title: sputum_76

description: Gene expression from sputum


title: sputum_75

status: Public on Apr 07 2014

type: RNA

city: New Haven

first: Geoffrey

middle: L.

last: Chupp

address: 300 Cedar St, S441

department: Department of Internal Medicine

country: USA

institute: Section of Pulmonary, Critical Care and Sleep Medicine

description: Gene expression from sputum

hyb_protocol: See manufacturer's protocol

scan_protocol: See manufacturer's protocol

data_processing: RMA was used to background correct, quantile normalize and summarize the gene expression levels across all arrays. Blood and sputum arrays were processed separately. Principal component analysis (PCA) was used to visualize the data and remove outliers. The batch effect was adjusted using Combat and the RIN number was adjusted using linear regression model.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: sputum

label_protocol: Purified RNA from the sputum or blood was processed for gene expression using the Affymetrix HuGene 1.0 ST gene arrays following manufacturer’s protocols.

growth_protocol: Sputum induction was performed with hypertonic saline, as previously described. Simply, by using a microscope, mucus plugs (cellular parts) from the sputum sample were dissected, separated and collected from aqueous compartments. Processing of the collected cellular part was done by mixing with  1 X Sputolysin Reagent (Calbiochem, cat# 560000) at a ratio of 1:4 (weight:volume), followed by vortexings at high speed for 30 seconds and low speed for 15 min, adding equal volume of PBS and a cell strainer filtration. Total cell count, viability, and differential, were determined by hemocytometer, trypan blue exclusion, and Wright-Geimsa stain, respectively. After centrifuged at 3,500 x g for 5 min, cell pellets were lysed in lysis solution of All-in-One Purification Kit (Product# 24200, Norgen Biotek Co, Thorhold, CAN) and stored at -80C until use.

extract_protocol: 10 ng of sputum RNA was amplified using the WT-Ovation Pico RNA amplification System (NuGen, San Carlos, CA) and processed per Affymetrix protocols. Total RNA from the blood was isolated using a column-based system (total-RNA kit, Norgen) and if needed, DNA contamination was removed using a DNA clear kit (Qiagen).  Hemoglobin reduction of blood samples was used to remove hemoglobin gene transcripts (GLOBINclear Kit, Ambion, Austin, TX) and samples were checked by Agilent bioanalyzer.

treatment_protocol: Sputum cell pellets were processed using the All-in-One purification kit (Norgen Biotek, Thorhold, CAN), checked on an Agilent bioanalyzer and, if needed, treated again to remove DNA contamination (Qiagen, Gaithersberg, MD).

tag: cluster assignment


title: sputum_72

description: Gene expression from sputum


title: MMP - 24 h - 4.41 mM - nr1

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Next, 0.0375 ng/ul of cRNA was hybridized on the Affymetrix HT MG-430 PM array. After hybridization, washing and staining was performed with the Affymetrix HWS Kit (#901530).

scan_protocol: The Array plates were scanned via the Affymetrix GeneTitan scanner. Data quality was checked by Affymetrix Expression Console software.

data_processing: Data was normalized using the Robust Multichip Average (RMA) algorithm, using an MBNI custom CDF version (http://brainarray.mbni.med.umich.edu) version 13.

organism: Mus musculus

source_name: ESCs_MMP_24 h_4.41 mM

label_protocol: Samples were randomized, blinded and further processed for array analysis at ServiceXS (Leiden, The Netherlands) using Affymetrix HT MG 430 PM array plates. Array analysis methods were according to manufacturer’s protocols. For each individual sample 100 ng RNA was  used for the labelling reaction. The Affymetrix 3 IVT-Express labelling kit (#901229) was used to synthesize biotin-labelled cRNA. Subsequently, 7.5 ug cRNA of each sample was fragmented using a hybridization cocktail.

growth_protocol: ES-D3 (ATCC) pluripotent embryonic stem cells (ESC) were cultured in complete medium (CM), consisting of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% foetal bovine serum, 1% non-essential amino acids, 2 mM l-glutamine, 1% 5000 IU/ml penicillin/5000 ug/ml streptomycin , and 0.1 mM b-mercaptoethanol . ESC pluripotency was maintained by adding leukaemia inhibitory factor (LIF), 1000 units/ml to the culture medium. ESC were kept for a maximum of 25 passages and are passaged every other day. Differentiation was initiated by culturing the cells via the ‘hanging drop method’ in which approximately 750 cells/drop were cultured in 56 droplets of 20 ul of CM, on the inner side of a lid of a Petri dish (94 mm × 16 mm), containing 5 ml phosphate buffered saline (PBS), Ca2+ and Mg2+ free . ESC were cultured in a humidified atmosphere (37 ◦C, 5% CO2) for three days during which the cells proliferated and formed cell aggregates (i.e. embryoid bodies (EB)). EB were transferred to a bacterial Petri dish (60 mm × 15 mm) containing 5 ml CM and cultured in a humidified atmosphere (37 ◦C, 5% CO2) for two days. Subsequently each individual EB was transferred to a single well of a 24-wells plate , containing 1 ml CM. Within 5 days aggregates further differentiated and displayed spontaneously contracting cell foci. At day 10, all wells were microscopically examined and scored based on the presence or absence of contracting cells.

extract_protocol: RNA was extracted by using the RNA Mini-extraction kit (Qiagen).The concentration of the RNA was measured by Nanodrop (Thermo Scientific). The quality of the RNA was checked using the 2100 Bio-Analyzer (Agilent) and Shimadzu MultiNA. Samples with a RNA Integrity Number (RIN) ≥ 8 were used for microarray analysis.

treatment_protocol: ESC were exposed to phthalate monoesters (MEHP, MBuP, MBzP, or MMP) in 0.3% DMSO during the differentiation protocol from day 3 onwards (time 0 h). Phthalates were dissolved in DMSO and tested in a concentration-response fashion (0.00441, 0.0143, 0.0441, 0.143, 0.441, 1.43 and 4.41 mM). Concurrent solvent control cultures (0.3% DMSO) were exposed from day 3 onward, and collected after 24 h (day 4, time 24 h). All groups contained 7–8 replicates, individually cultured. EB were collected in RNA protect in a 15 ml tube (Qiagen #76526) and stored at −20 ◦C prior to RNA extraction.

tag: cell line

value: ES-D3 (ATCC)

tag: cell type

value: murine pluripotent embryonic stem cells (ESC)

tag: time

tag: exposured to

value: monomethyl phthalate

tag: concentration


title: sputum_74

description: Gene expression from sputum


title: MMP - 24 h - 1.43 mM - nr6

source_name: ESCs_MMP_24 h_1.43 mM


title: MMP - 24 h - 1.43 mM - nr3


title: sputum_73

description: Gene expression from sputum


title: MMP - 24 h - 1.43 mM - nr5


title: MMP - 24 h - 4.41 mM - nr3


title: sputum_70

description: Gene expression from sputum


title: sputum_71

description: Gene expression from sputum


title: MMP - 24 h - 1.43 mM - nr2


title: MMP - 24 h - 1.43 mM - nr7


title: MMP - 24 h - 1.43 mM - nr4


title: MMP - 24 h - 4.41 mM - nr2


title: MMP - 24 h - 1.43 mM - nr1


title: sputum_69

description: Gene expression from sputum


title: MMP - 24 h - 0.441 mM - nr5

source_name: ESCs_MMP_24 h_0.441 mM


title: MMP - 24 h - 0.441 mM - nr4


title: MMP - 24 h - 0.441 mM - nr3


title: MMP - 24 h - 0.441 mM - nr6


title: sputum_67

description: Gene expression from sputum


title: MMP - 24 h - 0.441 mM - nr2


title: MMP - 24 h - 0.441 mM - nr1


title: MMP - 24 h - 0.441 mM - nr7


title: MMP - 24 h - 0.143 mM - nr8

source_name: ESCs_MMP_24 h_0.143 mM


title: sputum_65

description: Gene expression from sputum


title: MMP - 24 h - 0.143 mM - nr7


title: sputum_68

description: Gene expression from sputum


title: sputum_66

description: Gene expression from sputum


title: MMP - 24 h - 0.143 mM - nr6


title: ACC80

type: genomic

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

description: Adrenocortical carcinoma

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: standard Illumina protocol

extract_protocol: Tumor samples were powdered under liquid nitrogen. DNA was extracted and purified by cesium chloride gradient ultracentrifugation or by proteinase K digestion and ethanol extraction, followed by a clean-up step on columns (QIAGEN, Courtaboeuf, France).

tag: Sex

value: F

tag: age

value: Adrenocortical carcinoma


title: hip mutant KL2825, biological rep2

city: Boston

first: Kim

last: Lewis

state: MA

address: 360 Huntington Ave

institute: Northeastern University

description: Gene expression data from hip mutant strain stationary phase cells

hyb_protocol: Mixed fragmented and labeled RNA with Control Oligonucleotide B2, 20X Hybridization Controls, 2X Hybridization Mix DMSO and Nuclease-free Water. 2. Hyb on thermocycler for 5 mins at 99 degrees. 3. Incubateed the probe array filled with Pre-Hybridization Mix at 45 °C for 10 minutes with rotation. 4. Transfered the hybridization cocktail that has been heated at 99 °C, in Step 3, to a 45 °C heat block for 5 minutes. 5. Spun the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 6. Removed the array from the hybridization oven. Vented the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refiledl the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 7. Placed probe array into the hybridization oven, set to 45°C. 8. Rotated array at 60 rpm. 9. Hybridize for 16 hours

scan_protocol: Equipment and Consumables Required for Washing and Staining Arrays: GeneChip® Fluidics Station 450, GeneChip Scanner 3000 series, Affymetrix GeneChip® Command Console AGCC v1.1.

data_processing: Statistical analysis of the data was performed using R/Bioconductor with the oneChannelGUI package and comparing the twelve hip mutant strains to the wild type strain.

organism: Mycobacterium tuberculosis

source_name: hip mutant KL2825

label_protocol: At room temp, prepared an IVT Master Mix in a nuclease-free tube. Master mix consisted of: IVT Biotin Label, IVT Labeling Buffer and IVT Enzyme Mix. 2. Mixed well by pipetting up and down several times. 3. Transfered 30 µL of IVT Master Mix to each (30 µL) double-stranded cDNA sample. Mixed thoroughly. 4. Incubated the IVT reaction for 4 or 16 hours at 40 °C in a thermal cycler

growth_protocol: M. tuberculosis wild type strain (mc[2]6020) and hip mutants were grown in Middlebrook 7H9 broth (with supplements) at 37°C in a shaking incubator (200 rpm) to stationary phase (two weeks).

extract_protocol: Cells were resuspended in RNA Pro (MP Biochemicals) and lysed by bead beating. 2. Total RNA was extracted with chloroform and preciptated with isopropanol.

treatment_protocol: Stationary phase cultures were treated with two volumes RNA protect (Qiagen) prior to total RNA extraction.

tag: genotype/variation

value: hip mutant

tag: growth stage

value: stationary phase cells


title: sputum_63

description: Gene expression from sputum


title: hip mutant KL2849, biological rep2

source_name: hip mutant KL2849


title: hip mutant KL2849, biological rep1


title: MMP - 24 h - 0.143 mM - nr5


title: sputum_64

description: Gene expression from sputum


title: MMP - 24 h - 0.143 mM - nr4


title: sputum_62

description: Gene expression from sputum


title: ACC115

description: Adrenocortical carcinoma


title: sputum_61

description: Gene expression from sputum


title: hip mutant KL2825, biological rep1


title: MMP - 24 h - 0.143 mM - nr3


title: ACC58

description: Adrenocortical carcinoma

value: M


title: hip mutant KL2801, biological rep2

source_name: hip mutant KL2801


title: MMP - 24 h - 0.143 mM - nr2


title: sputum_60

description: Gene expression from sputum


title: ACC83

description: Adrenocortical carcinoma


title: ACC117

description: Adrenocortical carcinoma


title: ACC122

description: Adrenocortical carcinoma


title: hip mutant KL2801, biological rep1


title: MMP - 24 h - 0.143 mM - nr1


title: sputum_59

description: Gene expression from sputum


title: ACC124

description: Adrenocortical carcinoma


title: wild type (mc[2]6020), biological rep2

description: Gene expression data from wild type strain stationary phase cells

source_name: wild type (mc[2]6020)

value: wild type


title: sputum_58

description: Gene expression from sputum


title: MEHP - 24 h - 0.441 mM - nr8

source_name: ESCs_MEHP_24 h_0.441 mM

value: mono-(2-ethylhexyl) phthalate


title: sputum_56

description: Gene expression from sputum


title: MEHP - 24 h - 0.441 mM - nr7


title: wild type (mc[2]6020), biological rep1


title: ACC114

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.441 mM - nr4


title: hip mutant HT1170, biological rep2

source_name: hip mutant HT1170


title: hip mutant HT1137, biological rep2

source_name: hip mutant HT1137


title: sputum_55

description: Gene expression from sputum


title: MEHP - 24 h - 0.441 mM - nr5


title: MEHP - 24 h - 0.441 mM - nr6


title: hip mutant HT1137, biological rep1


title: sputum_53

description: Gene expression from sputum

value: CONTROL


title: sputum_57

description: Gene expression from sputum


title: hip mutant HT1170, biological rep1


title: sputum_54

description: Gene expression from sputum


title: ACC67

description: Adrenocortical carcinoma


title: ACC57

description: Adrenocortical carcinoma


title: ACC116

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.441 mM - nr3


title: hip mutant HT1130, biological rep2

source_name: hip mutant HT1130


title: ACC66

description: Adrenocortical carcinoma


title: hip mutant HT1134, biological rep2

source_name: hip mutant HT1134


title: MEHP - 24 h - 0.441 mM - nr1


title: MEHP - 24 h - 0.143 mM - nr8

source_name: ESCs_MEHP_24 h_0.143 mM


title: sputum_51

description: Gene expression from sputum


title: sputum_52

description: Gene expression from sputum


title: hip mutant HT1134, biological rep1


title: MEHP - 24 h - 0.441 mM - nr2


title: ACC60

description: Adrenocortical carcinoma


title: sputum_50

description: Gene expression from sputum


title: sputum_49

description: Gene expression from sputum


title: ACC73

description: Adrenocortical carcinoma


title: ACC95

description: Adrenocortical carcinoma


title: ACC118

description: Adrenocortical carcinoma


title: ACC69

description: Adrenocortical carcinoma


title: hip mutant HT1130, biological rep1


title: hip mutant HT1120, biological rep2

source_name: hip mutant HT1120


title: hip mutant HT1117, biological rep2

source_name: hip mutant HT1117


title: sputum_46

description: Gene expression from sputum

source_name: sputum


title: hip mutant HT1120, biological rep1


title: MEHP - 24 h - 0.143 mM - nr4


title: MEHP - 24 h - 0.143 mM - nr6


title: MEHP - 24 h - 0.143 mM - nr5


title: hip mutant HT1117, biological rep1


title: sputum_45

description: Gene expression from sputum


title: ACC106

description: Adrenocortical carcinoma


title: hip mutant HT1116, biological rep2

source_name: hip mutant HT1116


title: sputum_47

description: Gene expression from sputum


title: sputum_44

description: Gene expression from sputum


title: ACC128

description: Adrenocortical carcinoma


title: sputum_48

description: Gene expression from sputum


title: ACC75

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.143 mM - nr2


title: hip mutant HT1116, biological rep1


title: MEHP - 24 h - 0.143 mM - nr3


title: ACC70

description: Adrenocortical carcinoma


title: ACC127

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.143 mM - nr7


title: hip mutant HTS1105, biological rep2

source_name: hip mutant HTS1105


title: hip mutant HTS1105, biological rep1


title: sputum_41

description: Gene expression from sputum


title: MEHP - 24 h - 0.0441 mM - nr7

source_name: ESCs_MEHP_24 h_0.0441 mM


title: sputum_42

description: Gene expression from sputum


title: ACC59

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0441 mM - nr8


title: hip mutant HTS1090, biological rep2

source_name: hip mutant HTS1090


title: MEHP - 24 h - 0.0441 mM - nr6


title: sputum_43

description: Gene expression from sputum


title: MEHP - 24 h - 0.143 mM - nr1


title: sputum_40

description: Gene expression from sputum


title: ACC56

description: Adrenocortical carcinoma


title: sputum_39

description: Gene expression from sputum


title: hip mutant HTS1090, biological rep1


title: MEHP - 24 h - 0.0441 mM - nr5


title: MEHP - 24 h - 0.0441 mM - nr4


title: sputum_38

description: Gene expression from sputum


title: ACC74

description: Adrenocortical carcinoma


title: ACC129

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0441 mM - nr3


title: MEHP - 24 h - 0.0441 mM - nr2


title: sputum_35

description: Gene expression from sputum


title: sputum_37

description: Gene expression from sputum


title: ACC65

description: Adrenocortical carcinoma


title: ACC131

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0441 mM - nr1


title: ACC123

description: Adrenocortical carcinoma


title: ACC72

description: Adrenocortical carcinoma


title: ACC63

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr8

source_name: ESCs_MEHP_24 h_0.0143 mM


title: ACC68

description: Adrenocortical carcinoma


title: sputum_34

description: Gene expression from sputum


title: sputum_33

description: Gene expression from sputum


title: MEHP - 24 h - 0.0143 mM - nr7


title: MEHP - 24 h - 0.0143 mM - nr6


title: sputum_32

description: Gene expression from sputum


title: ACC125

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr5


title: sputum_36

description: Gene expression from sputum


title: ACC71

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr4


title: ACC130

description: Adrenocortical carcinoma


title: sputum_31

description: Gene expression from sputum


title: sputum_30

description: Gene expression from sputum


title: ACC119

description: Adrenocortical carcinoma


title: sputum_29

description: Gene expression from sputum


title: sputum_27

description: Gene expression from sputum


title: ACC121

description: Adrenocortical carcinoma


title: ACC62

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr2


title: ACC64

description: Adrenocortical carcinoma


title: ACC126

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr1


title: ACC61

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.0143 mM - nr3


title: ACC120

description: Adrenocortical carcinoma


title: sputum_28

description: Gene expression from sputum


title: ACC132

description: Adrenocortical carcinoma


title: sputum_26

description: Gene expression from sputum


title: MEHP - 24 h - 0.00441 mM - nr7


title: MEHP - 24 h - 0.00441 mM - nr6


title: ACC113

description: Adrenocortical carcinoma


title: sputum_25

description: Gene expression from sputum


title: MEHP - 24 h - 0.00441 mM - nr8


title: Sexual_Plant10-Cy3

city: Gatersleben

first: Timothy

last: Sharbel

address: Corrensstrasse 4

country: Germany

institute: IPK Gatersleben

scan_protocol: After hybridization, washing and drying (following the manufacturer’s protocols; Roche-NimblGen) the arrays were scanned at 2 µm double pass resolution with an Agilent Microarray G2565BA Fluorescent Scanner (Agilent Technologies). Each 3-plex image (3x720K) was split into three separate arrays and aligned for data extraction using the NimbleScan software (version 2.6; Roche-NimblGen). The NimbleScan software performs spatial correction of the data, thereby reducing artifacts and noise before applying q-spline fit normalization (Workman et al. 2002). Data in *unavg_segMNT.gff files represent raw data as coming from the NimbleScan software.

data_processing:
For the dye-swap experimental design, two CGH profiles (Cy3 and Cy5) were obtained, each representing the log2-ratios of measured fluorescence intensities for the test (sexual or apomictic genotype; Table 1) versus reference sample (mixture of different genotypes, see above) for all 719 346 probes on the array (720K minus control probes). Genome-wide CGH-profiles of each genotype were normalized by applying quantile normalization (Bolstad et al. 2003) to both CGH profiles from the dye swap.
All normalized CGH profiles were analyzed by a mixture model of three Gaussian distributions described in Seifert et al. (2012, PLoS Comp. Biol. 8: doi: 10.1371/journal.pcbi.1002286 ) to identify depletions, enrichment and unchanged regions between a test genotype and the reference sample by specifically adapting the parameters of the mixture model to both CGH profiles of each test genotype using a Bayesian Expectation Maximization (EM) algorithm.  Identification of depleted, unchanged, and enriched regions was done by performing a decoding of the measured log2-ratios into the most likely underlying state of each probe (depleted, unchanged, or enriched). Only probes that were identified as depleted or enriched in both CGH profiles (dye swap replicates) of a test sample (genotype) were considered as being depleted or enriched in this genotype, while all other probes were considered as being unchanged (i.e. no CNV variation with respect to the pooled reference). This resulted in a reproducible set of genomic regions affected by depletions or enrichment for each genotype.

organism: Boechera polyantha

label_protocol: DNA with concentrations between 450 ng/μl and 1.0 μg/μl and absorbance readings of A260/A280 > 1.8 and A260/A230 > 1.9 (recommended by Roche-NimbleGen) were used for the labeling procedure. A total of 1.0 µg of gDNA per sample was used for each labeling reaction and hybridization thereafter. A dye swap experimental design was used for technical replication, where both test and reference samples are interchangeably labeled with the two dyes (Cy3 and Cy5; following Roche-NimblGen standard protocols) in order to minimize error due to dye-bias.  A pooled reference sample was used, whereby an equal concentration of gDNA from each of the 20 genotypes was combined as a reference in each labeling reaction and hybridization (Scherer et al. 2007, Nat. Genet. 39:S7–S15.; Ju et al. 2010, Nucleic Acids Res. 1–11, doi:10.1093/nar/gkq730).

extract_protocol: Genomic DNA (gDNA) was extracted from the leaf tissue of a single plant of each of the 20 genotypes using a modified CTAB method described by Mace et al. (2003). Plant Mol. Biol. Report 21:459a-459h.

tag: ipk-plant id

tag: name

tag: es numbera

tag: species

value: B. polyantha

tag: reproduction

value: Sexual

tag: locality

value: Big Hole Pass

tag: u.s. state

value: MT

organism:
Boechera stricta
Boechera lignifera
Boechera divaricarpa
Boechera crandallii
Boechera retrofracta
Boechera schistacea
Boechera polyantha
Boechera retrofracta x Boechera stricta
Boechera duchesnensis

source_name: pooled reference sample (mixture of different genotypes)

tag: reference

value: mixture of all 20 genotypes


title: Sexual_Plant9-Cy5

hyb_protocol: A total of 1.0 µg of gDNA per sample was used for each labeling reaction and hybridization thereafter. A dye swap experimental design was used for technical replication, where both test and reference samples are interchangeably labeled with the two dyes (Cy3 and Cy5; following Roche-NimblGen standard protocols) in order to minimize error due to dye-bias.  A pooled reference sample was used, whereby an equal concentration of gDNA from each of the 20 genotypes was combined as a reference in each labeling reaction and hybridization (Scherer et al. 2007, Nat. Genet. 39:S7–S15.; Ju et al. 2010, Nucleic Acids Res. 1–11, doi:10.1093/nar/gkq730).

organism: Boechera schistacea

value: B. schistacea

value: Toiyabe

value: NV


title: sputum_23

description: Gene expression from sputum

tag: cluster assignment


title: Sexual_Plant8-Cy3

organism: Boechera stricta

value: B. stricta

value: Golden Gate B

value: CO


title: Sexual_Plant10-Cy5


title: sputum_24

description: Gene expression from sputum


title: ACC110

description: Adrenocortical carcinoma

tag: cell type

value: Adrenocortical carcinoma


title: Sexual_Plant8-Cy5


title: MEHP - 24 h - 0.00441 mM - nr5

tag: cell line

value: ES-D3 (ATCC)

value: murine pluripotent embryonic stem cells (ESC)

tag: time


title: sputum_22

description: Gene expression from sputum


title: Sexual_Plant9-Cy3


title: MEHP - 24 h - 0.00441 mM - nr4

tag: exposured to

tag: concentration


title: ACC108

description: Adrenocortical carcinoma

tag: Sex

value: F

tag: age


title: Sexual_Plant7-Cy3

value: Gold Creek


title: MEHP - 24 h - 0.00441 mM - nr2

value: mono-(2-ethylhexyl) phthalate


title: Sexual_Plant6-Cy5

value: B. polyantha

value: Trail Creek

value: ID


title: sputum_20

description: Gene expression from sputum


title: ACC111

description: Adrenocortical carcinoma


title: sputum_19

description: Gene expression from sputum


title: Sexual_Plant7-Cy5

value: Sexual


title: sputum_21

description: Gene expression from sputum


title: ACC112

description: Adrenocortical carcinoma

value: M


title: ACC109

description: Adrenocortical carcinoma


title: MEHP - 24 h - 0.00441 mM - nr3


title: Sexual_Plant6-Cy3

value: mixture of all 20 genotypes


title: MEHP - 24 h - 0.00441 mM - nr1


title: ACC101

description: Adrenocortical carcinoma


title: ACC102

description: Adrenocortical carcinoma


title: control - 48 h - 0 mM - nr8

source_name: ESCs_control_48 h_0 mM

value: none (unexposed control)


title: ACC104

description: Adrenocortical carcinoma


title: sputum_17

description: Gene expression from sputum


title: ACC96

description: Adrenocortical carcinoma


title: control - 48 h - 0 mM - nr7


title: sputum_16

description: Gene expression from sputum


title: control - 48 h - 0 mM - nr6


title: Sexual_Plant4-Cy5

value: Parker Meadow


title: Sexual_Plant5-Cy5

organism: Boechera crandallii

value: B. crandallii

value: Wood Gulch-south


title: Sexual_Plant5-Cy3

value: CO


title: sputum_18

description: Gene expression from sputum


title: Sexual_Plant4-Cy3


title: sputum_15

description: Gene expression from sputum


title: control - 48 h - 0 mM - nr5


title: sputum_14

description: Gene expression from sputum


title: Sexual_Plant3-Cy5

value: B. stricta

value: Sagebrush Meadow

value: MT


title: ACC100

description: Adrenocortical carcinoma

value: F

value: Adrenocortical carcinoma


title: control - 48 h - 0 mM - nr4

value: ES-D3 (ATCC)

value: murine pluripotent embryonic stem cells (ESC)


title: control - 48 h - 0 mM - nr3


title: ACC99

description: Adrenocortical carcinoma


title: control - 48 h - 0 mM - nr2


title: sputum_13

description: Gene expression from sputum


title: sputum_12

description: Gene expression from sputum


title: Sexual_Plant2-Cy5

value: Twin Saddle


title: sputum_11

description: Gene expression from sputum


title: control - 48 h - 0 mM - nr1


title: ACC98

description: Adrenocortical carcinoma


title: Sexual_Plant3-Cy3


title: ACC92

description: Adrenocortical carcinoma


title: Sexual_Plant2-Cy3

value: ID


title: control - 24 h - 0 mM - nr8

source_name: ESCs_control_24 h_0 mM


title: sputum_10

description: Gene expression from sputum


title: Sexual_Plant1-Cy3

value: B. polyantha

value: Sexual

value: Bandy Ranch


title: control - 24 h - 0 mM - nr7

value: none (unexposed control)


title: sputum_8

description: Gene expression from sputum


title: control - 24 h - 0 mM - nr6


title: sputum_9

description: Gene expression from sputum


title: Sexual_Plant1-Cy5

value: mixture of all 20 genotypes


title: ACC105

description: Adrenocortical carcinoma

value: M


title: ACC107

description: Adrenocortical carcinoma


title: ACC97

description: Adrenocortical carcinoma


title: sputum_7

description: Gene expression from sputum


title: Apomictic_Plant10-Cy3

organism: Boechera duchesnensis

value: B. duchesnensis

value: Apomictic

value: ES88/Map ID 80

value: UT


title: ACC103

description: Adrenocortical carcinoma


title: control - 24 h - 0 mM - nr5


title: sputum_6

description: Gene expression from sputum


title: control - 24 h - 0 mM - nr3


title: sputum_5

description: Gene expression from sputum


title: ACC85

description: Adrenocortical carcinoma


title: Apomictic_Plant8-Cy5

organism: Boechera divaricarpa

value: B. divaricarpa

value: Mule Ranch

value: MT


title: ACC87

description: Adrenocortical carcinoma

value: Adrenocortical carcinoma


title: ACC90

description: Adrenocortical carcinoma


title: ACC91

description: Adrenocortical carcinoma

value: F


title: ACC94

description: Adrenocortical carcinoma


title: Apomictic_Plant9-Cy5

value: Morgan Switch Back


title: control - 24 h - 0 mM - nr2

value: ES-D3 (ATCC)

value: murine pluripotent embryonic stem cells (ESC)


title: control - 24 h - 0 mM - nr4


title: sputum_4

description: Gene expression from sputum


title: sputum_3

description: Gene expression from sputum


title: ACC93

description: Adrenocortical carcinoma


title: Apomictic_Plant10-Cy5


title: Apomictic_Plant7-Cy5

value: B. polyantha

value: Ranch Creek


title: ACC88

description: Adrenocortical carcinoma


title: Apomictic_Plant9-Cy3

value: ID


title: sputum_2

description: Gene expression from sputum


title: control - 0 h - 0 mM - nr8

source_name: ESCs_control_0 h_0 mM

value: 0 h

value: none (unexposed control)


title: control - 24 h - 0 mM - nr1


title: control - 0 h - 0 mM - nr7


title: ACC86

description: Adrenocortical carcinoma


title: sputum_1

description: Gene expression from sputum


title: control - 0 h - 0 mM - nr5


title: control - 0 h - 0 mM - nr6


title: ddm1 F6 inflorescence replicate 3

city: Columbus

first: Richard

middle: Keith

last: Slotkin

state: OH

address: 318 West 12th Ave.

department: Molecular Genetics

institute: The Ohio State University

description: ddm1 F6

hyb_protocol: Hybridization was performed to ATH1 arrays in Affymetrix GeneChip® hybridization oven 645 and washed in Affymetrix GeneChip®  Fluidics Station 450 according to standard Affymetrix GeneChip® Hybridization and Wash protocols.

scan_protocol: Arrays were scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix protocols.

data_processing: The data were analyzed with the GeneSpring GX Software Suite using GC-RMA normalization

organism: Arabidopsis thaliana

source_name: ddm1, F6 inbred generation, inflorescence, unopened flower buds

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer and Nanodrop 8000 spectrophotometer. Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

growth_protocol: Plants were grown on soil in long day (18 hour) light at 23C

extract_protocol: Total RNA was extracted from unopened flower buds using Trizol reagent. Total RNA was further purified using a Qiagen MinElute RNA cleanup kit.

tag: tissue

value: unopened flower buds

tag: genotype/variation

value: ddm1, F6 inbred generation


title: ddm1 F6 inflorescence replicate 2

description: ddm1 F6


title: M3KO#3

city: Baltimore

first: Kunrong

last: Cheng

state: MD

address: 22 S. Greene St., N3W62

institute: University of Maryland Baltimore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization (IlluminaGUI).

source_name: colon tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using the RNeasy kit from Qiagen according to the manufacturer’s instructions. RNA was digested using the RNase-Free DNase set. Quality control was confirmed using a Bioanalyzer 2100 (Expression Analysis, Inc., Durham, NC).

tag: strain

value: 7 months

value: colon tumor


title: M3KO#2


title: Apomictic_Plant6-Cy5

organism: Boechera lignifera

tag: ipk-plant id

tag: name

tag: es numbera

value: B. lignifera

value: Apomictic

value: ES84/Map ID 74

value: UT

value: mixture of all 20 genotypes


title: Apomictic_Plant8-Cy3

tag: species

value: B. divaricarpa

tag: reproduction

tag: locality

value: Mule Ranch

value: MT


title: Apomictic_Plant7-Cy3

value: B. polyantha

tag: u.s. state

tag: reference


title: control - 0 h - 0 mM - nr4

tag: cell line

value: ES-D3 (ATCC)

tag: cell type

value: murine pluripotent embryonic stem cells (ESC)


title: ACC89

description: Adrenocortical carcinoma

value: F

value: Adrenocortical carcinoma


title: Apomictic_Plant5-Cy5

value: Vipond Park, Beaverhead


title: M3KO#1


title: ddm1 F6 inflorescence replicate 1

description: ddm1 F6

value: unopened flower buds

value: ddm1, F6 inbred generation


title: ACC84

description: Adrenocortical carcinoma

value: M


title: control - 0 h - 0 mM - nr2

tag: time

value: 0 h

tag: exposured to

value: none (unexposed control)


title: control - 0 h - 0 mM - nr3


title: WT#3

value: 7 months

value: colon tumor

value: wild type


title: WT#2


title: ACC82

description: Adrenocortical carcinoma

tag: Sex


title: wt Col inflorescence replicate 3

description: wt Col

source_name: wt Col inflorescence, unopened flower buds

value: wild type Col


title: wt Col inflorescence replicate 2

description: wt Col


title: WT#1

tag: age


title: Apomictic_Plant6-Cy3

value: B. lignifera

value: Apomictic

value: ES84/Map ID 74

value: UT

value: mixture of all 20 genotypes


title: ACC79

description: Adrenocortical carcinoma

value: F


title: Apomictic_Plant4-Cy5

value: B. divaricarpa

value: MT


title: Apomictic_Plant5-Cy3

value: Vipond Park, Beaverhead


title: ACC81

description: Adrenocortical carcinoma

value: Adrenocortical carcinoma


title: ACC76

description: Adrenocortical carcinoma


title: H3K79me3_NaCl_rep1

status: Public on Apr 06 2014

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110946_S01_ChIP_1010_Sep10

hyb_protocol: Labeled DNA was hybridized to the Yeast Whole Genome ChIP-on-chip Microarray (Agilent p/n G4491A, AMADID: 014741) according to manufacture instruction.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA)  following the Agilent protocol ChIP_1010_Sep10, grid template 014741_D_F_20091202  and the metric set ChIP_QCMT_Sep10.

data_processing: Agilent Feature Extraction Software (v10.10.1.1) was used for background subtraction and linear or lowess normalization.

organism: Saccharomyces cerevisiae

source_name: IP α-H3K79me3 (Abcam, 2621)

label_protocol: Labeling of DNA was obtained following the ‘Agilent Yeast ChIP-on-chip Analysis’ protocol Version 9.2 (Agilent Technologies, Palo Alto, California USA. p/n G4493-90010). 2000 ng of ChIP and reference samples were labeled respectively with Cyanine 5-dUTP and cyanine 3-dUTP using the ‘CGH Labeling Kit’ from Invitrogen (p/n 18095-011) according to the manufacturer’s instructions.

growth_protocol: Cells were grow exponentially in  rich medium (YPD)  to OD600 0.5-0.8.

extract_protocol: Chromatin immunoprecipitation was performed as previously described [Ren B, et al., 2000]. Briefly crosslinked cell pellets were resuspended in lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1mM PMSF, 1mM benzamidine and protease inhibitor cocktail from Roche) and lysed by vortexing at 4ºC by 45 min with glass beads. Chromatin was sonicated to 200–1000 bp (average of 400bp). Immunoprecipitation was carried for 4h using the specified Ab and 50 µL IgG M-280 Dynabeads. Beads were washed twice with lysis buffer, twice with 500 mM NaCl lysis buffer, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxycholate, 1 mM EDTA pH 8.0, 1 mM PMSF, 1 mM benzamidine and protease inhibitor cocktail from Roche), once with TE containing 1mM PMSF, and finally collected. Two successive elutions were performed with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubating 10 min at 65ºC. The eluted fraction was treated overnight at 65ºC to reverse the cross-linking. Proteins were degraded by proteinase K and DNA was purified by phenol/chloroform/isoamylic alcohol extraction. The sample as treated with RNAse A and purified. Ligation Mediated PCR was used for DNA amplification. Immunoprecipitated DNA was blunted by T4 phage DNA polymerase, phenol/chloroform/isoamylic alcohol extracted and ethanol precipitated. Sample was ligated to annealed linkers oJW102 and oJW103. The sample was PCR amplified and amplified size analyzed on a 1.2% agarose gel (average size of 150 bp).

treatment_protocol: Samples were  crosslinked with 1% formaldehyde for 30 min, quenched by adding glycine to a final concentration of 125 mM and washed three times with 30 mL of ice-cold PBS buffer. For saline stress samples, the cells were incubated with 0.4M NaCl for 10 min previous to the formaldehyde crosslink.

value: BY4742 strain

tag: antibody

tag: growth condition

value: 10 minutes after 0.4M NaCl stress

tag: normalization

value: Linear dye normalization

source_name: IP α-H3 (Abcam, 1791)


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 G183S, biological rep4

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Following fragmentation and labeling of 5.5 microgram of single strand DNA , the samples were hybridized for 17 hr at 45C on each Mouse Gene 1.0 ST arrays

scan_protocol: The arrays  were washed and stained in the Affymetrix 450 fluidics station. Then the GeneChips were scanned using Affymetrix GCS3000 7G scanner system.

data_processing: The data were analyzed with bioconductor, RMA and Partek Genomics Program Suite

source_name: J558 cell line

label_protocol: The Ambion® WT Expression Kit was used to generate sense strand cDNA from 100ng total RNA for subsequent fragmentation and labeling using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Cells were selected with puromycin after infection for 5-7 days, subsequently cells were sorted for GFP and IgM expression by FACS.

extract_protocol: Trizol used to extract RNA from J558 cell line transduced with MSCV-PIG constructs

value: J558 murine myeloma cells

tag: genotype/variation

value: Pax5 G183S mutant


title: Apomictic_Plant3-Cy3

organism: Boechera retrofracta x Boechera stricta

tag: ipk-plant id

tag: name

value: B. stricta x retrofracta

value: Mule Ranch


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 G183S, biological rep3


title: wt Col inflorescence replicate 1

description: wt Col

tag: tissue

value: unopened flower buds

value: wild type Col


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 G183S, biological rep2


title: ACC78

description: Adrenocortical carcinoma


title: Apomictic_Plant4-Cy3

tag: es numbera

tag: species

tag: reproduction

value: Apomictic


title: H3K4me1_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110949_S01_ChIP_1010_Sep10

source_name: IP α-H3K4me1 (Abcam, 8895)

tag: strain


title: H3K9ac_NaCl_rep2

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110548_S01_ChIP-v1_95_May07

source_name: IP α-H3K9ac (Upstate, 07-352)

value: IP α-H3K9ac (Upstate 06-942,lot 31636)


title: H3K9ac_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110943_S01_ChIP_1010_Sep10


title: H3K4me1_NaCl_rep2

description:
10 minutes after 0.4M NaCl stress - Lowess dye normalization
US45102947_251474110686_S01_ChIP-Low-alone

value: Lowess dye normalization


title: H3K14ac_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110546_S01_ChIP-v1_95_May07

source_name: IP α-H3K14ac (Upstate, 07-353)


title: control - 0 h - 0 mM - nr1

tag: cell line

value: ES-D3 (ATCC)

value: murine pluripotent embryonic stem cells (ESC)

value: 0 h

value: none (unexposed control)


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 WT, biological rep3

value: Pax5 WT


title: H3K4me3_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Lowess dye normalization
US45102947_251474110702_S01_ChIP-v1_Low alone_95

value: BY4742 strain


title: H3K36me3_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Lowess dye normalization
US45102947_251474110705_S01_ChIP_107_Sep09_Lowess

source_name: IP α-H3K36me3 (Abcam, 9050)

value: 10 minutes after 0.4M NaCl stress


title: Apomictic_Plant3-Cy5

tag: locality

tag: u.s. state

value: MT

tag: reference

value: mixture of all 20 genotypes


title: H3K79me2_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Lowess dye normalization
US45102947_251474110688_S01_ChIP-Low-alone

source_name: IP α-H3K79me2 (Abcam, 3594)


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 WT, biological rep2

value: J558 murine myeloma cells


title: H3K14ac_NaCl_rep2

description:
10 minutes after 0.4M NaCl stress - Linear dye normalization
US45102947_251474110945_S01_ChIP_1010_Sep10

value: Linear dye normalization


title: H3K79me3_YPD_rep1

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110944_S01_ChIP_1010_Sep10

value: exponential growth in YPD


title: Apomictic_Plant2-Cy3

organism: Boechera retrofracta

value: B. retrofracta

value: Ranch Creek


title: H3K79me2_YPD_rep1

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110687_S01_ChIP-Low-alone


title: Apomictic_Plant1-Cy3

value: B. polyantha

value: Apomictic

value: Birch Creek


title: J558 murine myeloma cells infected with MSCV-Puro-IRES-GFP (PIG) empty vector, biological rep3

value: control (empty vector)


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 WT, biological rep1


title: Apomictic_Plant1-Cy5


title: H3K4me3_YPD_rep1

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110707_S01_ChIP-v1_Low alone_95

source_name: IP α-H3K4me3 (Abcam, 8580)

value: Lowess dye normalization


title: J558 murine myeloma cells infected with MSCV-Puro-IRES-GFP (PIG) empty vector, biological rep2


title: H3K4me1_YPD_rep1

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110948_S01_ChIP_1010_Sep10


title: H4K8ac_YPD_rep2

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110696_S01_ChIP-v1_Low alone_95

source_name: IP α-H4K8ac (Abcam, 15823)


title: H3K4me1_YPD_rep2

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110684_S01_ChIP-Low-alone


title: H3K36me3_YPD_rep2

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110695_S01_ChIP-v1_Low alone_95


title: H3K36me3_YPD_rep1

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110703_S01_ChIP_107_Sep09_Lowess


title: CS_aspirin

status: Public on Apr 05 2014

city: Los Alamos

first: Chris

middle: J

last: Stubben

state: NM

address: MS M888

department: Bioscience Division

institute: Los Alamos National Lab

hyb_protocol: Hybridization followed standard Affymetrix procedures.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner.

data_processing: For each time course experiment, the samples were processed and normalized using RMA in the R affy package.

organism: Burkholderia thailandensis E264

source_name: CS salicylate

label_protocol: Microarray experiments were performed by the Genomics and Microarray Core at the University of Colorado, Denver in 2009.

extract_protocol: Total bacterial RNA for each experimental condition was extracted using the TRIzol method.

tag: medium

value: Calf serum

tag: temp °c

tag: ID


title: CS_antibiotic

description: carbenicillin (100 μg/ml), chloramphenicol (30 μg/ml), erythromycin (200 μg/ml, and kanamycin (50 μg/ml)

source_name: CS antbiotic


title: BHI_solid

source_name: BHI solid media

value: Brain heart


title: TS_wt

source_name: TS wt

value: Tryptic soy


title: TS_mut_KanR

description: spontaneous B. thailandensis mutant isolated in response to a sublethal exposure to kanamycin

source_name: TS kan


title: CS_37_rep2

source_name: CS 37°C


title: CS_37_rep1


title: Apomictic_Plant2-Cy5

source_name: pooled reference sample (mixture of different genotypes)


title: CS_EDTA_antibiotic

source_name: CS antibiotic + EDTA at 0.07g/L


title: CS_37_rep4


title: J558 murine myeloma cells infected with MSCV-PIG Pax5 G183S, biological rep1

value: Pax5 G183S mutant


title: LB_NaCl_rep1

source_name: LB high salt at 0.5M

value: Luria broth


title: H4K8ac_YPD_rep1

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110704_S01_ChIP_107_Sep09_Lowess

value: BY4742 strain

tag: antibody

tag: growth condition

value: IP α-H4 (Abcam 10158,lot GR 6858)


title: LB_H202_rep4

source_name: LB Peroxide


title: LB_NaCl_rep2


title: H3K14ac_YPD_rep2

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110947_S01_ChIP_1010_Sep10

tag: normalization

source_name: IP α-H3 (Abcam, 1791)


title: H3K14ac_YPD_rep1

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110545_S01_ChIP-v1_95_May07


title: H3K9ac_YPD_rep2

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110547_S01_ChIP-v1_95_May07

source_name: IP α-H3K9ac (Upstate, 07-352)

value: IP α-H3K9ac (Upstate 06-942,lot 31636)


title: H3K4me3_YPD_rep2

description:
exponential growth in YPD - Lowess dye normalization
US45102947_251474110761_S01_ChIP-Low-alone


title: H3K9ac_YPD_rep1

description:
exponential growth in YPD - Linear dye normalization
US45102947_251474110942_S01_ChIP_1010_Sep10

value: Linear dye normalization


title: LB_H202_rep1


title: LB_pH5_rep1

source_name: LB pH 5


title: LB_pH9_rep2

source_name: LB pH 9


title: LB_pH9_rep4


title: LB_pH5_rep4


title: LB_41_rep2

source_name: LB 41 °C


title: LB_pH5_rep2


title: LB_H202_rep2


title: LB_37_rep1

source_name: LB 37 °C


title: LB_41_rep3


title: LB_pH5_rep3


title: LB_H202_rep3


title: LB_37_rep4


title: LB_pH9_rep3


title: LB_25_rep4

source_name: LB 25 °C


title: LB_25_rep1


title: LB_pH9_rep1


title: LB_37_rep3


title: LB_41_rep4


title: LB_25_rep2


title: LB_25_rep3


title: LB_37_rep2


title: LB_41_rep1


title: M9_proline

source_name: M9 proline

value: M9 proline


title: M9_galactose

source_name: M9 galactose

value: M9 galactose


title: M9_glucose

source_name: M9 glucose at 25 °C

value: M9 glucose


title: CS_37_rep3


title: M9_ethanol

source_name: M9 +5% Ethanol

value: M9 succinate


title: M9_EDTA_limit

source_name: M9 EDTA with nutrient-limit (N, S, Mg)


title: J558 murine myeloma cells infected with MSCV-Puro-IRES-GFP (PIG) empty vector, biological rep1

source_name: J558 cell line

value: J558 murine myeloma cells

tag: genotype/variation


title: M9_EDTA

source_name: M9 EDTA at 0.07g/L


title: M9_bleach

source_name: M9 +200 ppm Bleach


title: M9_solid

source_name: M9 solid media


title: M9_low_Mg

source_name: M9 low Mg++ at 5 uM


title: M9_low_sulfur

source_name: M9 sulfur-limited at 0.02mM


title: M9_37_rep4

source_name: M9 37 °C


title: M9_37_rep2


title: M9_low_N

source_name: M9 nitrogen-limited


title: M9_high_Mg

source_name: M9 high Mg++ at 50 mM


title: M9_PO4

source_name: M9 phosphate at 70 mM


title: M9_37_rep1


title: M9_16_rep4

source_name: M9 16 °C


title: M9_N_CO2

source_name: Mp anaerobic N2 + CO2


title: H4K8ac_NaCl_rep1

description:
10 minutes after 0.4M NaCl stress - Lowess dye normalization
US45102947_251474110709_S01_ChIP_107_Sep09_Lowess

source_name: IP α-H4K8ac (Abcam, 15823)

value: 10 minutes after 0.4M NaCl stress


title: M9_phenol

source_name: M9 +0.1% phenol


title: M9_N

source_name: M9 anaerobic N2


title: M9_16_rep3


title: M9_16_rep1


title: PO4_t5_rep5

source_name: Phosphate limit, t5 at 20mM

tag: time since t0


title: M9_low_PO4

source_name: M9 phosphate at 40 mM


title: M9_16_rep2


title: PO4_t5_rep4


title: PO4_t5_rep1


title: PO4_t5_rep3


title: PO4_t4_rep4

source_name: Phosphate limit, t4 at 20mM


title: M9_37_rep3


title: PO4_t5_rep2


title: PO4_t4_rep3


title: PO4_t4_rep2


title: PO4_t3_rep2

source_name: Phosphate limit, t3 at 40mM


title: PO4_t4_rep1


title: PO4_t3_rep3


title: PO4_t1_rep3

source_name: Phosphate limit, t1 at 40mM


title: PO4_t4_rep5


title: PO4_t3_rep1


title: PO4_t2_rep4

source_name: Phosphate limit, t2 at 40mM


title: PO4_t2_rep2


title: PO4_t1_rep5


title: PO4_t3_rep4


title: PO4_t1_rep4


title: PO4_t2_rep5


title: PO4_t1_rep2


title: PO4_t1_rep1


title: PO4_t2_rep1


title: PO4_t3_rep5


title: PO4_t0_rep4

source_name: Phosphate limit, t0 at 80mM


title: PO4_t0_rep5


title: PO4_t0_rep3


title: PO4_t0_rep1


title: PO4_t0_rep2


title: salt_t4_rep4

source_name: Salt stress, t4 at 350mM

value: Nutrient broth


title: salt_t4_rep5


title: salt_t3_rep4

source_name: Salt stress, t3 at 350mM


title: PO4_t2_rep3


title: salt_t4_rep3


title: salt_t4_rep1


title: salt_t3_rep5


title: salt_t3_rep3


title: salt_t4_rep2


title: salt_t1_rep5

source_name: Salt stress, t1 at 350mM


title: salt_t3_rep2


title: salt_t2_rep1

source_name: Salt stress, t2 at 350mM


title: salt_t2_rep2


title: salt_t1_rep4


title: salt_t3_rep1


title: salt_t2_rep3


title: salt_t2_rep4


title: salt_t2_rep5


title: salt_t0_rep4

source_name: Salt stress, t0


title: salt_t1_rep3


title: salt_t0_rep5


title: salt_t1_rep1


title: salt_t0_rep3


title: C-BM-22

city: Izmir

first: Burak

last: Durmaz

address: Bornova

department: Medical Genetics

country: Turkey

institute: Ege University

hyb_protocol: According to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: The signal enhancement procedure was processed with Geniom Real Time Analyzer (GRTA) and detection pictures were evaluated by using Geniom Wizard Software. The signal intensities for all miRNAs were extracted from the raw data for each array. After background correction, the median signal intensity of the seven replicate intensity values of each miRNA was obtained. Normalization was conducted by using the freely available R software

source_name: RNA from bone marrow

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: After thawing 2.7 ml EDTA bone marrow was transferred into PAXgene Blood RNA Tubes (PreAnalytix GmbH) and total RNA was extracted using the miRNeasy kit (Qiagen GmbH).

treatment_protocol: Bone marrow sampling at ALL diagnosis (before treatment). Samples stored at -20 degree

tag: disease

value: healthy control

tag: gender

value: female

tag: year of birth


title: C-BM-20


title: C-BM-21

value: male


title: C-BM-23


title: C-BM-16


title: C-BM-17


title: C-BM-18


title: salt_t1_rep2


title: CC_B_rep3

city: Hefei

first: Dawei

state: Anhui

address: Huangshan Rd.

department: Life Sciences School

country: China

institute: USTC

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing: Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Intensity.xls. Normalization was performed using the Agilent GeneSpring GX v12.1 software.

source_name: bad quality embryo_CCs

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: embryo quality

value: bad quality

tag: tissue

value: oocytes at metaphase II stage

tag: cell type

value: Cumulus Cells


title: salt_t0_rep2


title: salt_t0_rep1


title: CC_A_rep3

source_name: good quality embryo_CCs

value: good quality


title: CC_B_rep2


title: CC_A_rep2


title: C-BM-15


title: C-BM-13


title: C-BM-14


title: C-BM-12


title: C-BM-09


title: C-BM-05


title: C-BM-08


title: ALL-BM-67

value: childhood acute lymphoblastic leukemia


title: ALL-BM-62


title: ALL-BM-63


title: ALL-BM-65


title: pH_t4_rep4

source_name: pH drop, t4 at pH 5


title: pH_t4_rep5


title: ALL-BM-61


title: pH_t4_rep3


title: pH_t4_rep2


title: pH_t3_rep3

source_name: pH drop, t3 at pH 4.5


title: ALL-BM-58


title: ALL-BM-60


title: Norm_ATF3KO_4

city: Cincinnati

first: Christopher

last: Karp

address: 3333 Burnet Ave

department: Molecular Immunology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression after 1 week in 4-OHT containing methylcellulose

hyb_protocol: Samples were hybridized to the SurePrint G3 Mouse GE 8x60K Microarray (AMADID 028005).

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner.

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE.txt files. Reading in the FE extraction files and extraction the median intensity values for each probe on the array. These intensities are not background corrected (this has been shown to only introduce noise), but are corrected for any scanner offset that was added to the original raw values. The dataset was filtered to remove positive control elements and any elements that have been flagged as outliers. Present (P), Marginal (M) or Absent (A) calls were made for each element on the array using in-house methodologies that take into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. The median green (Cy3) intensities were normalized between the arrays using the Quantile Normalization package in 'R' (Bolstad et al., 2003).

source_name: Norm_ATF3KO_bone marrow

label_protocol: Sample labeling and hybridization was performed according to the manufacturerÕs protocols using the One-Color Microarray-Based Gene Expression Analysis Manual (Low Input Quick Amp Version).

growth_protocol: Cells were flushed from tibias and femurs using cold HBSS with 0.1% BSA. Bone marrow cells were sorted by magnetic beads and RNA was isolated from the Ly6G+ fraction for microarray analysis.

extract_protocol: RNA was prepared using the Qiagen RNeasy kit following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer Lab-On-A-ChIP Agilent 6000 Series II (Agilent Technologies, Santa Clara, CA).

tag: strain background

value: ATF3 KO

value: bone marrow

value: Ly6G+ neutrophils


title: CC_B_rep1


title: ALL-BM-57


title: ALL-BM-55


title: pH_t3_rep2


title: Norm_ATF3WT_4

source_name: Norm_ATF3WT_bone marrow

value: WT


title: pH_t4_rep1


title: pH_t3_rep1


title: Norm_ATF3KO_1


title: Norm_ATF3KO_2


title: CC_A_rep1


title: Norm_ATF3WT_2


title: ALL-BM-52


title: ALL-BM-50


title: ALL-BM-51


title: Norm_ATF3WT_3


title: ALL-BM-45


title: ALL-BM-44


title: ALL-BM-53


title: ALL-BM-43


title: pH_t2_rep2

source_name: pH drop, t2 at pH 4.5


title: pH_t2_rep3


title: pH_t2_rep1


title: Norm_ATF3WT_1

description: Gene expression in unmanipulated


title: ALL-BM-42


title: ALL-BM-41


title: ALL-BM-47


title: ALL-BM-39


title: ALL-BM-46


title: pH_t1_rep4

source_name: pH drop, t1 at pH 4


title: ALL-BM-38


title: ALL-BM-35


title: ALL-BM-34


title: pH_t1_rep2


title: pH_t1_rep5


title: pH_t1_rep3


title: ALL-BM-33


title: pH_t0_rep5

source_name: pH drop, t0 at pH 9


title: CD4SP cells from LM, replicate2

city: Chicago

first: Rebecca

last: Mathew

state: IL

address: GCIS, 929 E 57th Street

institute: The University of Chicago

description: gene expression data from thymic CD4+ cells

hyb_protocol: Following fragmentation, 5 ug of biotin labeled cDNA was hybridized for 16 hr at 45C and 60 rpm on MG 430 2.0 array in an Affymetrix Hybridization Oven 640. Array was then washed and stained with steptavidin phycoerythrin in the GeneChip Fluidics Station 450 (Affymetrix,Inc).

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner  3000 7G

data_processing: CEL Intensity values were generated by Gene Chip Operating Software v.1.4 MicroArray Suite version 5.0 (Affymetrix) and scaled to an average intensity of 500.

source_name: mouse CD4SP thymocytes from LM replicate2

label_protocol: RNA of high integrity number (>9.7-10) was used for this study. Biotin labeled cRNA was generated and was processed to cDNA and amplified by WT-Ovation Pico RNA Amplification System (Nugen Technology)

growth_protocol: CD4 Cre-Cul3fl/fl (LM) and CD4 Cre+ Cul3fl/fl (KO) mice were in B6 background. All mice were raised in a specific pathogen-free environment at the University of Chicago and the experiments were performed in accordance with the guidelines of the Institutional Animal Care and use Committee

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

treatment_protocol: CD4 single positive thymocytes were sorted from LM or KO mice at 4C

value: CD4SP thymocytes

tag: genotype

value: CD4Cre-Cul3fl/fl (LM)

tag: genetic background


title: CD4SP cells from LM, replicate1

source_name: mouse CD4SP thymocytes from LM replicate1


title: ALL-BM-32


title: CD4SP cells from KO, replicate2

source_name: mouse CD4SP thymocytes from KO replicate2

value: CD4 Cre+Cul3fl/fl (KO)


title: pH_t0_rep3

tag: medium


title: pH_t1_rep1

tag: temp °c


title: pH_t0_rep1

tag: ID


title: ALL-BM-31


title: SCID_#525_Thymocytes DN3, biological rep4

city: North York

first: Yan Zhen

last: Zheng

address: 2075 Bayview Avenue

country: Canada

institute: Sunnybrook Research Institute

description: Gene expression from CD4& CD8 double negative; CD44 negative; CD25 positive thymocytes

hyb_protocol: Following Affymetrix protocol:Hybridization-EukGE-WS2v5 (GeneChip Gene Expression Experiment Report from TCAG, SickKids)

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix Expression Console MAS5.0 algorithm using Affymetrix default analysis settings, global scaling as normalization method (scaling factor 150)

source_name: SCID_Mouse #525_Thymocytes DN3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip Gene Expression Experiment Report from TCAG, SickKids).

growth_protocol: Mice were bred and maintained under pathogen-free conditions and monitored daily

treatment_protocol: Single cell suspensions of 6-8wks murine thymi were prepared in D-PBS containing 0.5% BSA (FACS buffer). CD25-APC (Clone PC61.5 dilution 1:300), CD44-PE (Clone IM7 1:200), CD4-PE-Cy7 (Clone RM4-5 dilution 1:200), CD8-APC-Cy7 (Clone: 53-6.7 1:200) were used to sort cells into stage DN1, DN2, and DN3.

value: thymocytes

value: HOX11 negative, B220 & CD3 negative

tag: age

value: 6~8 weeks

value: outbred ICR


title: CD4SP cells from KO, replicate1

source_name: mouse CD4SP thymocytes from KO replicate1


title: pH_t0_rep4

value: Nutrient broth


title: Norm_ATF3KO_3


title: SCID_#525_Thymocytes DN2, biological rep4

description: Gene expression from CD4& CD8 double negative; CD44 positive; CD25 positive thymocytes

source_name: SCID_Mouse #525_Thymocytes DN2

value: female


title: SCID_#525_Thymocytes DN1, biological rep4

description: Gene expression from CD4& CD8 double negative; CD44 positive; CD25 negative thymocytes

source_name: SCID_Mouse #525_Thymocytes DN1


title: temp_t4_rep5

source_name: Temperature shift, t4


title: ALL-BM-30

source_name: RNA from bone marrow

value: male


title: ALL-BM-29


title: temp_t4_rep4


title: HOXSCID_#535_Thymocytes DN2, biological rep4

source_name: HOXSCID_Mouse #535_Thymocytes DN2

value: HOX11 positive, B220 & CD3 negative


title: pH_t0_rep2


title: HOXSCID_#535_Thymocytes DN3, biological rep4

source_name: HOXSCID_Mouse #535_Thymocytes DN3


title: ALL-BM-28


title: ALL-BM-27


title: temp_t4_rep3


title: HOXSCID_#999_Thymocytes DN3, biological rep3

source_name: HOXSCID_Mouse #999_Thymocytes DN3


title: ALL-BM-26


title: HOXSCID_#535_Thymocytes DN1, biological rep4

source_name: HOXSCID_Mouse #535_Thymocytes DN1


title: temp_t4_rep1


title: temp_t4_rep2


title: HOXSCID_#999_Thymocytes DN1, biological rep3

source_name: HOXSCID_Mouse #999_Thymocytes DN1


title: ALL-BM-25


title: HOXSCID_#999_Thymocytes DN2, biological rep3

source_name: HOXSCID_Mouse #999_Thymocytes DN2


title: temp_t3_rep4

source_name: Temperature shift, t3


title: temp_t3_rep5


title: SCID_#686_Thymocytes DN3, biological rep3

source_name: SCID_Mouse #686_Thymocytes DN3


title: ALL-BM-23


title: SCID_#686_Thymocytes DN1, biological rep3

source_name: SCID_Mouse #686_Thymocytes DN1


title: SCID_#686_Thymocytes DN2,  biological rep3

source_name: SCID_Mouse #686_Thymocytes DN2


title: HOXSCID_#20_Thymocytes DN3, biological rep2

source_name: HOXSCID_Mouse #20_Thymocytes DN3


title: ALL-BM-18


title: temp_t3_rep3


title: temp_t3_rep2


title: ALL-BM-20


title: ALL-BM-17


title: temp_t3_rep1


title: HOXSCID_#20_Thymocytes DN1, biological rep2

source_name: HOXSCID_Mouse #20_Thymocytes DN1


title: ALL-BM-14


title: HOXSCID_#20_Thymocytes DN2, biological rep2

source_name: HOXSCID_Mouse #20_Thymocytes DN2


title: SCID_#50_Thymocytes DN3, biological  rep2

source_name: SCID_Mouse #50_Thymocytes DN3


title: ALL-BM-09


title: temp_t2_rep4

source_name: Temperature shift, t2


title: SCID_#50_Thymocytes DN2, biological rep2

source_name: SCID_Mouse #50_Thymocytes DN2


title: temp_t2_rep5


title: temp_t2_rep3


title: SCID_#50_Thymocytes DN1, biological rep2

source_name: SCID_Mouse #50_Thymocytes DN1


title: ALL-BM-07

source_name: RNA from bone marrow


title: SCID_#687_Thymocytes DN3, biological rep1

source_name: SCID_Mouse #687_Thymocytes DN3


title: ALL-BM-08


title: temp_t2_rep2


title: SCID_#687_Thymocytes DN2, biological rep1

source_name: SCID_Mouse #687_Thymocytes DN2


title: ALL-BM-04


title: SCID_#687_Thymocytes DN1, biological rep1

source_name: SCID_#687_Mouse Thymocytes DN1


title: saliva_IA20

city: Cambridge

first: Christina

middle: A

last: Eichstaedt

address: Fitzwilliam Street

department: Biological Anthropology

institute: University of Cambridge

description: Intermediate altitude sample

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

source_name: 1 ml saliva, lysed

growth_protocol: Saliva mixed with equal volume of lysis buffer (Quinque et al. 2006) to allow storage at room temperature

extract_protocol: Qiagen DNA Investigator Kit scaled up for 2 ml buffer-saliva mixture

treatment_protocol: Storage at room temperature for 2 weeks, 1-3 weeks at 4°C, centrifugation

tag: sampling location

value: Cachi, Argentina


title: saliva_IA22

description: Intermediate altitude sample


title: temp_t2_rep1


title: saliva_IA21

description: Intermediate altitude sample


title: ALL-BM-01

value: childhood acute lymphoblastic leukemia


title: saliva_IA24

description: Intermediate altitude sample


title: saliva_IA18

description: Intermediate altitude sample


title: temp_t1_rep4

source_name: Temperature shift, t1


title: temp_t1_rep5


title: saliva_IA23

description: Intermediate altitude sample


title: saliva_IA15

description: Intermediate altitude sample


title: saliva_IA16

description: Intermediate altitude sample


title: saliva_IA12

description: Intermediate altitude sample


title: HOXSCID_#19_Thymocytes DN3, biological  rep1

source_name: HOXSCID_Mouse #19_Thymocytes DN3


title: saliva_IA13

description: Intermediate altitude sample


title: temp_t1_rep3


title: saliva_IA17

description: Intermediate altitude sample


title: temp_t1_rep2


title: Normal ovary, rep 2

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans St. CRB-II, Room 305

institute: Johns Hopkins University School of Medicine

description:
O175
Replicate 2 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were background subtracted, quantile normalized, and log2 transformed using neqc function in limma package in R.

source_name: Mouse ovary

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit and cleaned-up with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain/background

value: mixed C57BL/6;BALB/c;129

value: Arid1a flox/flox;Pten flox/flox

tag: ovarian bursal injection

value: ovary


title: Normal ovary, rep 3

description:
O177
Replicate 3 of 4.

tag: genotype/variation


title: Het GMP, biological rep2

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from adult BM progenitors

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

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Arraystar version 4 (DNAStar) software with Robust Multichip Analysis ( RMA).

source_name: Mouse bone marrow GMP

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system

extract_protocol: NucleoSpin RNA XS kit (Macherey-Nagel)

value: Vav1-iCre x Cbfb(F/+)

value: GMP

tag: mouse genetic background

value: C57BL6 N12 backcrossed


title: Normal ovary, rep 1

description:
O173
Replicate 1 of 4.


title: temp_t1_rep1

tag: time since t0


title: Normal ovary, rep 4

description:
O176
Replicate 4 of 4.


title: saliva_IA10

description: Intermediate altitude sample

tag: gender


title: KO GMP, biological rep2

value: Vav1-iCre x Cbfb(F/F)


title: HOXSCID_#19_Thymocytes DN1, biological  rep1

source_name: HOXSCID_Mouse #19_Thymocytes DN1

value: thymocytes


title: Control ME (Cy5) x Treatment IE (Cy3)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of 6 wks ME vs IE rat hippocampi Pool 2

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner G2505C

data_processing: Software: Feature Extraction ver 9.5.3.1

organism: Rattus norvegicus

source_name: Treatment IE 6wks Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Eleven-week-old male Wistar rats (220-270 g; SLC, Saitama, Japan) were housed in polycarbonate steel cages with a 12-h light/dark schedule (lights on at 7:00 a.m.) and given ad libitum access to food and water.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Control ME 6 wks, Treatment IE 6 wks

value: Hippocampus

tag: strain

value: Wistar

source_name: Control ME 6 wks Cy5


title: KO GMP, biological rep1


title: HOXSCID_#19_Thymocytes DN2, biological  rep1

source_name: HOXSCID_Mouse #19_Thymocytes DN2

value: 6~8 weeks

value: outbred ICR


title: temp_t0_rep5

source_name: Temperature shift, t0

value: Nutrient broth


title: Het GMP, biological rep1


title: Control ME (Cy3) x Treatment IE (Cy5)

description: Dye-swap (Cy3/Cy5) of 6 wks ME vs IE rat hippocampi Pool 1

source_name: Control ME 6wks Cy3

tag: tissue

source_name: Treatment IE 6 wks Cy5


title: saliva_IA11

description: Intermediate altitude sample

organism: Homo sapiens

value: female


title: saliva_IA9

description: Intermediate altitude sample


title: KO LSK, biological rep2

organism: Mus musculus

source_name: Mouse bone marrow LSK

tag: cell type

value: LSK


title: temp_t0_rep4


title: saliva_IA14

description: Intermediate altitude sample

value: male

value: Cachi, Argentina


title: temp_t0_rep3


title: Ovarian tumor, rep 5

description:
T293
Replicate 5 of 5.

source_name: Mouse ovarian tumor

value: mixed C57BL/6;BALB/c;129

value: AdCre

value: ovarian tumor


title: Ovarian tumor, rep 3

description:
T976
Replicate 3 of 5.

value: Arid1a flox/flox;Pten flox/flox


title: saliva_IA8

description: Intermediate altitude sample


title: Het LSK, biological rep2

value: Vav1-iCre x Cbfb(F/+)


title: Control Sedentary (Cy5) x Treatment ME (Cy3)

description: Dye-swap (Cy5/Cy3) of 6 wks ME rat hippocampi Pool 2

scan_protocol: Scanner: Agilent DNA microarray Scaner G2505B

source_name: Treatment ME Cy3

treatment_protocol: Control Sedentary 6 wks, Treatment ME 6 wks, Treatment IE 6 wks

source_name: Control Cy5


title: Control Sedentary (Cy3) x Treatment IE (Cy5)

description: Dye-swap (Cy3/Cy5) of 6 wks IE rat hippocampi Pool 1

source_name: Control Cy3

source_name: Treatment IE Cy5


title: Control Sedentary (Cy5) x Treatment IE (Cy3)

description: Dye-swap (Cy5/Cy3) of 6 wks IE rat hippocampi Pool 2

source_name: Treatment IE Cy3


title: KO LSK, biological rep1

value: C57BL6 N12 backcrossed


title: Ovarian tumor, rep 4

description:
T287
Replicate 4 of 5.


title: temp_t0_rep1


title: Het LSK, biological rep1


title: saliva_IA5

description: Intermediate altitude sample

scan_protocol: standard Illumina protocol

source_name: 1 ml saliva, lysed


title: temp_t0_rep2


title: Ovarian tumor, rep 2

description:
T50
Replicate 2 of 5.


title: saliva_IA6

description: Intermediate altitude sample


title: SW620_100 μg/mL_48h_Replicate2

status: Public on Apr 04 2014

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

description: Treated - 100 μg/mL

hyb_protocol: Hybridization was performed in an Agilent G4112F platform (Whole Human Genome Microarray 44k, AMADID 14850) using the One-Color gene expression system (Agilent Technologies) according to the manufacturer’s instructions. These microarrays contain around 41,000 human genes and transcripts with one 60-mer oligonucleotide probe representing each sequence.

scan_protocol: Arrays were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

data_processing: Microarray data were extracted with Feature Extraction Software version 10.7 (Agilent Technologies)

source_name: SW620, 100 μg/mL, 48h, Replicate2

label_protocol: cRNA was labelled with cyanine-3 (Cy3) for hybridization in an Agilent platform, according to the manufacturer’s instructions.

growth_protocol: Cells were cultured under standard conditions of temperature (37ºC), humidity (95%) and carbon dioxide (5%).

extract_protocol: Total RNA was extracted with the RNEasy kit (Qiagen, Valencia, CA) following the manufacturer's instructions. RNA quality control was performed in a 2100 Bioanalyzer (Agilent Technologies). In all cases, RNA integrity number was above 8.

treatment_protocol: Supercritical rosemary extract was added to colon cancer cells in culture following overnight attachment and incubated for 48h.

value: colon cancer

tag: tumor type

value: adenocarcinoma

tag: treatment

value: 100 μg/mL


title: saliva_IA19

description: Intermediate altitude sample

hyb_protocol: standard Illumina protocol

label_protocol: standard Illumina protocol


title: Ovarian tumor, rep 1

description:
T375
Replicate 1 of 5.


title: SW620_60 μg/mL_48h_Replicate2

description: Treated - 60 μg/mL

source_name: SW620, 60 μg/mL, 48h, Replicate2

value: 60 μg/mL


title: saliva_IA4

description: Intermediate altitude sample


title: saliva_IA3

description: Intermediate altitude sample


title: SW620_0 μg/mL_48h_Replicate2

description: Control

source_name: SW620, 0 μg/mL, 48h, Replicate2


title: Control Sedentary (Cy3) x Treatment ME (Cy5)

description: Dye-swap (Cy3/Cy5) of 6 wks ME rat hippocampi Pool 1

value: Hippocampus

value: Wistar

source_name: Treatment ME Cy5


title: saliva_IA7

description: Intermediate altitude sample


title: SW620_30 μg/mL_48h_Replicate2

description: Treated - 30 μg/mL

source_name: SW620, 30 μg/mL, 48h, Replicate2

value: 30 μg/mL


title: SW620_30 μg/mL_48h_Replicate1

description: Treated - 30 μg/mL

source_name: SW620, 30 μg/mL, 48h, Replicate1


title: SW620_60 μg/mL_48h_Replicate1

description: Treated - 60 μg/mL

source_name: SW620, 60 μg/mL, 48h, Replicate1


title: SW620_100 μg/mL_48h_Replicate1

description: Treated - 100 μg/mL

source_name: SW620, 100 μg/mL, 48h, Replicate1


title: U1810 untreated, replicate 1

city: Stockholm

first: Lovisa

last: Lundholm

address: Karolinska Biomics Center Z5:01

department: Department of Oncology-Pathology

institute: Karolinska Institutet

description:
Untreated 1
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), untreated replicate 1.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000.

data_processing: Data processing was done through Affymetrix® GeneChip® Command Console® Software (AGCC) v 1.1 and downstream analysis was performed by Affymetrix Expression Console (EC) v 1.1. Probe logarithmic intensity error estimation (PLIER) was used to enhance probe signals by summarization, perfect match GC composition-based background correction (PM GCBG) was applied for background correction and global median to normalize the signals. For further analysis, genes with signal intensity below 10 after background correction were excluded to avoid taking genes whose alterations are not easily distinguished from noise into subsequent analyses. In addition, genes corresponding to uncharacterized proteins, hypothetical proteins prefixed with the letters LOC, and small nucleolar RNAs (SNORD) were also excluded from the analysis since in this study we aimed to focus on well annotated, protein-coding mRNAs. Due to variation between replicates, each experiment was compared to its control (Cisplatin 1 vs. Untreated 1, etc.)

source_name: U1810 residual clones 9 days after 1 h with no treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: U1810 cells were seeded at a density of 500 cells per plate the day before treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up by RNeasy mini kit (Qiagen).

treatment_protocol: The cells were treated with cisplatin for 1 hour, washed with PBS, and then grown in growth media for 9 days (media was replaced at day 5).

tag: cell line

value: Non-small cell lung carcinoma (NSCLC) cells


title: U1810 untreated, replicate 3

description:
Untreated 3
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), untreated replicate 3.


title: U1810 cisplatin, replicate 1

description:
Cisplatin 1
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), 1 h cisplatin replicate 1.

source_name: U1810 residual clones 9 days after 1 h of cisplatin (10 µM)

value: cisplatin


title: SW620_0 μg/mL_48h_Replicate1

description: Control

source_name: SW620, 0 μg/mL, 48h, Replicate1


title: megakaryocyte_ serotonin treated_24hrs_rep4

city: Little rock

first: fusun

last: kilic

state: AR

address: 4301 West Markham Street, Mail Slot 516,

department: Biochemistry

institute: UAMS

description: CD41+ cells selected

data_processing: The data were normalised using median after log transformation with IlluminaGUI in R

source_name: bone marrow_megakaryocytes

label_protocol: Biotin-cRNA was prepared from high quality total RNA samples with the TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina System (Epicentre Biotechnologies).

growth_protocol: Adult C57BL/6J male mice, 10-12 weeks old, body weight 25-30 grams. Animals were maintained in rooms at 24°C with 40% humidity and a 12 hour light/dark cycle and were provided food and water adlibitum until used.

extract_protocol: Femurs were removed and dissected from anesthetized mice and marrow cells were collected in MK buffer. Bone marrow cells were pooled (n=3-4 mice per sample) and enriched using Percoll gradient. After washing, the cellls were incubated with a monoclonal anti-mouse antibody directed against teh platelet glycoprotein IIb (CD41+) and suspended with the immunomagnetic beads coated with sheep anti-mouse IgG antibody. This isolation technique yields at least 96.6% pure MKs. Immunomagnetic beads bound to MK cells were dissolved in RTL lysis buffer from Qiagen and sonicated briefly. The beads were separated from the supernatant usign a magnet and total RNA was isolated using a Qiagen isolation kit as per manufacturer's protocol. Purified RNA was checked for integrity and quantified using a Pico Total RNA kit and the Agilent 2100 BioAnalyzer.

treatment_protocol: Osmotic pumps were implanted subcutaneously between the scapulae of the anesthetized mice using isofluorane (2.5% at 1.5 L/min oxygen). Animals were infused with 25.8 mM 5-HT (Sigma) by means of Alzet minipumps (model 1003D, at a rate of 1.66 ug/kg/hr over 24 hours. This treatment results in the plasma blood level of approximately 231 ng/ml which was verified by ELISA.

value: male

value: serotonin

value: bone marrow megakaryocytes


title: megakaryocyte_saline treated_24hrs_rep2

description: CD41+ cells selected

value: saline


title: U1810 cisplatin, replicate 3

description:
Cisplatin 3
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), 1 h cisplatin replicate 3.


title: U1810 untreated, replicate 2

description:
Untreated 2
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), untreated replicate 2.


title: megakaryocyte_ serotonin treated_24hrs_rep3

description: CD41+ cells selected


title: megakaryocyte_saline treated_24hrs_rep1

description: CD41+ cells selected


title: megakaryocyte_ serotonin treated_24hrs_rep1

description: CD41+ cells selected


title: megakaryocyte_saline treated_24hrs_rep3

description: CD41+ cells selected


title: megakaryocyte_ serotonin treated_24hrs_rep2

description: CD41+ cells selected


title: BMMs, untreated control, ko, Replicate 3

city: Vienna

first: Claus

last: Vogl

state: Vienna

address: Veterinaerplatz 1

department: Biomedical Sciences

country: Austria

institute: University of Veterinary Medicine, Vienna

hyb_protocol: Labeled samples were loaded and hybridized to GeneChip® Mouse Gene 1.0 ST Arrays for 16 hours over night at 45°C according to the manufacturer’s instructions rotating in a hybridization oven.

scan_protocol: Arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix protocols. Arrays were scanned with the GeneChip Scanner GCS3000.

data_processing: For generation of probe set expression values, CEL files containing probe level data were normalized using the robust multi-chip average (RMA) algorithm (including background correction, quantile normalization across all arrays, median polished summarization based on log transformed expression values) implemented in the Partek Software v.6.5 (Partek Inc, St Louis, MO).

source_name: BMMs_untreated control_ko

label_protocol: Fragmentation and labeling was performed using the GeneChip® WT Terminal Label & Controls Kit (Affymetrix, London) according to the manufacturer’s instructions.

growth_protocol: Bone marrow derived macrophages were cultivated as described in PMID 11070173.

extract_protocol: Total RNA was isolated according to the manufacturer's instructions (peqGOLDTriFast, PEQLAB). 100ng of total RNA was used for reverse transcription, cDNA synthesis and purification according to the manufacturer’s instructions (AmbionWT Expression Kit; Life Technologies; Carlsbad, California)

treatment_protocol: Recombinant mouse IFNγ was purchased from Calbiochem (Merck4Biosciences, Germany) and used at concentrations of 100 U/ml. The Listeria monocytogenes EGD strain (kindly provided by Thomas Decker from the MFPL, University of Vienna, Austria) was i.p. injected.

tag: strain background

value: Stat1 KO (ko)

value: Bone marrow derived macrophages (BMMs)

tag: treated with

value: none (untreated control)


title: U1810 cisplatin, replicate 2

description:
Cisplatin 2
Gene expression data from pooled surviving clones from NSCLC cell line (U-1810), 1 h cisplatin replicate 2.


title: BMMs, untreated control, db, Replicate 3

source_name: BMMs_untreated control_db

value: Stat1 delta beta (db)


title: BMMs, untreated control, da, Replicate 3

source_name: BMMs_untreated control_da

value: Stat1 delta alpha (da)


title: BMMs, untreated control, wt, Replicate 3

source_name: BMMs_untreated control_wt

value: Sta1 Wildtype (wt)


title: BMMs, untreated control, db, Replicate 1


title: BMMs, untreated control, ko, Replicate 2


title: BMMs, untreated control, da, Replicate 2


title: BMMs, untreated control, ko, Replicate 1


title: saliva_IA1

description: Intermediate altitude sample

source_name: 1 ml saliva, lysed

value: female

value: Cachi, Argentina


title: saliva_IA2

description: Intermediate altitude sample


title: BMMs, untreated control, db, Replicate 2


title: BMMs, untreated control, da, Replicate 1


title: BMMs, 6h IFNg, wt, Replicate 3

source_name: BMMs_6h IFNg_wt

value: 6h IFNg


title: BMMs, untreated control, wt, Replicate 2


title: BMMs, untreated control, wt, Replicate 1


title: BMMs, 6h IFNg, wt, Replicate 2


title: BMMs, 6h IFNg, db, Replicate 3

source_name: BMMs_6h IFNg_db


title: BMMs, 6h IFNg, ko, Replicate 2

source_name: BMMs_6h IFNg_ko


title: BMMs, 6h IFNg, da, Replicate 3

source_name: BMMs_6h IFNg_da


title: BMMs, 6h IFNg, ko, Replicate 3


title: BMMs, 6h IFNg, db, Replicate 1


title: BMMs, 24h IFNg, wt, Replicate 3

source_name: BMMs_24h IFNg_wt

value: 24 h IFGg


title: BMMs, 6h IFNg, db, Replicate 2


title: BMMs, 6h IFNg, wt, Replicate 1


title: BMMs, 6h IFNg, ko, Replicate 1


title: BMMs, 6h IFNg, da, Replicate 2


title: BMMs, 6h IFNg, da, Replicate 1


title: BMMs, 24h IFNg, ko, Replicate 3

source_name: BMMs_24h IFNg_ko


title: BMMs, 24h IFNg, db, Replicate 3

source_name: BMMs_24h IFNg_db


title: BMMs, 24h IFNg, da, Replicate 3

source_name: BMMs_24h IFNg_da


title: BMMs, 24h IFNg, ko, Replicate 2


title: BMMs, 24h IFNg, wt, Replicate 2


title: BMMs, 24h IFNg, da, Replicate 2


title: BMMs, 6h IFNg + Lis, wt, Replicate 3

source_name: BMMs_6h IFNg + Lis_wt

value: 6h IFNg + Listeria monocytogenes (Lis)


title: BMMs, 6h IFNg + Lis, ko, Replicate 3

source_name: BMMs_6h IFNg + Lis_ko


title: BMMs, 6h IFNg + Lis, db, Replicate 2

source_name: BMMs_6h IFNg + Lis_db


title: BMMs, 6h IFNg + Lis, da, Replicate 3

source_name: BMMs_6h IFNg + Lis_da


title: BMMs, 6h IFNg + Lis, ko, Replicate 2


title: BMMs, 24h IFNg, db, Replicate 2


title: BMMs, 24h IFNg, db, Replicate 1


title: BMMs, 24h IFNg, da, Replicate 1


title: BMMs, 24h IFNg, ko, Replicate 1


title: BMMs, 6h IFNg + Lis, db, Replicate 3


title: BMMs, 6h IFNg + Lis, da, Replicate 2


title: BMMs, 6h IFNg + Lis, wt, Replicate 1


title: BMMs, 6h IFNg + Lis, db, Replicate 1


title: BMMs, 6h IFNg + Lis, ko, Replicate 1


title: BMMs, 24h IFNg, wt, Replicate 1


title: BMMs, 6h IFNg + Lis, da, Replicate 1


title: ahl16 vs. Col, replicate 2

city: Shanghai

first: Zhong-Nan

last: Yang

address: Shanghai Guilin Road No.100

institute: Shanghai Normal University

description: Biological replicate 2 of 3.

hyb_protocol: Each Agilent-021169 slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent Technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent Technologies, Santa Clara, CA, US), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent Technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent Technologies, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent Technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Lowess (locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: Inflorescence of ahl16

label_protocol: Total RNA were amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent Technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE Healthcare Biosciences, Pittsburgh, PA, US), Cy5 NHS ester (Cat#PA15100, GE Healthcare Biosciences, Pittsburgh, PA, US) following the manufacture's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Arabidopsis, ecotype Columbia-0, was the source of both the wild-type and mutant plants. Plants were grown under long-day conditions (16-hour of light / 8-hour of dark) in a growth room at approximately 22°C.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

tag: ecotype

value: ahl16 mutant

value: bud

tag: developmental stage

value: closed buds (before flower stage 12)

source_name: Inflorescence of Col-0

value: wild type


title: ahl16 vs. Col, replicate 1

description: Biological replicate 1 of 3.


title: SCD_1

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

description: Gene expression data from pre-adipocytes from mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 20 hr at 48C on MoGene 1.1 ST arrays. GeneChips were washed and stained in the Gene Atlas Fluidics Station.

scan_protocol: MoGene 1.1 ST arrays were scanned using the Gene Atlas Imaging Station.

data_processing: The data was analyzed using R/Bioconductor and  normalized using the RMA method. An ANOVA was used to identify differentially expressed genes. A FDR of 0.05 was used to account for multiple testing.

source_name: Pre-adipocytes treated with SCD inhibitor (SDCinhib), replicate 1

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol using 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: 7 day differentiation, induced by isobutylmethylxanthine, dexamethasone and human insulin for 2 days, and differentiation was maintained with human insulin

extract_protocol: Total RNA was extracted on day 7 of differentiation using the Qiagen Rneasy Mini Kit (Qiagen, Mississauga, ON, Canada) according to manufacturer's instruction

treatment_protocol: Throughout differentiation cells were treated with either 1 µM of a commercially available SCD inhibitor or an equivalent volume of DMSO (control condition)

value: pre-adipocyte

value: SCD inhibitor


title: BMMs, 6h IFNg + Lis, wt, Replicate 2


title: SCD_2

source_name: Pre-adipocytes treated with SCD inhibitor (SDCinhib), replicate 2


title: DMSO_1

source_name: Pre-adipocytes maintained in DMSO (control), replicate 1

value: DMSO


title: SCD_3

source_name: Pre-adipocytes treated with SCD inhibitor (SDCinhib), replicate 3


title: DMSO_4

source_name: Pre-adipocytes maintained in DMSO (control), replicate 4


title: DMSO_3

source_name: Pre-adipocytes maintained in DMSO (control), replicate 3


title: DMSO_2

source_name: Pre-adipocytes maintained in DMSO (control), replicate 2


title: ahl16 vs. Col, replicate 3

description: Biological replicate 3 of 3.


title: cbs+/- HM vs WT - repeat 1 - mAdbID:94888

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

description: mAdb experiment ID: 94888

hyb_protocol: Hybridization of cDNA to mouse oligonucleotide slides (National Cancer Institute, Frederick, MD) was performed in triplicate at 43°C for 16 hours.

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [81987] ScanPower: 100;; 100 LaserPower: 1.95;; 3.55 Temperature: 20.53

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: cbs+/- HM

label_protocol: Cy3 Labeling Protocol: Total RNA was used to synthesize cDNA probes (FairPlay Microarray labeling kit; Stratagene, La Jolla, CA). These probes were labeled with Cy3 monofunctional reactive dye (Amersham Bioscience, Piscataway, NJ).

treatment_protocol:
Treatment type: compound
Agent: Methionine
Treatment dose: 0.5%
Treatment time: 5 weeks
In-vivo treatment: Mice were fed a special rodent diet (Teklad no. 8604; Harlan Laboratories, Indianapolis, IN) and given tap water ad libitum. To generate cbs+/- high-methionine mice (cbs+/- HM), cbs+/- mice were given tap water containing methionine (final concentration, 0.5%) starting from the weaning period. Wild type mice (cbs+/+) were also given tap water containing methionine (final concentration, 0.5%) starting from the weaning period.

tag: age

value: 5 weeks

value: neural retinas

source_name: cbs+/+ WT

label_protocol: Cy5 Labeling Protocol: Total RNA was used to synthesize cDNA probes (FairPlay Microarray labeling kit; Stratagene, La Jolla, CA). These probes were labeled with Cy5 monofunctional reactive dye (Amersham Bioscience, Piscataway, NJ).


title: cbs+/- HM vs WT - repeat 2 - mAdbID:94889

description: mAdb experiment ID: 94889

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [81987] ScanPower: 100;; 100 LaserPower: 2.08;; 3.54 Temperature: 21.66


title: cbs+/- HM vs WT - repeat 3 - mAdbID:94890

description: mAdb experiment ID: 94890

scan_protocol: Creator: GenePix Pro 4.1.1.4 Scanner: GenePix 4000B [81987] ScanPower: 100;; 100 LaserPower: 2.01;; 3.54 Temperature: 22.36


title: EC3b

city: Singapore

first: Shugui

last: Wang

address: Biopolis Way, Matrix

country: Singapore

institute: Danone Nutricia research

description: bacteria are from Infant stool

hyb_protocol: Hybridization were done using GEArray S Series Human Immunology Signaling Pathways Gene Array kit. In summary, before pre-hybridization, membranes were pre-wet by adding roughly 5ml of deionized water to the hybridization tube. Warm the GEAhyb Hybridization Solution (in the kit) to 60°C, and then add 2ml of the GEAhyb Hybridization Solution into each tube. The membranes were then pre-hybridized in the oven at 60°C for 24h with continuous agitation at 5-10rpm.  The hybridization step was done according to the manufacture’s instruction. The target hybridization solution was prepared by adding 5µg of biotin labeled cRNA to 1ml of prewarmed GEAhyb Hybridization solution. The solution was then mixed well by pipetting and kept at 60°C till use. The pre-hybridization solution from the hybridization tube was discarded and the Target Hybridization Mix was added into the membrane in the hybridization tube. The membranes were then hybridized overnight at 60°C with continuous agitation (5-10rpm). After hybridization, the Target Hybridization Mix was poured off. The membranes were washed by Wash Solution 1 (2x SSC, 1%SDS) 10min twice at 60°C and Wash Solution 2 (0.1x SSC, 0.5%SDS) 7min twice at 60°C with 20-30 rpm agitation.

scan_protocol: The signals were then detected using Chemiluminenscent detection Kit (Superarray, USA) according to the manufacture’s instruction. Image were acquired by exposing to X-ray film (Koda, USA), the images were then scanned using image scanner (Amersham, UK) and analyzed.

data_processing: The signals were analyzed using the web-based GEArray Expression Analysis Suite (Supperarray, US); Empty spots: positions 399, 398, 400; internal control spots: positions 411, 412, 413, 414, 415, 416

source_name: E.faecalis EC3 replicate 2

label_protocol: cDNA was synthesized using AmpoLabeling-LPR Kit. Briefly, Briefly, 1.5µg of total RNA was used for constructing the cDNA. RNA was mixed with 1µl RT primer and appropriate RNase free H2O to get a total volume of 10µl.  The contents were mixed well by gentle pipetting up and down 2 to 3 times followed by a brief centrifugation to collect the mixture at the bottom of the tube. The mixture was then incubated at 70°C for 3min followed by a brief centrifugation. Tubes were placed on ice immediately and kept at 37°C for 10min.  The cDNA Synthesis Master Mix was mixed well and put on ice for use. For each array, transfer 10µl of the cDNA Synthesis Master Mix to the 10µl Annealing Mixture. They were mixed well but gently with a pipetting up and down 2 to 3 times followed by a brief centrifugation to collect the mixture at the bottom of the tube. The mixtures were then continued to be incubated at 37°C for 25min.  After that, they were heated at 85°C for 5min to hydrolyze the RNA and to inactivate the reverse transcriptase. The finished RT Reactions were then held on ice until the next step. For each array, add 30µl of the LPR Cocktail to each RT reaction (20µl) and mixed well but gently with a pipettor. Before denaturing the probes for hybridization, the incorporation efficiency of dUTP with probe was checked according to the manufacture’s instruction (Superarray, USA).  The labeled cDNA probes were then denatured by heating the tube containing the LPR at 94°C for 2min, and quickly chilling on ice. The cDNA probe is now ready for hybridization.

growth_protocol: HCT116 cells were cultured in 24 well plate

extract_protocol: RNA was extracted after a 6h incubation of cell culture with 1 x 107 or 108cfu/ml of bacteria, using the High Pure RNA Isolation Kit (Roche Applied Science, Germany). The wells were washed once with 1ml of ice cold PBS to remove excess bacterial cells, and resuspended in 200μl of PBS. Lysis-binding buffer was added to each well (400μl per well) and residual cells were scrapped off the well bottom before adding the cell lysate to the filter and collection tubes. The tubes were centrifuged at 10,000g for 15sec to remove the buffer while RNA remained bound to the glass fiber fleece on the filter tubes. DNase was added to each tube to digest contaminating DNA for 15min. The RNA was purified from salts, proteins and other cellular impurities using the wash buffer provided in the kit followed by centrifugation before elution from the glass fiber fleece. RNA was then kept at -70°C immediately.

treatment_protocol: Cells were treated with different bacteria

value: E.faecalis EC3


title: EC3a

description: bacteria are from Infant stool

source_name: E.faecalis EC3 replicate 1


title: EC16b

description: bacteria are from Infant stool

source_name: E.faecalis EC16 replicate 2

value: E.faecalis EC16


title: EC16a

description: bacteria are from Infant stool

source_name: E.faecalis EC16 replicate 1


title: EC15b

description: bacteria are from Infant stool

source_name: E.faecalis EC15 replicate 2

value: E.faecalis EC15