city: Boston

first: Lorella

last: Marselli

state: MA

address: One Joslin Place

department: Joslin Diabetes Center and the Department of Medicine

institute: Harvard Medical School

description:
Gene expression data from surgical samples
Surgical-824

hyb_protocol: Biotinylated cRNA was fragmented to nucleotide stretches of 30-200 nucleotides and hybridized for 16hr at 45C to the Affymetrix Human X3P array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.

source_name: human beta-cells_non-diabetic

label_protocol: Amplified RNA  was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).

extract_protocol: Total RNA was extracted from each population of laser captured β–cells using PicoPure RNA Isolation Kit (Arcturus) and amplified by T7-based linear amplification using T7-oligo-dT-primers. RNA amplification was performed using RiboAmp HS RNA Amplification Kit (Arcturus) following the manufacture’s protocol.

treatment_protocol: Pancreas specimens obtained from surgical samples and islet grafts recovered from the transplanted mice were placed in cryomolds, embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed in diethylpyrocarbonate (DEPC)-treated water for 30 sec, and dehydrated in 70% ethanol for 30 sec, 100% ethanol (rinsing), 100% ethanol twice for 1 min, and xylene for 4 minutes. Sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer for 30 minutes at 42°C, and the samples stored at -80°C.

value: pancreatic islets

value: beta-cell

value: non-diabetic condition

tag: gender

value: male

tag: age (years)

tag: bmi (body mass index, kg/m2)


title: HeLa_Control (Cy5)_HeLa_MALAT-1 (Cy3)_Replication 2

description:
Mammalian non-coding transcript
Hela Malat 126-4


title: Caseum 2-B


title: Testis, Alkbh1 KO, biological replicate 1

description: Gene expression data


title: Astrocytes_R1 vs. Oligodendrocytes_R1

description: Astrocytes1 vs. Oligodendrocytes_R1


title: tomato PI365967 salt stressed 5 h rep3.

city: Beijing

first: Wei

last: Sun

address: 20 Nan Xin Cun

country: China

institute: Institute of Botany, Chinese Academy of Sciences

description: 6-leaf-old whole plant of PI365967, salt stressed for 5 h.

hyb_protocol: The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Tomato Genome Arrays according to the protocols provided by the manufacturer. Immediately following hybridization, the probe array underwent an automated washing and staining protocol on the fluidics station 450.

scan_protocol: Then arrays were scanned with Affymetrix® GeneChip® Scanner 3000, and the resulting images were analyzed with Affymetrix® GeneChip® Operating Software (GCOS 1.4).

data_processing: A dChip normalization method was employed to normalize the ratio values. Normalized ratio data were then log transformed. Differentially expressed genes were identified using SAM software and multiple test corrections were performed using False Discovery Rate (FDR).

organism: Solanum lycopersicum

source_name: PI365967, salt stressed, 5 h

label_protocol: 10 μg total RNA was first reverse transcribed using a T7-Oligo (dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

growth_protocol: Seeds of uniform size were surface-sterilized by soaking in 70% (v/v) ethanol for 2 min, then in 2.63% (w/v) NaOC1 for 30 min, and finally rinsed five times with sterile distilled water. The seeds were sown in petri dish containing 10 ml of double distilled H2O and germinated under 16 hr light (1500 lux) at 26℃ in a growth chamber. 7 d later, seedlings were planted in pots containing sterile sand supplemented with 1/4-strength Hoagland solution in a greenhouse.

extract_protocol:
In one treatment, 9 six-leaf-old tomato plants were divided into three biological replicates and treated hydroponically under sterile condition with 200 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip.
Total RNA was isolated using a hot phenol method (Kay et al., 1987).

treatment_protocol: For salt treatment, 4-week-old plants were transferred to aerated hydroponic tanks containing 1/4- strength Hoagland solution in a greenhouse. After acclimating for 3 d, tomato plants having six true leaves were treated with fresh 1/4-strength Hoagland solution with 200 mM NaCl.

tag: age of plant

value: whole plant

tag: treatment

value: salt stress

tag: treatment time


title: tomato PI365967 unstressed 5 h rep2.

description: 6-leaf-old whole plant of PI365967, unstressed for 5 h as a control.

source_name: PI365967, unstressed, 5 h

extract_protocol:
In one treatment, 9 six-leaf-old tomato plants were divided into three biological replicates and treated hydroponically under sterile condition with 0 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip.
Total RNA was isolated using a hot phenol method (Kay et al., 1987).

treatment_protocol: For salt treatment, 4-week-old plants were transferred to aerated hydroponic tanks containing 1/4- strength Hoagland solution in a greenhouse. After acclimating for 3 d, tomato plants having six true leaves were treated with fresh 1/4-strength Hoagland solution with 0 mM NaCl.

value: unstress


title: Testis, Alkbh1 KO, biological replicate 3

description: Gene expression data

value: testis


title: tomato PI365967 unstressed 5 h rep3.


title: Normal-A


title: tomato PI365967 salt stressed 5 h rep2.


title: tomato Moneymaker salt stressed 5 h rep3.

description: 6-leaf-old whole plant of Moneymaker, salt stressed for 5 h.

source_name: Moneymaker, salt stressed, 5 h

value: Moneymaker


title: Caseum 3


title: Caseum 1


title: tomato Moneymaker unstressed 5 h rep3.

description: 6-leaf-old whole plant of Moneymaker, unstressed for 5 h as a control.

source_name: Moneymaker, unstressed, 5 h


title: tomato PI365967 salt stressed 5 h rep1.


title: mature oligodendrocytes d6_Rep1

description: mature oligodendrocytes d6_Rep1

hyb_protocol: Refer to Agilent miRNA hybridisation protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B). Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Data were processed using alogorithms specified by the Agilent Feature Extraction software (version A.8.5.1.1). Subsequent statistical analysis (detection of candidates using linear models) of data were carried out using R.

source_name: mature oligodendrocytes d6_Rep1

label_protocol: Refer to Agilent miRNA labeling protocol

growth_protocol: Preparation of mouse oligodendrocyte primary cultures were performed as described previously (Simons et al., 2000). After shaking, cells were plated in Dulbecco's modified Eagle's medium (DMEM) with B27 supplement, 1% horse serum, L-thyroxine, tri-iodo-thyronine, glutamine and pyruvate on poly-L-lysinecoated dishes or glass coverslips.

treatment_protocol: No treatment but different time points were analyzed.

tag: genotype/variation

value: CNP-Cre

value: oligodendrocytes

tag: time point

tag: differentiation status

value: Mature


title: tomato Moneymaker salt stressed 5 h rep2.

tag: tissue


title: tomato Moneymaker unstressed 5 h rep2.

tag: genotype


title: tomato PI365967 unstressed 5 h rep1.


title: Immature oligodendrocytes d1_Rep2

description: Immature oligodendrocytes d1_Rep2

source_name: Immature oligodendrocytes d1_Rep2

value: Immature


title: mature oligodendrocytes d6_Rep2

description: mature oligodendrocytes d6_Rep2

source_name: mature oligodendrocytes d6_Rep2


title: mature oligodendrocytes d6_Rep3

description: mature oligodendrocytes d6_Rep3

source_name: mature oligodendrocytes d6_Rep3


title: Immature oligodendrocytes d0_Rep3

description: Immature oligodendrocytes d0_Rep3

source_name: Immature oligodendrocytes d0_Rep3


title: tomato Moneymaker salt stressed 5 h rep1.


title: Immature oligodendrocytes d0_Rep2

description: Immature oligodendrocytes d0_Rep2

source_name: Immature oligodendrocytes d0_Rep2


title: Immature oligodendrocytes d0_Rep1

description: Immature oligodendrocytes d0_Rep1

source_name: Immature oligodendrocytes d0_Rep1


title: Immature oligodendrocytes d1_Rep1

description: Immature oligodendrocytes d1_Rep1

source_name: Immature oligodendrocytes d1_Rep1


title: Nipponbare genome 40μg hydridization rep2

type: genomic

city: Mishima

first: Nori

last: Kurata

address: 1111 Yata

institute: National Institute of Genetics

description: Genome hybridization using total DNA from Nipponbare

hyb_protocol: Biotinylated fragments were treated the same as labeled cRNA in Affymetrix standard hybridization protocols. Biotinylated fragments were mixed in 〜225 µl with a final concentration of 0.1 mg/ml sonicated herring sperm DNA in a hybridization buffer with 100 mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCl, 20 mM EDTA and 0.01% Tween 20, denatured at 99ºC for 5 min and equilibrated at 45ºC for 5 min prior to hybridization. The hybridization mixture was hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm according to Affymetrix standard procedure. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray 3000 scanner.

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: Nipponbare genomic DNA

label_protocol: The biotin (biotin-dCTP) labeled DNA was prepared from 300ng purified DNA using bio-prime labeling kit (Invitrogen).

extract_protocol: genomic DNA was isolated from leaves by Qiagen DNA easy plant Mini kit.

value: leaves

tag: cultivar

value: Nipponbare


title: 9311 genome 40μg hydridization rep3

description: Genome hybridization using total DNA from 9311

organism: Oryza sativa Indica Group

source_name: 9311 genomic DNA


title: Nipponbare genome 40μg hydridization rep3


title: tomato Moneymaker unstressed 5 h rep1.

value: 5 h


title: 9311 genome 40μg hydridization rep2


title: 9311 genome 40μg hydridization rep4


title: Nipponbare genome 5μg hydridization rep4


title: 9311 genome 40μg hydridization rep1


title: 9311 genome 5μg hydridization rep2

hyb_protocol: Biotinylated fragments were treated the same as labeled cRNA in Affymetrix standard hybridization protocols. Biotinylated fragments were mixed in 〜225 µl with a final concentration of 0.1 mg/ml sonicated herring sperm DNA in a hybridization buffer with 100 mM 2-N-morpholino-ethane-sulphonic acid (MES), 1 M NaCl, 20 mM EDTA and 0.01% Tween 20, denatured at 99ºC for 5 min and equilibrated at 45ºC for 5 min prior to hybridization. The hybridization mixture  was hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm according to Affymetrix standard procedure. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station 450.

label_protocol: The biotin (biotin-dCTP) labeled  DNA was prepared from 300ng purified DNA using bio-prime labeling kit (Invitrogen).


title: 9311 genome 5μg hydridization rep1


title: Nipponbare genome 5μg hydridization rep3


title: Nipponbare genome 40μg hydridization rep4


title: 9311 genome 5μg hydridization rep4


title: Nipponbare genome 5μg hydridization rep2


title: Nipponbare genome 1μg hydridization rep1


title: 9311 genome 5μg hydridization rep3


title: 9311_shoot 3-4weeks, biological rep2

description: Gene expression data from rice shoot

hyb_protocol: According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.

source_name: shoot 3-4weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was isolated and purified by RNeasy Plant Mini Kit (QIAGEN)

value: shoot


title: Nipponbare_shoot 3-4weeks, biological rep5

description: Gene expression data from rice shoot


title: 9311_shoot 3-4weeks, biological rep4

description: Gene expression data from rice shoot


title: Nipponbare genome 40μg hydridization rep1


title: 9311_shoot 3-4weeks, biological rep3

description: Gene expression data from rice shoot


title: 9311_shoot 3-4weeks, biological rep5

description: Gene expression data from rice shoot


title: 9311_shoot 3-4weeks, biological rep1

description: Gene expression data from rice shoot


title: Nipponbare_shoot 3-4weeks, biological rep1

description: Gene expression data from rice shoot


title: Nipponbare_shoot 3-4weeks, biological rep2

description: Gene expression data from rice shoot


title: Nipponbare_shoot 3-4weeks, biological rep3

description: Gene expression data from rice shoot


title: TACSTD2.1.72h.5

first: Marian

last: Grade

address: Robert-Koch-Str. 40

department: Surgery

institute: University Medical Center Goettingen, Georg-August-University

description: siRNA-mediated knockdown of TACSTD2

hyb_protocol: After a two-hour reaction, 1.5 μg of purified, Cy3-labeled cRNA were hybridized to an oligonucleotide Whole Human Genome Microarray (4x44K, Agilent Technologies) for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner, and data were extracted using the Feature Extraction software version 9.5.1 (Agilent Technologies).

data_processing: Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: SW480, TACSTD2 knockdown, 72h after treatment

label_protocol: 600 ng of total RNA were reverse-transcribed and amplified, thereby incorporating Cyanine 3-CTP nucleotides, using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent One-Color Microarray-Based Gene Expression Analysis, protocol version 5.5, February 2007; Agilent Technologies).

growth_protocol: Cells were grown in RPMI-1640 containing 10% FBS and 1% Penecillin/Streptomycin.

extract_protocol: After transfection (48h or 72h), total RNA was isolated using TRIzol (Invitrogen, Gaithersburg, MD), and purified using the RNeasy Mini kit (Qiagen, Germantown, MD).  A detailed protocol can be found at www.riedlab.nci.nih.gov/.  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Only RNA samples with a RNA integrity number between 9.0 and 10.0 were considered for further analysis.

treatment_protocol: Reverse transfections were performed in 6-well plates. Briefly, 60 pmol siRNAs were diluted in 750 μl serum-free media. Subsequently, 1.8 μl Oligofectamine (Invitrogen, Carlsbad, CA) were mixed with 750 μl serum-free media. These solutions were combined to allow complex formation at ambient temperature. Next, tumor cells were dissolved in 1500 μl serum containing 20% FBS, and added to the reaction (20 nM siRNA). After 45-minute incubation at ambient temperature, plates were kept at 37°C in a humidified 5% CO2 atmosphere.

tag: cell line

value: SW480 human colon adenocarcinoma cell line

value: transfection

tag: targeted gene

tag: time

tag: replicate


title: TACSTD2.1.72h.4

description: siRNA-mediated knockdown of TACSTD2

tag: protocol

tag: sirna


title: RRM2.5.48h.1

description: siRNA-mediated knockdown of RRM2

source_name: SW480, RRM2 knockdown, 48h after treatment


title: TACSTD2.4.72h.5

description: siRNA-mediated knockdown of TACSTD2


title: RRM2.5.48h.2

description: siRNA-mediated knockdown of RRM2


title: TACSTD2.4.72h.6

description: siRNA-mediated knockdown of TACSTD2


title: RRM2.6.48h.3

description: siRNA-mediated knockdown of RRM2


title: RPS2.6.48h.1

description: siRNA-mediated knockdown of RPS2

source_name: SW480, RPS2 knockdown, 48h after treatment


title: RRM2.6.48h.1

description: siRNA-mediated knockdown of RRM2


title: RRM2.5.48h.3

description: siRNA-mediated knockdown of RRM2


title: RRM2.6.48h.2

description: siRNA-mediated knockdown of RRM2


title: NOL5A.5.72h.5

description: siRNA-mediated knockdown of NOL5A

source_name: SW480, NOL5A knockdown, 72h after treatment


title: TACSTD2.4.72h.4

description: siRNA-mediated knockdown of TACSTD2


title: RPS2.5.48h.2

description: siRNA-mediated knockdown of RPS2


title: NOL5A.5.72h.6

description: siRNA-mediated knockdown of NOL5A


title: TACSTD2.1.72h.6

description: siRNA-mediated knockdown of TACSTD2


title: RPS2.6.48h.3

description: siRNA-mediated knockdown of RPS2


title: Nipponbare genome 5μg hydridization rep1


title: NOL5A.1.72h.5

description: siRNA-mediated knockdown of NOL5A


title: Nipponbare_shoot 3-4weeks, biological rep4

description: Gene expression data from rice shoot


title: NOL5A.1.72h.6

description: siRNA-mediated knockdown of NOL5A


title: RPS2.5.48h.3

description: siRNA-mediated knockdown of RPS2


title: RPS2.5.48h.1

description: siRNA-mediated knockdown of RPS2


title: NOL5A.5.72h.4

description: siRNA-mediated knockdown of NOL5A


title: RPS2.6.48h.2

description: siRNA-mediated knockdown of RPS2


title: ICEclc_10mM3CBA_exponential_rep2

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description: Gene expression during mid-exponential phase (OD600=0.5) with 10mM trichlorobenzaote (3CBA) as substrate.

hyb_protocol: 60 ng of labeled cDNA was then loaded onto each microarray, hybridized for 17 hours at 65ºC, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60ºC for 30 minutes) was omitted.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR: Hi:100% and XDR Lo:10%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 020923_D_F_20080708) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were then transported to GeneSpring GX v10.0.2, Generic Single Color experiment, thresholding 1.0, Quantile normalization, no baseline transformation performed.

organism: Pseudomonas knackmussii

source_name: ICEclcB13 in Pseudomonas knackmussii strain B13

label_protocol: cDNA was synthesized from total RNA and directly labeled with cyanine-3-dCTP using a modification of a protocol described elsewhere (Charbonnier et al. 2005). Briefly, each 50-µL reaction contained 10 µg of total RNA, 1.25 µg of random hexanucleotide primers (Promega), 100 µM each of unlabeled dATP, dGTP, and dTTP (Invitrogen), 25 µM of unlabeled dCTP (Invitrogen), 25 µM of cyanine-3-labeled dCTP (Perkin-Elmer), 25 U SUPERase•In (Ambion), and 400 U Superscript II reverse transcriptase (Invitrogen). Reactions were performed by heating at 42ºC for 2 hours followed by 70ºC for 10 min. RNA was then removed by adding 100 mM NaOH, heating to 65ºC for 20 min, and neutralizing with 100 mM HCl and 300 mM sodium acetate (pH 5.2). Labeled cDNA products were purified using the MinElute PCR purification kit (Qiagen) and the quantity and incorporation frequency of cyanine-3-labeled dCTP were calculated using the MICROARRAY function on a NanoDrop Spectrophotometer.

growth_protocol: P. knackmussii B13, the original host of ICEclc, was cultivated in minimal medium (MM) based on the type 21C medium (Gerhardt et al. 1981). This MM was complemented with 10mM 3CBA and the bacteria were grown at 30°C. Bacterial growth was assessed from culture turbidity at 600 nm (OD600). Cells were recovered during exponential phase (OD600 of 0.4) or 48 h after the beginning of the stationary phase. For RNA isolation, 100 ml of culture was immediately harvested by centrifugation (at 15,000 × g for 1 min at 4°C) and the supernatant was decanted. Cell pellets were resuspended in 4 ml RNAprotect Bacteria Reagent (QIAGEN GmbH). After 5 min incubation, the suspensions were centrifuged again (at 5,000 × g for 5 min at room temperature); the supernatant was discarded and pellets were stored at -80°C.

extract_protocol: Prior to RNA extraction, pellets were slowly thawed, then resuspended in 0.5 ml TES buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 mM NaCl], followed by addition of and mixing with 0.25 ml lysis solution [20 mM sodium acetate (pH 5.5), 1 mM EDTA, 0.5% SDS]. After that, the total RNA was further purified by the hot acid-phenol method as described previously [Baumann et al. 1996]. RNA samples were purified from contaminating DNA by treatment with 50 U of DNase I (RNase free; Roche) during 1 h at 37°C. Finally, the RNA was dissolved in 50 µl diethylpyrocarbonate (DEPC)-treated water and quantified by absorbance at 260 and 280 nm on a NanoDrop spectrophotometer (Witec AG). The integrity of RNA was determined by agarose gel electrophoresis and the absence of DNA was verified by PCR.

tag: strain

tag: growth phase

value: exponential phase


title: ICEclc_10mM3CBA_stationary_rep2

description: Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.

value: stationary phase


title: ICEclc_10mM3CBA_stationary_rep3


title: Neg.2.72h.8

description: Transfection with a negative control siRNA

source_name: SW480, Negative Control siRNA, 72h after treatment

value: Negative Control siRNA


title: ICEclc_10mM3CBA_stationary_rep1


title: Neg.0.72h.1

description: Untransfected cells

source_name: SW480, untransfected control, 72h after treatment

value: Untransfected Control


title: NOL5A.1.72h.4

description: siRNA-mediated knockdown of NOL5A


title: Neg.0.72h.2

description: Untransfected cells


title: Neg.2.72h.2


title: Neg.2.48h.8

source_name: SW480, Negative Control siRNA, 48h after treatment


title: Neg.2.72h.4


title: Neg.2.48h.4


title: Neg.2.72h.1


title: Neg.2.72h.6


title: Neg.2.72h.3


title: Neg.2.48h.2


title: Neg.2.72h.7


title: Neg.2.48h.9


title: Neg.0.72h.3

description: Untransfected cells


title: Neg.2.72h.5


title: Neg.2.48h.7


title: Neg.2.48h.6


title: HMGA1.6.48h.3

description: siRNA-mediated knockdown of HMGA1

source_name: SW480, HMGA1 knockdown, 48h after treatment


title: Neg.2.48h.5


title: Neg.2.48h.1


title: HMGA1.6.48h.2

description: siRNA-mediated knockdown of HMGA1


title: ICEclc_10mM3CBA_exponential_rep3


title: Neg.2.48h.3


title: Neg.2.72h.9


title: ICEclc_10mM3CBA_exponential_rep1


title: HMGA1.5.48h.3

description: siRNA-mediated knockdown of HMGA1


title: MALT_Lymphoma_Translocation Negative_16

status: Public on May 31 2010

city: London

first: Rifat

last: Hamoudi

address: 67-73 Riding House Street

country: United Kingdom

institute: University College London

description: Gene expression data was obtained from fresh forzen biopsy at diagnosis.

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 A GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned  at pixel value 3um, wavelength 570 nm using the argon laser scanner the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Batch MAS5 Normalisation on all 24 MALT lymphoma samples ran on the HG-U133A GeneChips was carried out using the MAS5() function within the affy library version 1.20.0 in Bioconductor version 2.0. All MAS5 data were scaled to a target intensity of 100. Bioconductor was run on R version 2.8.0 (2008-10-20). The file was written out and split into each individual sample file with one column for probe and another for the MAS5 normalised value.

label: Biotin

source_name: Gastric MALT lymphoma

label_protocol: Biotin labelling of the cRNA was carried out using the Enzo labelling kit (Enzo life sciences) from 5ug total RNA.

extract_protocol: RNAeasy kit (Qiagen) was used to extract total RNA followed by treatment with Turbo DNAase (Ambion).

tag: lymphoma type

value: Gastric MALT lymphoma

tag: translocations


title: HMGA1.6.48h.1

description: siRNA-mediated knockdown of HMGA1


title: MALT_Lymphoma_Translocation Negative_21


title: HMGA1.5.48h.1

description: siRNA-mediated knockdown of HMGA1


title: MALT_Lymphoma_t(11;18)/API2-MALT1_9

scan_protocol: GeneChips were scanned at pixel value 3um, wavelength 570 nm using the argon laser Hewlett-Packard GeneArray Scanner G2500A.

source_name: Pulmonary MALT lymphoma

value: Pulmonary MALT lymphoma

tag: translocation


title: MALT_Lymphoma_t(11;18)/API2-MALT1_11


title: MALT_Lymphoma_Translocation Negative_22


title: MALT_Lymphoma_Translocation Negative_23


title: MALT_Lymphoma_t(11;18)/API2-MALT1_13


title: MALT_Lymphoma_t(11;18)/API2-MALT1_7


title: MALT_Lymphoma_Translocation Negative_19


title: MALT_Lymphoma_Translocation Negative_17


title: MALT_Lymphoma_t(11;18)/API2-MALT1_8


title: MALT_Lymphoma_Translocation Negative_18


title: MALT_Lymphoma_Translocation Negative_24


title: MALT_Lymphoma_t(11;18)/API2-MALT1_5


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_3


title: MALT_Lymphoma_t(11;18)/API2-MALT1_12


title: Astrocytes_R1 vs. Oligodendrocytes_R1

description: Astrocytes1 vs. Oligodendrocytes_R1

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

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (version A.8.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: Low RNA input Fluor linear Amp Kit 5184-3523(Agilent Technologies)following manufacturer's instructions

tag: cell type

value: Astrocytes

value: Oligodendrocytes


title: MALT_Lymphoma_t(14;18)/IGH-MALT1_15

source_name: Hepatic MALT lymphoma

value: Hepatic MALT lymphoma


title: MALT_Lymphoma_t(11;18)/API2-MALT1_6


title: HMGA1.5.48h.2

description: siRNA-mediated knockdown of HMGA1


title: Oligodendrocytes_R4 vs. Astrocytes_R4

description: Oligodendrocytes_R4 vs. Astrocytes_R4


title: MALT_Lymphoma_t(1;14)/BCL10-IGH_4


title: reduction mammoplasty breast epithelium sample 4

first: Kelly

last: Graham

address: 650 Albany Street

department: Hematology/Oncology

institute: Boston University School of Medicine

description: Gene Expression data from case 278R:Reduction Mammoplasty Epithelium

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: .cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.

source_name: Reduction Mammoplasty Epithelium

label_protocol: T7-based RNA ampliﬁcation was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.

tag: specimen

value: Reduction Mammoplasty

tag: disease state

value: control

value: breast epithelium


title: reduction mammoplasty breast epithelium sample 10

description: Gene Expression data from case 288R:Reduction Mammoplasty Epithelium

tag: tissue


title: MALT_Lymphoma_t(11;18)/API2-MALT1_10


title: Mantle_cell_lymphoma_3

hyb_protocol: Following fragmentation, 15ug of biotinylated cRNA was hybridized for 16 hours at 45 C on Human Genome HG-U133 plus2 GeneChips from Affymetrix. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned  at pixel value 2.5um, using the Affymetrix GeneChip Scanner 3000.

data_processing: Batch MAS5 Normalisation on all 7 follicular lymphoma and 8 mantle cell lymphoma samples ran on the HG-U133 plus2 GeneChips was carried out using the MAS5() function within the affy library version 1.20.0 in Bioconductor version 2.0. All MAS5 data were scaled to a target intensity of 100. Bioconductor was run on R version 2.8.0 (2008-10-20). The file was written out and split into each individual sample file with one column for probe and another for the MAS5 normalised value.

source_name: Lymph node from mantle cell lymphoma patient

label_protocol: Biotin labelling of the cRNA was carried out using the Affymetrix one cycle labelling kit from 1ug total RNA.

value: Mantle cell lymphoma


title: Follicular_Lymphoma_7

source_name: Lymph node from follicular lymphoma patient

value: Follicular lymphoma


title: Follicular_Lymphoma_2


title: MALT_Lymphoma_t(1;2)/BCL10-IGK_1

description: t(1;2)(p22;q32) translocation which is identical to the t(1;14) translocation.


title: Mantle_cell_lymphoma_7


title: HNSCC_N0_93_555

status: Public on May 28 2010

city: Sao Paulo

first: Anna

last: Coló

address: Rua Professor Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

description: Cell lines: Daudi, DLD-1, DU145, FaDu, GM637, H146, H1080, HB4α, HEK293, Jurkat, Saos-2, SK-BR-3, SK-MEL-28, T24, T98G.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deyonized formamide 50% / Temperature:42oC / Time:12-24h / Touch Down: 70, 55, 50, 42 Washing - Round 1 - Solution: 2X SSC 0,1% SDS / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 SSC 0,1% SSC / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 3 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar / Washing Number: 3 Washing - Round 4 - Solution: 0,1X SSC / Temperature:42 / Time:4 min / Washing Number: 4 Washing - Round 5 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar lâm por lâm / Washing Number: 5

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

label: Alexa 555

source_name: HNSCC, N0, 93

label_protocol: After NaOAc/ethanol precipitation, cDNA was with indirectly labeled with Alexa Dye 555 or 647 (Invitrogen, Carlsbad, CA) and purified using QIAquick PCR purification kit (Qiagen, Germany).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) and amplified by a T7-based protocol. Briefly, 3 ug of total RNA and 0,5 ug of oligo-dT(24)-T7 (Integrated DNA Technologies IDT, Coralville, IA) were denaturated at 70oC for 10 min and snap cooled on ice for 1 min. Reverse transcription was performed by adding 6 mM MgCl2, 1mM dNTP (Eppendorf, Germany), 1X First Strand Buffer, 20 units of RNasin and 1 ul of Improm II (Promega, Madison, WI) at 42oC for 2 hours. Second-strand synthesis was made by adding 0,2 mM dNTP (Eppendorf, Germany), 1X Second Strand Buffer, 0,6 units of RNase H (USB Corporation, Cleveland, OH), units of Ligase (New England Biolabs, Ipswich, MA) and 10 units of DNA Pol I (Invitrogen, Carlsbad, CA) at 16oC for 2 hours. Double-strand DNA was completed by adding 5 units of T4 DNA Pol (Invitrogen, Carlsbad, CA) and incubating at 16oC for 10 min. After phenol/chloroform extraction, in vitro transcription was carried out with RiboMax kit (Promega, Madison, WI) by adding 7,5mM rNTP, 1X Reaction buffer and 0.1 volume of Enzyme mix. Amplified RNA (aRNA) was extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 ug of aRNA and 10 ug of Random Hexamers (Amersham Biosciences, Piscataway, NJ) were denaturated at 70oC for 10 min and snap cooled on ice for 1 min. Reverse transcription was performed by adding 6 mM MgCl2, 0,5mM dNTP mix (Eppendorf, Germany) with Aminoallyl dUTP (Sigma-Aldrich, St. Louis, MO), 1X First Strand Buffer, 20 units of RNasin and 1 ul of Improm II (Promega, Madison, WI) at 42oC for 2 hours. aRNA was degradated with 0,42 M NaOH and 14 mM EDTA at 70oC for 10 min.

value: HNSCC, N0

tag: sample type

value: primary untreated SCC of the oral cavity pN0

label: Alexa 647

source_name: Reference RNA

value: 15 human cell lines


title: HNSCC_N+_89_647

description: non-recurrent HNSCC

scan_protocol: Hardware: Perkinelmer / Software: ScanArray Express Microarray Scanner, Image quantification: Scan Array Express version 3.0

data_processing: Normalization: Lowess, software R version 2.9.2 (2009-08-24)

value: 15 human cell lines (Daudi, DLD-1, DU145, FaDu, GM637, H146, H1080, HB4α, HEK293, Jurkat, Saos-2, SK-BR-3, SK-MEL-28, T24, T98G)

source_name: HNSCC, N+, 89

value: HNSCC, N+

value: primary untreated SCC of the oral cavity pN+


title: Follicular_Lymphoma_6


title: Mantle_cell_lymphoma_4


title: HNSCC_N+_90_555

description: non-recurrent HNSCC

value: primary untreated SCC of the oropharynx pN+


title: Follicular_Lymphoma_1


title: HNSCC_N+_91_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 91


title: HNSCC_N0_93_647


title: HNSCC_N+_99_647

description: recurrent HNSCC

source_name: HNSCC, N+, 99


title: Mantle_cell_lymphoma_6


title: HNSCC_N+_90_647

description: non-recurrent HNSCC


title: HNSCC_N+_92_647

description: recurrent HNSCC

source_name: HNSCC, N+, 92


title: HNSCC_N+_9_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 9


title: HNSCC_N+_99_555

description: recurrent HNSCC


title: HNSCC_N0_97_555

source_name: HNSCC, N0, 97


title: HNSCC_N+_9_647

description: non-recurrent HNSCC


title: Mantle_cell_lymphoma_5


title: HNSCC_N0_97_647


title: HNSCC_N+_92_555

description: recurrent HNSCC


title: HNSCC_N+_91_647

description: non-recurrent HNSCC


title: HNSCC_N+_89_555

description: non-recurrent HNSCC


title: Follicular_Lymphoma_3


title: Mantle_cell_lymphoma_1


title: HNSCC_N+_87_647

source_name: HNSCC, N+, 87


title: HNSCC_N+_76_647

description: recurrent HNSCC

source_name: HNSCC, N+, 76


title: HNSCC_N+_88_647

source_name: HNSCC, N+, 88


title: HNSCC_N+_76_555

description: recurrent HNSCC


title: HNSCC_N0_79_555

source_name: HNSCC, N0, 79

value: primary untreated SCC of the oropharynx pN0


title: HNSCC_N+_74_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 74


title: HNSCC_N+_88_555


title: HNSCC_N+_6_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 6


title: HNSCC_N0_73_555

source_name: HNSCC, N0, 73


title: HNSCC_N+_87_555


title: HNSCC_N+_68_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 68


title: HNSCC_N0_73_647


title: HNSCC_N+_70_555

source_name: HNSCC, N+, 70


title: HNSCC_N+_57_647

description: recurrent HNSCC

source_name: HNSCC, N+, 57


title: HNSCC_N+_6_555

description: non-recurrent HNSCC

source_name: Reference RNA


title: HNSCC_N+_69_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 69


title: HNSCC_N+_67_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 67


title: HNSCC_N+_67_555

description: non-recurrent HNSCC


title: HNSCC_N+_69_555

description: non-recurrent HNSCC


title: HNSCC_N+_57_555

description: recurrent HNSCC


title: HNSCC_N+_54_647

description: non-recurrent HNSCC

source_name: HNSCC, N+,54


title: HNSCC_N+_74_555

description: non-recurrent HNSCC


title: HNSCC_N+_5_555

description: recurrent HNSCC

source_name: HNSCC, N+, 5


title: HNSCC_N+_5_647

description: recurrent HNSCC


title: HNSCC_N+_70_647


title: HNSCC_N+_47_647

source_name: HNSCC, N+, 47


title: HNSCC_N+_47_555


title: HNSCC_N+_68_555

description: non-recurrent HNSCC


title: HNSCC_N+_38_647

description: recurrent HNSCC

source_name: HNSCC, N+, 38


title: HNSCC_N0_46_647

source_name: HNSCC, N0, 46


title: HNSCC_N0_37_647

source_name: HNSCC, N0, 37


title: HNSCC_N+_54_555

description: non-recurrent HNSCC


title: HNSCC_N+_52_647

source_name: HNSCC, N+, 52


title: HNSCC_N+_53_555

description: recurrent HNSCC

source_name: HNSCC, N+, 53


title: HNSCC_N+_42_555

source_name: HNSCC, N+, 42


title: HNSCC_N+_52_555


title: HNSCC_N+_53_647

description: recurrent HNSCC


title: HNSCC_N+_35_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 35


title: HNSCC_N+_38_555

description: recurrent HNSCC


title: Mantle_cell_lymphoma_2

source_name: Lymph node from mantle cell lymphoma patient


title: HNSCC_N+_4_647

description: recurrent HNSCC

source_name: HNSCC, N+, 4


title: HNSCC_N+_2_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 2


title: HNSCC_N+_35_647

description: non-recurrent HNSCC


title: HNSCC_N0_37_555


title: HNSCC_N+_32_647

source_name: HNSCC, N+, 32


title: HNSCC_N+_26_647

source_name: Reference RNA

source_name: HNSCC, N+, 26


title: HNSCC_N+_34_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 34


title: HNSCC_N+_26_555


title: HNSCC_N0_79_647

source_name: HNSCC, N0, 79


title: HNSCC_N+_23_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 23


title: HNSCC_N0_46_555


title: HNSCC_N+_4_555

description: recurrent HNSCC


title: HNSCC_N+_2_555

description: non-recurrent HNSCC


title: HNSCC_N+_22_647

source_name: HNSCC, N+, 22


title: HNSCC_N+_208_647

description: recurrent HNSCC

source_name: HNSCC, N+, 208


title: HNSCC_N+_34_555

description: non-recurrent HNSCC


title: HNSCC_N0_203_647

source_name: HNSCC, N0, 203


title: HNSCC_N0_201_647

source_name: HNSCC, N0, 201


title: HNSCC_N+_28_647

description: Cell lines: Daudi, DLD-1, DU145, FaDu, GM637, H146, H1080, HB4α, HEK293, Jurkat, Saos-2, SK-BR-3, SK-MEL-28, T24, T98G

source_name: HNSCC, N+, 28


title: HNSCC_N0_201_555


title: HNSCC_N+_23_647

description: non-recurrent HNSCC


title: HNSCC_N+_1_555

source_name: HNSCC, N+, 1


title: HNSCC_N+_209_555

source_name: HNSCC, N+, 209

value: 15 human cell line


title: HNSCC_N+_208_555

description: recurrent HNSCC


title: HNSCC_N+_209_647


title: HNSCC_N0_20_555

source_name: HNSCC, N0, 20


title: HNSCC_N+_194_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 194


title: HNSCC_N0_200_555

source_name: HNSCC, N0, 200


title: HNSCC_N+_194_555

description: non-recurrent HNSCC


title: HNSCC_N+_185_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 185


title: HNSCC_N+_22_555


title: HNSCC_N0_198_555

source_name: HNCSS, N0, 198


title: HNSCC_N0_198_647

source_name: Reference RNA


title: HNSCC_N0_191_647

source_name: HNSCC, N0, 191


title: HNSCC_N0_191_555


title: HNSCC_N+_28_555


title: HNSCC_N0_18_647

source_name: HNSCC, N0, 18


title: HNSCC_N0_18_555


title: HNSCC_N+_17_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 17


title: HNSCC_N+_184_647

description: recurrent HNSCC

source_name: HNSCC, N+, 184


title: HNSCC_N+_32_555

source_name: HNSCC, N+, 32


title: HNSCC_N+_189_555

source_name: HNSCC, N+, 189


title: HNSCC_N+_17_647

description: non-recurrent HNSCC


title: HNSCC_N+_189_647

label: total RNA


title: HNSCC_N+_42_647

source_name: HNSCC, N+, 42


title: HNSCC_N0_188_555

source_name: NHSCC, N0, 188


title: HNSCC_N+_185_647

description: non-recurrent HNSCC


title: HNSCC_N0_188_647


title: HNSCC_N+_173_647

source_name: HNSCC, N+, 173


title: NHSCC_N+_176_647

description: recurrent HNSCC

source_name: HNSCC, N+, 176


title: NHSCC_N+_176_555

description: recurrent HNSCC


title: HNSCC_N+_172_647

description: non-recurrent HNSCC

source_name: HNSSS, N+, 172


title: HNSCC_N+_180_647

description: recurrent HNSCC

source_name: HNSCC, N+, 180


title: HNSCC_N+_174_647

source_name: HNSCC, N+, 174


title: HNSCC_N+_184_555

description: recurrent HNSCC


title: HNSCC_N+_180_555

description: recurrent HNSCC


title: HNSCC_N+_168_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 168


title: HNSCC_N+_174_555


title: HNSCC_N0_203_555

source_name: HNSCC, N0, 203


title: HNSCC_N+_164_555

description: recurrent HNSCC

source_name: HNSCC, N+, 164


title: HNSCC_N+_169_555

source_name: HNSCC, N+, 169

source_name: Reference RNA


title: HNSCC_N+_169_647


title: HNSCC_N+_172_555

description: non-recurrent HNSCC


title: HNSCC_N+_173_555


title: HNSCC_N+_163_555

description: recurrent HNSCC

source_name: HNSCC, N+, 163


title: HNSCC_N+_163_647

description: recurrent HNSCC


title: HNSCC_N+_162_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 162


title: HNSCC_N+_168_555

description: non-recurrent HNSCC


title: HNSCC_N0_167_555

source_name: HNSCC, N0, 167


title: HNSCC_N0_167_647


title: HNSCC_N+_152_555

source_name: HNSCC, N+, 152


title: HNSCC_N0_20_647

source_name: HNSCC, N0, 20


title: HNSCC_N+_14_555

description: non-recurrent HNSCC

source_name: HNSCC, N+, 14


title: HNSCC_N+_164_647

description: recurrent HNSCC


title: HNSCC_N0_165_555

source_name: HNSCC, N0, 165


title: HNSCC_N0_156_555

source_name: HNSCC, N0, 156


title: HNSCC_N+_162_647

description: non-recurrent HNSCC


title: HNSCC_N0_156_647


title: HNSCC_N+_147_647

description: recurrent HNSCC

source_name: HNSCC, N+, 147


title: HNSCC_N0_145_555

source_name: HNSCC, N0, 145


title: HNSCC_N+_14_647

description: non-recurrent HNSCC


title: HNSCC_N+_152_647


title: HNSCC_N+_141_647

source_name: HNSCC, N+, 141


title: HNSCC_N0_142_647

source_name: HNSCC, N0, 142


title: HNSCC_N+_138_555

source_name: HNSCC, N+, 138


title: HNSCC_N+_141_555


title: HNSCC_N0_137_555

source_name: HNSCC, N0, 137


title: HNSCC_N0_137_647


title: HNSCC_N+_138_647


title: HNSCC_N0_200_647

source_name: HNSCC, N0, 200


title: HNSCC_N+_147_555

description: recurrent HNSCC


title: HNSCC_N0_165_647


title: HNSCC_N+_127_555

description: recurrent HNSCC

source_name: HNSCC, N+, 127


title: HNSCC_N+_107_555

source_name: HNSCC, N+, 107

source_name: Reference RNA


title: HNSCC_N+_11_647

description: recurrent HNSCC

source_name: HNSCC, N+, 11


title: HNSCC_N+_126_555

source_name: HNSCC, N+, 126


title: HNSCC_N0_145_647


title: HNSCC_N+_11_555

description: recurrent HNSCC


title: HNSCC_N+_126_647


title: HNSCC_N+_127_647

description: recurrent HNSCC


title: HNSCC_N+_105_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 105


title: HNSCC_N+_105_555

description: non-recurrent HNSCC


title: HNSCC_N+_101_647

description: non-recurrent HNSCC

source_name: HNSCC, N+, 101


title: HNSCC_N+_107_647


title: lytSR vs WT cDNA rep 1

status: Public on Mar 08 2010

city: Shanghai

first: Tao

last: Zhu

address: 138, Dongan Road

institute: Fudan university

description: gene expression data from wild type vs lytSR mutant biological rep 1 obtained by cDNA microarray

hyb_protocol: Microarray hybridization (at 42°C for 16 h) and washing of the slides at 50°C were performed according to the manufacturer’s instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Genespring 10 Software was used for background subtraction and LOWESS normalization.  Please see "README.txt" file available on the SERIES record for a description of the columns contained in the raw data files.

organism: Staphylococcus epidermidis

source_name: wild type biological rep 1-cDNA

label_protocol: Reverse transcription were performed using 2 µg of total RNA using T7 promoter primers and M-MLV reverse transcriptase (Promega, Madison, WI, USA), and then cRNA was transcribed from the resulting cDNA as template. cRNA prepared form the wild strain and lytSR mutant was labeled using the dyes Cy3 and Cy5 according to the manufacturer’s instructions(Amersham, Piscataway, New Jersey).

growth_protocol: For microarray experiments, overnight cultures of S. epidermidis were diluted 1:200 into fresh TSB and grown at 37 ℃ to the mid-exponential phase

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

value: 1457 strain

tag: genome/variation

value: wild type

source_name: lytSR mutant biological rep1-cDNA

value: lytSR mutant


title: HNSCC_N+_101_555

description: non-recurrent HNSCC


title: lytSR vs WT oligo rep 4

description: gene expression data from wild type vs lytSR mutant biological rep 4 obtained by oligo microarray

source_name: wild type biological rep 4-oligo

source_name: lytSR mutant biological rep4-oligo


title: healthy group

status: Public on Apr 15 2010

type: protein

city: Central

first: R A P

middle: M

last: Perera

address: 34, Hospital road

department: Faculty of Dentistry

country: Hong Kong

institute: The University of Hong kong

description:
Human UOPS male
42 subjects in this group

hyb_protocol: Samples were mixed with with C5a,  IL-4,  IL-32 alpha, CD40 ligand,  IL-5,  CXCL10/IP-10, G-CSF,  IL-6,  CXCL11/I-TAC, GM-CSF,  IL-8,  CCL2/MCP-1, CXCL1/GRO alpha,  IL-10,  MIF, CCL1/I-309,  IL-12 p70,  CCL3/MIP-1 alpha, ICAM-1,  IL-13,  CCL4/MIP-1 beta, IFN-gamma,  IL-16,  CCL5/RANTES, IL-1 alpha,  IL-17,  CXCL12/SDF-1, IL-1 beta,  IL-17E,  Serpin E1/PAI-1, IL-1ra,  IL-23,  TNF-alpha, IL-2 and  IL-27 and the hybridized with capture antibodies spotted in duplicate on nitrocellulose membranes. After over night incubation and 3 washing steps, Streptavidin-Horseradish Peroxidase and chemiluminescent detection reagents are added and the signal produced is in proportion to the amount of cytokine bound.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (R & D).

data_processing: Raw data were processed with the Optiquant Array Computational Tool (Packard Bioscience) for background correction and normalization. Data analysis and statistical evaluations were performed with SAM alogrthm (http://www-stat.stanford.edu/~tibs/SAM/sam.pdf)

molecule: protein

source_name: Healthy male

label_protocol: According to the manufacturer's instructions (R & D).

growth_protocol: Unstimulated whole saliva was collected by direct spitting into 50ml Falcon tubes placed on ice. Supernatant was obtained following centrifugation of whole saliva for 15 minutes at 2600 g.

treatment_protocol: Samples were lyophilized and diluted again in a protein buffer for homogenization

value: Pharyngeal secretions

tag: sex

value: male


title: NHAART group

description:
Human UOPS male
14 subjects in this group (Pt2 , Pt3, Pt6, Pt7, Pt8, Pt16, Pt17, Pt19, Pt20, Pt28, Pt34, Pt36, Pt71, Pt72)

source_name: NHAART


title: HAART group

description:
Human UOPS male
58 subjects in this group (Pt1, Pt4, Pt5, Pt9, Pt10, Pt11, Pt12, Pt13, Pt14, Pt15, Pt18, Pt21, Pt22, Pt23, Pt24, Pt25, Pt26, Pt27, Pt29, Pt30, Pt31, Pt32, Pt33, Pt35, Pt37, Pt38, Pt39, Pt40, Pt41, Pt42, Pt43, Pt44, Pt45, Pt46, Pt47, Pt48, Pt49, Pt50, Pt51, Pt52, Pt53, Pt54, Pt55, Pt56, Pt57, Pt58, Pt59, Pt60, Pt61, Pt62, Pt63, Pt64, Pt65, Pt66, Pt67, Pt68, Pt69, Pt70)

source_name: HAART


title: HNSCC_N0_142_555

source_name: HNSCC, N0, 142


title: HNSCC_N+_1_647

source_name: HNSCC, N+, 1


title: Larvae, Jpal-Per vs Ogasawara, Replicate 4-2

status: Public on Feb 23 2010

city: Shinjyuku-ku, Tokyo

first: Osamu

last: Komagata

address: Toyama 1-23-1

institute: National Institute of Infectious Diseases, Japan

description: Biological replicate 4 of 5

hyb_protocol: Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers under the Gene Expression Hybridization Kit (Agilent Technologies) protocol. After hybridization, slides were washed by Agilent's protocol.

scan_protocol: Scanned on an Agilent microarray scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing:
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
VALUEs in Sample data table represent log10 (resistant/susceptible) ratios.

organism: Culex quinquefasciatus

source_name: Ogasawara strain

label_protocol: Fluorescein-labeled cRNAs were synthesized with the Low RNA Input Linear Amplification Kit (Agilent Technologies) through the intermediary of double-stranded cDNA. The cRNA was labeled with either cyanine-3 (Cy-3) or cyanine-5 (Cy-5) CTP dye (Perkin-Elmer, Waltham, MA, USA) during cRNA amplification. cRNAs were then purified with the cRNA Cleanup Kit (Agilent Technologies) and measured for overall efficacy of cRNA synthesis and fluorescein-labeling using ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

growth_protocol: Larvae of both the strains were fed a diet of ground insect pellets.

extract_protocol: Total RNA for microarray analysis was extracted from day 2, fourth instar larvae and purified using the Total RNA Isolation Mini Kit (Agilent Technologies).

value: Ogasawara

tag: insecticide

value: susceptible

tag: developmental stage

value: fourth instar larvae, day 2

source_name: Jpal-Per strain

value: Jpal-per

value: resistant


title: zebrafish 12hpf Ovo1 morphant-2

status: Public on Apr 28 2010

city: Irvine

first: Sarah

last: Piloto

state: CA

address: 4462 Natural Sciences II, Dept. Dev. and Cell Biology

department: Developmental and Cell Biology

institute: University of California, Irvine

description: gene expression of wild type embryos injected with Ovo1 morpholino-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC with rotation on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip ® Scanner 3000.

data_processing: The results were quantified and analyzed using Expression Console ver. 1.1 software (Affimetrix, Inc.) using the PLIER algorithm default values.

organism: Danio rerio

source_name: zebrafish embryos 12 hpf

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix GeneChip Expression Analysis Technical Manual, 2002)

growth_protocol: Embryos were maintained in a  28.5oC incubator until 12 hpf (6 somites)

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

tag: tissue type

value: whole embryo

value: AB

tag: genotype/variation

value: Ovo1 morphant, sox10(7.2):gfp

tag: age

value: 12 hpf (6 somites)


title: zebrafish 12hpf control-3

description: gene expression of wild type control embryos-3

tag: strain

value: control


title: Larvae, Jpal-Per vs Ogasawara, Replicate 2-1

description: Biological replicate 2 of 5


title: Larvae, Jpal-Per vs Ogasawara, Replicate 1-1

description: Biological replicate 1 of 5


title: zebrafish 12hpf Ovo1 morphant-1

description: gene expression of wild type embryos injected with Ovo1 morpholino-1


title: Larvae, Jpal-Per vs Ogasawara, Replicate 5-2

description: Biological replicate 5 of 5


title: zebrafish 12hpf Ovo1 morphant-3

description: gene expression of wild type embryos injected with Ovo1 morpholino-3


title: Liver_thiamine-treated_51week_rep1

status: Public on Dec 07 2009

city: Takatsuki

first: Takao

last: Tanaka

state: Osaka

address: 4-20-1 Nasahara

description: We followed manufacturer's protocol.

hyb_protocol: We followed manufacturer's protocol. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

organism: Rattus norvegicus

source_name: liver, thiamine-treated, 51week

extract_protocol: QIAGEN RNeasy mini kit was used.

treatment_protocol:
The animal protocols were approved by the Institutional Animal Care and Use Committee of Osaka University of Pharmaceutical Sciences. Otsuka Long-Evans Tokushima Fatty (OLETF) male rats at 4 weeks of age were kindly supplied by the Tokushima Research Institute, Otsuka Pharmaceutical (Tokushima, Japan). OLETF rats were randomly divided into 2 groups of 8 each: untreated control and thiamine-treated animals. The latter group received 2 g thiamine/L in their drinking water. Rats were housed in standard cages (2 rats per cage) with free access to water and standard chow, unless noted otherwise. Cages were kept in temperature-controlled animal quarters (21°C) with a 0600-1800 light: 1800-0600 dark cycle, which was maintained throughout the experimental period. All animals were provided standard rodent chow (NMF, Oriental Yeast Co., Tokyo, Japan). Cages were changed at the beginning of each week and body weights were measured between 0800 and 1000. Body weight, food, and water intake were measured weekly throughout the investigation.
The control and treated rats were sacrificed at 55 weeks of age (thiamine treatments for 51 weeks; n = 8 per group). After 16 h of fasting, a rat was anesthetized with pentobarbital (50 mg/Kg), and an indwelling catheter was inserted in the right carotid artery. From exsanguinated animals, samples of liver were removed, and rinsed in ice-cold saline. Parts of liver were placed in RNAlater® (Ambion, Austin, TX) and stored at -80ºC, until further analysis. Individual samples were run on separate microarrays (n = 2, for both thiamine-treated and control groups); no samples were pooled.

value: Otsuka Long-Evans Tokushima Fatty (OLETF) rats

tag: gender

value: 55 weeks

value: liver

tag: intervention

value: 0.2% thiamine containing water free access for 51 weeks


title: zebrafish 12hpf control-2

description: gene expression of wild type control embryos-2


title: WN19 vs. WN39 T2

status: Public on Apr 06 2010

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

institute: King's College London

hyb_protocol: Microarrays were hybridized following the Genisphere Array 900 HS protocol with modifications.

scan_protocol: A Perkin & Elmer scanner was used to extract the raw intensities.

data_processing: Preprocessing and normalization was done in the R software [58] using Limma package [59]. Loess method [59] was used for normalization within arrays and normalization between arrays was done using aquantile method [60], both of them included in limma package.

organism: Caenorhabditis elegans

source_name: wn19 96  hours

label_protocol: Labeled cDNA was produced with Array 900 HS kit from Genisphere and Superscript II from Invitrogen. The Nucleospin kit () was used to clean the cDNA samples in order to reduce unspecific binding to the arrays.

growth_protocol: A set of 36 recombinant inbred lines (RILs) generated by crosses between N2 and CB4856 (Li et al., 2006) were used to generate genetical genomics data. The RILs were cultured on standard nematode growth medium (NGM) with E. coli OP50 as food source and a constant temperature of 24ºC. Populations were started with nonmated hermaphrodites and screened regularly to remove any occurring males.

extract_protocol: RNA from nematodes was extracted following the Trizol method, followed by the RNeasy Micro kit (Quiagen, Valencia, CA, USA) to clean up the samples.

treatment_protocol: Reproductive nematodes from 36 RILs were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect age synchronized eggs which were inoculated in 24 dishes (t0). After 40 hours (t1) nematodes from 6 dishes were collected in late L3 stage, frozen in liquid nitrogen and keep them at -80ºC until RNA extraction procedure. The remaining 18 dishes were kept in culture until hour 41 when the nematodes were transferred to fresh NGM dishes (with E. coli OP50) treated with 0.05-0.01 mg/ml of FUDR in order to avoid reproduction. After 30 hours in dishes with FUDR and when reproductive period is about to finish, nematodes were transferred to fresh dishes without FUDR, to prevent starvation. After 23 hours, 96 hours of total culture time (t2), nematodes from 6 dishes were collected and frozen in liquid nitrogen prior to RNA extraction. The remaining 12 dishes were kept at constant temperature until 214 hours of culture (t3), when they were harvest and frozen in liquid nitrogen. All the dishes were visually inspected before the harvest. Any population with contamination, more than one generation (reproduction) or starving nematodes (lacking bacteria) were discarded.

value: Late reproduction stage (96 hours at 24ºC).

tag: recombinant inbred line

source_name: wn39 96 hours


title: Liver_thiamine-untreated_51week_rep2

institute: Osaka University of Pharmaceutical Sciences

description: We followed manufacturer's protocol.

source_name: liver, thiamine-untreated, 51week

label_protocol:
We followed manufacturer's protocol.
http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

value: 0% thiamine containing water free access for 51 weeks


title: Larvae, Jpal-Per vs Ogasawara, Replicate 4-1

description: Biological replicate 4 of 5


title: pri-C1.2 hiPSC

status: Public on Apr 22 2010

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data of cell line pri-C1.2 hiPSC

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Affy and limma package (MAS5)

source_name: pri-C1.2 hiPSC

label_protocol: 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010

treatment_protocol: RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.

value: Human embryonic stem cells (hESC)

tag: cell subtype

value: pri-C1.2 hiPSC


title: zebrafish 12hpf control-1

description: gene expression of wild type control embryos-1


title: Larvae, Jpal-Per vs Ogasawara, Replicate 5-1

description: Biological replicate 5 of 5

value: Ogasawara

value: susceptible


title: Liver_thiamine-treated_51week_rep2

description: We followed manufacturer's protocol.

value: male


title: Liver_thiamine-untreated_51week_rep1

description: We followed manufacturer's protocol.


title: Larvae, Jpal-Per vs Ogasawara, Replicate 3-1

description: Biological replicate 3 of 5

value: Jpal-per

value: resistant

value: fourth instar larvae, day 2


title: Larvae, Jpal-Per vs Ogasawara, Replicate 2-2

description: Biological replicate 2 of 5


title: Larvae, Jpal-Per vs Ogasawara, Replicate 1-2

description: Biological replicate 1 of 5


title: Larvae, Jpal-Per vs Ogasawara, Replicate 3-2

description: Biological replicate 3 of 5


title: WN19 vs. WN39 T1

source_name: wn19 40 hours

value: Late L3 stage (40 hours at 24ºC).

source_name: wn39 40 hours


title: WT at DD48 + rifampicin, single experiment

status: Public on Aug 01 2009

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

description: Gene expression data from Synechococcus elongatus PCC 7942

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings, divided by corresponding genomic DNA signals (genomic DNA sample), and global scaling as normalization method except for samples under DD conditions. The trimmed average target intensity of each array was arbitrarily set to 1000. For data under DD, genomic-DNA-divided value is shown.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Synechococcus wild type cells collected at hour 48 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (46 micromol/m^2/sec) or the dark

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: Genotype

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: WN19 vs. WN39 T3

source_name: wn19 214 hours

value: Old adults stage (214 hours at 24ºC).

source_name: wn39 214 hours


title: WT at DD28 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 28 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD44 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 44 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD24 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 24 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD20 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 20 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD16 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 16 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD 8 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 8 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD12 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 12 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD 4 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 4 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD16, rep2

source_name: Synechococcus wild type cells collected at hour 16 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD20, rep2

source_name: Synechococcus wild type cells collected at hour 20 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD 0 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 0 (=ZT12, DD0) under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD36 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 36 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: WT at DD48, rep1

source_name: Synechococcus wild type cells collected at hour 48 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD52, rep1

source_name: Synechococcus wild type cells collected at hour 52 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD 0, rep2

source_name: Synechococcus wild type cells collected at hour 0 (=ZT12, DD0) under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture.


title: WT at DD 4, rep2

source_name: Synechococcus wild type cells collected at hour 4 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: Embryonic Drosophila cells, Kc167 cells, FAIRE, replicate 1

status: Public on Jan 06 2010

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: FAIRE untreated Kc cells

hyb_protocol: 13 µg labeled DNA per channel, 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 hybridiaztion 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: Slides were scanned on an Agilent scanner with 5 micron resolution at 30% intensity.

data_processing: Scans were processed with NimbleScan 2.4 using standard settings. Values of all reporters except NimbleGen control reporters were extracted from pair files and represented as log2-ratios and normalized using the the loess() function in R with parameter control=loess.control(trace.hat='approximate'). Values were median centered.

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, formaldehyde crosslinked

label_protocol: 1 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5/Cy3 nonamers per manufacturer's protocol (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: Cells were pelleted and washed twice with ice-cold PBS. Each pellet (0.1-0.15g of cells) was resuspended in 3 ml of buffer L1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 5% NP-40, 0.25% Triton X-100) and incubated 10 min. on ice with occasional inverting to mix. Cells were pelleted, resuspended in 3 ml of buffer L2 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min. at room temperature with agitation. Cells were pelleted and resuspended in 3.9 ml of buffer L3 (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 5 mg/ml N-lauroyl sarcosine, with Complete protease inhibitors (Roche)) and sonicated using the Bioruptor to yield mainly fragments smaller than 500 bp. DNA was isolated by two extractions in buffer-saturated phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated, RNA was removed with RNase A, and DNA was purified using Qiagen’s MinElute kit.

treatment_protocol: Cells grown in suspension were fixed by addition of formaldehyde to a final concentration of 2%. After incubating for 15 min at room temperature with agitation, glycine was added to 125 mM, and samples were incubated with tumbling for 5 min at room temperature.

tag: cell line

source_name: Embryonic Drosophila cells, Kc167 cells, not crosslinked

treatment_protocol: Untreated cells were used as a control in hybridizations.


title: WT at DD28, rep1

source_name: Synechococcus wild type cells collected at hour 28 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD36, rep1

source_name: Synechococcus wild type cells collected at hour 36 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD 8, rep2

source_name: Synechococcus wild type cells collected at hour 8 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3A+B RNAi, replicate 1

status: Public on Oct 15 2009

description: H1 DamID Kc167 cells H3.3A+B RNAi

hyb_protocol: Hybridizations were done by NimbleGen, Reykjavik.

scan_protocol: Scans were done by NimbleGen, Reykjavik.

data_processing: Scans were processed by NimbleGen, Reykjavik. 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 were median centered. Random probes and complementary probes (experimental probes with a non-chromosome SEQ_ID) were removed.

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-H1, H3.3A+B RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 10 μg/ul H3.3A dsRNA and 10 μg/ul H3.3B dsRNA. On day 7,  pGWNDamMyc-H1 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into 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) and cells were again treated with dsRNA.

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 treated with 10 μg/μl H3.3A dsRNA and 10 μg/μl H3.3B dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg H1-Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, H3.3A+B RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 10 μg/ul H3.3A dsRNA and 10 μg/ul H3.3B dsRNA. On day 7,  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 treated with 10 μg/μl H3.3A dsRNA and 10 μg/μl H3.3B dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8


title: WT at DD40, rep1

source_name: Synechococcus wild type cells collected at hour 40 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD32, rep1

source_name: Synechococcus wild type cells collected at hour 32 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD 8, rep1


title: WT at DD24, rep1

source_name: Synechococcus wild type cells collected at hour 24 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: Embryonic Drosophila cells, Kc167 cells, FAIRE, replicate 2

description: FAIRE untreated Kc cells


title: WT at DD16, rep1

source_name: Synechococcus wild type cells collected at hour 16 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD12, rep1

source_name: Synechococcus wild type cells collected at hour 12 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD 4, rep1


title: WT at DD32 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 32 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3A+B RNAi, replicate 2

description: H1 DamID Kc167 cells H3.3A+B RNAi


title: WT at DD 0, rep1


title: Embryonic Drosophila cells, Kc167 cells, RpII18 DamID, replicate 1

description: RpII18 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing RpII18-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. pNDamM-RNAPolII18kD (Moorman C. et al., Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A 103, 12027-32, 2006) 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 RpII18-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2

source_name: Embryonic Drosophila cells, Kc167 cells, expressing 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. 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


title: kaiC-overexpressor at LL33 +IPTG (hour 8), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL33 with 100 uM IPTG (hour 8 after IPTG-induction)

value: IPTG-inducible kaiC overexpressor strain containing a Ptrc::kaiC construct with a kanamycin-resistance gene at the neutral site II (NSII)


title: Embryonic Drosophila cells, Kc167 cells, RpII18 DamID, replicate 2

description: RpII18 DamID untreated Kc167 cells


title: kaiC-overexpressor at LL27 +IPTG (hour 2), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL27 with 100 uM IPTG (hour 2 after IPTG-induction)


title: kaiC-overexpressor at LL27 -IPTG (hour 2), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL27 without IPTG (control)


title: kaiC-overexpressor at LL33 -IPTG (hour 8), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL33 without IPTG (control)


title: kaiC-overexpressor at LL29 -IPTG (hour 4), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL29 without IPTG (control)


title: kaiC-overexpressor at LL29 +IPTG (hour 4), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL29 with 100 uM IPTG (hour 4 after IPTG-induction)


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3B RNAi, replicate 2

description: H1 DamID Kc167 cells H3.3B RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-H1, H3.3B RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul H3.3B dsRNA. On day 7,  pGWNDamMyc-H1 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into 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) and cells were again treated with dsRNA.

treatment_protocol: cells treated with 15 μg/μl H3.3B dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg H1-Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, H3.3B RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul H3.3B dsRNA. On day 7,  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 treated with 15 μg/μl H3.3B dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after H3.3B RNAi, replicate 1

description: H1 DamID Kc167 cells H3.3B RNAi


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after white RNAi, replicate 1

description: H1 DamID Kc167 cells w RNAi

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-H1, white RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 7,  pGWNDamMyc-H1 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) was transfected into 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) and cells were again treated with dsRNA.

treatment_protocol: cells treated with 15 μg/μl white dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg H1-Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam, white RNAi

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. On day 1, 3 and 5, cells were serum starved for 1h and treated with 15 μg/ul white dsRNA. On day 7,  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 treated with 15 μg/μl white dsRNA on days 1, 3, 5 and 7 and transfected with 20 μg Dam expression plasmid/2*10e6 cells on day 7; harvested on day 8


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 1

description: H1 DamID untreated Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam-H1

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-H1 (de Wit E. et al., Global chromatin domain organization of the Drosophila genome. PLoS Genet 4(3):e1000045, 2008) 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 H1-Dam expression plasmid/2*10e6 cells on day 1; harvested on day 2


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID, replicate 2

description: H1 DamID untreated Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, H1 DamID after white RNAi, replicate 2

description: H1 DamID Kc167 cells w RNAi


title: kaiC-overexpressor at LL25 +IPTG (hour 0), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL25 with 100 uM IPTG (hour 0 after IPTG-induction)


title: kaiC-overexpressor at LL25.5 -IPTG (hour 0.5), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL25.5 without IPTG (control)


title: kaiC-overexpressor at LL25.5 +IPTG (hour 0.5), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL25.5 with 100 uM IPTG (hour 0.5 after IPTG-induction)


title: kaiC-overexpressor at LL26 +IPTG (hour 1), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL26 with 100 uM IPTG (hour 1 after IPTG-induction)


title: kaiC-overexpressor at LL26 -IPTG (hour 1), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL26 without IPTG (control)


title: WT at DD40 + rifampicin, single experiment

source_name: Synechococcus wild type cells collected at hour 40 under continuous dark (DD) after two 12-h:12-h dark/lightcycles from a continuous culture. 200-ug/ml rifampicin was present from hour 0 under DD.


title: kaiC-overexpressor at LL33 +IPTG (hour 8), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL33 with 100 uM IPTG (hour 8 after IPTG-induction)


title: kaiC-overexpressor at LL25 -IPTG (hour 0), rep2

source_name: Synechococcus Ptrc::kaiC cells at LL25 without IPTG (control)


title: kaiC-overexpressor at LL27 +IPTG (hour 2), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL27 with 100 uM IPTG (hour 2 after IPTG-induction)


title: kaiC-overexpressor at LL27 -IPTG (hour 2), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL27 without IPTG (control)


title: kaiC-overexpressor at LL33 -IPTG (hour 8), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL33 without IPTG (control)


title: kaiC-overexpressor at LL29 +IPTG (hour 4), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL29 with 100 uM IPTG (hour 4 after IPTG-induction)


title: kaiC-overexpressor at LL25 +IPTG (hour 0), rep1


title: kaiC-overexpressor at LL26 +IPTG (hour 1), rep1


title: kaiC-overexpressor at LL25 -IPTG (hour 0), rep1


title: kaiC-overexpressor at LL25.5 -IPTG (hour 0.5), rep1


title: kaiC-overexpressor at LL29 -IPTG (hour 4), rep1

source_name: Synechococcus Ptrc::kaiC cells at LL29 without IPTG (control)


title: kaiABC-null at LL44, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 44 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.

value: kaiABC-null strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: kaiABC-null at LL40, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 40 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiC-overexpressor at LL26 -IPTG (hour 1), rep1


title: kaiC-overexpressor at LL25.5 +IPTG (hour 0.5), rep1


title: kaiABC-null at LL20, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 20 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL12, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 12 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL16, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 16 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL24, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 24 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL32, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 32 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL36, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 36 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL32, rep1


title: kaiABC-null at LL36, rep1


title: kaiABC-null at LL40, rep1


title: kaiABC-null at LL28, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 28 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL8, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 8 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL4, rep2

source_name: Synechococcus kaiABC-null mutant cells collected at hour 4 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: kaiABC-null at LL28, rep1


title: kaiABC-null at LL24, rep1


title: kaiABC-null at LL20, rep1


title: kaiABC-null at LL16, rep1


title: kaiABC-null at LL44, rep1


title: kaiABC-null at LL12, rep1


title: kaiABC-null at LL4, rep1


title: kaiABC-null at LL8, rep1


title: WT at LL52, rep2

source_name: Synechococcus wild type cells collected at hour 52 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL32, rep2

source_name: Synechococcus wild type cells collected at hour 32 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL40, rep2

source_name: Synechococcus wild type cells collected at hour 40 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL48, rep2

source_name: Synechococcus wild type cells collected at hour 48 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL36, rep2

source_name: Synechococcus wild type cells collected at hour 36 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL28, rep2

source_name: Synechococcus wild type cells collected at hour 28 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at DD12, rep2

source_name: Synechococcus wild type cells collected at hour 12 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at DD20, rep1

source_name: Synechococcus wild type cells collected at hour 20 under continuous dark (DD) after two 12-h:12-h dark/light cycles from a continuous culture.


title: WT at LL16, rep2

source_name: Synechococcus wild type cells collected at hour 16 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.


title: WT at LL12, rep2

source_name: Synechococcus wild type cells collected at hour 12 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture.