title: F1_whole seedlings without root, biological rep3

city: Canberra

first: Ryo

last: Fujimoto

state: ACT

address: Cnr Clunies Ross St & Barry Dr

institute: CSIRO

hyb_protocol: A total hybridisation volume of 300ul is prepared for each sample and 200ul loaded into a GeneChip.  The chip is hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.

scan_protocol: After hybridisation, the chip is washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.  Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

organism: Arabidopsis thaliana

source_name: F1_whole seedlings without root

label_protocol: 1-3ug of total RNA was labelled using a cDNA synthesis kit GeneChip Eukaryotic poly-A RNA spikes (Millenium Sciences cat no. 900433) were added to the reaction to determine the labelling efficiency.  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.  Samples that pass this checkpoint are then prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO.

growth_protocol: Controlled enviromental condition (22C) under fluorescent lights and a 16h/8h (day/light) photoperiod.

extract_protocol: Total RNA was isolated from whole plants without root using SV Total RNA Isolation system (Promega)

tag: ecotype

value: F1 hybrid of Col and C24

value: Seedlings


title: Hypoxia  5 days SG2_A5

status: Public on Feb 19 2013

type: RNA

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

country: USA

institute: Seattle Biomedical Research Institute

description:
SG2_A5
Hypoxia
5
days

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization with the 'affy' package for R.

molecule: total RNA

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: TFOE experiments done at indicated concentration of anhydrotetracycline.  Hypoxic experiments conducted as described previously (Rustad et al., 2008)

tag: experiment

tag: replicate

value: A

tag: time

value: 5 days

tag: treatment

value: Hypoxia


title: Kidney 20mgkg-1 rep2

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Probe quality and fragmentation were confirmed using Bioanalyser 2100 prior to microarray hybridisation. Fragmented and labelled probes were hybridised for 18 hours onto Affymetrix GeneChip® Mouse Genome 430 2.0 Array (cat. 900496, Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (cat. 900720-900722, Affymetrix).

scan_protocol: Microarrays were scanned using Genechip Scanner 3000 7G.

data_processing: The data in the matrix table were generated from raw CEL files using RMA normalisation method in Partek GS 6.5 software.

label: biotin

organism: Mus musculus

source_name: Kidney

label_protocol: 50ng RNA from each sample were used to generate complementary DNA strands using Ovation RNA Amplification System V2 (cat. 3100-12, Nugen) and 3.75ug of each cDNA were fragmented and biotin labelled using Encore™ Biotin Module (cat. 4200-12, Nugen).

extract_protocol: RNA extraction was performed in random batches by polytron homogenisation of tissue in Trizol (cat. 15596-026, Invitrogen) followed by phenol chloroform extraction. RNAs were quantitated and qualified using Nanodrop ND8000 (Thermo Scientific) and 2100 Bioanalyser (Agilent). Prior to cDNA probe generation RNAs were subjected to sample clean up and DNAse I treatment using RNEasy Micro (Qiagen) before repeat quantitation and qualification.

tag: tissue

value: Kidney

tag: mouse number

tag: dosage

value: 20 mg/kg

tag: ast (u/l)

tag: creatinine (umol/l)

tag: bun (mmol/l)

tag: ldh (u/l)

tag: ck (u/l)

tag: rna integrity number (rin)

tag: strain


title: Hypoxia  2 days SG2_A2

description:
SG2_A2
Hypoxia
2
days

value: 2 days


title: F1_whole seedlings without root, biological rep1

country: Australia


title: Kidney 6mgkg-1 rep3

value: 6 mg/kg


title: F1_whole seedlings without root, biological rep2


title: single clonally selected and synchronized C42B cell (#12)

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridization probes were prepared by combining 6 mg of Alexa Fluor® 3 labeled sample and 1 mg Alexa Fluor® 5 labeled reference and denatured at 95°C and hybridized at 63°C on Agilent Human 4x44K microarrays and processed following the manufacturer’s specifications.

scan_protocol: Fluorescence array images were collected for Alexa Fluor® 3 and Alexa Fluor® 5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Graphical examination of raw array signal indicated a batch effect in C42B data due to experimental processing day. We corrected for this effect by separately estimating mean  Alexa Fluor® 3 and mean Alexa Fluor® 5 signal within single-, 5-, and 10-cell C42B arrays between experimental days and adjusting values on the second day by the estimated difference.  We normalized day-effect-corrected signals for C42B data and raw patient data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of "null" to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers.  C42B and patient data further normalized (each set seperately) using between-array quantile normalization.  All normalizations were performed using the Limma package in R.

label: Alexa Fluor® 5

organism: Homo sapiens

label_protocol: Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen) (reference cDNA was labeled with Alexa Fluor® 5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications. The second round amplified amino-allyl RNA was then converted to first strand cDNA and labeled with Alexa Fluor® 5 using the BioPrime® Total Genomic labeling kit (Invitrogen).

tag: gender

value: male

tag: reference cell lines

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

label: Alexa Fluor® 3

extract_protocol: Total RNA was amplified from each sample using the WT-OviationTM one-direct system (NuGEN) according to the manufacturer’s directions. Amplified cDNA from each sample was labeled with Alexa Fluor® 3 using the BioPrime® Total Genomic labeling kit (Invitrogen).

value: Clonally selected and cultured single passage of cell cycle synchronized C4-2B PCa cells.  Single cells were isolated using a micromanipulator under direct visualization with an inverted microscope.


title: Normal brain

city: Lyon

first: jacques

last: champier

address: rue Guillaume Paradin

department: neuroonology

country: France

hyb_protocol: Biotin-labelled aRNA (10 ug) was fragmented using 5ug of fragmentation buffer in a final volume of 25 ul, then mixed with 240 ug of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected on Codelink Human whole Genome Bioarrays containing around 54,000 human oligonucleotide gene probes (GE Healthcare Europe GmbH, Freiburg, Germany). The arrays were hybridized overnight at 37°C at 15g in an incubator, then washed in stringent TNT buffer at 46°C for 1 h before performing the streptavidin-Cy5 (GE Healthcare) detection step.

scan_protocol: The arrays were scanned using a GenePix 4000B scanner (Axon, Union City, CA, USA) and GenePix software, with a laser set at 635 nm, the laser power at 60% and the photomultiplier tube voltage at 60%.

data_processing: The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.

source_name: Brain tissue from healthy donor

label_protocol: Total RNA (2ug) was amplified and biotin-labelled by a round of in vitro transcription using a MessageAmp aRNA kit (Ambion, Austin, Texas, USA).

extract_protocol: RNA from a whole normal adult male human brain (single donor, 72 years) in 0.1 mM EDTA, pH 8.0, was purchased from Stratagene (Stratagene Europe, Amsterdam, The Netherlands).

value: normal brain

tag: age

value: 72 years


title: Pineoblastoma_PB1

source_name: Tumor tissue, pineoblastoma

extract_protocol: Total RNA, extracted from the samples using the RNA Plus procedure (Qbiogen, Illkirch, France) based on the method of Chomczinski and Sacchi, was precipitated with ethanol. The quality of the isolated total RNA was evaluated on nanochips using an Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France).

value: pineoblastoma


title: C24_whole seedlings without root, biological rep1

source_name: C24_whole seedlings without root

tag: ecotype


title: Kidney 20mgkg-1 rep1


title: single clonally selected and synchronized C42B cell (#6)


title: C24_whole seedlings without root, biological rep2


title: Hypoxia  1 days SG2_A1

description:
SG2_A1
Hypoxia
1
days

tag: experiment

tag: replicate

value: 1 days


title: single clonally selected and synchronized C42B cell (#18)


title: Kidney 6mgkg-1 rep2

tag: treatment


title: Pineoblastoma_PB2

tag: tissue


title: C24_whole seedlings without root, biological rep3


title: Kidney vehicle rep3

tag: mouse number

value: Vehicle


title: Hypoxia  0 days SG2_A0

description:
SG2_A0
Hypoxia
0
days

tag: time

value: 0 days


title: Kidney 6mgkg-1 rep1

tag: dosage

tag: ast (u/l)


title: Kidney vehicle rep2

tag: creatinine (umol/l)

tag: bun (mmol/l)


title: Rv3133c OE by Atc & 2h 0.2% O2 gas 100 ng Atc 18 Hours pEXNF_3133c__hypoxic_100

description:
pEXNF_3133c__hypoxic_100
Rv3133c OE by Atc & 2h 0.2% O2 gas
18
Hours
100
ng

value: 18 Hours

tag: dose

value: 100 ng Atc

value: Rv3133c OE by Atc & 2h 0.2% O2 gas


title: Col_whole seedlings without root, biological rep3

source_name: Col_whole seedlings without root

value: Col

value: Seedlings


title: Kidney vehicle rep1

value: Kidney

tag: ldh (u/l)

tag: ck (u/l)

tag: rna integrity number (rin)


title: Col_whole seedlings without root, biological rep1


title: Heart 20mgkg-1 rep3

source_name: Heart

value: Heart

value: 20 mg/kg

tag: strain


title: Neurocytoma_CN4

source_name: Tumor tissue, neurocytoma

value: neurocytoma


title: Neurocytoma_CN_1


title: Rv3133c OE by Atc & 2h 0.2% O2 gas 10 ng Atc 18 Hours pEXNF_3133c__hypoxic_10

description:
pEXNF_3133c__hypoxic_10
Rv3133c OE by Atc & 2h 0.2% O2 gas
18
Hours
10
ng

value: Rv3133c-Atc dilution

value: 10 ng Atc


title: Pineocytoma_PC1

source_name: Tumor tissue, pineocytoma

value: pineocytoma


title: Rv3133c OE by Atc 100 ng Atc 18 Hours pEXNF_3133c__Aerobic_100

description:
pEXNF_3133c__Aerobic_100
Rv3133c OE by Atc
18
Hours
100
ng

value: Rv3133c OE by Atc


title: Rv3133c OE by Atc & 2h 0.2% O2 gas 1 ng Atc 18 Hours pEXNF_3133c__hypoxic_1

description:
pEXNF_3133c__hypoxic_1
Rv3133c OE by Atc & 2h 0.2% O2 gas
18
Hours
1
ng

value: 1 ng Atc


title: Heart 20mgkg-1 rep2


title: Neurocytoma_CN3


title: Rv3133c OE by Atc 10 ng Atc 18 Hours pEXNF_3133c__Aerobic_10

description:
pEXNF_3133c__Aerobic_10
Rv3133c OE by Atc
18
Hours
10
ng


title: Rv3133c OE by Atc 1 ng Atc 18 Hours pEXNF_3133c__Aerobic_1

description:
pEXNF_3133c__Aerobic_1
Rv3133c OE by Atc
18
Hours
1
ng


title: Neurocytoma_CN1


title: RAW-PruGRA15KOinfect,IFNg

city: Cambridge

first: Emily

middle: E

last: Rosowski

state: MA

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 5 ug of cDNA from samples were hybridized on GeneChip Mouse Genome 430A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Data was then normalized, setting all data to have a minimum value of 50.

source_name: RAW264.7, Pru ∆gra15 infected 18hr, IFNg 6hr

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: 1.5x106 RAW264.7 murine macrophages were plated in 6-well plates (BD Biosciences) and grown for 24 hours at 37C, 5% CO2.  Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

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

treatment_protocol: Parasite strains were syringe lysed, washed at least once with PBS, and added to plated RAW264.7 cells at an MOI ~5 for 18 hours.  Plaque assays were done to assess parasite viability.  Uninfected and infected cells were subsequently stimulated with murine IFN-γ for six hours.

value: RAW264.7 murine macrophages

tag: parasite strain

value: Pru A7 ∆gra15

tag: infected

value: yes

tag: stimulated


title: RAW-cepinfect,IFNg

source_name: RAW264.7, cep infected 18hr, IFNg 6hr

value: CEP ∆hxgprt C22


title: RAW-noinfection,IFNg-2

source_name: RAW264.7, uninfected, IFNg 6hr

value: no


title: Col_whole seedlings without root, biological rep2

tag: ecotype


title: RAW-Pruinfect,IFNg

source_name: RAW264.7, Pru infected 18hr, IFNg 6hr

value: Pru ∆hxgprt A7


title: Heart 6mgkg-1 rep3

value: 6 mg/kg

tag: treatment


title: Heart 6mgkg-1 rep1

tag: tissue


title: Heart 20mgkg-1 rep1

tag: mouse number


title: Neurocytoma_CN5


title: Pineocytoma_PC2


title: Rv0081 OE by Atc & 2h 0.2% O2 gas 100 ng Atc 18 Hours pEXCF_0081__hypoxic_100

description:
pEXCF_0081__hypoxic_100
Rv0081 OE by Atc & 2h 0.2% O2 gas
18
Hours
100
ng

tag: experiment

tag: replicate

value: A

tag: time

value: 18 Hours

value: 100 ng Atc

value: Rv0081 OE by Atc & 2h 0.2% O2 gas


title: Rv0081 OE by Atc & 2h 0.2% O2 gas 10 ng Atc 18 Hours pEXCF_0081__hypoxic_10

description:
pEXCF_0081__hypoxic_10
Rv0081 OE by Atc & 2h 0.2% O2 gas
18
Hours
10
ng

value: Rv0081-Atc dilution


title: Heart 6mgkg-1 rep2

value: Heart

tag: dosage

tag: ast (u/l)

tag: creatinine (umol/l)


title: Rv0081 OE by Atc & 2h 0.2% O2 gas 1 ng Atc 18 Hours pEXCF_0081__hypoxic_1

description:
pEXCF_0081__hypoxic_1
Rv0081 OE by Atc & 2h 0.2% O2 gas
18
Hours
1
ng

tag: dose


title: RAW-noinfection,nostim-2

source_name: RAW264.7, uninfected, unstimulated


title: RAW-RHinfect,IFNg

source_name: RAW264.7, RH infected 18hr, IFNg 6hr


title: Rv0081 OE by Atc & 2h 0.2% O2 gas 0.1 ng Atc 18 Hours pEXCF_0081__hypoxic_0.1

description:
pEXCF_0081__hypoxic_0.1
Rv0081 OE by Atc & 2h 0.2% O2 gas
18
Hours
0.1
ng

value: 0.1 ng Atc


title: Heart vehicle rep2

value: Vehicle

tag: bun (mmol/l)

tag: ldh (u/l)

tag: ck (u/l)


title: RAW-noinfection,IFNg-1

tag: parasite strain


title: Heart vehicle rep3

tag: rna integrity number (rin)

tag: strain


title: T4

status: Public on Feb 18 2013

type: genomic

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

description: A. thaliana tumor mCIP enrichment, biological replicate 3

hyb_protocol: Approximately 7 µg of amplified and terminally labeled DNA were hybridized to tiling arrays using the GeneChip HWS kit (Affymetrix). Array hybridization was carried out at 45°C at 60 rpm for 16 h in an Affymetrix hybridization oven. Prior to scanning, arrays were washed in the Fluidics Station (Affymetrix) using script FS450_0001.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000.

data_processing:
Data from mCIP and input pairs were loess normalized; log2(mCIP/input) signal log ratios (SLR) were reported in bedGraph files.  Coordinates of genomic probes were mapped to the A. thaliana TAIR9 sequence assembly. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).
Additional results files: K2_K3_K4_smoothed.bedGraph; T2_T3_T4_smoothed.bedGraph; unchanged_regions.bed; hypomethylated_regions.bed; hypermethylated_regions.bed
Results file descriptions: SLRs were quantiles normalized and subjected to a 500 bp sliding window median smoothing across biological replicates of the two experimental groups. The smoothed SLRs were reported in files K2_K3_K4_smoothed.bedGraph and T2_T3_T4_smoothed.bedGraph. The CMARRT algorithm was employed to define mCIP-enriched genomic regions in smoothed SLRs of the experimental groups. File unchanged_regions.bed reports enriched regions present in both groups, hypomethylated_regions.bed reports regions enriched only in tumor-free stalk tissue and hypermethylated_regions.bed reports regions enriched only in crown galls; these regions are discussed in the paper. Analyses were performed in R (http://www.r-project.org) with the Bioconductor package Starr (http://www.bioconductor.org).

molecule: genomic DNA

source_name: mCIP DNA from A. thaliana crown galls

label_protocol: Samples (approximately 7 µg of amplified DNA each) were fragmented and terminally labeled with biotin using the GeneChip Mapping 10K Xba kit (Affymetrix).

growth_protocol: Arabidopsis plants were cultivated in growth chambers at 22°C during the light and 16°C during the dark period in 12 h intervals.  Arabidopsis plants were cultivated in growth chambers at 22°C during the light and 16°C during the dark period in 12 h intervals.

extract_protocol: Tissue was separated from the host inflorescence stalk under a stereozoom microscope (Leica MZ6, Leica Microsystems GmbH) using a scalpel 28 d after inoculation. Genomic DNA of plant material was isolated wth the DNeasy Plant Mini Kit (Qiagen). Genomic DNA (1.1 µg) was sonicated to approximately 600 bp fragments using a Bioruptor (Diagenode), heated for 10 min at 99 °C and immediately cooled on ice for 10 min. 100 ng DNA were removed and used as input samples for array hybridization. Immunoprecipitation was performed by incubating 1 µg of sonicated DNA with 10 µg of 5-mC monoclonal antibody (Diagenode) in 600 µl IP-Buffer (10 mM Na-Phosphate Buffer, 0.14 M NaCl, 0.05 % Triton X-100, pH 7.0) at 4°C for 12 h. After addition of 100 µl of Dynabeads Protein G (Life Technologies) and incubation at 4°C for 3 h, Dynabeads were washed twice with 600 µl IP-Buffer for 10 min. DNA elution was performed by vortexing the dynabeads three times in 200 µl TE buffer with increasing SDS-concentrations (0.1%, 0.5%, 1.5%). DNA was purified by phenol-chloroform extraction and ethanol precipitation. Input DNA and mCIP eluate were processed with the Whole Genome Amplification kit (Sigma) until a DNA yield of >7 µg was reached.

value: crown galls from Agrobacterium tumefaciens strain C58noc inoculated inflorescence stalks

tag: antibody

value: 5-methylcytosine mouse monoclonal (Diagenode, cat# MAb-006-100, lot# DA-0018)

source_name: Input DNA from A. thaliana crown galls

value: none (input)


title: RAW-RHROP16KOinfect,IFNg

source_name: RAW264.7, RH ∆rop16 infected 18hr, IFNg 6hr

value: RAW264.7 murine macrophages

value: RH ROP16KO B23

tag: infected

tag: stimulated


title: T3

description: A. thaliana tumor mCIP enrichment, biological replicate 2

tag: tissue


title: T2

description: A. thaliana tumor mCIP enrichment, biological replicate 1


title: Heart vehicle rep1

tag: mouse number

tag: treatment


title: K3

description: A. thaliana control mCIP enrichment, biological replicate 2

source_name: mCIP DNA from A. thaliana stalks

value: mock-inoculated segments of tumor-free inflorescence stalks

source_name: Input DNA from A. thaliana stalks


title: G. metallireducens_Fe(III)Citrate_rep4

city: Amherst

first: Jessica

middle: Amber

last: Smith

address: 203 Morrill Science Center IVN

department: Microbiology

institute: UMASS Amherst

description: This sample is of Geobacter metallireducens GS-15. It is the fourth of four biological replicates grown with Fe(III) citrate provided as the electron acceptor used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Geobacter metallireducens GS-15

source_name: 10mM acetate as electron donor and 55mM Fe(III) citrate as electron acceptor

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Geobacter metallireducens (ATCC 53774 and GS-15) was obtained from our laboratory culture collection and was routinely cultured under strict anaerobic conditions with 10mM acetate provided as the sole electron donor as previously described (Lovley 1993). Either Fe(III) citrate (56 mM) or Fe(III) oxide (100 mmol l-1) were provided as the sole terminal electron acceptor for Fe(III) reduction studies.
Geobacter metallireducens (ATCC 53774 and GS-15) was obtained from our laboratory culture collection and was routinely cultured under strict anaerobic conditions with 10mM acetate provided as the sole electron donor as previously described (Lovley 1993). Either Fe(III) citrate (56 mM) or Fe(III) oxide (100 mmol l-1) were provided as the sole terminal electron acceptor for Fe(III) reduction studies.

extract_protocol: Total RNA for microarray analysis was extracted from triplicate cultures of G. metallireducens cells grown with acetate (10 mM)-Fe(III) citrate(55 mM) or acetate (10mM)-Fe(III) oxide (100 mmol l-1) during exponential growth using a previously described method (Holmes et al., 2011).  RNA samples were purified with the RNA Clean-Up kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, and treated with DNA-free DNASE (Ambion, Austin, TX, USA). The RNA samples were tested for genomic DNA contamination by PCR amplification of the 16S rRNA gene. The concentration and quality of the RNA samples were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). All RNA samples had A260/280 ratios, of 1.8–2.0, indicating high purity (Ausubel et al., 1997). cDNA was generated with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, St-Louis, MO, USA) according to manufacturer’s instructions.

treatment_protocol: Samples were flash frozen in liquid Nitrogen and stored at -80 celcius

tag: electron acceptor

value: Fe(III) Citrate

tag: electron donor type

value: 10mM acetate


title: WDR5_WT_NOdox_rep1

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: replicate 1

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

source_name: V6.5 Mouse embryonic stem cells

label_protocol: Affymetrix 3' IVT Express Kit

growth_protocol: Lentiviral infected GFP+ mouse embryonic stem cells were grown in full media with or without doxycycline (2 ug/mL)

extract_protocol: Trizol and qiagen RNeasy kits were used to isolate total RNA.

treatment_protocol: Lentiviral infection +/- doxycycline

tag: cell type

value: V6.5 Mouse embryonic stem cells

tag: transfection

value: WT

value: nodox


title: G. metallireducens_Fe(III)Citrate_rep2

description: This sample is of Geobacter metallireducens GS-15. It is the second of four biological replicates grown with Fe(III) citrate provided as the electron acceptor used in this experiment, each from separate cultures.


title: K2

description: A. thaliana control mCIP enrichment, biological replicate 1


title: WDR5_WT_dox_rep2

description: replicate 2

value: dox


title: G. metallireducens_Fe(III)Citrate_rep3

description: This sample is of Geobacter metallireducens GS-15. It is the third of four biological replicates grown with Fe(III) citrate provided as the electron acceptor used in this experiment, each from separate cultures.


title: G. metallireducens_Fe(III)Oxide_rep4

description: This sample is of Geobacter metallireducens GS-15. It is the fourth of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.

source_name: 10mM acetate as electron donor and 100mM Fe(III) oxide as electron acceptor

value: Fe(III) Oxide


title: NI12tot

status: Public on Feb 17 2013

city: Nantes

first: Cyrille

last: Féray

address: 1 rue Gaston Veil

institute: Faculté de médecine de Nantes

description: Total RNA from Huh7 cells (non-infected) - replicate 1

hyb_protocol: Each Cy3-labeled RNA was hybridized on an Agilent 8x15k human miRNA microarray slide.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The rawdata have been normalized with the quantile method (R software).

source_name: Huh7 cells (non-infected) - replicate 2

label_protocol: Cy3 labeling was performed with the Agilent kit, from 100 ng of total RNA.

extract_protocol: Total RNAs were then extracted with Trizol, and precipitated with isopropanol (Sigma).  The quality of RNAs was checked on an Agilent 2100 Bioanalyser.

tag: infection

value: Non-Infected


title: NI14tot

source_name: Huh7 cells (non-infected) - replicate 4


title: Inf14tot

description: Total RNA from Huh7 cells infected with HCV JFJ1 - replicate 4

value: Infected with HCV JFJ1


title: NI13tot

source_name: Huh7 cells (non-infected) - replicate 3


title: Inf13tot

description: Total RNA from Huh7 cells infected with HCV JFJ1 - replicate 3


title: WDR5_F266A_NOdox_rep2

description: replicate 2


title: RAW-noinfection,nostim-1

value: no


title: WDR5_WT_dox_rep1

description: replicate 1


title: WDR5_F266A_NOdox_rep1

description: replicate 1


title: WDR5_F266A_dox_rep1

description: replicate 1


title: G. metallireducens_Fe(III)Oxide_rep3

description: This sample is of Geobacter metallireducens GS-15. It is the third of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: G. metallireducens_Fe(III)Citrate_rep1

description: This sample is of Geobacter metallireducens GS-15. It is the first of four biological replicates grown with Fe(III) citrate provided as the electron acceptor used in this experiment, each from separate cultures.


title: G. metallireducens_Fe(III)Oxide_rep2

description: This sample is of Geobacter metallireducens GS-15. It is the second of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: Inf12tot

description: Total RNA from Huh7 cells infected with HCV JFJ1 - replicate 2


title: NI11tot

source_name: Huh7 cells (non-infected) - replicate 1


title: WDR5_F266A_dox_rep2

description: replicate 2


title: WDR5_WT_NOdox_rep2

description: replicate 2


title: G. metallireducens_Fe(III)Oxide_rep1

description: This sample is of Geobacter metallireducens GS-15. It is the first of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ES_2i_2

city: London

first: Kirsten

middle: R

last: McEwen

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

hyb_protocol: The Affymetrix GeneChip WT Terminal Labelling and Hybridisation kit was employed for hybridisation.

scan_protocol: GeneChip scanner.

data_processing: Quality control was undertaken using Affymetrix Expression Console software. Preprocesing by robust multiarray averaging (RMA) was performed in R using the Bioconductor limma package and batches were corrected using Combat.

label: Biotin

source_name: ESCs, cultured in 2i conditions

label_protocol: 100 ng of total RNA was processed using the Ambion WT Expression kit and Affymetrix GeneChip WT Terminal Labelling and Hybridisation kit.

growth_protocol: FCS medium consists of DMEM-F12 (Gibco) supplemented with 15% FCS, 0.1 mM MEM non-essential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mecaptanethanol and mouse LIF 10 µg/ml (prepared in house). Cells cultured in serum were maintained on a mouse embryonic fibroblast (MEF) feeder layer. 2i medium consists of the MEK inhibitor PD0325901 (PD) 1 mM, the GSK3 inhibitor CHIR99021 (CH) 3 mM and mouse LIF 10 µg/ml (as above) in N2B27 medium. Cells cultured in 2i were maintained on laminin (10 μg/ml, Sigma).

extract_protocol: The Qiagen RNeasy Mini kit was used for extraction of total RNA.

value: EGCs

value: 129SvEv x Oct4-delta-PE-GFP transgenic (mixed background)

tag: gender

value: Male

tag: batch


title: ES_FCS_5

source_name: ESCs, cultured in FCS conditions


title: ES_2i_4


title: ES_2i_3

value: Female


title: ES_2i_1


title: ES_2i_5


title: ES_FCS_4


title: RPE1_alpha-amanitin_ICRF193_5h_rep1

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

hyb_protocol: Standard Agilent protocols

scan_protocol: Standard Agilent protocols

data_processing: Array data was extracted using the RINGO bioconductor packaged. RNA expression and ChIP data was normalised within arrays (loess) and between arrays (scale). For bTMP-IP, arrays were VSN normalised

source_name: Input DNA from RPE1 cells 5 hrs alpha-amanitin and ICRF193 treatment

label_protocol: Samples were amplified using Sigma whole genome amplification kit and labeled using an ENZO labeling kit

growth_protocol: Cells were grown in DMEM:F12

extract_protocol: For total RNA, RNA was extracted using a Qiagen RNeasy minikit and labeled using the Invitrogen Superscript direct cDNA labeling system. ChIP was performed as described in Naughton et al. (2013) Nature Struct. Mol. Biol. For bTMP binding, cells or control genomic DNA were treated with various concentrations (50-500 μg.ml-1) of Biotinylated-TMP for 20 mins at RT in the dark. Biotinylated-TMP was UV cross-linked to DNA at 360 nm for 10 mins. DNA was purified from the cells using SDS/PK digestion followed by phenol:chloroform:isoamylaclohol extraction. DNA was fragmented by sonication (10 × 20s at 2 μ).  Biotin incorporation into the DNA was detected by dot blotting using an alkaline phosphatase conjugated avidin as a probe. The Biotinylated-psoralen DNA complex in TE was immunoprecipitated using avidin conjugated to magnetic beads for 2 hours at room temperature and then overnight at 4°C. Beads were washed sequentially for 5 min each at room temperature with TSE I (20 mM Tris pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100 and 0.1% SDS), TSE II (20 mM Tris pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100 and 0.1% SDS) and  buffer III (10 mM Tris pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP40 and 1% deoxycholate). Beads were then washed twice with TE buffer for 5 min. To extract the DNA and to release psoralen adducts the samples were boiled for 10 mins at 90°C in 50 μl of 95% Formamide with 10 mM EDTA. Samples were than made up to 200 μl with water and the DNA was purified using a Qiagen PCR purification Kit.

treatment_protocol: Cells were untreated or treated with alpha-amanitin (5h), topoisomerase inhibitors (5h) or bleomycin (10 min)

tag: cell line

source_name: bTMP-IP from RPE1 cells 5 hrs alpha-amanitin and ICRF193 treatment


title: ES_FCS_3


title: K4

description: A. thaliana control mCIP enrichment, biological replicate 3

value: 5-methylcytosine mouse monoclonal (Diagenode, cat# MAb-006-100, lot# DA-0018)

value: none (input)


title: RPE1_alpha-amanitin_Camptothecin_5h_rep1

source_name: Input DNA from RPE1 cells 5 hrs alpha-amanitin and camptothecin treatment

source_name: bTMP-IP from RPE1 cells 5 hrs alpha-amanitin and camptothecin treatment


title: RPE1_alpha-amanitin_ICRF193_5h_rep2


title: RPE1_alpha-amanitin_Camptothecin_5h_rep2


title: RPE1_ICRF193_5h_rep1

source_name: Input DNA from RPE1 cells 5 hrs ICRF193 treatment

source_name: bTMP-IP from RPE1 cells 5 hrs ICRF193 treatment


title: RPE1_Camptothecin_5h_rep2

source_name: bTMP-IP from RPE1 cells 5 hrs Camptothecin treatment

source_name: Input from RPE1 cells 5 hrs Camptothecin treatment


title: RPE1_Camptothecin_5h_rep1

source_name: Input DNA from RPE1 cells 5 hrs Camptothecin treatment

source_name: bTMP-IP DNA from RPE1 cells 5 hrs Camptothecin treatment


title: RPE1_recovery_2h_rep2

source_name: bTMP-IP from RPE1 cells 2 hours recovery after alpha-amanitin treatment

source_name: Input DNA from RPE1 cells 2 hours recovery after alpha-amanitin treatment


title: RPE1_ICRF193_5h_rep2


title: ES_FCS_2


title: ES_FCS_1


title: Slide 2-Array 3_rep 2

city: Ames

first: Derrick

middle: Jamaal

last: Coble

state: IA

address: 2254 Kildee Hall

department: Animal Science

institute: Iowa State University

description:
Gene expression of  Control and S. enteritidis-infected chickens
s2a3 raw data

hyb_protocol: Arrays were incubated at 65℃ for 17h in Agilent’s microarray hybridization chambers and subsequently washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) and Stabilization and Drying Solution (Agilent Technologies, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings, Scan resolution=5μm, PMT 100%, 10%

data_processing: Raw data were normalized using the LIMMA (Smyth, 2004) package developed in R, which utilizes empirical Bayes method for improved statistical inferences. False discovery rate (FDR) was controlled at the significance level 0.05 using the procedure developed by Storey and Tibshirani (2003).

organism: Gallus gallus

source_name: Mock-infected Chicken 7

label_protocol: Two µg of total RNA were reverse transcribed into cDNA. The synthesized cDNA was transcribed into cRNA and labeled with Cyanine 3 (Cy-3) or Cyanide 5 (Cy-5) dyes. Labeled cRNA was purified with QIAGEN RNeasy® Mini Kit (Qiagen, Valecia, CA). The same amounts (875 ng) of Cy-3 labeled cRNA and Cy-5 labeled cRNA, were hybridized onto Chicken 44K Agilent microarrays using a dye swap design for each array on each slide. The Cy-3 and Cy-5 dyes were applied to the two treatment (control treatment and infected treatment) levels respectively, and the dye assignment to treatment levels was swapped for each array in a slide. On each array, a S. enteritidis-infected and non-infected bird was represented.

extract_protocol: Liver samples of approximately 25 mg were homogenized in 0.6 ml of TRI Reagent Solution (Ambion) and total mRNA was isolated using the Ambion MagMax-96 kit protocol. To ensure high-quality RNA for microarray hybridization, samples were ethanol precipitated as follows. Samples were combined with 50 µL of RNAse free water to 100uL. Ten µL of 3M sodium acetate, 300µL 100% ethanol, and 20µg Glycogen were added to the water-RNA mixture. These samples were incubated at -80oC overnight and centrifuged at 4oC centrifuge for 25 minutes at 14,000rpm. The supernatant was aspirated and the pellets were washed with 500µl of 70% ethanol. This mixture was centrifuged again at 7600 x g for 5 minutes at 4oC. The supernatant was removed and the pellet was re-dissolved in RNAse free water. The samples were stored at -80oC until usage.

treatment_protocol: All birds were determined to be free of S. enteritidis by swabbing and plating cloacal samples prior to the experiment (Iowa State University, Veterinary Diagnostic Lab). Sixteen broiler hens of approximately 5 months (8 challenged orally with 1x108 S. enteritidis on each of three sequential days and 8 mock-challenged with phosphate buffered saline) were used. Livers were harvested at 10 days post infection and stored in RNALater (Ambion). All animal protocols, were approved by the Iowa State University Institutional Animal Care and Use Committee.

value: Liver

tag: developmental stage

value: 10 dpi

tag: infection status

value: Mock-infected

source_name: S. enteritidis-infected Chicken 7

value: S. enteritidis-infected


title: RPE1_recovery_2h_rep1


title: Slide 2-Array 4_rep 2

description:
Gene expression of  Control and S. enteritidis-infected chickens
s2a4 raw data

source_name: S. enteritidis-infected Chicken 8

source_name: Mock-infected Chicken 8


title: HAEC H3K9me2

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

scan_protocol: Performed according to standard NimbleGen protocol with NimbleGen software

data_processing: log2 IP/control after partial quantile normalization. The normalization method was described in a 2008 nature genetics paper (PMID 19151716)

source_name: ChIP against H3K9me2

label_protocol: Labels with Cy3 and Cy5 were performed according to standard NimbleGen protocol

extract_protocol: Human H1 ES and iPSCs38 cells were cultured as described (Park et al., Nature, 2008). Human astrocytes (HA) and aortic endothelial cells (HAEC) and were purchased from ScienCell Research Laboratories (San Diego, CA), and cultured as recommended by the company. Native chromatin IP against H3K9me2 antibody (Abcam 1220) were performed as described (Wen et al. Nat Genet., 2009).

value: primary aortic endothelial cell

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

tag: chip antibody catalog #

source_name: input DNA


title: Slide 2-Array 1_rep 1

description:
Gene expression of  Control and S. enteritidis-infected chickens
s2a1 raw data

source_name: Mock-infected Chicken 5

source_name: S. enteritidis-infected Chicken 5


title: RPE1_alpha-amanitin_5h_rep2

source_name: bTMP-IP from RPE1 cells 5 hrs alpha-amanitin treatment

source_name: Input DNA from RPE1 cells 5 hrs alpha-amanitin treatment


title: Slide 2-Array 2_rep 3

description:
Gene expression of  Control and S. enteritidis-infected chickens
s2a2 raw data

source_name: S. enteritidis-infected Chicken 6

source_name: Mock-infected Chicken 6


title: EG_2i_3

source_name: EGCs, cultured in 2i conditions

tag: strain


title: Slide 1-Array 4_rep 1

description:
Gene expression of  Control and S. enteritidis-infected chickens
s1a4 raw data

source_name: S. enteritidis-infected Chicken 4

tag: tissue

source_name: Mock-infected Chicken 4


title: EG_2i_4


title: HA H3K9me2

hyb_protocol: Performed according to standard NimbleGen protocol

value: primary astrocyte


title: RPE1_alpha-amanitin_5h_rep1


title: Slide 1-Array 3_rep 1

description:
Gene expression of  Control and S. enteritidis-infected chickens
s1a3 raw data

source_name: Mock-infected Chicken 3

source_name: S. enteritidis-infected Chicken 3


title: HPF H3K9me2

value: primary lung fibroblast


title: HAEC H3K9me2, array 4 of 4

description: Chip-chip Human aortic endothelial cells H3K9me2

data_processing: Partial quantile normalization as described in PMID: 19151716.

source_name: H3K9me2 ChIP DNA fromHuman aortic endothelial cells

growth_protocol: Human aortic endothelial cells  were purchased and cultured as recommended by ScienCell (San Diego, CA).

extract_protocol: Human H1 ES and iPSCs38 cells were cultured as described (Park et al., Nature, 2008). Human astrocytes (HA) and aortic endothelial cells (HAEC) and were purchased from ScienCell Research Laboratories (San Diego, CA), and cultured as recommended by the company. Native chromatin IP against H3K9me2 antibody [Abcam, catalog number: Ab1220, lot number: 935410] were performed as described (Wen et al. Nat Genet., 2009).

treatment_protocol: Native Chromatin Immunoprecipitation was conducted as described (Wen et al., Nature Genetics, 2009)

value: Human aortic endothelial cells

source_name: Input DNA fromHuman aortic endothelial cells


title: EG_2i_2


title: Slide 1-Array 2_rep 1

description:
Gene expression of  Control and S. enteritidis-infected chickens
s1a2 raw data

source_name: S. enteritidis-infected Chicken 2

source_name: Mock-infected Chicken 2


title: RPE1_genomic-DNA_rep1

description: bTMP binding to naked genomic DNA

hyb_protocol: Standard Nimblegen protocol

scan_protocol: Standard Nimblegen protocol

data_processing: Array data was extracted using the RINGO bioconductor packaged and VSN normalised

source_name: Input DNA from RPE1 cells

label_protocol: Samples were amplified using Sigma whole genome amplification kit and labeled using Nimblegen labeling kit

extract_protocol: Cells or control genomic DNA were treated with various concentrations (50-500 μg.ml-1) of Biotinylated-TMP for 20 mins at RT in the dark. Biotinylated-TMP was UV cross-linked to DNA at 360 nm for 10 mins. DNA was purified from the cells using SDS/PK digestion followed by phenol:chloroform:isoamylaclohol extraction. DNA was fragmented by sonication (10 × 20s at 2 μ).  Biotin incorporation into the DNA was detected by dot blotting using an alkaline phosphatase conjugated avidin as a probe. The Biotinylated-psoralen DNA complex in TE was immunoprecipitated using avidin conjugated to magnetic beads for 2 hours at room temperature and then overnight at 4°C. Beads were washed sequentially for 5 min each at room temperature with TSE I (20 mM Tris pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100 and 0.1% SDS), TSE II (20 mM Tris pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100 and 0.1% SDS) and  buffer III (10 mM Tris pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP40 and 1% deoxycholate). Beads were then washed twice with TE buffer for 5 min. To extract the DNA and to release psoralen adducts the samples were boiled for 10 mins at 90°C in 50 μl of 95% Formamide with 10 mM EDTA. Samples were than made up to 200 μl with water and the DNA was purified using a Qiagen PCR purification Kit.

treatment_protocol: Untreated

source_name: bTMP-IP from naked RPE1 genomic DNA


title: RPE1_recovery_2h_rep2

description: bTMP binding after recovery from alpha amanitin treated cells

source_name: Input DNA from RPE1 cells 2 hours recovery after alpha-amanitin treatment

treatment_protocol: 2h recovery after alpha-amanitin treatment

source_name: bTMP-IP from RPE1 cells 2 hours recovery after alpha-amanitin treatment


title: Slide 1-Array 1_rep 3

description:
Gene expression of  Control and S. enteritidis-infected chickens
s1a1 raw data

source_name: Mock-infected Chicken 1

source_name: S. enteritidis-infected Chicken 1


title: EG_2i_1


title: H1 H3K9me2, array 2 of 4

description: Chip-chip Human ESC H1 H3K9me2

source_name: H3K9me2 ChIP DNA from Human ESC H1

growth_protocol: Human ESCs were cultured by stardard protocol as described (Park et al., Cell, 2008)

value: Human ESC H1

source_name: Input DNA from Human ESC H1


title: RPE1_bleomycin_10min_rep2

description: bTMP binding after bleomycin treatment

source_name: Input DNA from RPE1 cells after bleomycin treatment

treatment_protocol: 10 min bleomycin

source_name: bTMP-IP from RPE1 cells after bleomycin treatment


title: RPE1_genomic-DNA_rep2

description: bTMP binding to naked genomic DNA


title: H1 H3K9me2, array 4 of 4

description: Chip-chip Human ESC H1 H3K9me2


title: RPE1_untreated_rep1

source_name: bTMP-IP from RPE1 cells


title: iPSC38 H3K9me2, array 2 of 4

description: Chip-chip Human iPSC ADA-38 H3K9me2

source_name: H3K9me2 ChIP DNA from Human iPSC ADA-38

growth_protocol: Human iPSCs were cultured by stardard protocol as described (Park et al., Cell, 2008)

value: Human iPSC ADA-38

source_name: Input DNA from Human iPSC ADA-38


title: iPSC38 H3K9me2

source_name: ChIP against H3K9me2

source_name: input DNA


title: EG_2is_4

source_name: EGCs, cultured in 2i after initial derivation in FCS conditions for 2 days

value: EGCs


title: RPE1_untreated_rep2


title: H1 H3K9me2


title: HA H3K9me2, array 2 of 4

description: Chip-chip Human Astrocytes H3K9me2

source_name: H3K9me2 ChIP DNA from Human astrocytes

growth_protocol: Human Astrocytes were purchased and cultured as recommended by ScienCell (San Diego, CA).

value: Human astrocytes

source_name: Input DNA from Human astrocytes


title: iPSC38 H3K9me2, array 4 of 4

description: Chip-chip Human iPSC ADA-38 H3K9me2


title: HA H3K9me2, array 4 of 4

description: Chip-chip Human Astrocytes H3K9me2


title: RPE1_recovery_2h_rep1


title: HAEC H3K9me2, array 2 of 4

source_name: H3K9me2 ChIP DNA fromHuman aortic endothelial cells

source_name: Input DNA fromHuman aortic endothelial cells


title: RPE1_alpha-amanitin_5h_rep2

description: bTMP binding to alpha amanitin treated cells

source_name: Input DNA from RPE1 cells 5 hrs alpha-amanitin treatment

treatment_protocol: 5h alpha-amanitin treatment

source_name: bTMP-IP from RPE1 cells 5 hrs alpha-amanitin treatment


title: RPE1_alpha-amanitin_5h_rep1


title: RPE1_bleomycin_10min_rep1

description: bTMP binding after bleomycin treatment


title: RPE1_untreated_rep2

description: bTMP binding to untreated cells

source_name: Input DNA from RPE1 cells


title: EG_2is_3

value: 129SvEv x Oct4-delta-PE-GFP transgenic (mixed background)


title: Normal male 3

city: Kansas City

first: Douglas

middle: C

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Kansas Medical Center Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data (CEL. files) were uploaded into Partek Genomics Suite software version 6.5 (Partek Inc, St. Louis) for normalization and statistical analysis. The Robust Multichip Analysis (RMA) was used for background correction followed by quantile normalization with baseline transformation to the median of the control samples. Probes with intensity values above 20% of the background value in at least one of the conditions, were included for additional analysis.  To overcome the limitation of having a single 15q13.3 homozygous deletion sample, we used a 1-way ANOVA model using the Method of Moments to test for statistical significance.26 Genes with p values < 0.01 were kept for further analysis

source_name: Normal male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit

growth_protocol: Lymphoblastoid cells were grown in RPMI 1640 media (Sigma, St Louis MO.) supplemented with 10% fetal calf serum and 1% penn/strep.

extract_protocol: RNA was isolated from rapidly growing cell cultures using a mirVana RNA isolation kit (Invitrogen; Grand Island, NY).

value: Lymphoblastoid

tag: phenotype

value: normal


title: Normal male 2


title: EG_FCS_3

source_name: EGCs, cultured in FCS conditions

value: Male


title: EG_FCS_4


title: EG_2is_1


title: Normal female 3

source_name: Normal female


title: Normal male 1


title: RPE1_untreated_rep1

description: bTMP binding to untreated cells


title: EG_2is_2


title: RPE1_genomic-DNA_rep2

source_name: bTMP-IP from naked RPE1 genomic DNA


title: RPE1_genomic-DNA_rep1


title: EG_FCS_2


title: RPE1_bleomycin_10min_rep1

source_name: Input DNA from RPE1 cells after bleomycin treatment

source_name: bTMP-IP from RPE1 cells after bleomycin treatment


title: EG_FCS_1

value: Female


title: RPE1_Topoisomerase_IIb_ChIP_rep1

source_name: untreated RPE1 TopoIIb ChIP

source_name: untreated RPE1 Input DNA


title: Normal female 2


title: Normal female 1


title: Normal boy 3

source_name: Normal boy


title: Paternal grandmother, homozygus deletion

value: homozygus deletion


title: Normal boy 1


title: RPE1_Topoisomerase_IIb_ChIP_rep2


title: RPE1_Topoisomerase_IIa_ChIP_rep1

source_name: untreated RPE1 TopoIIa ChIP


title: Normal boy 2


title: RPE1_Topoisomerase_IIa_ChIP_rep2


title: RPE1_bleomycin_10min_rep2


title: WT BMDM_polyIC 9h treated total RNA

city: Seoul

first: Byungil

last: Kim

address: 134 Shin-chon-dong, Seodaemun-gu

department: Biochemistry

country: South Korea

institute: Yonsei University

description: total RNA of wild-type BMDM treated with poly(I:C) for 9 h

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at DNA Link Inc. (Korea), an Affymetrix authorized service provider.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were extracted and normalized with Affymetrix GCOS software and the RMA (Robust Multi-array Average) Normalization method (DNA Link Inc., Korea). We compared these using Affymetrix Expression console1.1, TMEV4.4, DAVID.

source_name: wild-type, BMDM

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: BMDMs were differentiated for 7 days in basic medium [DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1X non-essential amino acids (Gibco), 10 mM HEPES (Gibco), 50 μM 2-mercaptoethanol (Sigma), 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco)] with 20% (v/v) L929 culture supernatant.

extract_protocol: RNA (3 samples per group, mixed) from poly(I:C)-treated WT and Oasl1-/- BMDMs were prepared using Trizol.

treatment_protocol: BMDMs treated with 5 µg/ml poly(I:C) for 9 h

value: BMDM

tag: genotype/variation

value: wild-type

tag: treatment

tag: dose

value: 5 µg/ml poly(I:C)

tag: time

value: 9 h

tag: fraction

value: total RNA


title: Proband double deletion

source_name: Proband double deletion

value: Proband double deletion


title: RPE1_Topoisomerase_I_ChIP_rep2

source_name: untreated RPE1 TopoI ChIP


title: OASL1 KO BMDM_polyIC 9h treated total RNA

description: total RNA fraction of Oasl1-/- BMDM treated with poly(I:C) for 9 h

source_name: Oasl1-/-, BMDM

tag: cell type


title: Father, homozugus deletion

source_name: Father, homozygus deletion


title: RPE1_Topoisomerase_I_ChIP_rep1


title: RPE1_untreated_rep2

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Raw data was taken from Illumina scanner and analysed using the LUMI Bioconductor package. Background corrected using minimum method. Data was normalised using variance stabilizing transformation and a robust spline normalisation

source_name: RPE1 cells untreated

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit, Ambion

growth_protocol: Cells were grown in standard DMEM:F12 media

extract_protocol: RNA extraction using Tri-Reagent


title: OASL1 KO BMDM_polyIC 12h treated polysomal RNA

description: polysome-associated mRNAs of Oasl1-/- BMDM treated with poly(I:C) for 12 h

data_processing: Data were extracted and normalized with Affymetrix GCOS software and the RMA (Robust Multi-array Average) Normalization method (DNA Link Inc., Korea). We compared these using Affymetrix Expression console1.1, R affy-package(2.9.2), DAVID.

molecule: cytoplasmic RNA

extract_protocol: For polysome analysis of cell lysates, BMDMs (4.5 × 107) treated with 10 µg/ml poly(I:C) for 12 h were washed twice with cold PBS containing 200 μg/ml CHX, suspended in 500 µl polysome lysis buffer [5 mM Tris-HCl (pH 7.5), 2.5 mM MgCl2, 1.5 mM KCl, 200 µg/ml CHX, 2,000 U/ml RNasin (Promega), 2 mM dithiothreitol, 0.5% Triton X-100 and the protease inhibitor cocktail] for 2 min, and centrifuged at 14,000 × g for 2 min at 4°C. The collected supernatant was then loaded onto a 10-50% sucrose gradient prepared in 20 mM HEPES-KOH (pH 7.5), 100 mM KCl and 5 mM MgCl2 and centrifuged at 35,000 rpm for 2 h at 4°C using an SW41 Ti rotor on an Optima LE-80K Ultracentrifuge (Beckman Coulter). After centrifugation, 16 fractions were collected from the top of the gradient by piercing the ultracentrifuge tube with a Brandel tube piercer and passing 60% sucrose through the bottom of the tube. The polysome-associated mRNAs (equivalent to fractions 9, 10 and 11) were prepared using Trizol.

treatment_protocol: BMDMs treated with 10 µg/ml poly(I:C) for 12 h

value: 10 µg/ml poly(I:C)

value: polysomal RNA


title: RPE1_untreated_rep3


title: RPE1_untreated_rep1


title: WT BMDM_polyIC 12h treated polysomal RNA

description: polysome-associated mRNAs of wild-type BMDM treated with poly(I:C) for 12 h


title: RPE1_RNA-polII_ChIP_rep2

source_name: untreated RPE1 Total RNA polymerase ChIP


title: RPE1_RNA-polII_ChIP_rep1


title: RPE1_RNA_untreated_rep1

description: Single Channel Analysis

source_name: untreated RPE1 Total RNA


title: RPE1_RNA_untreated_rep2

description: Single Channel Analysis


title: Sorted Cell Population CD 34+ 8

status: Public on Feb 16 2013

city: Linz

first: Johannes

last: Pröll

address: Krankenhausstrasse 7

country: Austria

institute: Red Cross Transfusion Service for Upper Austria

hyb_protocol: Samples were hybridized with GeneChip HG-133  Arrays (Affymetrix) and scanned at site.

data_processing: We determined the Gene Cell intensity scaling using GeneChip Operating Software. Partek genomics suite was used to normalize and to apply RMA.

source_name: Human Bone Marrow

growth_protocol: not applicable

extract_protocol: Trizol was applied for total RNA extraction according to the manufacturer`s instructions, appending a phenolchlorophorm step.

treatment_protocol: Cell sorting was performed using the Aria III sorter equipped with FACSDiva software Version 6.1.3 to obtain pure 95% subsets by sorting with specific marker combinations.

value: CD34-positive common precursor cells


title: Mother, homozygus deletion

source_name: Mother, homozygus deletion


title: Psoralen + CPT Raji cells Replicate 3

city: Bethesda

first: Damian

last: Wojtowicz

address: 8600 Rockville Pike; Rm 8N811N

institute: NCBI/NLM/NIH

description: Biological replicate 3 of 3. Raji cells in early G1 phase exposed to CPT and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.

hyb_protocol: Hybridization was performed by NimbleGen.

scan_protocol: Arrays were scaned by NimbleGen.

data_processing: Data extraction and quality assesment were performed by NimbleGen.

source_name: XL + CPT from Raji cells

label_protocol: DNA labeling was performed by NimbleGen.

growth_protocol: Raji cells were synchronized in early G1 phase of the cell cycle by treatment with 1.5% (v/v) DMSO for 96 hours. Cells were released from DMSO in fresh medium and experiments were conducted 6 hours later.

extract_protocol: 2x10^7 cells per 10 ml of media were treated with 140 μL of a 0.9 mg/ml solution of 4,5’,8-trimethylpsoralen in ethanol for 4 min at 37C. To photocross-link the DNA strands, plates with cells were exposed to 3.6 kJ m^-2 of 365 nm light (ultraviolet lamp, model B-100 A, Ultra-Violet Products). Cross-linked genomic DNA was isolated by RNase and Proteinase K treatment in lysis buffer (10 mM Tris-Cl pH 8.0, 100 mM EDTA, 0.5% SDS), followed by repetitive phenol/chloroform extraction and ethanol precipitation. Purified DNA was sonicated (Sonicator, Ultrasonic processor XL, MISONIX Inc. at 15% of power) to produce 250 bp average-size DNA fragments. DNA was then heat-denaturated and incubated at 55C for 1 hour in glyoxal buffer. Glyoxylated non-cross-linked and cross-linked DNA fragments were separated by electrophoresis (3% agarose gel electrophoresis in 10 mM sodium phosphate buffer (pH 7.0) at 2 volt/cm for 12 hours). After electrophoresis, the gel was incubated with denaturing solution (0.5 M NaOH, 1.5 M NaCl) at 65°C for 3 hours to reverse psoralen crosslinks and stained with SYBR-green. Cross-linked and non-cross-linked DNA fragments were purified by electroelution and hybridized in different combinations to NimbleGen ENCODE arrays (tiled with 12-bp overlapping, 50-mer probes across unique regions of ENCODE as well as 200 kb centered on the c-myc TSS).

treatment_protocol: Cells were exposed to 10uM camptothecin for 5 min.

value: Raji human B cells

tag: cell cycle

source_name: non-XL + CPT from Raji cells


title: Sorted Cell Population CD 105+ 9

value: CD105-positive erythroid cells


title: Sorted Cell Population CD 34+ 6


title: Sorted Cell Population CD 105+ 7


title: Psoralen + BLAP Raji cells Replicate 3

description: Biological replicate 3 of 3. Raji cells in early G1 phase exposed to BLAP and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.

source_name: XL + BLAP from Raji cells

treatment_protocol: Cells were exposed to 10uM beta-lapachone for 5 min.

source_name: non-XL + BLAP from Raji cells


title: Sorted Cell Population CD 34+ 4


title: Sorted Cell Population CD 105+ 5


title: Gene Expression Raji cells Replicate 2

type: mixed

description: Biological replicate 2 of 3. Gene expression of Raji cells in early G1 phase.

molecule: nuclear RNA

source_name: RNA from Raji cells

extract_protocol: Nuclear RNA was prepared using the Qiagen RNeasy kit. RNA was isolated from the nuclear pellets resuspended in the kit lysis buffer and processed according to the protocol. RNA was converted into double-stranded DNA by using SuperScript Choice System for cDNA synthesis (Invitrogen). cDNAs were sonicated to average fragments of 250 base pairs and hybridized to Nimblegene ENCODE arrays together with genomic DNA sonicated to similar size.

source_name: genomic DNA from Raji cells


title: Psoralen + CPT Raji cells Replicate 1

description: Biological replicate 1 of 3. Raji cells in early G1 phase exposed to CPT and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Sorted Cell Population CD 105+ 22


title: Sorted Cell Population CD 14+  23

value: CD14-positive cells


title: Psoralen Raji cells Replicate 2

description: Biological replicate 2 of 3. Raji cells in early G1 phase treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.

source_name: XL from Raji cells

source_name: non-XL from Raji cells


title: iPSC38 H3K9me2, array 1 of 4

description: Chip-chip Human iPSC ADA-38 H3K9me2

source_name: H3K9me2 ChIP DNA from Human iPSC ADA-38

value: Human iPSC ADA-38

source_name: Input DNA from Human iPSC ADA-38


title: Psoralen + BLAP Raji cells Replicate 2

description: Biological replicate 2 of 3. Raji cells in early G1 phase exposed to BLAP and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Psoralen + BLAP Raji cells Replicate 1

description: Biological replicate 1 of 3. Raji cells in early G1 phase exposed to BLAP and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Psoralen + DRB Raji cells Replicate 2

description: Biological replicate 2 of 3. Raji cells in early G1 phase exposed to DRB and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.

source_name: XL + DRB from Raji cells

treatment_protocol: Treatment with 40 uM of DRB for 30 minutes to inhibit transcription.

source_name: non-XL + DRB from Raji cells


title: H1 H3K9me2, array 1 of 4

description: Chip-chip Human ESC H1 H3K9me2

source_name: H3K9me2 ChIP DNA from Human ESC H1

value: Human ESC H1

source_name: Input DNA from Human ESC H1


title: Sorted Cell Population CD 34+ 21


title: Sorted Cell Population CD 105+ 3


title: Gene Expression Raji cells Replicate 3

description: Biological replicate 3 of 3. Gene expression of Raji cells in early G1 phase.


title: Psoralen + DRB Raji cells Replicate 3

description: Biological replicate 3 of 3. Raji cells in early G1 phase exposed to DRB and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Psoralen + DRB Raji cells Replicate 1

description: Biological replicate 1 of 3. Raji cells in early G1 phase exposed to DRB and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Psoralen Raji cells Replicate 3

description: Biological replicate 3 of 3. Raji cells in early G1 phase treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Psoralen + CPT Raji cells Replicate 2

description: Biological replicate 2 of 3. Raji cells in early G1 phase exposed to CPT and treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: Sorted Cell Population CD 105+ 20


title: H1 H3K9me2, array 3 of 4

description: Chip-chip Human ESC H1 H3K9me2


title: Psoralen Raji cells Replicate 1

description: Biological replicate 1 of 3. Raji cells in early G1 phase treated with psoralen and UV light. Cross-linked and uncross-linked genomic DNA were separated and hybridized to custmized NimbleGen ENCODE arrays.


title: iPSC38 H3K9me2, array 3 of 4

description: Chip-chip Human iPSC ADA-38 H3K9me2


title: Gene Expression Raji cells Replicate 1

description: Biological replicate 1 of 3. Gene expression of Raji cells in early G1 phase.


title: Sorted Cell Population CD 105+ 16


title: Sorted Cell Population CD 105+ 15


title: Sorted Cell Population CD 34+ 19


title: Sorted Cell Population CD 34+ 18


title: Sorted Cell Population CD 14+  17


title: Sorted Cell Population CD 105+ 14


title: Sorted Cell Population CD 14+  12


title: HAEC H3K9me2, array 1 of 4

description: Chip-chip Human aortic endothelial cells H3K9me2

source_name: H3K9me2 ChIP DNA fromHuman aortic endothelial cells

value: Human aortic endothelial cells

source_name: Input DNA fromHuman aortic endothelial cells


title: HA H3K9me2, array 3 of 4

description: Chip-chip Human Astrocytes H3K9me2

source_name: H3K9me2 ChIP DNA from Human astrocytes

value: Human astrocytes

source_name: Input DNA from Human astrocytes


title: Sorted Cell Population CD 105+ 10

source_name: Human Bone Marrow


title: Sorted Cell Population CD 105+  1


title: Sorted Cell Population CD 14+  11


title: Sorted Cell Population CD 14+  1


title: MAP_7H9+casitone_anaerobic_rep2

city: Ithaca

first: Jenn-Wei

last: Chen

institute: Cornell University

description:
Sample 23
Biological replicate 2.

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

scan_protocol: Scanned on aDNA Microarray Scanner With Surescan High-Resolution Technology G2505B. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1 ) was used for background subtraction and LOWESS normalization.

organism: Mycobacterium avium subsp. paratuberculosis

source_name: K-10, 7H9+Casitone anaerobic, 3 hrs

label_protocol: 3 ug of total RNA was used for cDNA synthesis with SuperScript III RTase (Invitrogen) at 42°C for 12 hrs. After cleaning up with the Qiagen Minelute kit, the cDNA was primed with 50 uM Exo-resistant random primer at 37°C for 12 hrs in the presence of 25 U of Klenow (NEB), and 150 uM of dATP, dGTP, dTTP, 30 uM dCTP, with 50 uM Cy3- or Cy5- dCTP.

growth_protocol: Cultured the MAP strains with 7H9 + Casitone medium at 37 °C in a T75 cell culture flask from OD600 around 0.05 to 0.7.

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

treatment_protocol: In the case of 7H9+Casitone, pH4.7, pH8.7, 42°C and anaerobic treatment, MAP bacteria were collected by centrifugation and resuspended with medium. After 3 hrs of incubation, the total RNA was purified. In the case of 7H9 treatment, the incbation time was 2 days.

tag: background strain

tag: genotype

value: wild type

value: anaerobic conditions

tag: treatment duration

value: 3 hrs

source_name: leuD mutant, 7H9+Casitone anaerobic, 3 hrs

value: leuD mutant


title: Sorted Cell Population CD 14+  13


title: MAP_7H9+casitone_pH8.7_rep1

description:
Sample 17
Biological replicate 1.

source_name: K-10, 7H9+Casitone pH8.7, 3 hrs

value: high pH

source_name: leuD mutant, 7H9+Casitone pH8.7, 3 hrs


title: MAP_7H9+casitone_pH8.7_rep2

description:
Sample 19
Biological replicate 2.


title: MAP_7H9+casitone_anaerobic_rep1, dye-swap

description:
Sample 22
Label swap of Sample 21.


title: zebrafish_30h_ras-hs_r2

city: Boston

first: Anthony

middle: Dominc

last: DiBiase

address: KFRB, 1 Blackfan St, Suite 8216

department: Hem/Onc

institute: Children's Hospital Boston

description: transgenic Tg(hsp70-hRASG12V)

hyb_protocol: Hybridization was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

data_processing: The probe-level data were normalized and translated to gene-level (SEQ_IDs) with custom python scripts, then analyzed with Goldenspike (http://www2.ccr.buffalo.edu/halfon/spike/). This R Goldenspike package background-corrects, normalizes, multiple-tests, and computes the sample statistics below.

organism: Danio rerio

source_name: whole embryo

label_protocol: Labeling was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: embryos were synchronized for the fertilization time and grew at 28.5 degrees C.

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

treatment_protocol: Embryos received heatshock at 37 degrees C for one hour at 24 hour-post fertilization (hpf) stage, and kept in 28.5 degrees C till 30hpf for RNA extraction.

value: transgenic Tg(hsp70-hRASG12V)


title: MAP_7H9+casitone_anaerobic_rep2, dye-swap

description:
Sample 24
Label swap of Sample 23.


title: zebrafish_30h_ab-hs_r1

description: wild type

value: heatshock at 37 degrees C for one hour at 24 hour-post fertilization (hpf) stage


title: zebrafish_30h_ras-hs_r1

description: transgenic Tg(hsp70-hRASG12V)


title: MAP_7H9+casitone_pH4.7_rep2

description:
Sample 15
Biological replicate 2.

source_name: K-10, 7H9+Casitone pH4.7, 3 hrs

value: low pH

source_name: leuD mutant, 7H9+Casitone pH4.7, 3 hrs


title: MAP_7H9+casitone_pH4.7_rep2, dye-swap

description:
Sample 16
Label swap of Sample 15.


title: MAP_7H9+casitone_pH4.7_rep1

description:
Sample 13
Biological replicate 1.


title: MAP_7H9+casitone_anaerobic_rep1

description:
Sample 21
Biological replicate 1.


title: MAP_7H9+casitone_42°C_rep2, dye-swap

description:
Sample 12
Label swap of Sample 11.

source_name: leuD mutant, 7H9+Casitone at 42°C, 3 hrs

value: high temperature

source_name: K-10, 7H9+Casitone at 42°C, 3 hrs


title: MAP_7H9+casitone_pH8.7_rep1, dye-swap

description:
Sample 18
Label swap of Sample 17.


title: MAP_7H9+casitone_pH4.7_rep1, dye-swap

description:
Sample 14
Label swap of Sample 13.


title: zebrafish_30h_ab-hs_r2

description: wild type


title: MAP_7H9+casitone_42°C_rep1

description:
Sample 9
Biological replicate 1.


title: Sorted Cell Population CD 34+ 24

value: CD34-positive common precursor cells


title: MAP_7H9+casitone_42°C_rep1, dye-swap

description:
Sample 10
Label swap of Sample 9.


title: MAP_7H9_2 days_rep2, dye-swap

description:
Sample 8
Label swap of Sample 7.

source_name: leuD mutant, 7H9, 2 days

value: no Casitone

value: 2 days


title: MAP_7H9_2 days_rep1, dye-swap

description:
Sample 6
Label swap of Sample 5.


title: MAP_7H9+casitone_42°C_rep2

description:
Sample 11
Biological replicate 2.


title: HA H3K9me2, array 1 of 4

description: Chip-chip Human Astrocytes H3K9me2


title: MAP_7H9_2 days_rep2

description:
Sample 7
Biological replicate 2.


title: MAP_7H9+casitone_3hrs_rep2, dye-swap

description:
Sample 4
Label swap of Sample 3.

source_name: leuD mutant, 7H9+Casitone, 3 hrs

source_name: K-10, 7H9+Casitone, 3 hrs


title: HAEC H3K9me2, array 3 of 4

source_name: H3K9me2 ChIP DNA fromHuman aortic endothelial cells


title: MAP_7H9+casitone_3hrs_rep1, dye-swap

description:
Sample 2
Label swap of Sample 1.


title: MAP_7H9_2 days_rep1

description:
Sample 5
Biological replicate 1.


title: MAP_7H9+casitone_pH8.7_rep2, dye-swap

description:
Sample 20
Label swap of Sample 19.


title: S22862_F_2m_Rep1

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor with RMA method.

source_name: OvarianGranulosa cells_Foxo1/3 dKO

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

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

tag: strain background

value: mixed background from FVB and C57BL/6

value: Foxo1 f/-;Foxo3 f/-; Amhr2-cre (Foxo1/3 dKO)

tag: age

value: 2 month

value: ovarian granulosa cells


title: WT_aorta_rep2

city: Minneapolis

first: Neeta

last: Adhikari

state: Minnesota

address: 312 Church Street SE

department: Lillehei Heart Institute

institute: University of Minnesota

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized by using Rank Invariant normalization using Genome Studio

label_protocol: Biotinylated cRNA were prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies, USA).

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up  with QIAGEN RNeasy mini kit in accordance with the manufacturer's protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Male

value: 3-4 months

value: Thoracic aorta


title: MAP_7H9+casitone_3hrs_rep1

description:
Sample 1
Biological replicate 1.

source_name: K-10, 7H9+Casitone, 3hrs

value: wild type

value: 3 hrs


title: MAP_7H9+casitone_3hrs_rep2

description:
Sample 3
Biological replicate 2.

value: leuD mutant


title: S22865_F_d25_Rep2


title: WT_aorta_rep3


title: TC-1.5 µM treament

city: Ann Arbor

first: Lihong

last: Shi

address: 3608 BSRB, 109 Zina Pitcher Place

institute: University of Michigan

description: gene expression data from 1.5 µM TC treated, day 8 in vitro differentiated human erythroid cells

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Perfect Match Peg Arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.0. RMA was used to normalize the data and fit log2 transformed expression values

source_name: human day 8 differentiated erythroid cells

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: From days 0 to 8, the cells were cultured in IMDM basic medium (Biochrom) supplemented with 40 µg of inositol/ml, 10 µg of folic acid/ml, 160 µM monothioglycerol, 120 µg of iron-saturated human transferrin/ ml, 10 µg of insulin/ml, 900 ng of ferrous sulfate/ml, 90 ng of ferric nitrate/ml, 1µM hydrocortisone, and 5 ng of interleukin-3 (IL-3)/ml, and 200 mM L-glutamine (Invitrogen), 1% deion- ized bovine serum albumin (Stemcell Technologies), 100 ng of stem cell factor (Prospec)/ml, and 3 IU of erythropoietin/ml. From day 8 through day 14, the cells were cultured in the same medium without hydrocortisone or IL-3.

treatment_protocol: Tranylcypromine (Tocris Bioscience) dissolved in water at 0.5, 1.5 and 5 µM was added to the culture medium on day 4 through day 14.

tag: drug treatment

value: TC-1.5 µM


title: S22861_wt_d25_Rep2

source_name: OvarianGranulosa cells_wild type


title: S22863_F_2m_Rep2


title: TC-0.5 µM treament

description: gene expression data from 0.5 µM TC treatment, day 8 in vitro differentiated human erythroid cells

value: TC-0.5 µM


title: S22864_F_d25_Rep1


title: S22860_wt_d25_Rep1


title: NDST_aorta_rep3

tag: strain


title: WT_aorta_rep1

tag: tissue


title: NDST_aorta_rep2


title: TC-5 µM treament

description: gene expression data from 5 µM TC treated, day 8 in vitro differentiated human erythroid cells

value: TC-5 µM


title: without TC treatment

description: gene expression data from none-treatment, day 8 in vitro differentiated human erythroid cells

value: TC-0 µM


title: NDST_aorta_rep1


title: 4184R2_recurring

status: Public on Feb 15 2013

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

description: SAMPLE 52

hyb_protocol: 1650ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 4x180K Custom Microarray (Design ID 032034 )

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour GEand 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.5.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities

source_name: LNCaP derived xenograft_recurring

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: Cell Culture. Cultured LNCaP cells (derived from the lymph node metastasis of a prostate cancer patient), passage 35–45, were maintained in RPMI 1640 with 5% FCS at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated using the mirVana™ miRNA Isolation Kit (Ambion AM1560)

tag: cell type origin

value: Cultured LNCaP cells

value: LNCaP derived xenograft

tag: harvest time point (along the psa curve)

value: recurring


title: 4179N_nadir

description: SAMPLE 51

source_name: LNCaP derived xenograft_nadir

value: nadir


title: 4179L2_CRPC

description: SAMPLE 50

source_name: LNCaP derived xenograft_CRPC

value: CRPC


title: 4183R1_CRPC

description: SAMPLE 48


title: 4182L2_resistant

description: SAMPLE 47

source_name: LNCaP derived xenograft_resistant

value: resistant


title: 4182N_intact

description: SAMPLE 49

source_name: LNCaP derived xenograft_intact

value: intact


title: 4179R1_nadir

description: SAMPLE 37


title: PBS treated EL4 Cell Replicate 2

city: Beijing

first: Li-Xin

last: Wang

address: Fuxing Road

department: Hematology

country: China

institute: Chinese PLA General Hospital

description:
Raw data file: 101221 10996A_EL4DAC2 cy5+10996A_EL4CTR2 cy3 035.LSR
Biological replicate 2 of 3. PBS treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4CTR2

hyb_protocol: Arrays  hybridization was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature)

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner .

data_processing: For individual channel data extract, faint spots were removed for which intensities were below 400 unit after background subtracted in both channels (Cy3 and Cy5). A space- and intensity-dependent normalization based on a LOWESS program was employed [SpotData software (CapitalBio Corp)]. To determine the significant differentially expressed genes, Significance Analysis of Microarrays (SAM) was performed.

source_name: Total RNA from 2×106 EL4 cells

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

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

treatment_protocol: DAC was added to cell culture medium to a final concentration of 0.25μM once daily for 3 consecutive days, the cells were cultured for another day, then were harvested for mRNA extraction.

tag: cell line

value: EL4 cells

tag: passage

value: T cell lymphoma cells

tag: agent

value: control


title: 4181R2_nadir

description: SAMPLE 42


title: PBS treated EL4 Cell Replicate 3

description:
Raw data file: 101221 10996A_EL4CTR3 cy5+10996A_EL4DAC3 cy3 036.LSR
Biological replicate 3 of 3. PBS treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4CTR3


title: 4187L1_nadir

description: SAMPLE 46


title: 4177L2_nadir

description: SAMPLE 36


title: 4186R1_intact

description: SAMPLE 44


title: 4178L2_regressing

description: SAMPLE 33

source_name: LNCaP derived xenograft_regressing

value: regressing


title: 4178R2_recurring

description: SAMPLE 32


title: 4182R2_intact

description: SAMPLE 40


title: 4187R2_regressing

description: SAMPLE 45


title: 4180L1_nadir

description: SAMPLE 41


title: 4179L1_CRPC

description: SAMPLE 34


title: 4181L2_intact

description: SAMPLE 35


title: 4188R2_intact

description: SAMPLE 43


title: 4186L2_CRPC

description: SAMPLE 31


title: 4177N_CRPC

description: SAMPLE 38


title: 4178N_recurring

description: SAMPLE 39


title: DAC treated EL4 Cell Replicate 3

description:
Raw data file: 101221 10996A_EL4CTR3 cy5+10996A_EL4DAC3 cy3 036.LSR
Biological replicate 3 of 3. DAC treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4DAC3

value: decitabine


title: DAC treated EL4 Cell Replicate 1

description:
Raw data file: 101221 10996A_EL4DAC1 cy5+10996A_EL4CTR1 cy3 026.LSR
Biological replicate 1 of 3. DAC treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4DAC1


title: 4187L2_nadir/recurring

description: SAMPLE 30

source_name: LNCaP derived xenograft_nadir/recurring

value: nadir/recurring


title: Monocyte H3K4Me3 from volunteer1

city: Duarte

first: Nancy

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: ChIP-chip Monocyte H3K4Me3 from volunteer1

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: mean-centered log2(Cy5/Cy3) in gff format. The gff files are combined to generate matrix dataset in R.

source_name: H3K4Me3  ChIP DNA from human monocytes

label_protocol: According to standard NimbleGen Protocol

growth_protocol: RPMI 1640 medium

extract_protocol: THP1 cells  or primary monocytes were crosslinked in 1% formaldehyde, sonicated to shear DNA, and IPs performed with antibodies. IP with no antibody was used as the Input control.

treatment_protocol: No Treatment

value: Monocyte

source_name: monocyte no antibody control

growth_protocol: RPMI medium


title: 4177R1_regressing

description: SAMPLE 27


title: 4181R1_nadir

description: SAMPLE 29


title: DAC treated EL4 Cell Replicate 2

description:
Raw data file: 101221 10996A_EL4DAC2 cy5+10996A_EL4CTR2 cy3 035.LSR
Biological replicate 2 of 3. DAC treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4DAC2


title: 4186L1_CRPC

description: SAMPLE 26


title: 4184L2_intact

description: SAMPLE 24


title: 4188L1_intact

description: SAMPLE 25


title: PBS treated EL4 Cell Replicate 1

description:
Raw data file: 101221 10996A_EL4DAC1 cy5+10996A_EL4CTR1 cy3 026.LSR
Biological replicate 1 of 3. PBS treated EL4 cells,  harvested 48 h after the last dose of treatment.
EL4CTR1


title: 4179R2_CRPC

description: SAMPLE 21


title: 4184N_CRPC

description: SAMPLE 28


title: 4183L2_resistant

description: SAMPLE 20


title: 4185L1_nadir/recurring

description: SAMPLE 19


title: THP1 Pol II Ser5P

description: ChIP-chip THP1 Pol II Ser5P

source_name: Pol II Ser5-P  ChIP DNA from THP1 cells

source_name: THP1 IgG control

value: THP1 cell line


title: Monocyte H3K4Me3 from volunteer 3

description: ChIP-chip Monocyte H3K4Me3 from volunteer 3


title: THP1 Pol II

description: ChIP-chip THP1 Pol II

source_name: Pol II ChIP DNA from THP1 cells


title: THP1 H3K9Ac

description: ChIP-chip THP1 H3K9Ac

source_name: H3K9Ac  ChIP DNA from THP1 cells


title: Marghera_December_DigestiveGland_POOL4

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Pool consisting of 5 digestive gland

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Ruditapes philippinarum

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Marghera (Venice Lagoon) in December

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: digestive gland


title: Marghera_November_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Marghera (Venice Lagoon) in September


title: 4184R1_CRPC

description: SAMPLE 18


title: Monocyte H3K4Me3 from volunteer 2

description: ChIP-chip Monocyte H3K4Me3 from volunteer 2


title: 4185R2_intact

description: SAMPLE 23


title: Marghera_November_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Marghera_June_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Marghera (Venice Lagoon) in June


title: Marghera_November_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: Marghera_December_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: 4176L1_regressing

description: SAMPLE 22


title: 4186R2_recurring

description: SAMPLE 17

source_name: LNCaP derived xenograft_recurring


title: Marghera_November_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: 4182R1_resistant

description: SAMPLE 15


title: Marghera_June_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: 4185N_intact

description: SAMPLE 16


title: Marghera_April_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in Marghera (Venice Lagoon) in April


title: Marghera_April_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Marghera_April_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: Marghera_June_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: Marghera_December_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Marghera_June_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: 4187R1_recurring

description: SAMPLE 13


title: 4176R1_CRPC

description: SAMPLE 10

source_name: LNCaP derived xenograft_CRPC


title: 4176L2_nadir

description: SAMPLE 11

source_name: LNCaP derived xenograft_nadir


title: 4177R2_regressing

description: SAMPLE 14


title: Marghera_April_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: 4185R1_resistant

description: SAMPLE 9

source_name: LNCaP derived xenograft_resistant


title: S.Erasmo_December_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in S.Erasmo (Venice Lagoon) in December


title: 4183L1_CRPC

description: SAMPLE 12


title: S.Erasmo_December_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: S.Erasmo_December_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: S.Erasmo_September_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in S.Erasmo (Venice Lagoon) in September


title: 4178R1_CRPC

description: SAMPLE 6


title: S.Erasmo_December_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: 4181N_nadir

description: SAMPLE 7


title: 4176N_regressing

description: SAMPLE 8

source_name: LNCaP derived xenograft_regressing


title: 4180N_nadir/recurring

description: SAMPLE 4

source_name: LNCaP derived xenograft_nadir/recurring


title: S.Erasmo_September_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland


title: 4188R1_intact

description: SAMPLE 5

source_name: LNCaP derived xenograft_intact


title: S.Erasmo_September_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: S.Erasmo_September_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: 4185L2_CRPC

description: SAMPLE 2


title: 4180R1_intact

description: SAMPLE 1


title: S.Erasmo_June_DigestiveGland_POOL4

description: Pool consisting of 5 digestive gland

source_name: Pool of Ruditapes philippinarum digestive gland sampled in S.Erasmo (Venice Lagoon) in June


title: Marghera_December_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: Control NCI-H295A cells, sample 2

city: San Francisco

last: Tee

address: HSE1401, 513 Parnassus Ave

institute: UCSF

description: Control NCI-H295A cells.

hyb_protocol: The chips were stained and washed using an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using a GCS 3000 scanner with auto-loader in the Genomics Core laboratory.

data_processing: Hybridization intensity signals from the scanned images were analyzed using Affymetrix GeneChip Operating Software (GCOS, version 1.3) to provide qualitative detection calls and quantitative estimates of gene expression levels (signal values).

source_name: cell line

label_protocol: 4 μg RNA was used to synthesize double-stranded cDNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX) with oligo-dT primer [5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24] to incorporate a T7 RNA polymerase promoter. Antisense cRNA was labeled with biotin-UTP using T7 RNA polymerase (Ambion), and the cRNA was fragmented to 35–200 nucleotides (nt) at 94 C for 35 min in 40 μl 40 mm Tris-acetate (pH 8.1), 100 mm KOAc, 30 mm MgOAc. The integrities of total RNAs, cRNAs, and fragmented cRNAs were assessed on a Bio-Rad (Hercules, CA) Experion BioAnalyzer.

growth_protocol: NCI-H295A adrenocortical cells were grown on 10-cm plates in RPMI 1640 with 2% fetal calf serum, gentamicin, insulin, and selenium. Three nearly confluent plates were incubated in the presence and absence of 1 mm 8-Br-cAMP for 18 h; the cells were washed with PBS and lysed with 1 ml Trizol (Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was purified further using RNeasy columns (QIAGEN, Valencia, CA).

tag: treatment

value: Control


title: KO RNA pooled from embryonic murine limb tissue

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from murine shox2 knockout pooled fore- and hindlimbs at stage E12.5.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of mouse430_2 -type from Affymetrix. A Custom CDF Version 11 with UniGene-based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: E12.5 pooled fore- and hindlimb tissue, Shox2 KO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Murine embryonic fore- and hindlimb tissue was dissected at stage E12.5.

extract_protocol: For total RNA isolation by TRIzol® (Invitrogen), samples from embryonic limbs (E12.5) of the same genotype (wildtype and Shox2-/-) were pooled. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue was stored at -80°C until RNA preparation.

tag: genotype/variation

value: Shox2 -/-

value: forelimbs and hindlimbs


title: cAMP-treated NCI-H295A cells, sample 3

description: NCI-H295A cells treated with 1 mM cAMP.

treatment_protocol: NCI-H295A cells were treated with 1 mM 8-Br-cAMP for 18 h.

value: 1 mM cAMP


title: 18.19Mxs.18.19M

city: Bloomington

first: Colin

middle: D

last: Meiklejohn

state: IN

address: Jordan Hall, 1001 E. 3rd St.

department: Biology Department

institute: Indiana University

hyb_protocol: Hybridization was done using the 3DNA Array50 kit following the manufacturer's protocols

scan_protocol: Slides were scanned in an Axon 4000B scanner and microarray images were processed with GenePix v5.0

data_processing: Spots were filtered using the following quality control criteria: 70% of the foreground pixels within a spot were required to have a signal intensity higher than two standard deviations above the median background signal intensity in at least one of the two channels (Cy3 or Cy5); the median foreground signal intensity was required to be at least three times as great as the median background signal intensity in at least one of the two channels; a spot must have more than 30 foreground pixels.  Spot-wise log2 ratios were normalized over overall spot signal intensity by loess smoothing using a span of 0.3.  To account for spatial variation in signal across arrays, spot-wise log2 ratios were subsequently normalized by a second loess smoothing over the physical location of the spots on the slide, using a span of 0.002, which corresponds to an effective neighborhood of ~ 250 spots.

molecule: polyA RNA

organism: Drosophila simulans

source_name: whole adult flies

label_protocol: At least 20μg total RNA was used as a template for cDNA synthesis and incorporation of fluorescent dyes was done using the 3DNA Array50 kit following the manufacturer’s protocols

growth_protocol: Flies were reared in three independent cohorts on standard media  at 25C on a 12:12 light:dark cycle.  Culture density was controlled by combining 15 parental males with 15 females per vial for homozygous introgression genotypes, and 10 males with 10 females for the simB, mau12, and heterozygous introgression genotypes.

extract_protocol: RNA was extracted from frozen flies using TRIzol, chloroform and phase-lock gel tubes

treatment_protocol: Adults were collected as virgins and the sexes were aged separately for 1-2 days before flash-freezing in liquid nitrogen and storage at -80C at the same time of day

tag: Sex

value: male

value: whole organism


title: S.Erasmo_June_DigestiveGland_POOL3

description: Pool consisting of 5 digestive gland


title: S.Erasmo_June_DigestiveGland_POOL1

description: Pool consisting of 5 digestive gland


title: Control NCI-H295A cells, sample 1

description: Control NCI-H295A cells.


title: Control NCI-H295A cells, sample 3

description: Control NCI-H295A cells.


title: cAMP-treated NCI-H295A cells, sample 2

description: NCI-H295A cells treated with 1 mM cAMP.


title: S.Erasmo_June_DigestiveGland_POOL2

description: Pool consisting of 5 digestive gland


title: LCMV-Clone 13 spleen day 30, rep4

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description:
5237
Gene expression data from spleens harvested at day 30, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks

hyb_protocol: Affymetrix Mouse Genes ST 1.0 microarray

scan_protocol: Affymetrix Expression Console

data_processing:
Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.
Relative expression levels for each probeset were calculated by normalization to the median value for all uninfected samples

source_name: LCMV-Clone 13-infected_spleen harvested on day 30

label_protocol: Ambion WT labeling kit

growth_protocol: Six-ten week old mice were used for all experiments, and were housed under pathogen-free conditions.

extract_protocol: Harvested spleens were frozen in RNA Later (Qiagen) at 1 mg/ml tissue.  Whole spleens were homogenized, and RNA from homogenates were isolated with Rneasy extraction kit (Qiagen).

treatment_protocol: Mice were infected intravenously via the retro-orbital sinus with 2x10^6 plaque forming unites of LCMV-Armstrong or LCMV-Clone 13.

value: 6-10 weeks

tag: infected with

value: LCMV clone 13

value: spleen

tag: harvest time point

value: day 30


title: LCMV-Clone 13 spleen day 30, rep2

description:
5235
Gene expression data from spleens harvested at day 30, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: LCMV-Clone 13 spleen day 30, rep3

description:
5236
Gene expression data from spleens harvested at day 30, from LCMV-Clone 13 infected C57BL7 mice aged 6-10 weeks


title: simBMx18.19M

value: simB


title: mau12Mx16.25M

organism: Drosophila mauritiana