title: C. owensensis versus C. saccharolyticus

city: Raleigh

first: Robert

last: Kelly

address: Campus Box 7905

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC

scan_protocol: Images were aquired with a scanarray 4000 (PE) with 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards

data_processing: Signals for each channel were obtained using ScanArray express and were background substrated using the median local intensity around the spot. Once all the slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 4.0 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Caldicellulosiruptor owensensis

source_name: C. owensensis

label_protocol: Genomic DNA was partially digested with Hae III (NEB) and amino allyl-dUTP plus dNTPs were incorporated using Klenow fragment (NEB) and random nonamers (Sigma-Aldrich).  Cy-NHS ester dyes (GE Healthcare) were incubated with aa-dUTP labeled DNA fragments to label genomic DNA fragments.  Unincorporated dye was removed using Qiaquick spin columns according to manufacturer’s recommendations (Qiagen).

growth_protocol: All Caldicellulosiruptor strains were initiated from axenic freeze-dried samples, except C. bescii, in their recommended growth medium per the DSMZ website at 70C.  After the Caldicellulosiruptor species were revived, cultures were subcultured three times onto DSMZ640 medium plus cellobiose.  500 mL of batch grown culture was harvested after overnight growth for genomicDNA harvesting.

extract_protocol: Cells were harvested by centrifugation at 5,000 rpm and DNA was isolated, as described by Geslin et al. (J Bacteriol 185:3888), with the addition of lysozyme during cell lysis.

organism: Caldicellulosiruptor saccharolyticus

source_name: C. saccharolyticus


title: Phan_010_KO.bleomycin rep1

status: Public on Nov 29 2010

type: RNA

city: Ann Arbor

first: Tianju

last: Liu

state: Michigan

address: 109 Zina pitcher pl

department: Pathology

country: USA

institute: University of Michigan

description: gene expression profile at day 21 after bleomycin endotracheal injection

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: bleomycin injected mouse lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

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

treatment_protocol: Bleomycin or saline was endotracheally injected into wild type and FIZZ2 knockout mice, then the lungs were purfused with PBS and harvested for total RNA isolation.

tag: strain

tag: tissue

value: Lung

tag: agent

value: bleomycin

tag: genotype/variation

value: FIZZ2 knockout


title: Phan_008_KO.saline rep2

description: gene expression profile at day 21 after saline endotracheal injection

source_name: saline injected mouse lung

value: saline


title: Phan_011_KO.bleomycin rep2


title: Phan_006_WT.bleomycin rep3

value: wild type


title: Phan_009_KO.saline rep3


title: Phan_005_WT.bleomycin rep2


title: C. kronotskyensis versus C. saccharolyticus

type: genomic

middle: M

state: MI

molecule: genomic DNA

organism: Caldicellulosiruptor kronotskyensis

source_name: C. kronotskyensis


title: C. lactoaceticus versus C. saccharolyticus

organism: Caldicellulosiruptor acetigenus

source_name: C. lactoaceticus


title: C. kristjanssonii versus C. saccharolyticus

source_name: C. kristjanssonii


title: Liver_infected_7weeks_1

status: Public on Nov 30 2010

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

description:
7wks69_D
Gene expression in the liver of BALB/c mice 7 weeks post infection with Schistosoma japonicum

hyb_protocol: cRNA was hybridised to Illumina MouseWG-6 v2 expression beadchip arrays according to the manufacturers instructions

scan_protocol: Microarrays were scanned using a Beadstation 500 at Green factor level 2

data_processing:
Data was analysed using the GenomeStudio v1.1.1 and Genespring GX 11 programs
Values reported were derived using Illumina GenomeStudio v1.1.1 and represent relative signal intensity normalized to background, Genespring GX 11 was used to normalise each chip to the 50th percentile and each gene to the median and uninfected controls, measurements less than 0.01 were set to 0.01

source_name: Liver homogenate, infected, 7 weeks

label_protocol: cRNA was synthesised from 100ng of total RNA from each individual mouse with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

extract_protocol: Total RNA was extracted from liver tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

treatment_protocol: Mice were euthanized and liver tissue was collected and stored in RNAlater for microarray analysis

value: BALB/c

tag: gender

value: Female

tag: age

value: 6 weeks

value: Liver

tag: infection

value: infection with 12 cercariae

tag: time

value: 7 weeks post infection


title: Obese Case 3

city: Augusta

first: Xiaoling

last: Wang

state: GA

address: 1120 15th street

department: Pediatrics

institute: Medical College of Georgia

description: Obese case

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Obese case

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from buffy coat using Qiagen® QiAamp® Blood Kit according to standard instructions

value: Male

tag: sample type

value: peripheral leukocyte

tag: disease state

value: Obese case


title: Obese Case 7

description: Obese case


title: Phan_001_WT.saline rep1


title: Obese Case 6

description: Obese case


title: Lean Control 6

description: Lean control

source_name: Lean control

value: Lean control


title: Obese Case 4

description: Obese case


title: Lean Control 7

description: Lean control


title: C. hydrothermalis versus C. saccharolyticus

organism: Caldicellulosiruptor hydrothermalis

source_name: C. hydrothermalis


title: Phan_003_WT.saline rep3


title: Lean Control 5

description: Lean control


title: Obese Case 5

description: Obese case


title: Lean Control 3

description: Lean control


title: Phan_002_WT.saline rep2


title: Granta 519CellLine_treated with sox11 siRNA_rep4

city: Stockholm

first: Birgitta

last: Sander

address: F56 Pathology, Karolinska University Huddinge hospital

country: Sweden

institute: Karolinska Institutet

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary ssDNA to Human Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Preprocessing was performed in Affymetrix Expression Console (v. 1.1) using the following methods: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median

source_name: Granta 519 cell line, treated with SOX11 siRNA

label_protocol: Total RNA were amplified and converted to cDNA and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37 °C and 5% CO2.

extract_protocol: cells were harvested in 20hs after siRNA transfection. Total RNA from individual transfection experiments was extracted with Qiagen Rneasy Plus Mini Kit. Both the quality and the quantity of RNA were assesed.

treatment_protocol: 4,000,000 Granta 519 cells were suspended in 100 μl human cell line nucleofector solution C with 100 pmol of either SOX11 siRNA or control siRNA using X-01 electroporation program.

tag: cell type

value: mantle cell lymphoma (MCL) cell line

tag: cell line

value: Granta 519

tag: sirna

value: treated with SOX11 siRNA


title: Lean Control 4

description: Lean control


title: Obese Case 2

description: Obese case


title: Granta 519CellLine_treated with control siRNA_rep4

source_name: Granta 519 cell line, treated with control siRNA

value: treated with control siRNA


title: C. bescii versus C. saccharolyticus

organism: Caldicellulosiruptor bescii

source_name: C. bescii


title: Granta 519CellLine_untreated_rep4

source_name: Granta 519 cell line, untreated

value: untreated


title: SON Mouse Dehydrated (48hrs) 3

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the Supraoptic nucleus from a single control animal

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS

label: Amino allyl UTP (biotin)

source_name: Mouse SON

label_protocol: MessegeAmp II aRNA amplification kit (Ambion).

extract_protocol: Mice were killed using cervical dislocation and the brain was carefully removed from the cranium and snap frozen using powdered dry ice and stored at -80oC for no more than 14 days. Sections of brain (14μm) were cut using an RNase free cryostat and mounted onto RNase free membrane coated glass slides (P.A.L.M. Membrane slides; P.A.L.M. Microlaser Technologies). Immediately after sectioning, frozen sections were thawed and fixed (30s; in 95% [v/v] EtOH), rehydrated (30s in each of 75% [v/v] and 50% [v/v] EtOH) before being stained (60s 1% [v/v] cresyl violet). Sections were then dehydrated in a graded EtOH series (30s in each of 50% [v/v], 75% [v/v] and 95% [v/v]. then 2x 30s in 100% [v/v]). Laser microdissection was performed using a P.A.L.M. MicrolaserSystem (P.A.L.M. Microlaser Technologies). The SON was identified with reference to Franklin and Paxinos and the tissue from each animal was independently pooled into collection vials containing RNAlater® (Ambion, Huntingdon, UK). A single operative carried out all dissections. Total RNA was isolated without delay (within 24h) according to standard procedures that accompany the Ambion RNAqueous MicroKit (Ambion).

value: Adult

value: Supraoptic nucleus


title: SON Mouse Dehydrated (48hrs) 2


title: Obese Case 1

description: Obese case


title: SON Mouse Dehydrated (48hrs) 4


title: Granta 519CellLine_untreated_rep3


title: Toxoplasma gondii RPS13 conditional mutant with ATc, 3

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

description: Toxoplasma gondii RPS13 conditional mutant with ATc.

hyb_protocol: Standard Affymetrix protocol with 5ug labeled cRNA.

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per chip normalize to 50th percentile/Per gene normalize to median.

organism: Toxoplasma gondii

source_name: Toxoplasma gondii RPS13 conditional mutant, +ATc

label_protocol: Affymetrix One Cycle: 3ug starting RNA - Standard One Cycle protocol

extract_protocol: Parasites were purified from host cells and RNA was extracted using the Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

value: RPS13 conditional mutant

tag: developmental stage

value: tachyzoite

tag: treatment

value: anhydrotetracycline (ATc)


title: Granta 519CellLine_treated with control siRNA_rep3


title: Lean Control 2

description: Lean control


title: Toxoplasma gondii RPS13 conditional mutant with ATc, 2


title: Granta 519CellLine_treated with sox11 siRNA_rep2


title: Granta 519CellLine_treated with control siRNA_rep2


title: SON Mouse Control 4


title: SON Mouse Dehydrated (48hrs) 1


title: Toxoplasma gondii RPS13 conditional mutant with ATc, 4


title: Granta 519CellLine_treated with sox11 siRNA_rep3


title: Granta 519CellLine_treated with control siRNA_rep1


title: SON Mouse Control 3


title: Toxoplasma gondii RPS13 conditional mutant without ATc, 4

description: Toxoplasma gondii RPS13 conditional mutant without ATc.

source_name: Toxoplasma gondii RPS13 conditional mutant, -ATc

value: without anhydrotetracycline (ATc)


title: Granta 519CellLine_untreated_rep2


title: SON Mouse Control 2


title: Granta 519CellLine_untreated_rep1


title: Toxoplasma gondii RPS13 conditional mutant with ATc, 1


title: Lean Control 1

description: Lean control


title: Toxoplasma gondii RPS13 conditional mutant without ATc, 1


title: Toxoplasma gondii RPS13 conditional mutant without ATc, 3


title: Granta 519CellLine_treated with sox11 siRNA_rep1


title: Phan_004_WT.bleomycin rep1

value: Lung

value: bleomycin

value: wild type


title: SON Mouse Control 1

value: Male


title: Toxoplasma gondii RPS13 conditional mutant without ATc, 2


title: H4_WT_vs_WCE_#2

status: Public on Nov 28 2010

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in WT cells

hyb_protocol: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 5mg/mL Salmon Sperm DNA, 20uL 8mg/mL yeast tRNA). Put at 95C for 3 minutes. Put at 65C while waiting for hybridization. Follow standard Agilent chamber hybridization protocols. Incubate 16-20h at 40C in hybridization oven at 20RPM rotation speed. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them, and allow them to air dry for 1 minute. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 500 ml of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.1.0.4).

data_processing:
The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005). The combined data were next transformed to Z-scores (discarding the mitochondrial values) for the analyses.

Bioconductor packages: Biobase version 1.12.1 and limma version 2.9.1; R version 2.4.0.

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to drynes+B33s. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).

growth_protocol: Cultures were started in 50mL YEP+2% Glucose from one colony of appropriate strain and incubated overnight to OD600 0.8-1.0. Cultures were poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde, and put on rotating wheel for 30min. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine.

extract_protocol: Crosslinked cells are pelleted at 3.7k RPM in Beckman centrifuge (GS 6R Rotor 3.8). Cells are resuspended in 40mL ice cold TBS and pelleted again. This is repeated a second time. Cell pellets are resuspended in the remaining liquid (approx. 1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells quick-frozen by immersion in liquid nitrogen. Cells are thawed on ice, and resuspended in 700mL lysis buffer with protease inhibitors (solution composition detailed at the end). 500uL of acid-washed glass beads (Sigma) are added, and the cells are lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow elution of lysate, but not of beads. The pierced tubes are put in 2mL collection tubes and spun briefly to 6000 RPM. The lysate is then homogenized by pipetting and sonicated 4x 20sec with a 1 minute break between sonication cycles. The sonicated lysates are centrifuged, and the supernatant is saved and frozen at -80C, or used immediately for ChIP. Lysis buffer: 50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate; 1mM PMSF; 1mM Benzamidine; 10ug/mL Aprotinin; 1ug/mL Leupeptin; 1ug/mL Pepstatin.    For the immunoprecipitation, beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 2mL PBS + 5% BSA. Antibodies (at the concentration indicated below) are added and incubated overnight at 4C in haematological mixer. Beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 30uL PBS + 5% BSA / ChIP. 400-500uL of lysate are added to 30uL beads, and incubated overnight at 4C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 45uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl, pH 8.0; 250mM LiCl; 0.5% NP40; 0.5% Na-deoxycholate; 1mM EDTA. Reference: Drouin S., Robert F. Methods (in press). The 9E11 antibody (provided by Alain Verreault, IRIC) was used (10uL / ChIP) with anti-mouse Dynabeads (50uL / ChIP). The 9E10 antibody (from the Young lab) was used (2uL / ChIP) with anti-mouse Dynabeads (50uL / ChIP). The RYH4 (provided by Alain Verreault, IRIC) and 8WG16 anti-Rpb1 CTD (from the Young lab) antibodies were used (2uL / ChIP) with protein G Dynabeads (50uL / ChIP). The H3K36me3 (Abcam ab9050) and H4K5Ac (Upstate 07-327) antibodies were used (4uL / ChIP) with protein G Dynabeads (50uL / ChIP). The H5 antibody (Covance Research, MMS-129R-200) was used (5uL / ChIP) with protein G Dynabeads (50uL / ChIP).    To clean up the DNA, beads are spun down and supernatant is transfered to a new 1.5mL tube. 350uL of a solution of 345uL TE / 3uL RNAse A (10mg/mL) / 2uL Glycogen (20mg/mL) is added to the supernatant and incubated at 37C for 2 hours. 15uL 10% SDS and 7.5uL Proteinase K are then added and incubated for another 2 hours at 37C. The samples are then extracted twice with 450uL phenol/chloroform/isoamyl alcohol (25:24:1). 16uL of 5M NaCl is added to the final extract of about 350uL. 2 volumes of freezing 100% EtOH (-20C) are added, and the samples are put at -80C for 30 minutes. They are then centrifuged at maximum velocity for 20 minutes at 4C. The supernatant is discarded, and the pellet is washed with 500uL 70% EtOH (-20C) and centrifuged 15 minutes at 4C. The supernatant is discarded, the pellet resuspended in 50uL TE and stored at -20C.

tag: antibody

value: RYH4 (Verreault Lab)


title: H4_WT_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in WT cells


title: H4_3xMTase-KO_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: H4_eaf3-dCHD_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in eaf3-dCHD cells


title: H4_spt4D_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in spt4D cells


title: H4_spt4D_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in spt4D cells


title: H4_H3K36A_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in H3K36A cells


title: H4_H3K36A_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in H3K36A cells


title: H4_rco1D_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in rco1D cells


title: H4_rpd3-H188A_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in rpd3-H188A cells


title: H4_rco1D_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in rco1D cells


title: H4K5Ac_rco1D_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in rco1D cells

value: H4K5Ac (Upstate)


title: H4K5Ac_spt4D_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in spt4D cells


title: H4_rco1-dPHD_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in rco1-dPHD cells


title: Stem-Cell vs Paneth-Cell sort_1

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction Software (V.9.5.3, Agilent Technologies).

source_name: FACS sorted epithelial intestinal cells cells from Lgr5-EGFP-ires-CreERT2 mice

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Intestinal cell fractions from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations: stem cells were sorted based on high level of GFP expression (GFPhi) and Paneth cells were sorted based on high level of CD24 expression (CD24hi) and high side-scatter (SSChi).

extract_protocol: Rna was isolated using Trizol (Invitrogen)

value: paneth cell

tag: cell phenotype

value: GFPhi

value: intestinal stem cell


title: H4_eaf3-dCHD_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in eaf3-dCHD cells

tag: strain


title: H4K5Ac_spt4D_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in spt4D cells


title: H4_rco1-dPHD_vs_WCE_#1

description: Biological replicate 1 of 2. H4 occupancy measured by the IP/input ratio in rco1-dPHD cells


title: H4K5Ac_rco1D_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in rco1D cells


title: H4K5Ac_eaf3-dCHD_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in eaf3-dCHD cells


title: H4K5Ac_rpd3-H188A_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in rpd3-H188A cells


title: H4K5Ac_rco1-dPHD_vs_WCE_#1

description: Biological replicate 1 of 1. H4K5Ac occupancy measured by the IP/input ratio in rco1-dPHD cells


title: H4K5Ac_eaf3-dCHD_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in eaf3-dCHD cells


title: Stem-Cell vs Paneth-Cell sort_1 swap

value: GFPhigh


title: H4K5Ac_rpd3-H188A_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in rpd3-H188A cells


title: H4K5Ac_3xMTase-KO_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: H4K5Ac_3xMTase-KO_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: H4K5Ac_H3K36A_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in H3K36A cells


title: H4K5Ac_H3K36A_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in H3K36A cells


title: H4K5Ac_WT_vs_WCE_#2

description: Biological replicate 2 of 2. H4K5Ac occupancy measured by the IP/input ratio in WT cells


title: H3K36me3_WT_vs_H4_#1

description: Biological replicate 1 of 1. H3K36me3 occupancy measured by the IP/H4 ratio in WT cells

value: H3K36me3 (Abcam)


title: RXT2-9Myc_WT_vs_NoTag_#1

description: Biological replicate 1 of 2. RXT2-9Myc occupancy measured by the IP/NoTag ratio in WT cells

value: Anti-Myc 9E10 (Young Lab)


title: SPT4-9Myc_WT_vs_NoTag_#2

description: Biological replicate 2 of 2. SPT4-9Myc occupancy measured by the IP/NoTag ratio in WT cells

value: Anti-Myc 9E11 (Verreault Lab)


title: RNAPII_spt4D_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in spt4D cells

value: 8WG16 (Young Lab)


title: RNAPII_rco1D_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in rco1D cells


title: RNAPII-Ser2-Pi_WT_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII-Ser2-Pi occupancy measured by the IP/input ratio in WT cells

value: H5 (Covance)


title: RNAPII-Ser2-Pi_WT_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII-Ser2-Pi occupancy measured by the IP/input ratio in WT cells


title: RNAPII_spt4D_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in spt4D cells


title: RXT2-9Myc_WT_vs_NoTag_#2

description: Biological replicate 2 of 2. RXT2-9Myc occupancy measured by the IP/NoTag ratio in WT cells


title: H4K5Ac_WT_vs_WCE_#1

description: Biological replicate 1 of 2. H4K5Ac occupancy measured by the IP/input ratio in WT cells


title: SDS3-9Myc_WT_vs_NoTag_#1

description: Biological replicate 1 of 1. SDS3-9Myc occupancy measured by the IP/NoTag ratio in WT cells


title: SPT4-9Myc_WT_vs_NoTag_#1

description: Biological replicate 1 of 2. SPT4-9Myc occupancy measured by the IP/NoTag ratio in WT cells


title: H4K5Ac_set2D_vs_H4_#1

description: Biological replicate 1 of 1. H4K5Ac occupancy measured by the IP/H4 ratio in set2D cells


title: RNAPII_rco1D_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in rco1D cells


title: RNAPII_rpd3-H188A_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in rpd3-H188A cells


title: RNAPII_rpd3-H188A_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in rpd3-H188A cells


title: RNAPII_eaf3-dCHD_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in eaf3-dCHD cells


title: RNAPII_rco1-dPHD_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in rco1-dPHD cells


title: RNAPII_3xMTase-KO_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: RNAPII_H3K36A_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in H3K36A cells


title: RNAPII_3xMTase-KO_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: RNAPII_H3K36A_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in H3K36A cells


title: RCO1-9Myc_kin28-AS_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in kin28-AS cells

growth_protocol: Cultures were started in 50mL YEP+2% Glucose from one colony of appropriate strain and incubated overnight to OD600 0.8-1.0. The NA-PP1 ATP analog was added at a final concentration of 6uM for 15min before harvesting. Cultures were poured in 50mL Falcon tube containing 1.6mL 32% paraformaldehyde, put on rotating wheel at room temperature for 30min, and then at 4C for 90min, still on the wheel. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine.

extract_protocol: Crosslinked cells were washed twice with 50mL ice cold TBS, resuspended in 500uL lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin) and acid-washed glass beads were added to the meniscus. Cells were lysed using bead-beater (3x1 min, with 5min breaks on ice). The whole cell extract was mixed with 500ul of lysis buffer and centrifuged at 14000rpm for 1 minute. The pellet was resuspended in 1 ml of lysis buffer and washed twice more. The resulting extract was sonicated 6x9 minutes (30 sec on/1 min off) using a Diagenode sonicator and subsequently centrifuged at 14000rpm for 5 minutes. The supernatant containing the sonicated chromatin was transferred to a new tube.    For the immunoprecipitation, beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 2mL PBS + 5% BSA. Antibodies (at the concentration indicated below) are added and incubated overnight at 4C in haematological mixer. Beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 30uL PBS + 5% BSA / ChIP. 400-500uL of lysate are added to 30uL beads, and incubated overnight at 4C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 45uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl, pH 8.0; 250mM LiCl; 0.5% NP40; 0.5% Na-deoxycholate; 1mM EDTA. Reference: Drouin S., Robert F. Methods (in press). The 9E11 antibody (provided by Alain Verreault, IRIC) was used (5uL / ChIP) with anti-mouse Dynabeads (50uL / ChIP).    To clean up the DNA, the chromatin-containing supernatant was mixed with 350ul of TE containing 3ul of RNAseA (10mg/mL) and 2ul of glycogen (20mg/mL) and incubated for 2 hours at 37C. To digest the proteins, 15ul of 10% SDS and 7.5ul Proteinase K (20mg/ml) were added and the mixture was incubated for an additional 2 hours at 37C. The samples were extracted 2x with 400uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated with 1 mL of 100% ethanol and 14uL of 5M NaCl, the samples were centrifuged at 14,000rpm for 20 minutes at 4C. The DNA pellet was washed in 1 mL of 70% ethanol, dried and resuspended in 60ul of TE.


title: RCO1-9Myc_spt4D_set2D_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D_set2D cells

growth_protocol: Cultures were started in 50mL YEP+2% Glucose from one colony of appropriate strain and incubated overnight to OD600 0.8-1.0. Cultures were poured in 50mL Falcon tube containing 1.6mL 32% paraformaldehyde, put on rotating wheel at room temperature for 30min, and then at 4C for 90min, still on the wheel. Crosslinking was stopped by addition of 2.5mL 2.5M Glycine.

extract_protocol: Crosslinked cells were washed twice with 50mL ice cold TBS, resuspended in 500uL lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin) and acid-washed glass beads were added to the meniscus. Cells were lysed using bead-beater (3x1 min, with 5min breaks on ice). The whole cell extract was mixed with 500ul of lysis buffer and centrifuged at 14000rpm for 1 minute. The pellet was resuspended in 1 ml of lysis buffer and washed twice more. The resulting extract was sonicated 6x9 minutes (30 sec on/1 min off) using a Diagenode sonicator and subsequently centrifuged at 14000rpm for 5 minutes. The supernatant containing the sonicated chromatin was transferred to a new tube.    For the immunoprecipitation, beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 2mL PBS + 5% BSA. Antibodies (at the concentration indicated below) are added and incubated overnight at 4C in haematological mixer. Beads are washed twice with 10mL PBS + 5% BSA (freshly made), and resuspended in 30uL PBS + 5% BSA / ChIP. 400-500uL of lysate are added to 30uL beads, and incubated overnight at 4C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and once with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 45uL TE + 1% SDS to 5uL WCE, and put overnight at 65C to reverse the crosslinks. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5; 140mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate. Wash Buffer: 10mM Tris-HCl, pH 8.0; 250mM LiCl; 0.5% NP40; 0.5% Na-deoxycholate; 1mM EDTA. Reference: Drouin S., Robert F. Methods (in press). The 9E11 antibody (provided by Alain Verreault, IRIC) was used (5-10uL / ChIP) with anti-mouse Dynabeads (50uL / ChIP).    To clean up the DNA, the chromatin-containing supernatant was mixed with 350ul of TE containing 3ul of RNAseA (10mg/mL) and 2ul of glycogen (20mg/mL) and incubated for 2 hours at 37C. To digest the proteins, 15ul of 10% SDS and 7.5ul Proteinase K (20mg/ml) were added and the mixture was incubated for an additional 2 hours at 37C. The samples were extracted 2x with 400uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated with 1 mL of 100% ethanol and 14uL of 5M NaCl, the samples were centrifuged at 14,000rpm for 20 minutes at 4C. The DNA pellet was washed in 1 mL of 70% ethanol, dried and resuspended in 60ul of TE.


title: RNAPII_WT_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in WT cells


title: RNAPII_rco1-dPHD_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in rco1-dPHD cells


title: RNAPII_set2D_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in set2D cells


title: RCO1-9Myc_bur1-AS_vs_NoTag_#1

description: Biological replicate 1 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in bur1-AS cells


title: RCO1-9Myc_ctk1D_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in ctk1D cells


title: RCO1-9Myc-dPHD_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in rco1-dPHD cells


title: RCO1-9Myc_spt4D_set2D_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D_set2D cells


title: RCO1-9Myc_spt4D_vs_NoTag_WT_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D cells


title: RCO1-9Myc_spt5-dCTD_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt5-dCTD cells


title: RCO1-9Myc_bur1-AS_vs_NoTag_#3

description: Biological replicate 3 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in bur1-AS cells


title: RCO1-9Myc_spt4D_ctk1D_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D_ctk1D cells


title: H4_3xMTase-KO_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in 3xMTase-KO cells


title: RCO1-9Myc-dPHD_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in rco1-dPHD cells


title: RCO1-9Myc_ctk1D_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in ctk1D cells


title: RCO1-9Myc_bur1-AS_vs_NoTag_#2

description: Biological replicate 2 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in bur1-AS cells


title: RNAPII_eaf3-dCHD_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in eaf3-dCHD cells


title: RCO1-9Myc_kin28-AS_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in kin28-AS cells


title: RNAPII_set2D_vs_WCE_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/input ratio in set2D cells


title: RCO1-9Myc_spt4D_vs_NoTag_WT_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D cells


title: RNAPII_WT_vs_WCE_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/input ratio in WT cells


title: H4_rpd3-H188A_vs_WCE_#2

description: Biological replicate 2 of 2. H4 occupancy measured by the IP/input ratio in rpd3-H188A cells


title: RCO1-9Myc_spt4D_ctk1D_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt4D_ctk1D cells


title: RCO1-9Myc_spt5-dCTD_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in spt5-dCTD cells


title: RCO1-9Myc_3xMTase-KO_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in 3xMTase-KO cells


title: RCO1-9Myc_eaf3-dCHD_vs_NoTag_#1

description: Biological replicate 1 of 1. RCO1-9Myc occupancy measured by the IP/NoTag ratio in eaf3-dCHD cells


title: RCO1-9Myc_H3K36A_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in H3K36A cells


title: RCO1-9Myc_H3K36A_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in H3K36A cells


title: RCO1-9Myc_3xMTase-KO_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in 3xMTase-KO cells


title: RCO1-9Myc_set2D_vs_NoTag_#2

description: Biological replicate 2 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in set2D cells


title: RCO1-9Myc_WT_vs_NoTag_#2

description: Biological replicate 2 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in WT cells


title: RCO1-9Myc_WT_vs_NoTag_#3

description: Biological replicate 3 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in WT cells


title: RCO1-9Myc_set2D_vs_NoTag_#1

description: Biological replicate 1 of 2. RCO1-9Myc occupancy measured by the IP/NoTag ratio in set2D cells


title: p4801_NSCLC - adenocarcinoma

status: Public on Nov 27 2010

city: Melbourne

first: Holger

last: Schlueter

state: Victoria

address: Locked Bag 1

department: Research

institute: Peter Mac Callum cancer Centre

hyb_protocol: Hybridisation: The dried pellet was resuspended in 4.7ul of 20x SSC and 15µl deionised formamide (filtered, 0.22 µm, Millipore), and the solution was heated at 100ºC for 3 minutes. 0.3 µl of 10% SDS (filtered, 0.22 µm, Millipore) was added, and then the denatured target was applied to a coverslip (24mm x 40mm, Menzel-Glaser) and transferred to a microarray slide by inverting the slide over the coverslip. The slide was immediately placed in the humidified chamber and hybridised at 42C for 14-16 hours. Between 1 and 6 microarrays were performed at a time. Washing: Following hybridisation, slides were washed to remove excess labeled target and reagents. All wash reagents were filtered through a 0.22 µm bottle-top filter and all steps were performed in light-proof containers. Coverslips were removed by immersion in 50ml of Wash 1 (0.5x SSC and 0.01% SDS) in a glass Coplin jar for approximately 60 seconds. Slides were then placed in a darkened container containing ~250ml of Wash 1 and agitated gently at room temperature for 1 minute. In new darkened containers, slides were washed for 3 minutes with ~250ml of Wash 2 (0.5x SSC), then ~250ml of Wash 3 (0.06x SSC). Wash 3 was repeated for 30 seconds prior to removing slides and drying in a centrifuge (Hareus Megafuge) at 800rpm for 5 minutes.

scan_protocol: Scanning of microarrays was performed using a dual laser microarray scanner (model G2505B, Agilent Technologies). The confocal laser used excitatory wavelengths of 532 nm and 635 nm for Cy3 and Cy5 channels, respectively.

data_processing:
Data was presented using Feature Extraction Software (Version 7.5, Agilent Technologies) as a 16-bit TIFF image for each channel, and was reviewed using a pseudo-colour overlay image of the Cy5/Cy3 channels, with red allocated to Cy5 and green to Cy3. The images allowed for visual assessment of spot morphology, signal intensity and background or other staining artifacts.
Genepix Pro software (version 5.1, Axon Instruments) was used to extract data from scanned TIFF images. This program defined each spot by a grid reference and quantified each channel separately. It calculated spot intensity by plotting intensity by area and calculating the area under the curve. The program also identified regions outside the area of maximum intensity as background and recorded this value in another field. For each channel (Cy3 and Cy5) there was a value for mean intensity and mean background, recorded in a text file that could be imported into appropriate software for data analysis and data imaging.

source_name: NSCLC - adenocarcinoma

label_protocol:
An aliquot of 4-10μg of amplified RNA (aRNA) was transferred to a dome cap 200 µl PCR tube (Scientific Specialties Inc.) which contained 2.5 µl of a set of exogenous RNA templates used for internal quality control (ScorecardTM, Amersham Biosciences), then random hexamer primer and Rnase-free water were added .After annealing at 70ºC for 10 minutes 5x RT buffer (Promega), Rnase-free water and reverse transcriptase MMLV Rnase H-point mutant were added, and the samples incubated at 42C for 2.5 hours, to facilitate reverse transcription. Each sample was then hydrolysed with the addition of 0.25M sodium hydroxide, 0.5M EDTA and 0.2M acetic acid. Test and reference samples were transferred to separate 1.5 ml tubes (Ependorf) containing 5 volumes (300 µl) of PB Buffer (Qiagen PCR purification kit, Qiagen). The PCR purification protocol was then used according to manufacturer’s instructions, with a vacuum used in place of centrifuging. All steps were carried out at room temperature using the mini Qiaquick PCR chromatography columns (800 µL column capacity), and separate columns were used for test and reference samples. Following purification, samples were not eluted and Cy-5 and Cy-3 dyes were added to test and reference columns respectively, then incubated for 1 hour at room temperature in the dark.
A second round of PCR purification followed, and labelled targets (Cy3-test and Cy5-reference) were eluted into a single eppendorf tube which contained a blocking mix consisting of: 3 µl tRNA (4 mg/ml), 3 µL Cot-1 DNA (10 mg/ml), 0.75 µL Poly dA (8 mg/ml) and 0.75 µl 50x Denhart’s containing herring sperm DNA that was designed to block non-specific hybridization. The solution was then dried in a vacuum centrifuge set at 60ºC for approximately 40 minutes.

extract_protocol:
Extraction of RNA was performed on each sample using an established technique at Peter Mac – ‘Trizol/RNeasy total RNA extraction for human/animal tissues’.
In summary, approximately 15-30mg of tissue was crushed on dry ice, combined with 2ml of Trizol and homogenised at room temperature using an Ultraturrax probe (John Morris Scientific). After the addition of 400μl chloroform, the homogenate was shaken vigorously for 30 seconds, then left to stand at room temperature for 5 minutes. Samples were then centrifuged at 11,000rpm at 4C for 15 minutes. The clear supernatant was carefully removed, without disturbing the interface, and transfered to a clean tube. The supernatant was mixed by vigorous shaking with an equal volume (~1-2ml) of 70% alcohol, then transferred to an RNeasy (Qiagen) column and placed on a vacuum. The column was washed with 700μl Buffer RW1 (Qiagen), followed by 2 washes with 500μl Buffer RPE (Qiagen). To ensure the membrane was clean and dry, the RNeasy (Qiagen) column was placed into a 2ml collection tube and centrifuged in a microcentrifuge at full speed for 1 minute. The flow through and collection tube was discarded. Finally, the column was eluted twice with 50ul RNase-free water, with collection of the eluate in a new 1.5ml collection tube. A spectrophotometer was used to measure RNA concentration by estimating absorbance at 260 nm and 280 nm. A ratio of <1.8 suggested poor quality RNA and was not used. Purified RNA was precipitated in 0.1 volumes of 3 M Sodium Acetate and 2 volumes of 100% ethanol and stored in a -20C freezer overnight. After centrifuging at 13,000rpm at 4C for 15 minutes, the supernatant was discarded and the pellet washed with 500μl 70% ethanol. The pellet was then resuspended in an appropriate volume of RNase-free water to give a final RNA concentration between 1 – 8ug/μl. A repeat assessment of RNA concentration was performed and samples were stored in -80C until required for transcriptional studies.  RNA yields of approximately 0.5-1.0μg per mg of tissue were typically obtained using this approach.
Reference sample is comprised of pooled RNA from following 11 cell lines: MCF7, breast adenocarcinoma-derived cell line, adherent, ATCC HTB-22; Hs578T, breast adenocarcinoma-derived cell line (stromal-like), adherent, ATCC HTB-126; NTERA2, teratoma-derived cell line, adherent, ATCC CRL-1973; Colo205, colon tumor-derived cell line, mixed, ATCC CCL-222; OVCAR-3, ovarian tumor-derived cell line, adherent, ATCC HTB-161; UACC-62, melanoma-derived cell line, adherent, Stinson et al. (1992); MOLT-4, T cell leukemia-derived cell line, suspension, ATCC CRL-1582; RPMI 8226, multiple myeloma-derived cell line, suspension, ATCC CCL-155; NB4+ATRA, acute promyelocytic leukemia-derived cell line, suspension, Lanotte et al. (1991); SW872, liposarcoma-derived cell line, adherent, ATCC HTB-92; HepG2, liver tumor-derived cell line, adherent, ATCC HB-8065

tag: tissue

value: non-small cell lung cancer

tag: tumor type

value: adenocarcinoma

value: male

tag: smoking status

value: Ex

tag: p53 mutation

value: y

tag: kras mutation

tag: pik3ca mutation

value: n

source_name: RNA from 11 pooled cell lines

tag: reference type

value: pooled RNA from 11 cell lines


title: p7769_NSCLC - large cell carcinoma

source_name: NSCLC - large cell carcinoma

value: large cell carcinoma

tag: gender

tag: time to recurrence or censorship (months)


title: P7759_NSCLC - adenocarcinoma


title: p7890_NSCLC - large cell carcinoma

value: exon 20 A3140G


title: p7941_NSCLC - squamous cell carcinoma

source_name: NSCLC - squamous cell carcinoma

value: squamous cell carcinoma


title: p7793_NSCLC - adenocarcinoma_rep1


title: p7793a_NSCLC - adenocarcinoma_rep2


title: P7870_NSCLC - large cell carcinoma

value: Never

value: u


title: P7876_NSCLC - adenocarcinoma


title: p959_NSCLC - large cell carcinoma


title: P7798_NSCLC - large cell carcinoma

value: female


title: P7815_NSCLC - adenocarcinoma

value: Current


title: p7622_NSCLC - adenocarcinoma


title: p7662_NSCLC - large cell carcinoma


title: RCO1-9Myc_WT_vs_NoTag_#1

description: Biological replicate 1 of 3. RCO1-9Myc occupancy measured by the IP/NoTag ratio in WT cells

value: Anti-Myc 9E11 (Verreault Lab)


title: p7501_NSCLC - adenocarcinoma


title: p7793c_NSCLC - adenocarcinoma_rep3


title: p7556_NSCLC - large cell carcinoma


title: p7797_NSCLC - adenocarcinoma

value: exon 9 A1634G


title: p7584_NSCLC - adenocarcinoma


title: p7381_NSCLC - squamous cell carcinoma


title: p7379_NSCLC - adenocarcinoma


title: p7386_NSCLC - squamous cell carcinoma


title: p7289_NSCLC - adenocarcinoma


title: p7443_NSCLC - squamous cell carcinoma


title: p7179_NSCLC - squamous cell carcinoma


title: p6832_NSCLC - adenocarcinoma


title: p7164_NSCLC - adenocarcinoma


title: p7041_NSCLC - large cell carcinoma


title: p7015a_NSCLC - squamous cell carcinoma_rep2


title: p6899_NSCLC - adenocarcinoma


title: p7015_NSCLC - squamous cell carcinoma_rep1


title: p6385_NSCLC - squamous cell carcinoma


title: p6988_NSCLC - adenocarcinoma_rep1


title: P6621_NSCLC - squamous cell carcinoma


title: p6139_NSCLC - adenocarcinoma


title: p6988a_NSCLC - adenocarcinoma_rep2


title: p5570_NSCLC - squamous cell carcinoma


title: p6930_NSCLC - adenocarcinoma


title: p5880_NSCLC - adenocarcinoma


title: p5872_NSCLC - large cell carcinoma


title: p6270_NSCLC - adenocarcinoma


title: p5927_NSCLC - large cell carcinoma


title: p6977_NSCLC - large cell carcinoma


title: p5493_NSCLC - squamous cell carcinoma


title: p5966_NSCLC - large cell carcinoma


title: p5449_NSCLC - adenocarcinoma


title: P5443_NSCLC - adenocarcinoma


title: P5412_NSCLC - squamous cell carcinoma


title: p4652_NSCLC - adenocarcinoma


title: p4801b_NSCLC - adenocarcinoma_rep2


title: p4759_NSCLC - adenocarcinoma


title: p4787_NSCLC - squamous cell carcinoma


title: P7743_NSCLC - large cell carcinoma


title: p4643_NSCLC - squamous cell carcinoma


title: p4801a_NSCLC - adenocarcinoma_rep1


title: p4433_NSCLC - adenocarcinoma


title: p4314_NSCLC - adenocarcinoma


title: p3298_NSCLC - adenocarcinoma


title: p4140_NSCLC - large cell carcinoma


title: p4333_NSCLC - adenocarcinoma


title: p4207_NSCLC - squamous cell carcinoma


title: p4162_NSCLC - large cell carcinoma


title: p3660_NSCLC - adenocarcinoma


title: p3938_NSCLC - large cell carcinoma


title: p3965_NSCLC - large cell carcinoma


title: p4125_NSCLC - squamous cell carcinoma


title: p2569_NSCLC - large cell carcinoma


title: p4081_NSCLC - squamous cell carcinoma


title: p2298_NSCLC - squamous cell carcinoma


title: p2198a_NSCLC - adenocarcinoma_rep2


title: p1983_NSCLC - squamous cell carcinoma_rep1


title: p1909_NSCLC - squamous cell carcinoma


title: p1906_NSCLC - squamous cell carcinoma


title: p4006_NSCLC - adenocarcinoma


title: p1983a_NSCLC - squamous cell carcinoma_rep2


title: p2176_NSCLC - large cell carcinoma


title: p1770_NSCLC - adenocarcinoma


title: p1706_NSCLC - squamous cell carcinoma


title: p2198_NSCLC - adenocarcinoma_rep1


title: p1666_NSCLC - squamous cell carcinoma


title: Non-instigator 2

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

institute: Lund University

description: Gene expression data from Sorted Sca1+/cKit- derived from mice breaing PC3 non-instigating tumor

hyb_protocol: Affymetrix standard protocol, Affymetrix MG-430A microarrays.

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protocol

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

source_name: Sca1+/cKit- BMCs

label_protocol: Biotinylated cRNA were prepared according to the standard NuGen Ovation Biotin labeling system

extract_protocol: Total RNA was extracted from BMCs using RNA extraction kits according to the manufacturer’s instructions (Qiagen)

tag: cell type

value: Sca1+/cKit- BMCs

tag: source

value: PC3 non-instigating tumor


title: Non-instigator 3


title: p1324_NSCLC - large cell carcinoma

value: non-small cell lung cancer


title: Non-instigator 4


title: p1409_NSCLC - squamous cell carcinoma

value: male


title: p1611_NSCLC - squamous cell carcinoma

value: Ex


title: p1082_NSCLC - adenocarcinoma

value: adenocarcinoma

value: y


title: p1323_NSCLC - squamous cell carcinoma

value: n

value: pooled RNA from 11 cell lines


title: Non-instigator 1


title: Non-instigator 5


title: Instigator 5

value: BPLER instigating tumor


title: Instigator 4

description: Gene expression data from Sorted Sca1+/cKit- derived from mice breaing BPLER instigating tumor


title: Instigator 3


title: Subject SP8 dye swap

city: Chieti

first: Rosa

last: Mancinelli

state: Chieti

address: via Dei Vestini 29

department: Dept. Basic and Applied Medical Sciences

country: Italy

institute: University "G. d'Annunzio" Chieti-Pescara, Chieti

hyb_protocol: Optimal amount of aRNA-Cy3 and aRNA-Cy5 were co-precipitated adding 4/5 volume of ammonium acetate 5 M and 2.5 volumes of absolute ethanol. The sample was dissolved using 120 μl of hybridization buffer (SSC 20 x 500 μL, SDS 10% 20 μL, formamide 1000 μL, distilled water 480 μL) and 3 μL of RNase-free water, denatured at 90 °C for 2 min and applied directly to the microarray slides then covered with a coverslip. The microarray slide was seeded and sealed in the hybridization chamber and incubate for two days in a bath at 48 °C. After hybridization, slides were washed sequentially with a 1 x SSC/0.2% (w/v) SDS solution, a 0.1 x SSC/0.2% (w/v) SDS solution, a 0.2 x SSC solution and a 0.1 x SSC solution (4 min for each wash) in the dark at room temperature.

scan_protocol: Array was scanned using a GSI Lumonics LITE dual confocal laser scanner with a ScanArray Microarray Analysis System (PerkinElmer).

data_processing: Raw images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). The expression levels of all spot replicates were normalized by applying the Lowess (Locfit) normalization procedure using MIDAS (the TIGR Microarray Data Analysis System) before performing any statistical analyses. The normalized and background corrected intensities are used to calculate a ratio value. Differentially expressed genes were identified using the SAM (Significant Analysis of Microarrays) permutation test procedure (STANFORD software, http://www-stat.stanford.edu/_tibs/SAM), which defines genes with a computed score larger than the threshold value as significant. Up-regulated genes have positive values, and down-regulated genes have negative values.

source_name: Vastus lateralis muscle pre-expedition

label_protocol: Aliquots (1 μg) of each RNA sample were reverse transcribed using the Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion). An aliquot of aaRNA modified was coupled with fluorofores Cy3 and Cy5 (CyDye Post-Labeling Reactive Dye Packs, # RPN5661, GE Healthcare).

extract_protocol: Total RNA from these Vastus Lateralis muscle biopsies was purified using the standard Tri Reagent protocol (#9424, Sigma-Aldrich).

value: Vastus lateralis needle biopsy

tag: condition

value: control

source_name: Vastus lateralis muscle post-expedition

value: high altitude hypoxia


title: test mouse 2

city: Buffalo

first: David

middle: W

last: Goodrich

state: NY

address: Elm and Carlton

department: Pharmacology&Therapeutics

institute: Roswell Park Cancer Institute

description: Test biological replicate 2 of 2

hyb_protocol: The arrays were secured in a SureHyb chamber and hybridized at 65°C for 17 hours, then washed with Agilent Gene Expression Wash Buffer.

scan_protocol: Array images were captured by scanning at 532nm and 635nm using a Agilent Technologies Scanner G2505B

data_processing: Agilent Feature Extraction Software version 8.5 was used for background subtraction and normalization.

source_name: Rb1R654W/F:Trp53F/F:PB-cre4 mouse

label_protocol: The cRNA probes were synthesized and directly labeled with Cy3-CTP or Cy5-CTP using Agilent's low RNA input linear amplification method per manufacturer's instructions.

growth_protocol: Mice kept under normal husbandry

extract_protocol: RNAeasy (Qiagen) according to instructions

treatment_protocol: No treatment

value: Prostate

tag: age

value: 60 days

value: mixed C57BL/6:129/SVJae:FVB

source_name: three pooled wild type mice


title: Subject SP8


title: Subject SP7 dye swap


title: Matrigel 4

description: Gene expression data from Sorted Sca1+/cKit- derived from mice breaing matrigel

value: Matrigel


title: Subject SP5 dye swap


title: Subject SP3


title: Matrigel 3

value: Sca1+/cKit- BMCs


title: Instigator 2


title: Instigator 1


title: control mouse 1

description: Control biological replicate 1 of 2

source_name: Rb1F/F:Trp53F/F:PB-Cre4 mouse


title: Subject SP3 dye swap


title: Subject SP5


title: control mouse 2

description: Control biological replicate 2 of 2


title: Matrigel 2


title: test mouse 1

description: Test biological replicate 1 of 2


title: Subject SP7


title: Matrigel 1


title: dsrAB_peatsoil_2007_30-40_coreA

status: Public on Nov 26 2010

city: Vienna

first: Doris

last: Steger

state: Vienna

address: Althanstrasse 14

department: Department of Microbial Ecology

country: Austria

institute: University of Vienna

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 30-40 cm, core A

hyb_protocol: For clones 80 ng and for environmental samples 500 ng of labeled dsrAB RNA fragments and defined amounts of labeled RNA targeting the control probes were mixed with 120 µl of hybridization buffer [0.1% SDS, 0.1% 100x Denhardt’s reagent (Invitrogen), 6x SSC and 15% formamide] and incubated at 65°C for 5-15 min prior to hybridization. The ThermoTWISTER incubator (Quantifoil Instruments GmbH, Jena, Germany) and the HybriWell Sealing System HBW2222-FL (Grace BioLabs) were used for hybridization. Microarrays were hybridized for 17 h at 55°C under continuous shaking at 400 rpm. Following hybridization, slides were washed by shaking at room temperature for 5 min in 2x SSC/0.1% SDS, for 5 min in 0.1x SSC, and finally for 20 s in ice-cold double-distilled water. Slides were dried by centrifugation (3 min, 300 g), stored at room temperature in the dark, and scanned the same day.

scan_protocol: Fluorescence images were recorded by scanning the slides at 10-μm resolution with a GenePix Personal 4100A array scanner (Axon Instruments, Molecular Devices Corporation, Sunnyvale, CA, USA). Each pixel line of the selected area was scanned three times and the obtained signals were averaged to generate the fluorescence image. Gain of the photo multiplier tube was adjusted to record images with signal intensities just below the saturation level. Scanned images were saved as multilayer tiff images and analyzed with the GenePix Pro 6.0 software (Axon Instruments). Low quality hybridizations were repeated.

data_processing:
Microarray hybridization results were first corrected for differences in the local background according to SBRPi=SPi ÷ BPi, where SBRPi is the signal-to-noise ratio of the probe spot Pi, SPi is the median pixel intensity of the specific probe spot and BPi is the median pixel intensity of the local background area around probe Pi. To account for variations between different hybridizations, the mean signal-to-noise ratio  SBRCi of ten internal control oligonucleotides (dsrCONT1 to 4, dsrCONT7 to 12) and differences in labeling efficiency were used to normalize the SBRPi using the following formula: nSBRPi = (SBRPi ÷ xSBRPi) ÷ [dye] × [template] × 100, where nSBRPi is the normalized signal-to-noise ratio of the probe spot Pi, [dye] is the concentration of incorporated Cy3 dye molecules in pmol/µl and [template] is the concentration of labeled RNA in ng/µl.
Clone evaluation: hybridization events with normalized signal-to-background ratios (nSBR) below 0.04 were considered negative.

organism: environmental samples

source_name: environmental sample

label_protocol: Target labeling was achieved by in vitro transcription according to the following protocol. 500 ng of purified PCR product, 4 μl 5x T3 RNA polymerase buffer (Fermentas), 2 μl dithiothreitol (100 mM), 0.5 μl RNAsin (40 U/μl) (Promega GmbH, Mannheim, Germany), 1 μl each of ATP, CTP, and GTP (each 10 mM), 0.5 μl UTP (10 mM), 2 μl T3 RNA polymerase (20 U/μl) (Fermentas) and 0.75 μl Cy3-UTP (5 mM) were adjusted with RNase-free water to a total volume of 20 µl and incubated at 37°C for 4 hours. The DNA template was subsequently degraded by adding 2 U DNase I (Fermentas) and incubation at 37°C for 15 min. Enzymatic digestion was stopped with 2 µl of EDTA (25 mM, Fermentas). Following adjustment of the volume to 100 µl with TE buffer (10 mM Tris-HCl, pH 7.5; 1 mM EDTA), RNA was precipitated with 10 µl of 5 M NaCl and 300 µl of ethanol. RNA was washed with 500 µl of ice-cold 70% ethanol and resuspended in 50 µl TE buffer. RNA concentration and the amount of incorporated dye were measured with a ND-1000 spectrophotometer (Nanodrop, Inc.). Labeled RNA was fragmented by incubating with 10 mM ZnCl2 and 20 mM Tris/HCl (pH 7.4) at 60°C for 30 min. Fragmentation was stopped by the addition of 10 mM EDTA pH 8.0. Labeled RNA was divided in several aliquots that were stored at -20°C.

extract_protocol: Environemtal DNA was extracted from approximately 250 mg (wet weight) of each soil sample using the Power SoilTM DNA Kit (MoBio Laboratories, Solana Beach, CA).

tag: target genes

value: dissimilatory (bi)sulfite reductase genes dsrAB

tag: sample type

value: peatsoil sample, 2007 30-40 cm, core A


title: dsrAB_peatsoil_2007_20-30_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 20-30 cm, core B

value: peatsoil sample, 2007 20-30 cm, core B


title: Subject SP1


title: dsrAB_peatsoil_2007_20-30_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 20-30 cm, core C

value: peatsoil sample, 2007 20-30 cm, core C


title: dsrAB_peatsoil_2007_20-30_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 20-30 cm, core A

value: peatsoil sample, 2007 20-30 cm, core A


title: dsrAB_peatsoil_2007_15-20_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 15-20 cm, core B

value: peatsoil sample, 2007 15-20 cm, core B


title: dsrAB_peatsoil_2007_15-20_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 15-20 cm, core A

value: peatsoil sample, 2007 15-20 cm, core A


title: dsrAB_peatsoil_2007_15-20_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 15-20 cm, core C

value: peatsoil sample, 2007 15-20 cm, core C


title: Subject SP1 dye swap


title: dsrAB_peatsoil_2007_30-40_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 30-40 cm, core B

value: peatsoil sample, 2007 30-40 cm, core B


title: KO2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

hyb_protocol: After hybridization the hybridization mixture is removed and the GeneChips® are washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: liver tissue from 21 days old mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA isolated from mouse liver

growth_protocol: Fed state 21 days old mice were taken away from their mother at 8-11am, euthanized and dissected. Livers were snap frozen in liquid N2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up on Qiagen RNeasy columns to remove traces of organic solvents.

treatment_protocol: 15 ACBP-/- and 15 +/+ mice were divided into 6 groups with 5 individuals in each. Thus, each sample is made from a pool of equal amounts of RNA from 5 ACBP-/- or +/+ individuals, respectively.

value: liver

tag: genotype/variation

value: ACBP-/- (KO)


title: WT1

tag: strain

value: wildtype


title: KO3

tag: tissue


title: KO1


title: WT2


title: dsrAB_peatsoil_2007_10-15_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 10-15 cm, core A

value: peatsoil sample, 2007 10-15 cm, core A


title: WT3


title: dsrAB_peatsoil_2007_10-15_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 10-15 cm, core C

value: peatsoil sample, 2007 10-15 cm, core C


title: dsrAB_peatsoil_2007_10-15_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 10-15 cm, core B

value: peatsoil sample, 2007 10-15 cm, core B


title: dsrAB_peatsoil_2007_5-10_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 5-10 cm, core A

value: peatsoil sample, 2007 5-10 cm, core A


title: dsrAB_peatsoil_2007_5-10_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 5-10 cm, core B

value: peatsoil sample, 2007 5-10 cm, core B


title: dsrAB_peatsoil_2007_0-5_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 0-5 cm, core A

value: dissimilatory (bi)sulfite reductase genes dsrAB

value: peatsoil sample, 2007 0-5 cm, core A


title: dsrAB_peatsoil_2007_0-5_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 0-5 cm, core B

value: peatsoil sample, 2007 0-5 cm, core B


title: dsrAB_peatsoil_2007_0-5_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 0-5 cm, core C

value: peatsoil sample, 2007 0-5 cm, core C


title: dsrAB_peatsoil_2004_15-20_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 15-20 cm, core A

value: peatsoil sample, 2004 15-20 cm, core A


title: dsrAB_peatsoil_2004_15-20_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 15-20 cm, core B

value: peatsoil sample, 2004 15-20 cm, core B


title: dsrAB_peatsoil_2004_10-15_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 10-15 cm, core C

value: peatsoil sample, 2004 10-15 cm, core C


title: dsrAB_peatsoil_2004_15-20_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 15-20 cm, core C

value: peatsoil sample, 2004 15-20 cm, core C


title: dsrAB_peatsoil_2004_10-15_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 10-15 cm, core A

value: peatsoil sample, 2004 10-15 cm, core A


title: dsrAB_peatsoil_2007_5-10_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2007 5-10 cm, core C

value: peatsoil sample, 2007 5-10 cm, core C


title: dsrAB_peatsoil_2004_10-15_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 10-15 cm, core B

value: peatsoil sample, 2004 10-15 cm, core B


title: dsrAB_peatsoil_2004_5-10_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 5-10 cm, core A

value: peatsoil sample, 2004 5-10 cm, core A


title: dsrAB_peatsoil_2004_5-10_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 5-10 cm, core C

value: peatsoil sample, 2004 5-10 cm, core C


title: dsrAB_peatsoil_2004_5-10_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 5-10 cm, core B

value: peatsoil sample, 2004 5-10 cm, core B


title: dsrAB_peatsoil_2001_25-30_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 25-30 cm, core B

value: peatsoil sample, 2001 25-30 cm, core B


title: dsrAB_peatsoil_2004_0-5_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 0-5 cm, core B

value: peatsoil sample, 2004 0-5 cm, core B


title: dsrAB_peatsoil_2004_0-5_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 0-5 cm, core A

value: peatsoil sample, 2004 0-5 cm, core A


title: dsrAB_peatsoil_2001_25-30_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 25-30 cm, core C

value: dissimilatory (bi)sulfite reductase genes dsrAB

value: peatsoil sample, 2001 25-30 cm, core C


title: dsrAB_peatsoil_2001_25-30_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 25-30 cm, core A

value: peatsoil sample, 2001 25-30 cm, core A


title: dsrAB_peatsoil_2001_17.5-25_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 17.5-25 cm, core B


title: dsrAB_peatsoil_2001_17.5-25_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 17.5-25 cm, core C


title: dsrAB_peatsoil_2001_17.5-25_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 17.5-25 cm, core A


title: dsrAB_peatsoil_2001_10-17.5_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 10-17.5 cm, core A


title: dsrAB_peatsoil_2001_10-17.5_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 10-17.5 cm, core B


title: dsrAB_peatsoil_2001_10-17.5_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 10-17.5 cm, core C


title: dsrAB_peatsoil_2001_0-10_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 0-10 cm, core C

value: peatsoil sample, 2001 0-10 cm, core C


title: dsrAB_peatsoil_2001_0-10_coreA

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 0-10 cm, core A

value: peatsoil sample, 2001 0-10 cm, core A


title: dsrAB_peatsoil_2004_0-5_coreC

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2004 0-5 cm, core C

value: peatsoil sample, 2004 0-5 cm, core C


title: dsrAB_spikeIn_experiment_100000copies

description: Labeled RNA (by in vitro transcription) from a peatsoil sample containing different concentrations of the clone dsr-36 for determination of detection limit


title: dsrAB_peatsoil_2001_0-10_coreB

description: Labeled dsrAB RNA (by in vitro tanscription) from peatsoil sample, 2001 0-10 cm, core B

value: peatsoil sample, 2001 0-10 cm, core B


title: dsrAB_spikeIn_experiment_10000copies

value: a peatsoil sample containing different concentrations of the clone dsr-36 for determination of detection limit


title: dsrAB clone dsr64

description: Labeled RNA (by in vitro transcription) from dsrAB clone for chip evaluation

organism: uncultured sulfate-reducing bacterium

source_name: dsrAB clone

tag: clone

value: dsrAB clone dsr64

value: dsrAB clone for chip evaluation


title: dsrAB_spikeIn_experiment_1000copies


title: dsrAB_spikeIn_experiment_1copy


title: dsrAB clone dsr3-1-1

value: dsrAB clone dsr3-1-1


title: dsrAB_spikeIn_experiment_10copies


title: dsrAB clone dsr54

value: dsrAB clone dsr54


title: dsrAB_spikeIn_experiment_100copies


title: dsrAB clone dsr88

value: dsrAB clone dsr88


title: dsrAB clone dsr60

value: dsrAB clone dsr60


title: dsrAB clone dsr39

value: dsrAB clone dsr39


title: dsrAB clone dsr82

value: dsrAB clone dsr82


title: dsrAB clone dsr75

value: dsrAB clone dsr75


title: dsrAB clone dsr36

value: dsrAB clone dsr36

value: dissimilatory (bi)sulfite reductase genes dsrAB


title: dsrAB clone dsr40

value: dsrAB clone dsr40


title: dsrAB clone dsr3

value: dsrAB clone dsr3


title: dsrAB clone 47c_20

value: dsrAB clone 47c_20


title: dsrAB clone dsr2

value: dsrAB clone dsr2


title: dsrAB clone 46c_20

value: dsrAB clone 46c_20


title: dsrAB clone 3c_20

value: dsrAB clone 3c_20


title: dsrAB clone 4_40

value: dsrAB clone 4_40


title: dsrAB clone 38c_20

value: dsrAB clone 38c_20

value: dsrAB clone for chip evaluation


title: dsrAB clone dsr9

value: dsrAB clone dsr9


title: dsrAB clone 35_05

value: dsrAB clone 35_05


title: dsrAB clone 34_40

value: dsrAB clone 34_40


title: dsrAB clone 2c_20

value: dsrAB clone 2c_20


title: dsrAB clone 28_05

value: dsrAB clone 28_05


title: dsrAB clone 25c_40

value: dsrAB clone 25c_40


title: dsrAB clone 24c_40

value: dsrAB clone 24c_40


title: dsrAB clone 21_40

value: dsrAB clone 21_40

value: dissimilatory (bi)sulfite reductase genes dsrAB


title: dsrAB clone 2_05

value: dsrAB clone 2_05


title: M229_R5_A_PLX

city: Los Angeles

first: Mikyung

last: Lee

state: CA

address: UCLA Med-Derm BOX 951781, 13-942 Factor, 13-952 Factor Los Angeles, CA 90095-1781

institute: UCLA

hyb_protocol: Labeled cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix) according to the manufacturer's protocol

scan_protocol: Array scanning was carried out with the GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's instructions

data_processing: Expression data were normalized, background-corrected, and log2-transformed for parametric analysis. Differentially expressed genes were identified using significance analysis of microarrays (SAM) with the R package 'samr' (FDR<0.05; fold change>2)

source_name: Human melanoma cell lines

label_protocol: cDNAs were generated from total RNA and biotinylated according to the standard Affymetrix protocol.

growth_protocol: Selected melanoma cell lines were grown in DMEM supplemented with 10% serum

extract_protocol: Total RNA was extracted using RiboPure Kit (Ambion) according to the manufacturer's instructions

treatment_protocol: Cell lines were treated with DMSO control or 1 uM PLX4032 for 6h

value: Human melanoma cell line

tag: cell line

tag: genotype

value: V600E BRAF mutant

tag: treatment group

value: 1 uM PLX4032 for 6h


title: M249_R4_A_PLX


title: M249_A_PLX


title: M229_B_PLX


title: M249_R4_B_PLX


title: M249_B_PLX


title: M229_R5_B_PLX


title: M229_A_PLX


title: dsrAB clone 19d_20

value: dsrAB clone 19d_20


title: M238_R1_B_PLX


title: M238_A_PLX


title: M238_R1_A_PLX


title: M238_B_DMSO

value: DMSO control


title: M249_A_DMSO


title: M238_B_PLX


title: M238_R1_B_DMSO


title: yeast_genomic_DNA_Repl4

first: Fernando

last: Carrillo Oesterreich

address: Pfotenhauerstr. 108

institute: MPI-CBG

description: Saccharomyces genomic DNA preparation Replicate 4

hyb_protocol: For each sample 7.5µg of DNA probes were hybridized using the Affymetrix hybridization kit. Hybridization was performed for 16h at 45°C (Affymetrix GeneChip Hybridization Oven 645).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000.

data_processing:
Raw intensities were extracted from the CEL files. Genomic positions and sequences were allocated for each intensity using the bpmap file. Log10 Intensities for perfect match (pm) and mismatch (mm) were generated. Difference of pm and mm was calculated for each microarray spot. All analysis was performed by user-written software.
results file descriptions: For each chromosomal probe present on the array, chromosome (chrID), chromosomal position (pos), Log10 intensity of perfect match probes (logipm) and mismatch probe (logimm) is given. Furthermore the difference between perfect match and mismatch intensity (gLog(pm-mm)) as well as probe sequence is listed.

organism: Saccharomyces

source_name: wild-type genomic RNA

label_protocol: RNA samples were reversed transcribed (GeneChip Whole Transcript Sense Labeling Kit, Affymetrix), enzymatically fragmented and end-labeled (GeneChip Double-Stranded DNA  Terminal Labeling Kit, Affymetrix). Genomic DNA samples were enzymatically fragmented and end-labeled (GeneChip Double-Stranded DNA  Terminal Labeling Kit, Affymetrix).

extract_protocol: Nascent RNA: Yeast cells were grown at 30C until reaching exponential phase. Cells were rapidly frozen. A chromatin fraction was generated and nascent RNA isolated by phenol-chloroform extraction.  mRNA: Yeast cells were grown at 30C until reaching exponential phase. Total RNA was isolated (Ribo-Pure Yeast Kit, Ambion) and polyadenylated mRNA extracted (MicroPoly(A)Purist Kit, Ambion).  Genomic DNA: Genomic DNA was extracted by phenol-chloroform digestion. Contaminating RNA was removed by enzymatic digestion.


title: yeast_genomic_DNA_Repl3

description: Saccharomyces genomic DNA preparation Replicate 3


title: dsrAB clone 19_20

value: dsrAB clone 19_20


title: dsrAB clone 17_05

value: dsrAB clone 17_05

value: dsrAB clone for chip evaluation


title: yeast_genomic_DNA_Repl2

description: Saccharomyces genomic DNA preparation Replicate 2


title: yeast_genomic_DNA_Repl1

description: Saccharomyces genomic DNA preparation Replicate 1


title: dsrAB clone 15_05

value: dsrAB clone 15_05


title: dsrAB clone 15d_20

value: dsrAB clone 15d_20


title: M229_B_DMSO


title: yeast_mRNA_Repl2

description: Saccharomyces mRNA preparation Replicate 2

source_name: wild-type messenger RNA


title: M229_R5_B_DMSO


title: M238_R1_A_DMSO


title: M238_A_DMSO


title: dsrAB clone 12_20

value: dsrAB clone 12_20


title: yeast_mRNA_Repl3

description: Saccharomyces mRNA preparation Replicate 3


title: dsrAB clone 14_40

value: dsrAB clone 14_40


title: M229_R5_A_DMSO


title: M249_R4_B_DMSO


title: yeast_mRNA_Repl1

description: Saccharomyces mRNA preparation Replicate 1


title: yeast_nascent_RNA_Repl3

type: other

description: Saccharomyces Nascent RNA preparation Replicate 3

molecule: other

source_name: wild-type nascent RNA


title: dsrAB clone 11c_20

value: dsrAB clone 11c_20


title: yeast_nascent_RNA_Repl1

description: Saccharomyces Nascent RNA preparation Replicate 1


title: dsrAB clone 10_05

value: dsrAB clone 10_05


title: dsrAB clone 1_20

value: dsrAB clone 1_20


title: M249_R4_A_DMSO


title: yeast_nascent_RNA_Repl2

description: Saccharomyces Nascent RNA preparation Replicate 2


title: M229_A_DMSO


title: M249_B_DMSO


title: Ol-11Pr [65a]

status: Public on Nov 25 2010

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
qPCR was performed using the 7900HT Fast Real-Time PCR System, TaqMan Universal PCR Master Mix and Taqman MiRNA Array A Card v2.0 (Applied Biosystems)
the qPCR data were processed and outputed by Sequence Dectection System (SDS) Software (Applied Biosystems); the undetermined data were set to the Ct value of 40. The raw Ct values were scrutinized to identify and remove technical sample outliers with exceptionally higher portion of undetermined miRNAs. The Ct values were then normalized by quantile normalization using R package HTqPCR.

label: syberGreen

extract_protocol:
Total RNA was extracted from FFPE tissue samples using RecoverAll Total Nucleic Acid Isolation Kit (Applied Biosystems).  Tissues of ≤80μm were sectioned into sizes of 5-20 μm and underwent deparaffinization, protease digestion, nucleic acid isolation, and nuclease digestion/purification according to the manufacture’s protocol for RNA isoloation.  Sample concentrations were determined using the Qubit Quantification Platform (Invitrogen) and normalized to 10 ng/μL.
cDNA were generated using 30ng of total RNA,  Megaplex RT Primers, Human Pool Set v2.0 and TaqMan MiRNA Reverse Transcription kit (Applied Biosystems)

tag: patient id

tag: classifier

value: Oligomets

tag: disease stage

value: Primary tumor


title: Ol-16Pr [60a]


title: Ol-12Pr [58a]


title: Pol-1Met1 [6b1]

value: Polymets

value: Metastasis


title: Pol-6Pr [4a]


title: Pol-1Met2 [6b2]


title: Pol-3Met [7b]


title: Ol-4Met [5b]


title: Pol-5Met [4b]


title: T. reesei RutC-30 replicate 3

city: VTT, Espoo

first: Marika

last: Vitikainen

address: Tietotie 2

country: Finland

institute: VTT Technical Research Centre

description: aCGH RutC-30.3/QM6a.3

hyb_protocol: According to RocheNimblegen's service workflow protocols

data_processing: RocheNimblegen carried out a 2D lowess spatial normalisation (Edwards et al.,,D. 2003).  Further normalisation was carried out with R  (R Development Core Team 2008) using Bioconductor  (Gentleman et al., 2004). Data was parsed to R with package Ringo (Toedling ea al., 2007) and snapCGH (Smith et al., 2006). The data was first normalised with-in arrays with lowess using package Limma (Smyth et al., 2004) and then normalized between arrays with variance stabilizing normalisation (VSN) (Huber et al., 2002).

organism: Trichoderma reesei

extract_protocol: For DNA isolation the strains were cultivated in Trichoderma minimal medium (Penttila et al., 1987) supplemented with 2 % glucose, 0.2 % peptone for 2 days at 28ºC. Mycelia were collected by filtering, washed with deionised water and lyophilized. DNA was isolated from three parallel cultivations of each strain. DNA was isolated according to Raeder et al., (1985) with modifications. Lyophilized mycelia (100 mg) were first grinded in liquid nitrogen. Mycelia powder was suspended in a buffer 200 mM Tris-HCl pH 8,5, 250 mM NaCl, 25 mM EDTA pH 8,0 and 0,5 % SDS. RNAse was added to the concentration 2,6 mg/ml and samples were incubated in 37°C at least 30 min. Samples were extracted with phenol-chloroform-isoamyl alcohol (24:1) three times followed by extraction with chloroform-isoamyl alcohol (24:1) three times. Isopropanol was added to the volume of 0.54 to precipitate DNA. DNA pellets were washed once with 70 % ethanol, air dried 5 min and suspended in deionised water. Quality and purity of the DNA were analyzed according to Roche NimbleGen guidelines (www.nimblegen.com).

treatment_protocol: no treatment

tag: phenotype

value: Cellulase hyperproducing mutant

value: wild-type QM6a


title: Pol-2Met [59b]


title: T. reesei QM9123 replicate 2

description: aCGH QM9123.2/QM6a.2

scan_protocol: According to RocheNimblegen's service workflow protocols


title: Ol-15Pr [57a]


title: Ol-13Pr [52a]


title: T. reesei RutC-30 replicate 1

description: aCGH RutC-30.1/QM6a.1

label_protocol: According to RocheNimblegen's service workflow protocols


title: Ol-8Met3 [49b2]


title: Pol-1Pr [2a]


title: T. reesei QM9123 replicate 1

description: aCGH QM9123.1/QM6a.1


title: T. reesei RutC-30 replicate 2

description: aCGH RutC-30.2/QM6a.2


title: T. reesei QM9414 replicate 3

description: aCGH QM9414.3/QM6a.3


title: Pol-3Pr [46a]


title: Ol-2Met [31b]


title: Ol-6Pr [244a]


title: Ol-8Met1 [49b1]


title: Pol-7Pr [39a]


title: Ol-7Met [23b]


title: Spleen_control_S4

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Spleen control S4

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Data were normalized using GC-RMA, using the gcrma package in Bioconductor.

source_name: normal spleen sample

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube.

extract_protocol: Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturer’s recommendations.  RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: tissue blocs were kept at -80° till use

value: normal spleen


title: Spleen_control_S5

description: Spleen control S5


title: T. reesei QM9414 replicate 1

description: aCGH QM9414.1/QM6a.1


title: T. reesei QM6a replicate 1

description: aCGH QM6a.1/QM6a.1 self-hybridization


title: Ol-5Pr [231a]


title: Ol-5Met [236b]


title: Spleen_control_S3

description: Spleen control S3


title: Ol-3Pr [26a]


title: T. reesei QM6a replicate 2

description: aCGH QM6a.2/QM6a.2 self-hybridization


title: Spleen_control_S2

description: Spleen control S2


title: Pol-4Pr [230a]


title: T. reesei QM6a replicate 3

description: aCGH QM6a.3/QM6a.3 self-hybridization


title: T. reesei NG14 replicate 3

description: aCGH NG14.3/QM6a.3


title: Ol-19Pr2 [22c]


title: T. reesei QM9414 replicate 2

description: aCGH QM9414.2/QM6a.2


title: MALT_Lymphoma_LLX1_t(11;18)-negative

description: MALT lymphoma LLX1

source_name: MALT lymphoma


title: Ol-9Met [22b]


title: Ol-7Pr [220a]


title: Ol-1Pr [221a]


title: T. reesei NG14 replicate 1

description: aCGH NG14.1/QM6a.1


title: T. reesei NG14 replicate 2

description: aCGH NG14.2/QM6a.2


title: Ol-2Pr [217a]


title: Ol-10Pr [209a]


title: Ol-4Pr [27a]


title: Ol-19Pr1 [22a]


title: MALT_Lymphoma_LL38_t(11;18)-negative

description: MALT lymphoma LL38


title: MALT_Lymphoma_LL69_t(11;18)-negative

description: MALT lymphoma LL69


title: MALT_Lymphoma_LL96_t(11;18)-positive

description: MALT lymphoma LL96


title: MALT_Lymphoma_LL18_t(11;18)-negative

description: MALT lymphoma LL18


title: MALT_Lymphoma_LL79_t(11;18)-positive

description: MALT lymphoma LL79


title: Spleen_control_MIX

description: Spleen control (MIX)

source_name: mix of normal spleen samples

value: multiple normal spleens


title: MALT_Lymphoma_LL29_t(11;18)-positive

description: MALT lymphoma LL29


title: MALT_Lymphoma_LL57_t(11;18)-positive

description: MALT lymphoma LL57


title: Ol-3Met [202b]


title: Spleen_control_S1

description: Spleen control S1


title: MALT_Lymphoma_LL65_t(11;18)-negative

description: MALT lymphoma LL65


title: Pol-4Met [204b]


title: Pol-5Pr [1a]


title: Ol-1Met [18b]


title: M229

hyb_protocol: Fragmented DNA was first precipitated and then hybridized to BeadChip (Infinium II Assay) according to manufacturer's protocol

data_processing: Scanned array data were imported into BeadStudio software (Illumina Inc.) for data processing

label: C-Bio and A-DNP

label_protocol: Fragmented template DNA was first captured on the BeadChip and then incorporation of labeled nucleotides during oligos extension were used to determine the genotype call for the sample

extract_protocol: Genomic DNA was extracted using FlexiGene DNA Kit (Qiagen) according to the manufacturer's protocol

tag: cell type

value: Human melanoma cell lines


title: Ol-9Pr [18a]


title: Ol-6Met1 [15b]


title: Pol-2Pr [06_03_10_6a]


title: M238


title: Ol-17Pr [15a]


title: Ol-8Pr [13a]


title: M238-R1


title: M229-R5


title: LPS

type: protein

city: louisville

first: huizhi

last: wang

state: kY

address: 501 S.Preston St. Room 211B

department: PEDH

institute: University of Louisville

hyb_protocol: Full Moon service

scan_protocol: Full Moon service

data_processing: Interarray quantile normalization performed by Full Moon service

molecule: protein

source_name: human monocytes stimulated with LPS alone

label_protocol: Full Moon service

extract_protocol: Protein was isolated according to the Full Moon protocol (available on Full Moon website)

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors as per protocols approved by the University of Louisville,

value: human monocytes isolated form healthy donor's PBMC

tag: agent

value: LPS


title: LPS+Rapamycin

source_name: human monocytes stimulated with LPS and rapamycin

value: LPS+Rapamycin


title: S-SS2cy3

city: Thiverval-Grignon

first: Marie-Pierre

last: FORQUIN

address: Aveniue de la Bretigniere

department: MICA

country: France

institute: INRA

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Array scanning was carried out with a GenePix 4000A dual-channel (635 nm and 532 nm) laser scanner (GenePix) with a resolution of 10 nm per pixel. The laser power was set at 100, and the photomultiplier tension was adjusted between 680 and 800 V, according to the average intensity of the hybridization of each slide in order to optimize the dynamic range of measurements.

data_processing: R limma package - Normalization : normalizeWithinArrays loess - Statistical analysis :R Anapuce R package.

organism: Brevibacterium aurantiacum

source_name: Sulfate

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP and cy5-UTP or cy3UTP dyes in the dark.

growth_protocol: B.aurantiacum ATCC9175 was grown in ESM in the presence of 500 µM sulfate or after resuspension of the cells after two hours in the absence of any sulfur source

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

value: ATCC 9175

source_name: Sulfate starvation


title: S-SS1cy3


title: MALT_Lymphoma_LL52_t(11;18)-negative

description: MALT lymphoma LL52


title: S-SS3cy5


title: S-SS2cy5


title: MALT_Lymphoma_LL39_t(11;18)-positive

description: MALT lymphoma LL39


title: S-SS3cy3


title: MALT_Lymphoma_LL27_t(11;18)-positive

description: MALT lymphoma LL27


title: MALT_Lymphoma_LL49_t(11;18)-negative

description: MALT lymphoma LL49


title: MALT_Lymphoma_LL5_t(11;18)-negative

description: MALT lymphoma LL5


title: S-MC1cy3

growth_protocol: B.aurantiacum ATCC9175 was grown in EDM in the presence of 500 µM sulfate or 10 mM Methionine plus 500 µM cystine until exponential growth phase.

source_name: Methionine plus Cystine


title: S-MC3cy3


title: S-MC2cy3


title: S-SS1cy5


title: S-MC2cy5


title: S-MC3cy5


title: S-MC1cy5


title: Ol-14Pr [228a]


title: S-C2cy3

growth_protocol: B.aurantiacum ATCC9175 was grown in EDM in the presence of 500 µM sulfate or 500 µM cystine until exponential growth phase.

source_name: Cystine


title: S-C1cy3


title: C-MC2cy5

growth_protocol: B.aurantiacum ATCC9175 was grown in EDM in the presence of 500 µM cystine or 10 mM Methionine plus 500 µM cystine until exponential growth phase.


title: C-MC1cy5


title: C-MC1cy3


title: C-MC2cy3


title: 2dpp testis culture win18446-2

city: Pullman

first: Ryan

last: Evanoff

state: WA

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression data from 2ddp testis cultured for 24h in presence of WIN 18,446.

hyb_protocol: Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Robust Multi-array Average(GC-RMA) using Genespring 11.0 default analysis settings as normalization method.

source_name: 2dpp 129 mouse

label_protocol: Approximately 100 ng total RNA from each sample was used to generate cDNA using the Ovation RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer's instructions.  3.75ug of the cDNA was then fragmented and labelled using the Encore Biotin Module (NuGEN, San Carlos, CA) according to the manufacturer's instructions.

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

treatment_protocol: Tissue was cultured in an agar block placed into a well of a 24-well plate containing 300 µl Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and cultured at 37°C with 5% CO2.  DMSO was used as the vehicle and WIN18,446 was used at a final concentration of 1 µM.

tag: Stage

value: 2 dpp

tag: treatment


title: S-C2cy5


title: S-C1cy5


title: 2dpp testis culture control-2

description: Gene expression data from 2ddp testis cultured for 24h in presence of vehicle.

value: control


title: 2dpp testis culture control-1


title: 2dpp testis culture win18446-1