title: EtOH treated H4Ac, replicate #2

description: ChIP-chip H4Ac EtOH-treated Drosophila heads.

source_name: H4Ac ChIP DNA from EtOH-treated Drosophila heads

treatment_protocol: Ethanol vapor exposure for 15 minutes, 6 hrs before chromatin extraction.

value: ethanol alcohol

treatment_protocol: Control: No EtOH exposure, 6 hrs before chromatin extraction.


title: EtOH treated H4Ac, replicate #1

status: Public on Sep 05 2013

type: genomic

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

country: USA

institute: University of Puerto Rico, Rio Piedras

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

molecule: genomic DNA

organism: Drosophila melanogaster

label_protocol: 1 µg amplified ChIP DNA prepared from fly heads was labeled by Klenow random priming with Cy5 or Cy3 nonamers per manufacturer's protocol, by Nimblegen personnel (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Adult Drosophila were raised on standard cornmeal agar medium in a 12/12 h light/dark cycle for 3-5 days.

extract_protocol: 500 wild-type flies were sedated with either ethanol, benzyl alcohol or mock sedated for 15 min and then were allowed to recover in a drug-free environment for 6 hours. After recovery, flies were collected, frozen in liquid nitrogen, and vortex decapitated, and then heads were collected by sieving. Heads were cross-linked with 2% formaldehyde for 5 min, and chromatin was solubilized and sonicated on ice 6x30 s, followed by 1 min cooling on ice to produce fragments of approximately 500 bp with a sonic Dismembrator 250 (Fisher Scientific). Chromatin samples (2 ug) were immunoprecipitated using a 1:200 dilution of ChIP grade antibody against acetylated histone H4 at lysine 5, 8, 12 and 16 (catalog # 06-866; EMD Millipore Corporation, Billerica, MA). A fraction (1/10) of the chromatin sample was left unprecipitated for use as input control. DNA from immunoprecipitated (ChIP) and input samples was washed, reversed cross-linked, and purified and subsequently amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO) following the manufacturer's protocol. Approximately 1 ug of amplified ChIP and input DNA from each sample was sent to NimbleGen (Roche NimbleGen, Inc. Madison, WI) for two-color hybridization to Drosophila ChIP-chip 2.1M Whole-Genome Tiling Arrays.

tag: genotype/variation

value: wild-type

tag: developmental stage

value: adult

tag: tissue

value: head

tag: treatment

tag: chip antibody

source_name: H4Ac ChIP DNA from untreated Drosophila heads


title: heart_HFD_RSG_1

type: RNA

city: Berlin

first: Christopher

last: Weidner

address: Ihnestraße 63

department: Otto Warburg Laboratory

country: Germany

institute: Max Planck-Institute for Molecular Genetics

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline normalization implemented in Illumina GenomeStudio V2011.1.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Heart_HFD_rosiglitazone posttreatment

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: Heart tissue was first lysed and homogenized in RLT buffer (QIAGEN) with 5 mm steel beads at 20 Hz for 4 min (TissueLyser, QIAGEN). Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser

tag: strain

tag: gender

value: male

tag: age

value: 21 wks

value: heart

tag: pre-treated with

value: high-fat diet (HFD) for 12 wks

tag: treated with

value: HFD with 4 mg/kg/d rosiglitazone (RGS) for 3 wks


title: heart_HFD_3

description: replicate 3

value: HFD without compound for 3wks


title: N/Tert-empty vector cell line #1, no MMC treatment, replicate 1

city: Philadelphia

first: Elizabeth

middle: A

last: White

state: PA

address: 3610 Hamilton Walk

department: Otorhinolaryngology

institute: University of Pennsylvania

description: gene expression data from untreated N/Tert cells

hyb_protocol: Hybridization was performed by injecting the hybridization cocktail containing fragmented aRNA into Array and incubated at 45oC for about 16 hours with 60 rpm rotation in GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: The image was acquired by scanning the arrays using GeneChip 7G Plus Scanner (Affymetrix).

data_processing: Raw data (.cel files) from individual gene chips were compiled and normalized using Affymetrix Power Tools using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization) then filtered to exclude expression values <80 using the preprocessDataset module in GenePattern software (Broad Institute).

label: biotin

organism: Homo sapiens

source_name: N/Tert-empty vector cells treated with vehicle control

label_protocol: Biotin-labeled aRNA was synthesized using GeneChip 3’ IVT Express Kit (Affymetrix P/N: 901229-A, 901229-D) in GeneAmp PCR System 9700 (Applied Biosystems)

growth_protocol: N/Tert-1 cells stably harboring empty or E6 expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 4 ug/ml hygromycin and 0.5 ug/ml puromycin

extract_protocol: RNA was extracted with the Qiagen RNeasy mini kit according to the manufacturer's protocol

treatment_protocol: Cells were treated with 2ug/ml mitomycin C or vehicle control (water) in K-SFM protio to harvest by trypsinization and freezing of cell pellets.

tag: cell line

tag: cell type

value: human foreskin keratinocytes immortalized with hTert

tag: retroviral vector

value: MSCV-IP N HAonly emptyV2


title: heart_HFD_1

description: replicate 1


title: N/Tert-empty vector cell line #1, no MMC treatment, replicate 2


title: Chorion_RUPP_3

city: Jackson

first: Eric

last: George

state: MS

address: 2500 N. State St

department: Physiology and Biophysics

institute: U of MS Medical Center

hyb_protocol: RNA samples were processed per manufactures directions for specific application [GeneChip® 1.0 ST] using Affymetrix equipment (Scanner 3000 7G System).

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

data_processing:
Analysis of microarray data was performed using software provided by Affymetrix (Affymetrix® Expression Console™ Software);
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061
Data were further analyzed using commercially available GeneSifter™ software platform (http://www.genesifter.net) and/or Array Star 5 (DNASTAR, Inc, WI). In brief, differentially expressed genes evaluated by t-test using two methods: (1) FWER (family-wise error rate) procedure, p<0.05 and fold-change ±1.2 or greater; and/or (2) Benjamani and Hochberg FDR (false discovery rate) which corrects for multiple comparison, using p<0.05, and fold-change ±1.2 or greater.  Two-way ANOVA using a p<0.01 or lower was performed to identify interaction effects between groups. Gene networks and functional analysis were evaluated through the use of Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com).

organism: Rattus norvegicus

source_name: placental chorion_5 days ischemia

extract_protocol: RNA was isolated using TRIzol and Invitrogen PureLink Kits per manufacturer protocols.

treatment_protocol: Pregnant rats which underwent mechanical blood flow restriction to the uteroplacental unit on gestational day 14.  Tissues harvested on gestational day 19

tag: strain background

value: Sprague Dawley

value: female

tag: sample group

value: 5 days ischemia

value: placental chorion


title: heart_HFD_2

description: replicate 2


title: Chorion_RUPP_4

label_protocol: RNA samples were processed per manufactures directions for specific application [GeneChip® 1.0 ST] using Affymetrix equipment (Scanner 3000 7G System).


title: Chorion_RUPP_5


title: Chorion_RUPP_6


title: Chorion_Ctrl_6

source_name: placental chorion_normal pregnancy

value: Normal control pregnant rats


title: Chorion_RUPP_2


title: BM-Vec

city: Taipei

first: Jui-Yu

last: Hsieh

address: No. 155, Sec 2, Li-Nong Street

country: Taiwan

institute: National Yang-Ming University

description: BM-MSC transduced with pCDH-CMV-MSC-EF1-copGFP

hyb_protocol: cRNA were hybridized, washed and stained on U133 plus 2.0 chips according to standard Affymetrix protocol.

scan_protocol: Chips are stained on Affymetrix GCS3000 scanner (scanner type M10)

data_processing: The CEL file was loaded to R/Bioconductor software and normalized by GC-RMA with default settings.

source_name: MSC, human bone marrow

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

growth_protocol: All MSCs were cultured in MesenCult® (Stem Cells Technology) medium at 37°C in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted by Tri-Reagent (Sigma) according to the manufacturer's instructions.

value: MSC, human bone marrow

tag: manipulation

value: transduced with pCDH-CMV-MSC-EF1-copGFP

tag: passages

value: < 10 passages


title: Chorion_Ctrl_5


title: WJ-si146a

description: WJ-MSCs transfected with si146a after 3 days

source_name: MSC, human Wharton's jelly of umbilical cord

value: transfected with si146a after 3 days


title: PBMCs from untreated pSS patient, pSS9

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

description: Total RNA from isolated PBMCs.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 80μl of hyb solution to each array, then tape holes and parafilm. Hybridize 17 hours at 45° at 60rpm.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
Probe group file: HuGene-1_0-st-v1.r4.pgf
Meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: Peripheral blood mononuclear cells (PBMCs), Sjögren's syndrome patient

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit.

growth_protocol: Not applicable.

extract_protocol: Peripheral blood was collected in heparinized tubes and peripheral blood mononuclear cells were isolated using Ficoll. Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN).

treatment_protocol: Not applicable.

tag: disease status

value: Sjögren's syndrome

value: peripheral blood mononuclear cells (PBMCs)


title: PBMCs from untreated pSS patient, pSS8

description: Total RNA from isolated PBMCs.


title: BM-146a

description: BM-MSC transduced with pCDH-146a

value: transduced with pCDH-146a


title: Chorion_RUPP_1


title: PBMCs from untreated pSS patient, pSS10

description: Total RNA from isolated PBMCs.


title: Chorion_Ctrl_4


title: PBMCs from untreated pSS patient, pSS11

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS7

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS6

description: Total RNA from isolated PBMCs.


title: WJ-siGFP

description: WJ-MSCs transfected with siGFP after 3 days

value: MSC, human Wharton's jelly of umbilical cord

value: transfected with siGFP after 3 days


title: PBMCs from healthy control, HC14

description: Total RNA from isolated PBMCs.

source_name: Peripheral blood mononuclear cells (PBMCs), healthy control

value: healthy


title: PBMCs from untreated pSS patient, pSS2

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC15

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS1

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC16

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS3

description: Total RNA from isolated PBMCs.


title: Chorion_Ctrl_2


title: PBMCs from healthy control, HC12

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS5

description: Total RNA from isolated PBMCs.


title: Chorion_Ctrl_3


title: GSC8_shScr_rep2

city: Kaifeng

first: Xiong

last: Jin

state: Henan

address: Jin Ming Avenue

department: School of Pharmacy

country: China

institute: Henan University

hyb_protocol: 0.75μg of cRNA were hybridized to the Illumina Human HT-12 Expression BeadChip according the protocols provided by the manufacturer.

scan_protocol: The arrays were scanned on illumine Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v20092 (Gene Expression Module v1.5.4). And there is a filtering and normalizing system performed by the manufacturer (Macrogen Inc. Republic of Korea). Filtering: Genes which detection p-value is less than 0.05 are selected. Detection p-value<0.05 means signal of the probe is higher than background. Transformation: All filtered genes are transformed by logarithm(base 2) for the purpose of decrease of signal range and less sensitivity to outliers. Normalization: Quantile normalization is used in this step to reduce the systematic biases from sample preparation, variability in hybridization,spatial effects, scanner settings, and experimenter bias.

source_name: Cultured GSC8

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

growth_protocol: All cells were cultured using Neurobasal medium (NBE; Invitrogen) supplemented with modified N2, B27, epidermal growth factor (EGF, 20 ng/ml; R&D Systems), and basic fibroblast growth factor (bFGF, 20 ng/ml; R&D Systems) in suspension.

extract_protocol: Total RNA was isolated from cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

value: glioma stem cells

value: GSC8 cells

tag: transfection

value: pSuper-GFP-Scramble-shRNA


title: PBMCs from healthy control, HC10

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC11

description: Total RNA from isolated PBMCs.


title: PBMCs from untreated pSS patient, pSS4

description: Total RNA from isolated PBMCs.


title: GSC8_shScr_rep3


title: PBMCs from healthy control, HC4

description: Total RNA from isolated PBMCs.


title: GSC2_shScr_rep3

source_name: Cultured GSC2

value: GSC2 cells


title: PBMCs from healthy control, HC5

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC9

description: Total RNA from isolated PBMCs.


title: Chorion_Ctrl_1

value: Sprague Dawley

value: female

tag: tissue


title: GSC8_shScr_rep1


title: GSC2_shScr_rep2


title: PBMCs from healthy control, HC2

description: Total RNA from isolated PBMCs.


title: GSC2_shScr_rep1


title: PBMCs from healthy control, HC7

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC3

description: Total RNA from isolated PBMCs.


title: Naïve

city: Portland

first: Theresa

last: Lusardi

state: Oregon

address: 2720 SW Moody Avenue

department: Knight Cancer Institute

institute: OHSU

description: Naïve

hyb_protocol: Samples were co-hybridized using the NimbleGen Hybridization System.

scan_protocol: Arrays were scanned using the Nimblegen MS 200 Microarray Scanner.

data_processing: Arrays were processed using Nimblescan V 2.6 software.

organism: Rattus rattus

source_name: naïve_5mC IP

label_protocol: Total and 5-mC enriched genomic DNA were labeled using the NimbleGen Dual-Color DNA Labeling Kit.

extract_protocol: Total genomic DNA was isolated from fresh frozen tissues using a DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA).

value: male

value: hippocampus

tag: molecule subtype

value: 5-mC enriched genomic DNA

source_name: naïve_total DNA


title: PBMCs from healthy control, HC1

description: Total RNA from isolated PBMCs.


title: PBMCs from healthy control, HC8

description: Total RNA from isolated PBMCs.


title: WB-RSV-m224

city: London

first: Jethro

last: Herberg

address: Norfolk Place

department: Section of Paediatrics

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

data_processing: The data were normalised using Genome Studio, with background subtracted and quantile normalised.

source_name: Whole Blood from patient with RSV infection

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

tag: infecting pathogen

value: RSV

value: whole blood


title: WB-RSV-m214


title: Epileptic + Adenosine treated

source_name: Epileptic_Adenosine 5d_5mC IP

treatment_protocol: Epileptic + 5 days adenosine

tag: strain

source_name: Epileptic_Adenosine 5d_total DNA


title: Epileptic

description: KA

source_name: Epileptic_5mC IP

treatment_protocol: Epileptic: 9 weeks post kainic acid induced status epilepticus

tag: gender

source_name: Epileptic_total DNA


title: PBMCs from healthy control, HC6

description: Total RNA from isolated PBMCs.


title: GSC8_shID1_rep2


title: GSC8_shID1_rep1


title: GSC2_shID1_rep2


title: GSC2_shID1_rep3


title: WB-RSV-m189


title: WB-RSV-m220


title: NL12_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters (Protocol:GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Normal liver tissue control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tumor stage

tag: etiology

tag: sample type

value: Normal liver tissue control

tag: material

tag: age (yrs)

tag: tumor size [cm]


title: GSC8_shID1_rep3

tag: cell type

tag: cell line


title: WB-RSV-m140


title: WB-RSV-m252


title: HCC-Grad:G2_9_B

source_name: HCC liver tissue

value: hepatocellular carcinoma (HCC)


title: WB-RSV-m153


title: GSC2_shID1_rep1


title: WB-RSV-m128


title: c-FostetON Keratinocyte. 72h. Replicate 4.

first: Marc

last: Zapatka

address: Im Neuenheimer Feld 580

department: B060 Molecular Genetics

institute: German Cancer Research Center

hyb_protocol: RNA of samples was hybridized to the Illumina MouseRef-8 V2 R3 BeadChip array according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Microarray scanning was done using a Beadstation array scanner.

data_processing:
Raw data files from the Illumina chip quantification.
Data preprocessing and quality control was conducted using packages of the Bioconductor project implemented in our in-house developed ChipYard framework for microarray data analysis (http://www.dkfz.de/genetics/ChipYard/). In summary microarray probes were annotated based on Ensembl (version 58) using an in house BLAST-based pipeline. Before normalization with variance-stabilizing transformation (VST) and robust spline normalization (RSN) algorithms beads with signals below the negative controls were removed and positive negative and hybridization controls were excluded.

source_name: Keratinocytes from the tail

label_protocol: Standard Illumina protocol

growth_protocol: Isolation and culture of mouse primary tail keratinocytes was performed as described elsewhere (Zenz et al., 2003). 24h after plating, keratinocyte media was changed to KC-SFM (Gibco). Keratinocytes were cultured at 32ºC. Medium was changed every other day and, if needed, supplemented with Dox at 1μg/L. Cells were collected at different time points after Dox treatment.

extract_protocol: RNA was extracted using Trizol.

treatment_protocol: c-FostetON keratinocytes were cultured in the presence/abscence of 1ug/ml of Doxicycline.

value: c-FostetON keratinocytes

tag: treatment

value: untreated

tag: time


title: WB-RSV-m142


title: c-FostetON Keratinocyte. 72h DOX. Replicate 3.

value: DOX


title: NL01_2


title: WB-RSV-m150


title: c-FostetON Keratinocyte. 72h DOX. Replicate 4.


title: WB-RSV-m135


title: WB-RSV-m78


title: WB-RSV-m129


title: NL10_2

value: Rx


title: WB-RSV-m158


title: WB-RSV-m147


title: WB-RSV-m137


title: WB-RSV-m92


title: c-FostetON Keratinocyte. 72h DOX. Replicate 2.


title: HCC-Grad:G2_8_B


title: WB-RSV-m70


title: c-FostetON Keratinocyte. 72h DOX. Replicate 1.


title: WB-RSV-m77


title: HCC-Grad:G2/3_3_B


title: WB-RSV-m19


title: c-FostetON Keratinocyte. 72h. Replicate 2.


title: HCC035: C2_C

value: alcohol abuse


title: WB-RSV-m69


title: c-FostetON Keratinocyte. 72h. Replicate 1.


title: HCC072: alpha1-Antitrypsinmangel_B

value: Alpha-1 antitrypsin deficiency

value: Tx


title: c-FostetON Keratinocyte. 72h. Replicate 3.


title: WB-H1N1-m12

source_name: Whole Blood from patient with H1N1/09 influenza infection

value: Influenza A H1N1/09


title: NL15


title: NL12_1


title: NL13


title: NL14


title: WB-H1N1-m138


title: WB-H1N1-m95


title: c-FostetON Keratinocyte. 48h DOX. Replicate 2.


title: c-FostetON Keratinocyte. 48h DOX. Replicate 1.


title: WB-H1N1-m73


title: WB-H1N1-m63


title: WB-H1N1-m72


title: WB-H1N1-m60


title: PBMCs from healthy control, HC13

description: Total RNA from isolated PBMCs.

tag: disease status

value: healthy

value: peripheral blood mononuclear cells (PBMCs)


title: WB-H1N1-m208

value: female


title: c-FostetON Keratinocyte. 48h. Replicate 3.


title: WB-H1N1-m51

value: male


title: WB-H1N1-m61


title: WB-H1N1-m94


title: c-FostetON Keratinocyte. 48h. Replicate 2.


title: c-FostetON Keratinocyte. 24h DOX. Replicate 3.


title: WB-H1N1-m57


title: WB-H1N1-m39


title: WB-H1N1-m155


title: NL10_1


title: WB-H1N1-m48


title: c-FostetON Keratinocyte. 48h. Replicate 1.


title: NL11


title: c-FostetON Keratinocyte. 24h DOX. Replicate 2.


title: HCC-Grad:G2_5 rep2


title: PLC

source_name: cell line control

value: cell line control


title: WB-H1N1-m37


title: WB-H1N1-m28


title: WB-control-m234

source_name: Whole Blood from healthy control


title: c-FostetON Keratinocyte. 24h DOX. Replicate 1.


title: WB-H1N1-m2


title: HCC035: C2_B


title: WB-H1N1-m1


title: NL01_1


title: M2-2

city: Kumamoto

first: Hidetaka

last: Sugihara

address: 1-1-1 Honjo

country: Japan

institute: Kumamoto university

description:
SAMPLE 3
253118112748_1_4
gastric cancer cell line and leukemia cell line
miRNA expression after 24hr incubation

hyb_protocol: Agilent Human 8 x 60K miRNA Array was performed on the two pooled samples. Hybridization was carried out according to the instructions of the Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09). Probe intensities were normalized using GeneSpring 12.0 through percentile shift normalization. Differentially expressed miRNAs were identified through Fold Change filtering (Fold change <0.5).

source_name: AGS co-cultured with M2 macrophage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Agilent's miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.

growth_protocol: AGS cancer cell lines  were cultured in 5% CO2 at 37°C in RPMI 1640 supplemented with 10% fetal bovine serum (FBS). THP-1 cancer cells were cultured under 5% CO2 at 37°C in RPMI 1640 supplemented with inactivated 10% FBS.

extract_protocol: miRNA was isolated from cell lines using a mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) following the manufacturer's recommendations. miRNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: M1- or M2-polarized THP-1 macrophages were co-cultured in upper inserts with AGS cells in 6-well plates (1 × 105 cells/well) without direct contact. After 24 h of co-culture, the upper inserts containing macrophages were discarded. AGS cells were collected.

value: AGS gastric cancer cell line

tag: co-cultured with

value: M2 macrophage


title: WB-control-m231

tag: tissue

value: whole blood


title: M1-2

description:
SAMPLE 2
253118112748_1_2
gastric cancer cell line and leukemia cell line
miRNA expression after 24hr incubation

source_name: AGS co-cultured with M1 macrophage

value: M1 macrophage


title: WB-control-m222


title: WB-control-m223


title: HCC-Grad:G2/3_5

value: hepatocellular carcinoma (HCC)


title: c-FostetON Keratinocyte. 24h. Replicate 3.

value: c-FostetON keratinocytes

value: untreated


title: c-FostetON Keratinocyte. 24h. Replicate 2.


title: HCC-Grad:G2/3_4


title: WB-control-m211


title: c-FostetON Keratinocyte. 24h. Replicate 1.


title: HCC-Grad:G3_2


title: WB-control-m212


title: HCC-Grad:G3_1


title: WB-control-m219


title: c-FostetON Keratinocyte. 12h DOX. Replicate 3.

value: DOX


title: HuH7


title: Control-2

description:
SAMPLE 1
253118112748_1_1
AGS gastric cancer cell line
miRNA expression after 24hr incubation

source_name: AGS only

value: control


title: c-FostetON Keratinocyte. 12h DOX. Replicate 1.


title: WB-control-m207


title: c-FostetON Keratinocyte. 12h DOX. Replicate 2.


title: c-FostetON Keratinocyte. 6h DOX. Replicate 3.


title: WB-control-m199


title: c-FostetON Keratinocyte. 12h. Replicate 2.


title: HepG2


title: HCC061: C2

value: alcohol abuse


title: WB-control-m190


title: WB-control-m200


title: HCC072: alpha1-Antitrypsinmangel_A

value: Alpha-1 antitrypsin deficiency

value: Tx


title: c-FostetON Keratinocyte. 6h DOX. Replicate 2.


title: WB-control-m201


title: HCC058: HFE

value: genetic hemochromatosis

value: x


title: WB-control-m198

value: female


title: c-FostetON Keratinocyte. 12h. Replicate 1.


title: c-FostetON Keratinocyte. 6h DOX. Replicate 1.


title: WB-control-m186

value: male


title: HCC015: HBV

value: HBV

value: Rx


title: WB-control-m185


title: HCC041: C2


title: c-FostetON Keratinocyte. 6h. Replicate 2.


title: HCC023: C2


title: c-FostetON Keratinocyte. 6h. Replicate 1.


title: HCC057: HBV


title: WB-control-m184


title: WB-RSV-m34

value: RSV


title: IMB-1 ChIP-chip in N2 mixed-stage embryos (387661)

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
SDQ4154_IMB1_EE6_N2_MXEMB
Mixed stage N2 C. elegans embryos

hyb_protocol: DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.

scan_protocol: Array scanning and raw data extraction were performed according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted and saved as .pair files by using NimbleScan software v2.5 according to the NimbleScan User's Guide

data_processing:
ChIP-chip_normalization_standard_MA2C_v2. First, all the IP and INPUT log ratio values are read from the pairdata file. Secondly, we build GC bins for INPUT and IP based on the GC counts for every probe sequence, which means that the INPUT or IP values for any probes which have the same GC counts will be put together. After that, for each GC bin, we calculate the mean for IP and INPUT data, and the covariance between this two channels. By default, the robust mean variance method is applied, which generalizes Tukey's theory of bi-weight estimation where the constant C is set to 2.  At last, we adjust the log ratio values for each probe by using the mean and covariance values for their corresponding GC bins, then these values are further normalized by their mean and standard derivation. In a single experiment, median within the sliding window defined by 2x bandwidth parameter is assigned as MA2C score at the center of each probe. In case of replicates, when we calculate the MA2Cscore afterwards, we take the median as the score from all the replicates for all the probes within the sliding window defined by 2x bandwidth parameter.  Processed data are obtained using following parameters: genome version is WS190
Genome_build: WS190
Supplementary_files_format_and_content:  .wig file reports MA2C score.

organism: Caenorhabditis elegans

growth_protocol: The C. elegans N2 strain animals in the liquid S-medium were fed with bacteria HB101 until becoming gravid adults. Mixed-stage embryos were harvested from the adults by hypochlorite treatment.

extract_protocol: The C. elegans N2 strain mixed-stage embryos were cross-linked in 2% formaldehyde for 30 min at 25ºC. Chromatin extract was prepared by sonication in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl). Five to ten micrograms of antibodies were immobilized on sepharose beads and incubated with the chromatin extract for >12 hours at 4ºC. After washing the immunoprecipitants followed by RNase treatment and reverse-crosslinking, DNA were extracted and purified.

treatment_protocol: For RNAi, the N2 strain worms were first arrested at the L1 larva stage in the liquid S medium for synchronization. Synchronized L1 worms were fed with a bacteria strain HB101, which do not contain induction vectors, at 20ºC for 36 hours (L4 stage) in the liquid S medium. L4 worms were harvested, washed and transferred to a new S medium supplemented with a bacteria strain HT115 expressing interfering double-strand RNA from L4440 vector under IPTG (RNAi bacteria). Worms were grown with the RNAi bacteria at 20ºC until the gravid stage. Embryos were harvested from the gravid adults by hypochlorite treatment and used in experiments. In parallel, worms were fed with HT115 bacteria bearing L4440 vector without target DNA insertion (empty vector RNAi).

value: no treatment

tag: chip antibody

value: SDQ4154_IMB1 [not commercial]

value: input control


title: IMB-1 ChIP-chip in N2 mixed-stage embryos (388119)

description:
SDQ4154_IMB1_EE8_N2_MXEMB
Mixed stage N2 C. elegans embryos

label_protocol: DNA was labeled and hybridized to NimbleGen C. elegans tiling array (HD2) according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008 with slight modifications. Briefly, amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42°C.


title: Met fl/fl_HPC 3

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by means of  Genome Studio v2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: Met fl/fl_HPC

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

tag: strain backgroud

tag: genotype/variation

value: Met fl/fl

value: liver

value: hepatic progenitor cells (HPC)


title: Met fl/fl_HPC 1

description: SAMPLE 4


title: HCC035: C2_A

value: hepatocellular carcinoma (HCC)

tag: gender


title: HCC-Grad:G2_8_A

tag: tumor stage


title: WB-control-m176

tag: infecting pathogen

value: whole blood


title: WB-control-m166


title: HCC-Grad:G2/3_3_A

tag: etiology

tag: sample type


title: Hippocampus, CASP 11-/-, young (1 month)-4

city: Baton Rouge

first: Ryan

last: Grant

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

hyb_protocol: Illumina Whole Genome Expression Direct Hybridization Assay Guide- 750 ng labeled aRNA hybridized to array

data_processing: Quantile normalization and background subtraction using Illumina GenomeStudio Gene Expression Module v1.9.0

label_protocol: Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina (TAN07924)-Manufacturer's protocol 200ng input total RNA

growth_protocol: Wild type and knockout mice were fed a chow diet after weaning for the entire duration of the experiment.  Young mice were sacrificed at 1 month and old mice were sacrificed at 21-23 months.

extract_protocol: RNA was extracted with Trizol reagent, and then transferred to QIAGEN RNeasy columns and Dnase I treated according to the prescribed protocol provided with the kit. Quality control and RNA concentration were determined using Nanodrop and Agilent Bioanalyser.

tag: background strain

tag: age

value: Young (1 month)

value: Hippocampus


title: HCC-Grad:G2_7

tag: material

tag: age (yrs)

tag: tumor size [cm]


title: HCC-Grad:G2/3_2


title: Egfr fl/fl_HPC 3

description: SAMPLE 3

source_name: Egfr fl/fl_HPC

value: Egfr fl/fl

tag: cell type


title: WB-control-m162


title: HCC-Grad:G2/3_1


title: Egfr fl/fl_HPC 1

description: SAMPLE 1


title: WB-control-m160


title: WB-control-m183


title: HCC-Grad:G2_9_A


title: Hippocampus, CASP 11-/-, young (1 month)-2


title: Hippocampus, CASP 11-/-, young (1 month)-3


title: PiCs_biological rep2c

city: Naples

first: Gabriella

last: Minchiotti

address: Via Pietro Castellino, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR

description: Gene expression data from mouse TBV2 (129/SvP) embryonic stem cells incubated for 5 days with L-Proline (500 μM)

hyb_protocol: Following fragmentation, labelled cRNA was hybridized on GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix), using Herring sperm DNA, Acetylated BSA, and BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences)

scan_protocol: Hybridyzed arrays were scanned with Gene ChIP Scanner 3000 7G using Command Console (Affymetrix)

data_processing:
The data were analysed with Microarray Analysis Suite (MAS5) and normalized using Robust Multi-array Average (RMA) method
The relative signal intensities of each probe across the six samples assayed for each cell line was evaluated selecting a false discovery rate (FDR) <0.05 to assess significant gene differential expressions

source_name: L-Pro treated ESCs

label_protocol: Biotin-labelled cRNA was generated by means of Enzo BioArray HighYield RNA Transcript Labeling kit

growth_protocol: Wild-type mouse TBV2 (129/SvP) embryonic stem cells (ESCs) were cultured in complete medium containing leukemia inhibitory factor (LIF) without non essential aminoacids.

extract_protocol: Total RNAs were isolated from untreated (ESCs) and L-Proline treated (PiCs) cells using RNeasy kit following manufacturer’s instructions. RNA was quantified using the NanoDrop spectrophotometer and quality was assessed using Agilent Bioanalyzer 2100 microfluidic electrophoresis (Agilent Technologies)

treatment_protocol: ESCs were seeded at low density on gelatin-coated feeder-free plates and incubated for 5 days in complete medium without (Control ESCs) or with L-Proline (500 μM) (L-Pro -induced cells; PiCs)

tag: strain

tag: cell line

value: TBV2 ES cell line

tag: agent

value: L-Proline


title: Met fl/fl_HPC 2

description: SAMPLE 5

tag: tissue


title: Egfr fl/fl_HPC 2

description: SAMPLE 2

tag: strain backgroud


title: WB-control-m144

value: female


title: WB-control-m161

value: male


title: HCC-Grad:G2_6


title: PiCs_biological rep2b


title: WB-control-m163


title: HCC-Grad:G2_5 rep1


title: HCC-Grad:G2_4


title: Lan-aCGH

city: Chongqing

first: Hong

last: Guo

address: 30# Gaotanyan St. Shapingba District

department: Medical Genetics

institute: Third Military Medical University

hyb_protocol: The labeled genomic DNA (31μg) was dried at 45℃ and diluted in 5.6 μl Sample Tracking Control. Then hybridized in 14.4 μl Hybridization solution (containing 2X Hybridization Buffer, Hybridization Component A, Alignment Oligo). Arrays were hybridized in Maui hybridization stations for 40-72 hr at 42 °C, and then washed in 42 °C with buffer (containing VWR Water, 10X Wash Buffer (I, II or III), 1M DTT) by using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed by using Nimblegen's standard protocol for SignalMap.

source_name: aCGH from human lymphocyte genomic DNA

label_protocol: 1. Add 4μL β-mercaptoethanol to 2200μL Random Primer Buffer, Mix by pulse-vortexing. Use 1050 μL Random Primer Buffer (containing β-mercaptoethanol) to dilute cy3-Random Nonamers and cy5-Random Nonamers respectively. 2. Add 500ng genomic DNA to LHC(Labeling and Hybridization Control). Then add 2μLLCH-1 to test Sample, and 2μLLCH-2 to Reference Sample, amount to 40μL respectively. Add test Sample (containing LLCH-1) to cy3-Random Nonamers, and Reference Sample (containing LLCH-2) to cy5-Random Nonamers, amount to 80μL respectively. 98 °C for 10 min，4°C for 2min. 3. Prepare dNTP/Klenow Master Mix (20μL): 8μL Nuclease-free Water, 10μL 10mM dNTP Mix, 2μL Klenow Fragment (3’->5’ exo-)50U/μl. 4. Add dNTP/Klenow Master Mix (20μL) to Sample mixtures (80μL) respectively. 37 °C  for 2 hr. 5. Add 21.5μL Stop Solution to stop reaction. 6. Then purify the label reaction liquid.

extract_protocol: Use QIAamp DNA Blood Mini kit to extract genomic DNA. 1. Pipet 20 μl QIAGEN Protease (or proteinase K) into the bottom of a 1.5 ml microcentrifuge tube. 2. Add 200 μl whole blood in 200 μl PBS. Add 4 μl of an RNase A stock solution (100 mg/ml) to the sample. 3. Add 200 μl Buffer AL to the sample. Mix by pulse-vortexing for 15 s. 4. Incubate at 56°C for 10 min. DNA yield reaches a maximum after lysis for 10 min at 56°C. 5. Briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 6. Add 200 μl ethanol (96–100%) to the sample, and mix again by pulse-vortexing for 15 s. After mixing, briefly centrifuge the 1.5 ml microcentrifuge tube to remove drops from the inside of the lid. 7. Carefully apply the mixture from step 6 to the QIAamp Mini spin column (in a 2 ml collection tube) without wetting the rim. Close the cap, and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the tube containing the filtrate. 8. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW1 without wetting the rim. Close the cap and centrifuge at 6000 x g (8000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the collection tube containing the filtrate. 9. Carefully open the QIAamp Mini spin column and add 500 μl Buffer AW2 without wetting the rim. Close the cap and centrifuge at full speed (20,000 x g; 14,000 rpm) for 3 min. 10. Recommended: Place the QIAamp Mini spin column in a new 2 ml collection tube and discard the old collection tube with the filtrate. Centrifuge at full speed for 1 min. 11. Place the QIAamp Mini spin column in a clean 1.5 ml microcentrifuge tube, and discard the collection tube containing the filtrate. Carefully open the QIAamp Mini spin column and add 200 μl Buffer AE or distilled water. Incubate at room temperature (15–25°C) for 1 min, and then centrifuge at 6000 x g (8000 rpm) for 1 min.

value: case

value: Chinese Han_male_lymphocyte

value: Chinese Han_female_lymphocyte

value: control


title: Hippocampus, CIAS -/-, old (23 month)-6

source_name: Hippocampus, CIAS -/-, old (23 month)

tag: genotype/variation

value: CIAS -/-

value: Old (23 month)


title: WB-control-m143

tag: gender


title: Hippocampus, CIAS -/-, old (23 month)-3


title: ESCs_biological rep2b

description: Gene expression data from mouse TBV2 (129/SvP) embryonic stem cells

source_name: untreated ESCs


title: WB-control-m80


title: WB-control-m68


title: WB-control-m56


title: WB-control-m96


title: PiCs_biological rep1b


title: Hippocampus, CIAS -/-, old (23 month)-2


title: ESCs_biological rep2a


title: ESCs_biological rep2c


title: Hippocampus, CIAS -/-, old (23 month)-5


title: HCC-Grad:G1_3

tag: tumor stage


title: PiCs_biological rep1a


title: PiCs_biological rep2a


title: PiCs_biological rep1c


title: HCC-Grad:G2_3


title: HCC-Grad:G2_2


title: WB-control-m107

tag: infecting pathogen


title: HCC-Grad:G1_4

tag: etiology


title: Hippocampus, CIAS -/-, old (23 month)-4


title: HCC-Grad:G1_2

tag: sample type


title: WB-control-m79


title: HCC-Grad:G2_1


title: Hippocampus, CIAS -/-, old (23 month)-1

tag: background strain


title: WB-control-m64


title: WB-bact-m102

source_name: Whole Blood from patient with gram positive bacterial infection

value: gram positive bacterial infection


title: WB-control-m9


title: HCC-Grad:G1_1


title: HCC006: HBV

value: HBV

value: Rx


title: Hippocampus, CIAS -/-, young (1 month)-2

source_name: Hippocampus, CIAS -/-, young (1 month)

tag: age


title: WB-bact-m236

value: whole blood


title: Hippocampus, ASC -/-, old (23 month)-4

source_name: Hippocampus, ASC -/-, old (23 month)

value: ASC -/-

value: Old (21 month)


title: CHOP-/- MEF cells 1uM MG132-replicate 3

city: Indianapolis

first: Ron

last: Wek

state: IN

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: CHOP-/- MEFs treated with proteasome inhibitor MG132 for 8 hours

hyb_protocol: Affymetrix standard protocol, except hybridization for 17 hours.

scan_protocol: Scanned using 3000-7G controlled by Affymetrix GCOS.

data_processing: Affymetrix MAS5 data scaled to intensity of 1000.

source_name: CHOP-/- MEF cells 1uM MG132

label_protocol: total RNA was labeled using the 3' IVT express kit from Affymetrix.

growth_protocol: Wildype and CHOP-/- mouse embryonic fibroblasts (MEF)  were grown in Dulbecco’s Modification of Eagle’s Medium (DMEM) (4.5 g/L glucose) and 10% Fetal Bovine Serum (FBS)

extract_protocol: Total RNA was extracted using the Trizol method higher quality RNA was then obtained using an RNeasy clean up kit (Qiagen)

treatment_protocol: 8 plates (10cm)  of WT and and 8 plates (10cm) of CHOP-/- MEF cells were subject to no stress (4 each for a total of 8) or treated for 8 hours with 1uM MG132 (4 each for a total of 8).  Unstressed cells were harvested at the same time as the stressed cells

tag: genotype

value: CHOP-/-

tag: treatment

value: 1uM MG132, 8 hr

value: embryonic fibroblasts


title: WB-bact-m239

value: female


title: CHOP-/- MEF cells 1uM MG132-replicate 2


title: WB-bact-m228


title: ESCs_biological rep1c

value: TBV2 ES cell line


title: Hippocampus, ASC -/-, old (23 month)-6

value: Hippocampus


title: Hippocampus, CASP 11-/-, young (1 month)-1

value: Young (1 month)


title: ESCs_biological rep1b


title: CHOP-/- MEF cells 1uM MG132-replicate 4


title: WB-bact-m238


title: Hippocampus, CIAS -/-, young (1 month)-4


title: Hippocampus, ASC -/-, old (23 month)-5


title: HCC056: HFE

source_name: HCC liver tissue

value: genetic hemochromatosis

value: hepatocellular carcinoma (HCC)

value: male

tag: material

tag: age (yrs)

tag: tumor size [cm]


title: HCC071: C2

value: alcohol abuse


title: HCC001: HBV


title: WB-bact-m226

value: gram positive bacterial infection


title: HCC063: kryptogen

value: cryptogenic


title: Hippocampus, CIAS -/-, young (1 month)-1

value: CIAS -/-


title: CHOP-/- MEF cells 1uM MG132-replicate 1

tag: cell type


title: WB-bact-m216

value: whole blood


title: Hippocampus, ASC -/-, old (23 month)-2

value: ASC -/-


title: Hippocampus, ASC -/-, old (23 month)-1

value: Old (23 month)


title: HCC044: kryptogen

value: Tx


title: HCC022: HCV

value: HCV


title: Hippocampus, ASC -/-, old (23 month)-3

value: Old (21 month)


title: WT MEF cells 1uM MG132-replicate 4

description: Wild type MEFs treated with proteasome inhibitor MG132 for 8 hours

source_name: WT MEF cells 1uM MG132

value: CHOP+/+

value: 1uM MG132, 8 hr

value: embryonic fibroblasts


title: WT MEF cells 1uM MG132-replicate 3


title: WB-bact-m191


title: Hippocampus, ASC -/-, young (1 month)-4

source_name: Hippocampus, ASC -/-, young (1 month)

value: Young (1 month)

value: Hippocampus


title: Hippocampus, ASC -/-, young (1 month)-2


title: WT MEF cells 1uM MG132-replicate 1


title: HCC019: HCV

value: hepatocellular carcinoma (HCC)


title: Hippocampus, Wild type, old (23 month)-6

source_name: Hippocampus, Wild type, old (23 month)

value: wild type


title: WB-bact-m192

value: male


title: WB-bact-m177

value: gram positive bacterial infection


title: CHOP-/- MEF cells untreated-replicate 4

description: CHOP-/- MEFs treated with DMSO for 8 hours

source_name: CHOP-/- MEF cells untreated

value: CHOP-/-


title: HCC042: kryptogen

value: cryptogenic

value: Rx (Netz)


title: ESCs_biological rep1a

tag: strain

tag: cell line

value: TBV2 ES cell line

tag: agent

value: control


title: Hippocampus, ASC -/-, young (1 month)-1

tag: genotype/variation

value: ASC -/-

tag: tissue


title: WB-bact-m179

tag: gender

value: female

value: whole blood


title: HCC045: HCV

tag: tumor stage

value: HCV

value: Tx


title: HCC005: HCV

tag: etiology


title: WT MEF cells 1uM MG132-replicate 2

value: CHOP+/+

value: 1uM MG132, 8 hr

value: embryonic fibroblasts


title: HCC053: HCV

tag: sample type

value: hepatocellular carcinoma (HCC)

value: Rx


title: WB-bact-m145

tag: infecting pathogen


title: CHOP-/- MEF cells untreated-replicate 3


title: Hippocampus, Wild type, old (23 month)-4

tag: background strain

value: wild type

tag: age

value: Old (23 month)

value: Hippocampus


title: Hippocampus, Wild type, old (23 month)-5


title: HCC018: HCV

value: male


title: HCC010: HCV


title: CHOP-/- MEF cells untreated-replicate 1

tag: genotype

value: CHOP-/-

tag: treatment


title: Hippocampus, Wild type, old (23 month)-2


title: WB-bact-m180

value: gram positive bacterial infection


title: WB-bact-m99


title: WB-bact-m173


title: WT MEF cells untreated-replicate 4

description: Wild type MEFs treated with DMSO as a vehicle control for 8 hours

source_name: WT MEF cells untreated


title: HCC074: kryptogen

value: cryptogenic

tag: material

tag: age (yrs)


title: WB-bact-m164


title: WT MEF cells untreated-replicate 3

tag: cell type


title: WB-bact-m120


title: Hippocampus, Wild type, young (1 month)-3

source_name: Hippocampus, Wild type, young (1 month)

value: Young (1 month)


title: WT MEF cells untreated-replicate 1


title: Hippocampus, Wild type, old (23 month)-3


title: Hippocampus, Wild type, old (23 month)-1


title: HCC040: HFE

value: genetic hemochromatosis

tag: tumor size [cm]


title: HCC011/016: HBV

value: HBV

value: female


title: Hippocampus, Wild type, young (1 month)-4


title: HCC046: HBV

value: Tx


title: HCC039: kryptogen


title: WT MEF cells untreated-replicate 2

value: CHOP+/+


title: WB-bact-m117

value: whole blood


title: DMSO_Macr_3

first: Christopher

last: Weidner

address: Ihnestraße 63

institute: Max Planck-Institute for Molecular Genetics

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

data_processing:
The data were normalized using cubic spline normalization and background subtraction implemented in Illumina GenomeStudio V2011.1.
Illumina GenomeStudio V2011.1 calculated intensity and detection P value.

source_name: Macrophages, DMSO

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: THP-1 cells were obtained from DSMZ and cultivated at 37 °C (5% CO2, 95% humidity) in RPMI 1640 (Invitrogen) supplemented with 10% FBS Superior (Biochrom). For macrophage generation, differentiation was induced by supplementation of 10-8 M Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) for 48 h.

extract_protocol: Total RNA was purified and isolated using the RNeasy Mini Kit (QIAGEN) according to their manual. Genomic DNA was digested on column using the DNase-Set (QIAGEN). Quality control was performed with Agilent Bioanalyser or agarose gel electrophoresis.

treatment_protocol: Ligand treatment of macrophages was performed for further 24 h with 10 µM T0901317 (Sigma-Aldrich) or 0.1% DMSO as vehicle control.

value: blood cell (leukemic monozyte)

tag: cell line


title: rep3 dye-swap_p53 WT/null kidneys

city: New Orleans

first: Yuwen

last: Li

address: 1430 Tulane Ave SL37 RM5534

department: Pediatrics

institute: Tulane University

description: rep3 dye-swap_p53 WT/null kidneys

hyb_protocol: Hybridization was performed following Agilent’s oligonucleotide microarray hybridization User’s Manual and Agilent’s in situ Hybridization Plus kit. The labeled cDNA was hybridized to Agilent 44K Whole Mouse Genome Oligonucleotide Microarray (containing ~41,000 genes).

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent).

data_processing: The data was then extracted from images by the Feature Extraction software 6.1 (Agilent). Lowess normalization was applied to correct for artifacts caused by non-linear rates of dye incorporation, as well as inconsistencies in the relative fluorescence intensity between some red and green dyes.

source_name: E15.5 p53 wild-type kidney

label_protocol: The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Fluorescently labeled cDNA was generated from 0.5 μg of total RNA in each reaction using the Agilent Fluorescent Direct Label Kit and 1.0 mM Cyanine 3- or 5- labeled dCTP (PerkinElmer, Boston, MA), and following the User’s Manual.

extract_protocol: Total RNA extracted with Rneasy Mini kit according to manufacturer's protocol.

tag: strain

value: p53 wild type

value: embryonic kidney

source_name: E15.5 p53 null kidney

value: p53 null

value: Embryonic kidney


title: HCC037: kryptogen

value: hepatocellular carcinoma (HCC)


title: CHOP-/- MEF cells untreated-replicate 2

value: embryonic fibroblasts


title: rep3_p53 null/WT kidneys

description: rep3_p53 null/WT kidneys

tag: genotype/variation


title: Hippocampus, Wild type, young (1 month)-2

value: wild type

tag: tissue

value: Hippocampus


title: DMSO_Macr_4

city: Berlin

description: replicate 4

tag: gender

value: male


title: HCC003: HCV

tag: tumor stage

value: HCV

value: Rx


title: DMSO_Macr_1

description: replicate 1


title: DMSO_Macr_2

description: replicate 2


title: Hippocampus, Wild type, young (1 month)-1

value: Young (1 month)


title: HCC008: HBV

tag: etiology

value: HBV

value: female


title: NIH3T3_GRHL2_3

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

institute: ZMNH

description: Gene expression Grhl2 transfected NIH3T3 cells

hyb_protocol: 1.5 μg of purified, Cy3-labeled cRNA was hybridized to Agilent Whole Genome Mouse Microarray 4x44K for 17 hours at 65˚C, then washed according to manufacturer's protocol.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' and images were processed with the Feature Extraction Software version 9.5 (Agilent).

data_processing: Signal intensities were converted to a log2 scale after quantile normalization using R/Bioconductor software (Agi4x44PreProcess). Signals from multiple probes relating to one transcript were averaged.

source_name: NIH3T3 GRHL2 expressing, replicate 3

label_protocol: 500 ng of total RNA were reverse-transcribed and amplified incorporating Cyanine 3-CTP nucleotides using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations ( Agilent Technologies).

growth_protocol: NIN3T3 cells were cultured in DMEM conaining 10% FCS in 10% CO2 atmosphere

extract_protocol: Total RNA was extracted from parental and GRHL2-expressing NIH3T3 cells using the RNeasy Kit (Qiagen). For each cell culture three samples taken from different passages were utilized for expression profiling.

treatment_protocol: FLAG-tagged human GRHL2 cDNA was subcloned into the pIRES-N1 expression vector under the control of cytomegalovirus promoter (pIRES-N1-GRHL2). NIH3T3 cells were transfected with pIRES-N1-GRHL2 using Lipofectamine 2000 (Invitrogen). Stably transfected cells were selected with 500 µg/ml G418.


title: rep2 dye-swap_p53 WT/null kidneys

description: rep2 dye-swap_p53 WT/null kidneys


title: NIH3T3_GRHL2_2

source_name: NIH3T3 GRHL2 expressing, replicate 2


title: HCC027: kryptogen

value: cryptogenic

tag: sample type


title: rep2_p53 null/WT kidneys

description: rep2_p53 null/WT kidneys


title: NIH3T3_GRHL2_1

source_name: NIH3T3 GRHL2 expressing, replicate 1


title: rep1 duplicate dye-swap_p53 WT/null kidneys


title: HCC007: HBV

value: Tx


title: rep1 dye-swap_p53 WT/null kidneys

description: rep1 dye-swap_p53 WT/null kidneys


title: HCC012/043: HCV


title: T09_Macr_2

description: replicate 2

scan_protocol: Standard Illumina scanning protocol.

source_name: Macrophages, T0901317

value: blood cell (leukemic monozyte)


title: rep1 duplicate_p53 null/WT kidneys

description: rep1 duplicate_p53 null/WT kidneys

value: p53 wild type


title: NIH3T3_parental_3

description: Gene expression parental NIH3T3 cells

source_name: NIH3T3, replicate 3


title: NIH3T3_parental_2

description: Gene expression parental NIH3T3 cells

source_name: NIH3T3, replicate 2


title: T09_Macr_1

description: replicate 1


title: NIH3T3_parental_1

description: Gene expression parental NIH3T3 cells

source_name: NIH3T3, replicate 1


title: T09_Macr_4

description: replicate 4


title: T09_Macr_3

description: replicate 3


title: T09_Foam_3

description: replicate 3

source_name: Foam cells, T0901317

growth_protocol: THP-1 cells were obtained from DSMZ and cultivated at 37 °C (5% CO2, 95% humidity) in RPMI 1640 (Invitrogen) supplemented with 10% FBS Superior (Biochrom). For macrophage generation, differentiation was induced by supplementation of 10-8 M Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) for 48 h. To induce foam cell formation macrophages were treated for additional 48 h with 100 µg/mL modified human oxidized low density lipoprotein (oxLDL) obtained from Source BioScience (RP-048).

treatment_protocol: Ligand treatment was performed simultaneously with foam cell formation with 10 µM T0901317 (Sigma-Aldrich) or 0.1% DMSO as vehicle control.


title: rep1_p53 null/WT kidneys

description: rep1_p53 null/WT kidneys

value: embryonic kidney


title: T09_Foam_2

description: replicate 2


title: HCC025: kryptogen

source_name: HCC liver tissue

value: x


title: HCC050: kryptogen


title: DMSO_Foam_4

description: replicate 4

source_name: Foam cells, DMSO


title: T09_Foam_1

description: replicate 1


title: HCC051: kryptogen


title: Nfix_depleted_rep2

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Labeled targets were hybridized on the HT_MG-430_PM plate array and processed using the GeneTitan system.

scan_protocol: Scanning uses the GeneTitan system.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 by the RMA method.

source_name: murine adult bone marrow

label_protocol: RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

growth_protocol: Isolated whole bone marrow Lineage- Sca-1 + c-Kit+ (LSK) cells were cultured in SFEM media (StemCell Technologies, Vancouver, British Columbia, Canada) supplemented with 2 mM glutamine, 30 U/mL penicillin/streptomycin, 10 ng/mL rmScf, 20 ng/mL rmTpo, 20 ng/mL rmIgf-2 (all from Peprotech, Rocky Hill, NJ), 10 ng/mL rhFGF-1 (R&D Systems, Minneapolis, MN) and 10 mg/ml heparin (Sigma, St Louis, MO) at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from 15,000 sorted mCherry+/LSK cells seven days post transduction using the Qiagen RNeasy Micro Kit (Qiagen, Santa Clarita, CA). RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module (NuGen, San Carlos, CA).

treatment_protocol: VSV-G pseudotyped pCL20c -MSCV-shRNAmir-PGK-mCherry carrying Control- or Nfix-shRNA was spinloaded in Retronectin (TaKaRA Bio USA, Madison, WI) coated 96 well plates. 15,000 freshly  isolated LSK cells from C57BL/6J mice cells resuspended in 200 ml of SFEM media was subsequently added per well.  Cells were incubated for 24 hours on virus and subsequently washed followed by six days of further culture.

value: LSK cells

value: Nfix depleted


title: HCC048: kryptogen

value: hepatocellular carcinoma (HCC)


title: Nfix_depleted_rep3


title: HCC038: C2

value: alcohol abuse


title: HCC029: C2


title: DMSO_Foam_3

description: replicate 3


title: HCC028: C2


title: wt_rep2

value: wt


title: DMSO_Foam_2

description: replicate 2

value: male


title: Nfix_depleted_rep1


title: wt_rep3


title: Slide 346848

status: Public on Sep 04 2013

city: Groningen

first: Arjan

middle: Oedse Geert

last: Oldebesten

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

hyb_protocol: Two biological replicates of labeled target and control cDNA was labeled twice with Cy3 and Cy5 dye [thermo fisher dylight 550/650] to provide 2 technical replicates in a dye swap, giving a total of 4 scanned slides. The B. subtilis 168 slides used were hybridized as described previously by Kloosterman et al., 2006 and produced as described by Kuipers et al., 2002. The slides contained three probe replicates for each gene of the B. subtilis 168 genome and are described in GPL15025 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15025).   The cDNA and the probes were hybridized overnight at 45° Celsius. The slides were subsequently washed using the ArrayIt® Microarray Wash Station and dried by centrifuging (2 min, 2000 rpm, RT). Slides were scanned using a Genepix Professional 4200AL (Axon instruments, Union City CA USA) array scanner, using the Genepix Pro 6.1 software (Axon instruments), default settings for Cy3/Cy5. From the scanned intensities the log ratio of target to control (rotten to fresh meat) was determined.

data_processing: Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). The obtained data was processed and normalized (Lowess normalization) using the in-house software MicroPrep (Van Hijum et. al, 2003). A statistical analysis was done using the webservice CyberT (Baldi et. al, 2001) A gene was considered differentially expressed when the Bayes p value was lower than 0.001 and the difference in expression (the fold) was >2 or <-2.   The genes obtained using the CyberT analysis were ordered by locus tag and fold. This list was processed further using different analysis tools. With use of the in-house software Genome2d (Baerends et. al, 2004), operons with expression difference were identified and figures showing these operons were made. Using the in-house software available online (http://server.molgenrug.nl/index.php?option=com_content&view=article&id=14&Itemid=15), the genes were ordered by COG, Gene Ontology and KEGG pathway description.   A quality control analysis was further done by hierarchical clustering (pearson correlation) of the three technical replicates of genes considered differentially expressed with the use of Multi Experiment Viewer (Tm4, Saeed et. al, 2006).

label: Dylight 550

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Net{A}

label_protocol: 15 µg of total RNA were primed with 2 µl of 1.6 µg/µL random nonamers at 70°C for 5 min, then reversed transcribed at 42°C for 18 h in the presence of 1.8 µL SuperScript III RTase (Invitrogen), 1.2 µL (25x) AA-dUTPs. Afterwards labeled with Dyelight (550/650) and incubated at room temperature in the dark for 70 min.

growth_protocol: Bacillus subtilis 168 was grown over night in Luria Broth, in a normal shake flask (37 degrees Celsius). We diluted the culture to OD(600) = 0.3 and let it grow in a normal shake flask (37 degrees Celsius) until the OD(600) was 0.8 (approximately 2 hours). At that point, the cultures was diluted to OD(600) = 0.1 and put it in our experimental setup (see treatment protocol). The setup was ran for two hours, until the OD(600) = 0.8.  We inoculated Bacillus subtilis from plate and let it grow over night in Luria Broth, in a normal shake flask (37 degrees Celsius). We diluted the culture to OD(600) = 0.3 and let it grow in a normal shake flask (37 degrees Celsius) until the OD(600) was 0.8 (approximately 2 hours). At that point, the cultures was diluted to OD(600) = 0.1 and put it in our experimental setup. The setup was ran for two hours, until the OD(600) = 0.8.

extract_protocol: RNA extraction using the Macaloïd/Roche method (Molgen GBB): cells disrupted using glass beads and macaloïd. The RNA was extracted using the protocol of Roche manufacturers.

treatment_protocol: A 100 mL culture bottle containing 40 mL of culture was connected to the headspace of  a 100 mL bottle containing 50 grams of 30% beef, 70% pork ground meat (rotten: 7 days, room temperature; or fresh: bought in the morning, see sample) on ice. The headspace was pumped around with a peristaltic pump; the whole setup was placed in a 37 degrees room.

tag: meat condition

value: Fresh

label: Dylight 650

source_name: Net{B}

value: Rotten


title: Slide 347185

scan_protocol: Slides were scanned using a Genepix Professional 4200AL (Axon instruments, Union City CA USA) array scanner, using the Genepix Pro 6.1 software (Axon instruments), default settings for Cy3/Cy5.


title: Slide 346845


title: DMSO_Foam_1

description: replicate 1


title: Atf6a-/- TM animal 1 (34h)

city: Iowa City

middle: Thomas

last: Rutkowski

state: IA

address: 51 Newton Rd.

department: Anatomy and Cell Biology

institute: University of Iowa Carver College of Medicine

description: Gene expression data from wild-type or Atf6a-/- animals challenged for 34h with vehicle or 1 mg/kg tunicamycin

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HT Mouse Genome MG-430A GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language version 2.8.0. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: total RNA from mouse liver homogenate following 8h treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were of variable age and gender, housed in a pathogen-free facility on a 12h light/dark cycle.

extract_protocol: 34h after injection, animals were euthanized by cervical dislocation, livers were resected and snap frozen in liquid nitrogen, and then frozen livers were homogenized in Trizol and RNA purified by the Trizol protocol. RNA was thenn further purified using RNeasy spin columns.

treatment_protocol: Animals were injected intraperitoneally with 1 mg/kg tunicamycin dissolved in 150 mM dextrose, or dextrose alone as a vehicle control.

value: liver homogenate

tag: atf6a genotype

tag: txt

value: 1 mg/kg tunicamycin


title: Muscle_Control_Rep3

city: Nagoya

first: Kinji

last: Ohno

address: 65 Tsurumai, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

hyb_protocol: According to standard Affymetrix protocol

data_processing: Normalized by RMA. Affymetrix Core probesets.

source_name: Muscle Control 3

tag: disease state

value: control


title: wt_rep1


title: Slide 347182


title: Vastus_OverExpressing_FRG1_Type_Sample871

city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

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

source_name: Vastus Lateralis Muscle

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

extract_protocol: Total RNA from skeletal muscle was extracted using RNeasy Fibrous Tissue Midi or Mini Kit (Qiagen), followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

value: female

tag: age

value: 4 weeks old

value: Over-expressing FRG1


title: Vastus_Wild_Type_Sample872

value: Wild Type


title: Atf6a-/- TM animal 3 (34h)


title: Vastus_Wild_Type_Sample923


title: Vastus_Wild_Type_Sample906


title: Muscle_Control_Rep2

scan_protocol: According to standard Affymetrix protocol

source_name: Muscle Control 2


title: Muscle DM1 Rep2

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM456nnn/GSM456440/suppl/GSM456440 DM1 Muscle Pt2.CEL.gz

source_name: Muscle DM1 2

label_protocol: According to standard Affymetrix protocol

value: myotonic dystrophy


title: wild-type TM animal 2 (34h)


title: Atf6a-/- TM animal 2 (34h)


title: wild-type TM animal 3 (34h)


title: wild-type TM animal 1 (34h)


title: Vastus_OverExpressing_FRG1_Type_Sample874


title: Atf6a-/- vehicle animal 3 (34h)

value: 150 mM dextrose (vehicle)


title: wild-type vehicle animal 3 (34h)


title: Muscle_Control_Rep1

source_name: Muscle Control 1

extract_protocol: According to standard Affymetrix protocol


title: Atf6a-/- vehicle animal 1 (34h)


title: Atf6a-/- vehicle animal 2 (34h)


title: Muscle_DM1_Rep3

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM456nnn/GSM456443/suppl/GSM456443 DM1 Muscle Pt3.CEL.gz

source_name: Muscle DM1 3


title: wild-type vehicle animal 1 (34h)


title: wild-type vehicle animal 2 (34h)


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD5

description:
3146_WD5_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD5 control eating typical Western diets.

data_processing: The data were normalized using quantile normalization with the Lumi package in R.

source_name: BJ human fibroblasts cell line, Western diet

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

extract_protocol: RNA was extracted using the kit mirVANA (Ambion, Inc.) according to the manufacturer's protocol.

treatment_protocol: Fetal Bovine Serum (FBS) was replaced with human serum from calorie-restricted (CR)  participants and controls eating a typical Western diet (WD).

value: BJ

value: foreskin fibroblast cell line

tag: diet of human sera

value: Western

tag: gender of human sera

tag: age of human sera


title: Vastus_OverExpressing_FRG1_Type_Sample873


title: wild-type TM animal 3 (8h)

description: Gene expression data from wild-type or Atf6a-/- animals challenged for 8h with vehicle or 2 mg/kg tunicamycin

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language version 2.6.0. RMA was used to normalize the data and fit log2 transformed expression values.

extract_protocol: 8h after injection, animals were euthanized by cervical dislocation, livers were resected and snap frozen in liquid nitrogen, and then frozen livers were homogenized in Trizol and RNA purified by the Trizol protocol. RNA was thenn further purified using RNeasy spin columns.

treatment_protocol: Animals were injected intraperitoneally with 2 mg/kg tunicamycin dissolved in 150 mM dextrose, or dextrose alone as a vehicle control.

value: 2 mg/kg tunicamycin


title: Atf6a-/- TM animal 2 (8h)


title: wild-type vehicle animal 2 (8h)


title: Atf6a-/- vehicle animal 2 (8h)


title: Atf6a-/- TM a animal 3 (8h)


title: wild-type TM animal 1 (8h)


title: wild-type TM animal 2 (8h)


title: Atf6a-/- TM animal 1 (8h)


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD4

description:
3145_WD4_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD4 control eating typical Western diets.

tag: cell type


title: wild-type vehicle animal 3 (8h)


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR2

description:
3276_CR2_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR2.

source_name: BJ human fibroblasts cell line, calorie-restricted diet

tag: cell line

value: calorie restricted


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD10

description:
3151_WD10_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD10 control eating typical Western diets.

value: male


title: Atf6a-/- vehicle animal 1 (8h)


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR12

description:
3279_CR12_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR12.


title: CD45.1+LSK_wild-type in RUNX1S291fs/Ezh2Δ/Δ

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

institute: Kumamoto University

description: Gene expression at 4 months post-transplantation in wild-type CD45.1+LSK cells isolated from (pre-MDS) RUNX1S291fs/Ezh2Δ/Δ mice

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner (Agilent Technologies)

data_processing: Standard Agilent protocol

source_name: Bone marrow CD45.1+LSK cells, isolated from RUNX1S291fs/Ezh2Δ/Δ mice, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

value: bone marrow LSKs

tag: disease stage

value: normal

tag: genotype

value: wild type

value: Bone marrow CD45.1+LSK cells

tag: genetic background


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD6

description:
3147_WD6_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD6control eating typical Western diets.


title: wild-type vehicle animal 1 (8h)

tag: tissue

value: liver homogenate


title: Atf6a-/- vehicle animal 3 (8h)


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR9

description:
3124_CR9_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR9.


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD9

description:
3150_WD9_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD9 control eating typical Western diets.


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR13

description:
3280_CR13_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR13.

value: female


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD8

description:
3149_WD8_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD8 control eating typical Western diets.


title: CD45.1+LSK_wild-type in RUNX1S291fs

description: Gene expression at 4 months post-transplantation in wild-type CD45.1+LSK cells isolated from (pre-MDS) RUNX1S291fs mice

source_name: Bone marrow CD45.1+LSK cells, isolated from RUNX1S291fs mice, replicate 1


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR11

description:
3126_CR11_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR11.


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD11

description:
3152_WD11_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD11 control eating typical Western diets.


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR7

description:
3122_CR7_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR7.


title: CD45.2+LSK_RUNX1S291fs/Ezh2Δ/Δ

description: Gene expression at 4 months post-transplantation in RUNX1S291fs/Ezh2Δ/Δ LSK cells

source_name: Bone marrow CD45.2+LSK cells, RUNX1S291fs/Ezh2Δ/Δ , replicate 1

value: normal, pre-MDS

value: Bone marrow CD45.2+LSK cells


title: CD45.2+LSK_RUNX1S291fs

description: Gene expression at 4 months post-transplantation in RUNX1S291fs LSK cells

source_name: Bone marrow CD45.2+LSK cells, RUNX1S291fs, replicate 1


title: CD45.2+LSK_Ezh2Δ/Δ

description: Gene expression at 4 months post-transplantation in Ezh2Δ/Δ LSK cells

source_name: Bone marrow CD45.2+LSK cells, Ezh2Δ/Δ, replicate 1


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD14

description:
3155_WD14_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD14 control eating typical Western diets.


title: CD45.2+LSK_RUNX1S291fs/Ezh2Δ/Δ-MDS

description: Gene expression in RUNX1S291fs/Ezh2Δ/Δ-LSK cells of moribund MDS mouse

source_name: Bone marrow CD45.2+LSK cells, RUNX1S291fs/Ezh2Δ/Δ-MDS, replicate 1

value: MDS


title: SAHA6hr_replicate3

city: Rochester

first: Jennifer

last: Westendorf

address: 200 1st St SW

institute: Mayo Clinic

hyb_protocol: cRNA products were column purified and hybridized onto Illumina Mouse Whole Genome 6 Beadchips for 16 hours at 58º C.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-cy3 conjugate, and then scanned in an Illumina BeadArray Reader.  All quality assessment parameters were determined to be within normal ranges before proceeding to the final data reduction.

data_processing: The data were normalized with the fastlo R package

source_name: calvaria

label_protocol: The quality of total RNA samples was assessed by using the Agilent Bioanalyzer 2100 (Santa Clara, CA).  Labeling of high quality samples was performed according to manufacturer’s instructions for the Illumina Total Prep RNA Amplification Kit (Life Technologies, Grand Island, NY).   Briefly, 200 ng of total RNA was reverse transcribed with T7 Oligo d(T) to create second strand cDNA.  Subsequently, the products were column purified and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: MC3T3 sc4 murine calvarial osteoblasts were maintained in α-Minimal Essential Medium without ascorbic acid containing 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin (maintenance medium).

extract_protocol: Collagenase digests were performed with 1 mg/ml type II collagenase and 1 mg/ml BSA (Sigma) in Hank’s balanced salt solution for 40 min (cells were exposed to SAHA or vehicle during this incubation).  Cells were then harvested and RNA isolated with RNeasy kit.

treatment_protocol: MC3T3 sc4 cells were plated in 10cm plates in maintenance medium.  At confluence, maintenance medium was replaced with osteogenic medium (α-Minimal Essential Medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin, 50 µg/ml ascorbic acid and 4 mM beta glycerol phosphate). Fresh differentiation medium was added three days later. On day four, fresh differeniation medium containing 20µM SAHA and/or its solvent (DMSO) were added for 2 hours. RNA was isolated and microarray analysis performed.

tag: time

value: 6 h

tag: treatment

value: suberoylanilidehydroxamic acid


title: CD45.2+LSK_WT

description: Gene expression at 4 months post-transplantation in WT LSK cells

source_name: Bone marrow CD45.2+LSK cells, WT, replicate 1


title: SAHA6hr_replicate4


title: F2_13.5h_6%_L

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

hyb_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

growth_protocol: Batch fermentations were conducted in approximately 2.5 L of RM medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, temperature and DOT probes and controls as described previously (Yang et al., 2008). Briefly, a single colony of Z. mobilis ZM4 was added to a test tube containing 5-mL RM broth and a 1/100 dilution was added into the pre-warmed RM broth (10 mL culture into 1000 mL RM), which was then cultured aerobically at 30oC. The optical density was measured with a spectrophotometer at 600nm and the inoculum was added to each fermentor so that the initial OD600nm was approximately 0.14 in each fermentor. Fermentors were sparged overnight with filter-sterilized N2 gas and for approximately one hour post-inoculation to maintain anaerobic conditions. The agitation rate was 700 rpm in each vessel. Three replicate fermentors were used for wild-type Zymomonas mobilis ZM4 in control (no ethanol supplementation) or ethanol treatment conditions. Growth was monitored turbidometrically by measuring optical density at 600nm with a model 8453 spectrophotometer (Hewlett-Packard, Palo Alto, CA.). Samples were harvested during fermentation at different time points.

extract_protocol: RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: agent

value: 6% EtOH


title: F2_26h_6%_S

scan_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.


title: F3_26h_6%_S

label_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD7

description:
3148_WD7_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD7 control eating typical Western diets.

value: BJ

value: foreskin fibroblast cell line


title: SAHA6hr_replicate2


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD3

description:
3144_WD3_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD3 control eating typical Western diets.

value: Western


title: F2_10h_6%_L


title: F3_10h_6%_L


title: SAHA2hr_replicate4


title: SAHA6hr_replicate1


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR8

description:
3123_CR8_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR8.

value: calorie restricted


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD12

description:
3153_WD12_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD12 control eating typical Western diets.

value: male


title: HU-replicate-2

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

hyb_protocol: Sample hybridization protocol provided and performed by NimbleGen.

scan_protocol: Sample scan protocol provided and performed by NimbleGen.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila

source_name: HU-treated WT427 cells

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: Cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking.

extract_protocol: Homogenization was done using a QIAshredder spin column, and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to the manufacturer's instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE), and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).

treatment_protocol: Three conditions: 1) TRX1 KO; 2) EZL2 KO; 3) HU was used to treat Tetrahymena thermophila WT427 cells for 48 hours.

tag: strain/background

value: hydroxyurea (HU)


title: F2_6h_6%_L


title: F3_13.5h_6%_L


title: CD45.2+LSK_RUNX1S291fs/Ezh2Δ/Δ-MDS/ML

city: Kumamoto

description: Gene expression in RUNX1S291fs/Ezh2Δ/Δ-LSK cells of moribund MDS/myeloid leukemia mouse

source_name: Bone marrow CD45.2+LSK cells, RUNX1S291fs/Ezh2Δ/Δ-MDS/ML, replicate 1

value: bone marrow LSKs

value: MDS/myeloid leukemia


title: HU-Mock-replicate-2

source_name: wild type (WT427 cells) in HU treatment experiments, untreated

value: wild type


title: TRX1condition-TRX1_KO_replicate-2

source_name: TRX1 KO cells, untreated

value: TRX1 KO


title: TRX1condition-TRX1_KO_replicate-1


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR5

description:
3121_CR5_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR5.


title: SAHA2hr_replicate2

value: 2 h


title: F3_6h_6%_L


title: HU-Mock-replicate-1


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD13

description:
3154_WD13_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD13 control eating typical Western diets.


title: DMSO_replicate4

value: control

value: DMSO


title: F1_26h_S

source_name: Control

value: Control


title: SAHA2hr_replicate1


title: HU-replicate-1


title: F4_26h_S


title: F1_13.5h_S


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR3

description:
3120_CR3_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR3.

value: female


title: Human foreskin fibroblasts, human sera obtained from control eating typical Western Diet, Sample WD2

description:
3143_WD2_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from Sample WD2 control eating typical Western diets.


title: F4_13.5h_S


title: TRX1condition-wildtype_replicate-1

source_name: wild type (WT427 cells), untreated


title: DMSO_replicate3


title: DMSO_replicate2


title: EZL2condition-EZL2_KO_replicate-2

source_name: EZL2 KO cells, untreated

value: EZL2 KO


title: F4_10h_S


title: DMSO_replicate1


title: EZL2condition-EZL2_KO_replicate-1


title: SAHA2hr_replicate3

value: suberoylanilidehydroxamic acid


title: F1_6h_L

value: 6 h


title: EZL2condition-wildtype_replicate-1


title: CB3 CTL, biological replicate 3

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression data from neonatal neutrophils

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (EukGE-Ws2v4).

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

data_processing: The digital data retrieved from the CEL files were processed by Partek Genomic Suite version 6.5 using modified RMA-algorithm.

source_name: neonatal neutrophil

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Two-Cycle cDNA Synthesis Kit and IVT labeling kit).

growth_protocol: PGN induced transcriptional changes in human neonatal neutrophils

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy micro kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: PGN treatment for 4 hours at 10 microgram / microliter

value: neonatal neutrophil

tag: source tissue

value: cord blood


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR10

description:
3125_CR10_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR10.

source_name: BJ human fibroblasts cell line, calorie-restricted diet

value: BJ

value: foreskin fibroblast cell line

value: calorie restricted


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR14

description:
3281_CR14_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR14.

value: male


title: F1_10h_S


title: Human foreskin fibroblasts, human sera obtained from Calorie-Restricted Diet, Sample CR1

description:
3118_CR1_BJ.AVG_Signal
Human foreskin fibroblasts cultured in media supplemented with human sera obtained from calorie-restricted diet Sample CR1.


title: F4_6h_S


title: TRX1condition-wildtype_replicate-2


title: LOXIMVI, rep 3

city: Houston

first: HAI

last: LONG

state: TX

address: 1515 Holcombe Blvd., Unit 425

department: Leukemia

institute: University of Texas MD Anderson Cancer Center

description: replicate 3

hyb_protocol: A total of 750ng of labelled cRNA was prepared for direct hybridization to the Sentrix HumanHT-12 v4 Beadchip as per Illumina’s protocol (Part # 11286340 Rev. A). All the four samples, each in triplicate, were loaded into 12 individual arrays on the same beadchip, and hybridized at 58°C for 16 hours on a rocking platform. After hybridization, the chip was washed, blocked, stained with Cy3 and washed again, and dried before scanning.

scan_protocol: Scanned by Illumina iScan system.

data_processing: Using the scanner operating software, GenomeStudio, signal on the array were converted into a TXT file as raw data. The data were normalized with quantile normalization for analysis.

source_name: melanoma cell line LOXIMVI

label_protocol: For each sample, 500ng of total RNA was amplified and labeled with biotin using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) as per standard protocol. The quantity of labelled product was determined using NanoDrop 1000 Spectrophotometer, and quality control was performed with Agilent 2100 Bioanalyzer.

growth_protocol: Melanoma cell lines SK-MEL-28 and LOXIMVI were cultured in Dulbecco’s modiﬁed Eagle's minimal essential medium (DMEM) and RPMI 1640 medium, respectively, supplemented with 2 mM L-glutamine and 10% fetal bovine serum. Two normal melanocytes, HEMn-LP and HEMa-LP, were purchased from Invitrogen (Carlsbad, CA) and grown in Medium 254 supplemented with HMGS-2 (Human Melanocyte Growth Supplement-2, PMA-Free) for 3-6 passages before we harvested them for RNA extraction. All cells were grown at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) as per manufacturer's protocol. The quantity of total RNA was determined with NanoDrop 1000 Spectrophotometer, and the quality control was performed with Agilent 2100 Bioanalyzer.

tag: gender

value: Male

value: 58 years adult

value: malignant melanoma, lymph node metastasis


title: LOXIMVI, rep 1

description: replicate 1


title: CB3-PGN, biological replicate 3

description: Gene expression data from PGN-stimulated neonatal neutrophils

value: peptidoglycan


title: LOXIMVI, rep 2

description: replicate 2


title: CB2-PGN, biological replicate 2


title: EZL2condition-wildtype_replicate-2

value: wild type


title: Muslce DM1 Rep1

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM456nnn/GSM456439/suppl/GSM456439 DM1 Muscle Pt1.CEL.gz

source_name: Muscle DM1 1

tag: disease state

value: myotonic dystrophy


title: CB2 CTL, biological replicate 2

value: control


title: SK-MEL-28, rep 3

description: replicate 3

source_name: melanoma cell line SK-MEL-28

tag: age

value: 51 years adult

value: malignant melanoma


title: CB1-PGN, biological replicate 1


title: athb17-1_root-quiescent-center_rep6

city: Hayward

first: Don

middle: R

last: Maszle

state: CA

address: 3935 Point Eden Way

institute: Mendel Biotechnology, Inc.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization Protocol

scan_protocol: Affymetrix Scan Protocol using GCOS and Agilent G2500A Scanner

data_processing: Used R/Bioconductor fitPLM procedure to fit a probe-level model after first performing RMA.2 background correction and quantile normalization

organism: Arabidopsis thaliana

source_name: athb17-1; root quiescent center; rep 6

label_protocol: Standard Biotin Label

growth_protocol: Stratified seeds were germinated on solid 80% MS medium (80% MS vitamins, 0.3% sucrose, 1% BactoAgar) with a 16:8 L:D photoperiod for 6 d. Seedlings were then transferred to vertical plates containing 80% MS (80% MS vitamins, 0.3% sucrose, 1% BactoAgar for an additional 5 d.

extract_protocol: Primary and lateral root tips from 11 d old seedlings were used for the collection of specific root tissues by laser microdissection. Preparation of paraffin sections (8 ??m) was performed as Jiao et al., 2009, with minor modifications. Tissue sections were imaged by fluorescene microscopy using the PALM MicroBeam System (Carl Zeiss, Germany), and quiescent center cells were were collected into adhesive caps. Three biological replicates, each pooled from 40 to 60 roots, were collected for each sample. Total RNA was prepared from the microdissected tissues using the PicroPure RNA isolation kit, and RiboAmp HS RNA amplification kit (Life Technologies, USA), and cRNA was generated using Turbo labeling Biotin Kit (Life Technologies, USA) according to the manual.

treatment_protocol: Seedlings were not treated.

tag: line

value: root quiescent center


title: athb17-1_root-quiescent-center_rep5

source_name: athb17-1; root quiescent center; rep 5


title: HEMa, rep 2

description: replicate 2

source_name: Human Epidermal Melanocytes, adult, lightly pigmented donor (HEMa-LP)

value: adult

value: normal skin


title: SK-MEL-28, rep 2

description: replicate 2


title: WT-SIB_root-quiescent-center_rep6

source_name: WT-SIB; root quiescent center; rep 6

value: WT sibling


title: HEMa, rep 3

description: replicate 3


title: WT-SIB_root-quiescent-center_rep5

source_name: WT-SIB; root quiescent center; rep 5


title: SK-MEL-28, rep 1

description: replicate 1


title: DP54-3%

status: Public on Sep 03 2013

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

description: Gene expression under 3% O2

hyb_protocol: Following labeling and clean up, the amplified RNA and dye incorporation were quantified using a ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE) and hybridized to Agilent whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies). After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Each sample was analyzed once.

data_processing: The level of gene expression was determined by using Agilent Feature Extraction Software..

label_protocol: After RNA was qualified by the Agilent 2100 Bioanalyzer, 250 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3-labeled CTP using the Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the protocol supplied by the manufacturer.

growth_protocol: Dental pulp cells were cultured in MSCGM medium (LONZA) under 21% and 3% oxygen concentration atomosphere.

extract_protocol: RNA extraction (RNeasy Plus Mini Kit; Qiagen, Valencia, CA, USA)

value: dental pulp cells

tag: oxygen concentration