title: primary glioblastoma NCH_m_9

status: Public on Dec 19 2009

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

country: Italy

institute: Salento University

description: Glioblastoma tissue vs non-neoplastic brain tissue

hyb_protocol: Purified tagged miRNA was hybridized to an epoxy-coated glass slide printed with miRNA probes in the antisense orientation. Purified tagged miRNA was diluted 1:1 in 2X Hybridization solution. The so obtained mix was held at the hybridization temperature (52°C) until loading the array. After loading the array, the chamber was sealed. Maintaining controlled humidity during hybridization is crucial for successful microarray experiments to prevent the slide from drying out. The hybridization chamber was placed in an incubator at 52°C, and incubated overnight (16–20 hours). Washing steps were performed as follows: array was washed in wash solution 1 (2X SSC/0.2% SDS) for 15 minutes at 50°C, in wash solution 2 (2X SSC) for 15 minutes at room temperature, and finally in wash solution 3 (0.2X SSC). Finally, array was dried by centrifugation.

scan_protocol: After hybridization, arrays were scanned using a confocal laser scanner (Affymetrix 428 scanner) at a resolution of 10 ?m. Data from the laser scans were collected as graphics (.tiff format) for each channel. To maximize the dynamic range of microarrays, the same arrays were scanned using different photo-multiplier settings (PMT). The use of different intensities allows the quantification of both the high and low copy expressed genes.

data_processing: The images were combined and processed using the ScanAnalyze program (written by Michael Eisen), and the positions on the images were assigned to grid coordinates for the matching of spot identity with average pixel intensity at that region. Background corrected, log converted intensity ratios were determined for each element of the array. The image processing analysis also extracted information regarding spot quality and assigned a quality score to each ratio measurement. The definition of the quality metric was based on the notion that unreliable data points usually result from weak target intensity, high local background, small target area, and inconsistent target intensity within a given target. Implementation of the quality metric enabled unified and universally applicable data filtering before downstream higher-level data analysis. ScanAlyze data was imported in GeneSpring and GenePattern for further elaboration (Silicon Genetics, Redwood City, CA). To import data a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. Parameters are not numerical but define the sample nature or tissue type. The normalization of each sample was performed by dividing each signal intensity by the 50th- percentile of all genes in that array. The normalization of each gene between samples was performed on the median of signal intensity of that gene in the reference sample. Genes were also analyzed using GeneSpring for differential expression between sample classes. The software allow the data filtering upon signal intensity and detection value. To select differentially expressed genes, we used several approaches: for two class matching we utilized the Scatter Plot selecting the genes with an expression fold >2. To identify differentially expressed genes in a multi class match, we calculated the log2 of normalized data. In this way, over-expressed genes were the ones with a value >0, while the down-expressed was the ones with a value <0. For statistical validation, we used t-test with a p-value of 0.01.

source_name: glioblastoma tissue

label_protocol: The labelling protocol consisted of two steps: a prehybridization target tagging and a post-hybridization incubation with capture labelled reagents. The target was tagged with the following steps: 1. miRNAs were added of a poly(A) tail using a polyA polymerase; 2. a short highly specific tag was ligated to each tailed miRNA using a bridging oligo. Following a purification, tagged miRNAs could be hybridized to the microarray.

extract_protocol: Total RNA was extracted from tissue using TRIZOL, after pulverizing the tissue in a stainless steel mortar and pestle that were chilled on liquid nitrogen. miRNA was isolated by PureLink™ miRNA Isolation Kit (Invitrogen) following manufacturer’s instructions.

tag: Age = 58

tag: Gender = M

tag: Tumour subtype = primary

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,6

source_name: non-neoplastic brain tissue

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_72

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: Age = 59

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,5


title: WildType_48hours

status: Public on Dec 25 2009

city: Los Angeles

first: Huanying

last: Ge

state: CA

address: 1050 Childs Way, RRI building 408D

department: Biology

country: USA

institute: Computational biology and bioinformatics

description: Microarray Experiment is done in UCLA DNA array Core Facility

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: we applied the Probe-Treatment-Reference (PTR) method coupled with sub-array normalization to the data. We choose target-reference relations illustrated in the paper to do the pairwise normalization.The normalized data are used to fit the three-factor PTR model according to the target-reference relations for each probe-set and the parameters are estimated by least absolute deviations (LAD).

label: biotin

organism: Saccharomyces cerevisiae

source_name: Wild Type

label_protocol: Standard Affymetrix protocol

growth_protocol: Both strains used were obtained from frozen stocks. Each strain was inoculated in 1 mL SDC and grown overnight. Saturated overnight cultures were then diluted. All samples were incubated at 30oC with shaking (220 rpm). Total RNA was isolated at different time points.

extract_protocol: Total RNA was isolated at each time point according to the acid phenol protocol.

treatment_protocol: No other treatment.

tag: Age

value: 48 hours


title: WildType_36hours

value: 36 hours


title: WildType_60hours

value: 60 hours


title: Sch9Mutant_60hours

source_name: Sch9 Mutant


title: secondary glioblastoma NCH_m_8

tag: Age = 45

tag: Gender = F

tag: Tumour subtype = secondary

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 7,6


title: primary glioblastoma NCH_m_69

tag: Age = 60

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 4,7


title: primary glioblastoma NCH_m_73

tag: Age = 58


title: primary glioblastoma NCH_m_68

tag: Age = 67

tag: Gender = M

tag: Tumour subtype = primary

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,2


title: primary glioblastoma NCH_m_65

tag: Age = 65

tag: Survival = 4,6

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_63

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,2


title: primary glioblastoma NCH_m_6

tag: Gender = F

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,3


title: primary glioblastoma NCH_m_59

tag: Age = 59

tag: Survival = 4,9


title: zebrafish eye_control replicate1,2,3,4

city: San Marcos

first: Dana

middle: M

last: Garcia

state: TX

address: 601 University Drive

institute: Texas State University-San Marcos

description: contains four biological replicates

hyb_protocol: aRNA sample was fragmented using Ambion RNA fragmentation reagents and added to hybridization solution (Ocimum Biosolutions.) Hybridization performed under 40 mmX22mm lifterslip by addition of 240 ul of labeled solution to zebrafish 14K OciChip

scan_protocol: Scanned using Affymetrix 428 Array scanner and analyzed with GenePix Pro 3.0 software.

data_processing: Array normalization and statistical analysis was performed using limma:Linear Models for Microarray Data library module (version 2.2.0) of the R statistical package (version 2.2.0).   Signal intensities of less than 1000 in all time points are marked as null in the Matrix datasheet and were removed from the analysis. One-way ANOVA was performed on ratios of triplicate time points. Slide intensity dara were normalized using the global LOWESS method with the least squares method used for linear model fit.

organism: Danio rerio

source_name: control fish left eye

label_protocol: 1 ug of RNA was labeled using Amino-AllylmessageAMP II aRNA Amplification Kit (ambion) labled with Cy3/Cy5

extract_protocol:
Total RNA extracted using TRI-reagent and cleaned-up with RNeasy spin columns per manufacturer's instructions
Quality assessment: RNA quality was assesed using a Nanodrop spectophotometer,  glyoxal gel electophoresis, and the Agilent BioAnalyzer.

tag: tissue

value: eye with lens and sclera removed

tag: genetic line

value: wildtype (zdr)

tag: light cycle

value: 12 hour light/dark

tag: time

value: 0 hr post surgery

tag: treatment

value: no treatment


title: primary glioblastoma NCH_m_62

tag: Age = 62

tag: Gender = M

tag: Tumour subtype = primary

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 4,3


title: zebrafish eye_168hr-replicate1,2,3

description: contains three biological replicates

source_name: optic nerve injured eye

value: 168 hr post surgery

value: Optic nerve severed

source_name: sham operated eye

value: Sham operated


title: secondary glioblastoma NCH_m_53

tag: Age = 41

tag: Tumour subtype = secondary

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 8,1

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_54

tag: Age = 75

tag: Survival = 5


title: primary glioblastoma NCH_m_57

tag: Age = 56

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,6


title: secondary glioblastoma NCH_m_56

tag: Age = 48

tag: Gender = F

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 8,3


title: primary glioblastoma NCH_m_48

tag: Age = 62

tag: Tumour subtype = primary

tag: Survival = 5,1


title: zebrafish eye_24hr-replicate1,2,3

description: contains three biological replicates

tag: tissue

tag: genetic line

tag: light cycle

tag: time

value: 24 hr post surgery

tag: treatment


title: secondary glioblastoma NCH_m_49

tag: Age = 42

tag: Gender = M

tag: Tumour subtype = secondary

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 7,2

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_5

tag: Age = 60

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,3


title: primary glioblastoma NCH_m_45

tag: Age = 65

tag: Gender = F

tag: Survival = 4,2


title: AVZ 48_GMCSF_Serum

status: Public on Dec 30 2009

city: Paris

first: Seraya

last: Maouche

state: Paris

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

country: France

institute: INSERM U937

hyb_protocol: Hybridizations were performed using the Agilent in situ hybridization kit. For each sample, 750 ng of Cy5-labeled, linearly amplified cRNA was mixed with equal amounts of Cy3-labelled, linearly amplified reference cRNA. The mixture was then fragmented by incubation with the fragmentation buffer at 60°C for 30 minutes. An equal amount of 2x hybridization buffer was added to the fragmented cRNA mixture and hybridized to whole-genome oligo arrays (Human-25K, Réseau National des Génopoles, France) at 60°C for 17 hours

scan_protocol: Fluorescent images of hybridized microarrays were obtained with a GenePix 4000 Axon Instruments scanner and provessed with the GenePix software (Axon Instruments).

data_processing: The Bioconductor packages marray and Limma were used to perform quality control and preprocessing. Background correction method: normexp Within array print-tip loess normalization was performed for each spot followed by between array quantile normalization. bad spots were filtered out. Log2 ch1/ch2.

source_name: GM-CSF monocyte-derived macrophage

label_protocol: RNA was amplified and labeled with Cy3 or Cy5

growth_protocol: The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and with 10 % FCS and 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA) or with 10 % FCS and 10 ng/ml of granulocyte macrophage colony-stimulation factor (GM-CSF, SIGM) or with 10 % human serum only. Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.

extract_protocol: RNA was extracted from monocytes derived macrohages using RNeasy mini kit of Qiagen.

treatment_protocol: For the isolation of PMBC from Buffy Coat and removal of dead cells, a density gradient centrifugation using Ficoll–Paque (GE Healthcare) gradient was used. PMBC were washed with PBS and the supernatant completely removed. The cell pellet was re-suspended in 80 µl of PBS/BSA buffer per 107 total cells and 10 µl of MACS CD14 (Miltenyi Biotec) were added carefully, mixed and incubated for 15 min at 6°-12°C. The cells were washed by adding 10-20X labelling volume of buffer, centrifuged at 300 g for 10 min. The cells were re-suspended in 500 µl of buffer before magnetic separation as described by the manufacturer.

tag: cell type

value: GM-CSF induced human monocyte-derived macrophage

source_name: peritoneal macrophage

value: peritoneal macrophage


title: secondary glioblastoma NCH_m_44

tag: Age = 46

tag: Survival = 7,6


title: secondary glioblastoma NCH_m_38

tag: Age = 43

tag: Survival = 8,3


title: zebrafish eye_3hr-replicate1,2,3

description: contains three biological replicates

tag: tissue

tag: genetic line

tag: light cycle

tag: time

value: 3 hr post surgery

tag: treatment


title: primary glioblastoma NCH_m_43

tag: Age = 63

tag: Gender = M

tag: Tumour subtype = primary

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 4,1

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_34

tag: Age = 62

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 5


title: primary glioblastoma NCH_m_39

tag: Age = 68

tag: Survival = 4,2


title: primary glioblastoma NCH_m_33

tag: Age = 69

tag: Gender = F

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,3


title: secondary glioblastoma NCH_m_35

tag: Age = 43

tag: Tumour subtype = secondary

tag: Survival = 7,5


title: primary glioblastoma NCH_m_27

tag: Age = 75

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,3


title: primary glioblastoma NCH_m_36

tag: Age = 65

tag: Tumour subtype = primary

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 4,6


title: primary glioblastoma NCH_m_31

tag: Age = 66

tag: Gender = M

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 4

tag: non-neoplastic adult brain tissue


title: secondary glioblastoma NCH_m_25

tag: Gender = F

tag: Survival = 8,7


title: secondary glioblastoma NCH_m_234

tag: Age = 50

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 7


title: primary glioblastoma NCH_m_233

tag: Age = 67

tag: Survival = 5,6


title: primary glioblastoma NCH_m_23

tag: Survival = 5


title: primary glioblastoma NCH_m_26

tag: Age = 60

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres


title: secondary glioblastoma NCH_m_216

tag: Age = 43

tag: Tumour subtype = secondary

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 7,6


title: secondary glioblastoma NCH_m_215

tag: Age = 47

tag: Gender = M

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 8,5


title: secondary glioblastoma NCH_m_213

tag: Age = 44

tag: Gender = F

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: non-neoplastic adult brain tissue


title: secondary glioblastoma NCH_m_214

tag: Age = 45

tag: Survival = 8,6


title: secondary glioblastoma NCH_m_212

tag: Age = 42

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres


title: secondary glioblastoma NCH_m_210

tag: Age = 40

tag: Survival = 7,9


title: secondary glioblastoma NCH_m_209

tag: Age = 50

tag: Tumour subtype = secondary

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 8,1


title: secondary glioblastoma NCH_m_211

tag: Age = 48


title: primary glioblastoma NCH_m_208

tag: Age = 64

tag: Gender = M

tag: Tumour subtype = primary

tag: Survival = 5,2


title: primary glioblastoma NCH_m_203

tag: Age = 69

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,4


title: primary glioblastoma NCH_m_205

tag: Survival = 4,5

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_204

tag: Age = 66

tag: Gender = F

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 4,1


title: primary glioblastoma NCH_m_206

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,1


title: secondary glioblastoma NCH_m_163

tag: Age = 43

tag: Tumour subtype = secondary

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 8


title: primary glioblastoma NCH_m_202

tag: Age = 64

tag: Tumour subtype = primary


title: secondary glioblastoma NCH_m_161

tag: Age = 48

tag: Gender = M

tag: Survival = 6,9


title: primary glioblastoma NCH_m_18

tag: Age = 63

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,3


title: secondary glioblastoma NCH_m_162

tag: Age = 41

tag: Gender = F

tag: Survival = 7,1

tag: non-neoplastic adult brain tissue


title: secondary glioblastoma NCH_m_160

tag: Age = 44

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 7,6


title: secondary glioblastoma NCH_m_16

tag: Age = 47

tag: Tumour subtype = secondary

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 8,1


title: secondary glioblastoma NCH_m_159

tag: Age = 48

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 7,7


title: primary glioblastoma NCH_m_17

tag: Age = 62

tag: Gender = M

tag: Tumour subtype = primary

tag: Survival = 4,9


title: secondary glioblastoma NCH_m_156

tag: Survival = 8,4


title: primary glioblastoma NCH_m_207

tag: Age = 65

tag: Survival = 5,5


title: primary glioblastoma NCH_m_2

tag: Age = 71

tag: Gender = F

tag: Survival = 4,5

tag: non-neoplastic adult brain tissue


title: secondary glioblastoma NCH_m_155

tag: Age = 44

tag: Tumour subtype = secondary


title: primary glioblastoma NCH_m_153

tag: Age = 68

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 5,6


title: primary glioblastoma NCH_m_154

tag: Age = 56

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres


title: primary glioblastoma NCH_m_201

tag: Age = 73

tag: Gender = M

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,2


title: primary glioblastoma NCH_m_147

tag: Age = 60

tag: Tumour subtype = primary

tag: Survival = 5,7


title: primary glioblastoma NCH_m_148

tag: Age = 62

tag: Survival = 4,6


title: primary glioblastoma NCH_m_151

tag: Age = 72

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 4,5

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_152

tag: Age = 61

tag: Gender = F

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres


title: secondary glioblastoma NCH_m_157

tag: Age = 48

tag: Tumour subtype = secondary

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 7,1


title: primary glioblastoma NCH_m_149

tag: Gender = M

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,3


title: secondary glioblastoma NCH_m_158

tag: Age = 46

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 7,4


title: primary glioblastoma NCH_m_144

tag: Age = 69

tag: Tumour subtype = primary

tag: Survival = 5


title: primary glioblastoma NCH_m_146

tag: Age = 71

tag: Survival = 4,4

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_143

tag: Survival = 5,6


title: primary glioblastoma NCH_m_141

tag: Age = 63


title: primary glioblastoma NCH_m_138

tag: Age = 58

tag: Gender = F

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,7


title: primary glioblastoma NCH_m_136

tag: Age = 56

tag: Gender = M

tag: Survival = 4,1


title: primary glioblastoma NCH_m_150

tag: Age = 54

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location


title: primary glioblastoma NCH_m_134

tag: Age = 62

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,8


title: primary glioblastoma NCH_m_14

tag: Tumour subtype = primary

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 3,9


title: primary glioblastoma NCH_m_139

tag: Survival = 5,5

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_133

tag: Age = 71

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres


title: primary glioblastoma NCH_m_145

tag: Age = 63

tag: Gender = F

tag: Survival = 5


title: primary glioblastoma NCH_m_131

tag: Age = 67

tag: Gender = M

tag: Tumour location = temporal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,3


title: primary glioblastoma NCH_m_132

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location


title: primary glioblastoma NCH_m_142

tag: Age = 57

tag: Tumour location = parietal subcortical white matter of the cerebral hemispheres

tag: Survival = 4,7


title: primary glioblastoma NCH_m_1

tag: Age = 62

tag: Tumour subtype = primary

tag: Survival = 4,9


title: primary glioblastoma NCH_m_135

tag: Age = 65

tag: Tumour location = occipital subcortical white matter of the cerebral hemispheres

tag: Survival = 5,1

tag: non-neoplastic adult brain tissue


title: primary glioblastoma NCH_m_128

tag: Age = 58

tag: Tumour location = frontal subcortical white matter of the cerebral hemispheres

tag: Survival = 5,4


title: primary glioblastoma NCH_m_137

tag: Age = 67

tag: Gender = M


title: primary glioblastoma NCH_m_12

tag: Age = 74

tag: Survival = 4,1


title: primary glioblastoma NCH_m_140

tag: Age = 68

tag: Survival = 4,3


title: ATSC differentiated toward the hepatic lineage (patient 1)

status: Public on Dec 15 2009

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

institute: Università Cattolica del Sacro Cuore di Roma

description:
Adipose tissue was retrieved from a female (42 year old) patient
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.

hyb_protocol: Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.

scan_protocol: Arrays were read with the geneChip Affymetrix 3000 7G scanner.

data_processing: Data were generated by using Affymetrix GCOS v1.2 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software.

label: Biotin

source_name: Human subcutaneous adipose tissue

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

growth_protocol: Adipose tissue was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro and harvested at culture passage 4 for this experiment.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure.

treatment_protocol: At passage culture 4, cells were submitted to the in vitro hepatogenic regimen. Briefly, serum was depleted for 48 hours. Cells were cultured for 2 weeks in the induction medium consisting in DMEM supplemented with 2% FBS, 4.9mM nicotinamide, 20ng/ml hepatocyte growth factor, and 10ng/ml fibroblast growth factor beta. Then, cells were cultured for 2 other weeks in maturation medium containing DMEM supplemented with 2% FBS, 4.9mM nicotinamdie and 20ng/ml oncostatin M.

tag: cell type

value: Adipose tissue-derived stromal cell differentiated toward the hepatic lineage


title: primary glioblastoma NCH_m_130

tag: Gender = F

tag: Tumour location = fronto-temporal subcortical white matter of the cerebral hemispheres location

tag: Survival = 5,2


title: Adipose tissue-derived MSC (patient 1)

value: Adipose tissue-derived mesenchymal-stromal cell


title: ATSC differentiated toward the hepatic lineage (patient 2)

description:
Adipose tissue was obtained from a male (49 year old ) patient
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.


title: primary glioblastoma NCH_m_129

tag: Age = 57

tag: Tumour subtype = primary

tag: Survival = 5


title: Adipose tissue-derived MSC (patient 3)

description:
Adipose tissue was retrieved from a female (51 year old) patient
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.


title: Adipose tissue-derived MSC (patient 2)

description:
Adipose tissue was retrieved from a male (49 year old) patient
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.


title: pH2A--WT_vs_H4_rep2

status: Public on Dec 01 2009

type: genomic

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 2 of 2. H2AS129pi enrichment measured in the same cells by the ratio WT/H4.

hyb_protocol: Resuspend Cy5 labeled sample in 4ul of water and combine with corresponding Cy3 labeled sample. Mix to 450ul of the hybridization buffer for each slide (45ul 0.5M Mes NaOH (pH 6.9), 135ul Formamide, 58.5ul 5M NaCl, 45ul 5% N-Lauroylsarcosine (FLUKA), 1ul 250 ug/ml Salmon Sperm DNA, 10ul 8 mg/ml yeast tRNA, 5.4ul 0.5 M EDTA, 150.1ul mQH2O). Boil samples for 3 minutes in 100ºC heat block. Transfer to 40ºC heat block for another 10 minutes. Follow standard Agilent chamber hybridization protocols. Incubate overnight at 40C in hybridization oven. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 1 L of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. Do not overboil it. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.0 and 6.1).

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

molecule: genomic DNA

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1) and 120 µL Chloroform/Isoamyl alcohol (24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -20C for 60 min, then spin 30 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.     Ligation: Thaw everything on ice, and do all manipulations on ice in the cold room. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL –20˚C 100% EtOH and centrifuge 30 minutes at 4˚C. Wash the pellet (should be a smear on the side of the tube) with 500uL –20˚C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and after 1 min of the first step (4 minutes at 55˚C) pause the program and add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase 2.5U/uL, 8uL ddH2O) before continuing the program. PCR cycling conditions: 1) 4:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer (see below) instead of their buffers PE and EB, respectively. Also, wash the columns twice (first time immediately after adding wash buffer, second time after 5 min incubation), and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness and store at –20˚C if desired. Resuspend the pellets with freshly made 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye and place in the dark. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Protecting samples from light as much as reasonably possible, purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash the columns twice (first time immediately after adding wash buffer, second time after 5 min incubation), and elute twice in 30uL EB. It is a good idea to mix both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until dryness (cover the chamber with tinfoil). Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4  0.1M Sodium Carbonate Buffer, pH 9.0 (50mL): 0.53g Na2CO3 + 40mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 50mL with ddH2O and pass through 0.22 µm filter. Make fresh each time. Derived from: Drouin S., Robert F. Methods (in press).

growth_protocol: Cultures of one colony of the appropriate strain were started in 10 mL XY (YEP supplemented with 0.02% tryptophan and 0.01% adenine) + 2% glucose and grown overnight at 30˚C.  The following morning, cells were subcultured into 50 or 100 mL fresh media at an OD600 of 0.1-0.15 and grown through the day until OD600 0.7-1.0 was reached.   Cultures were poured in 50mL Falcon tube(s) containing 1.4 mL 37% formaldehyde, and put on a rotating wheel at room temperature for 30 min.  Crosslinking was stopped by addition of 2.5mL 2.5M glycine.    For galactose induction experiments, cells grown overnight in XY + 2% glucose were washed twice in 10 mL sterile ddH2O, subcultured into XY + 2% galactose at an OD600 of 0.15 and grown for 7 h at 30˚C (final OD600 0.8-1.0)    For cell synchronization experiments, cells precultured overnight in XY + 2% glucose were subcultured into 200 mL of XY pH3.9 + 2% glucose (the lower pH inhibits the Bar1 protease to make the cells more sensitive to alpha-factor) to an OD600 of 0.5-0.6.  A 1 mL aliquot of cells was removed and fixed for FACS analysis in 70% ethanol (asynchronous).   Alpha-factor was added to a final concentration of 5 µg/mL (stock 5 mg/mL in DMSO) and growth was continued at 30˚C for 2 h (maximum -- to prevent toxicity from DMSO).  For G1-arrested cells, harvest and fix cells here (also remove a 1 mL aliquot of cells and fix for FACS analysis).  To enrich for S-phase cells, cells were harvested by centrifugation, washed twice in 200 mL sterile ddH2O and resuspended in 200 mL XY + 2% glucose (standard recipe, i.e. not pH’d) and returned to the 30˚C shaker.  Starting at 15 min post-release, and every 15 min after that, remove a 1 mL aliquot of cells to be fixed for FACS analysis and pour out 50 mL to be fixed for ChIP.  After fixation, washing and storage of ChIP samples, analyse FACS samples by Sytox Green staining and select the timepoint of release with desired DNA content for ChIP analysis.

extract_protocol: Crosslinked cells are pelleted at 3.5k RPM in a Beckman-Coulter Allegra X-15R centrifuge (SX4750 rotor). Cells are resuspended in 40mL ice cold TBS and pelleted again. This is repeated a second time. Cell pellets are resuspended in the remaining liquid (approx. 1mL) and transfered to 2 mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells quick-frozen by immersion in liquid nitrogen and stored at –80˚C. Cells are thawed on ice, and resuspended in 700 µL lysis buffer.   500uL of acid-washed glass beads (Sigma) are added, and the cells are lysed using the FastPrep FP120 (BIO101/Thermo Savant) bead-beater (8x20 sec cycles at power level 4.5, with 3min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow elution of lysate, but not of beads. The pierced tubes are suspended in 15mL collection tubes and spun for 2 min at 1000 x g. The supernatant is removed and the pellet is resuspended to a final volume of 1 mL in lysis buffer.  The lysate is sonicated (Misonix S3000) with a 5x 30 sec cycles (power 1 sec on, 1 sec off at output level 6) with a 5 minute break between sonication cycles. The sonicated lysates are centrifuged, and the supernatant is used immediately for ChIP. Lysis buffer: 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate with protease inhibitors (Complete EDTA-free Protease Inhibitors Cocktail without EDTA; Roche) and phosphatase inhibitors (Phosphatase Inhibitor Cocktail I; Sigma). Derived from: Drouin S., Robert F. Methods (in press).    For the immunoprecipitation, Anti-mouse Dynabeads or Protein G Dynabeads (50uL / ChIP) are washed three times with 1 mL PBS + 0.5% BSA  (passed through 0.22 µm filter), and resuspended in 1mL PBS + 0.5% BSA. After adding the antibody at the below indicated concentration, the mixture is incubated overnight at 4C in haematological mixer. Beads are washed three times with 1mL PBS + 0.5% BSA, and resuspended in 50uL lysis buffer / ChIP. 750-850 µL of lysate are added to 50uL beads, and incubated overnight at 4C in haematological mixer. Beads are then washed (using the Dynal magnet system) twice with 1mL ice cold Lysis Buffer (no protease inhibitors), twice with 1mL ice cold Lysis Buffer (no protease inhibitors) + additional 360mM NaCl (720uL of 5M NaCl per 10mL lysis buffer), twice with ice cold Wash Buffer, and twice with ice cold TE. Remaining liquid is removed by pipetting, and 50uL TE + 1% SDS is added. Beads are incubated overnight at 65C to reverse the crosslinks. Note for Whole Cell Extracts (WCE): WCE are included in the protocol only at the crosslink reversal step. Add 50uL TE + 1% SDS to 20uL WCE, and put overnight at 65C to reverse the crosslinks. Lysis Buffer (no protease inhibitors): 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate Wash Buffer: 10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA. Derived from: Drouin S., Robert F. Methods (in press).  The rabbit anti-phospho-histone H2A (Ser129), yeast-specific, (Upstate Cat# 07-745, lot# 30559) was used at 1.5 uL per immunoprecipitation.  The mouse 9E10 anti-c-Myc antibody (Santa Cruz) was used with 3 µl per immunoprecipitation.  The rabbit anti-histone H4 antibody (AV94 RyH4) was a kind gift from Alain Verreault and was used with 2 µL per immunoprecipitation.  The mouse anti-RNA polymerase II CTD antibody [8WG16] (AbCam ab817) was used with 0.5 µL per immunoprecipitation.  The mouse F-7 anti-HA antibody (Santa Cruz) was used with 15 µL per immunoprecipitation.    To clean-up the DNA, beads are spun down and supernatant is transfered to a new 1.5mL tube. 350uL of a solution of 345uL TE / 3uL RNAse A (10mg/mL) / 2uL Glycogen (20mg/mL) is added to the supernatant and incubated at 37C for 2 hours. 15uL 10% SDS and 7.5uL 10 mg/mL Proteinase K are then added and incubated for another 2 hours at 37C. The samples are then extracted 2-3 times with 450uL phenol/chloroform/isoamyl alcohol (25:24:1) and once with chloroform/isoamyl alcohol (24:1). 16uL of 5M NaCl is added to the final extract of about 350uL. 2 volumes of freezing 100% EtOH (-20C) are added, and the samples are put at –20˚C overnight. They are then centrifuged at maximum velocity for 30 minutes at 4˚C. The supernatant is discarded, and the pellet is washed with 500uL 70% EtOH (-20C) and centrifuged 15 minutes at 4C. The supernatant is discarded, the pellet resuspended in 50uL TE and stored at -20C. Derived from: Drouin S., Robert F. Methods (in press).

tag: strain

tag: antibody

value: anti-H2AS129pi (Upstate Catrep 07-745)

value: RYH4 anti-histone H4 (A.Verreault)


title: Cdc47-HA--Tag_vs_noTag_rep1

description: Biological replicate 1 of 2. DNA replication origin positions measured from Cdc47-HA in two cell lines by the ratio Tag/noTag.

value: F-7 anti-HA (Santa Cruz)


title: pH2A--rrm3D_vs_rrm3D_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the helicase mutant rrm3 delta measured in two cell lines by the ratio rrm3D/rrm3D_S129A.


title: pH2A--WT_vs_H4_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment measured in the same cells by the ratio WT/H4.


title: pH2A--WT_vs_S129A_rep3

description: Biological replicate 3 of 3. H2AS129pi enrichment measured in two cell lines by the ratio WT/S129A.


title: Cdc47-HA--Tag_vs_noTag_rep2

description: Biological replicate 2 of 2. DNA replication origin positions measured from Cdc47-HA in two cell lines by the ratio Tag/noTag.


title: ATSC differentiated toward the hepatic lineage (patient 3)

description:
Adipose tissue was obtained from a male (51 year old ) patient
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.


title: Cdc54-HA--Tag_vs_noTag_rep1

description: Biological replicate 1 of 2. DNA replication origin positions measured from Cdc54-HA in two cell lines by the ratio Tag/noTag.


title: Cdc54-HA--Tag_vs_noTag_rep2

description: Biological replicate 2 of 2. DNA replication origin positions measured from Cdc54-HA in two cell lines by the ratio Tag/noTag.


title: pH2A--rrm3D_vs_rrm3D_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the helicase mutant rrm3 delta measured in two cell lines by the ratio rrm3D/rrm3D_S129A.


title: pH2A--WT_vs_S129A_rep2

description: Biological replicate 2 of 3. H2AS129pi enrichment measured in two cell lines by the ratio WT/S129A.


title: pH2A--WT_vs_S129A_rep1

description: Biological replicate 1 of 3. H2AS129pi enrichment measured in two cell lines by the ratio WT/S129A.


title: 8mg/kg folate, TCE exposed rep2

city: tucson

first: ornella

last: selmin

state: AZ

address: 1177 east 4th st

department: nutritional sciences

institute: university of arizona

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 8mg/kg folate  and exposed to TCE. Two replicates of each samples were used for each hybridization

hyb_protocol: An aliquot of the labeled DNA was combined with the hybridization solution,  hybridized overnight  on the Mouse Gene 1.0ST array in an Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Once the wash and stain procedure was completed, the arrays were scanned using the Affymetrix GeneChip Scanner 3000 with 7G upgrade.

data_processing: The image generated was analyzed using the Affymetrix GeneChip Operating Software (GCOS) were .DAT (image), .CEL (cell intensity data), .CHP (probe analysis data) files were generated.The Affymetrix mouse gene ST arrays were processed with a bioconductor library (http://www.bioconductor.org) designed for this array.  The arrays were then normalized using the RMA function in the oligo library of bioconductor.  In order to identify poor quality arrays, Spearman correlation coefficients between all arrays were computed.  A plot of the coefficients revealed that correlations between the arrays were 0.98 or greater, indicating that a relatively small number of genes were changing in response to the treatments.  As a further control, the distribution of values for positive and negative control probes were examined on each array and found to have the correct expected separation.     Since there were only two biological replicates due to the complexity of the sample preparation, a specific approach was used that identified probes that showed a consistent change between biological duplicates. A cutoff value for the change between treatments of 1.5 fold was chosen based on an examination of the distribution of expression values on these arrays and identified between 200-1000 probes that were varying to the greatest extent.  Probe lists were generated as described below.  Briefly, the objective was to find genes that were changing between treatments while reducing the effects of the biological variation between duplicate samples.  To compare two treatments, probe expression ratios for all 4 possible combinations of the duplicate arrays were calculated.  If 2 or more of these ratios were 1.5 fold or greater, the gene was considered to be changed.

organism: Mus musculus

source_name: mouse cardiac tissue

label_protocol: The arrays were processed according to the protocol (GeneChip Whole Transcript(WT) Sense Target Labeling Assay Manual, version4) established by Affymetrix.  Briefly, 400ng of total RNA were reverse transcribed into double stranded cDNA by performing a two strand synthesis using the Affymetrix WT cDNA Synthesis and Amplification kit.  The entire cDNA was then in vitro transcribed overnight and cRNA cleaned using the Affymetrix GeneChip Sample Cleanup Module and quantified on a NanoDrop 1000(Thermo Scientific, Wilmington, DE).  Then, 8ug of cleaned-cRNA was reverse transcribed into  ssDNA, which was used as template for the labeling reaction.

growth_protocol: 129S1/Sv1mJ mice were obtained from Jackson Laboratories. Female mice were assigned to 3 different folate diets for four weeks before mating: 0, 2, or 8mg/kg folate (Dyets Inc), and received water ad libitum.

extract_protocol: Total RNA was extracted from pooled embryo hearts (n~ 35, corresponding to 4-6 litters) and purified using  Trizol /Rneasy Mini Kits (Qiagen, Valencia, CA)

treatment_protocol: The presence of a plug was indicative of day 0 pregnancy. At this time, each folate group was divided in two sub-groups of control (CTL) and trichloroethylene exposed mice (TCE), and maternal exposure to 10ppb TCE  was started via drinking water.

tag: age

value: Embryonal Day 10

tag: tissue

value: cardiac tissue


title: 2mg/kg folate, TCE exposed rep2

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 2mg/kg folate  and exposed to TCE. Two replicates of each samples were used for each hybridization


title: 8mg/kg folate, TCE exposed rep1


title: 0mg/kg folate, control rep2

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 0mg/kg folate. Two replicates of each samples were used for each hybridization


title: 0mg/kg folate, TCE exposed rep1

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 0mg/kg folate  and exposed to TCE. Two replicates of each samples were used for each hybridization


title: 8mg/kg folate, control rep2

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 8mg/kg folate. Two replicates of each samples were used for each hybridization


title: 0mg/kg folate, TCE exposed rep2


title: 2mg/kg folate, TCE exposed rep1


title: 2mg/kg folate, control rep1

description: Total RNA was extracted from 35 pooled cardiac tissues pooled from 4-6 different litters. Dams were kept on a diet containing 2mg/kg folate. Two replicates of each samples were used for each hybridization


title: 0mg/kg folate, control rep1


title: 8mg/kg folate, control rep1


title: MCL Long SAGE Library 04-26157

type: SAGE

anchor: NlaIII

city: Vancouver

first: Ronald

middle: J

last: deLeeuw

state: British Columbia

department: Cancer Genetics

institute: BC Cancer Research Centre

data_processing: Duplicate ditags have been removed prior to GEO submission

source_name: Lymph node biopsy

extract_protocol: Tissue sections were extracted in Invitrogen lysis/binding buffer as per I-SAGE protocol

tag: Classic MCL


title: MCL Long SAGE Library 03-10133

source_name: Lymph node Biopsy


title: 2mg/kg folate, control rep2


title: MCL Long SAGE Library 03-14255

tag: Lymph node tissue, 57yo male, classic MCL


title: Fe chlorosis replicate 2

city: Valencia

first: Miguel

last: Perez-Amador

state: Valencia

address: Avda. de los Naranjos s/n

country: Spain

institute: Inst. Biologia Molecular y Celular de Plantas (IBMCP-CSIC)

description: Stressed plants (Fe deficiency) labeled with Cy5,  compared to control plants labeled with Cy3; replicate 2

hyb_protocol: Microarray hybridization and washing were performed as described by Martinez-Godoy et al. (2008).

scan_protocol: Hybridized microarray slides were scanned at 532-nm for Cy3 and 635-nm for Cy5 dyes with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA) at 10-nm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus two standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

organism: Citrus trifoliata

source_name: Poncirus trifoliata (L.) Raf watered for 60 days without Fe-EDDHA (stress-2)

label_protocol: RNA was labeled using an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40ug) was used instead of poly(A)+ RNA.

growth_protocol: Seeds were harvested from mother seed trees held in the germplasm collection at IVIA (Instituto Valenciano de Investigaciones Agrarias). Seeds were sown on 55x40 cm trays containing a mixture of peat and siliceous sand (3:2, v/v) in an aphid-proof greenhouse between 15ºC and 28ºC at 80% relative humidity. Five-month old plants were transplanted into 5 liter pots containing siliceous sand (after peat remains were eliminated from the roots) and kept in the greenhouse. After transplanting, the plants were irrigated with water three times a week for two weeks for acclimation to the new substrate employed, and then for two weeks with nutrient solution (3 mM Ca(NO3)2, 3 mM KNO3, 2 mM MgSO4, 3 mM H3PO4, 18 uM Fe-EDDHA and trace elements according to Hoagland and Arnon (1950)).

extract_protocol: Total RNA was extracted from frozen roots according to the protocol described by Ancillo et al. (2007).

treatment_protocol: Plants were divided into two groups; one of them was kept in the conditions mentioned (18 uM Fe-EDDHA, control) while the other was watered with nutrient solution without Fe-EDDHA (0 uM Fe-EDDHA, iron deficiency). Plants were grown in these conditions for 60 days.

tag: authority

value: Poncirus trifoliata (L.) Raf

tag: developmental stage

value: 5 months old

value: root

tag: nutrient supplement

value: 0 uM Fe-EDDHA

source_name: Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA (control-2)

value: 18 uM Fe-EDDHA


title: Fe chlorosis replicate 4

description: Stressed plants (Fe deficiency) labeled with Cy5,  compared to control plants labeled with Cy3; replicate 4

source_name: Poncirus trifoliata (L.) Raf watered for 60 days without Fe-EDDHA (stress-4)

source_name: Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA (control-4)


title: Fe chlorosis replicate 1

description: Stressed plants (Fe deficiency) labeled with Cy3,  compared to control plants labeled with Cy5; replicate 1

source_name: Poncirus trifoliata (L.) Raf watered for 60 days without Fe-EDDHA (stress-1)

source_name: Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA (control-1)


title: outdoor_sow reared_day 5_5

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

description: Piglets were reared on the sow in indoor facilities, or in isolator units with daily antibiotics treatment, and the gene expression profile of ileal tissue was compared to that of piglets reared on the sow in outdoor facilities.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when p-value<0.01 and -2 ≤ Fold Change ≥ 2.

organism: Sus scrofa

source_name: ileal tissue, outdoor sow reared, 5 days

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.

growth_protocol: Animals were reared on the sow at an outdoor or indoor facility. Additional piglets from the indoor facility were transferred to individual isolator units at 24 hours of age, and given a daily dose of antibiotic cocktail for the duration of the study. Piglets were weaned at day 28. From day 29 onwards, piglets were fed creep feed ad libitum. Ileal tissue samples were excised at day 5, 28 and 56.

extract_protocol: Ileal tissue (75% in length from the pyloric sphincter) was excised, processed in ice-cold PBS, transferred to RNAlater (Ambion) and stored at -20 °C. Tissue was removed from RNAlater, lyzed in Trizol (Invitrogen), and RNA was extracted using chloroform/isopropanol steps. Total RNA was further treated with the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an RNase-free DNase I (Qiagen) digestion step.

treatment_protocol: The animal was reared on the sow at an outdoor facility. Ileal tissue was excised at day 5.

tag: animal

value: Large White × Landrace pig;

value: 5 days;

value: ileum, 75% in length from the pyloric sphincter


title: B. subtilis_salt stress_30min_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: B. subtilis grown in minimal medium

hyb_protocol: The microarray was prehybridized at 42 °C for 45 min in 4 x SSC, 0.5% SDS, 1% BSA. Afterwards, the slide was washed six times with deionized water and dried at 1,500 rpm for 5 min. Hybridization was performed using a SlideBooster (Advalytix). The labeled cDNA mixture was denatured for 2 min at 95 °C and then hybridized to the microarray for 16 h at 42 °C. Subsequently, the slide was washed at room temperature for 5 min in 0.2 x SSC, 0.1% SDS and two times for 5 min in 0.2 x SSC and then dried at 1,500 rpm for 5 min.

scan_protocol: The microarray was scanned using a ScanArray Express scanner (PerkinElmer Life and Analytical Sciences). Data were extracted using the ScanArray Express image analysis software. Intensity values for Cy3 and Cy5 (feature pixel median minus background pixel median) were used for further analysis.

data_processing: Intensity-dependent (Lowess) normalization was performed using the GeneSpring software (Agilent Technologies). The Cy5/Cy3 ratios of duplicate spots were averaged resulting in one value per gene. These values represent the ratio of an individual sample/ common reference pool.

organism: Bacillus subtilis

source_name: pooled RNA (equal amounts of RNA from all samples)

label_protocol: For cDNA synthesis, 25 µg of total RNA were mixed with a B. subtilis gene specific primer mix (ﬁnal concentration of 2.5 nM) (Eurogentec). As an external control, 1 ng of Arabidopsis thaliana rbcL RNA (Stratagene) was added. The RNA/primer mixture was incubated at 65 °C for 10 min followed by 10 min incubation at room temperature. Then, the following reagents were added: 10 µL of 5 x First Strand Buffer, 5 µl of 0.1 M DTT, 4 µL of dNTP mix (5 mM dATP; 5 mM dCTP; 5 mM dGTP; 2 mM dTTP) (Roche Diagnostics), 0.1 mM Cy3-dUTP or Cy5 dUTP (GE Healthcare), 1 µL SuperScript II reverse transcriptase (Invitrogen). The reaction mixture was incubated at 42 °C for 2 h. Subsequently, the RNA was hydrolyzed by incubation with 10 µL of 1M NaOH at 65 °C for 10 min. After adding 10 µL of 1M HCl and 200 µL of TE buffer (pH 8.0), the labeled cDNA was purified using the CyScribe GFX Purification Kit (GE Healthcare). After purification both samples were combined and the volume was reduced in a vacuum centrifuge. The labeled cDNA mixture was resuspended in 17 µL of hybridization buffer (MWG AG Biotech) and hybridized to the microarray.

growth_protocol: The B. subtilis 168 wild type strain was grown aerobically at 37 °C in BMM medium (Stülke et al., 1993) lacking glutamate to avoid its usage as precursor for biosynthesis of the compatible solute proline.

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002).

treatment_protocol: Exponentially growing B. subtilis cells (OD500nm of 0.4) were challenged with 6% (w/v) NaCl and samples were taken before and 10, 30, 60 and 120 minutes subsequent to the addition of NaCl.

value: wild type

tag: reference

source_name: salt stressed cells - 30 min after addition of 6% NaCl

tag: stress

value: salt

tag: time point

value: 30 min


title: B. subtilis_salt stress_60min_rep3

description: B. subtilis grown in minimal medium

value: pooled RNA (equal amounts of RNA from all samples)

source_name: salt stressed cells - 60 min after addition of 6% NaCl

value: 60 min


title: Fe chlorosis replicate 3

description: Stressed plants (Fe deficiency) labeled with Cy3,  compared to control plants labeled with Cy5; replicate 3

source_name: Poncirus trifoliata (L.) Raf watered for 60 days without Fe-EDDHA (stress-3)

source_name: Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA (control-3)


title: B. subtilis_salt stress_10min_rep3

description: B. subtilis grown in minimal medium

source_name: salt stressed cells - 10 min after addition of 6% NaCl

value: 10 min


title: B. subtilis_salt stress_120min_rep3

description: B. subtilis grown in minimal medium

source_name: salt stressed cells - 120 min after addition of 6% NaCl

value: 120 min


title: B. subtilis_salt stress_0min_rep3

description: B. subtilis grown in minimal medium

source_name: exponentially growing cells - before addition of NaCl

value: 0 min


title: outdoor_sow reared_day 5_3


title: B. subtilis_salt stress_30min_rep2

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_0min_rep2

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_120min_rep2

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_60min_rep2

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_10min_rep2

description: B. subtilis grown in minimal medium


title: outdoor_sow reared_day 5_4


title: outdoor_sow reared_day 5_2


title: outdoor_sow reared_day 5_6


title: outdoor_sow reared_day 5_1


title: B. subtilis_salt stress_120min_rep1

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_60min_rep1

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_10min_rep1

description: B. subtilis grown in minimal medium


title: B. subtilis_salt stress_30min_rep1

description: B. subtilis grown in minimal medium


title: indoor_sow reared_day 5_4

source_name: ileal tissue, indoor sow reared, 5 days

treatment_protocol: The animal was reared on the sow at an indoor facility. Ileal tissue was excised at day 5.


title: B. subtilis_salt stress_0min_rep1

description: B. subtilis grown in minimal medium


title: indoor_sow reared_day 5_3


title: indoor_sow reared_day 5_5


title: indoor_sow reared_day 5_2


title: indoor_sow reared_day 5_1


title: indoor_sow reared_day 5_6


title: indoor_isolator+antibiotics_day 5_6

source_name: ileal tissue, indoor isolator+antibiotics, 5 days

treatment_protocol: The animal was removed from the indoor facility at 24 hours of age, transferred to individual isolator units, and given a daily dose of antibiotic cocktail for the duration of the study. Ileal tissue was excised at day 5.


title: pH2A_S-phase--WT_vs_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment measured in S-phase-enriched cells in two cell lines by the ratio WT/S129A.

value: anti-H2AS129pi (Upstate Catrep 07-745)


title: pH2A_G1--WT_vs_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment measured in G1-arrested cells in two cell lines by the ratio WT/S129A.


title: pH2A_S-phase--WT_vs_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment measured in S-phase-enriched cells in two cell lines by the ratio WT/S129A.


title: outdoor_sow reared_day 28_4

source_name: ileal tissue, outdoor sow reared, 28 days

treatment_protocol: The animal was reared on the sow at an outdoor facility. Ileal tissue was excised at day 28.

value: 28 days;


title: pH2A--mec1D_sml1_tel1D_vs_triple_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the double PI-kinase mutant mec1 delta and tel1 delta (in the presence of sml1D) measured in two cell lines by the ratio mec1D_sml1D_tel1D/mec1D_sml1D_tel1D_S129A.


title: pH2A--tel1D_vs_tel1D_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the PI-kinase tel1 mutant delta measured in two cell lines by the ratio tel1D/tel1D_S129A.


title: indoor_isolator+antibiotics_day 5_4


title: indoor_isolator+antibiotics_day 5_5


title: outdoor_sow reared_day 28_3


title: indoor_isolator+antibiotics_day 5_3


title: pH2A--sml1D_vs_sml1D_S129A_rep4

description: Biological replicate 2 of 2. H2AS129pi enrichment in the suppressor of mec1 lethality sml1 delta measured in two cell lines by the ratio sml1D/sml1D_S129A.


title: pH2A_G1--WT_vs_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment measured in G1-arrested cells in two cell lines by the ratio WT/S129A.


title: pH2A--mec1D_sml1_tel1D_vs_triple_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the double PI-kinase mutant mec1 delta and tel1 delta (in the presence of sml1D) measured in two cell lines by the ratio mec1D_sml1D_tel1D/mec1D_sml1D_tel1D_S129A.


title: indoor_isolator+antibiotics_day 5_1


title: outdoor_sow reared_day 28_5


title: pH2A--mec1D_sml1D_vs_mec1D_sml1D_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the PI-kinase mutant mec1 delta (in the presence of sml1D) measured in two cell lines by the ratio mec1D_sml1D/mec1D_sml1D_S129A.


title: pH2A--mec1D_sml1D_vs_mec1D_sml1D_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the PI-kinase mutant mec1 delta (in the presence of sml1D) measured in two cell lines by the ratio mec1D_sml1D/mec1D_sml1D_S129A.


title: pH2A--sml1D_vs_sml1D_S129A_rep3

description: Biological replicate 1 of 2. H2AS129pi enrichment in the suppressor of mec1 lethality sml1 delta measured in two cell lines by the ratio sml1D/sml1D_S129A.


title: pH2A--tel1D_vs_tel1D_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the PI-kinase tel1 mutant delta measured in two cell lines by the ratio tel1D/tel1D_S129A.


title: outdoor_sow reared_day 28_6


title: pH2A--rpd3H188A_vs_rpd3H188A_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the HDAC rpd3 catalytic dead mutant measured in two cell lines by the ratio rpd3H188A/rpd3H188A_S129A.


title: outdoor_sow reared_day 28_2


title: indoor_isolator+antibiotics_day 5_2


title: indoor_sow reared_day 28_5

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

source_name: ileal tissue, indoor sow reared, 28 days

treatment_protocol: The animal was reared on the sow at an indoor facility. Ileal tissue was excised at day 28.


title: pH2A--rpd3H188A_vs_rpd3H188A_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the HDAC rpd3 catalytic dead mutant measured in two cell lines by the ratio rpd3H188A/rpd3H188A_S129A.


title: outdoor_sow reared_day 28_1


title: indoor_sow reared_day 28_6


title: pH2A--rpd3D_vs_rpd3D_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the HDAC mutant rpd3 delta measured in two cell lines by the ratio rpd3D/rpd3D_S129A.


title: RNAPII--IP_vs_Input_rep2

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

value: 8WG16 anti-CTD of Rpb1 (Abcam)


title: pH2A--hst1D_vs_hst1D_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment in the HDAC mutant hst1 delta measured in two cell lines by the ratio hst1D/hst1D_S129A.


title: pH2A_gal7h--WT_vs_S129A_rep2

description: Biological replicate 2 of 2. H2AS129pi enrichment measured following growth in galactose in two cell lines by the ratio WT/S129A.


title: pH2A_gal7h--WT_vs_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment measured following growth in galactose in two cell lines by the ratio WT/S129A.


title: pH2A--hst1D_vs_hst1D_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the HDAC mutant hst1 delta measured in two cell lines by the ratio hst1D/hst1D_S129A.


title: indoor_sow reared_day 28_4

description: Piglets were reared on the sow in indoor facilities, or in isolator units with daily antibiotics treatment, and the gene expression profile of ileal tissue was compared to that of piglets reared on the sow in outdoor facilities.


title: indoor_sow reared_day 28_3


title: indoor_sow reared_day 28_2


title: RNAPII--IP_vs_Input_rep1

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


title: indoor_isolator+antibiotics_day 28_6

source_name: ileal tissue, indoor isolator+antibiotics, 28 days

treatment_protocol: The animal was removed from the indoor facility at 24 hours of age, transferred to individual isolator units, and given a daily dose of antibiotic cocktail for the duration of the study. Ileal tissue was excised at day 28.


title: DNAP-myc--Tag_vs_noTag_rep1

description: Biological replicate 1 of 2. DNAP occupancy measured from Pol2-myc in two cell lines by the ratio Tag/noTag.

value: 9E10 anti-c-Myc (Santa Cruz)


title: indoor_sow reared_day 28_1


title: outdoor_sow reared_day 56_5

source_name: ileal tissue, outdoor sow reared, 56 days

treatment_protocol: The animal was reared on the sow at an outdoor facility. Weaning was performed at day 28. From day 29 onwards, the piglet was fed creep feed ad libitum. Ileal tissue was excised at day 56.

value: 56 days;


title: indoor_isolator+antibiotics_day 28_2


title: outdoor_sow reared_day 56_3


title: outdoor_sow reared_day 56_4


title: indoor_isolator+antibiotics_day 28_3


title: outdoor_sow reared_day 56_6


title: indoor_isolator+antibiotics_day 28_5


title: indoor_isolator+antibiotics_day 28_4


title: pH2A--rpd3D_vs_rpd3D_S129A_rep1

description: Biological replicate 1 of 2. H2AS129pi enrichment in the HDAC mutant rpd3 delta measured in two cell lines by the ratio rpd3D/rpd3D_S129A.


title: MCL Agilent 244K aCGH 03-14255

hyb_protocol: Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010.

scan_protocol: Agilent DNA Microarray Scanner p/n G2565BA. Scan Region: 61x21.6 mm Scan Resolution 5 micron Dye Channel Red & Green Red and Green PMT 100%

data_processing:
Value represent LOG10 Ratio (CH1/CH2) generated by Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx
Feature extraction protocol CGH-v4_91 was used.

label_protocol:
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010)

extract_protocol: Standard proteinaseK/RNAse followed by Phenol/Chlorofom extraction

tag: MCL Lymph node Biopsy

source_name: Promega Human Male DNA

extract_protocol: DNA provided by Promega Part Number G1471

tag: Normal Male DNA Promega


title: outdoor_sow reared_day 56_2


title: indoor_sow reared_day 56_6

source_name: ileal tissue, indoor sow reared, 56 days

treatment_protocol: The animal was reared on the sow at an indoor facility. Weaning was performed at day 28. From day 29 onwards, the piglet was fed creep feed ad libitum. Ileal tissue was excised at day 56.


title: indoor_isolator+antibiotics_day 28_1


title: outdoor_sow reared_day 56_1


title: MCL Agilent 244K aCGH 99-26032

data_processing: Value represent LOG10 Ratio (CH1/CH2) generated by Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx  Feature extraction protocol CGH-v4_91 was used.

tag: lymph node tissue, 63yo male, classic MCL

label_protocol:
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010


title: indoor_isolator+antibiotics_day 56_2

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. The moderated t-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when p-value<0.01 and -2 ≤ Fold Change ≥ 2

source_name: ileal tissue, indoor isolator+antibiotics, 56 days

treatment_protocol: The animal was removed from the indoor facility at 24 hours of age, transferred to individual isolator units, and given a daily dose of antibiotic cocktail for the duration of the study. From day 29 onwards, the piglet was fed creep feed ad libitum. Ileal tissue was excised at day 56.


title: indoor_sow reared_day 56_2


title: indoor_sow reared_day 56_1


title: indoor_sow reared_day 56_5


title: indoor_isolator+antibiotics_day 56_5


title: indoor_sow reared_day 56


title: indoor_isolator+antibiotics_day 56_3


title: indoor_sow reared_day 56_4


title: indoor_isolator+antibiotics_day 56_6


title: indoor_isolator+antibiotics_day 56_1


title: indoor_isolator+antibiotics_day 56

source_name: ileal tissue, indoor isolator+ antibiotics, 56 days


title: KIKO V vs._E2_24h

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: pooled RNA from three vehicle or three treated uteri

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

source_name: KIKO uterus, vehicle, 24h

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Trizol with Qiagen RNA easy clean up

tag: gender

value: female

value: 10+ weeks

value: uterus

source_name: KIKO uterus, E2, 24h

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.


title: aERKO V vs._E2_24h

source_name: aERKO uterus, vehicle, 24h

tag: strain

source_name: aERKO uterus, E2, 24h


title: E2_2h vs. aERKO V

source_name: aERKO uterus, E2, 2h

source_name: aERKO uterus, vehicle, 2h


title: WT V vs._E2_24h

source_name: WT uterus, vehicle, 24h

source_name: WT uterus, E2, 24h


title: E2_24h vs. WT V


title: E2_2h vs. KIKO V

source_name: KIKO uterus, E2, 2h

source_name: KIKO uterus, vehicle, 2h


title: KIKO V vs._E2_2h


title: E2_2h vs. WT V

source_name: WT uterus,  E2, 2h

source_name: WT uterus, vehicle, 2h


title: E2_24h vs. KIKO V


title: aERKO V vs._E2_2h


title: WT V vs._E2_2h

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

source_name: WT uterus, E2, 2h


title: E2_24h vs. aERKO V


title: WildType_1_1

status: Public on Nov 29 2009

city: Stanford

first: Alex

last: Morgan

address: 251 Campus Drive, MSOB X-215

department: Biomedical Informatics

institute: Stanford Medical School

description: B_NS2-WT #1_Mouse430_2

hyb_protocol: Microarray hybridization was performed at the Stanford PAN facility. RNA was reverse-transcribed to cDNA followed by in vitro transcription and biotinylation. Biotinylated cRNAs were then fragmented, mixed with control cRNA fragments, and hybridized to Affymetrix oligonucleotide arrays (Mouse Genome 430 2.0 Array).

scan_protocol: Microarray scanning was performed at the Stanford PAN facility.

data_processing: Microarray results were pre-processed by performing a background adjustment and normalization with RMA (robust multi-array analysis) using Bioconductor.

source_name: wild type

label_protocol: Biotin

growth_protocol: Mouse forebrains were finely minced, digested for 30 minutes at 37ºC in HBSS media containing 2.5 U/ml Papain (Worthington), 1U/ml Dispase (Roche or Stem Cell Technologies), and 250 U/ml DNase I (Sigma) and mechanically dissociated. NSC/progenitors were purified using two successive Percoll gradients (25% then 65%) (Amersham) and plated on uncoated tissue culture dishes at a density of 105 cells/cm2 in NeuroBasal-A medium supplemented with penicillin (100 U/ml)-streptomycin (100 mg/ml)-glutamine (292 µg/ml), serum-free B27 supplement without vitamin A (2%), bFGF (20 ng/ml), and EGF (20 ng/ml) (self-renewal/proliferation media). Cells were incubated at 37ºC.  Secondary neurospheres were collected 6 days   after initial plating at 50000 cells/ml.

extract_protocol: Total RNA was extracted using the mirVana isolation kit following the manufacturer’s protocol (Ambion)

treatment_protocol: NSC from neurospheres were enzymatically dissociated for 5-10 minutes at 37ºC with Accutase (Chemicon), then mechanically dissociated and seeded at a density of 5x104 cells/ml.

value: FVB/N

value: forebrain


title: Adipose-Long-Evans-Day4-FeedRestricted-rep3

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

data_processing: Quantitated array data (CEL files) were loaded into the R statistical environment (v2.9.1) using the Affy package (v1.22.1) of the BioConductor library. Data was investigated for spatial and distributional homogeneity, then pre-processed with the RMA algorithm (Irizarry et al. NAR). We employed an updated and remapped mapping of Probes to Entrez Gene IDs as implemented in the R package rat2302rnentrezgcdf (v12.0.0).

organism: Rattus norvegicus

source_name: Rat white adipose, Long-Evans strain, Day 4, Corn Oil Treated, Feed Restricted

growth_protocol: Animals were grown in a 12h/12h light/dark cycle housed in groups of 4 rats in suspended stainless-steel wire-mesh cages with pelleted R36 feed and tap water. The temperature was 21 +/- 1 degree Celcius and the relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). Total RNA yield was quantified by UV spectrophotometry and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: TCDD treated animals were treated with 100 ug/kg TCDD by oral gavage.

value: Long-Evans

value: male

value: 18-19 weeks

tag: tcdd dose

value: 0 ug/kg

tag: vehicle

value: Corn Oil

tag: exposure length

value: 96 hours

tag: feed restricted

value: Yes


title: Adipose-Long-Evans-Day4-CornOil-rep3

scan_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada

source_name: Rat white adipose, Long-Evans strain, Day 4, Corn Oil Treated

tag: age

value: No


title: Adipose-Long-Evans-Day4-FeedRestricted-rep1

label_protocol: Manufacturer's recommended protocols as followed by the TCAG Facility at the Hospital for Sick Kid's in Toronto, Canada


title: Adipose-Long-Evans-Day4-FeedRestricted-rep2


title: Adipose-Long-Evans-Day4-FeedRestricted-rep4


title: Adipose-Long-Evans-Day4-CornOil-rep2


title: Adipose-Long-Evans-Day4-CornOil-rep1


title: WildType_2_1

description: A_WT NS2 #1_Mouse430_2

tag: tissue


title: WildType_1_2

description: B_NS2-WT #2_Mouse430_2


title: FoxO3null_1_2

description: B_NS2-Fox03null #2_Mouse430_2

source_name: FoxO3 null mutant


title: Adipose-Long-Evans-Day4-TCDD-rep1

source_name: Rat white adipose, Long-Evans strain, Day 4, TCDD Treated

value: 100 ug/kg


title: Adipose-Long-Evans-Day4-TCDD-rep4


title: Adipose-Long-Evans-Day4-TCDD-rep3


title: Adipose-Long-Evans-Day4-TCDD-rep2


title: FoxO3null_1_1

description: B_NS2-Fox03null #1_Mouse430_2


title: Adipose-Long-Evans-Day4-CornOil-rep4


title: Adipose-Han/Wistar-Day1-CornOil-rep2

source_name: Rat white adipose, Han/Wistar strain, Day 1, Corn Oil Treated

value: Han/Wistar

value: 15-16 weeks

value: 24 hours


title: FoxO3null_2_2

description: A_F3 NS2 #2_Mouse430_2


title: Adipose-Han/Wistar-Day1-TCDD-rep4

source_name: Rat white adipose, Han/Wistar strain, Day 1, TCDD Treated


title: Adipose-Han/Wistar-Day1-TCDD-rep2


title: Adipose-Han/Wistar-Day1-CornOil-rep3


title: Adipose-Han/Wistar-Day1-CornOil-rep1


title: Adipose-Han/Wistar-Day1-TCDD-rep1


title: FoxO3null_2_1

description: A_F3 NS2 #1_Mouse430_2


title: Adipose-Han/Wistar-Day1-CornOil-rep4


title: WildType_2_2

description: A_WT NS2 #2_Mouse430_2


title: Adipose-Han/Wistar-Day1-TCDD-rep3


title: Adipose-Long-Evans-Day1-CornOil-rep4

source_name: Rat white adipose, Long-Evans strain, Day 1, Corn Oil Treated


title: Adipose-Long-Evans-Day1-TCDD-rep1

source_name: Rat white adipose, Long-Evans strain, Day 1, TCDD Treated


title: Adipose-Long-Evans-Day1-TCDD-rep4


title: Hypothalamus-Han/Wistar-TCDD-rep3

source_name: Rat hypothalamus, Han/Wistar strain, TCDD treated

value: 23 hours


title: Adipose-Long-Evans-Day1-CornOil-rep2


title: Adipose-Long-Evans-Day1-TCDD-rep2


title: Hypothalamus-Han/Wistar-CornOil-rep3

source_name: Rat hypothalamus, Han/Wistar strain, Corn Oil treated


title: Adipose-Long-Evans-Day1-CornOil-rep3


title: Hypothalamus-Han/Wistar-CornOil-rep4


title: Hypothalamus-Han/Wistar-CornOil-rep2


title: Hypothalamus-Han/Wistar-TCDD-rep1


title: DNAP-myc--Tag_vs_noTag_rep2

description: Biological replicate 2 of 2. DNAP occupancy measured from Pol2-myc in two cell lines by the ratio Tag/noTag.

tag: antibody

value: 9E10 anti-c-Myc (Santa Cruz)


title: Hypothalamus-Long-Evans-CornOil-rep2

source_name: Rat hypothalamus, Long-Evans strain, Corn Oil treated

value: 16-22 weeks


title: Adipose-Long-Evans-Day1-CornOil-rep1


title: Hypothalamus-Han/Wistar-TCDD-rep2


title: Hypothalamus-Long-Evans-TCDD-rep4

source_name: Rat hypothalamus, Long-Evans strain, TCDD treated


title: Adipose-Long-Evans-Day1-TCDD-rep3


title: Hypothalamus-Long-Evans-TCDD-rep3


title: Hypothalamus-Long-Evans-CornOil-rep1


title: Hypothalamus-Han/Wistar-CornOil-rep1


title: Hypothalamus-Long-Evans-TCDD-rep1


title: Wild Type exposed to ragweed: Mice 22

status: Public on Nov 22 2009

city: Galveston

first: Sanjiv

last: Sur

address: 301 University Blvd

institute: University of Texas Medial Branch

hyb_protocol: Follow fragmentation, 10ug of cRNA were hybridized for 16 hrs at 45C on Mouse 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Gene Array Scanner (Hewlett Packard) 3000

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling

source_name: BALB/c mice sensitized with ragweed extract and challenged with ragweed extract

label_protocol: Biotinylated cRNA were prepared accordiing to the standard Affymetrix protocol from 8.4 ug of total RNA

growth_protocol: Female Balb/c mice were purchased from Jackson Laboratory

extract_protocol: standard Affymetrix protocol

treatment_protocol: Mice were injected intraperitonealy with a mixture of ragweed and alum on days 0 and 4 to sensitize them, and challenged on day 11 with PBS or ragweed.  Lungs were dissected out 4 hours after challenge and total RNA was extracted from them.

value: Wild-type BALB/c mice


title: Hypothalamus-Long-Evans-TCDD-rep2


title: Wild Type exposed to ragweed: Mice 23


title: Wild Type treated with PBS: Mice 12

source_name: BALB/c mice sensitized with ragweed extract and challenged with PBS


title: Wild Type exposed to ragweed: Mice 21


title: Wild Type exposed to ragweed: Mice 27


title: Wild Type treated with PBS: Mice 13


title: Wild Type treated with PBS: Mice 11


title: Hypothalamus-Han/Wistar-TCDD-rep4


title: OKMS6 RepSox 24h rep3

status: Public on Nov 04 2009

city: Cambridge

first: Esther

middle: Yesde

last: Son

state: MA

address: 7 Divinity Avenue

department: Stem Cells and Regenerative Biology

institute: Harvard University

description: Non-normalized data file: RAW_2.txt

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic-spline normalization with BeadStudio.

source_name: Partially reprogrammed cell line derived from virally transduced MEFs

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA Amp kit.

growth_protocol: Cells were grown in a monolayer on gelatin-coated plates, either with or without an irradiated mouse embryonic fibroblast (MEF) feeder layer. They were given standard mES media containing either fetal bovine serum (FBS) or knock-out serum replacement (KSR).

extract_protocol: RNA was extracted with Trizol reagent in accordance with the prescribed protocol.

treatment_protocol: Cells were treated with small molecules as described in Ichida et al. (Cell Stem Cell, 2009).

tag: cell type

value: Partially reprogrammed Embryonic Stem Cells

tag: cell line

tag: genome/variation

value: viral Sox2

tag: small molecule treatment

value: RepSox at 24 hours


title: OKMS6 RepSox 24h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 48h rep2

description: Non-normalized data file: RAW_2.txt


title: OKMS6 48h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 24h rep2

description: Non-normalized data file: RAW_2.txt


title: OKMS6 RepSox 48h rep3

description: Non-normalized data file: RAW_2.txt

value: RepSox at 48 hours


title: RepSox iPS rep2

description: Non-normalized data file: RAW_1.txt

source_name: Mouse iPS line made with RepSox in lieu of viral Sox2

value: induced Pleuripotent Stem (iPS) Cell line

value: RepSox during derivation


title: OKMS6 24h rep3

description: Non-normalized data file: RAW_2.txt


title: RepSox iPS rep1

description: Non-normalized data file: RAW_1.txt


title: OKMS6 RepSox 10h rep3

description: Non-normalized data file: RAW_2.txt

value: RepSox at 10 hours


title: RepSox iPS rep3

description: Non-normalized data file: RAW_1.txt


title: OKMS6 RepSox 48h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 RepSox 10h rep2

description: Non-normalized data file: RAW_2.txt


title: OKMS6 RepSox 24h rep2

description: Non-normalized data file: RAW_2.txt


title: OKMS6 RepSox 10h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 10h rep3

description: Non-normalized data file: RAW_2.txt


title: OKMS6 24h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 48h rep3

description: Non-normalized data file: RAW_2.txt


title: OKMS6 10h rep2

description: Non-normalized data file: RAW_2.txt


title: OKMS6 10h rep1

description: Non-normalized data file: RAW_2.txt


title: OKMS6 RepSox 48h rep2

description: Non-normalized data file: RAW_2.txt


title: MEF rep2

description: Non-normalized data file: RAW_2.txt

source_name: Mouse embryonic fibroblasts (MEFs)

value: Embryonic Fibroblast Cells


title: MEF RepSox 1 week rep1

description: Non-normalized data file: RAW_2.txt

value: RepSox at 1 week


title: MEF RepSox 1 week rep3

description: Non-normalized data file: RAW_2.txt


title: V6.5 mES rep3

description: Non-normalized data file: RAW_2.txt

source_name: Mouse embryonic stem (mES) cell line V6.5

value: Embryonic Stem Cells


title: MEF rep3

description: Non-normalized data file: RAW_2.txt


title: Mse grown on tryptone + H2 + CO2 (M2) vs H2 + CO2 (A2)

status: Public on Nov 01 2009

city: Raleigh

first: Kathryne

middle: Sherlock

last: Auernik

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description: Scatterplots of signal intensities are reviewed to check for balance between channels.

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

scan_protocol: Images were aquired with a Perkin Elmer ScanArray scanner containing 2 lasers. Channels were balanced using the line scan feature and by balancing the overall signals without the use of external standards

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides are quantitated, data from all slides in loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001)].

organism: Metallosphaera sedula

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy3 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone and a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 6.2 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these mixotrophic conditions in DSMZ 88 media.

extract_protocol: At harvest, cells were quickly chilled and then centrifuged at 9510 x g for 15 minutes at 4C. RNA was extracted using Trizol (Invitrogen) and purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Harvest of final passage occurred at mid-10^7 cells/mL (~13hrs post-inoculation).

value: Metallosphaera sedula whole cells

label_protocol: Purified RNA was reverse transcribed using Superscript III (Invitrogen), re-purified, labeled with Cy5 dye (GE Healthcare), and hybridized to an Mse microarray slide (Corning).

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 1.1 x 10^7 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these autotrophic conditions in DSMZ 88 media.

treatment_protocol: Harvest of final passage occurred at mid-10^7 cells/mL (~22hrs post-inoculation).


title: Mse grown on tryptone + H2 + CO2 (M1) vs H2 + CO2 (A1)

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone and a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 6.3 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these mixotrophic conditions in DSMZ 88 media.

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 7.3 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these autotrophic conditions in DSMZ 88 media.


title: Mse grown on tryptone (H2) vs tryptone + H2 + CO2 (M2)

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone. An initial density of 1.0 x 10^7 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in 0.1% tryptone-supplemented DSMZ 88 media.

treatment_protocol: Harvest of final passage occurred at mid-10^7 cells/mL (~16hrs post-inoculation).

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone and a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 6.2 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these mixotrophic conditions in DSMZ 88 media.


title: V6.5 mES rep2

description: Non-normalized data file: RAW_2.txt


title: MEF RepSox 1 week rep2

description: Non-normalized data file: RAW_2.txt


title: R1 mES rep3

description: Non-normalized data file: RAW_2.txt

source_name: Mouse embryonic stem (mES) cell line R1


title: V6.5 mES rep1

description: Non-normalized data file: RAW_2.txt


title: R1 mES rep2

description: Non-normalized data file: RAW_2.txt


title: MEF rep1

description: Non-normalized data file: RAW_2.txt


title: Mse grown on H2 + CO2 (A2) vs tryptone (H2)

data_processing: Signals for each channel were obtained using ScanArray® Express 2.1 software using histogram quantitation and total normalization options to produce raw data, followed by manual verification of spot identification. Once all slides are quantitated, data from all slides in loop were analyzed with JMP Genomics 3.1 (SAS, NC), using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 1.1 x 10^7 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these autotrophic conditions in DSMZ 88 media.

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone. An initial density of 1.0 x 10^7 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times in 0.1% tryptone-supplemented DSMZ 88 media.


title: Mse grown on H2 + CO2 (A1) vs tryptone (H1)

growth_protocol:
Cells (DSMZ 5348) were grown at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), with a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 7.3 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these autotrophic conditions in DSMZ 88 media.


title: Mse grown on tryptone (H1) vs tryptone + H2 + CO2 (M1)

growth_protocol:
Cells (DSMZ 5348) were grown aerobically at 70C in an orbital shaking oil bath at 70 rpm on DSMZ 88 medium (pH 2), supplemented with 0.1% tryptone and a headspace containing 7% CO2, 14% O2, 28% H2, and the balance N2. An initial density of 6.3 x 10^6 cells/mL was used in two 1 L bottles containing 300 mL volume of the same medium.
Mse was subcultured at least 3 times under these mixotrophic conditions in DSMZ 88 media.


title: Mse grown on tryptone + H2 + CO2 (M1) vs tryptone + H2 + CO2 (M2)


title: Tumor sample ODG.25, anaplastic oligodendroglioma (WHO II)

city: New York

first: Cameron

last: Brennan

state: NY

address: 1275 York Avenue

institute: MSKCC

description: tumor profile

hyb_protocol: Microarray hybridization per manufacturer's instructions

scan_protocol: 2um scanner and Feature Extraction 9.5.3.1 (Agilent)

data_processing: Agilent Feature Extraction Software

source_name: Tumor specimen, snap frozen, -80c stored

label_protocol: Genomic DNA labeling kit PLUS (Agilent), per manufacturer's instructions

extract_protocol: DNeasy Blood and Tissue Kit (Qiagen), per manufacturer's instructions

treatment_protocol: Tumor samples snap-frozen and banked at -80c

tag: disease state

value: oligodendroglioma

source_name: Pooled normal genomic DNA, male

value: normal tissue


title: R1 mES rep1

description: Non-normalized data file: RAW_2.txt


title: Tumor sample AO.24, anaplastic oligodendroglioma

description: tumor profile

value: anaplastic oligodendroglioma


title: Tumor sample AA.26, anaplastic astrocytoma

description: tumor profile

value: anaplastic astrocytoma