title: KO comR vs. KO comX, replicate 2

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de louvain

description: Biological replicate 2 of 2.

hyb_protocol: Labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus) and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Streptococcus thermophilus

source_name: KO comR CDML, OD 0.4

label_protocol:
First strand cDNA was synthesized from 10 microg RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to the instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Strains LF148 and CB003 were grown at 37°C during 16h in M17 medium supplemented with lactose 1% (M17L), washed twice (5,000 x g, 9 min, room temperature) in one volume of CDM medium supplemented with lactose 1% (CDML) and resuspended in one volume of CDML. Cultures were then 30-fold diluted in CDML. When cells reached the mid-log phase (OD600 of 0.3~0.4), 25-ml aliquots were collected for total RNA extraction.

extract_protocol: Cells were harvested by centrifugation (7,000 x g for 4 min) and mechanically broken with 0.18-mm-diameter glass beads in a Braun Homogenizer (three 1-min periods of homogenization with 1-min intervals on ice). Total RNA was extracted using the High Pure RNA isolation kit (ROCHE, Basel, Switzerland).

tag: strain

value: LMD-9 comR::lox72

tag: isolate

value: clone 2

label: Alexa Fluor 647

source_name: KO comX CDML, OD 0.4

value: LMD-9 DcomX


title: 20 mM 2-oxoglutarate 1

status: Public on Feb 15 2014

type: RNA

city: Syracuse

first: Christopher

last: Nomura

state: NY

address: 1 Forestry Dr.

department: Chemistry

country: USA

institute: SUNY-ESF

description: Gene expression from cells grown in rich media induced with 20 mM 2-oxoglutarate

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 50C 60 rpm on GeneChip P. aeruginosa Genome Array with rotation at 60 rpm. GeneChips were processed with an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 P. aeruginosa array protocol (as specified in the Affymetrix GeneChip Expression Analysis Technical Manual), using stains from the Affymetrix Hybridization, Wash, and Stain Kit.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 7G Plus

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.

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa PAO1

source_name: Cells harvested at 30 min post induction

label_protocol: Samples were processed according to the Prokaryotic Target Preparation Protocol in Affymetrix GeneChip Expression Analysis Technical Manual.  Briefly, 10 ug of RNA was used to synthesize cDNA via random primers and SuperScript II reverse transcriptase.  cDNA was purified using Qiagen MinElute PCR purification columns.  The resulting cDNA was fragmented and labeled with biotin.

growth_protocol: P. aeruginosa PAO1 was grown in 1 mL of nutrient broth (Oxoid number 2) at 37 C, 200 rpm, until an OD 600 of 0.3 was reached.  Cells were induced with either 0 or 20 mM 2-oxoglutarate.

extract_protocol: RNA was isolated using the enzymatic lysis and proteinase K digestion method of Qiagen Rneasy with on-column DNA digestion.

treatment_protocol: At 30 min post induction with 2-oxoglutarate, 0.5 mL of culture was treated with 1.0 mL of RNAprotect Bacterial reagent (Qiagen).

tag: sub-strain

tag: genotype

value: wild-type


title: 20 mM 2-oxoglutarate 2


title: KO comR vs. KO comX, replicate 1

description: Biological replicate 1 of 2.

value: clone 1


title: Bat Hindlimb developmental stage CS16  (Biological Repeat 2)

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: Biological repeat 2 of 4. Gene expression levels in the CS16 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate

hyb_protocol: The Mus musculus (mouse) OpArray™  platform consists of activated epoxide coated slides printed with version 4.0 of the Mus musculus (mouse) Array Ready Oligo Set (AROS), which contains over 36 000 cDNA probes (OPERON Biotechnologies, Inc., Huntsville, AL, USA).  These Operon OpArray™ slides were printed by Operon and were treated according to the OpArray™ Protocol. Slides were prehybridised in OpArray Pre-Hyb Solution for 1 hr at 42 ºC then washed in a premixed OPERON wash solution for 5 min and rinsed in MilliQ water three times for 30 s each and dried by centrifugation. Pre-hybridised slides were placed on a solid heating block set at 50ºC and a hybridisation chamber created over the array using a LifterSlip™. The hybridisation solution consisted of 45 μL of OpArray Hyb Buffer, 250ng of Cy3-labelled target aRNA sample combined with 250ng of Cy5-labelled reference aRNA sample. This sample was denatured at 65 ºC for 5 min, centrifuged and loaded onto the array by pipetting the solution along the bottom edge of the LifterSlip™ allowing it to be evenly wicked over the array by capillary action. The slide was placed in hydrated hybridisation cassettes, which were sealed and incubated in the dark in a water bath at 42 ºC for 19 hrs. After hybridisation the slides were washed in three successive premixed wash solutions of increasing stringency (Wash1: 2X SSC and 0.1% SDS preheated to 42 ºC; Wash 2: 1X SSC; Wash 3: 0.2X SSC). The slides were transferred to a slide rack and gently agitated in Wash1 for 10 min. They were transferred to a clean slide rack and agitated in the Wash2 and then Wash 3 for 5 min each. Slides were immediately transferred to a dry slide rack and dried by centrifugation. They were kept in the sealed centrifuge until scanning which was performed within 6 hrs. After scanning, slides were placed in sealed, light free slide holders.

scan_protocol: Slides were scanned using the Genepix® 4000A scanner (Axon Instruments Inc., Molecular Devices, Sunnyvale, CA, USA). A low-resolution (40 µm/pixel) preview scan was performed to optimise the scanner settings. The gain of the Photomultiplier Tubes (PMT) for each wavelength of light emitted was adjusted to balance the signal from each channel. The signals from each channel were standardised by adjusting the PMTs until the count ratio was a value between 0.95 and 1.05 and the histogram of both channels had similar (overlapping) intensity profiles. Saturation thresholds were adjusted to ensure that the majority of the feature signals were below saturation level. The slides were then scanned with the optimised PMT gain settings. Data was captured and flagged using GenePix™ Pro (ver. 6.0) microarray analysis software (Amersham Biosciences, Piscataway, NJ, USA). A feature-indicator grid was aligned over the scanned array image capturing data associated with each feature and linking this to the Operon oligo identity number (using the Mus musculus OpArray Gal file). Each spot image was discriminated from the background and several measurements are taken. Spots were captured automatically as irregular features and were allowed to be resized from a maximum of 300% to a minimum of 33% of their original size (±100 µm). Background signal was calculated using the method of morphological closing followed by opening.

data_processing:
Features that could not be discriminated from the background, that were smaller than six pixels or that fell outside of the feature resizing threshold were automatically flagged as “Not Found” (given a flag value of -50). Found features were given a flagging value of 0. Features that had been captured automatically were checked manually and any automatic capture errors were corrected. During this time anomalous features were manually flagged as “Bad” (given a flag value of -100). These included spots that were discolored (over green) due to obvious wash effects; spots that were marked by the fluorescence of dust particles, hair or a scratch; and spots that had merged due to printing errors. Dye marker spots that occurred at the top, left-hand corner of each block were also marked “Bad”. Features were then automatically flagged as bad using the ‘Flag Features’ function. Spots were automatically flagged as “Bad” if they were: over saturated (greater than or equal to 10% saturated in either channel); misshapen (circularity of less than 35); very small (diameter of less than 80 or a number of pixels less than 40); or had an inconsistent spot signal (coefficient of variation of the pixels in either channel exceeded 99). These threshold parameters were determined by visual inspection of the scatter plots of these variables for each array in Genepix™ Pro. The latter three parameters exclude spots based on their morphology and the consistency of the signal across the spot. The raw data was then exported from Genepix™ Pro as Genepix results (.gpr) files.
Raw expression data were corrected for background effects, normalised and processed using the R programming language (ver. 2.6.0.) and associated R Bioconductor (ver. 2.1.) packages. The median foreground signal intensity of each spot for each of the channels, Cy5 (red) and Cy3 (green) as well as the median background intensity of each spot for each channel was imported into R. In addition to annotation, information weights matrix was generated, with all spots flagged as “Bad” (< -75) being weighted as 1. The 48 tiling spots (dye markers) were removed prior to normalization. The normexp background correction method was used with an offset of 32 to correct for any spatial artifacts that were present on the array. Data were adjusted within each array using a robust-spline normalisation function that was modified to accept an increased number of iterations. Data were adjusted between arrays using R-quantile normalisation which did not exclude weighted values. An estimated A value threshold for low signal (A = 7.1) was calculated using the distribution of the normalised values for the “null”, “buffer” and “negative control” spots. Genes that fell below this threshold across all arrays (“low intensity”) or that were weighted as “Bad” more than four times across all arrays were removed (values replaced with NA and then removed). Probe replicates were averaged Missing values were imputed using KNN imputation. Batch effects were corrected for using the R script COMBAT. Variance filtering (genes below the average standard deviation of all genes was classified as “Flat”) was performed to reduce the number of genes tested for differential expression. Features that did not contain mouse probe information (“Null”, “Dye”, “Buffer”, “alien spikes”) were removed. These steps reduced the dataset from 37 440 to 12 792 features (rows).
Matrix_B: Background corrected (normexp), normalised (within arrays using robust-spline, between arrays using Rquantile) log2 average signal (intensity) data (A values). Values weighted as “Bad” or filtered as “low intensity” have been replaced with “NA”.
Matrix_C: Background corrected (normexp), normalised (within arrays using robust-spline, between arrays using Rquantile) single channel data. Ch1 samples represent the signal from channel 1 (mouse reference samples) on each array while ch2 data represent the signal from ch2 (bat test samples). Values weighted as “Bad” or filtered as “low intensity” have been replaced with “NA”.

organism: Mus musculus

source_name: Common Reference: E13.5 mouse hand plate

label_protocol: These RNA samples were amplified and labelled using the Amino Allyl MessageAmp™ II Cy3 aRNA Amplification Kit (Ambion, Austin, TX, USA) as per manufacturer’s instructions. A fixed amount of 0.5 µg of input RNA was used in all experiments. Experiments were done in 4 batches with each biological repeat (1, 2, 3, 4) of the test conditions corresponding to an independent batch and being labelled with Cy3. In each batch the common reference was independently amplified and labelled with Cy5.

extract_protocol: Whole embryos were stored in RNAlater® (QIAGEN, Valancia, CA, USA) according to the manufacturer’s instructions. The autopods (distinguished as being the area of dorso-ventrally flattened tissue on the distal portion of the limb) were dissected off along the point of constriction of the presumptive wrist or ankle. This excluded the tissue associated with the stylopod and the zeugopod in addition to the tissue associated with the proto- and plagiopatagium of the bat. Total RNAs from these autopod tissues were extracted using QIAzol Lysis Reagent and purified using the RNeasy® Lipid Tissue Mini Kit (QIAGEN, Valancia, CA, USA). The quality of the RNA from the mouse hand plate pooled reference and ten randomly chosen bat limb samples was determined by the Centre for Proteomic and Genomic Research (CPGR, Cape Town, South Africa) using an Agilent 2100 Bioanalyser (Agilent Technologies, Stockport, UK). The RNA integrity of all samples was checked by visualization of 1 µg of RNA on a formaldehyde denaturing gel. The concentration and condition of each sample was determined using the Nanodrop® ND-1000 Uv-Vis Spectrophotometer (Nanodrop Technologies, Inc., Wilmington, DE, USA) prior to the experiment. These measurements were repeated three times and the average calculated.

tag: tissue

value: 24 Pooled left and right embryonic handplates

tag: developmental stage

organism: Miniopterus natalensis

source_name: CS16 bat footplate

value: Left and right embryonic footplate


title: microRNA_Monocytes_after exercise_14

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

description:
Mono14-miRNA-Peak.txt:gTotalProbeSignal(normalized)
microRNA expression after-exercise

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray.

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 10.2 (Agilent Technologies).

data_processing: The results were analyzed using GeneSpring GX 12.1 Software (Agilent Technologies, Inc).

organism: Homo sapiens

source_name: monocytes after 20 min bout of exercise

label_protocol: One hundred ng of total RNA was labeled with the fluorescent dye Cyanine 3-pCp (Cy3) using the microRNA Labeling Reagent and Hybridization Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol.

extract_protocol: Monocytes were isolated from PBMC using a negative magnetic cell separation methods (Miltenyi Biotec Monocyte Isolation Kit II, human  #130-091-153 and the autoMACS® Pro Separator).

treatment_protocol: Blood sample was drawn before and immediately after 20 min of exercise.

tag: gender

value: male

tag: age

value: 22-30 yr old

value: monocytes isolated from PBMC

tag: time point

value: after 20 min bout of exercise


title: no substrate 1

description: Gene expression from cells grown in rich media and induced with no substrate


title: no substrate 2


title: Bat Hindlimb developmental stage CS16  (Biological Repeat 4)

description: Biological repeat 4 of 4. Gene expression levels in the CS16 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Hepatocellular carcinoma [H85]

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

hyb_protocol: The hybridization was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA).

scan_protocol: The arrays were scanned by ScanArray scanner (Perkin-Elmer)

data_processing: Primary signal intensities were obtained using ImaGene 6.0 software (Bio-discovery, Marina del Rey, CA) and normalized using lowess and quantile method to eliminate intensity bias.

source_name: Normal liver tissue

label_protocol: The probe preparation was performed using 3DNA array detection system according to the manufacturer’s protocol (Genisphere, PA) with 20mg of total RNA.

extract_protocol: Total RNA was isolated from frozen tissue according to the manufacturer’s instructions (Qiagen), and quality of the total RNA was judged based on the ratio of 28S/18S RNA after agarose gel electrophoresis.

value: normal liver

source_name: Hepatocellular carcinoma

value: hepatocellular carcinoma


title: Hepatocellular carcinoma [H83]


title: Bat Hindlimb developmental stage CS16  (Biological Repeat 3)

description: Biological repeat 3 of 4. Gene expression levels in the CS16 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Bat Hindlimb developmental stage CS17  (Biological Repeat 4)

description: Biological repeat 4 of 4. Gene expression levels in the CS17 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate

source_name: CS17 bat footplate


title: Bat Forelimb developmental stage CS16  (Biological Repeat 2)

description: Biological repeat 2 of 4. Gene expression levels in the CS16 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate

source_name: CS16 bat handplate

value: Left and right embryonic handplate


title: Hepatocellular carcinoma [H80]


title: Gene expression of myoblasts 3 days after myogenic stimuli

city: Fukuoka-city

first: Kohei

last: Miyata

state: Fukuoka

address: 7-45-1 Nanakuma, Jounannku

department: Obstetrics and Gynecology

country: Japan

institute: Fukuoka University

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 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 100.

source_name: myoblasts

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Gene Profiling Regent User Guide (Affymetrix) from 200 ng of total RNA.

growth_protocol: Myoblasts were cultured with SkGM-2 medium (Lonza) at 37C 5% CO2.

extract_protocol: ISOGEN (Nippon gene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Differentiation to myotubes were stimulated by switching the culture medium to DMEM-F12 (Thermo scientific) with 2% horse serum (Sigma Aldrich) when cells were reachd about 50% confluent. Medium was replaced every other day, and changed to SkGM-2 medium at day 8. SkGM-2 medium was replaced every other day until day 15. Cells were collected on day 1, day 3, day 8 and day 15.

tag: ethnicity

value: Caucasian


title: Bat Forelimb developmental stage CS16  (Biological Repeat 4)

description: Biological repeat 4 of 4. Gene expression levels in the CS16 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Gene expression of myoblasts 8 days after myogenic stimuli


title: Bat Forelimb developmental stage CS16  (Biological Repeat 1)

description: Biological repeat 1 of 4. Gene expression levels in the CS16 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate

source_name: Common Reference: E13.5 mouse hand plates


title: Bat Hindlimb developmental stage CS17  (Biological Repeat 3)

description: Biological repeat 3 of 4. Gene expression levels in the CS17 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Bat Forelimb developmental stage CS17  (Biological Repeat 3)

description: Biological repeat 3 of 4. Gene expression levels in the CS17 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate

source_name: CS17 bat handplate


title: Hepatocellular carcinoma [H79]


title: Hepatocellular carcinoma [H78]


title: Gene expression of myoblasts 15 days after myogenic stimuli


title: Bat Forelimb developmental stage CS16  (Biological Repeat 3)

description: Biological repeat 3 of 4. Gene expression levels in the CS16 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Hepatocellular carcinoma [H81]


title: Bat Hindlimb developmental stage CS17  (Biological Repeat 2)

description: Biological repeat 2 of 4. Gene expression levels in the CS17 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Bat Hindlimb developmental stage CS17  (Biological Repeat 1)

description: Biological repeat 1 of 4. Gene expression levels in the CS17 bat foot plate relative to that in the Common reference pool of E13.5 mouse handplate


title: KO comR vs. KO comX, replicate 3

description: Biological replicate 1 of 2, dye swap.


title: Hepatocellular carcinoma [H77]


title: SM003_Mock_d7_4

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: Project name, virus strain, day, replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: Lung

tag: infection

value: Mock

value: 20 week

tag: time


title: Bat Forelimb developmental stage CS17  (Biological Repeat 4)

description: Biological repeat 4 of 4. Gene expression levels in the CS17 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Bat Forelimb developmental stage CS17  (Biological Repeat 2)

description: Biological repeat 2 of 4. Gene expression levels in the CS17 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Hepatocellular carcinoma [H76]


title: Bat Forelimb developmental stage CS17  (Biological Repeat 1)

description: Biological repeat 1 of 4. Gene expression levels in the CS17 bat hand plate relative to that in the Common reference pool of E13.5 mouse handplate


title: Gene expression of myoblasts before myogenic stimuli


title: Hepatocellular carcinoma [H75]


title: Hepatocellular carcinoma [H73]


title: Hepatocellular carcinoma [H74]


title: SM003_Mock_d4_2


title: SM003_Mock_d7_1


title: Hepatocellular carcinoma [H72]


title: Hepatocellular carcinoma [H63]


title: Hepatocellular carcinoma [H69]


title: SM003_Mock_d4_3


title: Hepatocellular carcinoma [H70]


title: SM003_Mock_d7_3


title: SM003_Mock_d4_4


title: SM003_Mock_d7_2


title: SM003_Mock_d1_4


title: SM003_Mock_d2_1


title: Hepatocellular carcinoma [H71]


title: SM003_Mock_d4_1


title: SM003_Mock_d1_2


title: Hepatocellular carcinoma [H62]


title: SM003_Mock_d2_3


title: SM003_Mock_d1_1


title: SM003_Mock_d1_3


title: SM003_icSARS_d7_5

value: SARS CoV


title: SM003_icSARS_d7_4


title: SM003_Mock_d2_2


title: SM003_Mock_d2_4


title: SM003_icSARS_d7_3


title: Hepatocellular carcinoma [H59]


title: Hepatocellular carcinoma [H61]


title: SM003_icSARS_d7_2


title: Hepatocellular carcinoma [H57]


title: Hepatocellular carcinoma [H55]


title: SM003_icSARS_d4_2


title: SM003_icSARS_d4_4


title: Hepatocellular carcinoma [H54]


title: SM003_icSARS_d4_1


title: SM003_icSARS_d7_1


title: SM003_icSARS_d4_5


title: SM003_icSARS_d1_4


title: SM003_icSARS_d4_3


title: SM003_icSARS_d1_3


title: SM003_icSARS_d2_3


title: SM003_icSARS_d2_4


title: SM003_icSARS_d2_5


title: Hepatocellular carcinoma [H51]


title: Hepatocellular carcinoma [H52]


title: SM003_icSARS_d2_2


title: SM003_icSARS_d1_1


title: SM003_BatSRBD_d7_5

value: SARS BatSRBD mutant


title: Hepatocellular carcinoma [H53]


title: SM003_icSARS_d1_2


title: SM003_icSARS_d2_1


title: Hepatocellular carcinoma [H50]


title: SM003_BatSRBD_d7_4


title: Hepatocellular carcinoma [H48]


title: SM003_BatSRBD_d7_1


title: SM003_BatSRBD_d4_5


title: Hepatocellular carcinoma [H47]


title: SM003_BatSRBD_d4_1


title: SM003_BatSRBD_d4_4


title: SM003_BatSRBD_d4_3


title: Hepatocellular carcinoma [H46]


title: Hepatocellular carcinoma [H45]


title: SM003_BatSRBD_d4_2


title: HumanHT1080 Lamin B2_repl1

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
ch1 raw data file= CMF_394589_S01_Cy3.pair
ch2 raw data file= CMF_394589_S01_Cy5.pair

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 50 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. The score was calculated as the log2 Dam-LaminB2 or Dam-BAF: Dam ratio of the normalized data.

molecule: genomic DNA

source_name: Dam-only DamID DNA from HT1080

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: For the Dam-BAF sample: 1-2x10e5 cells were infected with lenti-virus expressing  Dam. After 48 hours gDNA was isolated with  the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg  of gDNA was digested with DpnI (New England Biolabs)), adapters were  ligated with T4 ligase ((New England Biolabs)), and the ligation  reaction was subsequently digested with DpnII ((New England Biolabs)).  500 ng of the DpnII digested material was used as input for a PCR  amplification of methylated fragments (MePCR), see Vogel et al., 2008,  Nature Protocols for details. MePCR fragments were purified by Qiaquick  Spin columns (Qiagen).   For the Dam-Lamin2 sample: Same as for the Dam-BAF sample except  that Dam-Lamin B2 was introduced by a Lipofectamine (Invitrogen) transfection of 4μg plasmid.

tag: cell line

tag: expression

value: Dam

source_name: HumanHT1080 Lamin B2


title: SM003_BatSRBD_d2_5


title: HumanHT1080 Lamin B2_repl2

description:
ch1 raw data file= CMF_394596_S01_Cy5.pair
ch2 raw data file= CMF_394596_S01_Cy3.pair


title: SM003_BatSRBD_d2_4


title: Hepatocellular carcinoma [H44]


title: Hepatocellular carcinoma [H43]


title: HumanHT1080 BAF_repl2

description:
ch1 raw data file= CMF_512997_S01_Cy5.pair
ch2 raw data file= CMF_512997_S01_Cy3.pair

source_name: Dam-BAF DamID DNA from HT1080

value: Dam-BAF


title: SM003_BatSRBD_d7_3


title: SM003_BatSRBD_d1_5


title: SM003_BatSRBD_d2_3


title: Hepatocellular carcinoma [H38]


title: Hepatocellular carcinoma [H40]


title: SM003_BatSRBD_d1_4


title: SM003_BatSRBD_d2_2


title: Hepatocellular carcinoma [H36]


title: SM003_BatSRBD_d2_1


title: Hepatocellular carcinoma [H37]


title: HumanHT1080 BAF_repl1

description:
ch1 raw data file= CMF_355053_S01_Cy3.pair
ch2 raw data file= CMF_355053_S01_Cy5.pair


title: Hepatocellular carcinoma [H35]


title: Hepatocellular carcinoma [H41]


title: SM003_BatSRBD_d1_3


title: Hepatocellular carcinoma [H33]


title: SM003_BatSRBD_d1_2


title: SM003_10^5_MA15_d7_2

value: SARS MA15


title: SM003_BatSRBD_d1_1


title: 48 hpf 5 nM retinoic acid rep 1

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: This sample is comprised of 75 pooled embryos exposed to 5 nM retinoic acid from 6-24 hpf and harvested at 48 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.

hyb_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were background-subtracted, normalized by LOWESS (Locally-weighted Regression), and analyzed for differential expression by t-test (p<0.05). Data processing was performed by LC Sciences using proprietary software (Bolstad, BM et al. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193).

organism: Danio rerio

source_name: whole embryo 48 hpf

growth_protocol: Adult Tropical 5D strain zebrafish (Danio rerio) were raised according to Institutional Animal Care and Use Committee protocols in the Sinnhuber Aquatic Research Laboratory at Oregon State University. Adults were maintained on a 14 h light/10 h dark schedule on a recirculating system in which water was maintained at 28±1 °C. Following adult spawns, embryos were collected, rinsed, and housed at 28±1 °C in pools of 75 embryos until the start of the experiment.

extract_protocol: miRNA was isolated using a miRNeasy kit (Qiagen) from pooled tissue (75 embryos) harvested at 12-48 hpf (n=2).

treatment_protocol: Groups of embryos were waterborne exposed to 5 nM retinoic acid in buffered embryo medium or embryo medium alone in 20-ml glass vials sealed with Teflon-lined lids to prevent volatilization. Each exposure group was considered a single replicate. Based on previous studies, embryos were exposed to retinoic acid from 6-24 hpf, rinsed and embryo homogenate was collected at 12, 24, 36, or 48 hpf.

value: Tropical 5D

tag: agent

value: retinoic acid

tag: dose

tag: phenotype

value: posterior curved body axis


title: 48 hpf 5 nM retinoic acid rep 2

scan_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

tag: strain


title: 48 hpf control

description: This sample is comprised of 75 pooled embryos exposed to embryo medium control from 6-24 hpf and harvested at 48 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.

label_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications.

value: control

value: normal


title: 36 hpf control

description: This sample is comprised of 75 pooled embryos exposed to embryo medium control from 6-24 hpf and harvested at 36 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.

source_name: whole embryo 36 hpf


title: SM003_10^5_MA15_d7_3


title: Hepatocellular carcinoma [H39]

value: normal liver


title: SM003_10^5_MA15_d7_1


title: Hepatocellular carcinoma [H31]

value: hepatocellular carcinoma


title: 36 hpf 5 nM retinoic acid rep 2

description: This sample is comprised of 75 pooled embryos exposed to 5 nM retinoic acid from 6-24 hpf and harvested at 36 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.


title: Hepatocellular carcinoma [H27]


title: Hepatocellular carcinoma [H22]


title: Hepatocellular carcinoma [H25]


title: Hepatocellular carcinoma [H23]


title: 36 hpf 5 nM retinoic acid rep 1


title: Hepatocellular carcinoma [H21]


title: SM003_10^5_MA15_d4_3


title: SM003_10^5_MA15_d4_4


title: SM003_10^5_MA15_d4_5


title: 24 hpf control

description: This sample is comprised of 75 pooled embryos exposed to embryo medium control from 6-24 hpf and harvested at 24 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.

source_name: whole embryo 24 hpf


title: Mono_after exercise_12

description:
mono13_PRE.CEL(normalized)
Before exercise

hyb_protocol: 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix U133 plus 2 arrays.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.  Arrays were scanned using GeneChip® Scanner 3000 7G and Command Console Software v 3.2.3. to produce *.CEL intensity files.

data_processing: The results were analyzed using GeneSpring GX 12.1 Software  (Agilent Technologies, Inc).

label_protocol: First-strand cDNA is synthesized from 250ng of isolated total RNA using an oligo-dT primer with an attached T7 promoter sequence.  After making the complementary second strand, the double-stranded cDNA is used to generate biotin-tagged cRNA from an in- vitro transcription (IVT) using T7 RNA polymerase. 15ug of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® IVT 3’IVT Express Kit User Manual).

value: male

value: 22-30 yr old

value: monocytes isolated from PBMC

value: after 20 min bout of exercise


title: Mono_before exercise_13

description:
mono14_PEAK.CEL(normalized)
Immediately after exercise

source_name: monocytes before exercise

value: before exercise


title: Mono_before exercise_14

description:
mono15_PEAK.CEL(normalized)
Immediately after exercise


title: Mono_after exercise_14

description:
mono15_PRE.CEL(normalized)
Before exercise


title: Mono_before exercise_12

description:
mono13_PEAK.CEL(normalized)
Immediately after exercise


title: SM003_10^5_MA15_d4_1

value: Lung

value: 20 week


title: Mono_after exercise_13

description:
mono14_PRE.CEL(normalized)
Before exercise


title: SM003_10^5_MA15_d2_4


title: 24 hpf 5 nM retinoic acid rep 1

description: This sample is comprised of 75 pooled embryos exposed to 5 nM retinoic acid from 6-24 hpf and harvested at 24 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.


title: 12 hpf control

description: This sample is comprised of 75 pooled embryos exposed to embryo medium control from 6-12 hpf and harvested at 12 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.

source_name: whole embryo 12 hpf


title: SM003_10^5_MA15_d4_2


title: 24 hpf 5 nM retinoic acid rep 2


title: 12 hpf 5 nM retinoic acid rep 2

description: This sample is comprised of 75 pooled embryos exposed to 5 nM retinoic acid from 6-12 hpf and harvested at 12 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.


title: 12 hpf 5 nM retinoic acid rep 1


title: Hepatocellular carcinoma [H19]


title: Mono_after exercise_11

description:
mono12_PRE.CEL(normalized)
Before exercise

source_name: monocytes after 20 min bout of exercise


title: Mono_before exercise_11

description:
mono12_PEAK.CEL(normalized)
Immediately after exercise


title: Hepatocellular carcinoma [H17]

source_name: Normal liver tissue


title: Hepatocellular carcinoma [H15]

source_name: Hepatocellular carcinoma


title: SM003_10^5_MA15_d2_2


title: Hepatocellular carcinoma [H18]


title: Mono_before exercise_09

description:
mono11_PEAK.CEL(normalized)
Immediately after exercise


title: Mono_after exercise_07

description:
mono09_PRE.CEL(normalized)
Before exercise


title: Hepatocellular carcinoma [H11]


title: sample j_obese diet rat

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

country: Spain

institute: IDIBAPS

hyb_protocol: Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project (R v.2.7.0 . Affy package  Bioconductor v.2.0.1).

organism: Rattus norvegicus

source_name: obese_pancreatic islets

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug total RNA by means of cDNA synthesis (One-Cycle cDNA Synthesis Kit, Affymetrix Inc, Santa Clara, CA) followed by an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT Labeling Kit, Affymetrix Inc, Santa Clara, CA)

extract_protocol:
Immediately after animal sacrification, pancreatic islets were obtained by collagenase digestion.
10ug RNA was extracted from pancreatic islets with Trizol reagent (Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.

value: Wistar

tag: diet group

value: high-caloric cafeteria diet

value: pancreatic islets


title: Mono_before exercise_07

description:
mono09_PEAK.CEL(normalized)
Immediately after exercise


title: Mono_before exercise_08

description:
mono10_PEAK.CEL(normalized)
Immediately after exercise


title: SM003_10^5_MA15_d2_3

value: SARS MA15


title: SM003_10^5_MA15_d1_1


title: SM003_10^5_MA15_d1_4


title: SM003_10^5_MA15_d2_1


title: Hepatocellular carcinoma [H14]


title: Mono_after exercise_09

description:
mono11_PRE.CEL(normalized)
Before exercise


title: sample k_obese diet rat


title: Hepatocellular carcinoma [H13]


title: Mono_after exercise_08

description:
mono10_PRE.CEL(normalized)
Before exercise


title: SM003_10^5_MA15_d1_2


title: Hepatocellular carcinoma [H20]


title: SM003_10^4_MA15_d7_4


title: SM003_10^5_MA15_d1_3


title: Hepatocellular carcinoma [H12]


title: sample i_obese diet rat


title: Hepatocellular carcinoma [H28]


title: Hepatocellular carcinoma [H9]


title: Mono_after exercise_06

description:
mono08_PRE.CEL(normalized)
Before exercise


title: SM003_10^4_MA15_d7_3


title: SM003_10^4_MA15_d7_1


title: SM003_10^4_MA15_d7_2


title: sample h_obese diet rat


title: Hepatocellular carcinoma [H7]


title: Hepatocellular carcinoma [H10]


title: Mono_before exercise_05

description:
mono05_PEAK.CEL(normalized)
Immediately after exercise


title: Hepatocellular carcinoma [H5]


title: Hepatocellular carcinoma [H6]


title: sample g_obese diet rat


title: Mono_after exercise_05

description:
mono05_PRE.CEL(normalized)
Before exercise


title: SM003_10^4_MA15_d4_4


title: Hepatocellular carcinoma [H8]


title: Mono_before exercise_04

description:
mono04_PEAK.CEL(normalized)
Immediately after exercise


title: sample f_lean rat

source_name: lean_pancreatic islets

value: standard chow diet


title: sample c_lean rat


title: sample 42_obese diet rat

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project.

source_name: obese_adipose peripancreatic tissue

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug total RNA by means of cDNA synthesis (One-Cycle cDNA Synthesis Kit, Affymetrix Inc, Santa Clara, CA) followed by an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT Labeling Kit, Affymetrix Inc, Santa Clara, CA).

extract_protocol:
Immediately after animal sacrification, visceral pancreatic adipose tissue was excised, weighed, cut, and rapidly frozen in liquid nitrogen for RNA isolation.
10 ug RNA was extracted from adipose tissue with Trizol reagent (RNA Easy Lipid Mini Kit, Invitrogen Life Tecnologies, Paisley, Scotland, UK) according to the manufactures instructions.

value: adipose peripancreatic tissue


title: Hepatocellular carcinoma [H4]


title: Mono_before exercise_06

description:
mono08_PEAK.CEL(normalized)
Immediately after exercise


title: SM003_10^4_MA15_d4_2


title: Mono_after exercise_03

description:
mono03_PRE.CEL(normalized)
Before exercise


title: sample d_lean rat


title: SM003_10^4_MA15_d4_1


title: Hepatocellular carcinoma [H3]


title: sample e_lean rat


title: SM003_10^4_MA15_d4_3


title: Hepatocellular carcinoma [H2]


title: Mono_after exercise_04

description:
mono04_PRE.CEL(normalized)
Before exercise


title: SM003_10^4_MA15_d2_3


title: sample 29_obese diet rat

description:
R29
re-analysis of GSM906555


title: sample 32_obese diet rat

description:
R32
re-analysis of GSM906556


title: sample 19_lean rat

description:
R19
re-analysis of GSM906559

source_name: lean_adipose peripancreatic tissue


title: SM003_10^4_MA15_d2_4


title: Mono_after exercise_01

description:
mono02_PRE.CEL(normalized)
Before exercise


title: SM003_10^4_MA15_d1_4


title: Mono_before exercise_01

description:
mono02_PEAK.CEL(normalized)
Immediately after exercise


title: planktonic bacteria, biological rep2

city: Muttenz

first: Laura

last: Sutter-Dick

state: Basel-Land

address: Hofackerstrasse 30

department: Institute of Chemistry and Bioanalytics

country: Switzerland

institute: FHNW

description: Gene expression data from bacteria incubated with RPMI supplemented with 10% FBS media for 24 hrs (planktonic bacteria)

hyb_protocol: Labeled target aRNA was prepared from mycobacterium avium total RNA using protocols from Ambion MessageAmp II Bacteria kit. 10 ug labeled fragmented cRNA from each sample ws hybridized for 18 hours at 50C to an Affymetrix Mavi (M. avium) Array

scan_protocol: Washing, staining and scanning follows the Affymetrix GeneChip Expression Analysis Manual 702232 rev3 protocols, using AGCC software for a Fluidics Station 450, (wash protocol an altered protocol FlexFS450_0005_Gcrich) and a GeneChip Scanner 3000 with autoloader.

data_processing: Image processing and data extraction were perfomed using AGCC software version 3.0. The data were processed and normalized with ArrayStar5 using default analysis settings.

organism: Mycobacterium avium 104

source_name: Mycobacterial RNA extracted from planktonic bacteria

label_protocol: Biotinylated aRNA were prepared according to the standard Ambion MessageAmp II Bacteria kit.

growth_protocol: MAC104 was grown on 7H10 agar at 37C for 7days.

extract_protocol: The bacterial suspension was pelleted at 4°C and resuspended with 0.7 ml of RNA detergent (500mM sodium acetate, pH4 (Sigma), 1% triton X-100 (Sigma) and 0.6% sodium dodecyl sulfate (Sigma) in nuclease-free water) and 0.6 ml of acid phenol (Sigma) and transferred to a bead-beating tube with 300 μl of 0.1 mm glass beads (Sigma). The bacteria were bead-beated 6 times at maximum speed for 20 seconds, allowing each sample to chill between bead-beatings. The tubes were then centrifuged for 5 minutes at 4°C at 9,000 x g. The upper aqueous phase was carefully transferred to a clean 1.5 ml eppendorf tube. Then 0.2 ml of RNA detergent and 0.6 ml of chilled acid phenol were added to each sample and vortexed. The same procedure was repeated and the upper aqueous phase was again carefully transferred to a clean tube where an additional 0.6 ml of acid phenol was added to each sample. The same procedure was repeated and the upper aqueous layer was transferred to a clean tube and 0.6 ml of chloroform:isoamyl alcohol 25:1 (Sigma) was added. The same procedure was repeated again, and the aqueous layer was split into two tubes per sample and underwent an ethanol precipitation. Four volumes of 95%-100% ethanol (Sigma) were added to each tube. The tubes were vortexed in a bead-beater for 10 seconds and incubated for 30 minutes at -20°C. The samples were centrifuged at 4°C at 9,000 x g and supernatant removed. The pellet was resuspended with 1 ml of 75% ethanol, agitated and centrifuged at 4°C at 9,000 x g. The supernatant was removed and the pellet was resuspended in 100% ethanol. The sample was centrifuged at 4°C at 9,000 x g and supernatant removed and spun a second time allowed to sit at 4°C to remove any excess ethanol. The pellet was then resuspended in 0.2 ml of nuclease-free water (Ambion, Austin, TX), and corresponding samples were combined. Samples were treated with recombinant DNase I (Roche, Indianapolis, IN) and RNaseOUT recombinant ribonuclease inhibitor (Invitorgen, Carlsbad, CA) as per manufacturers protocol. One milliliter of Trizol reagent (Invitrogen, Carlsbad, CA) and 0.2 ml of cholorform (Sigma) were added to each sample and beadless bead-beated for 5 seconds. The samples were then centrifuged at 9,000 x g. The upper aqueous phase was transferred to a clean tube and 0.6 ml of chloroform:isoamly alcohol (24:1) (Sigma) was added to each sample. Each sample was then vortexed followed by centrifugation at 4°C at 3,000 x g for 10 minutes. The samples were then split into two tubes again and underwent a second ethanol precipitation, as previously described. The pellet was resuspended in 15 μl of TE buffer (10 mM Tris-HCl and 1mM EDTA) and corresponding samples were combined. MICROBEnrich kit (Ambion, Austin, TX) was used according to manufacturers protocol on each sample to remove mammalian RNA from the samples. The final purified samples were resuspended in 5 μl of nuclease-free water. The purified bacterial RNA samples were amplified using MessageAmp II-Bacteria kit according to manufacturers (Ambion, Austin, TX). Samples were eluted in nuclease-free water and vacuum centrifuged at 4°C at 9,000 x g to a final concentration of 1 μg/ml. Concentration, quality, and purity of bacterial RNA was then checked using a Nanodrop 2000 (Thermo Scientific, Wilmington, DE) as well as electrophoresis DNA gel.

treatment_protocol: For microaggregates,  Hep-2 cells were infected with MAC104 at an MOI of 100 in a T75 flask for 24hrs at 37C and 5% CO2 in RPMI supplemented with 10% FBS. Planktonic bacteria were incubated in RPMI supplemented with 10% FBS for 24 hrs in the same conditions as microaggregates.

tag: growth phase

value: log-phase


title: planktonic bacteria, biological rep3


title: planktonic bacteria, biological rep1


title: SM003_10^4_MA15_d1_2

source_name: Project name, virus strain, day, replicate


title: SM003_10^4_MA15_d2_2


title: sample 18_lean rat

description:
R18
re-analysis of GSM906558


title: SM003_10^4_MA15_d2_1


title: Microaggregates, biological rep2

description: Gene expression data from bacteria incubated with Hep-2 epithelial cells in RPMI supplemented with 10% FBS media for 24 hrs (microaggregate bacteria)

source_name: Mycobacterial RNA extracted from mycobacterial microaggregates


title: SM003_10^4_MA15_d1_3


title: sample 14_lean rat

description:
R14
re-analysis of GSM906557


title: lung_saline_avg

city: Denver

first: Rafeul

last: Alam

state: CO

address: 1400 Jackson St. K609

institute: National Jewish Health

description: mean normalized signal intensity

hyb_protocol: labeling, hybridization, scanning, and data processing were completed according to Phalanx Biotech protocols. See: http://www.phalanxbiotech.com/tech_support/MOAv2_UserGuide.pdf for technical details and http://www.phalanxbiotech.com/products/MOA.php for general information

source_name: lung, control

growth_protocol: Mice were allowed to eat and drink ad libitum

extract_protocol: Lungs were perfused with 0.9% saline and total RNA extracted according to Qiagen RNA extraction kit directions.

treatment_protocol: Acute asthma was produced by immunization twice, one week apart, of Balb/C mice 8-12 weeks of age with Aspergillus species (5 μg) in adjuvant (1:1 vol/vol). Adjuvant was aluminum and magnesium hydroxide (Pierce). Asthma was initiated by three consecutive intranasal exposures to Aspergillus species (5μg in 15μL saline) and asthma was evaluated 72 hours after the final exposure.  Tolerant asthma was produced by intranasal delivery of Aspergillus species (5μg in 15μL saline) twice a week for six consecutive weeks to Balb/C mice 8-12 weeks of age. Asthma was evaluated after mice were rested for an additional three weeks. Chronic asthma was produced by intranasal delivery of the Dustmite/ Ragweed/ Aspergillus (5,50,5ug in 15ul saline) mixture twice a week for six consecutive weeks in female mice  Balb/C mice 8-12 weeks of age. Asthma was evaluated 3 weeks after cessation of allergen exposure. Saline control mice were treated intransally with 15ul of saline twice a week for 6 weeks. Asthma was assesed 3 weeks after the final exposure

value: whole lung

value: Balb/C


title: lung_tolerant asthma_avg

description: mean normalized signal intensity

scan_protocol: labeling, hybridization, scanning, and data processing were completed according to Phalanx Biotech protocols. See: http://www.phalanxbiotech.com/tech_support/MOAv2_UserGuide.pdf for technical details and http://www.phalanxbiotech.com/products/MOA.php for general information

source_name: lung, tolerant asthma


title: lung_acute asthma_avg

description: mean normalized signal intensity

data_processing: labeling, hybridization, scanning, and data processing were completed according to Phalanx Biotech protocols. See: http://www.phalanxbiotech.com/tech_support/MOAv2_UserGuide.pdf for technical details and http://www.phalanxbiotech.com/products/MOA.php for general information

source_name: lung, acute asthma


title: Mono_before exercise_03

description:
mono03_PEAK.CEL(normalized)
Immediately after exercise


title: lung_chronic asthma_avg

description: mean normalized signal intensity

source_name: lung, chronic asthma

label_protocol: labeling, hybridization, scanning, and data processing were completed according to Phalanx Biotech protocols. See: http://www.phalanxbiotech.com/tech_support/MOAv2_UserGuide.pdf for technical details and http://www.phalanxbiotech.com/products/MOA.php for general information


title: Fruit of eggplant cv. PPL at 50 dpa, biological replicate 3

status: Public on Feb 14 2014

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

description: Gene expression profiles of fruit of eggplant cv. PPL at 50 dpa, biological replicate 3

scan_protocol: The tomato GeneChip Genome arrays were scanned on a GeneChip scanner 3000.

data_processing: After scannig CEL files were analyzed using GeneSpring GX 11.5 software. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

organism: Solanum virginianum

source_name: Fruit of eggplant cv. PPL at 50 dpa

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix tomato Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

extract_protocol: Total RNA was isolated using Spectrum Plant Total RNA Kit (Sigma, USA) from eggplant fruits of different stages.

treatment_protocol: Eggplant plants were grown under controlled conditions in glasshouse. Flowers were hand-pollinated at anthesis and samples were collected at 0, 5, 10, 20 and 50 days post anthesis (dpa). Harvested fruits were immediately frozen in liquid nitrogen and stored at -70 °C until used for total RNA extraction.

value: fruit

value: 50 dpa

tag: cultivar

value: PPL


title: Fruit of eggplant cv. PPL at 50 dpa, biological replicate 2

description: Gene expression profiles of fruit of eggplant cv. PPL at 50 dpa, biological replicate 2

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on Affymertix tomato Genechip Genome array. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix fluidics station 450.

growth_protocol: Eggplant plants were grown under controlled conditions in glasshouse.

tag: tissue


title: Crtam KO CD4+ IEL T cells

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from Crtam-/- small intestine intraepithelial CD4+ T cells 8 days after T. gondii infection.

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc.) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings (Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: small intestine intraepithelial CD4+ T cells, Crtam-/-, 8 days after T. gondii infection

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA.

extract_protocol:
Small intestines were isolated, washed twice with HBSS-EDTA to obtain the intraepithelial fraction. Stained with mAb to CD4, CD8, CD3 and CD45 and cell sorted.
RNA was extracted with the RNeasy microkit from Qiagen following the manufacturer's instructions.

treatment_protocol: Small intestine intraepithelial CD4+CD8-CD3+CD45+ T cells were cell sorted from small intestines of WT or Crtam-/- mice 8 days post oral infection with 5 cysts of Toxoplasma gondii prugniaud-luc.

tag: strain/background

tag: genotype/variation

value: Crtam-/-

tag: cell type

tag: treatment

value: Toxoplasma gondii infection

tag: timepoint

value: 8 days post infection


title: SM003_10^4_MA15_d1_1

value: Lung

tag: infection

tag: age


title: Microaggregates, biological rep1


title: WT CD4+ IEL T cells

description: Gene expression data from WT small intestine intraepithelial CD4+ T cells 8 days after T. gondii infection.

source_name: small intestine intraepithelial CD4+ T cells, WT, 8 days after T. gondii infection

value: WT


title: Fruit of eggplant cv. PPL at 50 dpa, biological replicate 1

description: Gene expression profiles of fruit of eggplant cv. PPL at 50 dpa, biological replicate 1


title: Fruit of eggplant cv. PPL at 20 dpa, biological replicate 1

description: Gene expression profiles of fruit of eggplant cv. PPL at 20 dpa, biological replicate 1

source_name: Fruit of eggplant cv. PPL at 20 dpa

value: 20 dpa


title: Fruit of eggplant cv. PPL at 20 dpa, biological replicate 2

description: Gene expression profiles of fruit of eggplant cv. PPL at 20 dpa, biological replicate 2


title: Fruit of eggplant cv. PPL at 10 dpa, biological replicate 2

description: Gene expression profiles of fruit of eggplant cv. PPL at 10 dpa, biological replicate 2

source_name: Fruit of eggplant cv. PPL at 10 dpa

value: 10 dpa


title: Microaggregates, biological rep3


title: Fruit of eggplant cv. PPL at 10 dpa, biological replicate 1

description: Gene expression profiles of fruit of eggplant cv. PPL at 10 dpa, biological replicate 1


title: Fruit of eggplant cv. PPL at 10 dpa, biological replicate 3

description: Gene expression profiles of fruit of eggplant cv. PPL at 10 dpa, biological replicate 3


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 2 (normalized with 50 dpa)

description: Gene expression profiles of fruit of eggplant cv. PPL at 0 dpa, biological replicate 2.

source_name: Fruit of eggplant cv. PPL at 0 dpa

value: 0 dpa


title: Fruit of eggplant cv. PPL at 20 dpa, biological replicate 3

description: Gene expression profiles of fruit of eggplant cv. PPL at 20 dpa, biological replicate 3


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 2 (normalized with 10 dpa)


title: Fruit of eggplant cv. PPL at 5 dpa, biological replicate 3

description: Gene expression profiles of fruit of eggplant cv. PPL at 5 dpa, biological replicate 3

source_name: Fruit of eggplant cv. PPL at 5 dpa

value: 5 dpa


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 3 (normalized with 10 dpa)

description: Gene expression profiles of fruit of eggplant cv. PPL at 0 dpa, biological replicate 3.


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 3 (normalized with 20 dpa)


title: Fruit of eggplant cv. PPL at 5 dpa, biological replicate 2

description: Gene expression profiles of fruit of eggplant cv. PPL at 5 dpa, biological replicate 2


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 1 (normalized with 20 dpa)

description: Gene expression profiles of fruit of eggplant cv. PPL at 0 dpa, biological replicate 1.


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 2 (normalized with 20 dpa)


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 3 (normalized with 50 dpa)


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 2 (normalized with 5 dpa)


title: Fruit of eggplant cv. PPL at 5 dpa, biological replicate 1

description: Gene expression profiles of fruit of eggplant cv. PPL at 5 dpa, biological replicate 1


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 3 (normalized with 5 dpa)


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 1 (normalized with 10 dpa)


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 1 (normalized with 5 dpa)


title: Fruit of eggplant cv PPL at 0 dpa, biological replicate 1 (normalized with 50 dpa)


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate7

city: Napoli

first: Liberato

middle: Pia

last: Berrino

address: via costantinopoli

department: Medicina Sperimentale

country: Italy

institute: Seconda Università degli Studi di Napoli

description:
Biological replicate 1 of 7. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061103_S01_GE2_105_Dec08_1_1.txt

hyb_protocol: After the RNA fragmentation 55 µl of 2x Gex Hybridization Buffer HI-RPM were added to the 4*44K array, microarrayswere enclosed in Agilent SureHyb chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505 C micro array scanner.

data_processing: Agilent Feature Extraction Software (v 10.2) was used for background subtraction and LOWESS normalization.

source_name: ECs_CS_ACS patient

label_protocol: 825ng of total RNA were converted in cDNA and then in cRNA following manufacturer's instruction (Agilent Technologies, Two-color). cRNA were labeled with Cy3-CTP and Cy5-CTP.

growth_protocol: Human coronary artery endothelial cells (ECs) were stimulated in vitro for 12 hours with plasma obtained from the coronary sinus (CS) and the aorta (Ao) of patients with ACS (n=28), or patients with stable angina (SA, n=16). For each patient, gene expression profile was evaluated by microarray technology in ECs exposed to plasma obtained from CS and compared to that of ECs exposed to plasma sampled from Ao.

extract_protocol: Total RNA extracted using Pure Link RNA mini kit following manufacturer's instructions (Ambion, Life Technologies)

value: coronary artery endothelial cells (ECs)

tag: stimulated with

value: plasma obtained from the coronary sinus (CS) of ACS patients

source_name: ECs_Ao_ACS patient

value: plasma obtained from the aorta (Ao) of ACS patients


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate4

description:
Biological replicate 1 of 4. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061103_S01_GE2_105_Dec08_1_4.txt


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate1

description:
Biological replicate 1 of 1. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061104_S01_GE2_105_Dec08_1_4.txt


title: SA_Coronary sinus (CS) vs aorta (Ao) replicate4

description:
Biological replicate 1 of 4. SA_ Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485054748_S01_ GE2_105_Dec08_1_4.txt

source_name: ECs_CS_SA patient

value: plasma obtained from the coronary sinus (CS) of SA patients

source_name: ECs_Ao_SA patient

value: plasma obtained from the aorta (Ao) of SA patients


title: islets of 10 days post partum, biological rep 4

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

institute: KULeuven

description: Gene expression data from islets of lactating mice 10 days post partum

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data were analyzed with RMA sketch using the standard settings for Gene 1.0 ST arrays of Expression Console in the AGCC software (affymetrix).

source_name: mouse islets, C57bl6/J, 10dpp

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: The absolute RNA microprep kit of Strategene was used to extract total RNA according to the manufacturer's instructions. The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: genotype

value: wild type

tag: pregnancy day

value: pancreatic islets


title: SA_Coronary sinus (CS) vs aorta (Ao) replicate1

description:
Biological replicate 1 of 1. SA_ Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485054748_S01_GE2_105_Dec08_1_1.txt


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate5

description:
Biological replicate 1 of 5. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061103_S01_GE2_105_Dec08_1_3.txt


title: islets of pregnancy day 15.5, biological rep 1

description: Gene expression data from islets of mice that were 15.5 day pregnant

source_name: mouse islets, C57bl6/J, P15.5


title: islets of pregnancy day 18.5, biological rep 3

description: Gene expression data from islets of mice that were 18.5 day pregnant

source_name: mouse islets, C57bl6/J, P18.5


title: SA_Coronary sinus (CS) vs aorta (Ao) replicate2

description:
Biological replicate 1 of 2. SA_ Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485054748_S01_GE2_105_Dec08_1_2.txt


title: islets of 10 days post partum, biological rep 1


title: islets of pregnancy day 15.5, biological rep 4


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate3

description:
Biological replicate 1 of 3. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061104_S01_GE2_105_Dec08_1_2.txt


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate6

description:
Biological replicate 1 of 6. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061103_S01_GE2_105_Dec08_1_2.txt


title: islets of 10 days post partum, biological rep 2


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate2

description:
Biological replicate 1 of 2. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061104_S01_GE2_105_Dec08_1_3.txt


title: islets of pregnancy day 6.5, biological rep 3

description: Gene expression data from islets of mice that were 6.5 day pregnant

source_name: mouse islets, C57bl6/J, P6.5


title: islets of pregnancy day 18.5, biological rep 2


title: islets of pregnancy day 18.5, biological rep 1


title: islets of pregnancy day 9.5; biological rep 2

description: Gene expression data from islets of mice that were 9.5 day pregnant

source_name: mouse islets, C57bl6/J, P9.5


title: SA_Coronary sinus (CS) vs aorta (Ao) replicate3

description:
Biological replicate 1 of 3. SA_ Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485054748_S01_GE2_105_Dec08_1_3.txt


title: islets of pregnancy day 9.5, biological rep 3


title: islets of pregnancy day 18.5, biological rep 4


title: islets of 10 days post partum, biological rep 3


title: islets of pregnancy day 15.5, biological rep 2


title: islets of pregnancy day 15.5, biological rep 3


title: islets of pregnancy day 9.5, biological rep 4


title: islets of pregnancy day 6.5, biological rep 4


title: islets of pregnancy day 9.5, biological rep 1


title: islets of pregnancy day 3.5, biological rep 2

description: Gene expression data from islets of mice that were 3.5 day pregnant

source_name: mouse islets, C57bl6/J, P3.5


title: islets of pregnancy day 6.5, biological rep 1


title: Islets of Pdx1-creLate mouse, biological rep 3

description: Gene expression data from islets of Pdx1-creLate

source_name: mouse islets, Pdx1-creLate, NP

value: Pdx1-creLate backcross generation N8

value: NP


title: Islets of control mouse, biological rep 1

description: Gene expression data from islets of WT littermates of Pdx1-creLate

source_name: mouse islets, control, NP


title: islets of pregnancy day 3.5, biological rep 1


title: Islets of Pdx1-creLate mouse, biological rep 2


title: islets of pregnancy day 6.5, biological rep 2


title: Islets of control mouse, biological rep 4


title: Islets of control mouse, biological rep 3


title: Islets of Pdx1-creLate mouse, biological rep 1


title: islets of pregnancy day 3.5, biological rep 3


title: NXF1 KD Cytoplasmic RNA Experiment 3

city: Cambridge

first: Vihandha

last: Wickramasinghe

address: Hills Road

country: United Kingdom

institute: MRC Cancer Unit, Hutchison/MRC Research Centre

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with R package lumi

molecule: cytoplasmic RNA

source_name: HCT116 cells

label_protocol: Biotinylated cRNA was prepared with the Illumina 96-well Total Prep RNA Amplification Kit (Ambion)

extract_protocol: RNA was extracted from cytoplasmic fraction of cells (obtained by digitonin permeabilisation) with QIAGEN RNeasy mini kit according to manufacturers instructions. RNA was treated with RNase free DNase (Qiagen) prior to elution. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with Control siRNA, GANP siRNA or NXF1 siRNA and cytoplasmic RNA was harvested 72 hours post-transfection.

tag: cell line

tag: transfection

value: NXF1 siRNA


title: Control Cytoplasmic RNA Experiment 3

value: Control siRNA


title: Islets of Pdx1-creLate mouse, biological rep 4

tag: strain


title: Control Cytoplasmic RNA Experiment 2


title: NXF1 KD Cytoplasmic RNA Experiment 2


title: Islets of control mouse, biological rep 2


title: GANP KD Cytoplasmic RNA Experiment 1

value: GANP siRNA


title: GANP KD Cytoplasmic RNA Experiment 2


title: GANP KD Cytoplasmic RNA Experiment 3


title: Control Cytoplasmic RNA Experiment 1


title: NXF1 KD Cytoplasmic RNA Experiment 1


title: HepG2_0.5_%_DMSO_7_24h_rep2

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files v15 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the Arrayanalysis.org web service. This resulted in 18,988 probe sets.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Total RNA was isolated after 24 hours of incubation with compound or solvent control in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% v/v DMSO or PBS)

value: hepatocellular carcinoma

tag: compound, dose

tag: treatment time


title: HepG2_2000_µM_Tolbutamide_24h_rep1

value: TOL, 2000 µM


title: HepG2_106.25_µM_Nifedipine_24h_rep1


title: HepG2_0.5_%_DMSO_7_24h_rep3


title: HepG2_106.25_µM_Nifedipine_24h_rep2


title: HepG2_500_µM_Clonidine_24h_rep3

value: CLO, 500 µM


title: HepG2_0.5_%_DMSO_7_24h_rep1


title: HepG2_500_µM_Clonidine_24h_rep2


title: HepG2_2000_µM_Tolbutamide_24h_rep3


title: HepG2_2000_µM_Tolbutamide_24h_rep2


title: HepG2_106.25_µM_Nifedipine_24h_rep3


title: ACS_Coronary sinus (CS) vs aorta (Ao) replicate8

description:
Biological replicate 1 of 8. ACS_Coronary sinus culture condition versus standard (Aorta) condition
US90403629_251485061104_S01_ GE2_105_Dec08_1_1.txt


title: HepG2_20_µM_Cisplatin_24h_rep3

value: cisPt, 20 µM


title: HepG2_500_µM_Clonidine_24h_rep1


title: HepG2_250_µM_D-mannitol_24h_rep2

value: Dman, 250 µM


title: HepG2_20_µM_Cisplatin_24h_rep1


title: HepG2_250_µM_D-mannitol_24h_rep3


title: HepG2_250_µM_D-mannitol_24h_rep1


title: HepG2_0.2_µM_MitomycinC_24h_rep3

value: MMC, 0.2 µM


title: HepG2_20_µM_Cisplatin_24h_rep2


title: HepG2_0.2_µM_MitomycinC_24h_rep2


title: Greek20

city: Oxford

first: George

last: Busby

state: OXON

address: Roosevelt Drive

institute: Wellcome Trust Centre for Human Genetics

hyb_protocol: Followed Illumina Standard Protocol

scan_protocol: Followed Illumina Standard Protocol

data_processing: Image was analyzed using Illumina GenomeStudio v2009.2.0.29803

source_name: saliva

label_protocol: Followed Illumina Standard Protocol

extract_protocol: Extraction of genomic DNA from saliva and blood using common laboratory protocols.

tag: gender

value: male

tag: nationality

value: Greek


title: Greek18


title: Greek16


title: Greek19


title: Greek17


title: Greek13


title: HepG2_0.5_%_PBS_4_24h_rep3


title: HepG2_0.2_µM_MitomycinC_24h_rep1


title: Greek15


title: Greek14


title: Greek12


title: UAE10

value: UAE


title: Tunisian12

value: Tunisian


title: HepG2_0.5_%_DMSO_6_24h_rep3


title: UAE3


title: HepG2_0.5_%_DMSO_6_24h_rep2


title: HepG2_0.5_%_PBS_4_24h_rep2


title: UAE14


title: UAE12


title: HepG2_0.5_%_DMSO_6_24h_rep1


title: UAE9


title: UAE4


title: UAE8


title: UAE13


title: UAE11


title: HepG2_0.5_%_PBS_4_24h_rep1


title: Tunisian11


title: UAE6


title: UAE5


title: HepG2_250_µM_Azathioprine_24h_rep1

value: AZA, 250 µM


title: HepG2_0.5_%_PBS_3_24h_rep2


title: UAE1


title: HepG2_0.5_%_PBS_3_24h_rep3


title: Tunisian9


title: HepG2_0.5_%_DMSO_5_24h_rep3


title: HepG2_250_µM_Azathioprine_24h_rep2


title: HepG2_0.5_%_DMSO_5_24h_rep2


title: HepG2_0.5_%_PBS_3_24h_rep1


title: Tunisian10


title: HepG2_250_µM_Azathioprine_24h_rep3


title: HepG2_0.5_%_DMSO_5_24h_rep1


title: UAE2


title: Castrtaed G-1 4

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
SAMPLE 16
In a castrated host, treated with G-1 (Mouse #4)

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer’s instructions

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF (Entrez Gene, version 13)

source_name: LNCaP xenograft_castrated_G-1_16 days

label_protocol: Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer’s instructions

growth_protocol: LNCaP xenograft grown in male nude mice

extract_protocol: Tumor were homogenized in Trizol reagent and total RNA was extracted according to the manufacturer's instructions. Purified total RNA was DNase treated and quality was checked by an Agilent Bioanalyser. Samples with a RIN number >8 were used for microarray experiments.

treatment_protocol: 16 days

tag: xenograft host

value: male nude mice

tag: tissue

value: Prostate cancer xenograft

tag: sample group

value: castrated

tag: injected with

value: G-1 (4 mg/kg/day) for 16 days


title: HepG2_1000_µM_Phenobarbital_24h_rep3

tag: cell type

value: PhB, 1000 µM


title: HepG2_1000_µM_Phenobarbital_24h_rep2


title: Castrtaed G-1 3

description:
SAMPLE 15
In a castrated host, treated with G-1 (Mouse #3)


title: Castrtaed G-1 2

description:
SAMPLE 14
In a castrated host, treated with G-1 (Mouse #2)


title: HepG2_1000_µM_Phenobarbital_24h_rep1


title: HepG2_0.5_%_DMSO_4_24h_rep3


title: Tunisian8


title: Castrtaed G-1 1

description:
SAMPLE 13
In a castrated host, treated with G-1 (Mouse #1)


title: HepG2_0.5_%_DMSO_4_24h_rep1


title: Castrated Vehicle 4

description:
SAMPLE 12
In a castrated host, treated with vehicle (Mouse #4)

value: vehicle alone for 16 days


title: Castrated Vehicle 3

description:
SAMPLE 11
In a castrated host, treated with vehicle (Mouse #3)


title: Tunisian6


title: HepG2_30_µM_17-beta_Estradiol_24h_rep2

value: hepatocellular carcinoma


title: HepG2_30_µM_17-beta_Estradiol_24h_rep3


title: HepG2_30_µM_17-beta_Estradiol_24h_rep1


title: Castrated Vehicle 2

description:
SAMPLE 10
In a castrated host, treated with vehicle (Mouse #2)


title: Castrated Vehicle 1

description:
SAMPLE 9
In a castrated host, treated with vehicle (Mouse #1)


title: Tunisian1


title: Tunisian4


title: Intact G-1 4

description:
SAMPLE 8
In an intact host, treated with G-1 (Mouse #4)

source_name: LNCaP xenograft_intact_G-1_16 days

value: intact (androgen-sensitive tumor)


title: Tunisian7


title: HepG2_0.5_%_DMSO_4_24h_rep2


title: Intact G-1 3

description:
SAMPLE 7
In an intact host, treated with G-1 (Mouse #3)


title: HepG2_3_µM_CyclosporinA_24h_rep3

value: CsA, 3 µM


title: UAE7


title: WestSicilian10

value: WestSicilian


title: HepG2_3_µM_CyclosporinA_24h_rep2


title: Intact G-1 2

description:
SAMPLE 6
In an intact host, treated with G-1 (Mouse #2)


title: Intact Vehicle 4

description:
SAMPLE 4
In an intact host, treated with vehicle (Mouse #4)

source_name: LNCaP xenograft_intact_vehicle_16 days


title: Intact G-1 1

description:
SAMPLE 5
In an intact host, treated with G-1 (Mouse #1)


title: Tunisian5


title: Tunisian3


title: WestSicilian9


title: WestSicilian2


title: WestSicilian3


title: Tunisian2


title: WestSicilian6


title: HepG2_3_µM_CyclosporinA_24h_rep1


title: Intact Vehicle 3

description:
SAMPLE 3
In an intact host, treated with vehicle (Mouse #3)


title: WestSicilian4


title: WestSicilian5


title: HepG2_2000_µM_Cyclophosphamide_24h_rep1


title: HepG2_2000_µM_Cyclophosphamide_24h_rep2


title: Intact Vehicle 2

description:
SAMPLE 2
In an intact host, treated with vehicle (Mouse #2)


title: WestSicilian7


title: WestSicilian8


title: EastSicilian9

value: EastSicilian


title: WestSicilian1


title: HepG2_2000_µM_Cyclophosphamide_24h_rep3


title: HepG2_2000_µM_Valproic_Acid_24h_rep2

value: VPA, 2000 µM


title: HepG2_2000_µM_Valproic_Acid_24h_rep3


title: EastSicilian6

value: male


title: HepG2_2000_µM_Valproic_Acid_24h_rep1


title: HepG2_2000_µM_Tetracycline_24h_rep2

value: TET, 2000 µM


title: HepG2_2000_µM_Tetracycline_24h_rep3


title: HepG2_0.5_%_PBS_1_24h_rep3


title: HepG2_0.5_%_PBS_2_24h_rep3


title: EastSicilian10


title: EastSicilian8


title: HepG2_0.5_%_PBS_2_24h_rep2


title: HepG2_0.5_%_PBS_1_24h_rep1


title: HepG2_0.5_%_PBS_1_24h_rep2


title: HepG2_0.5_%_PBS_2_24h_rep1


title: EastSicilian5


title: Intact Vehicle 1

description:
SAMPLE 1
In an intact host, treated with vehicle (Mouse #1)


title: EastSicilian7


title: HepG2_120_µM_Paraquat_24h_rep3

value: PAQ, 120 µM


title: EastSicilian3


title: HepG2_120_µM_Paraquat_24h_rep2


title: HepG2_120_µM_Paraquat_24h_rep1


title: HepG2_2000_µM_Lithium_Carbonate_24h_rep3

value: LiC, 2000 µM


title: HepG2_2000_µM_Lithium_Carbonate_24h_rep2


title: EastSicilian4


title: HepG2_2000_µM_Tetracycline_24h_rep1


title: HepG2_2000_µM_Lithium_Carbonate_24h_rep1


title: EastSicilian2


title: Spain33

value: Spanish


title: HepG2_2000_µM_Isoniazid_24h_rep3

value: ISO, 2000 µM


title: HepG2_2000_µM_Isoniazid_24h_rep2


title: HepG2_2000_µM_Isoniazid_24h_rep1


title: EastSicilian1


title: Spain32


title: HepG2_90_µM_Ethinyl_estradiol_24h_rep2

value: Et, 90 µM


title: HepG2_90_µM_Ethinyl_estradiol_24h_rep3


title: Spain30


title: Spain34


title: Spain35


title: HepG2_90_µM_Ethinyl_estradiol_24h_rep1


title: Spain29


title: Spain24


title: Spain21

value: female


title: HepG2_0.5_%_DMSO_3_24h_rep3


title: Norwegian15

value: Norwegian


title: Spain31


title: Polish15

value: Polish


title: Spain16


title: HepG2_0.5_%_DMSO_3_24h_rep2


title: Norwegian2


title: HepG2_0.5_%_DMSO_3_24h_rep1


title: Spain20


title: Spain22


title: HepG2_0.5_%_DMSO_2_24h_rep3


title: HepG2_0.5_%_DMSO_1_24h_rep2


title: HepG2_0.5_%_DMSO_1_24h_rep3


title: Spain18


title: Spain15


title: Polish16


title: Polish14


title: Spain23


title: HepG2_0.5_%_DMSO_1_24h_rep1


title: HepG2_0.5_%_DMSO_2_24h_rep1


title: HepG2_2000_µM_D-mannitol_24h_rep3

value: MAN, 2000 µM


title: Polish10


title: Polish9


title: Polish8


title: Polish12


title: Polish13


title: Polish11


title: HepG2_550_µM_Diclofenac_24h_rep2

value: hepatocellular carcinoma

value: DIC, 550 µM


title: HepG2_550_µM_Diclofenac_24h_rep3


title: HepG2_2000_µM_D-mannitol_24h_rep2


title: HepG2_20_µM_CyclosporinA_24h_rep2

value: CsA, 20 µM


title: Spain14


title: HepG2_20_µM_CyclosporinA_24h_rep1


title: HepG2_550_µM_Diclofenac_24h_rep1


title: HepG2_20_µM_CyclosporinA_24h_rep3


title: HepG2_20_µM_Chlorpromazine_24h_rep3

value: CLP, 20 µM


title: HepG2_20_µM_Chlorpromazine_24h_rep2


title: HepG2_0.5_%_DMSO_2_24h_rep2


title: HepG2_20_µM_Chlorpromazine_24h_rep1


title: HepG2_2000_µM_D-mannitol_24h_rep1


title: HepG2_15_µM_Amiodarone_24h_rep2

value: Amio, 15 µM


title: HepG2_15_µM_Amiodarone_24h_rep1


title: HepG2_15_µM_Amiodarone_24h_rep3


title: Polish7


title: Liver_SRC-2 Knockout_Rep3

city: East Lansing

first: Jae-Wook

last: Jeong

state: Michigan

address: 965 Fee Road

department: Department of Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

label: Biotin

source_name: SRC-2 null mouse, liver

label_protocol: Standard Affymetrix procedures

growth_protocol: Mice were maintained in the designated animal care facility at the Baylor College of Medicine according to the institutional guideline for the care and use of laboratory animals. SRC-2-/- and wild-type mice were ovariectomized at 6 wk of age. Two weeks later, the mice were killed by cervical dislocation after placing the mice under anesthesia, Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich,St. Louis, MO).

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy total RNA isolation kit and transcribed to cDNA

treatment_protocol: Liver tissues were flash frozen at the time of dissection and stored at -80 C

value: SRC-2 null

value: Liver

tag: genetic background

tag: Sex

value: Female


title: HepG2_50_µM_Adefovir_24h_rep3

value: ADF, 50 µM


title: HepG2_50_µM_Adefovir_24h_rep2


title: Spain19

value: male


title: HepG2_50_µM_Adefovir_24h_rep1


title: Norwegian12


title: Liver_SRC-2 Knockout_Rep2


title: Norwegian4


title: HepG2_10000_µM_Acetominophen_24h_rep2

value: APAP, 10000 µM


title: Norwegian10


title: Norwegian14


title: Norwegian11


title: Liver_SRC-2 Knockout_Rep1


title: HepG2_10000_µM_Acetominophen_24h_rep3


title: Norwegian9


title: Liver_Wildtype_Rep3

source_name: Wildtype mouse, liver

value: Wildtype


title: HepG2_10000_µM_Acetominophen_24h_rep1


title: Norwegian8


title: Moroccan15

value: Moroccan


title: Norwegian7


title: Moroccan14


title: Spain17

value: Spanish


title: Liver_Wildtype_Rep2


title: Thymus_Tcf-/-_tumor_mouse8

city: Leiden

first: Martijn

middle: H

last: Brugman

address: Albinusdreef 2

department: IHB

institute: LUMC

hyb_protocol: The samples were hybridized overnight at 42°C to GeneChip mouse genome 430 2.0 Arrays (Affymetrix). Washing and staining steps were performed on a Fluidics station 450 (Affymetrix).

scan_protocol: Genechips were scanned using a GeneChip scanner 3000 (Affymetrix) according to the manufacturer's instructions.

data_processing: Raw data were normalized and summarized using Robust Multichip Average (RMA) method. Array analysis was performed using R-2.14 (http://cran.r-project.org/) and Bioconductor 2.9 software (http://www.bioconductor.org/)

source_name: Thymus, homogenized

label_protocol: One µg of RNA was used to generate cRNA using Affymetrix One cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA), after which the samples were biotinylated using an Affymetrix IVT labeling kit.

growth_protocol: direct isolation from homogenized thymus tissue

extract_protocol: Qiagen RNeasy minicolumns, accoding to manufacturer's protocol

value: C57Bl/6 Tcf1−/− ΔVII/ΔVII

value: thymus


title: Moroccan9


title: Thymus_Tcf-/-_tumor_mouse7


title: Liver_Wildtype_Rep1


title: Norwegian3

value: Norwegian


title: WT_vs_sconB

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to A. nidulans 70-mer oligonucleotide microarrays (FGSC_A4, version 2) obtained from the Pathogen Functional Genomics Resource Center (PFGRC; J. Craig Venter Institute) using LifterSlips, in hybridization buffer containing formamide for 17 hours at 42°C.

scan_protocol: After washing the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.0 (Molecular Devices, USA).

data_processing: The excessively high background fluorescence of the slide area outside the spots containing the DNA probes resulted in the presence of negative spots. Consequently, the default background subtraction method based on calculated median of local background as well as any other methods available in GenePix Pro software turned out ineffective resulting in enormous number of spots with negative fluorescence value leading to exclusion of numerous, otherwise useful data. Therefore prior to further analysis, the raw GPR files were subject to simple post processing in which the [F635 Median - B635] and [F532 Median - B532] column values and derivative [Ratio of Medians (635/532)], [Sum of Medians (635/532)] and [Log Ratio (635/532)] column values were recalculated. The recalculation was done individually for each block on the slide assuming the fluorescence of the darkest spot in any given block as the background value for that block. After background subtraction all fluorescence values that were lower than 150 were reset to 150. This last step of post processing helped to avoid excessive false positives resulting from calculations done on small numbers got after background subtraction. The 150 threshold value was chosen arbitrarily as the value close to the average of SDs for low intensity spots. The whole post processing was done with Microsoft Excel.  Post processed GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized log2 ratio data from biological replicates and technical replicates (dye swap) were averaged and the statistical significance (p-value) was calculated.

organism: Aspergillus nidulans

source_name: mycelium

label_protocol: Samples of total RNA (50μg) were subjected to the first strand cDNA synthesis with oligo dT as primer using RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas) according to the manufacturer’s protocol. The nascent cDNA was simultaneously labeled using fluorescent dyes DY-547-aadUTP or DY-647-aadUTP (Dyomics, Germany).

growth_protocol: 100 ml of minimal medium (MM) supplemented with 2 mM sulfate and 0.0005 mg/ml pyridoxine in 300-ml Erlenmeyer flasks was inoculated with 2-5x108 conidia collected with 2-3 ml of 0,01% Tween-80 from fresh (48-72h, 37oC) solid complete medium cultures. Mycelia were grown for 18-21 h at 30oC in orbital shaker set to 200 rpm up to approximately 1 g of wet weight. Mycelia were then harvested by filtration, washed with distilled water, dried on filter paper, weighed, frozen in liquid nitrogen and kept at –80oC.

extract_protocol: 300 mg of mycelia were powdered in liquid nitrogen and total RNA was isolated using TRI Reagent (Molecular Research Center) according to the manufacturer’s protocol. RNA was further purified by precipitation with lithium chloride added to a final concentration of 3.42 M. Purified RNA was stored at -80°C.

tag: genotype/variation

value: Wild-type

value: mycelium

value: sconB mutant


title: WT_vs_sconC

value: sconC mutant


title: Norwegian6


title: Thymus_Tcf-/-_tumor_mouse5


title: WT_vs_cysB

value: cysB mutant


title: Norwegian1


title: Thymus_Tcf+/-_mouse5

value: C57Bl/6 Tcf1+/− wt/ΔVII


title: Thymus_Tcf-/-_tumor_mouse6


title: Norwegian13


title: Thymus_Tcf-/-_tumor_mouse4


title: Moroccan11


title: Moroccan12


title: Moroccan10


title: Moroccan7


title: Thymus_Tcf-/-_tumor_mouse3


title: Thymus_Tcf+/-_mouse4


title: Moroccan6


title: Thymus_Tcf+/-_mouse3


title: Polish6

value: Polish


title: Thymus_Tcf-/-_mouse4


title: Thymus_Tcf+/-_mouse2


title: Thymus_Tcf+/-_mouse1


title: Thymus_Tcf-/-_tumor_mouse2


title: Moroccan5


title: Thymus_Tcf-/-_mouse2


title: Thymus_Tcf-/-_tumor_mouse1


title: Moroccan3


title: Moroccan4


title: Moroccan8


title: a1H knockout embryo trachea at E16 rep2

city: iowa city

first: xinchang

last: zhou

state: IA

address: 200 Hawkins Dr

department: Otolaryngology

institute: university of iowa

description: Gene expression data from embryos trachea at E 16.

hyb_protocol: Following fragmentation, the resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer, placed onto Affymetrix Mouse Genome 430 2.0 arrays (Cat #900495), and incubated at 45º C for 18 h with 60 rpms rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: GeneChips were scanned with the Affymetrix Model 3000 scanner with 7G upgrade

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 100.

source_name: Mouse embryo E16 trachea

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the Ovation Pico RNA Amplification System, v2 (NuGEN Technologies, Cat. #3100) according to the manufacturer’s recommended protocol. 3.75ug of cDNAt were biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

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

value: trachea

tag: genotype

value: a1H knockout

tag: age

value: embryonic day 16


title: Thymus_Tcf-/-_mouse3


title: Moroccan1

value: male


title: Thymus_Tcf-/-_mouse1


title: a1H knockout embryo trachea at E16 rep1


title: Greek9

value: Greek


title: Greek11


title: Moroccan2

value: Moroccan


title: DNA input1

type: SRA

city: New York

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: mixed 6 input reps; The original fastq files are not available

library_source: genomic

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Illumina ELAND with default configurations
Uniquely aligned reads were kept and further filtered with PCR redundancy (See Supplemental for details).
Differential sites were found by diffReps (http://code.google.com/p/diffreps/) with window size 200bp and step size 20bp. An FDR<10% was used as cutoff.
genome build: mm9
processed data files format and content: diffReps output is a tab-delimited text file which contains information for each differential site. Each differential site is also annotated by its proximity to genes or heterochromatic regions.
processed data files format and content: BED files contain six columns that represent uniquely aligned, PCR redundancy removed alignments. Columns 4 and 5 are not used.
processed data files format and content: bigWig files are binary representation of wiggle files (http://genome.ucsc.edu/goldenPath/help/bigWig.html). They are converted from the BED files above using the BedTools (https://code.google.com/p/bedtools/).

source_name: NAc dissection from 3-5 animals

extract_protocol: Crosslink with 1% formaldehyde for 10 min and pool 20 NAc for one replicate. Homogenize and sonicate by using bioruptor.  Antibodies were all ChIP grade from Abcam. Around ten nanograms of input DNA or pull-down DNA was used for sequencing library prep following the instructions of Illumina’s ChIP-seq sample prep kit (cat#IP-102-1001). In brief, DNA fragment overhangs were converted into phosphorylated blunt ends, using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. An “A” base was then added to the DNA fragments to enable ligation to the adapters, which have a single “T” overhang. The constructed library was then run on a 2% agarose gel and size selected between 175-300 bp. Lastly, gel-extracted DNA was further enriched by PCR and run on a bioanalyzer to validate size distribution and concentration.

tag: passages

value: nucleus accumbens

tag: treatment

value: Repeated saline I.P. injection for 1w as control

tag: chip antibody


title: Greek8


title: Norwegian5


title: Greek7


title: Greek4


title: Moroccan13


title: WT embryo trachea at E16 rep1

value: wild type


title: Greek10


title: Greek5


title: Bulgarian12

value: Bulgarian


title: WT embryo trachea at E16 rep2


title: Bulgarian16


title: Bulgarian14


title: H3K4me3 ChIP-seq Sal Rep3

description:
The original fastq files are not available
diff.k4m3.res.annotated

extract_protocol:
Crosslink with 1% formaldehyde for 10 min and pool 20 NAc for one replicate. Homogenize and sonicate by using bioruptor.
Antibodies were all ChIP grade from Abcam. Around ten nanograms of input DNA or pull-down DNA was used for sequencing library prep following the instructions of Illumina’s ChIP-seq sample prep kit (cat#IP-102-1001). In brief, DNA fragment overhangs were converted into phosphorylated blunt ends, using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. An “A” base was then added to the DNA fragments to enable ligation to the adapters, which have a single “T” overhang. The constructed library was then run on a 2% agarose gel and size selected between 175-300 bp. Lastly, gel-extracted DNA was further enriched by PCR and run on a bioanalyzer to validate size distribution and concentration.

tag: strain

tag: chip antibody vendor/catalog

value: Abcam Cat#ab8580


title: Bulgarian11

tag: gender


title: Bulgarian15

tag: nationality


title: H3K4me3 ChIP-seq Sal Rep2


title: Bulgarian10


title: H3K4me3 ChIP-seq Sal Rep1


title: Bulgarian9


title: Greek6


title: Bulgarian8


title: Bulgarian7


title: H3K4me3 ChIP-seq Coc Rep2

value: Repeated cocaine I.P. injection for 1w at 20mg/kg


title: H3K4me3 ChIP-seq Coc Rep3


title: Bulgarian18


title: Bulgarian17


title: Bulgarian5


title: H3K4me3 ChIP-seq Coc Rep1