title: MEFs

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: MEFs are mesenchymal cells showing flat and elongated morphology.

hyb_protocol: The fragmented cRNA was hybridized to Affymetrix GeneChip arrays for 16 h.

scan_protocol: The Chips were washed and stained using an Affymetrix Fluidics Station and fluorescence was detected using the Affymetrix Imaging Station.

data_processing:
Raw data were background-corrected and subsequently normalized using Partek Express Affymetrix Edition under the Robust Microarray Analysis (RMA) algorithm.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

source_name: Primary mouse embryonic fibroblasts

label_protocol: 100 ng of total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: MEFs were maintained in Dulbecco’s modiﬁed Eagle medium (DMEM, Biowest) high glucose, 10% FBS (Biowest), 1X MEM non-essential amino acids, 1X L-Glutamine with Pen/Strep, and 0.1 mM β-mercaptoethanol (all GIBCO). Both iNSC and cNSCs were cultured in standard NSC medium: DMEM/F-12 supplemented with N2 or B27 supplements (Gibco-BRL), 10 ng/ml EGF, 10 ng/ml bFGF (both from Invitrogen), and 1XL-Glutamine with Pen/Strep(Gibco-BRL).

extract_protocol: Total RNA was prepared from MEFs, cNSCs and iNSCs using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Fibroblasts were transduced with replication-defective retroviral particles coding for Sox2, Klf4, c-Myc, and Brn4. After 48 h, the transduced fibroblasts were cultured in standard NSC medium.

tag: age

value: embryonic day (E)13.5

value: Mouse embryonic fibroblasts (MEFs)


title: Nasal_DNA_Methylation_Nonsmoker1

status: Public on Oct 01 2013

type: genomic

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

country: USA

institute: UNC-Chapel Hill

description:
Nasal epithelial cells extracted from human volunteers not exposed to cigarette smoke
Gene methylation data from nonsmokers

hyb_protocol: Samples were hybridized to IlluminaMethylation BeadChips array

scan_protocol: BeadChips were coated and then imaged on an Illumina iScan Reader

data_processing: Data were analyzed with GenomeStudio software (version 3.2) methylation module

label: Bisulfite converted DNA

molecule: genomic DNA

organism: Homo sapiens

source_name: nasal epithelial cells, nonsmoker

label_protocol: IlluminaHumanMethylation27 BeadChip bisulfite conversion with Zymo EZ DNA Methylation kit

growth_protocol: Primary human nasal epithelial cells were expanded to passage 2 in bronchial epithelial growth medium and then plated on collagen-coated filter supports with a 0.4 uM pore size, and cultured in a 1:1 mixture of bronchial epithelial cell basic medium and DMEM-H with SingleQuot supplements, bovine pituitary extracts (13mg/ml), bovine serum albumin (BSA, 1.5 ug/ml), and nystatin (20 units). Upon confluency, all-trans retinoic acid was added to the medium and air liquid interface culture conditions (removal of the apical medium) were created to promote differentiation.

extract_protocol: TRIzol DNA Extraction

treatment_protocol: Nasal epithelial cells were extracted from volunteers and grown until fully differentiated. DNA was then extracted.

tag: cell type

value: Nasal epithelial cells

tag: agent

tag: dose

value: no exposure

tag: disease state

value: healthy


title: Nasal_DNA_Methylation_Smoker2

description:
Nasal epithelial cells extracted from human volunteers chronically exposed to cigarette smoke
Gene methylation data from smokers

source_name: nasal epithelial cells, smoker

value: tobacco smoke

value: exposure


title: Nasal_DNA_Methylation_Smoker5


title: Nasal_DNA_Methylation_Smoker1


title: 156404_BAT_TLE3_CR

status: Public on Sep 27 2013

type: RNA

city: Los Angeles

first: Claudio

last: Villanueva

state: CA

address: 610 Charles E. Young Drive East Box 957239

department: Integrative Biology and Physiology

institute: UCLA

hyb_protocol: 5.5ug of cDNA was hybridized to Mouse Gene ST 1.0 Array for 16 hours.  Washing and Staining was completed on the Affymetrix Fluidic Station 450.

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method, which is implemented as a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). As part of the normalization process, a custom chip-definition file (ver. 17.1.0) from the BrainArray resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes. The number of 35,557 microarray probe sets was mapped to 21,187 genes.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Brown Adipose Tissue

label_protocol: Fragmenting and labeling was completed with the Affymetrix Gene Chip WT Terminal labeling for Gene ST 1.0 Array.

growth_protocol: Mice were allowed free access to water and placed at 4C or RT for 5 hours.

extract_protocol: RNA from each sample was prepared using manufacturer recommended protocols and the Qiagen RNAEasy columns.  250ng of RNA was used to prepare each sample using the Ambion WT Expression Kit for Gene ST 1.0 Array.

tag: strain

tag: genotype/variation

value: expressing TLE3 from the aP2 enhancer; aP2-TLE3 Tg

tag: gender

value: male

value: 3 months

tag: placed at

value: 4C (cold room) for 5 hrs

tag: tissue

value: brown adipose tissue


title: OsWRKY53SD over-expressing rice leaves (line 40) replicate 4

status: Public on Aug 31 2013

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Biological replicate 4 of 4.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2565

data_processing: After data was analyzed by Fearure Extraction software (version 11, Agilent), data normalization was performed using Partek Genomics Suite software (ver. 6.5; Partek software) by quantile normalization method.

organism: Oryza sativa

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Rice plants were grown in a chamber under a 14-h-light (28℃) and 10-h-dark (24℃) cycle in hydroponic culture.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Fourth leaves were harvested from WT, OsWRKY53-overexpressing rice plants and OsWRKY53SD-overexpressing rice plants at the four-leaf stage.


title: Royan_B20_2i_R1

status: Public on Oct 21 2013

city: Tehran

first: Hossein

last: Baharvand

address: Hafez St., Bani Hashem St.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

description:
Replicate 1 of 2
7991003089_G

hyb_protocol: Illumina BeadStation (Illumina)

scan_protocol: Illumina BeadStation (Illumina)

data_processing: The raw signal intensities of regular and control probes were extracted from Illumina® GenomeStudio software and used for normexp (Ritchie et al., 2007) background correction followed by quantile normalization using the limma (Smyth and Ritchie, 2011) package. For most of the bioinformatics analysis, we developed several scripts in R statistical language (R Core Team, 2012).

label: Biotin

source_name: Royan B20 mESC line cultured in 2i condition

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: mESC lines, Royan B20 and Royan B18, were generated from C57BL/6 mouse strains blastocysts in N2B27 medium supplemented with PD0325901 (PD)+SB431542 (SB)+LIF and mainteined as the same for more than 10 passages

extract_protocol: RNeasy Mini Kit

treatment_protocol: mESC lines, Royan B20 and Royan B18, were passaged simultaneously in N2B27 medium supplemented with PD+LIFor SB+LIF or 2i (PD+CHIR99021)+LIF for 10 passages.

tag: culture condition

tag: cell line

value: Embryonic Stem Cell (ESC)


title: OsWRKY53SD over-expressing rice leaves (line 40) replicate 3

description: Biological replicate 3 of 4.


title: 156401_BAT_WT_RT

value: wild type

value: room temperature for 5hrs


title: OsWRKY53SD over-expressing rice leaves (line 38) replicate 1

description: Biological replicate 1 of 4.


title: OsWRKY53SD over-expressing rice leaves (line 38) replicate 4

description: Biological replicate 4 of 4.


title: OsWRKY53SD over-expressing rice leaves (line 38) replicate 3

description: Biological replicate 3 of 4.


title: OsWRKY53 over-expressing rice leaves (line 10) replicate 2

description: Biological replicate 2 of 4.

value: water


title: OsWRKY53 over-expressing rice leaves (line 8) replicate 2

description: Biological replicate 2 of 4.


title: OsWRKY53SD over-expressing rice leaves (line 40) replicate 1

description: Biological replicate 1 of 4.


title: OsWRKY53 over-expressing rice leaves (line 8) replicate 1

description: Biological replicate 1 of 4.


title: OsWRKY53 over-expressing rice leaves (line 8) replicate 4

description: Biological replicate 4 of 4.


title: OsWRKY53SD over-expressing rice leaves (line 38) replicate 2

description: Biological replicate 2 of 4.


title: OsWRKY53 over-expressing rice leaves (line 10) replicate 1

description: Biological replicate 1 of 4.


title: Wild-type rice leaves replicate 4

description: Biological replicate 4 of 4.

source_name: Wild-type rice leaves

value: Wild-type rice leaves


title: MCF7_MBD3_Rep2 [GPL16734]

status: Public on Oct 31 2013

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

hyb_protocol: Hybridizaion was performed followed by NimbleGen Arrays User's Guide (version 6.2)

scan_protocol: Scanning was performed as described in Lai AY et al. (J Exp Med. 2010 Aug 30;207(9):1939-50)

data_processing: The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173. The normalized values presented here are the residuals obtained from loess regression (log2(cy5) was treated as dependent and log2(cy3) as explanatory variables) for CG count bin. These approach is similar to localized MA loess normalization the difference being that instead of predicting M (log2(Cy5/cy3)) using A (log2(cy5*cy3)) locally (using subset of probes) we attempt to predict log2(cy5) using log2(cy3) using probes that are similar in terms of their CG count. The multiple signal values from same probe within array were averaged. Furthermore, the resulting signal values for MIRA and ChIP-antibody samples were quantile normalized independently to adjust for between sample variations.

source_name: MBD3-Dam bound DNA from MCF-7 cells

label_protocol: 1ug DNA was labeled with Nimblegen Dual-Color DNA labeling kit followed by NimbleGen Arrays User's Guide (version 6.2)

growth_protocol: Cells were cultured with DMEM/F12 supplemented with 10% fetal bovine serum

extract_protocol: Genomic DNA was purified and processed for DamID as described in Nature Protocol 2007;2(6):1467-78.

treatment_protocol: Not applicable

tag: replicate

tag: fraction

value: MBD3-Dam bound DNA

source_name: Dam bound DNA from MCF-7 cells

value: Dam bound DNA


title: OsWRKY53 over-expressing rice leaves (line 10) replicate 3

description: Biological replicate 3 of 4.


title: Wild-type rice leaves replicate 1

description: Biological replicate 1 of 4.


title: OsWRKY53 over-expressing rice leaves (line 10) replicate 4

description: Biological replicate 4 of 4.


title: OsWRKY53SD over-expressing rice leaves (line 40) replicate 2

description: Biological replicate 2 of 4.


title: Wild-type rice leaves replicate 3

description: Biological replicate 3 of 4.


title: Wild-type rice leaves replicate 2

description: Biological replicate 2 of 4.


title: OsWRKY53 over-expressing rice leaves (line 8) replicate 3

description: Biological replicate 3 of 4.


title: MCF7_MBD3_Rep1 [GPL13848]


title: MCF7_MBD3_Rep3 [GPL16734]


title: MDA231_MBD3_Rep2 [GPL16734]

source_name: MBD3-Dam bound DNA from MDA-231 cells

source_name: Dam bound DNA from MDA-231 cells


title: MDA231_MBD3_Rep1 [GPL10671]


title: MCF7_MBD3_Rep1 [GPL10671]


title: MDA231_MBD3_Rep3 [GPL16734]


title: MDA231_MBD3_Rep1 [GPL13848]


title: NifAmut_WT_rep3

status: Public on Aug 15 2013

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

country: Germany

institute: University Bremen

description:
302728_rep3
Biological replicate 3 of 3

hyb_protocol: The combined Cy3/Cy5-labelled targets were dried in a speed vac and further dissolved in 60 µl DIG Easy hybridization solution (Roche, Mannheim, Germany). 1 µl of sonicated salmon sperm (5 µg/µl) was further added. The transcriptome microarray spotted on epoxysilane-coated Nexterion Slide E (Schott) (CeBiTec, University Bielefeld)  contained 70mer oligonucleotide probes for the 3,989 predicted protein-coding genes from Azoarcus sp. strain BH72 in four replicates (Hauberg 2012). Before hybridization, the targets were denatured at 65°C for 10 min. The hybridization of fluorescently labelled cDNA targets to oligonucleotide microarrays was performed at 42°C in a hybridization chamber (ArrayIt, Sunnyvale, CA, USA) in a water bath for 14 to 18 hours. followed by appropriate  washing steps as recommended.

scan_protocol: The Cy3- and Cy5-fluorescence was scanned at 532 nm and 635 nm with the GenePix Scanner 4000A (Molecular Devices, Sunnyvale, CA, USA) with a pixel size of 10 µm.The image analysis was performed with the GenePix 4.1 program and the subsequent analyses were carried out with the open-source software Microarray Data Analysis System (MIDAS v2.19) of TM4 (Saeed et al. 2003, http://www.tm4.org/). After scanning, raw data images of the slides that contain information about gene expression levels were obtained by the GenePix software. These images were analyzed by identifying each spot on the array (with the help of an array layout template) with measurements of its fluorescence intensity and the corresponding background intensity.

data_processing:
With the file transformation tool Express Converter v.2.1 (http://www.tm4.org/utilities.html), data files generated from GenePix (.gpr) were converted to TM4 files (.mev) that could be uploaded to the MIDAS platform. Normalization with MIDAS (TM4 suite) was done in order to reduce variability by appropriately adjusting the data. In this study, the LOWESS (locally weighted scattered plot smoothing) normalization was performed using the block mode as set-up parameter as this mode allowed correction of systematic spatial variation between the grids of the array. The normalized data for each spot were exported to Excel and aligned to the corresponding Azoarcus sp. BH72 gene name. Overall, three independent experiments (biological experiments) were performed. Average expression fold were determined from normalized values of the three sets. Statistical analysis was performed using the intensity values in a one tail paired t-test.
Genes with an expression factor ≥ 1.8 and P value ≤ 0.05 were considered as differentially expressed.

organism: Azoarcus sp.

source_name: Test: pure culture of bacteria, strain BHLAO (nitrogen fixing condition)

label_protocol: For transcriptome microarray analysis, 20 µg of total RNA was reverse transcribed with BioScript RT in respective reaction buffer (Bioline) with random hexamers and 4:1 aminomodified-dUTP/dTTP nucleotide mix for 90 min at 42°C. For coupling of fluorescent dyes to the aminoallyl-labelled first strand cDNA, aliquots of Cy3-NHS or Cy5-NHS esters (GE Healthcare) were dissolved in 60 µl of first strand cDNA, mixed and incubated for 90 min at room temperature in the dark. Blocking of all remaining dyes (quenching) was necessary after labelling. This quenching was achieved by adding 4.5 µl hydroxylamine (4 M) to the sample solution, followed by an incubation for 15 min at room temperature. Subsequent cleaning up of labelled cDNA from remaining dyes was performed with the CyScribe GFX Purification Kit (GE Healthcare) according to manufacturer’s instructions. The Cy5- and Cy3-labelled cDNA that was used in one hybridization experiment were cleaned up together. The labelled cDNA (60 µl) was stored at -20°C until microarray hybridization (Hauberg et al. 2012).

growth_protocol: Azoarcus sp. wild type strain BH72 or nifLA mutant strain BHLAO were grown respectively in an oxygen-controlled bioreactor (Biostat B; B. Braun Melsungen AG, Melsungen, Germany) at 37°C with stirring at 6000 r.p.m, under microaerobic (0.6% oxygen concentration) nitrogen fixing conditions with  10 mM glutamate (poor nitrogen source)

extract_protocol: The cell pellets were re-suspended in a 1:1 mixture of pre-warmed phenol-chloroform-isoamylalcohol (25:24:1, pH 4.7) and NAES solution (50 mM sodium acetate, 10 mM EDTA, 1 % SDS, pH 5.1). This suspension was incubated for 5 min at 65°C in a water bath, followed by 10 min incubation on ice. For phase separation, the mixture was centrifuged for 10 min at 12°C and 8000 x g. The upper phase was transferred and mixed with the same volume of phenol-chloroform-isoamylalcohol. This phenol extraction was repeated three times, followed by an extraction with equal volume of chloroform isoamylalcohol (24:1). RNA precipitation was performed with the same volume of isopropanol for 45 min on ice. The RNA was pelleted by centrifugation (12900 x g, 10 min at 4°C) and salts were removed with 1 ml of Ethanol (70 %). The dried RNA was dissolved in 100 µl 1 x RNAsecure, frozen in liquid nitrogen and kept at -80°C until further processing. Contaminating DNA was removed from RNA preparations by DNase I using Qiagen columns (RNeasy Mini Kit, Qiagen, Hilden, Germany) according to manufacturer’s instructions. The DNase I treated RNA was eluted twice in 30 µL of elution buffer, pooled and finally stored in 1x RNA secure in -80°C.

treatment_protocol: The cells were pelleted by centrifugation (6000 rpm, 28°C, 10 min), pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: BHLAO

value: nifA mutant

source_name: Reference: pure culture of bacteria, wild type (nitrogen fixing condition)


title: MCF7_MBD3_Rep2 [GPL10671]


title: NifAmut_WT_rep1

description:
301719_rep1
Biological replicate 1 of 3


title: 156402_BAT_TLE3_RT


title: CNS derived Microglia-3

status: Public on Jul 08 2013

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring v12.5 software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
meta-probeset file: MoEx-1_0-st-v1.na30.mm9.probeset

source_name: wild-type, brain and spinal cord derived CD11b+CD45Low microglia

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

growth_protocol: Mouse brains, spinal cords and spleens were dissected from 8-10 weeks mice

extract_protocol: Total RNA was isolated from adult brain sorted adult CD11b+/CD45Low microglia and splenic CD11b+/Ly6C+ monocytes from 20-30 mice per sample in biological triplicates.

value: wild-type

tag: developmental stage

value: adult

value: 8-10 weeks

value: Pool of brains and spinal cords

value: CD11b+CD45Low microglia


title: NifAmut_WT_rep2

description:
301720_rep2
Biological replicate 2 of 3


title: CNS derived Microglia-1


title: MDA231_MBD3_Rep2 [GPL10671]


title: DNA_Normal_rep1

status: Public on Jun 20 2013

city: Philadelphia

first: Kenneth

middle: S.

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

hyb_protocol: Labeled genomic DNA was co-hybridized by the Penn Microarray facility according to manufacturer instructions (briefly: 1 - add 71 mL hybridization mix including labeled sample (Agilent) to 39 mL probe; 2 - incubate 95 deg 3 min; 3 - incubate 37 deg 30 min; 4 - centrifuge 17kg 2 min; 5 - hybridize 65 deg 24 hrs).

scan_protocol: Arrays were scanned with an Agilent Scanner System.

data_processing: Data analyzed by using GeneSpring GX7.3.1 software (Agilent).

source_name: Tumor-adjacent pancreas

label_protocol: We amplified and labeled genomic DNA by using the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis enzymatic labeling kit (Agilent, Santa Clara CA), according to the manufacturer (briefly: 1 - add 5ml random primers to 24ul digested gDNA; 2 - incubate 95 deg 3 min; 3 - cool on ice 5 min; 4 - add digestion master mix (Agilent) to a final volume of 50 mL; 5 - incubate 37 deg 2 hrs; 6 - incubate 65 deg 10 min, then cool to 4 deg).

growth_protocol: Human pancreatic ductal carcinoma cell lines PanC-1 and MIAPaCa-2 were maintained in 90% Dulbecco's Modified Essential Medium (DMEM) supplemented with 10% FBS and fed every other day. H1 and iPS-like clones were generally maintained in 80% DMEM /F12 supplemented with 20% KNOCKOUT serum replacement, 0.1 mM nonessential amino acids, 0.1 mM beta-mercaptoethanol, and 10 ng/ml human basic fibroblast growth factor (bFGF).

extract_protocol: Total genomic DNA was isolated from epithelial cells and iPS-like clones by proteinase K/phenol-chloroform.

treatment_protocol: Human ES/iPS-like clones were grown onto irradiated MEFs in 0.1% gelatinized tissue culture dishes. Cells were fed every day and passaged once a week. For passaging, human ES cells were detached by treatment with 1 mg/ml collagenase IV (Invitrogen) for 3 min at 37 ˚C, centrifuged, resuspended with human ES media supplemented with 10 µm Y 27632 (Calbiochem, Darmstadt, Germany), and then seeded onto irradiated MEFs. The iPS-like lines were passaged mechanically with needles every 5-7 days. PanC-1 and MIAPaCa-2 human pancreatic adenocarcinoma cell lines were infected with the Tet0-mouse four transcription factors (Oct4, Sox2, Klf4, and c-Myc) and the pWPTrtTA expressing lentivirus, followed by splitting onto irradiated MEFs 48 h post-infection. By the time of splitting, infected cells reached a confluence of 60-80%. Culture media was switched to huES media supplemented with 4 ng/ml Fgf2, 10 uM Y27632, 0.5 ug/ml doxcycycline at 24 h post plating and cells were fed every day. HuES like clones were picked by manually at day 27, 28, 29 post-induction with dox and characterized by immunostaining for SSEA4 and AP and teratoma assays.

tag: tissue derivation

value: normal pancreas from margin of tumor

value: epithelial cells

tag: experiment


title: 156403_BAT_WT_CR

value: male

tag: age

value: 3 months

value: 4C (cold room) for 5 hrs

value: brown adipose tissue


title: AM PIE5 7h

status: Public on Apr 13 2013

city: St Lucia

first: ronan

last: kapetanovic

state: QLD

address: The University of Queensland

country: Australia

institute: Institute for Molecular Bioscience

hyb_protocol: The fragmented and biotin labelled cDNA was hybridised to the Snowball arrays, using the Affymetrix HybWashStain Kit and Affymetrix standard protocols.

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner.

data_processing: A total of 140 Affymetrix SNOWBALLs520824F_v1 arrays were QC analysed. Normalisation of the 47845 features across all arrays was achieved using the robust multi-array average (RMA) expression measure (Partek Genomic Suite, Partek, St. Louis, USA).  Statistical anlysis was performed by Partek and using Biolayout Express 3D.

organism: Sus scrofa

source_name: PIE_AM_stimulated with LPS

label_protocol: 500 ng of total RNA was amplified using the Ambion WT Expression Kit (Affymetrix).  5µg of the resulting cDNA was fragmented and labelled using the Affymetrix Terminal Labelling Kit.

growth_protocol: Cells were recovered from -155°C by quickly thawing them at 37 °C, then slowly diluting the freezing medium by dropwise addition of 40 ml of warm PBS over 2-3 min to avoid the shock of sudden dilution of DMSO. In order to obtain macrophages, bone-marrow cells and PBMC were cultured 5-7 days in large 100 mm2 sterile petri dishes in 20 ml of complete medium: RPMI-1640, Glutamax supplement (35050-61; Invitrogen), 10% heat-inactivated FCS (PAA Laboratories), penicillin/streptomycin (15140; Invitrogen, Paisley, U.K.) in the presence of rhCSF-1 (104 U/ml; a gift of Chiron, Emeryville, CA). Bone marrow-derived macrophages (BMDM), monocyte-derived macrophages (MDM) or alveolar macrophages (AM) were then seeded at 106 cells/ml in 6-wells plates in complete medium with rhCSF-1 and left overnight.

extract_protocol: RNA extraction was carried out using RNA-Bee (Fischer) following manual instruction and RNA quantified using a Nanodrop (Nanodrop, USA). RNA quality was assessed using Agilent nanochip (Agilent)

treatment_protocol: The next day, non-adherent cells were removed, fresh complete medium was added and cells were stimulated with LPS from Salmonella enterica serotype minnesota Re 595 (100 ng/ml; L9764; Sigma-Aldrich).

tag: breed

value: PIE

tag: pig number

value: female

tag: cell type

value: alveolar macrophages (AM)

tag: time point

tag: sample group

value: LPS-stimulated


title: AM HAM3 7h

source_name: HAM_AM_stimulated with LPS

value: HAM


title: AM PIE1 7h


title: AM HAM47h


title: AM PIE3 7h


title: CD8+ Foxo1fl/fl

status: Public on May 16 2013

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

description: Gene expression from GzmB-cre Foxo1fl/fl CD27hi KLRG1lo OT-I CD8+ T cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using GeneChip Affymetrix scanner 3000 7G

data_processing: The data was analyzed using the RMA and limma methods to assess differential expression

source_name: CD8+ FOXO1fl/fl

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: miRNeasy kit extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

tag: strain

value: OT-I CD8+ T cells

tag: genotype/variation

value: GzmB-cre Foxo1fl/fl CD27hi KLRG1lo


title: CD8+ wild-type

description: Gene expression from wild-type CD27hi KLRG1lo OT-I CD8+ T cells

source_name: CD8+ wild-type

value: wild-type CD27hi KLRG1lo


title: DNA_Tumor_rep1

source_name: Pancreatic tail tumor

value: pancreatic ductal adenocarcinoma tumor


title: AM HAM5 7h

tag: gender


title: Splenic Ly6C+ monocytes-1

source_name: wild-type, splenic Ly6C+/CD11b+ monocytes

value: wild-type

value: adult

value: 8-10 weeks

tag: tissue

value: Spleen

value: Ly6C+/CD11b+ monocytes


title: AM PIE2 7h


title: AM HAM1 7h

value: male


title: AM PIE4 7h


title: AM HAM2 7h


title: AM DR4 7h

source_name: DR_AM_stimulated with LPS

value: DR


title: AM DR5 7h


title: AM LW4 7h

source_name: LW_AM_stimulated with LPS

value: LW


title: AM LR3 7h

source_name: LR_AM_stimulated with LPS

value: LR


title: AM LW2 7h

value: female


title: AM LR5 7h

value: alveolar macrophages (AM)


title: AM LW5 7h

value: LPS-stimulated


title: CNS derived Microglia-2

value: Pool of brains and spinal cords

value: CD11b+CD45Low microglia


title: AM LW1 7h


title: AM LW3 7h


title: DNA_Normal-IPS-12_rep1

source_name: Tumor-adjacent pancreas, IPS-induced

value: normal pancreas from margin of tumor

value: IPS-induced epithelial cells

value: epithelial cells


title: AM LR4 7h


title: AM HAM5 0h

value: HAM

value: untreated


title: Splenic Ly6C+ monocytes-2

value: wild-type

value: adult

value: 8-10 weeks


title: AM LR2 7h


title: Splenic Ly6C+ monocytes-3

value: Spleen

value: Ly6C+/CD11b+ monocytes


title: DNA_Tumor-IPS-22_rep1

source_name: Pancreatic tail tumor, IPS-induced

value: pancreatic ductal adenocarcinoma tumor


title: AM HAM3 0h

value: male


title: AM HAM2 0h

value: female


title: AM HAM4 0h

value: alveolar macrophages (AM)


title: AM DR4 0h

value: DR


title: AM DR3 7h

value: LPS-stimulated


title: AM PIE3 0h

value: PIE


title: AM PIE1 0h


title: AM DR5 0h


title: AM HAM1 0h


title: AM PIE5 0h


title: AM LR1 7h

value: LR


title: AM PIE4 0h


title: AM PIE2 0h


title: AM DR3 0h


title: AM LW2 0h

value: LW


title: AM LR2 0h


title: AM LR4 0h


title: AM LW4 0h


title: AM LR5 0h


title: AM LW3 0h


title: AM LR1 0h


title: BMDM HAM4 7h

source_name: HAM_BMDM_stimulated with LPS

value: Bone marrow-derived macrophages (BMDM)


title: AM LW5 0h


title: BMDM HAM3 7h

value: HAM


title: BMDM HAM5 7h


title: BMDM PIE5 7h

source_name: PIE_BMDM_stimulated with LPS


title: BMDM PIE3 7h


title: BMDM PIE2 7h


title: BMDM PIE1 7h


title: BMDM DR5 7h

source_name: DR_BMDM_stimulated with LPS


title: BMDM LW5 7h

source_name: LW_BMDM_stimulated with LPS


title: BMDM DR1 7h


title: BMDM DR4 7h


title: BMDM LW3 7h


title: BMDM DR3 7h


title: BMDM LW2 7h


title: BMDM HAM2 7h


title: BMDM LW4 7h


title: BMDM LW1 7h


title: BMDM PIE4 7h


title: BMDM LR3 7h

source_name: LR_BMDM_stimulated with LPS


title: BMDM LR2 7h


title: BMDM HAM4 0h

value: untreated


title: BMDM LR1 7h


title: BMDM PIE1 0h


title: BMDM LR5 0h


title: BMDM HAM2 0h


title: BMDM PIE5 0h


title: BMDM LW5 0h


title: BMDM HAM3 0h


title: BMDM  HAM1 0h


title: BMDM DR1 0h


title: BMDM LR4 7h


title: BMDM LR5 7h


title: BMDM PIE3 0h


title: BMDM PIE4 0h


title: BMDM DR4 0h


title: BMDM LR2 0h


title: BMDM LW4 0h


title: BMDM LW2 0h


title: BMDM LR4 0h


title: BMDM DR2 0h


title: BMDM LR3 0h


title: BMDM DR3 0h


title: BMDM DR5 0h


title: BMDM LR1 0h


title: BMDM LW3 0h


title: BMDM LW1 0h


title: BMDM HAM5 0h


title: BMDM PIE2 0h


title: MDM HAM3 7h

source_name: HAM_MDM_stimulated with LPS

value: monocyte-derived macrophages (MDM)


title: MDM PIE1 7h

source_name: PIE_MDM_stimulated with LPS


title: MDM HAM1 7h


title: MDM PIE5 7h


title: MDM HAM5 7h


title: MDM HAM4 7h


title: MDM PIE4 7h


title: MDM HAM2 7h


title: MDM DR4 7h

source_name: DR_MDM_stimulated with LPS


title: MDM DR2 7h


title: MDM LW1 7h

source_name: LW_MDM_stimulated with LPS


title: MDM PIE3 7h


title: MDM DR1 7h


title: MDM LW2 7h


title: MDM LR1 7h

source_name: LR_MDM_stimulated with LPS


title: MDM DR3 7h


title: MDM DR5 7h


title: MDM LW3 7h


title: MDM LW5 7h


title: MDM LR3 7h


title: MDM HAM4 0h


title: MDM LW4 7h


title: MDM LR4 7h


title: MDM LR5 7h


title: MDM HAM2 0h


title: MDM LR2 7h


title: MDM HAM3 0h


title: MDM HAM5 0h


title: MDM HAM1 0h


title: MDM PIE4 0h


title: MDM PIE1 0h


title: MDM DR4 0h


title: MDM LR3 0h


title: MDM DR3 0h


title: AS2 overexpressing shoot apex

status: Public on Mar 01 2013

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

institute: Kanazawa University

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChipR Scanner 3000 7G system.

data_processing: The data were analyzed with MSA5.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Arabidopsis thaliana

source_name: AS2 overexpressing shoot apex

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

growth_protocol: Plants were grown on soil under long day condition (16 hours light and 8 hours dark). for 14 days.

extract_protocol: total RNAs were extracted using RNeasy (QIAGEN)

treatment_protocol: Shoot apices were harvested.

tag: genotype

value: AS2 overexpressing mutant

tag: genetic background

value: shoot apex containing leaf primordia


title: MDM LW5 0h


title: as2-1 shoot apex

source_name: as2-1 shoot apex

value: as2-1 mutant


title: MDM PIE5 0h


title: MDM LW4 0h


title: MDM DR1 0h


title: MDM DR2 0h


title: MDM DR5 0h


title: MDM LW2 0h


title: MDM LW1 0h


title: MDM LR2 0h


title: MDM LR5 0h


title: MDM LW3 0h


title: HUH7-asynch-3

status: Public on Mar 31 2013

description: Gene expression data from asynchronously cycling HUH7 cells

hyb_protocol: Standard manufacturer's protocol - Affymetrix GeneChip Technical Manual

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Data was imported into Partek and the GCRMA background-subtraction method was applied. The replicates were then quantile-normalized to each other and median polished.

label: TdT label

source_name: HUH7 cells, asynchronously cycling

growth_protocol: HUH7 cells were plated in fresh DMEM High Glucose with L-glutamine (Invitrogen; Carlsbad, CA; 11965) containing 10% FBS (HyClone, Logan, UT) and 1% penicillin-streptomycin (Invitrogen) and grown overnight to 75% confluence.

extract_protocol: Total RNA was collected from three different plates with asynchronous Huh7 cells using the RNeasy mini kit (Qiagen Valencia CA).

treatment_protocol: Asynchronously cycling cells were not subjected to any special treatment protocol.

tag: cycling state

value: asynchronous


title: MDM LR4 0h


title: MDM LR1 0h


title: wild type shoot apex

source_name: wild type shoot apex

value: wild type


title: as1-1 shoot apex

source_name: as1-1 shoot apex

value: as1-1 mutant


title: cavernous nerve injury _2

status: Public on Dec 31 2012

city: Seoul

first: SungWon

last: Lee

state: Seoul

address: 50 Irwon-dong

department: Urology

institute: Samsung Medical Center

description: At 12 weeks after bilateral CN resection , penile tissue was harvested and total RNA was extracted.

hyb_protocol: The Cy3-labeled RNAs were resuspended in 10 ㎕ of hybridization solution. The resuspended RNAs were placed on Agilent Rat genome 4x44K array ) and covered by  the A4 hybridization mixer. The slides were hybridized for 12 hr at 42 ℃ MAUI hybridization system.

scan_protocol: Hybridized slides were scanned with the Axon Instruments Agilent scanner The scanned images were analyzed with the software program Feature Extraction v10.7.3.1 (Agilent technologies, Santa Clara, CA) and GeneSpring GX 11.0 (Agilent technologies, Santa Clara, CA).

data_processing: The data were processed based on median polish normalization method using the GeneSpring GX 11.0 (Agilent technologies, CA). Spots that were judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

organism: Rattus norvegicus

source_name: The corpus cavernosum of penis

label_protocol: Each total 1 ug of RNA sample was labeled and amplified using Universal Linkage System (ULS) RNA labeling kit.

growth_protocol: At 12 weeks after sham or bilateral CN resection, penile tissue was harvested.

extract_protocol: Total RNA was extracted from the rat penile tissue sample using the TRI Reagent following manufacturer's instructions

value: Male

value: Week 12

value: Penile tissue

tag: treatment

value: bilateral CN resection


title: HUH7-asynch-2

label_protocol: Standard manufacturer's protocol - Affymetrix GeneChip Technical Manual


title: cavernous nerve injury_3

description: At 12 weeks after bilateral CN resection, penile tissue was harvested and total RNA was extracted.


title: Sept Large 1 vs Small 1 [liver]

status: Public on Nov 29 2012

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

state: Ontario

address: Science Complex, University of Guelph

department: Intergrative Biology

country: Canada

institute: University of Guelph

description:
mRNA pooled from 5 fish
A758L-1

hyb_protocol: cDNA was hybridized according to Preventing Ozone Related Problems version of the the hybridization protocol described in Two-Color Microarray-Based Gene Expression Analysis (Agilent Technologies) in Agilent hybridization chambers.

scan_protocol: Images were scanned on a GenePix 4200A scanner. Images were quantified using Genepix Pro software (version 6.1).

data_processing: Genespring GX (v.7.3.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 647

organism: Oncorhynchus mykiss

source_name: liver from small fish

label_protocol: cDNA was prepared from 0.5 ug mRNA using a SuperScript® Plus Direct cDNA Labeling System with Alexa Fluor® aha-dUTPs and labelled with either Alexa Fluor 555 or Alexa Fluor 647 according to the manufacturer's instructions.

growth_protocol: Rainbow trout from the Lyndon strain were reared at Alma Aquaculture Research Station and fed ad libitum.

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions.
mRNA was extracted from total RNA using μMACS mRNA Isolation Kits – Small Scale  according to the manufacturer's instructions.

tag: hatching time

value: Sept

value: Lyndon

tag: FISH size

value: small

value: liver

label: Alexa Fluor 555

source_name: liver from large fish

value: large


title: cavernous nerve injury_1


title: HUH7-asynch-1


title: Dec Small 1 vs Large 1 [liver]

description:
mRNA pooled from 5 fish
A128L-2

value: Dec


title: MDM PIE3 0h

value: PIE

value: male

value: monocyte-derived macrophages (MDM)

value: untreated


title: Dec Large 2 vs Small 2 [liver]

description:
mRNA pooled from 5 fish
A128L-3


title: Dec Small 2 vs Large 2 [muscle]

description:
mRNA pooled from 5 fish
A128M-4

scan_protocol: Images were scanned on a GenePix 4200A scanner Images were quantified using Genepix Pro software (version 6.1).

source_name: muscle from large fish

growth_protocol: Rainbow trout from the Lyndon strain were reared at Alma Aquaculture Research Station and fed ad libitum

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
mRNA was extracted from total RNA using μMACS mRNA Isolation Kits – Small Scale  according to the manufacturer's instructions.

value: muscle

source_name: muscle from small fish


title: Sept Small 1 vs Large 1 [liver]

description:
mRNA pooled from 5 fish
A758L-2


title: Dec Large 2 vs Small 2 [muscle]

description:
mRNA pooled from 5 fish
A128M-3


title: sham operation normal_3

description: At 12 weeks after sham operation (resection), penile tissue was harvested and total RNA was extracted.

value: sham operation


title: Dec Small 2 vs Large 2 [liver]

description:
mRNA pooled from 5 fish
A128L-4


title: Sept Small 2 vs Large 2 [liver]

description:
mRNA pooled from 5 fish
A758L-4


title: Dec Large 1 vs Small 1 [liver]

description:
mRNA pooled from 5 fish
A128L-1


title: sham operation normal_1


title: Sept Large 2 vs Small 2 [muscle]

description:
mRNA pooled from 5 fish
A758M-3


title: Dec Large 1 vs Small 1 [muscle]

description:
mRNA pooled from 5 fish
A128M-1


title: Sept Large 2 vs Small 2 [liver]

description:
mRNA pooled from 5 fish
A758L-3


title: Sept Small 1 vs Large 1 [muscle]

description:
mRNA pooled from 5 fish
A758M-2


title: Dec Small 1 vs Large 1 [muscle]

description:
mRNA pooled from 5 fish
A128M-2


title: HBEC34-KT

status: Public on Oct 25 2012

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Immortalized human bronchial epithelial cells

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: KSFM

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell line

value: HBEC-KT cell line (normal lung cells immortalized with CDK4 and hTERT)

tag: cell line name

tag: histology

value: Immortalized Normal

value: F


title: Sept Small 2 vs Large 2 [muscle]

description:
mRNA pooled from 5 fish
A758M-4


title: Nose_6ppmFormaldehyde_repA

status: Public on Sep 01 2012

description:
6ppm_A
Nasal tissue from nonhuman primate exposed to 6 ppm gaseous formaldehyde, 6 hours/day, for 2 days

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent Human miRNA Microarray, ver 1.

scan_protocol: Microarrays were scanned using Agilent Microarray Scanner.

data_processing: Data were normalized by quantile (Partek Genomics Suite software (version 6.5))

label: Cyanine 3-Cytidine bisphosphate (pCp) reagent

organism: Macaca fascicularis

source_name: nasal tissue_exposed to 6 ppm formaldehyde

label_protocol: Labeled cRNA were prepared according to the standard Agilent protocol.

growth_protocol: Monkeys were cared for at the Lovelace Research Institute. Animals were approximately 6 years of age during treatment. Animals were conditioned to whole body exposure chambers for 30, 60, 180, and 360 minutes prior to the first day of exposure.

extract_protocol: Approximately 15 minutes after the second exposure period, animals were serially sedated and euthanized with Euthasol. One animal underwent necropsy at a time, and each necropsy required approximately 45 minutes. All samples were collected within 3 hours post-exposure. During necropsy, nasal epithelial tissues from the maxilloturbinate regions were collected, stored in RNAlater® (Qiagen, Valencia, CA), and stored at -80°C. Small RNAs were extracted using the RNAeasy mini kit (Qiagen).

treatment_protocol: Animals received two days of formaldehyde exposure for six hours using whole body exposure chambers. Target exposure concentrations were 0, 2, and 6 ppm formaldehyde. Exposure conditions were created by vaporizing [13CD2]-paraformaldehyde.

tag: age

value: approximately 6 years of age

value: nasal maxilloturbinate region


title: Nose_2ppmFormaldehyde_repB

description:
2ppm_B
Nasal tissue from nonhuman primate exposed to 2 ppm gaseous formaldehyde, 6 hours/day, for 2 days

source_name: nasal tissue_exposed to 2 ppm formaldehyde


title: Nose_2ppmFormaldehyde_repA

description:
2ppm_A
Nasal tissue from nonhuman primate exposed to 2 ppm gaseous formaldehyde, 6 hours/day, for 2 days


title: Nose_6ppmFormaldehyde_repC

description:
6ppm_C
Nasal tissue from nonhuman primate exposed to 6 ppm gaseous formaldehyde, 6 hours/day, for 2 days


title: Nose_2ppmFormaldehyde_repC

description:
2ppm_C
Nasal tissue from nonhuman primate exposed to 2 ppm gaseous formaldehyde, 6 hours/day, for 2 days


title: Nose_6ppmFormaldehyde_repB

description:
6ppm_B
Nasal tissue from nonhuman primate exposed to 6 ppm gaseous formaldehyde, 6 hours/day, for 2 days


title: Nose_unexposed_repB

description:
Control_B
Nasal tissue from nonhuman primate control

source_name: nasal tissue_unexposed


title: Sept Large 1 vs Small 1 [muscle]

description:
mRNA pooled from 5 fish
A758M-1

value: Sept


title: HBEC30-KT

tag: race

value: Caucasian


title: Nose_unexposed_repA

description:
Control_A
Nasal tissue from nonhuman primate control


title: sham operation normal_2

value: Male

value: Week 12

value: Penile tissue


title: Cholangiocarcinoma Tumor 37

status: Public on Feb 25 2012

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by means of  Genome Studio v2010 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

source_name: Cholangiocarcinoma Tumor37

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: sample id

value: Cholangiocarcinoma


title: Cholangiocarcinoma Tumor 28

source_name: Cholangiocarcinoma Tumor28


title: Cholangiocarcinoma Tumor 35

source_name: Cholangiocarcinoma Tumor35


title: Cholangiocarcinoma Tumor 34

source_name: Cholangiocarcinoma Tumor34


title: Cholangiocarcinoma Tumor 26

source_name: Cholangiocarcinoma Tumor26


title: Cholangiocarcinoma Tumor 33

source_name: Cholangiocarcinoma Tumor33


title: Cholangiocarcinoma Tumor 36

source_name: Cholangiocarcinoma Tumor36


title: Cholangiocarcinoma Tumor 31

source_name: Cholangiocarcinoma Tumor31


title: Cholangiocarcinoma Tumor 27

source_name: Cholangiocarcinoma Tumor27


title: Cholangiocarcinoma Tumor 22

source_name: Cholangiocarcinoma Tumor22


title: Cholangiocarcinoma Tumor 30

source_name: Cholangiocarcinoma Tumor30


title: Cholangiocarcinoma Tumor 24

source_name: Cholangiocarcinoma Tumor24


title: Cholangiocarcinoma Tumor 13

source_name: Cholangiocarcinoma Tumor13


title: Cholangiocarcinoma Tumor 21

source_name: Cholangiocarcinoma Tumor21


title: Cholangiocarcinoma Tumor 32

source_name: Cholangiocarcinoma Tumor32


title: Cholangiocarcinoma Tumor 23

source_name: Cholangiocarcinoma Tumor23


title: Cholangiocarcinoma Tumor 14

source_name: Cholangiocarcinoma Tumor14


title: Cholangiocarcinoma Tumor 16

source_name: Cholangiocarcinoma Tumor16


title: Cholangiocarcinoma Tumor 19

source_name: Cholangiocarcinoma Tumor19


title: Cholangiocarcinoma Tumor 18

source_name: Cholangiocarcinoma Tumor18


title: Cholangiocarcinoma Tumor 12

source_name: Cholangiocarcinoma Tumor12


title: Cholangiocarcinoma Tumor 7

source_name: Cholangiocarcinoma Tumor7


title: Cholangiocarcinoma Tumor 15

source_name: Cholangiocarcinoma Tumor15


title: Cholangiocarcinoma Tumor 17

source_name: Cholangiocarcinoma Tumor17


title: Cholangiocarcinoma Tumor 10

source_name: Cholangiocarcinoma Tumor10


title: Cholangiocarcinoma Tumor 8

source_name: Cholangiocarcinoma Tumor8


title: Cholangiocarcinoma Tumor 4

source_name: Cholangiocarcinoma Tumor4


title: Cholangiocarcinoma Tumor 5

source_name: Cholangiocarcinoma Tumor5


title: Cholangiocarcinoma Tumor 9

source_name: Cholangiocarcinoma Tumor9


title: Cholangiocarcinoma Tumor 6

source_name: Cholangiocarcinoma Tumor6


title: Cholangiocarcinoma Tumor 11

source_name: Cholangiocarcinoma Tumor11


title: Cholangiocarcinoma Tumor 20

source_name: Cholangiocarcinoma Tumor20


title: Cholangiocarcinoma Tumor 1

source_name: Cholangiocarcinoma Tumor1


title: Cholangiocarcinoma Tumor 25

source_name: Cholangiocarcinoma Tumor25


title: Cholangiocarcinoma Tumor 3

source_name: Cholangiocarcinoma Tumor3


title: Surrounding liver SL59

description: matched

source_name: Surrounding liver SL59

value: Surrounding liver


title: Surrounding liver SL56

description: matched

source_name: Surrounding liver SL56


title: Surrounding liver SL55

description: matched

source_name: Surrounding liver SL55


title: Cholangiocarcinoma Tumor 2

source_name: Cholangiocarcinoma Tumor2


title: Surrounding liver SL58

description: matched

source_name: Surrounding liver SL58


title: Surrounding liver SL53

description: matched

source_name: Surrounding liver SL53


title: Surrounding liver SL52

description: matched

source_name: Surrounding liver SL52


title: Surrounding liver SL54

description: matched

source_name: Surrounding liver SL54


title: Surrounding liver SL57

description: matched

source_name: Surrounding liver SL57


title: Surrounding liver SL50

description: matched

source_name: Surrounding liver SL50


title: Surrounding liver SL51

description: matched

source_name: Surrounding liver SL51


title: Surrounding liver SL49

description: matched

source_name: Surrounding liver SL49


title: Surrounding liver SL42

description: matched

source_name: Surrounding liver SL42


title: Surrounding liver SL47

description: matched

source_name: Surrounding liver SL47


title: Surrounding liver SL37

description: matched

source_name: Surrounding liver SL37


title: Surrounding liver SL48

description: matched

source_name: Surrounding liver SL48


title: Surrounding liver SL45

description: matched

source_name: Surrounding liver SL45


title: Surrounding liver SL44

description: matched

source_name: Surrounding liver SL44


title: Surrounding liver SL39

description: matched

source_name: Surrounding liver SL39


title: Surrounding liver SL38

description: matched

source_name: Surrounding liver SL38


title: Surrounding liver SL33

description: matched

source_name: Surrounding liver SL33


title: Surrounding liver SL36

description: matched

source_name: Surrounding liver SL36


title: Surrounding liver SL43

description: matched

source_name: Surrounding liver SL43


title: Surrounding liver SL35

description: matched

source_name: Surrounding liver SL35


title: Surrounding liver SL40

description: matched

source_name: Surrounding liver SL40


title: Surrounding liver SL32

description: matched

source_name: Surrounding liver SL32


title: Surrounding liver SL46

description: matched

source_name: Surrounding liver SL46


title: Surrounding liver SL34

description: matched

source_name: Surrounding liver SL34


title: Surrounding liver SL29

description: matched

source_name: Surrounding liver SL29


title: Surrounding liver SL30

description: matched

source_name: Surrounding liver SL30


title: Surrounding liver SL41

description: matched

source_name: Surrounding liver SL41


title: Surrounding liver SL28

description: matched

source_name: Surrounding liver SL28


title: Surrounding liver SL27

description: matched

source_name: Surrounding liver SL27


title: Surrounding liver SL26

description: matched

source_name: Surrounding liver SL26


title: Surrounding liver SL25

description: matched

source_name: Surrounding liver SL25


title: Surrounding liver SL23

description: matched

source_name: Surrounding liver SL23


title: Surrounding liver SL31

description: matched

source_name: Surrounding liver SL31


title: Surrounding liver SL24

description: matched

source_name: Surrounding liver SL24


title: Surrounding liver SL21

description: matched

source_name: Surrounding liver SL21


title: Surrounding liver SL22

description: matched

source_name: Surrounding liver SL22


title: Surrounding liver SL19

description: matched

source_name: Surrounding liver SL19


title: Surrounding liver SL15

description: matched

source_name: Surrounding liver SL15


title: Surrounding liver SL20

description: matched

source_name: Surrounding liver SL20


title: Surrounding liver SL18

description: matched

source_name: Surrounding liver SL18


title: Surrounding liver SL11

description: matched

source_name: Surrounding liver SL11


title: Surrounding liver SL13

description: matched

source_name: Surrounding liver SL13


title: Surrounding liver SL17

description: matched

source_name: Surrounding liver SL17


title: Surrounding liver SL10

description: matched

source_name: Surrounding liver SL10


title: Surrounding liver SL16

description: matched

source_name: Surrounding liver SL16


title: Surrounding liver SL8

description: matched

source_name: Surrounding liver SL8


title: Surrounding liver SL6

description: matched

source_name: Surrounding liver SL6


title: Surrounding liver SL7

description: matched

source_name: Surrounding liver SL7


title: Surrounding liver SL12

description: matched

source_name: Surrounding liver SL12


title: Surrounding liver SL3

description: matched

source_name: Surrounding liver SL3


title: Surrounding liver SL9

description: matched

source_name: Surrounding liver SL9


title: Surrounding liver SL4

description: matched

source_name: Surrounding liver SL4


title: Surrounding liver SL14

description: matched

source_name: Surrounding liver SL14


title: Cholangiocarcinoma Tumor 29

source_name: Cholangiocarcinoma Tumor29


title: Surrounding liver SL5

description: matched

source_name: Surrounding liver SL5


title: Surrounding liver SL2

description: matched

source_name: Surrounding liver SL2


title: Surrounding liver SL1

description: matched

source_name: Surrounding liver SL1


title: Normal intrahepatic bile duct 5

source_name: Normal intrahepatic bile duct 5

value: Normal intrahepatic bile duct


title: Normal intrahepatic bile duct 3

source_name: Normal intrahepatic bile duct 3


title: Normal intrahepatic bile duct 2

source_name: Normal intrahepatic bile duct 2


title: Normal intrahepatic bile duct 1

source_name: Normal intrahepatic bile duct 1


title: Normal intrahepatic bile duct 4

source_name: Normal intrahepatic bile duct 4


title: Cholangiocarcinoma Tumor 100

source_name: Cholangiocarcinoma Tumor100


title: Normal intrahepatic bile duct 6

source_name: Normal intrahepatic bile duct 6


title: Cholangiocarcinoma Tumor 91

source_name: Cholangiocarcinoma Tumor91


title: Cholangiocarcinoma Tumor 102

source_name: Cholangiocarcinoma Tumor102


title: Cholangiocarcinoma Tumor 101

source_name: Cholangiocarcinoma Tumor101


title: Cholangiocarcinoma Tumor 90

source_name: Cholangiocarcinoma Tumor90


title: Cholangiocarcinoma Tumor 99

source_name: Cholangiocarcinoma Tumor99


title: Cholangiocarcinoma Tumor 98

source_name: Cholangiocarcinoma Tumor98


title: Cholangiocarcinoma Tumor 103

source_name: Cholangiocarcinoma Tumor103


title: Cholangiocarcinoma Tumor 87

source_name: Cholangiocarcinoma Tumor87


title: Cholangiocarcinoma Tumor 85

source_name: Cholangiocarcinoma Tumor85


title: Cholangiocarcinoma Tumor 97

source_name: Cholangiocarcinoma Tumor97


title: Cholangiocarcinoma Tumor 104

source_name: Cholangiocarcinoma Tumor104


title: Cholangiocarcinoma Tumor 96

source_name: Cholangiocarcinoma Tumor96


title: Cholangiocarcinoma Tumor 86

source_name: Cholangiocarcinoma Tumor86


title: Cholangiocarcinoma Tumor 92

source_name: Cholangiocarcinoma Tumor92


title: Cholangiocarcinoma Tumor 95

source_name: Cholangiocarcinoma Tumor95


title: Cholangiocarcinoma Tumor 94

source_name: Cholangiocarcinoma Tumor94


title: Cholangiocarcinoma Tumor 89

source_name: Cholangiocarcinoma Tumor89


title: Cholangiocarcinoma Tumor 81

source_name: Cholangiocarcinoma Tumor81


title: Cholangiocarcinoma Tumor 88

source_name: Cholangiocarcinoma Tumor88


title: Cholangiocarcinoma Tumor 80

source_name: Cholangiocarcinoma Tumor80


title: Cholangiocarcinoma Tumor 79

source_name: Cholangiocarcinoma Tumor79


title: Cholangiocarcinoma Tumor 84

source_name: Cholangiocarcinoma Tumor84


title: Cholangiocarcinoma Tumor 83

source_name: Cholangiocarcinoma Tumor83


title: Cholangiocarcinoma Tumor 82

source_name: Cholangiocarcinoma Tumor82


title: Cholangiocarcinoma Tumor 73

source_name: Cholangiocarcinoma Tumor73


title: Cholangiocarcinoma Tumor 77

source_name: Cholangiocarcinoma Tumor77


title: Cholangiocarcinoma Tumor 72

source_name: Cholangiocarcinoma Tumor72


title: Cholangiocarcinoma Tumor 78

source_name: Cholangiocarcinoma Tumor78


title: Cholangiocarcinoma Tumor 68

source_name: Cholangiocarcinoma Tumor68


title: Cholangiocarcinoma Tumor 71

source_name: Cholangiocarcinoma Tumor71


title: Cholangiocarcinoma Tumor 67

source_name: Cholangiocarcinoma Tumor67


title: Cholangiocarcinoma Tumor 65

source_name: Cholangiocarcinoma Tumor65


title: Cholangiocarcinoma Tumor 70

source_name: Cholangiocarcinoma Tumor70


title: Cholangiocarcinoma Tumor 74

source_name: Cholangiocarcinoma Tumor74


title: Cholangiocarcinoma Tumor 62

source_name: Cholangiocarcinoma Tumor62


title: Cholangiocarcinoma Tumor 66

source_name: Cholangiocarcinoma Tumor66


title: Cholangiocarcinoma Tumor 58

source_name: Cholangiocarcinoma Tumor58


title: Cholangiocarcinoma Tumor 75

source_name: Cholangiocarcinoma Tumor75


title: Cholangiocarcinoma Tumor 60

source_name: Cholangiocarcinoma Tumor60


title: Cholangiocarcinoma Tumor 76

source_name: Cholangiocarcinoma Tumor76


title: Cholangiocarcinoma Tumor 59

source_name: Cholangiocarcinoma Tumor59


title: Cholangiocarcinoma Tumor 61

source_name: Cholangiocarcinoma Tumor61


title: Cholangiocarcinoma Tumor 69

source_name: Cholangiocarcinoma Tumor69


title: Cholangiocarcinoma Tumor 57

source_name: Cholangiocarcinoma Tumor57


title: Cholangiocarcinoma Tumor 63

source_name: Cholangiocarcinoma Tumor63


title: Cholangiocarcinoma Tumor 55

source_name: Cholangiocarcinoma Tumor55


title: Cholangiocarcinoma Tumor 64

source_name: Cholangiocarcinoma Tumor64


title: Cholangiocarcinoma Tumor 56

source_name: Cholangiocarcinoma Tumor56


title: Cholangiocarcinoma Tumor 53

source_name: Cholangiocarcinoma Tumor53


title: Cholangiocarcinoma Tumor 50

source_name: Cholangiocarcinoma Tumor50


title: Cholangiocarcinoma Tumor 49

source_name: Cholangiocarcinoma Tumor49


title: Cholangiocarcinoma Tumor 54

source_name: Cholangiocarcinoma Tumor54


title: Cholangiocarcinoma Tumor 48

source_name: Cholangiocarcinoma Tumor48


title: Cholangiocarcinoma Tumor 52

source_name: Cholangiocarcinoma Tumor52


title: Cholangiocarcinoma Tumor 47

source_name: Cholangiocarcinoma Tumor47


title: Cholangiocarcinoma Tumor 51

source_name: Cholangiocarcinoma Tumor51


title: Cholangiocarcinoma Tumor 44

source_name: Cholangiocarcinoma Tumor44


title: Cholangiocarcinoma Tumor 46

source_name: Cholangiocarcinoma Tumor46


title: Cholangiocarcinoma Tumor 42

source_name: Cholangiocarcinoma Tumor42


title: Cholangiocarcinoma Tumor 43

source_name: Cholangiocarcinoma Tumor43


title: Cholangiocarcinoma Tumor 41

source_name: Cholangiocarcinoma Tumor41


title: Cholangiocarcinoma Tumor 45

source_name: Cholangiocarcinoma Tumor45


title: Cholangiocarcinoma Tumor 40

source_name: Cholangiocarcinoma Tumor40


title: Cholangiocarcinoma Tumor 38

source_name: Cholangiocarcinoma Tumor38


title: Cholangiocarcinoma Tumor 39

source_name: Cholangiocarcinoma Tumor39


title: E9.5 VEGF120 ms. Forebrain, rep 4

status: Public on Dec 01 2011

city: Grand Forks

first: Diane

last: Darland

state: ND

address: 10 Cornell Street/Campus Drive

department: Department of Biology

institute: University of North Dakota

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip 430.2 arrays (Affymetrix; catalog no. 901230). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.

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

data_processing: The data were analyzed with AGCC and MAS 5.0 in Expression Console using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity (TGT) of each array was set to 250.

source_name: E9.5 VEGF120 ms. Forebrain

label_protocol: Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the 3' IVT Express kit (Affymetrix), according to the manufacturer's instructions.

growth_protocol: The mice were generated by knock-in cDNA with the VEGF120 isoform of the VEGF-A gene [Carmeliet et al., Nature Medicine 1999; 5(5):495-502].

extract_protocol: Extraction of total RNA was performed using PicoPure™ RNA isolation kit (Applied Biosystems), according to the manufacturer's instructions. RNA purity was checked by OD260/280 readings and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: Embryonic timed pregnancies were collected at E9.5 and the forebrain microdissected.  The VEGF120 mice express only the VEGF120 isoform and lack the other isoforms of the VEGF-A gene.

value: forebrain

value: knock-in cDNA with the VEGF120 isoform of the VEGF-A gene, VEGF164 deficient


title: E9.5 wildtype ms. Forebrain, rep 1

source_name: E9.5 wildtype ms. Forebrain

value: wild type


title: E9.5 VEGF120 ms. Forebrain, rep 2


title: E9.5 wildtype ms. Forebrain, rep 3


title: E9.5 VEGF120 ms. Forebrain, rep 3


title: Healthy-5 baseline

status: Public on Nov 30 2011

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Healthy-5 baseline

extract_protocol: Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: disease state

value: healthy

tag: group

value: baseline


title: E9.5 wildtype ms. Forebrain, rep 4


title: Healthy-9 baseline

source_name: Healthy-9 baseline

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )


title: Healthy-8 baseline

source_name: Healthy-8 baseline


title: E9.5 VEGF120 ms. Forebrain, rep 1


title: LWL3 - duplicate LPS 7h

status: Public on Sep 01 2011

hyb_protocol: Molecules of cRNA were hybridized to each GeneChip array according to the standard procedures provided by the manufacturer.

scan_protocol: The arrays were scanned on the 7G Affymetrix scanner

data_processing: CEL files have been read into R using the function ReadAffy in the Bioconductor package affy. Raw data has been converted to probe set expression measures using the rma function (Robust Multi-Array Average expression measure) with default arguments.

source_name: pig BMDM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the Affymetrix IVT Express kit which uses 100ng input RNA

growth_protocol: Pig bone marrow cells were cultured 5-7 days with rhCSF1 (10e4 U/ml). Cells were then seeded in 6 wells plates at 10e6 cells/ml and left overnight.

extract_protocol: At different timepoints (0h, 2h, 7h, 24h), supernatant was remove and cells lysed with RTL buffer according to the manufacturer's instructions (Quiagen RNA-easy).

treatment_protocol: The next day BMDM were stimulated with 100ng/ml of LPS (Salmonella enterica serotype minnesota Re 595 - Sigma-Aldrich L9764).

tag: breed

value: largeWhite x Landrace F1

tag: cell type

value: bone marrow-derived macrophages

tag: pig

value: male

tag: timepoint


title: Healthy-10 baseline

source_name: Healthy-10 baseline


title: Healthy-7 baseline

source_name: Healthy-7 baseline


title: E9.5 wildtype ms. Forebrain, rep 2

tag: genetic background

tag: tissue

tag: genotype


title: LWL3 - LPS 7h

tag: gender


title: LWL3 - duplicate LPS 2h


title: LWL3 - duplicate unstimulated


title: Healthy-6 baseline

source_name: Healthy-6 baseline


title: LWL3 - LPS 24h


title: LWL3 - LPS 2h


title: LWL2 - duplicate LPS 24h

value: female


title: LWL2 - duplicate LPS 7h


title: LWL3 - unstimulated


title: LWL2 - duplicate unstimulated


title: LWL2 - duplicate LPS 2h


title: Healthy-4 baseline

source_name: Healthy-4 baseline


title: Healthy-3 baseline

source_name: Healthy-3 baseline


title: Cholangiocarcinoma Tumor 93

source_name: Cholangiocarcinoma Tumor93


title: LWL1 - unstimulated


title: LWL2 - LPS 7h


title: LWL2 - LPS 2h


title: Healthy-2 baseline

source_name: Healthy-2 baseline


title: LWL2 - unstimulated


title: LWL1 - duplicate LPS 7h


title: LWL1 - duplicate unstimulated


title: LWL1 - duplicate LPS 24h


title: LWL2 - LPS 24h


title: LWL1 - LPS 7h


title: LWL1 - LPS 24h


title: LWL1 - duplicate LPS 2h


title: Healthy-1 baseline

source_name: Healthy-1 baseline


title: LWL1 - LPS 2h


title: PC-3_Vehicle_3

status: Public on Aug 31 2011

first: Ju-Hong

last: Jeon

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

description: Vehicle effect on gene expression profile in PC-3 cells

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 1.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Affymetrix Human Gene 1.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

source_name: Prostate cancer cell line PC-3

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed  using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: The cells were maintained under DMEM medium containing 10% FBS.

extract_protocol: Total RNA was extracted from the cells and processed according to the manufacturer’s guideline (Affymetrix).

treatment_protocol: Either nothing or menthol was dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells.

value: Androgen-independent prostate carcinoma (PC-3) cell line

tag: agent

value: control


title: PC-3_Vehicle_1

tag: cell line


title: PC-3_Menthol_3

description: Menthol effect on gene expression profile in PC-3 cells

value: menthol


title: PC-3_Menthol_1


title: PC-3_Menthol_2


title: PC-3_Vehicle_2


title: miRNA OSE 665

status: Public on Jul 29 2011

city: Atlanta

first: Shubin

last: Shahab

state: GA

address: 310 Ferst Drive

department: Biology

institute: Georgia Institute of Technology

description: Ovarian surface epithelia brushing from ovaries described by pathology as within normal limits.

hyb_protocol: Hybridization was performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Scanning was performed according to Affymetrix-recommended procedures. The fluorecence data is extracted at 1.4 micron pixel resolution using the Affymetrix 3000 7G scanner

data_processing: For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes. A two-sample t-Test, with assumption of equal variance, was applied for statistical hypothesis testing. This test defined which probes are considered to be significantly differentially expressed based on a p-value of 0.01 and log2 difference ≥ 1.

source_name: Healthy ovarian surface epithelial cells

label_protocol: The 3’ ends of the RNA molecules were tailed and biotin-labeled using the mirVana™ miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit’s dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

extract_protocol: For miRNA extraction from normal ovarian surface epithelia, the cells were spun down and resuspended in lysis buffer from the mirVana miRNA Isolation Kit, and total RNA was extracted following the manufacturer's recommended protocol (Ambion, Austin, TX).  The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits (Ambion Inc., Austin, TX).

treatment_protocol: Normal ovarian surface epithelial (OSE) cells were collected from ovaries at time of surgery using a Cytobrush Â® Plus (Medscand) and immediately stabilized in RNAlater (Ambion) and stored at â€“20 degrees C.

tag: tumor stage/grade

tag: age at surgery


title: 246634

status: Public on May 20 2011

city: St Louis

first: Jacqueline

last: Payton

state: MO

address: 4320 Forest Park Avenue, Suite 211

institute: Washington University School of Medicine

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data scaled to array mean of 1500

source_name: Bone marrow specimen from Tumor cells

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Bone marrow specimen from tumor cells

extract_protocol: Trizol reagent standard protocol

value: bone marrow

tag: age

tag: Sex

value: M

value: W

tag: fab

tag: cytogenetics

value: normal

tag: %bm blast

tag: pb wbc@ presentation

tag: %pb blast

tag: vital status

value: Dead

tag: efs months (3.31.10)


title: miRNA CEPI 588

description: Serous ovarian tumor tissues were placed in cryotubes and immediately (<1 minute) frozen in liquid nitrogen following resection.

source_name: Laser captured microdissected ovarian cancer epithelial cells

extract_protocol: Fresh frozen tissues from tumors were cut into seven-micron sections, applied to non-charged slides, then fixed in 75% ethanol for 30 seconds, stained and dehydrated using the HistoGene LCM Frozen Section Staining Kit (Arcturus, Mountain View, CA). LCM was performed with an AutoPix Automated Laser Capture Microdissection System using the CapSure Macro Caps (Arcturus, Mountain View, CA). Approximately 10,000 cells were captured on each of 5-6 caps per sample. MiRNA was extracted from captured cells using the mirVana miRNA Isolation Kit (Ambion, Austin, TX).

treatment_protocol: Following pathological verification, a serous papillary epithelial cancer sample was embedded in cryomatrix (Shandon).  Seven micron frozen sections were cut and attached to uncharged microscope slides for each sample.  Immediately following dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slides were processed in an Autopixâ€˜ instrument (Arcturus) for laser capture microdissection (LCM) of cells to CapSure Macro LCM Caps.  Approximately 30,000 epithelia were collected from each cancer sample.


title: 972783

tag: race


title: miRNA OSE 482


title: miRNA OSE 783


title: miRNA CEPI 551


title: 325028

tag: tissue

value: complex [no favorable]


title: 345701

value: F

value: Alive


title: 387919

tag: flt3 d835


title: 322110

tag: flt3 itd

value: ITD


title: 225373


title: 332131


title: 851929


title: miRNA CEPI 489


title: 290344


title: 944281


title: Liver FoxA2/IgG

status: Public on Jul 19 2011

description:
FoxA2 vs non-specific hybridization in liver
FOXA2 antibody from Upstate, Catalog No. 07-633

hyb_protocol: For ChIP-chip analysis three competitive hybridizations were performed (FoxA2 vs IgG, FoxA2 vs input DNA, IgG vs input DNA). DNA hybridization was performed per Nimblegen protocol.

scan_protocol: standard Nimblegen protocol

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

source_name: FOXA2 chIP DNA from liver cells

label_protocol: We pooled the DNA recovered from triplicate immunoprecipitations, amplified the material by ligation-mediated PCR and then labeled the DNA with cyanine dye as described in the Samples section and hybridized it to the endoderm array.

extract_protocol: Mouse livers from C3H strain were crosslinked by perfusion through the portal vein and nuclei were isolated. Nuclei were resuspended in liver sonication buffer (50 mM Tris, 2mM EDTA, 0.5% N-laurylsarcosine, 50 mM PMSF, protease inhibitors) held on ice for 5 min, then sheared in a bath sonicator for 10 min with 30 sec ON/OFF intervals. RNAse was added to 40 ng/ml and chromatin was dialyzed to TE overnight 4°C, DNA was quantitated, and adjusted to 50 µg per ChIP reaction in 1X RIPA buffer. Immune complexes formed overnight at 4°C,  and were recovered with 40 µl 50% pre-cleared protein A beads for 2 hr at 4° C. Beads were washed 6 times with high salt RIPA and eluted twice with 100 ul elution buffer (1% SDS, 0.1 M sodium bicarbonate) at 42°C. Protein-DNA crosslinks were reversed overnight at 68°C, and DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation and resuspension in dH20.

treatment_protocol: We isolated chromatin from adult mouse livers which were perfused with formaldehyde in situ.

value: Liver

tag: strain

tag: antibody

source_name: IgG chIP DNA from liver cells

value: IgG


title: 721214

value: failed


title: Liver IgG/Input

description:
Non-specific antibody vs DNA input hybridization in liver
FOXA2 antibody from Upstate, Catalog No. 07-633

source_name: Input DNA from liver cells

value: Input


title: 335640


title: 258135


title: Liver FoxA2/Input

description:
FoxA2 vs DNA input hybridization in liver
FOXA2 antibody from Upstate, Catalog No. 07-633


title: A549 cells exposed to aged urban mix 1

status: Public on Feb 01 2011

city: Chapel Hill

first: Rebecca

last: Fry

address: 1213 MHRC

institute: UNC-Chapel Hill

description: Gene expression data from aged urban mix treated lung cells

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Human Gene 1.0 ST array

scan_protocol: GeneChips were scanned using Affymetrix scanner

data_processing: Data were analyzed with Robust multichip analysis in Partek version 6.4.

source_name: A549 cells

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

growth_protocol: A549 cells were grown in F-12K media

extract_protocol: Qiagen RNeasy Kit

treatment_protocol: Cells at air-liquid interface exposed to aged urban mix for 4 hrs

tag: cell line

value: A549 cells

tag: treatment group

value: exposed to aged urban mix


title: A549 cells exposed to aged urban mix 2


title: Control A549 cells for aged exposure 1

description: Gene expression data from untreated lung cells

treatment_protocol: Cells at air-liquid interface exposed to humidified air for 4 hrs

value: aged exposure


title: Control A549 cells for aged exposure 2


title: 548327

tag: age


title: A549 cells exposed to fresh urban mix 2

description: Gene expression data from fresh urban mix treated lung cells

treatment_protocol: Cells at air-liquid interface exposed to fresh urban mix for 4 hrs

value: exposed to fresh urban mix


title: Blood_DNA_Methylation_AsUnexposed_4

status: Public on Dec 16 2010

description: Platform GPL5082

hyb_protocol: Samples were hybridized to Affymetrix Human Promoter 1.0R Array (GPL5082)

scan_protocol: Chips were scanned using Affymetrix scanner

data_processing: Data were analyzed with Robust multichip analysis in Partek Genomics Suite (version 6.4). RMA normalized data are provided as a supplementary file on the Series record.

label_protocol: Affymetrix GeneChip WT dsDNA labeling kit (TdT)

extract_protocol: QiagenDNA Extraction Kit. CpG-methylated DNA was pulled down using a methyl binding domain protein complex. Samples were labeled with the Affymetrix GeneChip WT dsDNA labeling kit and hybridized to Affymetrix Human Promoter 1.0R arrays.

value: blood

tag: Sex

value: Female


title: Blood_DNA_Methylation_AsExposed_11

description: Platform GPL5082


title: Blood_DNA_Methylation_AsExposed_15

description: Platform GPL5082


title: Blood_DNA_Methylation_AsUnexposed_7

description: Platform GPL5082


title: Blood_DNA_Methylation_AsExposed_10

description: Platform GPL5082


title: Blood_DNA_Methylation_AsExposed_9

description: Platform GPL5082


title: Blood_DNA_Methylation_AsUnexposed_5

description: Platform GPL5082


title: Blood_DNA_Methylation_AsExposed_12

description: Platform GPL5082


title: Control A549 cells for fresh exposure 2

value: fresh exposure


title: Blood_DNA_Methylation_AsExposed_13

description: Platform GPL5082


title: Blood_DNA_Methylation_AsUnexposed_2

description: Platform GPL5082


title: 275786

value: bone marrow

value: M

value: W

tag: fab


title: Control A549 cells for fresh exposure 1


title: 753374

tag: cytogenetics

value: normal

value: Dead


title: Blood_DNA_Methylation_AsUnexposed_1

description: Platform GPL5082


title: A549 cells exposed to fresh urban mix 1


title: Blood_DNA_Methylation_AsExposed_16

description: Platform GPL5082


title: Blood_DNA_Methylation_AsUnexposed_8

description: Platform GPL5082


title: Blood_DNA_Methylation_AsExposed_14

description: Platform GPL5082


title: 758168

value: F

tag: %bm blast

value: Alive


title: Blood_DNA_Methylation_AsUnexposed_6

description: Platform GPL5082


title: Blood_DNA_Methylation_AsUnexposed_3

description: Platform GPL5082


title: DM1 myoblasts R068

status: Public on Oct 01 2010

description: Gene expression data from DM1 myoblasts

hyb_protocol: Following fragmentation, cRNA was hybridized on HuEx-1_0-st-v1-01 arrays

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were analyzed with Robust multichip analysis in Partek

source_name: human myoblasts

extract_protocol: RNAeasey extraction

tag: cell type

value: DM1 myoblast


title: A549 controls 3

description: miRNA expression data from untreated lung cells

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent Human miRNA Microarray, ver 1

scan_protocol: Microarrays were scanned using Agilent Microarray Scanner

data_processing: data were lowess normalized using Agilent software

label_protocol: Labeled cRNA were prepared according to the standard Agilent protocol

growth_protocol: A549 cells were grown in F-12K

extract_protocol: Qiagen miRNeasy kit

tag: treatment

value: untreated


title: Tk6 treated with arsenic rep2

status: Public on Apr 01 2010

description: Gene expression data from TK6 cells treated with inorganic arsenic

source_name: TK6 cells

growth_protocol: TK6 were grown in RPMI

extract_protocol: Qiagen Rneasy kit

treatment_protocol: Log-phase TK6 cells exposed to 0.1 uM arsenic for 24 hrs

value: inorganic arsenic 0.1 uM

value: TK6 cells


title: normal myoblasts R065

description: Gene expression data from normal myoblasts

value: normal myoblasts


title: Tk6 untreated controls for cadmium exposure rep2

description: Gene expression data from untreated TK6 cells

treatment_protocol: Log-phase TK6 cells were unexposed

value: untreated in parallel to cadmium treated cells


title: Tk6 treated with arsenic rep1


title: normal myoblasts H427


title: DM1 myoblasts H429

description: Gene expression data from DM1 myoblasts


title: Tk6 untreated controls for arsenic exposure rep2

value: untreated in parallel to arsenic treated cells


title: A549 treated with formaldehyde 2

description: miRNA expression data from lung cells treated with formaldehyde

treatment_protocol: Cells at air-liquid interface exposed to 1 ppm formaldehyde for 4 hrs

value: 1 ppm formaldehyde


title: normal myoblasts R066


title: Tk6 treated with cadmium rep1

description: Gene expression data from TK6 cells treated with cadmium chloride

treatment_protocol: Log-phase TK6 cells exposed to 0.1 uM cadmium for 24 hrs

value: cadmium chloride 0.1 uM


title: A549 controls 2


title: A549 treated with formaldehyde 3


title: Tk6 untreated controls for arsenic exposure rep1


title: A549 controls 1


title: Tk6 treated with cadmium rep2


title: DM1 myoblasts H428

description: Gene expression data from DM1 myoblasts


title: A549 treated with formaldehyde 1


title: Tk6 untreated controls for cadmium exposure rep1


title: DM1 myoblasts R067

description: Gene expression data from DM1 myoblasts


title: normal myoblasts H426


title: N_LS_Time0

status: Public on Oct 30 2009

description: Psoriasis patient

hyb_protocol: 15mg of the biotinylated cRNA was hybridized to Affymetrix Human Genome U133A 2.0 Array (22200 probe sets) (Affymetrix Inc.). The chips were washed and stained with streptavidin-phycoerythin.

source_name: Patient  N, lesion, time: 0

label_protocol: For each Affymetrix genechip, 4mg total RNA was reverse-transcribed, amplified, and labeled using BioArray High Yield RNA Transcription Labeling Kit (Enzo Biochem Inc.).

extract_protocol: Cells were lysed in RLT with Beta-2-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen), and DNA was removed with on-column DNAse digestion using RNAse-free DNAse Set (Qiagen). RNA was used for either RT-PCR or gene array.

tag: Patient

value: N

tag: Time

tag: Group

value: responder

tag: Condition

value: lesional


title: J_LS_Time0

description: Psoriasis patient

source_name: Patient  J, lesion, time: 0

value: J

value: non-responder


title: O_LS_Time0

description: Psoriasis patient

source_name: Patient  O, lesion, time: 0

value: O


title: K_LS_Time0

description: Psoriasis patient

source_name: Patient  K, lesion, time: 0

value: K


title: G_LS_Time0

description: Psoriasis patient

source_name: Patient  G, lesion, time: 0

value: G


title: M_LS_Time0

description: Psoriasis patient

source_name: Patient  M, lesion, time: 0

value: M


title: I_LS_Time0

description: Psoriasis patient

source_name: Patient  I, lesion, time: 0

value: I


title: H_LS_Time0

description: Psoriasis patient

source_name: Patient  H, lesion, time: 0

value: H


title: L_LS_Time0

description: Psoriasis patient

source_name: Patient  L, lesion, time: 0

value: L


title: F_LS_Time0

description: Psoriasis patient

source_name: Patient  F, lesion, time: 0

value: F


title: E_LS_Time0

description: Psoriasis patient

source_name: Patient  E, lesion, time: 0

value: E


title: Lame 48

status: Public on Sep 01 2009

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

country: France

institute: INRA

description: Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

hyb_protocol: All microarrays slides were prehybridized using 100 µL of DIG easy buffer (Roche) in humidified chambers for 1 hr at 42°C. Slides were then washed with distilled water for 10 min with mild agitation. The hybridization solution contained 80 µl of DIG easy buffer, 2.5 µl of yeast tRNA, 2.5 µl DNA salmon sperm (10µg/ µl) and 2 µl PolyA RNA (1µg/µl). An equal amount of Alexa 555- and Alexa 647-labelled cDNA probes from two samples was added to the mixture, which was denatured at 100°C for 2 min. The mixture of Alexa® 555 and Alexa 647® labeled samples was pipetted onto the slides, which were covered with a Lifter cover slips in hybridization chambers and the microarray hybridized for 16 hr at 42°C. The slides were washed in 0.2X saline sodium citrate (SSC) buffer and 0.1% sodium dodecyl sulfate (SDS) for 15 min at 42°C. The slides were washed a second time with 0.2x SSC for 15 min at room temperature. Finally, the slides were rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm for Alexa® 555 and 635 nm for Alexa® 647 using a GenePix 4000B microarray scanner. The GenePix Pro 6.0 software was used to acquire the fluorescent images, align the spots, quantify their intensity and finally export GenePix report (GPR) files containing spot intensity raw data. The GPR files were stored in the BioArray Software Environment (BASE) of SIGENAE (Système d'Information du projet d'Analyse des Genomes des Animaux d'Elevage) for further processing and analysis.

data_processing: The identification of differentially expressed genes was performed using anapuce package. Spot intensities were calculated using the median value that was logarithm transformed (log2). A normalization consisting of global locally-weighted regression (LOWESS) was applied on the overall intensity log ratio to remove the bias due to fluorescence incorporation. A block effect was also corrected by subtracting the median value of the block. Differential analysis was performed on data where at least four repeated expressions by gene were available. The gene variance was a mixture model by using the varmixt method. On both dataset, unilateral statistical t-test was performed according to varmixt method. Taking into account that all tests were simultaneous, P-values were adjusted by a Benjamini-Hochberg (BH) multiple testing procedures, to control False Discovery Rate to less than 0.05.

organism: Gallus gallus

source_name: Poule IsaBrown 29 stade 18h03

label_protocol: The methods for generating fluorescently labelled cDNA were performed according to the procedure recommended by the manufacturer (Invitrogen, USA). Twenty micrograms of total RNA from various regions of oviduct were used to produce fluorescently labelled cDNA with the Superscript Indirect cDNA Labelling System (Invitrogen, USA). After synthesis and purification, the cDNA was assessed with a Nanodrop ND 1000 (Nanodrop, Nyxor biotech, France). cDNA was used to perform fluorescent dye coupling reaction. The experimental design used a dye switch procedure in which half of samples were labelled with Alexa 555 fluorescent probe and the other half using Alexa 647 (Fisher Scientific BioBLock, France). The dye incorporation rate was assessed with a Nanodrop ND 1000. Only cDNA-probes with frequency of incorporation (Dye molecules/1000 bases) > 11.4 were used for hybridization.

extract_protocol: Total RNA was extracted from frozen tissue samples using a commercial kit (RNeasy mini kit, Qiagen, France) and simultaneously treated with DNase (RNase-free DNase set, Qiagen, France) according to the manufacture procedure. RNA concentrations were measured by absorption at 260 nm. The integrity of RNA was electrophoretically evaluated on a 1% agarose gel and using an agilent 2100 bio analyzer (Agilent technology, USA). Only RNA samples with a 28S/18S ratio > 1.3 were considered as good enough quality and used for hybridization experiments.

tag: tissue

value: uterus

source_name: poule IsaBrown 29 stade 18h03

value: white isthmus


title: Aag MMS treated mouse liver 24 hours replicate 2

status: Public on Feb 04 2009

hyb_protocol: Following fragmentation, cRNA was hybridized on MGU74v2

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust multichip analysis

source_name: mouse liver

extract_protocol: rna easy extraction

treatment_protocol: Mice were exposed to MMS (alkylating agent)

tag: Aag MMS treated mouse liver 24 hours


title: Lame 21

source_name: Poule IsaBrown 24 stade 17h57


title: Aag MMS treated mouse liver 48 hours replicate 3

description: Aag MMS treated mouse liver 48 hours  replicate 1

tag: Aag MMS treated mouse liver 48 hours


title: Aag MMS treated mouse liver 24 hours replicate 4


title: Aag MMS treated mouse liver 24 hours replicate 3


title: B_LS_Time0

description: Psoriasis patient

source_name: Patient  B, lesion, time: 0

value: B


title: Aag MMS treated mouse liver 24 hours replicate 1


title: C_LS_Time0

description: Psoriasis patient

source_name: Patient  C, lesion, time: 0

value: C


title: A_LS_Time0

description: Psoriasis patient

source_name: Patient  A, lesion, time: 0

value: A

value: responder


title: Lame 43

source_name: Poule IsaBrown 38 stade 17h57


title: D_LS_Time0

description: Psoriasis patient

source_name: Patient  D, lesion, time: 0

value: D

value: lesional


title: Aag MMS treated mouse liver 48 hours replicate 1


title: Aag MMS treated mouse liver 48 hours replicate 2


title: Aag MMS treated mouse liver 6 hours replicate 3

tag: Aag MMS treated mouse liver 6 hours


title: Aag MMS treated mouse liver 6 hours replicate 1


title: WT MMS treated mouse liver 48 hours replicate 1

tag: WT MMS treated mouse liver 48 hours


title: Lame 33

source_name: Poule IsaBrown 51 stade 17h44


title: Aag MMS treated mouse liver 12 hours replicate 1

tag: Aag MMS treated mouse liver 12 hours


title: Lame 4

source_name: Poule ISA BRown 19 stade 17h59

source_name: Poule Isa Brown 19 stade 17h59


title: Aag MMS treated mouse liver 12 hours replicate 2

description: Aag MMS treated mouse liver 12 hours  replicate 1


title: Lame 12

source_name: Poule IsaBrown 56 stade 17h50


title: Aag MMS treated mouse liver 6 hours replicate 2


title: WT MMS treated mouse liver 12 hours replicate 3

tag: WT MMS treated mouse liver 12 hours


title: WT MMS treated mouse liver 24 hours replicate 2

tag: WT MMS treated mouse liver 24 hours


title: WT MMS treated mouse liver 48 hours replicate 2


title: WT MMS treated mouse liver 24 hours replicate 1


title: Lame 2

source_name: Poule IsaBrown 23 stade 17h51


title: Aag untreated mouse liver replicate 1

description: Aag untreated mouse liver replicate 1

treatment_protocol: Untreated

tag: Aag untreated mouse liver


title: Aag untreated mouse liver replicate 3

description: Aag untreated mouse liver replicate 3


title: WT MMS treated mouse liver 12 hours replicate 1


title: WT MMS treated mouse liver 6 hours replicate 1

tag: WT MMS treated mouse liver 6 hours


title: Aag untreated mouse liver replicate 4

description: Aag untreated mouse liver replicate 4


title: Aag untreated mouse liver replicate 2

description: Aag untreated mouse liver replicate 2


title: WT MMS treated mouse liver 6 hours replicate 2


title: WT untreated mouse liver replicate 2

description: WT untreated mouse liver replicate 2

tag: WT untreated mouse liver


title: WT MMS treated mouse liver 12 hours replicate 2


title: WT untreated mouse liver replicate 1

description: WT untreated mouse liver replicate 1


title: anc1 treated replicate 2

status: Public on Nov 01 2008

description: Gene expression data from anc1 null yeast

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Yeast S98.

data_processing: The data were analyzed with Robust multichip analysis in RMA express

organism: Saccharomyces cerevisiae

source_name: anc1  null yeast treated

growth_protocol: yeast were grown in YPD  to mid-log phase

extract_protocol: RNA easy extraction of  total RNA was performed

treatment_protocol: anc1 null yeast were grown to mid log phase

tag: anc1 null yeast


title: anc1 treated replicate 3

description: Gene expression data from WT yeast

source_name: anc1 yeast treated with MMS


title: anc1 untreated replicate 1

description: Gene expression data from WT yeast

source_name: anc1 yeast untreated

treatment_protocol: anc1  yeast were grown to mid log phase

tag: anc1  yeast

tag: anc1 yeast


title: WT untreated mouse liver replicate 3

description: WT untreated mouse liver replicate 3


title: Wild type treated replicate 1

description: Gene expression data from WT yeast

source_name: Wt yeast untreated

treatment_protocol: Wt yeast were grown to mid log phase

tag: WT yeast


title: Wild type untreated replicate 1

description: Gene expression data from WT yeast


title: anc1 untreated replicate 2

source_name: anc1 null yeast untreated


title: anc1 treated replicate 1

description: Gene expression data from anc1  yeast

source_name: anc1  yeast treated

treatment_protocol: anc1 yeast were grown to mid log phase


title: Lame 36

source_name: Poule IsaBrown 8 stade 18h01


title: Wild type untreated replicate 2

description: Gene expression data from WT yeast


title: wt3

status: Public on Nov 30 2007

description: Gene expression data from wild type yeast (background BGY111)

source_name: wild type yeast (background BGY111)

growth_protocol: yeast were grown in SD-ura+gal to mid-log phase

extract_protocol: hot phenol extraction of total RNA was performed

treatment_protocol: wild type yeast (background BGY111) were grown to 10X7 cell/ml

tag: wild type yeast (background BGY111)


title: da2

description: Gene expression data from yeast overexpressing apn1 in apn1 null background

source_name: yeast overexpressing apn1 in apn1 null background replicate 2

treatment_protocol: Yeast overexpressing apn1 in apn1 null background were grown to 10X7 cell/ml

tag: Yeast strain overexpressing apn1 in apn1 null background


title: da3

source_name: yeast overexpressing apn1 in apn1 null background replicate 3

tag: Yeast overexpressing apn1  in apn1 null background


title: wt1


title: Wild type treated replicate 3

description: Gene expression data from WT yeast


title: Wild type untreated replicate 3

description: Gene expression data from WT yeast


title: anc1 untreated replicate 3

description: Gene expression data from WT yeast


title: Wild type treated replicate 2

description: Gene expression data from WT yeast


title: da1

source_name: yeast overexpressing apn1 in apn1 null background replicate 1


title: wt2


title: dm3

description: Gene expression data from yeast overexpressing mag in apn1 null background

source_name: yeast overexpressing mag in apn1 null background replicate 3

treatment_protocol: Yeast overexpressing mag in apn1 null background were grown to 10X7 cell/ml

tag: Yeast strain overexpressing mag in apn1 null background


title: dm2

source_name: yeast overexpressing mag in apn1 null background replicate 2

tag: Yeast overexpressing mag  in apn1 null background


title: m2

description: Gene expression data from yeast overexpressing mag

source_name: Yeast overexpressing mag

treatment_protocol: Yeast overexpressing mag were grown to 10X7 cell/ml

tag: Yeast strain overexpressing mag  in BGY111 background

tag: Yeast overexpressing mag expression


title: dm1

source_name: yeast overexpressing mag in apn1 null background replicate 1


title: dma3

description: Gene expression data from overexpressing mag and apn1 in apn1 null background

source_name: yeast overexpressing mag and apn1 in apn1 null background replicate 3

treatment_protocol: Yeast overexpressing mag and apn1 in apn1 null background were grown to 10X7 cell/ml

tag: Yeast strain overexpressing mag and apn1 in apn1 null background


title: dma2

source_name: yeast overexpressing mag and apn1 in apn1 null background replicate 2

tag: Yeast overexpressing mag and apn1 in apn1 null background


title: m1


title: d2

description: Gene expression data from yeast null for expression of apn2

source_name: Yeast null for apn1 expression

treatment_protocol: Yeast null for apn1 expression were grown to 10X7 cell/ml

tag: Yeast strain null for apn1 expression in BGY111 background

tag: Yeast null for apn1 expression


title: m3


title: dma1

source_name: yeast overexpressing mag and apn1 in apn1 null background replicate 1


title: d1

description: Gene expression data from yeast null for expression of apn1


title: d3

description: Gene expression data from yeast null for expression of apn3


title: neocarzinostatin, biological rep1

status: Public on Oct 16 2006

description: Gene expression data from yeast treated with neocarzinostatin

source_name: Yeast treated with neocarzinostatin

growth_protocol: yeast were grown in YPD to mid-log phase and treated with agent

treatment_protocol: Yeast strain DBY747 was treated with neocarzinostatin for 15min resulting in 20-25% lethality

tag: Yeast strain DBY747 treated with neocarzinostatin

tag: Yeast treated with neocarzinostatin


title: Calicheamicin, biological rep1

description: Gene expression data from yeast treated with calicheamicin

source_name: Yeast treated with Calicheamicin

treatment_protocol: Yeast strain DBY747 was treated with calicheamicin for 15min resulting in 20-25% lethality

tag: Yeast strain DBY747 treated with calicheamicin

tag: Yeast treated with calicheamicin


title: Esperamicin, biological rep1

description: Gene expression data from yeast treated with esperamicin

source_name: Yeast treated with Esperamicin

treatment_protocol: Yeast strain DBY747 was treated with esperamicin for 15min resulting in 20-25% lethality

tag: Yeast strain DBY747 treated with esperamicin

tag: Yeast treated with esperamicin


title: yeast treated with mock gamma, biological rep2

status: Public on Jan 27 2007

description: Gene expression data from yeast treated with mock gamma

source_name: Yeast treated with mock gamma

treatment_protocol: Yeast strain DBY747 was treated with mock gamma

tag: Yeast strain DBY747 treated with mock gamma

tag: Yeast treated with mock gamma


title: gamma radiation, biological rep2

description: Gene expression data from yeast treated with gamma radiation

source_name: Yeast treated with gamma radiation

treatment_protocol: Yeast strain DBY747 was treated with gamma radiation resulting in 20-25% lethality

tag: Yeast strain DBY747 treated with gamma radiation

tag: Yeast treated with gamma radiation


title: neocarzinostatin, biological rep2


title: yeast treated with mock gamma, biological rep1


title: Esperamicin, biological rep2


title: methanol, biological rep3

description: Gene expression data from yeast treated with methanol

source_name: Yeast treated with methanol

treatment_protocol: Yeast strain DBY747 was treated with methanol

tag: Yeast strain DBY747 treated with methanol

tag: Yeast treated with methanol


title: yeast treated with mock gamma, biological rep3


title: Calicheamicin, biological rep2


title: Esperamicin, biological rep3


title: gamma radiation, biological rep3


title: Calicheamicin, biological rep3


title: gamma radiation, biological rep1


title: methanol, biological rep2


title: neocarzinostatin, biological rep3


title: yeast treated with methanol, biological rep1