title: ScaPC_sarcoma_03

city: Boston

first: Amy

middle: J

last: Wagers

state: MA

address: 1 Joslin Place

department: Islet Cell and Regenerative Biology

institute: Joslin Diabetes Center

description: Gene expression data from sarcomas of ScaPC origin.

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

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

data_processing: CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons.  Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.

source_name: GFP-positive fraction of sarcoma, ScaPC

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

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

treatment_protocol: Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.

value: mixed B6.129 background

value: sarcoma

tag: sarcoma cell-of-origin

value: non-myogenic progenitors (ScaPCs)

tag: oncogenes

value: KRAS(G12V), p16p19null

tag: gfp status

value: positive


title: Left Leg-3hrs_S8-3L

status: Public on Nov 10 2011

type: RNA

city: Novato

first: Simon

last: Melov

state: CA

address: 8001 Redwood Blvd

country: USA

institute: Buck Institute for Research on Aging

description:
362503A11.pair
S8-3L

hyb_protocol: The resulting hybridized chips were then scanned and quantitated via a GenePix 4200 Scanner (Molecular Devices, Sunnyvale, CA, USA), and the quantitated images were used to evaluate relative gene expression between samples.

scan_protocol: As per GenePix 4200 standard protocol.

data_processing: To minimize nuisance experimental variation among the  data, we used between array loess normalization using the affy package in the Bioconductor repository.  We used a mixed model approach to estimate the differential expression (at the log2 scale) of massage.  Specifically, we fit a model, for each probe separately. Thus, the p-value, by probe (and time t=0 minutes and 2.5 hours) is that for the null, where the Wald statistic is returned by the mixed model procedure. We performed these regressions both by probe and post-baseline time of measurement (0 minutes and 2.5 hours).  For each of the sets by time, we adjusted for multiple testing using family-wise error rate.

molecule: total RNA

organism: Homo sapiens

source_name: vastus lateralis

label_protocol: Samples were reverse transcribed and amplified with one round of whole-transcriptome amplification via the WTA2  complete whole transcriptome kit from Sigma (Sigma-Aldrich, St. Louis, MO, USA). After amplification, the resulting omniplex cDNA library was then further purified using a Qiagen PCR purification chip (Qiagen), and further evaluated for integrity and yield via Bioanalyzer. cDNA libraries were then labeled, hybridized and washed onto 12-plex 135K (HG18) Nimblegen oligonucleotide whole genome microarrays (Roche Nimblegen, Madison, WI, USA), via the one color Nimblegen labeling kit as per the manufacturers instructions.

extract_protocol: RNA was extracted from whole muscle using an automated homogenization and extraction apparatus (QiaCube, Qiagen, Valencia, CA, USA) according to the manufacturers’ protocols for the RNeasy mini kit.  RNA yield and integrity was then evaluated via Bioanalyzer (Agilent, Santa Clara, CA, USA)

tag: subject

tag: massage leg

value: R

tag: time

tag: biopsy leg

value: L

tag: tissue

value: vastus lateralis


title: ScaPC_sarcoma_01

label: biotin

organism: Mus musculus

tag: strain


title: ScaPC_sarcoma_02


title: Left Leg-30min_S8-2L

description:
363189A06.pair
S8-2L


title: Untreated XEN cells rep1

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description: Gene expression data of untreated XEN cells

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: GCOS 1.4; Algorithm: ExpressionStat 5.0

source_name: IM8A1 XEN cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: IM8A1 XEN cells were grown in GMEM+10%FBS at 37oC, 5%CO2 in a humidified environment

extract_protocol: Total RNA was isolated with QIAGEN's RNeasy Midi kit, and cDNA was prepared using Affymetrix one-cycle kit.

treatment_protocol: XEN cells were treated with BMP2 (20 ng/ml), activin A (30 ng/ml), both or niether for 6 days.

value: PO strain

tag: treatment group

value: untreated


title: fm17_animal_700_muscle

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

description: Muscle samples were biopsied from Longissimus lumborum muscle 20' after stunning and exsanguination

hyb_protocol: The labelled RNA of each muscle sample was hybridized at 68°C for 24 h to a single array containing. The hybridization images from vector and complex targets were quantified using the semi-automated software, BZScan (15). Fixed circle segmentation, i.e. a grid process with a fixed spot diameter was applied. The grid obtained with vector hybridization images was used to assess the reproducibility of the quantification signals between array replicates and also to analyze the complex target hybridization images. The complex hybridization images were quantified by extracting the intensity of each spot.

scan_protocol: BAS-5000 Fuji - BZScan software

data_processing: Data from BZScan outputs were normalized by the median of each array. To minimize the effect of the amount of DNA products spotted at each spot, data were divided by vector oligonucleotide values. Data were obtained from two different hybridization experiments; data were centered with the median value obtained from the arrays within each hybridization experiment. Then data were logarithmically (log10) transformed. Finally, 2,464 clones with signal intensity higher than 2 times the median value of background (water, plasmid and empty spots) were further analyzed using R software (R, language and environment for statistical computing, R Foundation for statistical computing, Vienna, Austria, http://www.cran.r-project.org).

organism: Sus scrofa

label_protocol: cDNA was synthesized and labeled from 5 µg total RNA by simultaneous reverse transcription of mRNA using SuperScript II RNase H-Reverse Transcriptase (Invitrogen SARL, Life Technologies, Cergy Pontoise) and alpha-33P-deoxy-CTP.

extract_protocol: Total RNA was isolated from each of the 57 muscle samples. Briefly, the muscle samples were disrupted, homogenized and ground to a fine powder by rapid agitation for 1 min in a liquid-nitrogen cooled grinder with stainless steel beads. An aliquot of 250-300 mg of the fine powder was then processed for total RNA isolation and purification using RNeasy\ Fibrous Tissue Midi kit according to the manufacturers instructions (Qiagen SA France, Courtaboeuf, France). The method included a proteinase K digestion step to remove proteins and a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 300 µl of RNase-free water and stored at -80°C. RNA quality and concentration were controlled using an AGILENT 2100 bioanalyzer (RNA solutions and RNA 6000 Nano Lab-Chip Kit, Agilent Technologies France, Massy, France).

value: skeletal muscle

tag: animalnumber


title: fm17_animal_780_muscle


title: ScaPC_sarcoma_04


title: cell line-PC-3

city: Dublin

first: Antoinette

last: Perry

address: Room 2.15, Institute of Molecular Medicine, Trinity Centre, St. James's Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

description: test; androgen independent metastatic prostate cancer cell line

data_processing: RQ data from TLDAs were analyzed using Real Time StatMiner® v3.1 (Integromics, Granada, Spain). The optimal endogenous control was selected using the minimal variance of median algorithm. Differences in gene expression were assessed for significance using the Limma test and adjusted for a false discovery rate using the Benjamini-Hochberg method. Hierarchical clustering was performed by complete linkage analysis with similarity measured by Euclidean distance. Values in the Fold Change worksheet report fold change in expression for each target relative to control sample. For tissues this is BPH. For cell lines, this is PWR1E.

label: FAM

source_name: cell line

label_protocol: qPCR gene expression profiling was performed using TLDA Human Wnt Gene set v1.0 microfluidic card (Applied Biosystems, Foster City, CA). TaqMan® reactions were performed in duplicate on a 7900HT Sequence Detection System.

growth_protocol: Cell lines were obtained from the American Type Culture Collection, except human RC58/T prostate cancer cells, which were kindly provided by Prof. Rhim, Center for Prostate Disease Research, Uniformed Service University of Health Sciences, Bethesda, MD. All cell lines were maintained under standard cell culture conditions.

extract_protocol: Total RNA was isolated from cell lines using a QIAamp® RNeasy kit (Qiagen, UK) and from FFPE tissue sections using a RecoverAll Total Nucleic Acid Isolation Kit (Ambion Inc, Austin, TX). RNA samples from FFPE specimens were pooled to create 5 different pools, The high capacity cDNA Archive Kit (Applied Biosystems) was used to reverse transcribe pooled RNA (400ng).

treatment_protocol: PC-3 cells were treated with 1µM 5-Aza-2’Deoxycytidine (5-Aza-CdR) at 48-hour intervals over a period of 1 week in induce global demethylation.

tag: cell line

tag: mean age years (range)

tag: mean psa (ng/ml) (range)


title: Right Leg-3hrs_S7-3R

description:
363189A03.pair
S7-3R


title: cell line-PC-3 + 5azaCdR


title: tissue-22Rv1

description: test; androgen sensitive primary prostate cancer cell line


title: Pre_S8-1R

description:
363676A04.pair
S8-1R

value: Pre


title: CXCR4neg_sarcoma_02

description: Gene expression data from sarcomas of CD45-MAC1-TER119-Sca1-CXCR4- cellular origin.

source_name: GFP-positive fraction of sarcoma, CXCR4-

value: CD45-MAC1-TER119-Sca1-CXCR4- cells


title: CXCR4neg_sarcoma_03


title: cell line-LNCaP

description: test; androgen dependent metastatic prostate cancer cell line

value: LNCaP


title: fm17_animal_N40_muscle


title: CXCR4neg_sarcoma_01


title: SMP_sarcoma_03

description: Gene expression data from sarcomas of SMP origin.

source_name: GFP-positive fraction of sarcoma, SMP

value: skeletal muscle precursor cells (SMPs)


title: Left Leg-3hrs_S7-3L

description:
363676A02.pair
S7-3L


title: SMP_sarcoma_04


title: CXCR4neg_sarcoma_04


title: cell line-PWR1E

description: control; benign prostate cell line


title: fm17_animal_794_muscle


title: SMP_sarcoma_02


title: fm17_animal_350_muscle


title: Right Leg-30min_S7-2R

description:
363676A08.pair
S7-2R


title: fm17_animal_380_muscle


title: tissue-BPH-BR1

description: benign prostatic hyperplasia, biological replicate 1

source_name: FFPE prostate tissue

value: benign prostatic hyperplasia


title: HD3_KO_IL4_Hyb14

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description: Raw data file: 251486828386_4.txt

hyb_protocol: Labeled samples were hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.

scan_protocol: Arrays were washed and then scanned with the model G2565B Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Median intensities of each element on the array were captured with Agilent Feature Extraction version 9.53 (Agilent Technologies). Quality control diagnostic plots were prepared for each array, and those failing to exhibit high-quality hybridizations were excluded from further analysis, resulting in the final dataset containing four biological replicates for each condition. The subsequent analysis was performed as previously (Rieck et al. 2009).  Data was quantile normalized in R with the limma package's function normalizeBetweenArray.  FDRs were calculated using the SAMR package.

source_name: Bone Marrow-Derived Macrophages, HDAC3-Null, IL4 Treatment

label_protocol: RNA was amplified and labeled using the Ovation V2 Amplification Kit (NuGEN).

growth_protocol: Bone marrow derived macrophages were obtained by culturing bone marrow from 12-16 week old male C57Bl/6J mice in 30% L929 conditioned medium for six days, changing the media on the fourth day of culture.  Cells were replated on day 6, allowed to rest overnight and then treated accordingly.  Control macrophages were from mice with exons 4-7 of HDAC3 floxed with loxP sites (HDAC3 floxed).  HDAC3 KO macrophages were from mice expressing Cre recombinase under the control of the lysozyme M promoter and with floxed HDAC3.

extract_protocol: RNA was isolated using the Qiagen Rneasy Kit

treatment_protocol: Macrophages were treated with either control vehicle, 0.1% bovine serum albumin (BSA) or 10ng/mL of IL-4 for 24 hours.

value: Bone Marrow

tag: cell type

value: Macrophage

tag: genotype/variation

value: LysM Cre+, HDAC3 floxed

tag: agent


title: HD3_KO_IL4_Hyb15

description: Raw data file: 251486828387_4.txt


title: SMP_sarcoma_01

value: mixed B6.129 background

value: sarcoma

tag: sarcoma cell-of-origin


title: Left Leg-30min_S7-2L

description:
362503A06.pair
S7-2L


title: fm17_animal_792_muscle


title: tissue-BPH-BR2

description: benign prostatic hyperplasia, biological replicate 2


title: fm17_animal_701_muscle


title: fm17_animal_774_muscle


title: Control_IL4_Hyb12

description: Raw data file: 251486828392_3.txt

source_name: Bone Marrow-Derived Macrophages, Control, IL4 Treatment

value: HDAC3 floxed


title: fm17_animal_358_muscle


title: Right Leg-3hrs_S6-3R

description:
362503A01.pair
S6-3R

value: R


title: Left Leg-3hrs_S6-3L

description:
363189A02.pair
S6-3L

value: L


title: tissue-benign-BR1

description: histologically benign prostate adjacent to tumor, biological replicate 1

value: benign prostate adjacent to tumor


title: Control_IL4_Hyb10

description: Raw data file: 251486828386_3.txt


title: tissue-HGPIN-BR2

description: High grade prostatic intraepithelial neoplasia, biological replicate 2


title: HD3_KO_IL4_Hyb13

description: Raw data file: 251486828385_4.txt


title: fm17_animal_751_muscle


title: Control_IL4_Hyb9

description: Raw data file: 251486828385_3.txt


title: tissue-benign-BR2

description: histologically benign prostate adjacent to tumor, biological replicate 2


title: Pre_S6-1R

description:
363419A09.pair
S6-1R

value: vastus lateralis


title: Right Leg-30min_S6-2R

description:
363419A05.pair
S6-2R


title: Left Leg-30min_S6-2L

description:
362468A04.pair
S6-2L


title: tissue-HGPIN-BR1

description: High grade prostatic intraepithelial neoplasia, biological replicate 1


title: fm17_animal_N72_muscle


title: HD3_KO_No_treatment_Hyb7

description: Raw data file: 251486828387_2.txt

source_name: Bone Marrow-Derived Macrophages, HDAC3-Null, No Treatment

value: BSA


title: fm17_animal_364_muscle

value: skeletal muscle


title: HD3_KO_No_treatment_Hyb6

description: Raw data file: 251486828386_2.txt


title: Right Leg-3hrs_S5-3R

description:
362503A02.pair
S5-3R


title: Left Leg-3hrs_S5-3L

description:
362468A10.pair
S5-3L


title: Pre_S7-1R

description:
363676A10.pair
S7-1R

value: Pre


title: tissue-high grade prostate cancer-BR2

description: tumour, Gleason score 7, biological replicate 2

value: tumour

tag: disease state

value: prostate cancer

tag: gleason score 7


title: HD3_KO_No_treatment_Hyb5

description: Raw data file: 251486828385_2.txt


title: fm17_animal_687_muscle


title: tissue-low grade prostate cancer-BR2

description: tumour, Gleason score 6, biological replicate 2

tag: gleason score 6


title: tissue-low grade prostate cancer-BR1

description: tumour, Gleason score 6, biological replicate 1


title: fm17_animal_393_muscle


title: fm17_animal_803_muscle


title: tissue-high grade prostate cancer-BR1

description: tumour, Gleason score 7, biological replicate 1


title: fm17_animal_696_muscle


title: fm17_animal_759_muscle


title: Right Leg-30min_S5-2R

description:
363189A11.pair
S5-2R

tag: subject

tag: massage leg


title: fm17_animal_N16_muscle


title: Control_No_treatment_Hyb4

description: Raw data file: 251486828392_1.txt

source_name: Bone Marrow-Derived Macrophages, Control, No Treatment


title: Control_No_treatment_Hyb3

description: Raw data file: 251486828387_1.txt


title: Control_No_treatment_Hyb2

description: Raw data file: 251486828386_1.txt


title: Control_No_treatment_Hyb1

description: Raw data file: 251486828385_1.txt


title: BMP2-treated XEN cells rep1

description: Gene expression data of BMP2-treated XEN cells

value: PO strain


title: Pre_S5-1R

description:
363419A04.pair
S5-1R

tag: time

tag: biopsy leg


title: Left Leg-30min_S5-2L

description:
363676A06.pair
S5-2L

tag: tissue


title: fm17_animal_N32_muscle

description: Muscle samples were biopsied from Longissimus lumborum muscle 20' after stunning and exsanguination


title: Right Leg-3hrs_S4-3R

description:
363419A03.pair
S4-3R


title: Left Leg-3hrs_S4-3L

description:
362468A02.pair
S4-3L


title: HUVEC Dex 16h

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

description: Gene expression data from HUVEC treated for 16h with 10 uM dexamethasone

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HUVEC treated for 16h with dexamethasone

label_protocol: cRNA were prepared and labeled according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) from 5 ug total RNA.

extract_protocol: Total RNA extracted according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA).

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: fm17_animal_N13_muscle


title: HUVEC Dex 4h

description: Gene expression data from HUVEC treated for 4h with 10 uM dexamethasone

source_name: HUVEC treated for 4h with dexamethasone


title: fm17_animal_795_muscle


title: fm17_animal_362_muscle


title: fm17_animal_762_muscle


title: fm17_animal_733_muscle


title: Right Leg-30min_S4-2R

description:
363189A12.pair
S4-2R


title: Left Leg-30min_S4-2L

description:
363419A11.pair
S4-2L


title: HUVEC control 16h

description: Gene expression data from untreated HUVEC after 16h of culture time.

source_name: HUVEC control 16h culture time


title: putamen_PD patient LRRK2 G2019S mutation carrier 3

city: Barcelona

first: Teresa

last: Botta

address: Casanova 143

department: Serveis Científicotècnics

country: Spain

institute: IDIBAPS-Universitat de Barcelona-Hospital Clínic

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: putamen, PD with mutation

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT sense target labelling and control reagents kit (Affymetrix)

growth_protocol: not applicable

extract_protocol: Brain samples were obtained by donation to Neurological Tissue Bank (Universitat de Barcelona-Hospital Clínic-IDIBAPS) with a postmortem delay of less than 24h. After histopathological confirmation for Parkinson's disease and genetic study for LRRK2 mutation, putamen tissue samples were dissected from corresponding brain sections stored at -80ºC. 30-50 ngr of putamen tissue were homogenised with a high-speed homogeniser Polytron, and the RNA extrated using Rneasy lipid Tissue MiniKit (Qiagen) according to the manufacturer’s instructions and including a DNase digestion with RNase-Free DNase Set (Qiagen). The RNA concentration was measured with Nanodrop 1000 Spectrophotometer (Thermo Fisher Scientific), and determination of the absorbance at 260 nm and RNA quality were evaluated by 2100 Bioanalyzer (Agilent) assessing the presence of ribosomal RNA 18S and 28S. Isolated RNAs were stored at -80ºC. For real-time qRT-PCR array validation, 2 µgr of total RNA were retrotranscribed by using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). The real-time TaqMan-PCR assays for each gene were carried out with duplicates of cDNA in 96-well optical plates on a StepOnePlus Real-time PCR System (Applied Biosystems). Pre-designed TaqMan® Gene Expression Assays (AppliedBiosystems) were used for gene amplification.

treatment_protocol: Putamen samples from brain sections frozen at -80ºC

tag: neuropathological diagnosis

value: non-specific nigral degeneration

tag: gender

value: female

tag: family history of pd

value: tremor (mother and oncle)

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

value: yes

tag: dopamine-agonists treatment

tag: l-dopa response (degree if available)

value: good

tag: dyskinesia (degree if available)

value: yes (mild-moderated)

tag: dyskinesia (years after treatment start)

tag: motor fluctuations

tag: cognitive impairment

tag: hallucinations

value: no


title: putamen_asymptomatic G2019S LRRK2 carrier (mutation carrier control)

description: MC

source_name: putamen, control with mutation

value: no pathological changes (NPC)

value: male

value: not known


title: Right Leg-3hrs_S3-3R

description:
363189A05.pair
S3-3R

tag: subject

tag: massage leg

value: L

tag: time

value: R

value: vastus lateralis


title: fm17_animal_N58_muscle

tag: tissue

value: skeletal muscle

tag: animalnumber


title: Right Leg-30min_S3-2R

description:
363676A12.pair
S3-2R

tag: biopsy leg


title: putamen_PD patient LRRK2 G2019S mutation carrier 2

tag: neuropathological diagnosis

value: LBP (4) + ARP (IV-C)

tag: gender

tag: family history of pd

tag: age at onset (years)


title: putamen_PD patient LRRK2 G2019S mutation carrier 1

value: LBP (4)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

tag: dopamine-agonists treatment

value: moderated

value: yes (severe)


title: fm17_animal_702_muscle


title: putamen_idiopathic PD patient5

source_name: putamen, PD

value: LBP (3-4) + ARP (III/A)

value: tremor (father)

tag: l-dopa response (degree if available)

tag: dyskinesia (degree if available)

tag: dyskinesia (years after treatment start)

tag: motor fluctuations


title: Pre_S4-1R

description:
362468A06.pair
S4-1R

tag: subject

tag: massage leg

value: Pre


title: Left Leg-30min_S3-2L

description:
362503A05.pair
S3-2L

tag: time

tag: tissue


title: fm17_animal_379_muscle

tag: animalnumber


title: fm17_animal_343_muscle


title: Left Leg-3hrs_S3-3L

description:
362468A03.pair
S3-3L

tag: biopsy leg


title: HUVEC control 4h

description: Gene expression data from untreated HUVEC after 4h of culture time.

source_name: HUVEC control 4h culture time

tag: cell type

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: Pre_S3-1R

description:
363419A10.pair
S3-1R

source_name: vastus lateralis


title: putamen_idiopathic PD patient3

tag: neuropathological diagnosis

tag: gender

value: female

tag: family history of pd

value: yes

value: good

tag: cognitive impairment

tag: hallucinations


title: fm17_animal_348_muscle


title: fm17_animal_789_muscle


title: putamen_idiopathic PD patient4

value: LBP + ARP (III)

value: tremor (mother)

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

tag: dopamine-agonists treatment

value: no

value: partial


title: putamen_control5

source_name: putamen, control

value: NPC

value: not known

tag: l-dopa response (degree if available)

tag: dyskinesia (degree if available)

tag: dyskinesia (years after treatment start)

tag: motor fluctuations


title: fm17_animal_692_muscle

tag: tissue

value: skeletal muscle

tag: animalnumber


title: putamen_idiopathic PD patient2

value: male


title: Right Leg-30min_S2-2R

description:
362468A09.pair
S2-2R

tag: subject

tag: massage leg

value: L

tag: time

tag: biopsy leg

value: R

value: vastus lateralis


title: Right Leg-3hrs_S2-3R

description:
362468A11.pair
S2-3R


title: Left Leg-3hrs_S2-3L

description:
363676A03.pair
S2-3L


title: putamen_idiopathic PD patient1

tag: neuropathological diagnosis

value: Lewy body pathology (LBP,3-4) + Alzheimer related pathology (ARP, I)

tag: gender

tag: family history of pd

tag: cognitive impairment


title: Left Leg-30min_S2-2L

description:
363419A02.pair
S2-2L


title: putamen_control4

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: hallucinations


title: Right Leg-3hrs_S1-3R

description:
363676A09.pair
S1-3R


title: fm17_animal_756_muscle


title: Pre_S2-1R

description:
363676A01.pair
S2-1R

value: Pre


title: fm17_animal_418_muscle


title: Left Leg-3hrs_S1-3L

description:
363189A04.pair
S1-3L


title: putamen_control2

tag: l-dopa treatment

tag: dopamine-agonists treatment

tag: l-dopa response (degree if available)

tag: dyskinesia (degree if available)


title: putamen_control3

tag: dyskinesia (years after treatment start)

tag: motor fluctuations


title: fm17_animal_382_muscle

tag: tissue

tag: animalnumber


title: putamen_control1

value: no pathological changes (NPC)


title: Pre_S1-1R

description:
362468A08.pair
S1-1R

tag: subject

tag: massage leg

tag: time

tag: biopsy leg


title: Right Leg-30min_S1-2R

description:
362503A10.pair
S1-2R


title: Left Leg-30min_S1-2L

description:
363419A01.pair
S1-2L


title: L2.3-day3-3

status: Public on Nov 09 2011

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Multipotential neural precursor

hyb_protocol: All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's Expression console.

data_processing: The image data was processed utilizing the Affymetrix GCOS algorithm and the Robust Multiarray Average (RMA) method to determine the specific hybridizing signal for each gene.

organism: Rattus norvegicus

label_protocol: All target-labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1.2 ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System.

growth_protocol: Clones were cultured on poly-lysine/laminin-coated substrates in FGF2 containing DMEM/F12 culture medium.

extract_protocol: RNA was prepared with Trizol lysis buffer (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions.

treatment_protocol: For differentiation, the medium was removed and replaced with DMEM/F12/B27 medium lacking FGF2 (DMEM/F12) (differentiation medium) and 0.5% fetal bovine serum (FBS) was added to promote cell survival.

tag: day

tag: replicate


title: L2.3-day3-1

description: Multipotential neural precursor


title: L2.3-day0-1

description: Multipotential neural precursor


title: L2.3-day7-2

description: Multipotential neural precursor


title: L2.2-day7-3

description: Interneuronal precursor


title: L2.3-day7-1

description: Multipotential neural precursor


title: L2.3-day3-2

description: Multipotential neural precursor


title: L2.2-day3-3

description: Interneuronal precursor


title: L2.2-day7-1

description: Interneuronal precursor


title: L2.3-day0-3

description: Multipotential neural precursor


title: L2.3-day0-2

description: Multipotential neural precursor


title: L2.2-day3-1

description: Interneuronal precursor


title: L2.3-day7-3

description: Multipotential neural precursor


title: L2.2-day0-3

description: Interneuronal precursor


title: Ge6-day7-1

description: GABAergic neuronal precursor


title: Ge6-day3-2

description: GABAergic neuronal precursor


title: Ge6-day3-1

description: GABAergic neuronal precursor


title: L2.2-day3-2

description: Interneuronal precursor


title: Ge6-day0-2

description: GABAergic neuronal precursor


title: Ge6-day3-3

description: GABAergic neuronal precursor


title: Ge6-day7-3

description: GABAergic neuronal precursor


title: L2.2-day7-2

description: Interneuronal precursor


title: Ge6-day0-1

description: GABAergic neuronal precursor


title: Ge6-day7-2

description: GABAergic neuronal precursor


title: Ge2-day7-1

description: Nonneuronal neural precursor


title: Ge6-day0-3

description: GABAergic neuronal precursor


title: L2.2-day0-1

description: Interneuronal precursor


title: Ge2-day3-3

description: Nonneuronal neural precursor


title: Ctx8-day7-3

description: Multipotential neural precursor


title: Ge2-day3-1

description: Nonneuronal neural precursor


title: Ctx8-day3-2

description: Multipotential neural precursor


title: Ctx8-day3-3

description: Multipotential neural precursor


title: Ge2-day3-2

description: Nonneuronal neural precursor


title: Ctx8-day7-2

description: Multipotential neural precursor


title: Ge2-day7-3

description: Nonneuronal neural precursor


title: Ctx8-day0-1

description: Multipotential neural precursor


title: Ge2-day0-1

description: Nonneuronal neural precursor


title: Ge2-day7-2

description: Nonneuronal neural precursor


title: Ctx8-day0-2

description: Multipotential neural precursor


title: Ctx8-day0-3

description: Multipotential neural precursor


title: Ctx8-day3-1

description: Multipotential neural precursor


title: Ge2-day0-2

description: Nonneuronal neural precursor


title: Ge2-day0-3

description: Nonneuronal neural precursor


title: Ctx8-day7-1

description: Multipotential neural precursor


title: KO_3w-1

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description: Replicate 1 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was subtracted and quantile normalization was applied.

source_name: Knockout, 3w

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays.

growth_protocol: All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.

extract_protocol: Total RNA was extracted with the Qiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and the Agilent Bioanalyser.

treatment_protocol: 8- and 9-week-old female homozygote and control animals (C57/129) were injected i.p. with CCl4 (1ul/g) in mineral oil (Sigma) twice weekly for a period of 4 weeks. Liver samples were collected at various time-points after fibrosis induction using CCL4 ranging from 0 weeks to 3 weeks. Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.

tag: strain/background

tag: genotype

tag: gender

value: female

value: liver

tag: treatment

value: 3 weeks


title: KO_3w-2

description: Replicate 2 of 4.


title: KO_3w-3

description: Replicate 3 of 4.


title: KO_3w-4

description: Replicate 4 of 4.


title: KO_2w-1

description: Replicate 1 of 4.

source_name: Knockout, 2w

value: 2 weeks


title: KO_2w-3

description: Replicate 3 of 4.


title: KO_2w-2

description: Replicate 2 of 4.


title: KO_2w-4

description: Replicate 4 of 4.


title: KO_1d-4

description: Replicate 4 of 4.

source_name: Knockout, 1d

value: 1 day


title: KO_1w-4

description: Replicate 4 of 4.

source_name: Knockout, 1w

value: 1 week


title: KO_1d-2

description: Replicate 2 of 4.


title: KO_1w-3

description: Replicate 3 of 4.


title: KO_1d-3

description: Replicate 3 of 4.


title: KO_0w-3

description: Replicate 3 of 4.

source_name: Knockout, 0w

value: 0 weeks


title: WT_3w-3

description: Replicate 3 of 4.

source_name: Wildtype, 3w

value: wildtype


title: Flush subclinical bioligical replicate 1

city: Bonn

first: Michael

last: Hoelker

address: Endenicher Allee 15

institute: Universtity of Bonn

hyb_protocol: Array hybridization was performed after mixing appropriative amount of hybridization components, fragmented and labelled cRNA, control oligonucleotide B2 (3 nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix , DMSO and RNAse free water.The hybridization mix was heated to 99°C for 5 min followed by heating at 45°C for 5 min. Following this the samples were hybridized to the GeneChip® Bovine Genome Array (Affymetrix, CA, USA) for 16 h at 45°C. Three biotin labeled cRNA hybridizations were performed for endometrial samples of each category (HE-0, SE-0, HE-7, SE-7)

scan_protocol: After 16 h of hybridization, the arrays washing and staining was performed using the Fluidics Station 450/250 integrated as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731 (Affymetrix). The arrays were then scanned using affymetrix®GeneChip™3000 slide scanner (Affymetrix, CA, USA).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma). The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA). For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

organism: Bos taurus

source_name: Endometrial cytobrush samples collected from animals which exhibit subclinical endometritis at time of embryo flushing (SE-7)

label_protocol: The cRNA was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual (P/N 702232)

extract_protocol:
Total RNA was isolated from three pools of endometrial cytobrush samples derived from healthy or subclinical animals both at the time of insemination or flushing using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol
Two rounds of RNA amplification were performed as described by GeneChip® Expression Analysis Technical Manual using 15 ng of total RNA as a starting material using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA)

value: Endometrial cytobrush

tag: disease state


title: KO_0w-4

description: Replicate 4 of 4.


title: KO_1w-1

description: Replicate 1 of 4.


title: WT_3w-4

description: Replicate 4 of 4.


title: Flush subclinical bioligical replicate 2

value: subclinical endometritis at time of embryo flushing (SE-7)


title: Flush healthy biological replicate 2

source_name: Endometrial cytobrush samples collected from animals which were healthy at time of embryo flushing (HE-7)


title: Flush subclinical bioligical replicate 3


title: Flush healthy biological replicate 1

value: healthy at time of embryo flushing (HE-7)


title: KO_0w-1

description: Replicate 1 of 4.


title: AI subclinical bioligical replicate 1

source_name: Endometrial cytobrush samples collected from animals which exhibit subclinical endometritis at time of insemination (SE-0)


title: KO_0w-2

description: Replicate 2 of 4.


title: KO_1d-1

description: Replicate 1 of 4.


title: AI subclinical bioligical replicate 3

value: subclinical endometritis at time of insemination (SE-0)


title: WT_3w-2

description: Replicate 2 of 4.


title: WT_3w-1

description: Replicate 1 of 4.


title: AI subclinical bioligical replicate 2


title: KO_1w-2

description: Replicate 2 of 4.


title: Blastocyst subclinical 2 biological rep2

source_name: Blastocysts flushed from animals affected by subclinical endometritis (SE-7)

extract_protocol:
Total RNA was isolated from three pools of blastocysts each pool consiting of 10 blastocysts derived from healthy (HE-7) or subclinical (SE-7)animals both at the time of insemination or flushing using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol
Two rounds of RNA amplification were performed as described by GeneChip® Expression Analysis Technical Manual using 15 ng of total RNA as a starting material using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA)

value: Blastocysts

value: subclinical endometritis (SE-7)


title: AI healthy biological replicate 2

source_name: Endometrial cytobrush samples collected from animals which were healthy at time of insemination (HE-0)

value: healthy at time of insemination (HE-0)


title: AI healthy biological replicate 3


title: AI healthy biological replicate 1


title: Blastocyst subclinical 3 biological rep3


title: Blastocyst subclinical 1 biological rep1


title: WT_2w-3

description: Replicate 3 of 4.

source_name: Wildtype, 2w


title: WT_2w-4

description: Replicate 4 of 4.


title: WT_2w-2

description: Replicate 2 of 4.


title: WT_1d-3

description: Replicate 3 of 4.

source_name: Wildtype, 1d


title: WT_1d-2

description: Replicate 2 of 4.


title: WT_1w-3

description: Replicate 3 of 4.

source_name: Wildtype, 1w


title: WT_1w-2

description: Replicate 2 of 4.


title: WT_1w-4

description: Replicate 4 of 4.


title: WT_1d-4

description: Replicate 4 of 4.


title: WT_0w-4

description: Replicate 4 of 4.

source_name: Wildtype, 0w


title: Blastocyst healthy 2 biological rep1

source_name: Blastocysts flushed from healthy animals (HE-7)

value: healthy animals (HE-7)


title: Blastocyst healthy 3 biological rep2


title: WT_0w-3

description: Replicate 3 of 4.


title: WT_1d-1

description: Replicate 1 of 4.


title: E. coli ZK126 pure culture rep2

city: San Marcos

first: Robert

middle: JC

last: McLean

state: TX

address: 601 University Drive

department: Biology

institute: Texas State University-San Marcos

description: Gene expression data from pure culture

hyb_protocol: Following fragmentation, 4-6ug cDNA was hybridized to E coli or P aeruginosa gene chips

scan_protocol: Gene chips were scanned using an Affymetrix Model 3000 GeneArray scanner

data_processing: Microarray .cel files were analyzed by multiarray analysis method using the Affy package (version 1.18.2, Affymetrix) using default options.

organism: Escherichia coli

source_name: E. coli pure culture

label_protocol: Enzo Bioarray Terminal Labeling Kit (Affymetrix cat # 900181) according to manufacturer's instructions

growth_protocol: E coli and P aeruginosa cells were grown aerobically at 37C in pure and mixed culture in LB broth

extract_protocol: Qiagen RNA extraction following manufacturer's protocol

treatment_protocol: Following incubation samples were stabilized with RNA later (Ambion) and stored at 4C prior to RNA extraction

tag: strain

tag: culture

value: E. coli pure culture


title: WT_2w-1

description: Replicate 1 of 4.

value: female


title: E. coli ZK126 and P. aeruginosa culture rep2

description: Gene expression data from mixed culture

source_name: E. coli and P. aer. Mixed culture

value: E. coli and P. aeruginosa culture


title: E. coli ZK126 and P. aeruginosa culture rep1

description: Gene expression data from mixed culture


title: WT_0w-2

description: Replicate 2 of 4.

value: liver


title: E. coli ZK126 pure culture rep1

description: Gene expression data from pure culture


title: WT_1w-1

description: Replicate 1 of 4.


title: WT_0w-1

description: Replicate 1 of 4.


title: AtGATA2ox, rep3

city: Beijing

first: wenhui

last: lin

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of Botany, CAS

description: Gene expression data from overexpression line of AtGATA2 gene, repeat 3.

hyb_protocol: 20 μg of labeled and fragmented cRNA were hybridized with the Arabidopsis ATH1 genome array according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned using the Agilent GeneArray Scanner.

data_processing: Microarray data were analyzed using Genespring software (version 7, Silicon Genetics). Data that were flagged as absent using mismatch probes were removed from the analysis.  GC-RMA signal intensities were generated.  However, note that MAS5.0 signal intensities are presented in the table below. ANOVA was used to find genes whose expression was different between AtGATA2ox and Col or between AtGATA2ox and bri1-116.

organism: Arabidopsis thaliana

source_name: Overexpression line of AtGATA2 in Columbia background

label_protocol: Biotinylated cRNA were prepared from 10ug of total RNA according to the Eukaryotic Target Protocol (Affymetrix).

growth_protocol: Seedlings were grown on solid ½ MS medium with 1% sucrose in the dark for 108 hours.

extract_protocol: Total RNA was extracted by the Plant RNA Purification Reagent (Invitrogen), treated with RNase-free DNase I (Qiagen), and cleaned up using the RNeasy Plant Mini column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The seedlings were frozen in liquid nitrogen in complete darkness, and then the homozygote seedlings of bri1-116 were picked individually from the heterozygous population.

tag: ecotype

value: Columbia-0 (Col-0)

tag: genotype/variation

value: AtGATA2ox transgenic

value: seedling


title: APP-1_time4_rep2

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

description: Two biological repetitions were combined

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit (Agilent). 1μg of cRNA were mixed with blocking agent, fragmentation buffer and incubated at 60°C for 30 min for fragmentation. GEx Hybridization Buffer were added and 100 μl mixture were hybridized at 65°C for 17 hours with 10 rpm rotation. The arrays were washed two times using wash buffer 1 and 2 from Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Arrays were scanned using Agilent Microarray Scanner System G2565BA (Agilent) with resolution of 5μm. The scanner uses 100% and 10% PTM respectively and combines the two data automatically.

data_processing: The data were analyzed using Feature Extraction Software (Agilent). The signal intensity were normalized and transformed into log2 values.

organism: Actinobacillus pleuropneumoniae

source_name: Reference strain of serovar 1, WT

label_protocol: cDNA were transcribed into cRNA using T7 RNA Polymerase and aaUTP (Ambion). cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN). 4μg cRNA were combined with DMSO and 0.3M NaHCO3 and then were added into Cy3 NHS ester (GE healthcare). The mixture were incubated at 25°C for 1 hour. 4M Hydroxylamine were added and incubated at 25°C for 15min. The labeled cRNA were purified using QIAGEN RNeasy Mini kit (QIAGEN).

growth_protocol: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v) filtered cattle serum at 37°C.The samples were collected from early exponential phase, middle exponential phase, late exponential phase and stationary phase respectively and the total RNA were extracted using Trizol reagent according to the manufacturer’s instructions.

extract_protocol: RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. Total RNA were purified using QIAGEN RNeasy Mini Kit (QIAGEN).

tag: phase

value: stationary


title: AtGATA2ox, rep2

description: Gene expression data from overexpression line of AtGATA2 gene, repeat 2.

tag: tissue


title: FTC-238/hrTPO/RSK008 treated with Vinclozolin Array 1

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

description: Vinclozolin vs DMSO

hyb_protocol: Stratagene FairPlay III microarray labeling kit

scan_protocol: PixelSize=5 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000 ). A significance analysis of microarray (SAM) was performed for genes with significant changes in expression. Spots that were adjudged as substandard via the visual examination of each slide were flagged and excluded from further analysis. Spots that harbored dust artifacts or spatial defects were manually flagged and excluded. And in an attepmt to filter out the unreliable data, spots with signal-to-noise (signal-background-background SD) ratios below 10 were not included in the data.

source_name: FTC-238/hrTPO/RSK008 treated Vinclozolin labeled with Cy5

extract_protocol: TRIzol extraction

tag: cell line

source_name: FTC-238/hrTPO/RSK008 treated Vinclozolin labeled with Cy3


title: Mutant_time4_rep1

source_name: Mutant strain of A. pleuropneumoniae, luxS negative

tag: type

value: luxS negative


title: Mutant_time4_rep2


title: FTC-238/hrTPO/RSK008 treated with Vinclozolin Array 2

description: Vinclozolin vs DMSO

label_protocol: Stratagene FairPlay III microarray labeling kit


title: WT.DMSO_rep6

city: Seattle

last: Coon

state: WA

address: 4225 Roosevelt Way N.E., Suite 100

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Affymetrix Expression Console v1.1 RMA normalization log2

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Genome ST 1.0 microarrays.  Processing of the RNA samples was carried out using the Affymetrix GeneChip Whole Transcript Sense Target labeling protocol (for details see http://www.affymetrix.com/index.affx). The work was done in a core facility in the Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health at the University of Washington.

extract_protocol: Bisected cerebellum were incubated in RNAlater for 12 h at 4oC, then stored at -20oC.  Total RNA was isolated using TRIZOL Reagent and the QIAamp Tissue Kit from QIAGEN Inc., according to the manufacturer’s established protocols.

treatment_protocol: Chlorpyrifos (CPO) or vehicle (DMSO) injected S.Q.(1 uL/g bodyweight) daily from PND 4 to PND 21. CPO at 0.35 mg*kg-1*day-1 or 0.5 mg*kg-1*day-1

value: cerebellum

tag: age (at weaning)

value: PND 22


title: AtGATA2ox, rep1

description: Gene expression data from overexpression line of AtGATA2 gene, repeat 1.


title: FTC-238/hrTPO/RSK008 treated with Vinclozolin Array 3

description: Vinclozolin vs DMSO


title: FTC-238/hrTPO/RSK008 treated with Carbaryl Array 4

description: Carbaryl vs DMSO

source_name: FTC-238/hrTPO/RSK008 treated Carbaryl labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated Carbaryl labeled with Cy3


title: FTC-238/hrTPO/RSK008 treated with dibutyl phthalate Array 4

description: Dibutyl phthalate vs DMSO

source_name: FTC-238/hrTPO/RSK008 treated dibutyl phthalate labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated dibutyl phthalate labeled with Cy3


title: Mutant_time3_rep1

value: late exponential


title: WT.DMSO_rep3

department: Center for Ecogenetics and Environmental Health


title: FTC-238/hrTPO/RSK008 treated with dibutyl phthalate Array 2

description: Dibutyl phthalate vs DMSO


title: WT.DMSO_rep5


title: FTC-238/hrTPO/RSK008 treated with dibutyl phthalate Array 1

description: Dibutyl phthalate vs DMSO


title: FTC-238/hrTPO/RSK008 treated with dibutyl phthalate Array 3

description: Dibutyl phthalate vs DMSO


title: FTC-238/hrTPO/RSK008 treated with Carbaryl Array 3

description: Carbaryl vs DMSO


title: WT.DMSO_rep4


title: APP-1_time4_rep1


title: Mutant_time3_rep2


title: WT.DMSO_rep2


title: FTC-238/hrTPO/RSK008 treated with Carbaryl Array 2

description: Carbaryl vs DMSO


title: FTC-238/hrTPO/RSK008 treated with BP-2 Array 4

description: BP-2 vs DMSO

source_name: FTC-238/hrTPO/RSK008 treated BP-2 labeled with Cy5

source_name: FTC-238/hrTPO/RSK008 treated DMSO labeled with Cy3


title: APP-1_time3_rep1


title: Mutant_time2_rep2

value: middle exponential


title: APP-1_time3_rep2


title: WT.DMSO_rep1


title: Mutant_time2_rep1


title: FTC-238/hrTPO/RSK008 treated with BP-2 Array 3

description: BP-2 vs DMSO

source_name: FTC-238/hrTPO/RSK008 treated BP-2 labeled with Cy3


title: APP-1_time2_rep2


title: FTC-238/hrTPO/RSK008 treated with BP-2 Array 2

description: BP-2 vs DMSO

scan_protocol: PixelSize=5 DateTime=2006/10/02 10:15:03 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

source_name: FTC-238/hrTPO/RSK008 treated DMSO labeled with Cy5


title: WT.0.5_rep3


title: FTC-238/hrTPO/RSK008 treated with BP-2 Array 1

description: BP-2 vs DMSO


title: WT.0.35_rep4


title: WT.0.5_rep1


title: FTC-238/hrTPO/RSK008 treated with Carbaryl Array 1

description: Carbaryl vs DMSO


title: APP-1_time2_rep1


title: APP-1_time1_rep2

value: early exponential


title: Mutant_time1_rep1


title: WT.0.35_rep6


title: WT.0.35_rep5


title: Mutant_time1_rep2


title: WT.0.35_rep3


title: WT.0.5_rep2


title: WT.0.35_rep2


title: WT.0.35_rep1


title: APP-1_time1_rep1


title: P300+ sample

type: genomic

city: Ann Arbor

first: Yongsheng

last: Huang

state: MI

address: 100 Washtenaw Ave

department: Bioinformatics

institute: University of Michigan

hyb_protocol: Hybridization was performed by Nimblegen, using manufacturer's protocol

scan_protocol: Roche NimbleGen NimbleScan software

data_processing: MA2C (Song et al., 2007) with Median polish and bandwidth 150bp

molecule: genomic DNA

source_name: P300 ChIP DNA

label_protocol: Labeling was done by Nimblegen, using manufacturer's protocol

extract_protocol: A total of 150 million cells were crosslinked sequentially with disuccinimidylglutarate (45 min RT) and 1% formaldehyde (15 min RT).  Hoxa9 and Meis1 immunoprecipitation was performed with anti-HA antibody (Abcam) pre-conjugated to Protein G magnetic beads (Dynal/Invitrogen).  For C/ebpα ChIP, rabbit anti-C/ebpα (Santa Cruz) was compared with pre-immune rabbit IgG.  4-hour incubation (4°C with gentle rotation) was followed by washes using Low Salt, High Salt, LiCl, and Tris-EDTA buffers (Upstate/Millipore).  Immunoprecipitates were eluted with 0.1% SDS/0.1M NaHCO3 and DNA-protein crosslinks were reversed overnight at 65° in 0.2M NaCl.  DNA was RNAse treated and column purified (Qiaquick, Qiagen).  For ChIP-seq, size selection and sequencing were performed at the BC Cancer Agency Genome Sciences Centre (Vancouver, BC) as described previously (Robertson et al. 2007).    For ChIP-Chip, DNA was amplified prior to dual hybridization (performed at Nimblegen Systems) of input and immunoprecipitate on a custom tiled mouse genomic array containing putative Hoxa9 and Meis1 target genes (50-mer probes with an average spacing of 35 bp; 15 megabases of total sequence).

tag: age

value: 6-8 week old

value: murine bone marrow transduced with epitope tagged forms of Hoxa9

tag: cell type

value: Hoxa9-ER cells

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody catalog number

source_name: Input DNA

tag: sample type

value: input DNA


title: PON1.R192.DMSO_rep4

tag: genotype


title: CBP+ sample

source_name: CBP ChIP DNA

tag: gender

value: female

value: CBP

value: Abcam


title: H3 acetyl+ sample

source_name: H3 acetylation ChIP DNA

tag: strain

value: H3 acetylation

value: Millipore


title: PON1.R192.DMSO_rep2


title: TR MG132 2h recovery, rep2

city: Seoul

first: Kong-Joo

last: Lee

address: Seodaemun-gu

department: College of Pharmacy

institute: Ewha Womans Univ.

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8 Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3  (Gene Expression Module v3.3.8).

source_name: TR, MD132, 2h recovery

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent.

value: TR

value: fibrosarcoma

tag: thermotolerance

value: thermotolerant

tag: treatment

tag: recovery time


title: TR DMSO control, rep2

source_name: TR, control


title: TR MG132 8.5h recovery, rep2

source_name: TR, MD132, 8.5h recovery


title: TR MG132 18h recovery, rep1

source_name: TR, MD132, 18h recovery


title: PON1.R192.DMSO_rep1

value: cerebellum

value: PND 22


title: TR MG132 18h recovery, rep2


title: H3K4me1+ sample

source_name: H3 K4 mono-methylation ChIP DNA

value: H3 K4 mono-methylation


title: H4 acetyl+ sample

source_name: H4 acetylation ChIP DNA

value: H4 acetylation


title: PON1.R192.0.5_rep4


title: PON1.R192.0.5_rep5


title: TR MG132 8.5h recovery, rep1


title: PON1.R192.DMSO_rep3


title: TR DMSO control, rep1


title: TR MG132 2h recovery, rep1


title: PON1.R192.0.5_rep3


title: PON1.R192.0.5_rep2


title: PON1.R192.0.5_rep1


title: RIF-1 MG132 8.5h recovery, rep2

source_name: RIF-1, MD132, 8.5h recovery

value: normal


title: RIF-1 MG132 18h recovery, rep2

source_name: RIF-1, MD132, 18h recovery


title: PON1.R192.0.35_rep5


title: RIF-1 MG132 2h recovery, rep2

source_name: RIF-1, MD132, 2h recovery


title: PON1.R192.0.35_rep4


title: RIF-1 DMSO control, rep2

source_name: RIF-1, control


title: H3K4K9ac biological replicate 3 [298468A01]

city: Madison

first: Yufeng

last: Wu

state: WI

address: 1575 Linden Drive

institute: UW-Madison

hyb_protocol: The combined and resuspended samples were then hybridized to the array for 16-20 hours at 42°C degrees with mixing.  Arrays were washed using Roche NimbleGen Wash Buffer System and dried using the NimbleGen Microarray Dryer (Roche NimbleGen, Inc).

scan_protocol: Arrays were scanned at 5 µm resolution using the GenePix4000B scanner (Axon Instruments).

data_processing: Data was extracted from scanned images using NimbleScan v2.4 data extraction software, which allows for extraction, grid alignment, and generation of data files. Raw data of H3K4me3, H3K36me3 and H3K4K9Ac were normalized by Biweight method.  Raw data of H3K4me2 was normalized by MA2C method (Song et al., 2007). All normalized data follow Gaussian distribution, which was required for the ChIPOTle (Buck et al., 2005), the method we used to identify the enriched region.  To remove the variance of replicates, the data were processed with Quantile normalization and then averaged.  Regions enriched with one of the four histone modifications were identified by ChIPOTle (Buck et al., 2005) program (version 1.11, slide window=600bp, step=150bp, α=0.01 after BH multiple comparison correction).  A minimum of five consecutive probes was required to be identified as an enriched region.

organism: Oryza sativa

source_name: H3K4K9ac ChIP

label_protocol: 1 μg of ChIP DNA and 1 μg of Input DNA were labeled using 5’ Cy3 or Cy5-labeled Random Nonamers, respectively (NimbleGen Dual Color DNA labeling Kit).  DNA was incubated for 3 hours at 37°C with 100 units (exo-) Klenow fragment and 10 μl of 10 mM dNTP mix (NimbleGen Dual Color DNA labeling Kit).  The labeled samples were then precipitated with NaCl and isopropanol and then rehydrated in 25 μl of VWR H20.  The IP and Input samples were combined in a 1.5 ml tube and dried down by SpeedVac.  Samples were resuspended in 5.6 μl of H20 and 14.4 μl of Roche NimbleGen Hybridization Buffer (NimbleGen Hybridization and Sample Tracking Control Kit) and incubated at 95°C.

extract_protocol: Approximately 5 g leaf tissue from 2-week old seedlings of rice variety Nipponbare was used in each ChIP experiment.  Rabbit polyclonal antibodies against H3K4me2 (Upstate 07-030), H3K4me2 (Abcam ab8580), H3K36me3 (Abcam ab9050,) and H3K4K9Ac (Upstate 06-599) were used in ChIP and rabbit normal serum for in Mock experiments.  We also took an aliquot from chromatin solution for input DNA, and the input DNA was not immunoprecipitated.  All DNAs from ChIP experiments were amplified using the GenomePlexTM Whole Genome Amplification (WGA) kit (Sigma-Aldrich) method with fragmentation reaction.  To reduce the bias of the amplification, amplifications were performed in eight tubes and mix into one tube.  The amplified DNAs were purified using PCR purification kit (Qiagen) with PB buffer instead PBI buffer

tag: developmental stage

value: seedling

value: leaf

tag: antibody

value: H3K4K9Ac (Upstate 06-599)

source_name: H3K4K9ac Input

value: none (input)


title: H3K4K9ac biological replicate 3 [298184A03]

tag: tissue


title: H3K4K9ac biological replicate 3 [298377A01]


title: H3K4K9ac biological replicate 3 [298375A03]


title: H3K4K9ac biological replicate 2 [298377A02]


title: H3K4K9ac biological replicate 2 [298468A03]


title: RIF-1 MG132 18h recovery, rep1

tag: cell line


title: PON1.R192.0.35_rep3

tag: age (at weaning)


title: PON1.R192.0.35_rep1


title: H3K4K9ac biological replicate 3 [298379A02]


title: H3K4K9ac biological replicate 2 [298184A02]


title: H3K4K9ac biological replicate 2 [298375A01]


title: PON1.Q192.DMSO_rep4


title: H3K4K9ac biological replicate 2 [298379A01]


title: RIF-1 MG132 2h recovery, rep1


title: RIF-1 MG132 8.5h recovery, rep1


title: H3K4K9ac biological replicate 2 [298378A03]


title: H3K4me2 biological replicate 3 [355377A01]

source_name: H3K4me2 ChIP

value: H3K4me2 (Upstate 07-030)

source_name: H3K4me2 Input


title: H3K4K9ac biological replicate 1 [298468A02]


title: H3K4K9ac biological replicate 1 [298378A01]


title: H3K4K9ac biological replicate 1 [298377A03]


title: H3K4me2 biological replicate 3 [357111A02]


title: H3K4K9ac biological replicate 3 [298378A02]


title: PON1.R192.0.35_rep2


title: H3K4K9ac biological replicate 1 [298184A01]


title: H3K4me2 biological replicate 3 [355990A02]


title: PON1.Q192.DMSO_rep3


title: TR heat shock 24h recovery, rep2

source_name: TR, heat shock, 24h recovery

value: heat shock


title: H3K4K9ac biological replicate 1 [298375A02]


title: PON1.Q192.DMSO_rep2


title: H3K4me2 biological replicate 3 [357415A03]


title: PON1.Q192.DMSO_rep1


title: H3K4me2 biological replicate 3 [358115A03]


title: H3K4me2 biological replicate 3 [357601A01]


title: PON1.Q192.0.5_rep5


title: H3K4K9ac biological replicate 1 [298379A03]


title: TR heat shock 4h recovery, rep2

source_name: TR, heat shock, 4h recovery


title: PON1.Q192.0.5_rep3


title: TR heat shock 12h recovery, rep2

source_name: TR, heat shock, 12h recovery


title: TR heat shock control, rep2

source_name: TR, heat shock, control


title: PON1.Q192.0.5_rep4


title: TR heat shock 24h recovery, rep1


title: H3K4me2 biological replicate 2 [355377A03]


title: H3K4me2 biological replicate 2 [358115A01]


title: H3K4me2 biological replicate 2 [357601A02]


title: RIF-1 DMSO control, rep1


title: PON1.Q192.0.5_rep2


title: H3K4me2 biological replicate 2 [357111A01]


title: TR heat shock 12h recovery, rep1


title: PON1.Q192.0.5_rep1


title: H3K4me2 biological replicate 2 [357415A02]


title: PON1.Q192.0.35_rep5


title: H3K4me2 biological replicate 1 [357111A03]


title: HeLa_Heat-shock_Rep3

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

country: India

institute: CSIR-Institute Of Genomics and Integrative Biology

description:
Sample Identifier
4090082075_F	Heat-shock_treated_Rep3

hyb_protocol: Samples were hybridized on Illumina Human WG-6 v2.0 Expression BeadChip using Illumina Protocol.

scan_protocol: After Hybridization and washing, the BeadChips were scanned using Illumina BeadArray Reader

data_processing: Scanned images were analyzed using Illumina BeadStudio software. Background subtraction was done and Average Normalization used. For differential expression Illumina Custom Error model was used and transcripts selected using Diff Score threshold of ±13 (equivalent to p-value 0.05).

source_name: HeLa cell line, Heat-shock treated

label_protocol: Sample was labelled using Illumina TotalPrep RNA Amplification Kit from Ambion.

growth_protocol: Cells were cultured in DMEM-High Glucose (SIGMA) supplemented with heat-inactivated 10% FCS and antibiotic mix (HiMedia)

extract_protocol: RNA was isolated using Trizol (Invitrogen). Purification was done using RNeasy Kit (Qiagen) to remove aromatic remnants.

treatment_protocol: Heat-shock treatment was given at 45 degree Celsius for 30 min. in water bath. This was followed by incubation of 2 hours for heat-shock recovery and response, at 37 degree Celsius and 5% CO2.

value: HeLa

value: Cervix

value: Female


title: PON1.Q192.0.35_rep4


title: HeLa_Untreated_Rep3

description:
Sample Identifier
4090082075_E	Untreated_Rep3

source_name: HeLa cell line, untreated control


title: TR heat shock 4h recovery, rep1

value: TR


title: RIF-1 heat shock 12h recovery, rep2

source_name: RIF-1, heat shock, 12h recovery

value: fibrosarcoma


title: PON1.Q192.0.35_rep3


title: H3K4me2 biological replicate 1 [358115A02]


title: HeLa_Heat-shock_Rep2

description:
Sample Identifier
4090082075_D	Heat-shock_treated_Rep2


title: H3K36me3 biological replicate 3 [290339A03]

source_name: H3K36me3 ChIP

value: H3K36me3 (Abcam ab9050)

source_name: H3K36me3 Input


title: H3K4me2 biological replicate 1 [357415A01]


title: HeLa_Untreated_Rep2

description:
Sample Identifier
4090082075_C	Untreated_Rep2


title: RIF-1 heat shock 4h recovery, rep2

source_name: RIF-1, heat shock, 4h recovery


title: H3K4me2 biological replicate 1 [355377A02]


title: H3K4me2 biological replicate 1 [357601A03]


title: H3K4me2 biological replicate 1 [355990A01]


title: TR heat shock control, rep1

value: thermotolerant


title: RIF-1 heat shock 24h recovery, rep2

source_name: RIF-1, heat shock, 24h recovery


title: H3K4me2 biological replicate 2 [355990A03]


title: H3K36me3 biological replicate 3 [287780A01]


title: HeLa_Heat-shock_Rep1

description:
Sample Identifier
4090082075_B	Heat-shock_treated_Rep1


title: RIF-1 heat shock control, rep2

source_name: RIF-1, heat shock, control


title: RIF-1 heat shock 24h recovery, rep1


title: PON1.Q192.0.35_rep2

value: cerebellum

value: PND 22


title: P. aeruginosa pure culture rep2

description: Gene expression data from pure culture

organism: Pseudomonas aeruginosa PAO1

source_name: P. aer. Pure culture

tag: culture

value: P. aeruginosa pure culture


title: H3K36me3 biological replicate 2 [290339A01]


title: PON1.KO.DMSO_rep3


title: PON1.KO.DMSO_rep4


title: H3K36me3 biological replicate 2 [290305A02]


title: H3K36me3 biological replicate 3 [290305A01]


title: HeLa_Untreated_Rep1

description:
Sample Identifier
4090082075_A	Untreated_Rep1


title: RIF-1 heat shock 12h recovery, rep1

tag: cell type

value: normal


title: P. aeruginosa pure culture rep1

description: Gene expression data from pure culture


title: H3K36me3 biological replicate 3 [290313A01]

value: seedling


title: H3K36me3 biological replicate 3 [287780A02]

value: leaf


title: H3K36me3 biological replicate 2 [287779A03]


title: PON1.KO.DMSO_rep2


title: RIF-1 heat shock 4h recovery, rep1


title: RIF-1 heat shock control, rep1


title: WT seed sibling to ise2, biological replicate 3

city: Berkeley

first: Patricia

last: Zambryski

address: 281 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

hyb_protocol: cDNA hybridization to chips was performed according to Affymetrix protocols for Arabidopsis GeneChip® 1.0R tiling arrays (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: Arabidopsis GeneChip® 1.0R tiling array slides were scanned using a GeneChip® Scanner 3000 7G following Affymetrix recommendations.

data_processing: Data analysis was performed with the Partek ®TM (Partek Incorporated, St. Louis, MO). Robust Multiarray Averaging (RMA) was used for normalization of expression values (log2) among replicates and background correction. All necessary quality control steps including examination of correlations between samples were taken. Genes with > 2-fold change were identified with one-way ANOVA (p<0.05).

label_protocol: DNA hybridization to the arrays was performed using the ApplauseTM WT-Amp Plus ST System (NuGen Technologies Inc, San Carlos, CA) according to the manufacturer’s instructions.

growth_protocol: Heterozygous ise1-1 and ise2-1 A. thaliana plants were grown in long day conditions (16 hr light/8 hr dark) in a growth chamber at 22oC under 120 µmol photons m-2 s–1 light.

extract_protocol: Fifty uL of RNA Later (Ambion, Austin, TX) were added to each of the three biological replicates in microcentrifuge tubes and samples were ground with pestles. Total RNA was extracted using Plant RNeasy Mini Kit (QIAGEN, Valencia, CA), following the manufacturer’s instructions.  The extracted RNA was quantified using a 2100 Bioanalyzer (Agilent, Santa Clara, CA). 400 ng total RNA from each sample was converted to cDNA, amplified to give 4 ug DNA.

treatment_protocol: Mutant seeds were identified by their white color compared to green wild-type seedlings, and collected and placed in liquid nitrogen before transferring to -80oC freezer for storage. Wild-type sibling embryos also were collected and frozen. Approximately 100 mutant seeds were collected for each of the 3 genotypes. Duplicate sets of seeds were collected 3 times from independent groups of plants grown under identical conditions for a total of 18 samples.

value: WT

value: seed

tag: ecotype

value: Landsberg


title: PON1.Q192.0.35_rep1


title: PON1.KO.DMSO_rep1


title: H3K36me3 biological replicate 2 [287779A02]

value: none (input)


title: H3K36me3 biological replicate 3 [287780A03]


title: P. aeruginosa and E. coli ZK126 culture rep1

description: Gene expression data from mixed culture

source_name: E. coli and P. aer. Mixed culture

value: P. aeruginosa and E. coli culture


title: PON1.KO.0.5_rep3


title: H3K36me3 biological replicate 2 [290313A03]


title: P. aeruginosa and E. coli ZK126 culture rep2

description: Gene expression data from mixed culture


title: ise2 mutant seed, biological replicate 3


title: H3K36me3 biological replicate 1 [290339A02]


title: WT seed sibling to ise2, biological replicate 1


title: CUTLL1 cells treated 48 hours with PF-03084014 plus dexamethasone (both 1 microM) 2

city: New York

first: Adolfo

last: Ferrando

state: NY

address: 1130 St. Nicholas Avenue, Irving Cancer Research Center, Room 402A

department: Institute for Cancer Genetics

institute: Columbia University

description: Second replica of CUTLL1 cells treated with PF-03084014 and dexamethasone in combination for 48h

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing: The samples were normalized using dChip and analyzed using the GenePattern software suite

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA using the GeneChip Affymetrix 3' IVT express kit

growth_protocol: CUTLL1 cells were grown in RPMI+20% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit according to manufacturers' instructions.

treatment_protocol: CUTLL1 cells were seeded 5e5 cells per mL media. The following morning, cells were treated with 1mL/mL DMSO, 1 microM PF-03084014, 1 microM dexamethasone, or 1 microM PF-03084014 plus 1 microM dexamethasone. Cells were cultured for 48 hours.


title: PON1.KO.0.5_rep1


title: ise2 mutant seed, biological replicate 2


title: H3K36me3 biological replicate 1 [290313A02]


title: CUTLL1 cells treated 48 hours with PF-03084014 plus dexamethasone (both 1 microM) 1

description: First replica of CUTLL1 cells treated with PF-03084014 and dexamethasone in combination for 48h


title: PON1.KO.0.35_rep4


title: PON1.KO.0.35_rep5


title: CUTLL1 cells treated 48 hours with 1 microM dexamethasone 1

description: First replica of CUTLL1 cells treated with dexamethasone for 48h

value: 1 microM dexamethasone


title: ise2 mutant seed, biological replicate 1


title: CUTLL1 cells treated 48 hours with 1 microM dexamethasone 2

description: Second replica of CUTLL1 cells treated with dexamethasone for 48h


title: H3K36me3 biological replicate 2 [287779A01]


title: CUTLL1 cells treated 48 hours with 1 microM PF-03084014 2

description: Second replica of CUTLL1 cells treated with PF-03084014 for 48h


title: WT seed sibling to ise1, biological replicate 2


title: PON1.KO.0.5_rep2


title: PON1.KO.0.35_rep3


title: PON1.KO.0.35_rep1


title: PON1.KO.0.35_rep2


title: WT seed sibling to ise1, biological replicate 1


title: CUTLL1 cells treated 48 hours with 1 microM PF-03084014 1

description: First replica of CUTLL1 cells treated with PF-03084014 for 48h


title: H3K36me3 biological replicate 1 [290305A03]


title: H3K36me3 biological replicate 1 [287762A02]


title: ise1 mutant seed, biological replicate 2


title: ise1 mutant seed, biological replicate 3


title: ise1 mutant seed, biological replicate 1


title: H3K36me3 biological replicate 1 [287762A03]


title: CUTLL1 cells treated 48 hours with DMSO 1

description: First replica of CUTLL1 cells treated with vehicle (DMSO) for 48h

source_name: CUTLL1 cells treated 48 hours with DMSO

value: DMSO


title: WT seed sibling to ise1, biological replicate 3


title: H3K36me3 biological replicate 1 [287762A01]


title: 066

city: North Grafton

first: Giovanni

last: Widmer

address: 200 Westboro Rd

institute: Tufts University

description: This set includes 7003 oligonucleotides, has 20160 spots distributed in 48 blocks. Protocol: 2QGL, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000

hyb_protocol: Oligonucleotides microarrays were from NIAID Pathogen Functional Genomics Research Center. The arrays (Giardia lamblia microarray version 2) contain 19,230 elements consisting of duplicates of 70-mer oligomers derived from 9,115 predicated open-reading frames (ORFs) including the clearly indentified 6,470 ORFs of the genome of G. lamblia WB C6 as described in the Giardia database and of 500 Arabidopsis thaliana control oligomers. To prehybridize, slides were placed in a coplin jar containing 50 ml preheated prehybridization buffer (20x SSC, 10% SDS, 0.5 g BSA) and incubated at 42˚C for 2 hr. Slides were then washed using filtered distilled water. Then the slides were washed in isopropyl alcohol for 2 m and dried by centrifugation. To perform hybridization, dried Cy3 labeled cDNA was dissolved in 50 µl of hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.1 M DTT).  In some experiments 2 µl of universal microarray standard set was added to the probe mixture, and denatured for 10 min at 95˚C. Then 50 µl of probe mixture was added to microarray slide and covered with LifterSlip coverslips (Erie Scientific). Slides were incubated in a 42˚C water bath for 16-20 hr. For post-hybridization wash slides were first submerged into a low stringency solution (2x SSC, 0.1% SDS) preheated to 55°C and washed twice for 5 m each on a shaker. Slides were subsequently washed twice in medium stringency solution (0.1x SSC, 0.1% SDS), followed by two more 5-m washes at high stringency (0.1x SSC) at room temperature.

scan_protocol: Slides were dried in a centrifuge and scanned with an Agilent scanner.

data_processing: Files in TIFF format generated by the microarray scanner were imported into TIGR Spotfinder 3.1.1. Spots were manually curated to exclude artifactual spots and background cut-off was set at 5%. Cy3 fluorescence values output by Spotfinder were exported to Microsoft Excel.

organism: Giardia duodenalis

source_name: trophozoites

label_protocol: A total of 2 µg cDNA was labelled using a Genomic DNA Enzymatic Labeling Kit from Agilent.

growth_protocol: Trophozoites of assemblage A isolate WB were cultured in TYI-S-33 medium.

extract_protocol: Total RNA for microarray analysis was isolated using Trizol from trophozoites and cysts following 3 cycles of freeze/thawing.  DNA was removed using the TurboDNase kit from Ambion and the RNA extracted with Qiagen RNeasy columns according to the RNA cleanup protocol. RNA was amplified in vitro with the WT-Ovation Pico RNA Amplification System (NuGEN).  For the amplification reaction up to 5 µl of total RNA sample (50 ng) was used as substrate.

treatment_protocol: G. lamblia cysts of assemblage B isolate H3 were purchased from Waterborne (New Orleans, LA).To induce excystation cysts were subjected to a two-step procedure (Bingham & Meyer, 1979) modified according to al-Tukhi et al.  (al-Tukhi et al., 1991). A suspension of 5 x 106 G. lamblia cyst was washed in PBS, mixed with nine parts of 1 N HCl and incubated at 37°C for 1 hr.  The suspension was then centrifuged at 800 × g for 10 min and the cyst pellet washed once with warm PBS. The cysts were then re-suspended in TYI-S-33 medium (Keister, 1983) pre-warmed to 37°C, and incubated at 37°C for 4hr.

tag: Stage

value: trophozoites


title: H3K4me3 biological replicate 3 [246177A02]

source_name: H3K4me3 ChIP

value: H3K4me3 (Abcam ab8580)

source_name: H3K4me3 Input


title: hematopoetic progenitor cell from human

city: Rochester

first: Yasuhiro

last: Ikeda

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description:
Gene expression data from blood-derived iPS cells.
HPC A1

hyb_protocol: The IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips at 45C for 16 h.

scan_protocol: Microarray analysis was performed using the Affymetrix HG-U133 Plus2 GeneChip Array platform, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip Scanner 3000 (Santa Clara, CA).

data_processing: The data were analyzed with a third party software to Affymetrix,  using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Pluripotent cells derived from human hematopoetic progenitor cell - de-identified

label_protocol: Briefly, RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA. Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: After vector infection, cells were maintained in HEScGRO medium (100 ml, Millipore) supplemented with mTeSR-1 maintenance media (25 ml, Stemcell Technologies). Seven  to ten days after vector infection, the reprogrammed cells began to form colonies with iPS morphology.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified using RNeasy Plus spin columns (QIAGEN). Turbo DNA-free DNase (Ambion, Austin, TX) was used to digest all genomic DNA that could lead to false positive gene expression results. The RNA quantity and purity was measured with a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE) and the RNA integrity determined using the Agilent 2100 Bioanalyzer (Santa Clara, CA).

treatment_protocol: iPSCs were grown on matrigel-treated plates were collected for RNA isolation.

value: DA1-derived iPS clone, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: human keratinocytes derived from surgical waste (#3)

description:
Gene expression data from human keratinocyte cells.
SW3 HK

source_name: Primary human keratinocytes

value: Human keratinocytes derived from an elderly 56-year-old female


title: human keratinocyte (SW4)-derived iPSC

description:
Gene expression data from human keratinocyte-derived iPS cells.
iPSC SW4 #N1

source_name: Pluripotent cells derived from primary human keratinocytes

value: SW4-derived iPS clone, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: WT seed sibling to ise2, biological replicate 2


title: H3K4me3 biological replicate 3 [246177A03]


title: H3K4me3 biological replicate 3 [239086A02]


title: human keratinocyte (SW3)-derived iPSC

description:
Gene expression data from human keratinocyte-derived iPS cells.
iPSC SW3 #b

value: SW3-derived iPS clone, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: H3K4me3 biological replicate 3 [246206A03]


title: human keratinocytes derived from surgical waste (#4)

description:
Gene expression data from human keratinocyte cells.
SW4 HK

value: Human keratinocytes derived from an elderly 57-year-old female


title: 750


title: 751


title: 749

source_name: cysts

value: cysts


title: H3K4me3 biological replicate 3 [246177A01]

value: seedling


title: iPSC from human PBMC (#1)

description:
Gene expression data from blood-derived iPS cells.
iPSC S1

source_name: Pluripotent cells derived from human blood cells - de-identified

value: Blood DS1-derived iPS clone, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: 747


title: iPSC from human cardiac fibroblasts

description:
Gene expression data from hematopoeitic progenitor cell-derived iPS cells.
iPSC HCF1

source_name: Pluripotent stem cells derived from primary HCFs (Thatava, T. et. al., Gene Therapy, 2011)

value: HCF-derived pluripotent stem cell, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: 065


title: 070


title: H3K4me3 biological replicate 2 [245565A03]

value: leaf


title: H3K4me3 biological replicate 2 [245565A02]


title: 069


title: Sample-57K TumKer

status: Public on Nov 08 2011

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Illumina Beadstudio 2.3, Bioconductor BeadarraSNP

source_name: FFPE Uterine cervix tumor, keratin positive, G0G1 population

label_protocol: DNA was prepared according to the standard Illumina protocol from 400 to 1000 ng of DNA

extract_protocol: DNA was isolated using an overnight digestion with proteinase K at 56 C. DNA was purified using the Promega Protein Precipitation solution.

treatment_protocol: The G0G1 vimentin-positive, keratin-negative stromal cell fractions and the vimentin-negative, keratin-positive tumour cells were flow-sorted using a FACSAria I flow-sorter at 40 psi with a 0.100 mm nozzle at a frequency of approximately 52.4 kHz in purity mode. The 488 nm and the 407 nm laser line were used for excitation.

tag: sample id

value: Uterine cervix tumor

tag: fraction

value: keratin positive, vimentin negative tumour cells

tag: dnaindex


title: H3K4me3 biological replicate 3 [235862A01]

value: none (input)


title: H3K4me3 biological replicate 2 [235862A03]


title: 128


title: iPSC from human PBMC (#3)

description:
Gene expression data from blood-derived iPS cells.
iPSC S3

value: Blood DS3-derived iPS clone, expressing 4 reprogramming factors (Klf4, c-Myc, Sox2, and Oct4)


title: Sample-56K TumKer


title: H3K4me3 biological replicate 2 [245565A01]


title: human keratinocytes derived from surgical waste (#8)

description:
Gene expression data from human keratinocyte cells.
SW8 HK

value: Human keratinocytes derived from a type-2 diabetic elderly female


title: Sample-55K TumKer


title: CUTLL1 cells treated 48 hours with DMSO 2

description: Second replica of CUTLL1 cells treated with vehicle (DMSO) for 48h

value: DMSO


title: H3K4me3 biological replicate 2 [246206A02]

value: H3K4me3 (Abcam ab8580)


title: Sample-7K TumKer


title: Sample-10K TumKer


title: Sample-58E Endometrium

source_name: FFPE endometrium, vimentin positive, G0G1 population

value: Endometrium

value: keratin negative, vimentin positive non-tumor cells


title: Sample-58V TumVim

source_name: FFPE Uterine cervix tumor, vimentin positive, G0G1 population

value: keratin negative, vimentin positive stromal cells


title: H3K4me3 biological replicate 1 [245552A01]


title: Sample-57V TumVim


title: Sample-57E Endometrium


title: Sample-56E Endometrium


title: H3K4me3 biological replicate 1 [245552A03]


title: H3K4me3 biological replicate 2 [239086A01]


title: Sample-53V TumVim


title: H3K4me3 biological replicate 1 [245552A02]


title: Sample-55V TumVim


title: Sample-52E Endometrium


title: Sample-52V TumVim


title: Sample-53E Endometrium


title: Sample-51V TumVim


title: Sample-56V TumVim


title: Sample-50E Endometrium


title: Sample-49V TumVim


title: Sample-54V TumVim


title: Stat5 SCBT

source_name: STAT5 ChIP DNA

tag: gender

value: female

tag: age

value: 6-8 week old

value: murine bone marrow transduced with epitope tagged forms of Hoxa9

value: Hoxa9-ER cells

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody catalog number

source_name: Input DNA

tag: sample type

value: input DNA


title: Sample-55E Endometrium


title: Sample-50V TumVim


title: H3K4trimethyl+

source_name: H3K4trimethyl ChIP DNA

tag: strain

value: Millipore


title: H3K4me3 biological replicate 1 [235862A02]

tag: developmental stage

value: seedling

tag: tissue

value: leaf

tag: antibody


title: Sample-49E Endometrium


title: Cebpa F

source_name: Cebpa ChIP DNA

tag: cell line

value: Cebpa

value: sc-61 X


title: Hoxa9

source_name: Hoxa9 ChIP DNA

tag: cell type


title: Sample-54E Endometrium


title: Sample-51E Endometrium


title: H3K4me3 biological replicate 1 [246206A01]

value: none (input)


title: Sample-45V TumVim

value: Uterine cervix tumor


title: Pu.1 SCBT

source_name: PU.1 ChIP DNA


title: Sample-47V TumVim


title: Sample-46E Endometrium


title: Sample-44E Endometrium


title: Sample-42E Endometrium


title: Sample-44V TumVim


title: Sample-48V TumVim


title: Sample-42V TumVim


title: Sample-43V TumVim


title: Sample-41E Endometrium


title: Sample-37E Endometrium


title: Sample-39E Endometrium


title: Sample-37V TumVim


title: Sample-43E Endometrium


title: H3K27trimethyl+

source_name: H3K27trimethyl ChIP DNA


title: Sample-46V TumVim


title: H3K4me3 biological replicate 1 [239086A03]

source_name: H3K4me3 ChIP

value: H3K4me3 (Abcam ab8580)

source_name: H3K4me3 Input


title: Sample-41V TumVim


title: Sample-39V TumVim


title: Sample-40V TumVim


title: Sample-40E Endometrium

value: Endometrium


title: Sample-38E Endometrium

value: keratin negative, vimentin positive non-tumor cells


title: Sample-36E Endometrium


title: Sample-36V TumVim

value: keratin negative, vimentin positive stromal cells


title: Sample-45E Endometrium


title: Sample-38V TumVim


title: Sample-35V TumVim


title: Sample-34E Endometrium


title: Sample-35E Endometrium


title: Sample-33E Endometrium


title: Sample-33V TumVim


title: Sample-32V TumVim


title: Sample-32E Endometrium


title: Sample-31V TumVim


title: Sample-48E Endometrium


title: Sample-30V TumVim


title: Sample-28V TumVim


title: Sample-31E Endometrium


title: Sample-30E Endometrium


title: Sample-29V TumVim


title: Sample-25E Endometrium


title: Sample-25V TumVim


title: Sample-34V TumVim


title: Sample-27V TumVim


title: Sample-27E Endometrium


title: Sample-26V TumVim


title: Sample-47E Endometrium


title: Sample-28E Endometrium


title: Sample-26E Endometrium


title: Sample-24E Endometrium


title: Sample-24V TumVim


title: Sample-22E Endometrium


title: Sample-29E Endometrium


title: Sample-23E Endometrium


title: Sample-21V TumVim


title: Sample-23V TumVim


title: Sample-18E Endometrium


title: Sample-12E Endometrium


title: Sample-15V TumVim


title: Sample-19V TumVim


title: Sample-17V TumVim


title: Sample-19E Endometrium


title: Sample-11V TumVim


title: Sample-20V TumVim


title: Sample-22V TumVim


title: Sample-20E Endometrium


title: Sample-18V TumVim


title: Sample-21E Endometrium


title: Sample-11E Endometrium


title: Sample-14E Endometrium


title: Sample-17E Endometrium


title: Sample-13E Endometrium


title: Sample-16V TumVim


title: Sample-15E Endometrium


title: Sample-12V TumVim


title: Sample-13V TumVim


title: Sample-14V TumVim


title: Sample-16E Endometrium


title: Sample-10E Endometrium


title: Sample-9V TumVim


title: Sample-9E Endometrium


title: Sample-8V TumVim


title: Sample-8E Endometrium


title: Sample-10V TumVim


title: Sample-7E Endometrium


title: Sample-7V TumVim


title: Sample-6V TumVim


title: Sample-5E Endometrium


title: Sample-1V TumVim


title: CPV Treatment of S. aureus - Experiment 2A

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

hyb_protocol: Labeled cDNA was purified using a Qiagen PCR purification kit and the purified labeled cDNA was hybridized with S. aureus genome microarrays  provided by the Pathogen Functional Genomics Resource Center (PFGRC). Before hybridization, slides were pre-hybridized with pre-hybridization buffer at 42˚C for 45 min. Pre-hybridized slides were washed with water (4 times) and isopropanol (3 times) for 2 min each and dried by centrifugation. Purified probes were speed-vaced and resuspended in hybridization buffer. The probes in hybridization buffer were applied to the microarray slides covered with lifterslips (Erie Scientific Co.). Hybridized slides were sealed in a water tight hybridization chamber. These chambers were incubated for 14-16 h in a 42˚C water bath. Hybridized arrays were then washed 2 times with low stringency, medium stringency, and high stringency buffers for 10 min at room temperature using a reciprocal shaking table.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 6.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html) software using one class mode.

organism: Staphylococcus aureus

source_name: CPV Treatment S. aureus - Control 2A

label_protocol: cDNA was generated by using random hexamers (Invitrogen) as primers for reverse transcription. The primers were annealed (70°C for 10 min, followed by snap-freezing in ice for 1 min) to total RNA (2 μg) and were extended with SuperScript II reverse transcriptase (Invitrogen) with 0.1 M dithiothreitol 12.5 mM dNTP/ aa-UTP (Ambion, Austin, TX) mix at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then labeled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instruction.

extract_protocol: Total bacterial RNA was extracted from 3 ml of culture which was mixed with 6 ml of bacterial RNA protect solution (Qiagen, Valencia, CA) and the mixture was centrifuged at 3000 rpm for 20 min in swinging-bucket rotor centrifuge to collect the cells. Pellets were resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY) and the cells were broken using the FastPrep system (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds. From the broken cell lysate RNA was extracted as per the manufacturer’s instructions. Extracted RNA was purified using the RNeasy mini kit (Qiagen). DNase treated and purified mRNA was used for microarray analysis.

treatment_protocol: For the transcriptional profiling study overnight grown S. aureus COL was inoculated in TSB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 600 nm until OD reached approximately 0.4.  Based on the GIC study ½ x MIC concentration of EO was added for 15 min of challenge. Control cultures were not challenged with EO and were also incubated for 15 min.

value: COL

tag: treatment

value: no EO

source_name: CPV Treatment S.aureus - Treatment 2A

value: EO


title: CPV Treatment of S. aureus - Experiment 1B

source_name: CPV Treatment S. aureus - Control 1B

treatment_protocol: For the transcriptional profiling study overnight grown S. aureus COL was inoculated in TSB medium (20 ml) in a 50 ml Erlenmeyer flask and incubated at 37°C, with shaking at 200 rpm. Growth was measured at regular intervals at 600 nm until OD reached approximately 0.4.  Based on the GIC study ½ x MIC concentration of EO was added for 15 min of challenge.


title: CPV Treatment of S. aureus - Experiment 2B

source_name: CPV Treatment S. aureus - Control 2B

source_name: CPV Treatment S. aureus - Treatment 2B


title: CPV Treatment of S. aureus - Experiment 3A

source_name: CPV Treatment S. aureus - Control 3A

source_name: CPV Treatment S. aureus - Treatment 3A


title: CPV Treatment of S. aureus - Experiment 1A

source_name: CPV Treatment S. aureus - Control 1A

source_name: CPV Treatment S. aureus - Treatment 1A


title: Sample-4V TumVim

source_name: FFPE Uterine cervix tumor, vimentin positive, G0G1 population


title: Sample-1E Endometrium

source_name: FFPE endometrium, vimentin positive, G0G1 population


title: Sample-6E Endometrium


title: Sample-5V TumVim


title: Sample-2E Endometrium


title: Sample-3V TumVim


title: Sample-4E Endometrium


title: CPV Treatment of S. aureus - Experiment 3B

source_name: CPV Treatment S. aureus - Control 3B

source_name: CPV Treatment S. aureus - Treatment 3B


title: UMA07192

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description: A_4×44K_251485053225-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7192

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction Mammoplasty

extract_protocol: Qiagen RNeasy Kit.

value: normal breast

tag: bmi


title: UMA07199

description: A_4×44K_251485053221-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7199

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).


title: UMA07198

description: A_4×44K_251485053225-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7198


title: Sample-2V TumVim

tag: sample id

tag: fraction


title: Sample-3E Endometrium

tag: dnaindex


title: UMA07194

description: A_4×44K_251485053225-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7194


title: UMA07190

description: A_4×44K_251485053224-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7190


title: UMA07195

description: A_4×44K_251485053225-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7195


title: UMA07181

description: A_4×44K_251485053223-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7181


title: UMA07189

description: A_4×44K_251485053333-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7189


title: UMA07177

description: A_4×44K_251485053224-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7177


title: UMA07180

description: A_4×44K_251485053223-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7180


title: UMA07177_rep1

description: A_4×44K_251485053333-2Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7177


title: UMA07188

description: A_4×44K_251485053224-3Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7188


title: UMA07170

description: A_4×44K_251485051501-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7170


title: UMA07179

description: A_4×44K_251485053223-1Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7179


title: UMA07178

description: A_4×44K_251485053222-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7178


title: Subject 10_t=30days_placebo

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Human Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. For this experiment 20 arrays were used. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0).

source_name: after 30 days intervention with placebo

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Ten healthy obese men (age 45–65 years; BMI 30-35 kg/m2) participated in a double-blind randomized cross-over study. Exclusion criteria were unstable body weight (weight gain or loss > 3 kg in the last three months), total body fat (%) < 25%, fasting plasma glucose > 6.1 mmol/l, hemoglobin < 7.8 mmol/l, engagement in programmed exercise > 2 hours total per week, impaired kidney and/ or hepatic function, first- or second-degree family member with type 2 diabetes mellitus, any medical condition requiring treatment and/or medication use, intake of dietary supplements except vitamins and minerals, unwilling to restrict high-resveratrol-containing foods, current alcohol consumption > 20 grams/day, participation in another biomedical study within 1 month before the first screening visit, a contraindication to MRI scanning. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

extract_protocol: Skeletal muscle biopsies were taken in the morning of day 30 after an overnight fast. Biopsies were obtained from the vastus lateralis muscle under local anesthesia of the skin and fascia using the Bergström method with suction, cleaned from any visible fat and blood, immediately frozen in isopentane at its melting point, and stored at −80C until analysis.

treatment_protocol: The design of the study was a randomized cross-over design with two different treatments: placebo and resVida (150mg/day trans-resveratrol). Subjects were instructed to take the first supplement on the day after baseline measurements (d1) and the last supplement in the evening on day 29. In the morning of day 30, after a 36h in the respiration chamber, a muscle biopsy was taken, which was followed by the withdrawal of a fasting blood sample.

tag: ethnic background

value: Caucasian

tag: gender

value: male

tag: age

value: 45-65 years

value: vastus lateralis muscle


title: UMA07185

description: A_4×44K_251485053223-4Agilent Catalog 4 by 44k whole genome array of reduction mammoplasty patient7185


title: Subject 8_t=30days_resveratrol

source_name: after 30 days intervention with resveratrol


title: Subject 9_t=30days_resveratrol