title: Ler- vs wt at Early Stationary Replicate 4

status: Public on Mar 31 2013

type: RNA

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: Equal quantities (300ng) of Cy5- and Cy3-labeled aRNA were added to hybridization solution, and hybridization was performed using the Gene Expression hybridization kit (Agilent Technologies).

scan_protocol: Slides were analysed using an Axon Genepix 4000B microarray scanner, and Genepix 6 software (Axon Scientific).

data_processing: Data was analysed using GeneSpring, version 7 (Agilent). A Lowess curve (locally weighted linear regression curve) was fitted to the plot of log intensity versus log ratio, and 40% of the data were used to calculate the Lowess fit at each point.

molecule: total RNA

organism: Escherichia coli O127:H6 str. E2348/69

source_name: Escherichia coli 0127:H6 E2348/69 ler- OD 0.9

label_protocol: Five hundred nanograms of total RNA was used for labeling, and aRNA was synthesized with the Ambion MessageAmp™ II-Bacteria RNA Amplification Kit according to the recommendations of the manufacturer and labeled with the Cy3 or Cy5 monoreactive dye pack (GE Healthcare). Labeled aRNA was purified with Qiagen RNeasy MinElute clean up kit according to the manufacturer's instructions and quantified using a spectrophotometer (ND-1000; NanoDrop).

growth_protocol: DMEM buffered with 25 mM HEPES ; OD 0.9

extract_protocol: Qiagen RNeasy midi kit as per manufacturer's instructions

tag: strain

tag: genotype/variation

value: ler-

source_name: Escherichia coli 0127:H6 E2348/69 wt OD 0.9

value: ler+/wt


title: Ler- vs wt at Early Stationary Replicate 3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Ler- vs wt at Mid Log Replicate 4

source_name: Escherichia coli 0127:H6 E2348/69 ler- OD 0.3

growth_protocol: DMEM buffered with 25 mM HEPES ; OD 0.3

source_name: Escherichia coli 0127:H6 E2348/69 wt OD 0.3


title: Ler- vs wt at Early Stationary Replicate 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Ler- vs wt at Mid Log Replicate 1

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Ler- vs wt at Mid Log Replicate 2


title: Ler- vs wt at Early Stationary Replicate 1


title: Ler- vs wt at Mid Log Replicate 3


title: Cervical cancer biopsy R443

city: Distrito Federal

first: Ana María

last: Espinosa

state: Cuauhtemoc

address: Dr. Balmis No. 148

department: Unidad de Medicina Genómica

country: Mexico

institute: Hospital General de México O.D.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C and 60 rpm on Human Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_001

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) with GeneChip Scanner 3000

data_processing: Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console.

label: Biotin

organism: Homo sapiens

source_name: Cervical cancer biopsy

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

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

tag: clinic

value: Case

tag: sample id

tag: tissue

value: HPV16-positive cervical cancer specimen


title: Cervical cancer biopsy R446


title: Cervical cancer biopsy R434


title: Cervical cancer biopsy R411


title: Cervical cancer biopsy R415


title: Cervical cancer biopsy R482


title: Cervical cancer biopsy R441


title: Cervical cancer biopsy R409


title: Cervical cancer biopsy R396


title: Cervical cancer biopsy R412


title: P 27 Si RNA

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Illumina HT-12 v4 expression arrays

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring Gx v 12.0

source_name: Tiam1 silenced Y79 cells

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

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

tag: cell line

tag: passage

tag: cell type

value: Retinoblastoma


title: Cervical cancer biopsy R403


title: P 29 Si RNA

description: Illumina HT-12 v4 expression arrays


title: P 27 Control

description: Illumina HT-12 v4 expression arrays

source_name: Untreated Y79 cells


title: P 25 Control

description: Illumina HT-12 v4 expression arrays


title: Cervical cancer biopsy R378


title: P 29 Control

description: Illumina HT-12 v4 expression arrays


title: Cervical cancer biopsy R339


title: Cervical cancer biopsy R369


title: P 25 Si RNA

description: Illumina HT-12 v4 expression arrays


title: Cervical cancer biopsy R324


title: Cervical cancer biopsy R330


title: Cervical cancer biopsy R315


title: Cervical cancer biopsy R336


title: Cervical cancer biopsy R333


title: Cervical cancer biopsy R284


title: Cervical cancer biopsy R308


title: Cervical cancer biopsy R265


title: Cervical cancer biopsy R255


title: Cervical cancer biopsy R258


title: Cervical cancer biopsy R245


title: Cervical cancer biopsy R240


title: Cervical cancer biopsy R189


title: Cervical cancer biopsy R221


title: Cervical cancer biopsy R230


title: Cervical cancer biopsy R183


title: Cervical cancer biopsy R335


title: Cervical cancer biopsy R232


title: Cervical cancer biopsy R124


title: Cervical cancer biopsy R170


title: Cervical cancer biopsy R094


title: Cervical cancer biopsy R093


title: Cervical cancer biopsy R312


title: Healthy female endocervix CN19E

source_name: Healthy female endocervix

value: Control

value: Healthy endocervix


title: Cervical cancer biopsy R072


title: Cervical cancer biopsy R057


title: Healthy female exocervix CN19X

source_name: Healthy female exocervix

value: Healthy exocervix


title: Healthy female endocervix CN10E


title: Cervical cancer biopsy R052


title: Healthy female exocervix CN13X


title: Healthy female exocervix CN10X


title: Healthy female endocervix CN06E


title: Cervical cancer biopsy R015


title: Cervical cancer biopsy R035


title: Healthy female exocervix CN07X


title: Healthy female endocervix CN13E


title: Healthy female endocervix CN03E


title: Healthy female exocervix CN05X


title: Healthy female exocervix CN01X


title: Healthy female endocervix CN01E


title: CpG-ODN_2

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were processed and normalized using quantile normalization with BeadStudio software.

source_name: IGROV1, CpG-ODN

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

extract_protocol: RNA was extracted with the QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: ovarian carcinoma cell line

tag: treatment

value: CpG-ODN


title: CpG-ODN_3


title: CpG-ODN_4


title: pool_children_3

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

institute: IRCCS Ospedale Policlinico San Martino

description: Gene expression analysis

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 100 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 50 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm). Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%. Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (Agilent protocol GE1-v5_95_Feb07). The output of Feature Extraction was analyzed with the Agi4x44PreProcess package to obtain background subtracted (Agilent parameter gBGSubSignal). Only spots with signal minus background  flagged as “positive and significant” (FE field name gIsPosAndSignif)  and not flagged as ControlType or IsManualFlag were used. Probe intensities were log base 2 transformed and normalized across arrays  with the scale normalization method implemented in the function normalizeBetweenArrays of the R package ‘limma’ version 3.10.2. Within each array, log base 2 intensities of probes with identic ProbeName were averaged using the function avereps of limma

source_name: normal cerebellum sample

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com).  Dye incorporation and cRNA yield were checked with the Nanodrop.

extract_protocol: Total RNA was isolated by using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol. Total RNA was quantified and quality control assessed by Nano LabChip® assay on the 2100 Bioanalyzer (Agilent Technologies). Only samples with a RNA Integrity Number >7 were included in the study.

value: Cerebellum

tag: disease state

value: normal

tag: gender

value: unknown

tag: age (months)


title: CpG-ODN_1


title: poolClontech_bis

description: Gene expression analysis


title: poolClontech

description: Gene expression analysis


title: pool_children_1

description: Gene expression analysis


title: MB011_bis

description: Gene expression analysis

source_name: medulloblastoma tumor sample

value: medulloblastoma

value: female


title: HEK 293T Embelin-2

first: Tapas

middle: Kumar

last: Kundu

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

hyb_protocol: RNA was fragmented by metallic cleavage using manufacturar's protocol. Array lanes were blocked using ssDNA and subsequently samples were hybridized at 65oC for 17h. Array was washed with wash buffer with and without DNA. Finally array was dried.

scan_protocol: Samples were scanned in Agilent microarray scanner.

data_processing: Data was analyzed by Genespring GX11.5 software.

source_name: HEK 293T cells after 24h embelin treatment

label_protocol: The product cDNA is converted into cRNA by T7 polymerase and labelled with Cy3 (labelled on cytosine) using Agilent kit.

growth_protocol: HEK 293T cells were grown in DMEM medium with high glucose and 10% FBS at 37oC and 5% CO2 till ~60% confluency.

extract_protocol: Total RNA was extracted by Trizol method. RNA was cleaned up using RNeasy MinElute Cleanup Kit (Qiagen) and reverse transcribed.

treatment_protocol: Cells were treated with either DMSO solvent of 20uM embelin (dissolved in DMSO) for 24h under the same growth conditions mentioned above.

value: HEK 293T


title: #232

description: Gene expression analysis

value: male


title: HEK 293T Embelin-1


title: #203

description: Gene expression analysis


title: HEK 293T DMSO-1

source_name: HEK 293T cells after 24h DMSO treatment


title: #165

description: Gene expression analysis


title: #106

description: Gene expression analysis


title: MB010

description: Gene expression analysis


title: WT ligament tissue

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

country: Japan

institute: Kurume Universuty

description: Sample 3

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray Kit; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with Bioconductor.

organism: Mus musculus

source_name: ligament tissue from wild type mice

label_protocol: cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Mesenchymal stem cells (sample 1) derived from mouse embryos were obtained from the Cell Bank RIKEN Bioresource Center, Japan. The cells were suspended in E-MEM and Dulbecco’s Modified Eagle’s medium containing 10% foetal bovine serum (FBS) to a final concentration of 1.5 × 10^5 cells/ml, were seeded into dishes or flasks (2.0 × 10^4 cells/cm2), and were statically cultured at 37°C under 5% CO2. For the expression of murine proteins, the synthesized mouse A sequence was inserted into XhoI of the pCAGGS vector, which was then cloned and transfected into mouse mesenchymal stem cells. Protein expression in the culture supernatant was confirmed by Western blotting (sample 4). The plasmid DNA pCAGGS-XhoI-A-XhoI was used for introduction of the gene into 58 fertilized mouse eggs. These were then implanted into surrogate mouse mothers. A section of tail tissue was cut from 20 of the resulting newborn mice, and DNA was extracted using the DNA mini kit (QIAGEN). PCR was performed to determine whether the samples contained the exogenous gene. Comparison of microarray analyses with mesenchymal stem cells showed homology between the extracellular matrix of the ligament tissues of Wt mice (sample 3), the ligament tissues of mice transgenic for A (sample 2), and mesenchymal stem cell-derived ligament-like tissue.

extract_protocol: Total RNA was prepared from cells using an AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

tag: background strain

tag: genotype

value: wild type

value: ligament


title: HEK 293T DMSO-2


title: pool_children_2

description: Gene expression analysis


title: MB008

description: Gene expression analysis


title: sh-Ikaros-#3

city: Tokyo

first: Kazumi

last: Nakano

address: 4-6-1, Sirokanedai, Minatoku

department: Department of Medical Genome Sciences, Graduate School of Frontier Sciences

institute: The University of Tokyo

description: mRNA expression in Jurkat cells

hyb_protocol: 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent)  for 1min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel was set to Green, and No extended dynamic range was selected).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09  and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Jurkat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations.  The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Jurkat cells were transfected with the empty vector or ATL-type Helios expression plasmid by Lipophectamine2000 (Invitrogen). Also, Jurkat cells were transduced with recombinant retroviruses expressing sh-scramble, sh-Helios1, or sh-Ikaros.  Cells were selected by neomycin or puromycin for 2 weeks, respectively.

tag: cell-line

value: T-cell from ALL

value: Transduction of shIkaros by retrovirus

value: WT-Ikaros knockdown


title: #93

description: Gene expression analysis


title: Saline_4

source_name: IGROV1, saline

value: saline


title: Stem cells

description: Sample 1

source_name: C3H stem cells

value: mesenchymal stem cells


title: Tg ligament tissue

description: Sample 2

source_name: ligament tissue from transgenic mice

value: A transgenic


title: Stem cell-origin ligament tissue

description: Sample 4

source_name: ligament-like tissue from transfected stem cells

value: ligament-like tissue


title: Saline_2

value: ovarian carcinoma cell line


title: Saline_3


title: Saline_1


title: MB009

description: Gene expression analysis

value: Cerebellum


title: MB002

description: Gene expression analysis


title: sh-Ikaros-#2

description: mRNA expression in Jurkat cells


title: MB004

description: Gene expression analysis


title: Cervical cancer biopsy R412ST

hyb_protocol: Following fragmentation, ssDNA were hybridized for 16 hr at 45C and 60 rpm on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 protocol FS450_0007

data_processing: Microarrays were normalized using the RMA algorithm (Robust Multichip Average) in the Affymetrix Expression Console. The analysis was done at Gene Level Default: RMA-Sketch

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

value: Case

value: HPV16-positive  cervical cancer biopsy specimen


title: 154904

description: Gene expression analysis

value: medulloblastoma


title: sh-Helios1-#3

description: mRNA expression in Jurkat cells

value: Transduction of shHelios1 by retrovirus

value: WT-Helios knockdown


title: sh-Ikaros-#1

description: mRNA expression in Jurkat cells


title: MB001

description: Gene expression analysis

value: male


title: 193263

description: Gene expression analysis


title: 153342

description: Gene expression analysis

value: female


title: 181900

description: Gene expression analysis


title: sh-Helios1-#2

description: mRNA expression in Jurkat cells


title: 188181

description: Gene expression analysis


title: sh-Scramble-#2

description: mRNA expression in Jurkat cells

value: Transduction of sh-scramble by retrovirus

value: Control (sh-scramble)


title: sh-Scramble-#3

description: mRNA expression in Jurkat cells

value: T-cell from ALL


title: MB007

description: Gene expression analysis


title: Cervical cancer biopsy R359

value: HPV16-positive cervical cancer specimen


title: Cervical cancer biopsy R411ST


title: 195589

description: Gene expression analysis


title: sch9-deleted rep2

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample from 59A sch9-deleted strain, biological rep 2

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7

data_processing: Data normalization and statistical analysis were performed using R 2.14.2 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

source_name: 59A sch9-deleted

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: 59A control strain and 59A sch9-deleted strain used in this study were precultured in a nutrient medium containing Yeast Nitrogen Base (YNB) without amino acids (6.7 g/L) and glucose (20 g/L), for 24h at 28°C in Erlenmeyer flasks. The fermentation medium was inoculated at 1 106 cell/mL from preculture. Yeast cultures were carried out in fermenters (1.2 L, containing 1 L medium), with fermentation locks (CO2 bubbling outlets filled with water). Fermentation media were normally deaerated prior to inoculation by bubbling pure argon 5 min. Filling conditions were controlled and fermentations were carried out under anaerobic conditions with permanent stirring (300 rpm) under isothermal conditions (24°C).

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: Fermentation condition was established with 230 g/L glucose + fructose, 5% lipid factor and 142 mg/L assimilable nitrogen in synthetic medium.

value: 59A sch9-deleted

tag: array

tag: block


title: 59A rep1

description: Gene expression in sample from 59A strain, biological rep 1

tag: strain


title: sh-Helios1-#1

description: mRNA expression in Jurkat cells

tag: genotype/variation


title: MB011

description: Gene expression analysis


title: sch9-deleted rep1

description: Gene expression in sample from 59A sch9-deleted strain, biological rep 1


title: Cervical cancer biopsy R378ST

source_name: Cervical cancer biopsy

tag: clinic


title: Cervical cancer biopsy R409ST

tag: sample id


title: ATL-type Helios-#2

description: mRNA expression in Jurkat cells

value: transfection of ATL-type Helios expression plasmid and selection for 2weeks with neomycin

value: ATL-type Helios overexpression


title: ATL-type Helios-#3

description: mRNA expression in Jurkat cells


title: ATL-type Helios-#1

description: mRNA expression in Jurkat cells


title: Cervical cancer biopsy R369ST

tag: tissue


title: 59A rep2

description: Gene expression in sample from 59A strain, biological rep 2


title: empty vector-#3

description: mRNA expression in Jurkat cells

value: transfection of empty vector and selection for 2weeks with neomycin

value: Control (empty vector)


title: Cervical cancer biopsy R336ST


title: Cervical cancer biopsy R339ST


title: Cervical cancer biopsy R330ST


title: Cervical cancer biopsy R315ST


title: Cervical cancer biopsy R324ST


title: empty vector-#1

description: mRNA expression in Jurkat cells


title: empty vector-#2

description: mRNA expression in Jurkat cells


title: Cervical cancer biopsy R265ST


title: Cervical cancer biopsy R230ST


title: Cervical cancer biopsy R240ST


title: endometrium_control_day12_rep2

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: endometrial tissue sample collected from day 12 non-pregnant mare

hyb_protocol: Microarray analysis was performed using Agilent 4x44k Horse Gene Expression microarrays (AMADID 021322). Labeled cRNA was hybridized to the microarrays according the manufacturer’s instructions.

scan_protocol: Hybridized and washed slides were scanned at 3 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies). Processed signals were filtered based on “Well above background” flags (detection in 3 of 4 samples in either one of the two experimental groups) and subsequently normalized with the BioConductor package vsn.

organism: Equus caballus

source_name: endometrium, day 12, non-pregnant

label_protocol: Cy3-labeled cRNA was produced using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from the 8 endometrial biopsy samples using Trizol® Reagent (Invitrogen GmbH, Karlsruhe, Germany) according to the manufacturer’s instructions. Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany). Quality of total RNA was determined by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). RNA integrity (RIN) values ranged from 8.3 to 9.2.

tag: breed

value: Bavarian Warmblood

tag: mare #

tag: pregnancy status

value: control


title: MEF_TF Group 3_1

city: Durham

first: Nicolas

last: Christoforou

state: North Carolina

address: 136 Hudson Hall

department: Biomedical Engineering

country: USA

institute: Duke University

description: Mouse Embryonic Fibroblasts, TF Group 3, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, MYOCD, SRF, Biological Replicate 1

hyb_protocol: The entire labeling, hybridization, and scanning procedure was performed by the Duke University Genomics Microarray facility. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® 430A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: CEL files were imported and normalized using the RMA algorithm in the Partek Genomic Suite

growth_protocol: Mouse embryonic fibroblasts were cultured in standand growth medium (DMEM.HG, 10%FBS, Glutamine, Sodium Pyruvate, Non Essential Amino Acids, beta Mercaptoethanol). Cells within each sample were pretranduced with individual lentiviral vectors allowing the inducible overexpression of the reported transcription factors.

extract_protocol: Total RNA was extracted from the 12 samples using the Qiagen Rneasy Mini kit according to the manufacturer's specifications.

treatment_protocol: Transcription factor overexpression was induced through the addition of Dox for 7 days at which point total RNA was isolated.

tag: cell type

value: mouse embryonic fibroblasts

tag: transduction

value: overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, MYOCD, SRF


title: MEF_TF Group 3_2

description: Mouse Embryonic Fibroblasts, TF Group 3, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, MYOCD, SRF, Biological Replicate 2

scan_protocol: The entire labeling, hybridization, and scanning procedure was performed by the Duke University Genomics Microarray facility. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® 430A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).


title: MEF_TF Group 3_3

description: Mouse Embryonic Fibroblasts, TF Group 3, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, MYOCD, SRF, Biological Replicate 3

label_protocol: The entire labeling, hybridization, and scanning procedure was performed by the Duke University Genomics Microarray facility. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® 430A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).


title: MEF_TF Group 2_3

description: Mouse Embryonic Fibroblasts, TF Group 2, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, Biological Replicate 3

value: overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3


title: MEF_TF Group 2_2

description: Mouse Embryonic Fibroblasts, TF Group 2, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, Biological Replicate 2


title: endometrium_control_day12_rep3


title: MEF_TF Group 2_1

description: Mouse Embryonic Fibroblasts, TF Group 2, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Mesp1, SMARCD3, Biological Replicate 1


title: sh-Scramble-#1

description: mRNA expression in Jurkat cells

tag: treatment


title: MEF_TF Group 1_2

description: Mouse Embryonic Fibroblasts, TF Group 1, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Biological Replicate 2

value: overexpression of M2rtTA, GATA4, TBX5, MEF2C


title: endometrium_pregnant_day16_rep3

description: endometrial tissue sample collected from day 16 pregnant mare after embryo recovery

source_name: endometrium, day 16, pregnant

value: pregnant


title: Cervical cancer biopsy R221ST

value: Case

value: HPV16-positive  cervical cancer biopsy specimen


title: MEF_TF Group 1_3

description: Mouse Embryonic Fibroblasts, TF Group 1, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Biological Replicate 3


title: Lung-PR8-24h-S2

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Lung tissue after stimulation with either PR8, VN, X31 or Mock for 24 hours

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent G3-1-color scan setting for 8x60k arrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029).

source_name: wild-type C57BL/6J mice lung tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and

extract_protocol: Mice were sacrificed by CO2 inhalation. Whole lungs (right side) removed and homogenized (with bead homogenizer) in 1 ml Trizol. Samples snap frozen in liquid nitrogen.

treatment_protocol: Virus aliquots stored at -80C; quick thaw to RT and immediate dilution. Viruses diluted to 1x10^5 PFU/30ul (3.33x10^6 PFU/ml) in ice-cold 1x PBS in polystyrene tubes. Virus dilution maintained at 4C until use. Mice are all female C57BL/6J from Jackson Lab.

tag: infection (influenza strain)

tag: time (hours)


title: Lung-X31-16h-S1

description: Lung tissue after stimulation with either PR8, VN, X31 or Mock for 16 hours


title: endometrium_pregnant_day16_rep2


title: endometrium_control_day12_rep4


title: endometrium_pregnant_day16_rep4


title: Cervical cancer biopsy R183ST


title: Lung-PR8-16h-S2


title: endometrium_control_day12_rep1


title: MEF_Negative Control 3

description: Mouse Embryonic Fibroblasts, Negative Control, Overexpression of M2rtTA, Biological Replicate 3

value: overexpression of M2rtTA


title: endometrium_pregnant_day16_rep1


title: MEF_TF Group 1_1

description: Mouse Embryonic Fibroblasts, TF Group 1, Overexpression of M2rtTA, GATA4, TBX5, MEF2C, Biological Replicate 1


title: Lung-Mock-16h-1


title: MEF_Negative Control 2

description: Mouse Embryonic Fibroblasts, Negative Control, Overexpression of M2rtTA, Biological Replicate 2


title: Cervical cancer biopsy R189ST


title: Lung-X31-16h-S4


title: Cervical cancer biopsy R035ST


title: Cervical cancer biopsy R072ST


title: Cervical cancer biopsy R124ST


title: MEF_Negative Control 1

description: Mouse Embryonic Fibroblasts, Negative Control, Overexpression of M2rtTA, Biological Replicate 1


title: Healthy female exocervix CEXO-7

source_name: Healthy female exocervix

value: Control

value: Healthy exocervix


title: Lung-VN62-24h-S4


title: Lung-VN62-16h-S5


title: Healthy female exocervix CEXO-5


title: WNV day 7 rep1

city: New Haven

first: Tonya

middle: M

last: Colpitts

state: CT

address: 300 Cedar St, TAC S410

department: Internal Medicine, Section of Infectious Diseases

institute: Yale University School of Medicine

description: This sample is of RNA from day 7, Aedes aegypti mosquitoes infected with West Nile virus analyses on each experiment

hyb_protocol: Hybridization was performed by Yale University Keck Facilities (New Haven, CT) following the Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Yale University Keck Facilities (New Haven, CT) following the Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: Data normalization was quantile normalization. (reference: Bolstad B, et al.  (Bioinformatics, 19:185-193, 2003)

organism: Aedes aegypti

source_name: West Nile virus strain 2741

label_protocol: Labeling was performed by Yale University Keck Facilities (New Haven, CT) following the Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: mosquitoes grown at 28 degrees C, 80% humidity

extract_protocol: RNA extracted using Rneasy kit, Qiagen

treatment_protocol: 5-7 day post-eclosion Ae. aegypti mosquitoes were infected with WNV (strain 2741), YFV (Asibi strain) or DEN-2 (strain New Guinea C) via a 300 nL intra-thoracic inoculation of 5 log mosquito infectious dose 50% of virus

value: Rockefeller

tag: disease state

value: West Nile strain 2741


title: WNV day 7 rep3


title: WNV day 2 rep3

description: This sample is of RNA from day 2, Aedes aegypti mosquitoes infected with West Nile virus analyses on each experiment


title: WNV day 2 rep1


title: Healthy female exocervix CEXO-19


title: Healthy female exocervix CEXO-10


title: WNV day 2 rep2


title: WNV day 1 rep3

description: This sample is of RNA from day 1, Aedes aegypti mosquitoes infected with West Nile virus analyses on each experiment


title: Lung-PR8-24h-S5


title: WNV day 7 rep2


title: Lung-X31-12h-S4

description: Lung tissue after stimulation with either PR8, VN, X31 or Mock for 12 hours


title: Lung-X31-12h-S3


title: WNV day 1 rep2


title: Lung-X31-24h-S1


title: Lung-VN62-12h-S1


title: Lung-Mock-24h-1


title: Lung-PR8-12h-S5


title: WNV day 1 rep1


title: Healthy female exocervix CEXO-13


title: YFV day 7 rep3

description: This sample is of RNA from day 1, Aedes aegypti mosquitoes infected with yellow fever virus analyses on each experiment

source_name: yellow fever virus Asibi strain

value: yellow fever wildtype Asibi


title: mutant_ANT_PDE_A6

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.
CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: mutant_embryonic brain_rostral

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Pregnant female mice were euthanized at E8.0/8.5, embryos were collected and tissue samples were quickly dissected, by sectioning with fine tweezers and freezing in liquid nitrogen. Extra-embryonic membranes were used for genotyping of the embryos. The mice used for this study harbor the Raldh2 knockout allele.

extract_protocol: Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from individual embryonic samples.

tag: strain background

value: Raldh2 null mutant; Raldh2 -/-

value: embryonic brain

tag: tissue region

value: Rostral/Anterior

tag: developmental stage

value: 14 somite stage


title: Lung-Mock-12h-1

tag: strain


title: Lung-X31-24h-S3


title: mutant_ANT_PDE_21

tag: genotype/variation


title: YFV day 7 rep1

description: This sample is of RNA from day 7, Aedes aegypti mosquitoes infected with yellow fever virus analyses on each experiment


title: mutant_ANT_PDE_10-1


title: Lung-X31-24h-S4


title: Lung-VN62-16h-S1


title: mutant_ANT_PDE_9-1


title: YFV day 2 rep4


title: Lung-VN62-24h-S2


title: Lung-PR8-12h-S1


title: Lung-PR8-16h-S1


title: YFV day 1 rep3


title: YFV day 2 rep3

description: This sample is of RNA from day 2, Aedes aegypti mosquitoes infected with yellow fever virus analyses on each experiment


title: YFV day 2 rep1


title: WT_ANT_PDE_B1

source_name: WT_embryonic brain_rostral

value: wild type; Raldh2 +/+


title: mutant_ANT_PDE_22


title: YFV day 2 rep2


title: WT_POST_PDE_050

source_name: WT_embryonic brain_posterior

value: posterior

value: 4 somite stage


title: Lung-VN62-16h-S4


title: WT_POST_PDE_059


title: WT_ANT_PDE_B2


title: WT_ANT_PDE_2-wt


title: YFV day 1 rep1


title: DENV2 NGC day 7 rep3

description: This sample is of RNA from day 7, Aedes aegypti mosquitoes infected with dengue virus analyses on each experiment

source_name: dengue virus 2 New Guinea C

value: DENV2 New Guinea C


title: Lung-VN62-12h-S3


title: DENV2 NGC day 7 rep2


title: WT_POST_PDE_041


title: YFV day 1 rep2


title: Lung-X31-16h-S5


title: Lung-VN62-24h-S5


title: DENV2 NGC day 7 rep1


title: mutant_POST_PDE_046

source_name: mutant_embryonic brain_posterior


title: Lung-X31-12h-S1


title: Lung-PR8-24h-S1


title: Lung-VN62-12h-S4


title: Lung-PR8-12h-S2


title: DENV2 NGC day 1 rep3

description: This sample is of RNA from day 1, Aedes aegypti mosquitoes infected with dengue virus analyses on each experiment


title: WT_POST_PDE_042


title: mutant_POST_PDE_036


title: DENV2 NGC day 2 rep2

description: This sample is of RNA from day 2, Aedes aegypti mosquitoes infected with dengue virus analyses on each experiment


title: mutant_POST_PDE_053


title: WT_POST_PDE_049


title: DENV2 NGC day 1 rep2


title: DENV2 NGC day 2 rep1


title: DENV2 NGC day 1 rep1


title: Mouse maxillary molar 2

description: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix)

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Mouse maxillary molar

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

growth_protocol: Pregnant female mice (C57Bl6 genetic background) were euthanized at 14.5 days of gestation (E14.5), embryos were collected and tooth samples (lower incisors, mandibular and maxillary first molars) were microdissected

extract_protocol: Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from pools of 4 tooth germs to obtain enough RNA for subsequent microarray hybridization.

value: maxillary molar

tag: age

tag: genetic background


title: aedes mock D7 rep3

source_name: mosquito not infected


title: DENV2 NGC day 2 rep3


title: Du-het

city: Kumamoto

first: Satomi

middle: S

last: Tanaka

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description: whole embryo

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Dullard-heterozygous

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.nomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNAs were extracted using RNeasy Plus Micro RNA extraction kits (Qiagen, Hilden, Germany) from the embryos. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: whole embryo

value: Dullard-heterozygous


title: Mouse maxillary molar 3


title: mutant_POST_PDE_060


title: Du-mut

description: whole embryo

source_name: Dullard-homozygous

value: Dullard-homozygous


title: Lung-PR8-16h-S3


title: Mouse maxillary molar 4


title: 05_EOB-G(+)A(+)_No_1218_(Mouse430_2)

city: Nagoya

first: Yasuhiro

last: Fujii

department: Nephro-urology

institute: Nagoya City University

description: Gene expression data from kidney.

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Kidney

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: On day0 and day6, kidneys were extracted, and right kidney specimens were stored at -70 temparature.

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

treatment_protocol: Lean(Wild type) and ob/ob mice were treated by glyoxylate(G) and adiponectin(A) for a week.

value: Kidney

value: ob/ob

value: glyoxylate(+) and adiponectin(+)


title: Mouse maxillary molar 1


title: 04_DL-G(+)A(-)_No_1218_(Mouse430_2)

description: Gene expression data from kidney.

value: Lean (Wild type)

value: glyoxylate(+) and adiponectin(-)


title: WM115-FOXD3

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Labeled aRNA (825ng of each sample being co-hybridized, 40-45 pmol/ug dye intensity), in the presence of Agilent Gene Expression Blocking Agent, was fragmented (60C for 30 minutes) and hybridized to an Agilent Whole Human Genome, 4x44K (AMADID 014850) microarray using the Agilent Gene Expression Hybridization kit (Agilent Ref. 5190-0404). Hybridization was carried out in an Agilent SureHyb hybridization chamber in an Agilent Hybridization over at 65C and 10 rpm for 17 hours.

scan_protocol: The microarray slide was disassembled and washed using Agilent Gene Expression Wash Buffers (Agilent Ref. 5188-5327) and scanned using an Agilent B scanner with extended dynamic range (H: 100% PMT, L:  10% PMT).

data_processing: Data was extracted using Agilent Feature Extraction software (version 9.5.3.1).  Basic analysis was generated using Rosetta Luminator software.

source_name: melanoma cell line

label_protocol: Total RNA (500ng, 260/280 > 1.8, 260/230 > 2.0) was amplified using Agilent Low Input Linear Amplification Kit (discontinued; equivalent to Agilent Low-Input Quick Amp Labeling Kit, no dye; Agilent Ref. 5190-2308). aRNA was purified using Zymo Research RNA - IIc spin columns (discontinued; equivalent to Zymo RNA Clean and Concentrator Kit) and quantitated by Nanodrop. All processing steps from this point forward were carried out in an ozone regulated (< 5 ppb) environment to protect against ozone degradation of Cy5 relative to Cy3. Light exposure was minimized in order to avoid photo bleaching of cyanine dyes. aRNA was labeled using Perkin Elmer Micromax Direct Labeling Kit (discontinued; equivalent to Kreatech ULS aRNA Labeling Kit - with Cy3 and Cy5; Kreatech Ref. EA-006).  Labeled aRNA was purified using Zymo RNA - Ic spin columns (discontinued; equivalent to Zymo RNA Clean and Concentrator Kit) and quantitated by Nanodrop (Microarray protocol).

growth_protocol: A375TR cells expressing doxycycline-inducible FOXD3 were cultured in DMEM with 10% FBS and non-essential amino acids.  WM793TR and WM115TR cells expressing doxycycline-inducible FOXD3 were cultured in MCDB 153 medium containing 20% Leibovitz L-15 medium, 2% fetal bovine serum, 0.2% sodium bicarbonate, and 5μg/ml insulin.

extract_protocol: Total cellular RNA was extracted using the PerfectPure RNA Cultured Cell Kit (5 Prime, Gaithersburg, MD).  Total RNA was quantitated using a Nanodrop ND-1000 spectrophotometer (Nucleic Acid protocol).  RNA integrity (RIN: 9.9-10) was determined by Bioanalyzer 2100 using an RNA6000 Nano chip kit (Eukaryotic total RNA protocol).

treatment_protocol: Cells were treated for 5 days with 100ng/ml doxycycline.

tag: cell line

tag: transgene

value: LacZ


title: aedes mock D7 rep2

value: Rockefeller


title: YFV day 7 rep2

value: yellow fever wildtype Asibi


title: aedes mock D7 rep1


title: A375-FOXD3


title: aedes mock D2 rep2


title: aedes mock D2 rep1


title: 02_BOB-G(+)A(-)_No_1218_(Mouse430_2)

description: Gene expression data from kidney.


title: 506A_KO_FA

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

description: uterus at E3.5, KO, folinic acid, biological rep3

hyb_protocol: GeneChip arrays were hybridized overnight in the Affymetrix hybridization oven at 42oC. Washing and scanning was performed using the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: uterus, KO, folinic acid injection

label_protocol: Biotin-labeled samples were generated using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay.

growth_protocol: Animals were housed in a 12 h dark/light cycle and fed a Chow diet (LabDiet 5001). WT and Folr4-/- females received two intraperitoneal injections of 12.5mg/kg Folinic acid, one at 10 days and one at 3 days before mating. The morning with presence of a vaginal plug being counted as 0.5 days.

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

treatment_protocol: Uterus tissue was dissected at 3.5 days of gestation and stored in Trizol at minus 80 deg Celsius.

tag: background strain

value: uterus


title: aedes mock D2 rep3


title: 01_AL-G(-)A(-)_No_1218_(Mouse430_2)

description: Gene expression data from kidney.

value: glyoxylate(-) and adiponectin(-)


title: WM793-FOXD3


title: 03_COB-G(-)A(-)_No_1218_(Mouse430_2)

description: Gene expression data from kidney.


title: 548B_KO_FA

description: uterus at E3.5, KO, folinic acid, biological rep4


title: aedes mock D1 rep1


title: aedes mock D1 rep3


title: 437A_KO_FA

description: uterus at E3.5, KO, folinic acid, biological rep2


title: mutant_ANT_PDE_A4

value: Raldh2 null mutant; Raldh2 -/-

value: embryonic brain

value: Rostral/Anterior

value: 14 somite stage


title: aedes mock D1 rep2


title: 415B_KO_FA

description: uterus at E3.5, KO, folinic acid, biological rep1


title: 545A_KO

description: uterus at E3.5, KO, saline, biological rep3

source_name: uterus, KO, saline injection


title: Mouse lower incisor 4

source_name: Mouse lower Incisor

value: lower incisor


title: 490A_KO

description: uterus at E3.5, KO, saline, biological rep2


title: tga1_tga4_root_2h_KNO3_rep3

city: Santiago

first: Jose

middle: Miguel

last: Alvarez

state: Santiago

address: Alameda 340

department: Genética Molecular y Microbiología

country: Chile

institute: Pontificia Universidad Católica

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KNO3 2H R3

hyb_protocol: ATH1 chips were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G and the Affymetrix GeneChip Command Console Scan Control 1.1.0.845 software

data_processing: The summarized probe set data was generated using R/bioconductor (affy library). Normalization of the data was performed using rma. Normalized data was subjected to a two-way ANOVA analysis with a false discovery rate of 5 %.

organism: Arabidopsis thaliana

source_name: tga1_tga4 roots, treated with 5 mM KNO3 for 2 hours

label_protocol: Bioitinylated cRNA was prepared using the GeneChip 3'IVT kit from Affymetrix

growth_protocol: Arabidopsis seedlings of the Col 0 and tga1/tga4 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days.

extract_protocol: Total RNA was extracted using the TriZol reagent as indicated by the manufacturer.

treatment_protocol: Plants were treated at the onset of the light period on day 15 with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Roots were cut and frozen on liquid nitrogen.

value: TGA1 and TGA4 double mutant

value: root

value: 15 days old

value: seedling

value: 5 mM KNO3

tag: time

value: 2 hours


title: Mouse lower incisor 2


title: 462A_WT_FA

description: uterus at E3.5, control, folinic acid, biological rep3

source_name: uterus, WT, folinic acid injection

value: wild type


title: tak:anti-IgM6h-rep

city: Yokohama

first: Hisaaki

last: Shinohara

address: 1-7-22 Suehiro-cho

department: RCAI

institute: RIKEN

hyb_protocol: Affymetrix standard procedures

scan_protocol: GeneChip Scanner 3000

data_processing: CEL files were processed by RMA method to obtain normalized gene expression level (Affymetrix® Expression Console Software v.1.0).

source_name: tak_B cell_anti-IgM_6h

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

growth_protocol: Splenic B cells were purified by depleting CD43+ cells with magnetic beads using AutoMACS (Miltenyi Biotec).  Purified B Cells were cultured with RPMI containing 10% FBS

extract_protocol: TotalRNA was purified using the Qiagen RNeasy mini kit.

treatment_protocol: Purified B Cells were stimulated with 10 ug/ml of anti-IgM for 1, 3, 6, or 24hr.

value: TAK1-deleted; mb-1/TAK1f/f

tag: gender

value: mix

value: 8-12 weeks

tag: cell type

value: Splenic B cells

tag: stimulation

value: 10 µg/ml of anti-IgM for 6hr


title: Mouse lower incisor 3


title: tga1_tga4_root_2h_KCl_rep3

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KCl 2H R3

source_name: tga1_tga4 roots, treated with 5 mM KCl for 2 hours

tag: treatment

value: 5 mM KCl


title: 405B_WT_FA

description: uterus at E3.5, control, folinic acid, biological rep2

value: uterus


title: Mouse lower incisor 1


title: 485A_KO

description: uterus at E3.5, KO, saline, biological rep1


title: Col 0_root_2h_KNO3_rep3

description:
Col 0 wild-type seedlings, treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KNO3 2H R3

source_name: Col 0 roots, treated with 5 mM KNO3 for 2 hours

value: wild-type


title: tga1_tga4_root_2h_KNO3_rep1

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KNO3 2H R1


title: tak:anti-IgM24h-rep

source_name: tak_B cell_anti-IgM_24h

value: 10 µg/ml of anti-IgM for 24hr


title: tak:anti-IgM1h-rep

source_name: tak_B cell_anti-IgM_1h

value: 10 µg/ml of anti-IgM for 1hr


title: tak:anti-IgM0h-rep

source_name: tak_B cell_control

value: none (control)


title: wt:anti-IgM24h-rep

source_name: WT_B cell_anti-IgM_24h

value: wild type; mb-1/TAK1+/+


title: tak:anti-IgM3h-rep

source_name: tak_B cell_anti-IgM_3h

value: 10 µg/ml of anti-IgM for 3hr


title: Col 0_root_2h_KNO3_rep1

description:
Col 0 wild-type seedlings, treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KNO3 2H R1

value: root

value: 15 days old

value: seedling


title: tga1_tga4_root_2h_KCl_rep1

description:
TGA1 and TGA4 double mutant seedlings (tga1/tga4), treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
tga1_tga4 KCl 2H R1

value: TGA1 and TGA4 double mutant

value: 2 hours


title: 405A_WT_FA

description: uterus at E3.5, control, folinic acid, biological rep1

value: wild type


title: Col 0_root_2h_KCl_rep3

description:
Col 0 wild-type seedlings, treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KCl 2H R3

source_name: Col 0 roots, treated with 5 mM KCl for 2 hours


title: wt:anti-IgM6h-rep

source_name: WT_B cell_anti-IgM_6h

value: mix

value: 8-12 weeks


title: 514A_WT

description: uterus at E3.5, control, saline, biological rep4

source_name: uterus, WT, saline injection


title: 511B_WT

description: uterus at E3.5, control, saline, biological rep3


title: 511A_WT

description: uterus at E3.5, control, saline, biological rep2


title: Col 0_root_2h_KCl_rep2

description:
Col 0 wild-type seedlings, treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KCl 2H R2


title: wt:anti-IgM3h-rep

source_name: WT_B cell_anti-IgM_3h

value: Splenic B cells


title: Col 0_root_2h_KCl_rep1

description:
Col 0 wild-type seedlings, treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.
Col 0 KCl 2H R1

value: 5 mM KCl


title: 443A_WT

description: uterus at E3.5, control, saline, biological rep1

value: uterus


title: wt:anti-IgM1h-rep

source_name: WT_B cell_anti-IgM_1h


title: wt:anti-IgM0-rep

source_name: WT_B cell_control


title: tak:anti-IgM3h

value: TAK1-deleted; mb-1/TAK1f/f


title: GMP from Pbx1-Mutant Mouse #7, biological rep4

city: Rozzano

first: Francesca

last: Ficara

state: MI

address: via Manzoni 56

institute: CNR/Istituto Clinico Humanitas

description: Gene expression data Pbx1-null GMPs (GMP7)

hyb_protocol: Hybridization was performed in the Stanford PAN Facility using Affymetrix 430-2.0 arrays.

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.

data_processing: Microarray data were normalized with Expression Console software (Affymetrix), using RMA algorithms (no-log2, non-median-centered output) then further normalized with dCHip (Li and Wong 2001).  Low signals (below 60) were filtered out using the PreprocessDataset module in GenePattern (http://www.broad.mit.edu/cancer/software/genepattern/).

source_name: Mutant GMPs

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol

growth_protocol: Mice were maintained in the Stanford animal facility. To generate Pbx1-mutant and control mice, Pbx1 floxed/floxed mice were crossed with Tie2Cre+,Pbx1+/- mice.

extract_protocol: RNA was purified using Trizol followed by RNeasy MinElute Cleanup Kit (Qiagen), then subjected to amplification with the Affymetrix 3' IVT Express kit (Affymetrix, Santa Clara).

treatment_protocol: BM cells were obtained from multiple bones of individual mice, and maintained on ice when possible through all procedures. After immunomagnetic beads-mediated enrichment of cKit+ cells, CMPs and GMPs were sorted by flow cytometry into RNAlater (Ambion).

value: Bone Marrow

tag: genotype

value: 3 weeks old


title: tak:anti-IgM0h

tag: strain background

value: none (control)


title: GMP from Pbx1-Mutant Mouse #5, biological rep3

description: Gene expression data Pbx1-null GMPs (GMP5)


title: GMP from Pbx1-Mutant Mouse #2, biological rep2

description: Gene expression data Pbx1-null GMPs (GMP2)

value: 5 weeks old


title: tak:anti-IgM6h

value: 10 µg/ml of anti-IgM for 6hr


title: Human CSCs #6 Automatic, rep2

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description:
hRAS6A-A
Right auricle-derived cells.

hyb_protocol: Hybridization and washing steps were performed using the Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75th percentile (median).

source_name: Human CSCs #6, automatic culture

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Human CSCs were cultured in growth medium, DMEM/F12 supplemented with 10% FBS and 40 ng/ml basic FGF, in a humidified 37ºC incubator with 5% CO2.

extract_protocol: Total RNA samples were extracted from human CSCs with the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: For manual culture for cell expansion, the CSCs were seeded at 1 x 10^5 cells per 100 mm of culture dish (BD), and cultivated for 5-7 days. The cells were split at 1:10 ratio at the time of 80-90% confluent. The basic culture medium was replaced every 3 or 4 days. For automated culture, the first cell-seeding into a culture dish was performed by manual handling. After seeding, culture dishes were reposed in AutoCulture, and transferred into a CO2 incubator by AutoCulture. The CSCs were sub-cultured at about 1:10 split ratio onto a new culture dish, and returned the culture dish to a CO2 incubator.

value: cardiac stem cells (CSCs)

tag: culture type

value: automated


title: tak:anti-IgM1h

value: 10 µg/ml of anti-IgM for 1hr


title: tak:anti-IgM24h

value: 10 µg/ml of anti-IgM for 24hr


title: wt:anti-IgM24h

value: wild type; mb-1/TAK1+/+


title: GMP from Pbx1-Mutant Mouse #9, biological rep5

description: Gene expression data Pbx1-null GMPs (GMP9)


title: Human CSCs #6 Manual, rep2

description:
hRAS6A-H
Right auricle-derived cells.

source_name: Human CSCs #6, manual culture

value: manual


title: Human CSCs #6 Manual, rep1

description:
hRAS6P4
Right auricle-derived cells.


title: GMP from Pbx1-Mutant Mouse #1, biological rep1

description: Gene expression data Pbx1-null GMPs (GMP1)


title: CMP from Pbx1-Mutant Mouse #7, biological rep4

description: Gene expression data Pbx1-null CMPs (CMP7)

source_name: Mutant CMPs


title: GMP from Control Mouse #10, biological rep5

description: Gene expression data from normal GMPs (GMP10)

source_name: Control GMPs


title: CMP from Pbx1-Mutant Mouse #5, biological rep3

description: Gene expression data Pbx1-null CMPs (CMP5)


title: CMP from Pbx1-Mutant Mouse #1, biological rep1

description: Gene expression data Pbx1-null CMPs (CMP1)


title: wt:anti-IgM1h

value: mix


title: Human CSCs #6 Automatic, rep1

description:
hRAS6A
Right auricle-derived cells.


title: wt:anti-IgM3h

value: 8-12 weeks

value: 10 µg/ml of anti-IgM for 3hr


title: wt:anti-IgM6h

value: Splenic B cells


title: wt:anti-IgM0


title: CSP1 immonoprecipitated RNA from 35S:AtCSP1-FH#11, non-stress rep 2

city: Riverside

first: Piyada

last: Juntawong

state: CA

address: 900 University ave

department: Botany and Plant Sciences

institute: University of California Riverside

description: SAMPLE 29

hyb_protocol: Hybridizations were performed at 45 °C for 16 h, in a rotating platform with 10 µg of biotin-labeled aRNA for total and polysome RNAs and 7-10 µg of biotin-labeled aRNA for IP RNA.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: R/Bioconductor (v. 2.12.0), RMA normalization

label_protocol: Amplified RNA (aRNA) synthesis and biotin-labeling was conducted with 150 total or polysomal RNA, or 3-6 ng immunoprecipitated (IP) RNA using GeneChip® 3’ IVT expression  (Affymetrix)

growth_protocol: Plants were grown in soil (Sunshine Mix LC1, JM McConkey, Sumner, WA) containing 150 g Osmocote 14-14-14 fertilizer (Scotts catalog #90036) and 75 g Marathon pesticide (Crop production services, Riverside, CA) per 3.8 ft3 of soil in a controlled environmental growth room (16 h at ~100 uE sec-1m-2 light: 8 h dark at 23C).

extract_protocol:
Extraction of polysome by differential centrifugation through sucrose gradients was based on the procedures of Zanetti et al. (2005) and Mustroph et al. (2009); Total RNA and polysomal RNA (≥ 2 ribosomes per mRNA; typically gradient fractions 7 to 13) were extracted by use of TRIzol solution (Invitrogen) according to the manufacturer’s protocol. Total RNAs were subjected to DNAse treatment by use of RNase-Free DNAse Set (Qiagen, Chatsworth, CA) according to the manufacturer’s protocol. Total and polysomal RNA were cleaned by use of the RNAeasy Plant mini kit (Qiagen).

For CSP immunopurification for RNA analyses, rosette leaves of 25-d-old plants were collected and cross-linked with formaldehyde solution (Niranjanakumari et al., 2002). Briefly, leaves were washed with ice-cold ddH2O and cross-linked by bathing in 1% (v/v) formaldehyde (Molecular biology grade, Fisher, Fremont, CA) for 15 min by vacuum infiltration. Cross-linking was stopped by addition of 2 M glycine [pH 7.0] to a final concentration of 125 mM and vacuum-infiltrated for 5 min. Leaves were washed twice with ice-cold ddH2O, ground in liquid nitrogen and stored at -80 °C. One mL pulverized frozen plant tissue was thawed in 2 mL extraction buffer, mixed and centrifuged at 16,000 g at 4°C for 15 min to obtain a supernatant and passed through Miracloth. The clarified extracts were added to the antibody-coated Protein A beads (described above) and incubated at 4°C for 2 h with gentle shaking. The supernatant (Unbound fraction) was removed and the beads were washed 4 times by resuspension in 6 mL wash buffer (200 mM Tris-HCl [pH 9.0], 200 mM KCl, 36 mM MgCl2, 25 mM EGTA, 5 mM DTT, 1 mM PMSF, 50 μg/mL cycloheximide, 50 μg/mL chloramphenicol, 1.125 % (v/v) Triton X-100, 0.125 % (v/v) Brij-35, 0.125 % (v/v) Tween-40, 0.125 % (v/v) NP-40) and centrifuged to discard the wash solution. To elute the bound CSP1 and any associated molecules, 150 μL elution buffer (100 mM Tris-HCL [pH 8.0], 25 mM EDTA, 1 % (w/v) SDS) was added to the beads, which were incubated 10 min at room temperature with shaking, and centrifuged to obtain the eluate fraction. Elution were repeated by addition of 150 μL elution buffer following by incubation at 65°C for 10 min. The eluate was combined and 2 μL proteinase K (20 μg/mL) was added, and incubated at 65°C for 1 h to reverse the cross-linking. Immunopurified RNAs were extracted with TRIzol (Invitrogen) according to the manufacturer’s protocol and further purified by use of the RNAeasy plant mini kit column (Qiagen).

anti-CSP1 antibody: the rabbit polyclonal antiserum was generated against  a peptide (C15 AGNGDQRGATKGGN163) specific to *Arabidopsis thaliana *CSP1(At4g36020). The antiserum was subsequently affinity purified using the CSP1 peptide (anti-CSP1, Gencript, Piscataway, NJ)

treatment_protocol: 25-d-old plants grown in 5.08cm square pots were placed in a 4C chamber (16 h, ~ 50 uE sec-1 m-2 light: 8 h dark) for 12 h or in a 23C growth chamber (16 h, ~ 100 uE sec-1 m-2 light: 8 h dark). Cold treatment began 2 h following the initiation of light period (ZT2). Cold-treated or control rosette leaves were collected at specific time points, flash frozen in liquid nitrogen unless otherwise indicated and stored at -80C.

tag: ecotype

value: 25 days

value: 12h non-stress

value: rosettes

tag: ip antibody

tag: ip antibody vendor

value: Gencript

tag: molecule subtype

value: CSP1 immonoprecipitated RNA


title: CSP1 immonoprecipitated RNA from 35S:AtCSP1-FH#11, cold rep 2

description: SAMPLE 30

tag: genotype/variation

tag: age

value: 12h cold (4C)


title: GMP from Control Mouse #8, biological rep4

description: Gene expression data from normal GMPs (GMP8)

tag: tissue

value: Bone Marrow

value: 3 weeks old


title: CMP from Pbx1-Mutant Mouse #2, biological rep2

description: Gene expression data Pbx1-null CMPs (CMP2)

value: 5 weeks old


title: GMP from Control Mouse #3, biological rep1

description: Gene expression data from normal GMPs (GMP3)


title: GMP from Control Mouse #6, biological rep3

description: Gene expression data from normal GMPs (GMP6)


title: Ler- vs wt at Early Stationary Replicate 3

city: Birmingham

first: Chrystala

last: Constantinidou

department: School of Biosciences

institute: University of Birmingham

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: Equal quantities (300ng) of Cy5- and Cy3-labeled aRNA were added to hybridization solution, and hybridization was performed using the Gene Expression hybridization kit (Agilent Technologies).

scan_protocol: Slides were analysed using an Axon Genepix 4000B microarray scanner, and Genepix 6 software (Axon Scientific).

data_processing: Data was analysed using GeneSpring, version 7 (Agilent). A Lowess curve (locally weighted linear regression curve) was fitted to the plot of log intensity versus log ratio, and 40% of the data were used to calculate the Lowess fit at each point.

organism: Escherichia coli O157:H7 str. EDL933

source_name: Escherichia coli O157:H7 str. EDL933 ler- OD 0.9

label_protocol: Five hundred nanograms of total RNA was used for labeling, and aRNA was synthesized with the Ambion MessageAmp™ II-Bacteria RNA Amplification Kit according to the recommendations of the manufacturer and labeled with the Cy3 or Cy5 monoreactive dye pack (GE Healthcare). Labeled aRNA was purified with Qiagen RNeasy MinElute clean up kit according to the manufacturer's instructions and quantified using a spectrophotometer (ND-1000; NanoDrop).

growth_protocol: DMEM buffered with 25 mM HEPES ; OD 0.9

extract_protocol: Qiagen RNeasy midi kit as per manufacturer's instructions

tag: strain

value: ler-

source_name: Escherichia coli O157:H7 str. EDL933 wt OD 0.9

value: ler+/wt


title: Ler- vs wt at Early Stationary Replicate 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: NG3597_4-1_HF

type: genomic

city: Kyoto

first: Hideaki

last: Abe

state: Kyoto

address: 2-24 Tanaka-Sekiden-cho, Sakyo

department: Wildlife Research Center

institute: Kyoto University

hyb_protocol: The corresponding Cy3- and Cy5-labeled DNA were combined and hybridized at 65 C for 24 hours to Agilent customized Chicken CGH Microarray 4x180K, using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent customized Chicken CGH Microarrays were  detected using Agilent's DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image files. The weighted average of the log ratio values for the replicated probes was  given by the Agilent Feature Extraction program. Agilent Genomic Workbench uses an error model that is based on the log ratio error values in the FE files. Aberrant points were identified with log2 ratios > +0.5 (duplication) and with log2 ratios < -0.5 (deletion).

molecule: genomic DNA

organism: Gallus gallus

source_name: high fear

label_protocol: The digested DNA was used as template for a genomic DNA labeling reaction using the Genomic Enzymatic DNA Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Genomic DNA was isolated by PUREGENE DNA Purification Kit (Gentra Systems, Minneapolis, USA)

tag: breed

value: Nagoya

source_name: Low fear


title: Ler- vs wt at Early Stationary Replicate 4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: NG4692_2-1_HF


title: NG3557_3-1_HF


title: GMP from Control Mouse #4, biological rep2

description: Gene expression data from normal GMPs (GMP4)


title: Ler- vs wt at Early Stationary Replicate 1

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: Sorghum propinquum-young leaf, biological rep1

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

country: China

institute: Chinese Acadamy of agricultural science

description:
5-YL1
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 1 of 3. Young leaf.

hyb_protocol: Labeled test and control samples labeled with Cy5-dCTP and Cy3-dCTP, respectively, were dissolved in 80 uL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt's solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Array hybridization was performed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃, and arrays were washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (both from CapitalBio). For individual channel data extraction, faint spots were removed for which intensities were below 400 units after background was subtracted in both channels (Cy3 and Cy5).

data_processing: A space- and intensity-dependent normalization based on a LOWESS program was employed. To determine the significant differentially expressed genes, Significance Analysis of Microarrays (SAM, version 3.02) was performed.

organism: Sorghum propinquum

source_name: Young leaf, active tillering stage

label_protocol: The Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript Ⅱ reverse transcriptase. Briefly, 2 ug amplified RNA was mixed with 4 ug random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 uL of 4×first-strand buffer, 2 uL of 0.1M DTT, and 1.5 uL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 uL. The cDNA was mixed with 4 ug random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 uL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 uM dATP, 240 uM dGTP, 240 uM dTTP, 120 uM dCTP, and 40 uM Cy-dCTP. 1.2 uL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

growth_protocol: Plants of an S. propinquum vegetative clone (unnamed accession) with vigorous rhizomes were cultured in the greenhouse.

extract_protocol: Total RNA were extracted using TRIzol reagent according to the instructions and then purified and concentrated using the RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: At the active tillering stage, five tissues from rhizome tip (RT, distal 1 cm of the young rhizome), rhizome internodes (RI), shoot tip (ST, distal 5 mm of the tiller after removing all leaves), shoot internodes (SI) and young leaf (YL) were collected for total RNA extraction. Three independent biological replicates for each sample from individual plants were sampled, and all collected samples were snap-frozen in liquid nitrogen and kept in a -70℃ freezer.

tag: developmental stage

value: active tillering stage

value: young leaf

source_name: Equivalent to a mix of shoot tip, rhizome tip, rhizome internodes, shoot internodes and young leaf, active tillering stage

tag: sample type

value: reference


title: Sorghum propinquum-young leaf, biological rep2

description:
5-YL2
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 2 of 3. Young leaf.

value: mix of shoot tip, rhizome tip, rhizome internodes, shoot internodes and young leaf


title: NG993_1-1_HF


title: CMP from Control Mouse #6, biological rep3

description: Gene expression data from normal CMPs (CMP6)

source_name: Control CMPs


title: CMP from Control Mouse #8, biological rep4

description: Gene expression data from normal CMPs (CMP8)


title: Ler- vs wt at Mid Log Replicate 3

source_name: Escherichia coli O157:H7 str. EDL933 ler- OD 0.3

growth_protocol: DMEM buffered with 25 mM HEPES ; OD 0.3

source_name: Escherichia coli O157:H7 str. EDL933 wt OD 0.3


title: CSP1 immonoprecipitated RNA from 35S:AtCSP1-FH#11, cold rep 1

description: SAMPLE 24


title: Ler- vs wt at Mid Log Replicate 2


title: Ler- vs wt at Mid Log Replicate 4


title: CMP from Control Mouse #10, biological rep5

description: Gene expression data from normal CMPs (CMP10)


title: CMP from Control Mouse #4, biological rep2

description: Gene expression data from normal CMPs (CMP4)


title: Ler- vs wt at Mid Log Replicate 1


title: CMP from Control Mouse #3, biological rep1

description: Gene expression data from normal CMPs (CMP3)


title: Sorghum propinquum-shoot internodes, biological rep2

description:
4-SI2
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 2 of 3. Shoot internodes.

source_name: Shoot internodes, active tillering stage

value: shoot internodes


title: Sorghum propinquum-young leaf, biological rep3

description:
5-YL3
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 3 of 3. Young leaf.


title: CSP1 immonoprecipitated RNA from 35S:AtCSP1-FH#11, non-stress rep 1

description: SAMPLE 23

value: 25 days


title: Sorghum propinquum-shoot internodes, biological rep1

description:
4-SI1
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 1 of 3. Shoot internodes.


title: Sorghum propinquum-shoot internodes, biological rep3

description:
4-SI3
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 3 of 3. Shoot internodes.


title: Sorghum propinquum-rhizome internodes, biological rep2

description:
3-RI2
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 2 of 3. Rhizome internodes.

source_name: Rhizome internodes, active tillering stage

value: rhizome internodes


title: Sorghum propinquum-rhizome internodes, biological rep3

description:
3-RI3
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 3 of 3. Rhizome internodes.


title: Sorghum propinquum-rhizome internodes, biological rep1

description:
3-RI1
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 1 of 3. Rhizome internodes.


title: Sorghum propinquum-rhizome tip, biological rep3

description:
2-RT3
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 3 of 3. Rhizome tip.

source_name: Rhizome tip, active tillering stage

value: rhizome tip


title: LNCaP-D1b-DHT-3

hyb_protocol: 20ug labeled extract was hybridized 16hrs at 45degrees while rotating in a Affymetrix GeneChip Hybridization Oven 640; washed with an Affymetrix Fluidics Station 450; stain: Molecular Probes R-Phycoerythrin Streptavidin, antibody: Vector Laboratories Anti-Streptavidin (goat) biotinylated.

scan_protocol: GeneChips were quantified with an Affymetrix Gene Array Scanner (software version 1.4, default settings), and then “CEL” files were generated using Affymetrix Microarray Suite 5.0.

data_processing: RMA summarization, PM BG correction, and quantile normalization were performed in RMAExpress 1.0

label_protocol: Total RNA samples (0.5 µg) for each treatment condition were labeled using the standard labeling protocol (small scale protocol version 2.0).

growth_protocol: Cells were cultured in 5 % charcoal dextran treated media for a total of 72 hours to minimize AR signaling

treatment_protocol: Cells were treated with equivalent titers of viral contructs for 24 hours, washed, and then stimulated with 1nM DHT or EtOH control for 16 hours.

tag: cell line

value: LNCaP

tag: cell type

value: androgen-sensitive human prostate adenocarcinoma cells

tag: transduced with

value: virus encoding Cyclin D1b for 24 hrs

tag: stimulated with

value: 1nM DHT for 16 hrs


title: LNCaP-D1b-DHT-2


title: Sorghum propinquum-rhizome tip, biological rep1

description:
2-RT1
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 1 of 3. Rhizome tip.


title: Sorghum propinquum-rhizome tip, biological rep2

description:
2-RT2
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 2 of 3. Rhizome tip.


title: Sorghum propinquum-shoot tip, biological rep1

description:
1-ST1
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 1 of 3. Shoot tip.

source_name: Shoot tip, active tillering stage

value: shoot tip


title: LNCaP-D1b-DHT-1


title: Heart_atorvastatin_rep3

city: Shimotsuke

first: Masafumi

last: Kumazaki

state: Tochigi

address: 3311-1 Yakushiji

department: Pharmacology

institute: Jichi Medical University

hyb_protocol: The fragmented and labeled amplified cDNA was hybridized to a GeneChip Mouse Genome 430 2.0 Array (Affymetrix) for 18 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with Workstation (Affymetrix).

data_processing: The CEL file data were analyzed with Microarray Suite version 5.0 (MAS 5.0) to generate CHP files (represented in Sample tables below). Subsequent data processing involved normalizing to the median expression value of all samples with GeneSpring GX version 11.0 software (Agilent Technologies).

source_name: Mouse heart treated with atorvastatin_3

label_protocol: Amplified cDNA was prepared from 100 ng of total RNA using an Ovation RNA Amplification System V2 Kit (NuGEN Technologies) and purified using a PCR purification kit (Qiagen). According to the manufacturer’s instructions, 3.75 µg of purified cDNA was fragmented and labeled using an FL-Ovation cDNA Biotin Module V2 Kit (NuGEN Technologies).

growth_protocol: Male C57BL/6J mice (n = 20) were obtained from Charles River Laboratories Japan (Yokohama, Japan) at six weeks of age and maintained under specific pathogen-free conditions with controlled temperature and humidity and a 12-h light/12-h dark cycle. They were given standard chow (CE-2; CLEA Japan, Tokyo, Japan) and water ad libitum.

extract_protocol: Total RNA was isolated from the left ventricle of each animal using an RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: After two weeks of acclimation, the mice were divided into the following five groups: (1) control, (2) 4.5 mg/kg/day pitavastatin calcium (Livalo tablet, Kowa, Nagoya, Japan), (3) 21.0 mg/kg/day pravastatin sodium (Mevalotin tablet, Daiichi-Sankyo, Tokyo, Japan), (4) 10.9 mg/kg/day rosuvastatin calcium (Crestor tablet, Shionogi, Osaka, Japan), and (5) 11.4 mg/kg/day atorvastatin calcium hydrate (Lipitor tablet, Astellas, Tokyo, Japan). Each statin tablet was powdered and given as a food admixture; the doses were calculated on the basis of daily food consumption (0.15 g/gBW). After four weeks, heart samples were obtained from each mouse under diethyl ether anesthesia.

tag: gender

value: male

value: left ventricle of heart

tag: agent

value: atorvastatin (Lipitor)


title: Heart_atorvastatin_rep4

source_name: Mouse heart treated with atorvastatin_4


title: Heart_atorvastatin_rep1

source_name: Mouse heart treated with atorvastatin_1


title: LNCaP-D1b-EtOH-1

value: 0.01% EtOH (vehicle control) for 16 hrs


title: Sorghum propinquum-shoot tip, biological rep3

description:
1-ST3
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 3 of 3. Shoot tip.

value: active tillering stage


title: Heart_atorvastatin_rep2

source_name: Mouse heart treated with atorvastatin_2


title: LNCaP-D1b-EtOH-3


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, cold rep 3

description: SAMPLE 18

tag: ecotype

tag: treatment

value: 12h cold (4C)

value: rosettes

value: Gencript

value: CSP1 immonoprecipitated RNA


title: Heart_rosuvastatin_rep2

source_name: Mouse heart treated with rosuvastatin_2

value: rosuvastatin (Crestor)


title: Heart_rosuvastatin_rep3

source_name: Mouse heart treated with rosuvastatin_3


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, non-stress rep 3

description: SAMPLE 17

value: 25 days

value: 12h non-stress

tag: ip antibody

tag: ip antibody vendor


title: Heart_rosuvastatin_rep4

source_name: Mouse heart treated with rosuvastatin_4


title: Sorghum propinquum-shoot tip, biological rep2

description:
1-ST2
Sorghum propinquum, wild sorghum with long and strong rhizomes.
Biological replicate 2 of 3. Shoot tip.

value: mix of shoot tip, rhizome tip, rhizome internodes, shoot internodes and young leaf

value: reference


title: LNCaP-D1a-DHT-2

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma cells

value: virus encoding Cyclin D1a for 24 hrs


title: LNCaP-D1b-EtOH-2

value: virus encoding Cyclin D1b for 24 hrs


title: LNCaP-D1a-DHT-3

value: 1nM DHT for 16 hrs


title: Heart_rosuvastatin_rep1

source_name: Mouse heart treated with rosuvastatin_1

value: male

value: left ventricle of heart


title: EMBLIN_D2_rep2

city: Bangalore

first: Tapas

last: Kundu

address: Jakkur P.O.

department: Molecular Biology & Genetics Unit

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

description: Gene expression after 48h 10uM embelin treatment in differentiation medium

hyb_protocol: RNA was fragmented by metallic cleavage using manufacturar's protocol. Array lanes were blocked using ssDNA and subsequently samples were hybridized at 65oC for 17h. Array was washed with wash buffer with and without DNA. Finally array was dried.

scan_protocol: Arrays were scanned on Illumina iScan system.

data_processing: Initial data was extracted by gene-expression module of GenomeStudio version 2010.2. Data was analyzed by Genespring GX12.0 software.

source_name: 48h embelin treated C2C12 cells in DM

label_protocol: The product cDNA is converted into cRNA by T7 polymerase and labelled with Cy3 (labelled on cytosine) using Agilent kit.

growth_protocol: C2C12 cells were cultured in growth medium (GM) containing Dulbecco’s modified Eagle’s medium (DMEM) with 20% fetal bovine serum (FBS), and differentiated in DMEM containing 2% horse serum (DM).

extract_protocol: Total RNA was extracted by Trizol method. RNA was cleaned up using RNeasy MinElute Cleanup Kit (Qiagen) and reverse transcribed.

treatment_protocol: C2C12 cells were treated with either DMSO or 10uM embelin in GM/DM for either 24 or 48h.


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, non-stress rep 2

description: SAMPLE 11

tag: genotype/variation

tag: molecule subtype


title: DMSO_D2_rep2

description: Gene expression after 48h DMSO treatment in differentiation medium

source_name: 48h DMSO treated C2C12 cells in DM


title: EMBLIN_D1_rep2

description: Gene expression after 24h 10uM embelin treatment in differentiation medium

source_name: 24h embelin treated C2C12 cells in DM


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, cold rep 2

description: SAMPLE 12

tag: age

tag: tissue


title: Heart_pravastatin_rep3

source_name: Mouse heart treated with pravastatin_3

tag: strain

value: pravastatin (Mevalotin)


title: Heart_pravastatin_rep2

source_name: Mouse heart treated with pravastatin_2


title: LNCaP-D1a-DHT-1


title: Heart_pravastatin_rep1

source_name: Mouse heart treated with pravastatin_1


title: LNCaP-D1a-EtOH-3

value: 0.01% EtOH (vehicle control) for 16 hrs


title: LNCaP-D1a-EtOH-2


title: DMSO_D1_rep2

description: Gene expression after 24h DMSO treatment in differentiation medium

source_name: 24h DMSO treated C2C12 cells in DM


title: Heart_pitavastatin_rep3

source_name: Mouse heart treated with pitavastatin_3

value: pitavastatin (Livalo)


title: EMBLIN_D1_rep1


title: LNCaP-GFP-DHT-3

source_name: LNCaP-GFP-DHT

value: virus encoding control GFP for 24 hrs


title: Heart_pitavastatin_rep2

source_name: Mouse heart treated with pitavastatin_2


title: EMBLIN_D2_rep1


title: Heart_control_rep4

source_name: Mouse heart treated with standard chow_4

value: control


title: DMSO_D0_rep2

description: Gene expression after 24h DMSO treatment in growth medium

source_name: 0h DMSO treated C2C12 cells in GM


title: LNCaP-GFP-DHT-1


title: LNCaP-D1a-EtOH-1


title: Heart_pitavastatin_rep4

source_name: Mouse heart treated with pitavastatin_4


title: EMBLIN_D0_rep2

description: Gene expression after 24h 10uM embelin treatment in growth medium

source_name: 0h embelin treated C2C12 cells in GM


title: LNCaP-GFP-EtOH-3

source_name: LNCaP-GFP-EtOH


title: LNCaP-GFP-DHT-2


title: DMSO_D1_rep1


title: Heart_pitavastatin_rep1

source_name: Mouse heart treated with pitavastatin_1


title: LNCaP-GFP-EtOH-1


title: LNCaP-GFP-EtOH-2


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, non-stress rep 1

description: SAMPLE 5

value: rosettes

value: Gencript

value: CSP1 immonoprecipitated RNA


title: EMBLIN_D0_rep1


title: DMSO_D2_rep1


title: Heart_control_rep3

source_name: Mouse heart treated with standard chow_3


title: Heart_control_rep2

source_name: Mouse heart treated with standard chow_2


title: Heart_control_rep1

source_name: Mouse heart treated with standard chow_1


title: DMSO_D0_rep1


title: CSP1 immonoprecipitated RNA from 35S:HF-RPL18, cold rep 1

description: SAMPLE 6

value: 25 days

value: 12h cold (4C)


title: EBE-XVE-line 14 seedlings treated with estradiol, biol. rep 3

status: Public on Mar 30 2013

city: Potsdam

first: Mohammad

last: Mehrnia

state: Brandenburg

address: Am Muhlenberg 1

department: Stitt

country: Germany

institute: Max-Planck-Institut für Molekulare Pflanzenphysiologie

description: Gene expression data from EBE-XVE-line 14, 45 min after estradiol treatment

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

source_name: Arabidopsis EBE-XVE-line 14 Seedlings treated with Est

growth_protocol: EBE-XVE and wild-type (control) seeds were cultured on MS agar plates at 22˚C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime.

treatment_protocol: After three weeks, seedlings were transferred to MS liquid medium while shaking. Sixteen hours later, β-estradiol (Sigma-Aldrich) was added to the medium to a final concentration of 2 μM. Subsequently, shoots were harvested at 45 min after estradiol addition.

value: shoot

tag: genotype

value: EBE-XVE (col-0)

value: 3-week-old seedling


title: EBE-XVE-line 14 seedlings treated with estradiol, biol. rep 2

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: WT-Col-0 seedlings treated with estradiol, biol. rep 2

description: Gene expression data from WT-Col-0, 45 min after estradiol treatment

source_name: Arabidopsis WT-Col-0 Seedlings treated with Est

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

tag: cultivar

value: WT


title: WT-Col-0 seedlings treated with estradiol, biol. rep 1


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC42

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 21
Sentrix_ID 4
Sentrix_Position K
BS conversion C1 Grn 876
BS conversion C2 Grn 651
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: BeadStudio software v3.2

source_name: genomic DNA from cervical smear cells LBC42

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: DNA was extracted from liquid based cytology samples of women using the Qiagen DNeasy Blood and Tissue kit (Qiagen Ltd, UK)

tag: sample type

tag: cytology

value: HPV+ve/Cyto+ve


title: Sham-GA-7Days-3

city: Bronx

first: christopher

middle: p

last: cardozo

state: NY

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

description: Sample name: 1454

hyb_protocol: according the the manufacturers recommended procedures

data_processing: Preprocessing was performed using the RMA function of the Oligo package for Bioconductor.

organism: Rattus norvegicus

source_name: soleus

extract_protocol: Pieces of muscle weighing approximately 20 g were homogenized in Trizol reagent.  Total RNA was then extracted following the manufacturers recommended procedures and further purified on RNAeasy columns (Qiagen) then quantified by absorbance at 260 nm.  RNA integrity numbers were greater than 8.0 for all samples.

value: Wistar

value: Female

tag: spine surgery

tag: electrical stimulation (es)

value: No

tag: gastrocnemius ablation (ga)

value: Sham

tag: time after es/ga (days)

value: soleus


title: HPV+ve/Cyto-ve Liquid Based Cytology Cervical Smear Sample LBC06

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto-ve
Age 55
Sentrix_ID 4
Sentrix_Position H
BS conversion C1 Grn 980
BS conversion C2 Grn 1039
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC06

value: HPV+ve/Cyto-ve


title: Sham-GA-1Day-1

description: Sample name: 1460

scan_protocol: according the the manufacturers recommended procedures

tag: gender


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC31

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 33
Sentrix_ID 4
Sentrix_Position G
BS conversion C1 Grn 1077
BS conversion C2 Grn 754
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC31


title: Sham-GA-7Days-2

description: Sample name: 1453

label_protocol: according the the manufacturers recommended procedures


title: Sham-GA-1Day-3

description: Sample name: 1464


title: EBE-XVE-line 14 seedlings treated with estradiol, biol. rep 1


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC33

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 42
Sentrix_ID 4
Sentrix_Position I
BS conversion C1 Grn 613
BS conversion C2 Grn 598
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC33


title: GA-7Days-2

description: Sample name: 1448

value: Yes


title: GA-7Days-3

description: Sample name: 1451


title: HPV+ve/Cyto+ve Liquid Based Cytology Cervical Smear Sample LBC44

description:
CIN2+(=Cyto+ve)/Normal(=Cyto-ve) HPV+ve/Cyto+ve
Age 20
Sentrix_ID 4
Sentrix_Position F
BS conversion C1 Grn 792
BS conversion C2 Grn 856
Liquid Based Cytology samples from the uterine cervix were collected from 48 women who all tested positive for HPV. Of the 48 samples, 24 were of normal cytology, while the rest exhibited morphological transformation (cervical intraepithelial neoplasia of grade 2 or higher - CIN2+)

source_name: genomic DNA from cervical smear cells LBC44


title: WT-Col-0 seedlings treated with estradiol, biol. rep 3