title: ESC UNDIFF LINE WA07 PASSAGE 43

description: ESC UNDIFF LINE WA07 PASSAGE 43

source_name: ESC UNDIFF LINE WA07 PASSAGE 43


title: ESC UNDIFF LINE UC06 PASSAGE 114

status: Public on Oct 31 2012

type: RNA

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

description: ESC UNDIFF LINE UC06 PASSAGE 114

hyb_protocol: The entire purified labeled miRNA sample was dried using a speed-vac on medium setting and resuspended in 18ul of DNase/RNase-free water. To each sample, 4.5ul of 10x GE Blocking Agent and 22.5ul of 2x Hybridization Buffer (Agilent) were added. Samples were gently vortexed, incubated at 100oC for 5 minutes and chilled in an ice water bath for 5 minutes. The entire volume of each sample was hybridized to Agilent Human miRNA microarray kit (G4470A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 5uM scanning mode ‘Single Pass’, eXtended Dynamic range selected, Dye channel set to Green and Green PMT set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 016436_D_20070426) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: ESC UNDIFF LINE UC06 PASSAGE 114

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.1 ug RNA using the miRNA Labeling Reagent and Hybridization kit (Agilent) according to the manufacturer's instructions, followed by purification using Micro Bio-spin 6 columns (Bio-Rad).

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: Total RNA was extracted using the mirVana RNA Isolation kit (Ambion) as recommended by the vendor for array-based assays. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: ESC

tag: condition

value: UNDIFF

tag: line

tag: passage

tag: gender

value: FEMALE

tag: processing control


title: ESC UNDIFF LINE WA01 PASSAGE 56

description: ESC UNDIFF LINE WA01 PASSAGE 56

source_name: ESC UNDIFF LINE WA01 PASSAGE 56

value: MALE


title: ESC UNDIFF LINE WA01 PASSAGE 52

description: ESC UNDIFF LINE WA01 PASSAGE 52

source_name: ESC UNDIFF LINE WA01 PASSAGE 52


title: ESC UNDIFF LINE WA09 PASSAGE 45

description: ESC UNDIFF LINE WA09 PASSAGE 45

source_name: ESC UNDIFF LINE WA09 PASSAGE 45


title: Somatic Tissue Ovary

description: Somatic Tissue Ovary

source_name: Somatic Tissue Ovary

value: Somatic Tissue


title: ESC UNDIFF LINE ES02 PASSAGE 45

type: genomic

description: ESC UNDIFF LINE ES02 PASSAGE 45

hyb_protocol: see Agilent CGH 244k standard protocols.

data_processing: Agilent Feature Extraction ver9.5.1.1, protocol name: CGH-v4_95_Feb07.

molecule: genomic DNA

source_name: ESC UNDIFF LINE ES02 PASSAGE 45

label_protocol: Cy5 and Cy3 (see Agilent CGH 244k standard protocols).

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human pluripotent stem cells were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. Pluripotent stem cells were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer’s instructions. Control male and female genomic DNA was purchased from Promega.

tag: cell type

value: embryonic stem cells

value: undifferentiated

tag: cell line

source_name: Promega Human Female

tag: catalog number

tag: lot number


title: ESC UNDIFF LINE UC06 PASSAGE 110

description: ESC UNDIFF LINE UC06 PASSAGE 110

source_name: ESC UNDIFF LINE UC06 PASSAGE 110


title: ESC UNDIFF LINE UC01 PASSAGE 56

description: ESC UNDIFF LINE UC01 PASSAGE 56

source_name: ESC UNDIFF LINE UC01 PASSAGE 56


title: ESC UNDIFF LINE TE06 PASSAGE 64

description: ESC UNDIFF LINE TE06 PASSAGE 64

source_name: ESC UNDIFF LINE TE06 PASSAGE 64


title: ESC UNDIFF LINE SA01 PASSAGE 32

description: ESC UNDIFF LINE SA01 PASSAGE 32

source_name: ESC UNDIFF LINE SA01 PASSAGE 32


title: ESC UNDIFF LINE TE06 PASSAGE 60

description: ESC UNDIFF LINE TE06 PASSAGE 60

source_name: ESC UNDIFF LINE TE06 PASSAGE 60


title: ESC UNDIFF LINE SA02 PASSAGE 35

description: ESC UNDIFF LINE SA02 PASSAGE 35

source_name: ESC UNDIFF LINE SA02 PASSAGE 35


title: ESC UNDIFF LINE SA01 PASSAGE 28

description: ESC UNDIFF LINE SA01 PASSAGE 28

source_name: ESC UNDIFF LINE SA01 PASSAGE 28


title: ESC UNDIFF LINE UC01 PASSAGE 60

description: ESC UNDIFF LINE UC01 PASSAGE 60

source_name: ESC UNDIFF LINE UC01 PASSAGE 60


title: ESC UNDIFF LINE TE03 PASSAGE 66

description: ESC UNDIFF LINE TE03 PASSAGE 66

source_name: ESC UNDIFF LINE TE03 PASSAGE 66


title: ESC UNDIFF LINE ES06 PASSAGE 62

description: ESC UNDIFF LINE ES06 PASSAGE 62

source_name: ESC UNDIFF LINE ES06 PASSAGE 62


title: ESC UNDIFF LINE TE03 PASSAGE 70

description: ESC UNDIFF LINE TE03 PASSAGE 70

source_name: ESC UNDIFF LINE TE03 PASSAGE 70


title: ESC UNDIFF LINE ES04 PASSAGE 76

description: ESC UNDIFF LINE ES04 PASSAGE 76

source_name: ESC UNDIFF LINE ES04 PASSAGE 76


title: ESC UNDIFF LINE ES05 PASSAGE 59

description: ESC UNDIFF LINE ES05 PASSAGE 59

source_name: ESC UNDIFF LINE ES05 PASSAGE 59


title: ESC UNDIFF LINE ES06 PASSAGE 58

description: ESC UNDIFF LINE ES06 PASSAGE 58

source_name: ESC UNDIFF LINE ES06 PASSAGE 58


title: ESC UNDIFF LINE ES05 PASSAGE 55

description: ESC UNDIFF LINE ES05 PASSAGE 55

source_name: ESC UNDIFF LINE ES05 PASSAGE 55


title: ESC UNDIFF LINE ES04 PASSAGE 72

description: ESC UNDIFF LINE ES04 PASSAGE 72

source_name: ESC UNDIFF LINE ES04 PASSAGE 72


title: ESC UNDIFF LINE ES03 PASSAGE 84

description: ESC UNDIFF LINE ES03 PASSAGE 84

source_name: ESC UNDIFF LINE ES03 PASSAGE 84


title: ESC UNDIFF LINE ES03 PASSAGE 88

description: ESC UNDIFF LINE ES03 PASSAGE 88

source_name: ESC UNDIFF LINE ES03 PASSAGE 88


title: ESC UNDIFF LINE ES02 PASSAGE 49

description: ESC UNDIFF LINE ES02 PASSAGE 49

source_name: ESC UNDIFF LINE ES02 PASSAGE 49


title: ESC UNDIFF LINE ES02 PASSAGE 45

description: ESC UNDIFF LINE ES02 PASSAGE 45

source_name: ESC UNDIFF LINE ES02 PASSAGE 45


title: ESC UNDIFF LINE SA02 PASSAGE 39

description: ESC UNDIFF LINE SA02 PASSAGE 39

source_name: ESC UNDIFF LINE SA02 PASSAGE 39


title: ESC UNDIFF LINE BG03 PASSAGE 54

description: ESC UNDIFF LINE BG03 PASSAGE 54

source_name: ESC UNDIFF LINE BG03 PASSAGE 54


title: ESC UNDIFF LINE ES01 PASSAGE 67

description: ESC UNDIFF LINE ES01 PASSAGE 67

source_name: ESC UNDIFF LINE ES01 PASSAGE 67


title: ESC UNDIFF LINE ES01 PASSAGE 71

description: ESC UNDIFF LINE ES01 PASSAGE 71

source_name: ESC UNDIFF LINE ES01 PASSAGE 71


title: ESC UNDIFF LINE TE06 PASSAGE 60

description: ESC UNDIFF LINE TE06 PASSAGE 60

scan_protocol: see Agilent CGH 244k standard protocols.

source_name: ESC UNDIFF LINE TE06 PASSAGE 60

source_name: Promega Human Male


title: ESC UNDIFF LINE BG03 PASSAGE 50

description: ESC UNDIFF LINE BG03 PASSAGE 50

source_name: ESC UNDIFF LINE BG03 PASSAGE 50


title: ESC UNDIFF LINE BG02 PASSAGE 50

description: ESC UNDIFF LINE BG02 PASSAGE 50

source_name: ESC UNDIFF LINE BG02 PASSAGE 50


title: ESC UNDIFF LINE BG02 PASSAGE 54

description: ESC UNDIFF LINE BG02 PASSAGE 54

source_name: ESC UNDIFF LINE BG02 PASSAGE 54


title: ESC UNDIFF LINE BG01 PASSAGE 63

description: ESC UNDIFF LINE BG01 PASSAGE 63

source_name: ESC UNDIFF LINE BG01 PASSAGE 63


title: ESC UNDIFF LINE BG01 PASSAGE 67

description: ESC UNDIFF LINE BG01 PASSAGE 67

source_name: ESC UNDIFF LINE BG01 PASSAGE 67


title: MG1655 H-NS 1

status: Public on Nov 01 2012

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

department: Biochemistry

institute: UW-Madison

description: ChIP-chip MG1655 cells H-NS

hyb_protocol: Samples were hybridized to arrays by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

scan_protocol: Arrays were scanned by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

data_processing: Datasets were normalized using locally weighted linear regression (LOWESS) normalization on raw Cy3 and Cy5 signals to correct for intensity-dependent dye effects within each array using the “normalizeWithinArrays” function in the limma package for the statistical program R (v.2.14.2).

organism: Escherichia coli K-12

source_name: H-NS ChIP DNA from MG1655 cells

label_protocol: Samples were labeled by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

growth_protocol: Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4).

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 µM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 µM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 µl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

treatment_protocol: Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final).

tag: strain

tag: genotype/variation

value: wild-type

value: bacterial cells

tag: chip antibody

value: anti-H-NS

source_name: Input DNA from MG1655 cells

tag: sample type

value: input DNA


title: 24 Hour vehicle treated_6116750018_I

status: Public on Oct 29 2012

city: Los Angeles

first: sanjeev

middle: k

last: baniwal

address: 2220 Alcazar street

department: Orthopaedics

institute: University of Southern California

description: control sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw signal intensities were imported and analyzed using the GenomeStudio® data software.  After background subtraction and quantile normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.

label: biotin

source_name: T47D breast cancer cells

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

growth_protocol: T47D cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum from Clontech, CA.

extract_protocol: RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations.

treatment_protocol: Doxycycline was added to the culture mdium for either for 24 or 48 hours to induce the knockdown of PIP mRNA. Control samples were prepared by treating the cells with equal volume of water (usually 2.5 uL per mL).

tag: agent

value: vehicle

tag: time point

value: 24 Hour

tag: shRNA

value: Dox-inducible shRNA for PIP


title: 48 Hour Doxycycline treated_6116750017_K

description: Dox treatment knocksdown PIP mRNA levels

value: Doxycycline

value: 48 Hour


title: 24 Hour Doxycycline treated_6116750017_I


title: 24 Hour Doxycycline treated_6116750017_J


title: Patient 363, female, large

status: Public on Oct 12 2012

city: Uppsala

first: Patrick

last: Micke

address: Rudbeck laboratory

country: Sweden

institute: Uppsala University

description: gene expression data from non small lung cancer frozen sample of patient 363

hyb_protocol: For each sample, 2µg of total RNA from each sample was used to prepare biotinylated fragmented cRNA for analysis on Affymetrix Human Genome U133 plus 2 arrays (54675 probe sets, Affymetrix Inc., Santa Clara, U.S.A.). Sample preparation, processing and hybridization were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 5).

scan_protocol: The arrays were washed and stained using a Fluidics Station 450 and finally scanned using a GeneChip® Scanner 3000 7G.

data_processing: Biocondoctor affy package standard RMA preprocessing in Matrix Template

source_name: cancer cells from patient 363

growth_protocol: no in vitro data

extract_protocol: Five to ten sections (10µm) were cut from each frozen tissue block and collected into a tube with Buffer RLT (Qiagen, Hilden, Germany). Total RNA was extracted using the RNeasy Mini Kit following instructions from the manufacturer (Qiagen). RNA concentrations were measured with a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, U.S.A.), and the quality (RNA Integrity Number, RIN) was assessed using the Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, U.S.A.).

treatment_protocol: no treatment

tag: dead

value: yes

tag: days to determined death status

tag: histology

value: large

tag: tumor stage

tag: performance status corresponding to who criteria

tag: age

value: female

tag: adjuvant treatment

value: not known

tag: recurrence

tag: days to recurrence / to last visit


title: 24 Hour Doxycycline treated_6116750018_L


title: Patient 354, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 354

source_name: cancer cells from patient 354

label_protocol: For each sample, 2µg of total RNA from each sample was used to prepare biotinylated fragmented cRNA for analysis on Affymetrix Human Genome U133 plus 2 arrays (54675 probe sets, Affymetrix Inc., Santa Clara, U.S.A.). Sample preparation, processing and hybridization were performed according to the GeneChip® Expression Analysis Technical Manual (Affymetrix Inc., Rev. 5).

value: squamous

tag: gender

value: male

value: no


title: 48 Hour vehicle treated_6116750018_B

description: control sample


title: Patient 353, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 353

source_name: cancer cells from patient 353

value: adeno


title: Patient 327, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 327

source_name: cancer cells from patient 327


title: Patient 334, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 334

source_name: cancer cells from patient 334


title: 48 Hour Doxycycline treated_6116750018_A


title: Patient 360, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 360

source_name: cancer cells from patient 360


title: 48 Hour vehicle treated_6116750018_D

description: control sample


title: 24 Hour vehicle treated_6116750018_J

description: control sample


title: 48 Hour vehicle treated_6116750018_C

description: control sample


title: 48 Hour Doxycycline treated_6116750017_L


title: Patient 321, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 321

source_name: cancer cells from patient 321


title: Patient 350, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 350

source_name: cancer cells from patient 350


title: Patient 329, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 329

source_name: cancer cells from patient 329


title: Patient 320, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 320

source_name: cancer cells from patient 320


title: Patient 348, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 348

source_name: cancer cells from patient 348


title: Patient 294, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 294

source_name: cancer cells from patient 294


title: Patient 312, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 312

source_name: cancer cells from patient 312


title: Patient 285, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 285

source_name: cancer cells from patient 285


title: Patient 336, female, large

description: gene expression data from non small lung cancer frozen sample of patient 336

source_name: cancer cells from patient 336


title: Patient 318, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 318

source_name: cancer cells from patient 318


title: Patient 287, female, large

description: gene expression data from non small lung cancer frozen sample of patient 287

source_name: cancer cells from patient 287


title: Patient 290, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 290

source_name: cancer cells from patient 290


title: 24 Hour vehicle treated_6116750018_K

description: control sample

source_name: T47D breast cancer cells


title: Patient 277, female, large

description: gene expression data from non small lung cancer frozen sample of patient 277

source_name: cancer cells from patient 277


title: Patient 254, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 254

source_name: cancer cells from patient 254


title: Patient 257, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 257

source_name: cancer cells from patient 257


title: Patient 276, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 276

source_name: cancer cells from patient 276


title: Patient 275, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 275

source_name: cancer cells from patient 275


title: Patient 204, female, large

description: gene expression data from non small lung cancer frozen sample of patient 204

source_name: cancer cells from patient 204


title: Patient 209, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 209

source_name: cancer cells from patient 209


title: Patient 190, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 190

source_name: cancer cells from patient 190


title: Patient 226, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 226

source_name: cancer cells from patient 226


title: Patient 244, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 244

source_name: cancer cells from patient 244


title: Patient 218, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 218

source_name: cancer cells from patient 218


title: Patient 241, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 241

source_name: cancer cells from patient 241


title: Patient 236, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 236

source_name: cancer cells from patient 236


title: Patient 239, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 239

source_name: cancer cells from patient 239


title: Patient 263, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 263

source_name: cancer cells from patient 263


title: Patient 220, female, large

description: gene expression data from non small lung cancer frozen sample of patient 220

source_name: cancer cells from patient 220


title: Patient 187, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 187

source_name: cancer cells from patient 187


title: Patient 180, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 180

source_name: cancer cells from patient 180


title: Patient 156, male, large

description: gene expression data from non small lung cancer frozen sample of patient 156

source_name: cancer cells from patient 156


title: Patient 184, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 184

source_name: cancer cells from patient 184


title: Patient 154, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 154

source_name: cancer cells from patient 154


title: Patient 173, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 173

source_name: cancer cells from patient 173


title: Patient 179, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 179

source_name: cancer cells from patient 179


title: Patient 168, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 168

source_name: cancer cells from patient 168


title: Patient 163, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 163

source_name: cancer cells from patient 163


title: Patient 178, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 178

source_name: cancer cells from patient 178


title: Patient 186, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 186

source_name: cancer cells from patient 186


title: Patient 164, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 164

source_name: cancer cells from patient 164


title: Patient 182, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 182

source_name: cancer cells from patient 182


title: Patient 160, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 160

source_name: cancer cells from patient 160


title: Patient 149, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 149

source_name: cancer cells from patient 149


title: Patient 135, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 135

source_name: cancer cells from patient 135


title: Patient 139, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 139

source_name: cancer cells from patient 139


title: Patient 147, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 147

source_name: cancer cells from patient 147


title: Patient 116, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 116

source_name: cancer cells from patient 116


title: Patient 150, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 150

source_name: cancer cells from patient 150


title: Patient 138, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 138

source_name: cancer cells from patient 138


title: Patient 111, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 111

source_name: cancer cells from patient 111


title: Patient 123, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 123

source_name: cancer cells from patient 123


title: Patient 105, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 105

source_name: cancer cells from patient 105


title: Patient 130, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 130

source_name: cancer cells from patient 130


title: Patient 92, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 92

source_name: cancer cells from patient 92


title: Patient 76, male, large

description: gene expression data from non small lung cancer frozen sample of patient 76

source_name: cancer cells from patient 76


title: Patient 107, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 107

source_name: cancer cells from patient 107


title: Patient 78, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 78

source_name: cancer cells from patient 78


title: Patient 101, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 101

source_name: cancer cells from patient 101


title: Patient 66, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 66

source_name: cancer cells from patient 66


title: Patient 75, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 75

source_name: cancer cells from patient 75


title: Patient 74, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 74

source_name: cancer cells from patient 74


title: Patient 114, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 114

source_name: cancer cells from patient 114


title: Patient 96, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 96

source_name: cancer cells from patient 96


title: Patient 110, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 110

source_name: cancer cells from patient 110


title: Patient 84, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 84

source_name: cancer cells from patient 84


title: Patient 93, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 93

source_name: cancer cells from patient 93


title: Patient 79, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 79

source_name: cancer cells from patient 79


title: Patient 128, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 128

source_name: cancer cells from patient 128


title: Patient 68, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 68

source_name: cancer cells from patient 68


title: Patient 80, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 80

source_name: cancer cells from patient 80


title: Patient 62, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 62

source_name: cancer cells from patient 62


title: Patient 59, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 59

source_name: cancer cells from patient 59


title: Patient 36, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 36

source_name: cancer cells from patient 36


title: Patient 38, male, large

description: gene expression data from non small lung cancer frozen sample of patient 38

source_name: cancer cells from patient 38


title: Patient 43, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 43

source_name: cancer cells from patient 43


title: Patient 58, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 58

source_name: cancer cells from patient 58


title: Patient 56, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 56

source_name: cancer cells from patient 56


title: Patient 30, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 30

source_name: cancer cells from patient 30


title: Patient 7, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 7

source_name: cancer cells from patient 7


title: Patient 55, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 55

source_name: cancer cells from patient 55


title: Patient 41, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 41

source_name: cancer cells from patient 41


title: Patient 10, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 10

source_name: cancer cells from patient 10


title: Patient 29, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 29

source_name: cancer cells from patient 29


title: Patient 20, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 20

source_name: cancer cells from patient 20


title: Patient 8, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 8

source_name: cancer cells from patient 8


title: Patient 16, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 16

source_name: cancer cells from patient 16


title: Patient 359, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 359

source_name: cancer cells from patient 359


title: Patient 52, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 52

source_name: cancer cells from patient 52


title: Patient 357, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 357

source_name: cancer cells from patient 357


title: Patient 375, female, large

description: gene expression data from non small lung cancer frozen sample of patient 375

source_name: cancer cells from patient 375


title: Patient 373, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 373

source_name: cancer cells from patient 373


title: Patient 347, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 347

source_name: cancer cells from patient 347


title: Patient 361, male, large

description: gene expression data from non small lung cancer frozen sample of patient 361

source_name: cancer cells from patient 361


title: Patient 369, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 369

source_name: cancer cells from patient 369


title: Patient 365, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 365

source_name: cancer cells from patient 365


title: Patient 5, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 5

source_name: cancer cells from patient 5


title: Patient 367, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 367

source_name: cancer cells from patient 367


title: Patient 370, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 370

source_name: cancer cells from patient 370


title: Patient 28, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 28

source_name: cancer cells from patient 28


title: Patient 344, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 344

source_name: cancer cells from patient 344


title: Patient 319, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 319

source_name: cancer cells from patient 319


title: Patient 332, male, large

description: gene expression data from non small lung cancer frozen sample of patient 332

source_name: cancer cells from patient 332


title: Patient 341, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 341

source_name: cancer cells from patient 341


title: Patient 342, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 342

source_name: cancer cells from patient 342


title: Patient 331, male, large

description: gene expression data from non small lung cancer frozen sample of patient 331

source_name: cancer cells from patient 331


title: Patient 317, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 317

source_name: cancer cells from patient 317


title: Patient 311, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 311

source_name: cancer cells from patient 311


title: Patient 297, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 297

source_name: cancer cells from patient 297


title: Patient 314, male, large

description: gene expression data from non small lung cancer frozen sample of patient 314

source_name: cancer cells from patient 314


title: Patient 295, female, large

description: gene expression data from non small lung cancer frozen sample of patient 295

source_name: cancer cells from patient 295


title: Patient 338, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 338

source_name: cancer cells from patient 338


title: Patient 300, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 300

source_name: cancer cells from patient 300


title: Patient 302, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 302

source_name: cancer cells from patient 302


title: Patient 305, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 305

source_name: cancer cells from patient 305


title: Patient 310, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 310

source_name: cancer cells from patient 310


title: Patient 292, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 292

source_name: cancer cells from patient 292


title: Patient 301, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 301

source_name: cancer cells from patient 301


title: Patient 299, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 299

source_name: cancer cells from patient 299


title: Patient 282, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 282

source_name: cancer cells from patient 282


title: Patient 291, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 291

source_name: cancer cells from patient 291


title: Patient 288, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 288

source_name: cancer cells from patient 288


title: Patient 309, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 309

source_name: cancer cells from patient 309


title: Patient 284, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 284

source_name: cancer cells from patient 284


title: Patient 274, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 274

source_name: cancer cells from patient 274


title: Patient 272, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 272

source_name: cancer cells from patient 272


title: Patient 296, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 296

source_name: cancer cells from patient 296


title: Patient 278, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 278

source_name: cancer cells from patient 278


title: Patient 271, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 271

source_name: cancer cells from patient 271


title: Patient 265, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 265

source_name: cancer cells from patient 265


title: Patient 234, male, large

description: gene expression data from non small lung cancer frozen sample of patient 234

source_name: cancer cells from patient 234


title: Patient 258, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 258

source_name: cancer cells from patient 258


title: Patient 260, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 260

source_name: cancer cells from patient 260


title: Patient 249, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 249

source_name: cancer cells from patient 249


title: Patient 223, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 223

source_name: cancer cells from patient 223


title: Patient 228, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 228

source_name: cancer cells from patient 228


title: Patient 217, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 217

source_name: cancer cells from patient 217


title: Patient 235, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 235

source_name: cancer cells from patient 235


title: Patient 64, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 64

source_name: cancer cells from patient 64


title: Patient 196, male, large

description: gene expression data from non small lung cancer frozen sample of patient 196

source_name: cancer cells from patient 196


title: Patient 215, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 215

source_name: cancer cells from patient 215


title: Patient 212, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 212

source_name: cancer cells from patient 212


title: Patient 207, male, large

description: gene expression data from non small lung cancer frozen sample of patient 207

source_name: cancer cells from patient 207


title: Patient 214, male, large

description: gene expression data from non small lung cancer frozen sample of patient 214

source_name: cancer cells from patient 214


title: Patient 224, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 224

source_name: cancer cells from patient 224


title: Patient 243, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 243

source_name: cancer cells from patient 243


title: Patient 193, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 193

source_name: cancer cells from patient 193


title: Patient 247, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 247

source_name: cancer cells from patient 247


title: Patient 213, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 213

source_name: cancer cells from patient 213


title: Patient 197, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 197

source_name: cancer cells from patient 197


title: Patient 192, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 192

source_name: cancer cells from patient 192


title: Patient 255, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 255

source_name: cancer cells from patient 255


title: Patient 200, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 200

source_name: cancer cells from patient 200


title: Patient 256, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 256

source_name: cancer cells from patient 256


title: Patient 202, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 202

source_name: cancer cells from patient 202


title: Patient 229, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 229

source_name: cancer cells from patient 229


title: Patient 203, male, large

description: gene expression data from non small lung cancer frozen sample of patient 203

source_name: cancer cells from patient 203


title: Patient 201, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 201

source_name: cancer cells from patient 201


title: Patient 195, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 195

source_name: cancer cells from patient 195


title: Patient 189, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 189

source_name: cancer cells from patient 189


title: Patient 175, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 175

source_name: cancer cells from patient 175


title: Patient 174, male, large

description: gene expression data from non small lung cancer frozen sample of patient 174

source_name: cancer cells from patient 174


title: Patient 172, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 172

source_name: cancer cells from patient 172


title: Patient 81, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 81

source_name: cancer cells from patient 81


title: Patient 165, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 165

source_name: cancer cells from patient 165


title: Patient 98, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 98

source_name: cancer cells from patient 98


title: Patient 133, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 133

source_name: cancer cells from patient 133


title: Patient 169, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 169

source_name: cancer cells from patient 169


title: Patient 87, female, large

description: gene expression data from non small lung cancer frozen sample of patient 87

source_name: cancer cells from patient 87


title: Patient 112, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 112

source_name: cancer cells from patient 112


title: Patient 171, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 171

source_name: cancer cells from patient 171


title: Patient 48, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 48

source_name: cancer cells from patient 48


title: Patient 39, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 39

source_name: cancer cells from patient 39


title: Patient 162, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 162

source_name: cancer cells from patient 162


title: Patient 88, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 88

source_name: cancer cells from patient 88


title: Patient 158, male, large

description: gene expression data from non small lung cancer frozen sample of patient 158

source_name: cancer cells from patient 158


title: Patient 32, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 32

source_name: cancer cells from patient 32


title: Patient 33, male, large

description: gene expression data from non small lung cancer frozen sample of patient 33

source_name: cancer cells from patient 33


title: Patient 35, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 35

source_name: cancer cells from patient 35


title: Patient 61, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 61

source_name: cancer cells from patient 61


title: Patient 131, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 131

source_name: cancer cells from patient 131


title: Patient 27, female, squamous

description: gene expression data from non small lung cancer frozen sample of patient 27

source_name: cancer cells from patient 27


title: Patient 19, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 19

source_name: cancer cells from patient 19


title: Patient 23, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 23

source_name: cancer cells from patient 23


title: Patient 12, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 12

source_name: cancer cells from patient 12


title: Patient 13, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 13

source_name: cancer cells from patient 13


title: Patient 37, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 37

source_name: cancer cells from patient 37


title: Patient 22, male, adeno

description: gene expression data from non small lung cancer frozen sample of patient 22

source_name: cancer cells from patient 22


title: T6

status: Public on Oct 01 2012

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

description: comparison between MBL and normal genomic DNA

hyb_protocol: The labeled DNA were purified with the Millipore Amicon 30 kDa centrifugal filter device (Billerica, MA) and mixed in equal proportion for hybridization to the array in the presence of Cot-1 DNA (Invitrogen, Carlsbad, CA) using the Agilent Oligo aCGH Hybridization Kit.

scan_protocol: Washed slides were scanned using the Agilent G2565CA Microarray Scanner.  Microarray TIFF (.tif)

data_processing: Images were processed and analyzed with Agilent CytoGenomics v1.5 software. Copy number aberration calls were made with a minimum regional absolute average log base 2 ratio of 0.25 and minimum contiguous probe count of 5.  All array data were also manually reviewed for subtle copy number changes not detected by the software.

source_name: Brain Tumor

label_protocol: Control and tumor DNA were labeled by random priming with CY3- and CY5-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.

extract_protocol: Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue using the QIAamp Blood Mini Kit using a modified protocol incorporating deparaffinization and protease digestion (QIAGEN, Valencia, CA).

tag: tissue

value: brain tumor

tag: disease state

value: Medulloblastoma

source_name: Control

value: control

value: blood


title: T5


title: T3


title: T4


title: T1


title: D341

source_name: Cell line

value: cell line

tag: cell line


title: Patient 11, female, adeno

description: gene expression data from non small lung cancer frozen sample of patient 11

source_name: cancer cells from patient 11


title: Patient 14, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 14

source_name: cancer cells from patient 14


title: 14286369 - 6.3 Repet2 vs GUS Repet2

status: Public on Oct 10 2012

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Transcriptional comparison between 2 TOR RNAi mutants versus GUS control.

hyb_protocol: GUS Repet2 Cy5 / 6.3 Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: GUS Repet2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: hypocotyl - Media=MS 1/5, 10mM ethanol, 8g/l agar hygrometry=in vitro, Room 70% Temperature=20°C Light=DARK

extract_protocol: GUS Repet2:1.4ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.

treatment_protocol: Name:Ethanol induction - induction - compound addition,ethanol:quantity 10mM . Ethanol inducible lines, control: 35S:AlcR pAlcA:GUS, TOR RNAi 35S:AlcR pAlcA:TOR RNAi (FRB domain).

tag: ecotype

value: landsberg erecta

tag: genotype/variation

value: gus control

tag: dev.stage (boyes et al. plant cell 2001)

source_name: 6.3 Repet2

extract_protocol: 6.3 Repet2:3.06ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.


title: T2


title: D283


title: 14286354 - 5.2 Repet1 vs GUS Repet1

hyb_protocol: GUS Repet1 Cy5 / 5.2 Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: GUS Repet1

extract_protocol: GUS Repet1:2.07ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.

source_name: 5.2 Repet1

extract_protocol: 5.2 Repet1:1.48ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.


title: 14286368 - GUS Repet2 vs 6.3 Repet2

hyb_protocol: 6.3 Repet2 Cy5 / GUS Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286355 - GUS Repet1 vs 6.3 Repet1

hyb_protocol: 6.3 Repet1 Cy5 / GUS Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 6.3 Repet1

extract_protocol: 6.3 Repet1:3.11ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.


title: 14286367 - 5.2 Repet2 vs GUS Repet2

hyb_protocol: GUS Repet2 Cy5 / 5.2 Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 5.2 Repet2

extract_protocol: 5.2 Repet2:1ug. (Amplification_Ambion.txt) Amplification of messenger RNA (aRNA Amplification Kit AMBION MessageAmp # 1750) The kit consists of 3 parts: enzymatic reagents at -20 ° C, purification buffer at 4 ° C and columns at room temperature.


title: 14286365 - 6.3 Repet1 vs GUS Repet1

hyb_protocol: GUS Repet1 Cy5 / 6.3 Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Tumor-normal sample pair 9

status: Public on Sep 14 2012

city: Heidelberg

first: Marta

last: Faryna

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: Tumor and normal samples were paired randomly (except for Array 10 where matching normal tissue was available). Samples were hybridized to Human CpG Island microarrays (Agilent Technologies, Santa Clara, CA, USA) using the Oligo aCGH Hybridization Kit (Agilent). Array hybridization and washing was carried out according to the Agilent Microarray Analysis of Methylated DNA Immunoprecipitation protocol (Version 1.0, May 2008; Agilent Technologies).

scan_protocol: Arrays were scanned with Agilent Technologies Scanner G2505B US22502640.

data_processing: Micorarray data were extracted with Agilent Feature Extraction Software 10.5 using CGH_105_Dec08 protocol. Since normal tissue was detected in red channel and tumor tissue in green channel, in order to obtain LogRatio(Tumor/Normal) the LogRatio values from original extraction files  were multiplied by -1. Array data were corrected for GC content as reported previously by Schilling et al. (Genome Res, 2009, 19(11): p. 2028-35).

label: Alexa Fluor 3

source_name: Invasive ductal carcinoma

label_protocol: Samples were labelled with (BioPrime Total Genomic Labeling System, Invitrogen): tumor with Alexa Fluor 3 and normal with Alexa Fluor 5.

extract_protocol: Genomic DNA was extracted according to the Tissue Protocol of the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). After incubation with AL buffer an additional centrifugation step (2000 x g, 10 min) was added for fat removal. In Methyl-CpG Immunoprecipitation (MCIp) two µg ultrasonicated DNA (with an average fragment size of 400-500 bp) were immunoprecipitated with 60 µg MBD-Fc protein. MDB-Fc protein was produced according to a protocol described by Gebhard et al. (Cancer Res, 2006, 66 (12): p. 6118-28). Unbound DNA was recovered by centrifugation, bound DNA eluted twice with buffers containing increasing NaCl concentrations (400, 500, 550, 600 and 1000 mM NaCl). Eluates were desalted and fractions containing highly methylated DNA (600 and 1000 mM fractions) were combined for each sample.

tag: tissue type

value: Breast carcinoma

tag: histological assessment

value: Invasive ductal carcinoma

label: Alexa Fluor 5

source_name: Normal breast

value: Normal breast

value: Normal breast tissue


title: Tumor-normal sample pair 4

source_name: Ductal carcinoma in situ

value: Ductal carcinoma in situ


title: Tumor-normal sample pair 5

source_name: Lobular carcinoma in situ

value: Lobular carcinoma in situ


title: Patient 6, male, squamous

description: gene expression data from non small lung cancer frozen sample of patient 6

source_name: cancer cells from patient 6

tag: dead

tag: days to determined death status

value: squamous


title: 14286353 - GUS Repet1 vs 5.2 Repet1

hyb_protocol: 5.2 Repet1 Cy5 / GUS Repet1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Tumor-normal sample pair 6

source_name: Tubulo-lobular carcinoma

value: Tubulo-lobular carcinoma


title: Tumor-normal sample pair 2


title: Tumor-normal sample pair 7

source_name: Tubular carcinoma

value: Tubular carcinoma


title: Tumor-normal sample pair 10


title: Tumor-normal sample pair 8


title: Tumor-normal sample pair 3


title: Tumor-normal sample pair 1


title: WB_HFS172

status: Public on Sep 04 2012

city: Raleigh

first: Youssef

last: Idaghdour

state: NC

address: Gardner Hall NCSU Campus

department: Genetics

institute: NCSU

data_processing: The data were normalised using quantile normalisation with JMP Genomics

label: Biotin

source_name: Whole blood, age-matched control

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted from whole blood collected in Tempus tubes using the Tempus Spin RNA Isolation kit (Applied Biosystems). Total RNA was then globin-mRNA-depleted using GlobinClear kit (Ambion). Quality control was performed with Agilent Bioanalyser.

tag: sample name

tag: genotypic pc1

tag: genotypic pc2

tag: genotypic pc3

tag: location

value: Cotonou

value: F

tag: age (years)

tag: malaria rd test

value: NEGATIF

tag: parasitemia

tag: log2 parasitemia

tag: parasitemia category

value: C

tag: red blood cells

tag: white blood cells

tag: hemoglobin genotype

value: AA


title: WB_HFS169

tag: gender

value: M


title: WB_HFS170

value: AS


title: 14286366 - GUS Repet2 vs 5.2 Repet2

hyb_protocol: 5.2 Repet2 Cy5 / GUS Repet2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

value: landsberg erecta

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)

value: gus control


title: WB_HFS171

tag: sample name


title: WB_HFS167

tag: genotypic pc1


title: WB_HFS173

tag: genotypic pc2


title: WB_HFS164

tag: genotypic pc3


title: WB_HFS162

tag: location


title: WB_HFS163

tag: age (years)


title: WB_HFS166

tag: malaria rd test


title: WB_HFS165

tag: parasitemia


title: WB_HFS158

tag: log2 parasitemia


title: WB_HFS168

tag: parasitemia category


title: WB_HFS160

tag: red blood cells

value: AC


title: WB_HFS153

tag: white blood cells


title: WB_HFS154

tag: hemoglobin genotype


title: WB_HFS152

tag: gender


title: WB_HFS161


title: WB_HFS157


title: WB_HFS146


title: WB_HFS144


title: WB_HFS149


title: WB_HFS148


title: WB_HFS159


title: WB_HFS150


title: WB_HFS147


title: WB_HFS151


title: pb treated mouse 4 liver 5mC profile (28 d)

status: Public on Sep 12 2012

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: PB exposed mouse liver tissue

hyb_protocol: Labelled samples were applied commercially to a Nimblegen 2.1M Deluxe promoter array by Nimblegen, Iceland

scan_protocol: Arrays were scanned commercially by Nimblegen, Iceland

data_processing: Pair files normalised within arrays (loess), normalised between arrays (sclae normalisation), log2(IP/input)

organism: Mus musculus

source_name: 28 day PB exposed whole liver

label_protocol: Amplification of DNA samples was carried out commercially by NimbleGen, Iceland  (Cy5- (IP) or Cy3- (Input) labelled)

growth_protocol: PB exposed mouse liver tissue

extract_protocol: Genomic DNA (5mC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of -5mC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

treatment_protocol: genomic DNA extracted from mouse liver following 28 day exposed to Phenobarbital

tag: treatment

value: phenobarbital

tag: tissue

value: liver

tag: antibody

tag: antibody manufacturer

value: Eurogentec

tag: time

source_name: PB exposed mouse liver tissue

value: none (Input)


title: WB_HFS145

tag: sample name

tag: genotypic pc1

tag: genotypic pc2


title: control mouse 3 liver 5mC profile (28 d)

description: normal whole brain genomic DNA

source_name: normal whole liver

growth_protocol: normal mouse liver tissue

treatment_protocol: genomic DNA extracted from normal mouse liver

value: control


title: control mouse 4 liver 5mC profile (28 d)

description: normal whole brain genomic DNA


title: control mouse 5 liver 5mC profile (28 d)

description: normal whole brain genomic DNA


title: WB_HFS138

tag: genotypic pc3

tag: location

tag: age (years)


title: WB_HFS139

tag: malaria rd test

tag: parasitemia

tag: log2 parasitemia


title: control mouse 1 liver 5mC profile (28 d)

description: normal whole brain genomic DNA


title: WB_HFS140

tag: parasitemia category

tag: red blood cells

tag: white blood cells


title: pb treated mouse 2 liver 5hmC profile (28 d)

description: PB exposed mouse liver tissue

data_processing: Normalised data after normalised within arrays (loess) and between arrays (sclae normalisation) resulting in log2(IP/input) scores for each probe

extract_protocol: Genomic DNA (5hmC-IP - 2.5 µg in 450 µl TE), sonicated to yield a fragment distribution of approximately 300-1000 bp, was denatured by incubation at 100°C for 10 min. Samples were rapidly chilled on wet-ice. At this point, 45 µl (10%) of denatured sample was removed and saved as input, and 45 µl of 10X IP buffer (100 mM Na-Phosphate pH 7.0  (mono and dibasic), 1.4 M NaCl, 0.5 % Triton X-100) and 1 µg of -5hmC (ActiveMotif; #39769) antibody were added to the remaining sample. Samples were incubated at 4C with gentle agitation overnight. Then, 40 µl of magnetic beads (Dynabeads® Protein G, Invitrogen, UK) in 1X IP buffer were added to each sample to allow magnetic separation of the antibody from the unbound DNA using a magnetic tube rack. Samples were incubated at 4C for 1 hr with gentle agitation. Beads were collected with a magnetic rack and washed with 1000 µl of 1X IP buffer at RT for 10 min with gentle agitation; washing was repeated three times. Beads were collected with a magnetic rack and re-suspended in 250 µl of digestion buffer (50 mM Tris pH 8.0, 10 mM EDTA , 0.5 % SDS) followed by addition of 10 µl of proteinase K  (20 mg/ml; Roche Applied Science, Mannheim, Germany) and incubation at 52C for 1.5 hr with constant shaking (≥800 rpm). Finally, beads were removed using a magnetic rack and DNA was purified from the remaining sample using a QIAquick PCR Purification Kit (QIAGEN,CA, USA), eluting in a final volume of 40 µl dH2O. Inputs were also purified using a QIAquick PCR Purification Kit and eluted in 40 µl dH2O. Subsequently, 10 ng of input and IP DNA was subjected to whole genome amplification (WGA) using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich, UK) as per the manufacturer's instructions. Amplified DNA was run on a 1.2% agarose gel to confirm consistency of fragment size between samples.

tag: treatment

tag: gender

value: Active Motif


title: control mouse 4 liver 5hmC profile (28 d)

description: normal whole brain genomic DNA

tag: tissue

tag: antibody


title: WB_HFS156

tag: hemoglobin genotype


title: pb treated mouse 1 liver 5hmC profile (28 d)

description: PB exposed mouse liver tissue

tag: antibody manufacturer

tag: time


title: control mouse 3 liver 5hmC profile (28 d)

description: normal whole brain genomic DNA


title: control mouse 2 liver 5hmC profile (28 d)

description: normal whole brain genomic DNA


title: WB_HFS132

tag: sample name

tag: genotypic pc1

tag: genotypic pc2


title: WB_HFS141

tag: genotypic pc3

tag: location

tag: age (years)


title: control mouse 5 liver 5hmC profile (28 d)

description: normal whole brain genomic DNA


title: WB_HFS134

tag: malaria rd test

tag: parasitemia

tag: log2 parasitemia


title: pb treated mouse 5 liver 5hmC profile (28 d)

description: PB exposed mouse liver tissue


title: pb treated mouse 4 liver 5hmC profile (28 d)

description: PB exposed mouse liver tissue


title: pb treated mouse 2 liver 5mC profile (28 d)

description: PB exposed mouse liver tissue


title: pb treated mouse 3 liver 5hmC profile (28 d)

description: PB exposed mouse liver tissue


title: WB_HFS126

tag: parasitemia category

tag: red blood cells

tag: white blood cells


title: WB_HFS127

tag: gender


title: WB_HFS143


title: WB_HFS131


title: WB_HFS130


title: pb treated mouse 1 liver 5mC profile (28 d)

description: PB exposed mouse liver tissue

tag: treatment

tag: tissue

tag: antibody


title: WB_HFS124

tag: hemoglobin genotype


title: WB_HFS122

tag: sample name


title: WB_HFS135

tag: genotypic pc1


title: WB_HFS120

tag: genotypic pc2


title: WB_HFS136

tag: genotypic pc3


title: WB_HFS118

tag: location


title: WB_HFS119

tag: age (years)


title: control mouse 2 liver 5mC profile (28 d)

description: normal whole brain genomic DNA

tag: antibody manufacturer


title: WB_HFS117

tag: malaria rd test

tag: parasitemia


title: control mouse 1 liver 5hmC profile (28 d)

description: normal whole brain genomic DNA


title: WB_HFS114

tag: log2 parasitemia

tag: parasitemia category


title: WB_HFS111

tag: red blood cells

tag: white blood cells


title: WB_HFS112

tag: gender


title: WB_HFS106


title: WB_HFS105


title: WB_C0037

description: globin mRNA-depleted total RNA

source_name: Whole blood, symptomatic

value: POSITIF

value: Low Parasitemia


title: pb treated mouse 3 liver 5mC profile (28 d)

description: PB exposed mouse liver tissue

tag: treatment

tag: tissue

tag: time


title: WB_C0039

description: globin mRNA-depleted total RNA

tag: sample name

value: Cotonou

value: F

tag: hemoglobin genotype


title: WB_HFS101

description: globin mRNA-depleted total RNA

tag: genotypic pc1

tag: genotypic pc2

value: NEGATIF

value: C


title: WB_HFS115

tag: genotypic pc3

tag: location

value: M

value: AA


title: WB_C0036

description: globin mRNA-depleted total RNA

tag: age (years)

value: High Parasitemia


title: WB_C0034

description: globin mRNA-depleted total RNA

tag: malaria rd test


title: WB_C0035

description: globin mRNA-depleted total RNA

tag: parasitemia


title: pb treated mouse 5 liver 5mC profile (28 d)

description: PB exposed mouse liver tissue

tag: antibody

tag: antibody manufacturer


title: WB_HFS137

tag: log2 parasitemia

tag: parasitemia category

tag: red blood cells

value: AS


title: WB_HFS129

tag: gender

tag: white blood cells


title: WB_C0026

description: globin mRNA-depleted total RNA


title: WB_HFS109


title: WB_C0032

description: globin mRNA-depleted total RNA


title: WB_C0019

description: globin mRNA-depleted total RNA


title: WB_C0029

description: globin mRNA-depleted total RNA


title: WB_C0015

description: globin mRNA-depleted total RNA


title: WB_C0023

description: globin mRNA-depleted total RNA


title: WB_C0018

description: globin mRNA-depleted total RNA

value: AC


title: WB_C0028

description: globin mRNA-depleted total RNA


title: WB_C0030

description: globin mRNA-depleted total RNA


title: WB_HFS116


title: WB_HFS113


title: WB_C0027

description: globin mRNA-depleted total RNA


title: WB_C0024

description: globin mRNA-depleted total RNA


title: WB_C0021

description: globin mRNA-depleted total RNA


title: WB_C0020

description: globin mRNA-depleted total RNA


title: WB_C0022

description: globin mRNA-depleted total RNA


title: WB_C0025

description: globin mRNA-depleted total RNA


title: WB_C0031

description: globin mRNA-depleted total RNA


title: WB_C0017

description: globin mRNA-depleted total RNA


title: WB_C0033

description: globin mRNA-depleted total RNA


title: WB_C0014

description: globin mRNA-depleted total RNA


title: WB_C0016

description: globin mRNA-depleted total RNA


title: WB_C0013

description: globin mRNA-depleted total RNA


title: WB_C0011

description: globin mRNA-depleted total RNA


title: WB_C0012

description: globin mRNA-depleted total RNA


title: WB_C0010

description: globin mRNA-depleted total RNA


title: WB_C0038

description: globin mRNA-depleted total RNA


title: WB_HFS110


title: WB_C0008

description: globin mRNA-depleted total RNA


title: WB_C0007

description: globin mRNA-depleted total RNA


title: WB_C0009

description: globin mRNA-depleted total RNA


title: WB_B0054

description: globin mRNA-depleted total RNA

value: Zinvie


title: WB_C0005

description: globin mRNA-depleted total RNA


title: WB_C0002

description: globin mRNA-depleted total RNA


title: WB_B0055

description: globin mRNA-depleted total RNA


title: WB_C0006

description: globin mRNA-depleted total RNA


title: WB_C0003

description: globin mRNA-depleted total RNA


title: WB_C0004

description: globin mRNA-depleted total RNA


title: WB_C0001

description: globin mRNA-depleted total RNA


title: WB_B0046

description: globin mRNA-depleted total RNA


title: WB_B0051

description: globin mRNA-depleted total RNA


title: WB_B0050

description: globin mRNA-depleted total RNA


title: WB_B0049

description: globin mRNA-depleted total RNA


title: WB_B0056

description: globin mRNA-depleted total RNA


title: WB_B0043

description: globin mRNA-depleted total RNA


title: WB_B0047

description: globin mRNA-depleted total RNA


title: WB_B0053

description: globin mRNA-depleted total RNA


title: WB_B0048

description: globin mRNA-depleted total RNA


title: WB_B0040

description: globin mRNA-depleted total RNA


title: WB_B0045

description: globin mRNA-depleted total RNA


title: WB_B0037

description: globin mRNA-depleted total RNA


title: WB_B0041

description: globin mRNA-depleted total RNA


title: WB_B0038

description: globin mRNA-depleted total RNA


title: WB_B0036

description: globin mRNA-depleted total RNA


title: WB_B0033

description: globin mRNA-depleted total RNA


title: WB_B0028

description: globin mRNA-depleted total RNA


title: WB_B0025

description: globin mRNA-depleted total RNA


title: WB_B0039

description: globin mRNA-depleted total RNA


title: WB_B0034

description: globin mRNA-depleted total RNA


title: WB_B0018

description: globin mRNA-depleted total RNA


title: WB_B0035

description: globin mRNA-depleted total RNA


title: WB_B0026

description: globin mRNA-depleted total RNA


title: WB_B0032

description: globin mRNA-depleted total RNA


title: WB_B0015

description: globin mRNA-depleted total RNA


title: WB_B0021

description: globin mRNA-depleted total RNA


title: WB_B0012

description: globin mRNA-depleted total RNA


title: WB_B0024

description: globin mRNA-depleted total RNA


title: WB_B0027

description: globin mRNA-depleted total RNA


title: WB_B0023

description: globin mRNA-depleted total RNA


title: WB_B0014

description: globin mRNA-depleted total RNA


title: WB_B0029

description: globin mRNA-depleted total RNA


title: WB_B0013

description: globin mRNA-depleted total RNA


title: WB_B0017

description: globin mRNA-depleted total RNA


title: WB_B0030

description: globin mRNA-depleted total RNA


title: WB_B0019

description: globin mRNA-depleted total RNA


title: WB_B0031

description: globin mRNA-depleted total RNA


title: WB_B0011

description: globin mRNA-depleted total RNA


title: WB_B0010

description: globin mRNA-depleted total RNA


title: WB_B0009

description: globin mRNA-depleted total RNA


title: WB_B0005

description: globin mRNA-depleted total RNA


title: WB_B0020

description: globin mRNA-depleted total RNA


title: WB_B0008

description: globin mRNA-depleted total RNA


title: WB_B0006

description: globin mRNA-depleted total RNA


title: WB_B0007

description: globin mRNA-depleted total RNA


title: WB_B0002

description: globin mRNA-depleted total RNA


title: Wt WBM 5

status: Public on Sep 01 2012

first: Rachel

middle: Lynn

last: Novak

state: Maryland

address: 41 Center Drive

institute: NCI

hyb_protocol: Samples are hybridized overnight to Affymetrix GeneChip microarrays. Wash/stain/scan of the microarray is carried out under strictly controlled conditions with the Affymetrix Fluidics Station.

scan_protocol: Affymetrix Scanner

data_processing: Gene expression data was analyzed using BRB Array Tools version 4.2.1 using the RMA method. To generate tables of differentially expressed genes, genes with a 1.5 fold difference in expression and a parametric p-value less than 0.05 were tabulated. Probe sets with log2 transformed geometric mean intensities below 100 were not included in the analysis. For the analysis of leukemia samples, obtained from infiltrated spleens, genes increased 5.0 fold in normal spleens compared to normal BM were filtered out

source_name: Wildtype whole bone marrow

label_protocol: 100ng of RNA are reverse transcribed and labeled with biotin

growth_protocol: Mice were sacrificed when clincal signs of leukemia manifested. Wildtype hematopoetic tissue was taken from age-matched litter mates if possible. Clincally Healthy hematopoietic tissue was taken taken from transgenic animals which did not have any clincal signs of leukemia.

extract_protocol: RNA was extracted from the spleen, thymus, and bone marrow using Trizol according to the manufacturers protocol.

treatment_protocol: Mice were not on a treatment protocol

tag: genotype/variation

value: wildtype

tag: tissue

value: bone marrow


title: Wt WBM C57B6 1

description: Wt WBM C57B6


title: WB_B0004

description: globin mRNA-depleted total RNA

tag: sample name

tag: hemoglobin genotype


title: Wt WBM 1


title: Wt WBM C57B6 3

description: Wt WBM C57B6


title: Wt Thymus 2

source_name: Wildtype Thymus

value: thymus


title: Wt WBM 3


title: Wt WBM 4


title: Wt WBM C57B6 2

description: Wt WBM C57B6


title: Wt Thymus 5


title: Wt Thymus 3


title: Wt WBM 6


title: Wt Thymus 7


title: Wt WBM 2


title: Wt Thymus 4


title: Wt Thymus 6


title: WB_B0001

description: globin mRNA-depleted total RNA

tag: genotypic pc1

tag: genotypic pc2


title: WB_B0016

description: globin mRNA-depleted total RNA

tag: genotypic pc3

tag: location


title: WB_B0003

description: globin mRNA-depleted total RNA

tag: age (years)

tag: malaria rd test


title: WB_B0052

description: globin mRNA-depleted total RNA

tag: parasitemia


title: Wt Thymus 1


title: Wt LN BM 2

source_name: Wildtype lineage negative bone marrow


title: NHD13 CH WBM 2

description: NHD13_Clincally_Healthy_whole_bone_marrow

source_name: clinically healthy whole bone marrow from NHD13 transgenic mice


title: Wt Spleen 2

source_name: Wildtype spleen

value: spleen


title: Wt LN BM 3


title: WB_B0044

description: globin mRNA-depleted total RNA


title: NHD13 CH Thymus 2

source_name: clincally healthy thymus from NHD13 transgenic mice


title: NHD13 CH LN BM 2

description: NHD13_Clincally_Healthy_lineage_negative_bone_marrow

source_name: clincally healthy lineage negative bone marrow from NHD13 transgenic mice


title: NHD13 CH LN BM 3


title: NHD13 CH LN BM 1


title: NHD13 tumor 5

source_name: leukemic spleens from NHD13 transgenic mice


title: NHD13 CH Thymus 3


title: NHD13 CH Thymus 1


title: NHD13 tumor 6


title: NHD13 tumor 3


title: C10  tumor 5

source_name: leukemic spleens from CA10 transgenic mice


title: NHD13 CH WBM 3


title: NHD13 tumor 2


title: NHD13 tumor 1


title: C10  tumor 1


title: Wt LN BM 1


title: C10  tumor 4


title: C10  tumor 2


title: NHD13 CH WBM 1


title: NHD13 tumor 4


title: C10  tumor 3


title: C10 CH WBM 3

description: CA10_Clincally_Healthy_whole_bone_marrow

source_name: clinically healthy whole bone marrow from CA10 transgenic mice


title: C10 CH WBM 2


title: C10 CH WBM 1


title: C10 CH Thymus 4

source_name: clincally healthy thymus from CA10 transgenic mice


title: C10 CH Thymus 2


title: C10  tumor 6


title: C10 CH Thymus 3


title: C10 CH Spleen 1

source_name: clincally healthy spleens from CA10 transgenic mice


title: C10 CH Spleen 4


title: C10 CH Thymus 1


title: C10 CH Spleen 2


title: WB_B0022

description: globin mRNA-depleted total RNA


title: C10 CH LN BM 3

description: CA10_Clincally_Healthy_lineage_negative_bone_marrow

source_name: clincally healthy lineage negative bone marrow from CA10 transgenic mice


title: Wt Spleen 1


title: C10 CH Spleen 5


title: C10 CH LN BM 2


title: C10 CH Spleen 3


title: C10 CH LN BM 1


title: Liver B&E Rep 4

status: Public on Aug 31 2012

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

hyb_protocol: The microarrays were hybridized in Agilent hybridization chambers and incubated overnight (17 hrs.) in a rotisserie oven (Model G2545A, Agilent) at 65°C.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and raw images were processed using Agilent’s Feature Extraction Software, Version 10.1.1.1.

data_processing: Gene Spring version GX11;  any value <1.0 was set to 1.0;  No baseline transformation. Data were normalized using LOWESS (Locally Weighted Least Squares Regression). No MTC applied.

organism: Micropterus dolomieu

source_name: Liver

label_protocol: Total RNA samples (900 ng each) were labeled using Agilent’s Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), version 5.7, March 2008 (no. 5190-4444).

growth_protocol: Adults used

extract_protocol: RNA extractions were done with an Omega BioTek EZNA Total RNA kit, following manufacturer's instructions, with on-column DNase digestion

tag: sample id

tag: treatment

value: Bacteria & estradiol

tag: Sex

value: Female

organism: Micropterus salmoides

source_name: Liver (n=8 pooled sample)

value: Male


title: Liver B&E Rep 3


title: Liver Bacteria Rep 2

value: bacteria


title: Liver Control Rep 4

value: control


title: Liver Bacteria Rep 4


title: Liver Bacteria Rep 3


title: Liver Estradiol Rep 3

value: estradiol


title: Liver Control Rep 3


title: Liver Control Rep 2


title: Liver Bacteria Rep 1


title: Liver B&E Rep 2


title: Liver B&E Rep 1


title: Liver Estradiol Rep 4


title: Liver Estradiol Rep 2


title: Liver Control Rep 1


title: Gill Control Rep 4

source_name: Gill


title: Gill B&E Rep 4


title: Heart TAC surgery 20 days after

status: Public on Jun 09 2012

city: Guangzhou

first: Wei

last: Ouyang

state: Guangdong

address: 253 Gongyedadao Road, Guangzhou, People's Republic of China

department: Department of Nuclear Medicine,Zhujiang Hospital, Southern Medical University,Guangzhou,  People's Republic of China

country: China

description: The miRNAs in Sham-operated rats were set up as the blank control.

hyb_protocol: After the labeling procedure, the Hy3TM-labeled samples were hybridized to a miRCURYTM LNA Array (v.16.0) (Exiqon),which contains more than 1,891 capture probes covering all of the human, mouse and rat miRs annotated in miRBase 16.0, as well as all viral miRs related to these species.

scan_protocol: The images on the chip were scanned and imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: The 5 replicates were averaged, and the miRs that underwent a >= 2-fold change in expression between the TAC and sham groups were selected for analysisand.Meanwhile,the miRs with intensities > 50 in all samples were used to calculate the normalization factor. Expression data were normalized using the median normalization. After normalization, differentially expressed miRs were identified by fold change filtering (fold change >= 2). Hierarchical clustering was performed using MEV software (v4.6, TIGR).

organism: Rattus norvegicus

source_name: Hearts of 5 Rattus norvegicuses, TAC surgery, 20 days after

label_protocol: After RNA isolation from the hearts, one microgram of each sample was 3'-end-labeled with a Hy3TM fluorescent label (Exiqon, Denmark) using T4 RNA ligase.

growth_protocol: SD male rats (6-8 weeks old, 200-300 g) were housed at 20±2°C and 55±20% humidity with 12-hr light/dark cycles and free access to food and water in the Animal Care Facility at the Sun Yat-sen University (SYSU) School of Medicine.

extract_protocol: Total RNA was isolated from hearts at 5, 10, 15 and 20 days after TAC or sham surgery using TRIzol (Invitrogen，Life Technologies，New York， USA) and an miRNeasy Mini kit (QIAGEN, Valencia, CA, USA) according to the manufacturer’s instructions. RNA quality and quantity were measured using a Nanodrop spectrophotometer (ND-1000, Thermo Fisher Scientific, Wilmington, DE, USA), and RNA integrity was determined by denaturing agarose gel electrophoresis.

treatment_protocol: The SD rats were subjected to transverse aortic constriction surgery. Rats were anesthetized with barbital sodium administrated intraperitoneally at 200 mg/kg body weight. An approximately two-centimeter incision was made at the level of the cricoid process and dissected down to the clavicle. After cutting the right clavicle, the thymus was retracted gently, and the aortic arch was exposed. A constriction of the aortic arch was conducted between both carotid arteries using an 18 gauge angiocatheter. Sham-operated rats were underwent a similar surgical procedure without constriction of the aorta. After TAC surgery, the chest was closed with a 5-0 nylon suture, and mice were placed on a heating pad at 37°C until they had completely recovered from anesthesia.

tag: strain

value: SD

tag: surgery

value: TAC

tag: sample time after surgery

value: 20 days


title: Heart TAC surgery 15 days after

institute: Zhujiang Hospital, Southern Medical University,Guangzhou,  People's Republic of China

source_name: Hearts of 5 Rattus norvegicuses, TAC surgery, 15 days after

tag: gender

value: 15 days


title: Gill Estradiol Rep 3


title: Heart TAC surgery 10 days after

source_name: Hearts of 5 Rattus norvegicuses, TAC surgery, 10 days after

value: 10 days


title: Gill Control Rep 2


title: Gill B&E Rep 1


title: Gill Estradiol Rep 4


title: Gill Control Rep 3


title: Gill Bacteria Rep 4


title: Gill Estradiol Rep 2


title: Gill B&E Rep 2


title: Gill Estradiol Rep 1


title: Gill B&E Rep 3


title: Gill Bacteria Rep 1