title: 4hr_C57_GSS_102_lung

description:
4320221051_G
replicate 3


title: malignant mesothelioma, Y-MESO-8D

status: Public on Dec 18 2011

type: RNA

city: Nagoya

first: Futoshi

last: Ishiguro

address: 1-1 Kanokoden, Chikusa-ku

department: Molecular Oncology

country: Japan

institute: Aichi Cancer Center Research Institute

description: Biological replicate 11 of 20. malignant mesothlioma cell lines, harvested after several passages.

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing: Scanned images were analyzed with the Agilent Feature Extraction Program ver. 10.7.

molecule: total RNA

organism: Homo sapiens

source_name: human malignant mesothlioma

label_protocol: The cRNA from MM cell lines or reference samples were labeled with Cy5-CTP or Cy3-CTP fluorophores, respectively. 825 ng of each labeled cRNA was mixed, and hybridizations were performed on 4×44 K oligonucleotide-based whole human genome microarrays (Agilent Technologies) at 65oC for 17 hours. After hybridization, arrays were washed.

growth_protocol: Cells were seeded on flat-bottomed 24-well plates and grown in RPMI1640 medium with 10% FCS.

extract_protocol: Total RNA was prepared using RNeasy Plus RNA extraction kit (Qiagen K.K.) according to the manufacturer's protocol. By using 150 ng of total RNA, cRNA was generated and labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: After 90 hours, total RNA was extracted following manufacturer's instructions

tag: tissue

value: malignant meshelioma

source_name: normal mesothelial cells

value: normal mesothelial cells


title: malignant mesothelioma, Y-MESO-25

description: Biological replicate 15 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: malignant mesothelioma, MSTO-211H

description: Biological replicate 10 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: 28d_C57_Air_115_lung

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

country: USA

institute: CDC/NIOSH

description:
4309267044_D
replicate 4

hyb_protocol: 20 hour hybridization period at 58°C

scan_protocol: Illumina BeadStation 500G - BeadArray Reader standard

data_processing: Force positive background correction, variance stabilizing transformation, robust spline normalization

label: biotin

organism: Mus musculus

source_name: lung

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791)

extract_protocol: Lung RNA isolated from whole lung homogenates using the TRIzol method and cleaned with a Rneasy Mini Kit. Aorta was homogenized with a Qiagen Tissue Lyser and RNA was isolated using the Rneasy fibrous mini kit. Whole blood RNA was isolated using the Mouse RiboPure Blood RNA Isolation Kit and globin RNA was removed using the GLOBINclear kit.

treatment_protocol: Mice were exposed to either air or gas metal arc-stainless steel welding fume for 10 days (3 hours/day) at 40 mg/m3

tag: strain

tag: exposure

value: Air

tag: recovery time


title: 4hr_C57_Air_97_lung

description:
4320221051_B
replicate 2


title: 4hr_C57_Air_99_lung

description:
4320221051_D
replicate 4


title: 28d_C57_GSS_117_lung

description:
4309267044_F
replicate 2

value: GMA-SS


title: 4hr_C57_Air_42_blood

description:
4560232069_B
replicate 2

source_name: blood


title: 28d_C57_GSS_116_lung

description:
4309267044_E
replicate 1


title: 28d_C57_GSS_118_lung

description:
4309267044_G
replicate 3


title: 4hr_C57_GSS_101_lung

description:
4320221051_F
replicate 2


title: 28d_C57_Air_114_lung

description:
4309267044_C
replicate 3


title: 28d_C57_GSS_119_lung

description:
4309267044_H
replicate 4


title: 28d_C57_Air_112_lung

description:
4309267044_A
replicate 1


title: 4hr_C57_Air_96_lung

description:
4320221051_A
replicate 1


title: 4hr_C57_GSS_64_blood

description:
4560232069_H
replicate 4


title: 28d_C57_GSS_80_aorta

description:
4844850027_H
replicate 4

source_name: aorta


title: 4hr_C57_GSS_100_lung

description:
4320221051_E
replicate 1


title: malignant mesothelioma, NCI-H28

description: Biological replicate 8 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: 28d_C57_Air_58_aorta

description:
4844850027_B
replicate 2


title: 4hr_C57_GSS_63_aorta

description:
4844850024_G
replicate 3


title: 28d_C57_Air_59_aorta

description:
4844850027_C
replicate 3


title: 28d_C57_GSS_78_aorta

description:
4844850027_F
replicate 2


title: 4hr_C57_Air_98_lung

description:
4320221051_C
replicate 3


title: 28d_C57_Air_113_lung

description:
4309267044_B
replicate 2


title: 4hr_C57_Air_45_aorta

description:
4844850024_D
replicate 4


title: 28d_C57_Air_60_aorta

description:
4844850027_D
replicate 4


title: 4hr_C57_GSS_62_aorta

description:
4844850024_F
replicate 2


title: 4hr_C57_Air_43_aorta

description:
4844850024_C
replicate 3


title: 28d_C57_GSS_79_aorta

description:
4844850027_G
replicate 3


title: 4hr_C57_GSS_61_aorta

description:
4844850024_E
replicate 1


title: 28d_C57_GSS_77_aorta

description:
4844850027_E
replicate 1


title: 4hr_C57_Air_41_aorta

description:
4844850024_A
replicate 1


title: liver rep2

city: Yokohama

first: Alistair

middle: R

last: Forrest

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN OMICS science centre

institute: RIKEN

description:
liver-2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: mouse liver tissue

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

extract_protocol: Total RNA was extracted using QIAGEN Rneasy mini kit

tag: Sex

value: male

tag: age

value: 7 weeks

value: liver


title: mesothelium (peritoneum) rep2

description:
mesothelium (peritoneum)-2
replicate 2

source_name: mouse mesothelium (peritoneum) tissue

value: mesothelium (peritoneum)


title: fat rep2

description:
fat-2
replicate 2

source_name: mouse fat tissue

value: fat


title: bladder rep2

description:
bladder-2
replicate 2

source_name: mouse bladder tissue

value: bladder


title: skeletal muscle rep3

description:
skeletal muscle-3
replicate 3

source_name: mouse skeletal muscle tissue

value: skeletal muscle


title: mesothelium (plaura and pericardium) rep2

description:
mesothelium (plaura and pericardium)-2
replicate 2

source_name: mouse mesothelium (plaura and pericardium) tissue

value: mesothelium (plaura and pericardium)


title: lung rep1

description:
lung-1
replicate 1

source_name: mouse lung tissue

value: lung


title: fat rep1

description:
fat-1
replicate 1


title: mesothelium (peritoneum) rep1

description:
mesothelium (peritoneum)-1
replicate 1


title: heart rep2

description:
heart-2
replicate 2

source_name: mouse heart tissue

value: heart


title: malignant mesothelioma, Y-MESO-14

description: Biological replicate 7 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: liver rep1

description:
liver-1
replicate 1


title: malignant mesothelioma, Y-MESO-9

description: Biological replicate 6 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: skeletal muscle rep1

description:
skeletal muscle-1
replicate 1


title: skeletal muscle rep2

description:
skeletal muscle-2
replicate 2


title: malignant mesothelioma, NCI-H2373

description: Biological replicate 5 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: lung rep3

description:
lung-3
replicate 3


title: mesothelium (plaura and pericardium) rep1

description:
mesothelium (plaura and pericardium)-1
replicate 1


title: JNKi_batch1_a [Affy]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: probesets were summarized and probeset-level values normalized with rma (target=core) function from R/Bioconductor package oligo (version 1.14.0)

source_name: Terminally differentiated Neurons (TN)

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: Cells were grown at 37°C cell culture incubator in complete media

extract_protocol: RNA was isolated from cells using Rneasy kit from Qiagen

treatment_protocol: Cells were treated with either DMSO or 25 uM of the drug three times at an interval of 2 hours

tag: cell type

value: Terminally differentiated Neurons (TN)

tag: agent

tag: agent batch

tag: protocol

value: JNK inhibition

tag: biological replicate

value: a


title: bladder rep1

description:
bladder-1
replicate 1


title: fat rep3

description:
fat-3
replicate 3


title: JNKi_batch2_d [Affy]

value: d


title: DMSO_batch2_e [Affy]

value: DMSO

value: control

value: e


title: liver rep3

description:
liver-3
replicate 3

value: male


title: malignant mesothelioma, Y-MESO-12

value: malignant meshelioma

value: normal mesothelial cells


title: heart rep1

description:
heart-1
replicate 1

value: 7 weeks


title: malignant mesothelioma, NCI-H290

description: Biological replicate 3 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: JNKi_batch2_e [Affy]


title: malignant mesothelioma, ACC-MESO-4

description: Biological replicate 2 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: mesothelium (peritoneum) rep3

description:
mesothelium (peritoneum)-3
replicate 3

value: mesothelium (peritoneum)


title: malignant mesothelioma, NCI-H2052

description: Biological replicate 4 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: JNKi_batch1_b [Affy]

value: b


title: malignant mesothelioma, ACC-MESO-1

description: Biological replicate 1 of 20. malignant mesothlioma cell lines, harvested after several passages.


title: JNKi_batch2_c [Affy]

value: c


title: DMSO_batch2_d [Affy]


title: lung rep2

description:
lung-2
replicate 2


title: DMSO_batch1_a [Affy]


title: bladder rep3

description:
bladder-3
replicate 3

value: bladder


title: DMSO_batch2_c [Affy]


title: DMSO_batch1_b [Affy]


title: heart rep3

description:
heart-3
replicate 3


title: B1

status: Public on Dec 17 2011

city: blacksburg

first: rujuan

last: dai

state: VA

address: 1410 price fork RD

department: CMMID

institute: virginia Tech

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating  Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: The data processing began with background subtraction using a regression-based background mapping method and then normalization using Variance Stabilization Normalization (VSN) method (VSN was done in three groups(each group contain 8 samples): W and BW, MRL and Mlpr, B and Blpr). The normalized data were log2 transformed for further statistical analysis by using LIMMA program in R language (R2.10). The generated raw p-values were corrected by the Benjamini and Hochberg false-discovery rate test.

source_name: whole splenocytes

label_protocol: The assay started from 5 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA, containing miRNA, was isolated from whole splenocytes using mirVana miRNA isolation kits (Ambion) following manufactory’s instructions.

value: whole splenocytes

tag: gender

value: female


title: B2


title: blpr-4


title: blpr-1


title: Mlpr-4

value: MRL/MpJ-Faslpr/J


title: B3


title: B4


title: Mlpr-3


title: blpr-3


title: Mlpr-2


title: DU-145 control VPA 2 days  versus DU-145 control VPA 4 days

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

hyb_protocol: Fragmentation was carried out by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility by incubating at 60 degrees Celsius for 30 minutes and stopped by adding equal volume of 2x hybridization buffer (Agilent Technologies). Fragmented targets were added on 22 human 1Av2 Microarrays (Agilent Technologies). The microarrays were assembled into a hybridization chamber (Agilent Technologies) and hybridized at 60 degrees Celsius for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol. For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

scan_protocol: Microarrays were scanned by the Sidney Kimmel Comprehensive Cancer Center Microarray Core Facility with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micometer resolutions. Data was extracted using Feature Extraction Software version 8.1 (Agilent Technologies). For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

data_processing: Loess

label_protocol: Total RNA (1 microgram) was reverse transcribed into first- and second-strand cDNA by MMLV-RT using an oligo(dT) primer that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and cyanine-labeled CTPs. The labeled cRNA was purified using RNeasy mini kit (Qiagen) and followed by quantification on both concentrations of cRNA and dye labeled. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification and labeled according to manufacturer’s protocol. In total, 0.75 mircrogram of each sample labeled with Cy3 or Cy5 was mixed with control targets (Agilent Technologies). For target fragmentation, hybridization, and scanning, the experiment was split evenly into three distinct batches.

growth_protocol: DU-145 control VPA 2 days

extract_protocol: Total RNA was isolated from DU-145 and PC3 cells using a combination of TRIzol and RNeasy Kit (Qiagen), with slight modifications to manufacturer's protocols. Briefly, cells were harvested in TRIzol. After addition of chloroform and centrifugation, the aqueous phase was separated. This was ~50% of the initial TRIzol volume. Next, an equal volume of 70% ethanol was added to the supernatant. Because the final alcohol concentration now was only 30%, the RNA did not precipitate. The mixture was then passed through RNeasy column and further purification carried out according to the manufacturer's instructions. A DNase step was also included to ensure removal of any contaminating DNA.

treatment_protocol: DU-145 and PC3 cells were plated and treated with RPMI 1640 medium (Life Technologies), with and without addition of HDAC inhibitors. Vorinostat (SAHA) was obtained from Aton Pharma/Merck, and Valproic acid (VPA) from Sigma-Aldrich)

tag: cell line

tag: treatment

value: Control VPA

tag: time

value: 2 days

growth_protocol: DU-145 control VPA 4 days

value: 4 days


title: DU-145 VPA treated 4 days versus DU-145 VPA treated 2 days

growth_protocol: DU-145 VPA treated 4 days

value: VPA treated

growth_protocol: DU-145 VPA treated 2 days


title: DU-145 VPA treated 2 days versus DU-145 control VPA 2 days


title: MRL-4

value: MRL/MpJ


title: Mlpr-1


title: MRL-3


title: DU-145 VPA treated 2 days versus DU-145 SAHA treated 2 days

growth_protocol: DU-145 SAHA treated 2 days

value: SAHA treated


title: DU-145 control SAHA 2 days versus DU-145 SAHA treated 2 days

growth_protocol: DU-145 control SAHA 2 days

value: Control SAHA


title: MRL-2


title: PC3 VPA treated 2 days versus PC3 VPA treated 4 days

growth_protocol: PC3 VPA treated 2 days

growth_protocol: PC3 VPA treated 4 days


title: DU-145 control VPA 4 days  versus DU-145 VPA treated 4 days


title: BW4


title: MRL-1


title: 4hr_C57_Air_42_aorta

description:
4844850024_B
replicate 2

value: Air


title: BW3


title: PC3 SAHA treated 4 days versus DU-145 SAHA treated 4 days

growth_protocol: PC3 SAHA treated 4 days

growth_protocol: DU-145 SAHA treated 4 days


title: BW2


title: DU-145 SAHA treated 2 days versus DU-145 SAHA treated 4 days


title: PC3 control VPA 2 days versus PC3 VPA treated 2 days

growth_protocol: PC3 control VPA 2 days


title: W4

value: NZW/LacJ


title: W3


title: BW1


title: PC3 VPA treated 4 days versus PC3 control VPA 4 days

growth_protocol: PC3 control VPA 4 days


title: W2


title: 28d_C57_Air_57_aorta

description:
4844850027_A
replicate 1


title: PC3 SAHA treated 2 days versus PC3 control SAHA 2 days

growth_protocol: PC3 SAHA treated 2 days

growth_protocol: PC3 control SAHA 2 days


title: PC3 SAHA treated 2 days versus PC3 VPA treated 2 days


title: W1


title: PC3 SAHA treated 4 days versus PC3 SAHA treated 2 days


title: PC3 VPA treated 2 days versus DU-145 VPA treated 2 days


title: DU-145 VPA treated 4 days versus PC3 VPA treated 4 days


title: PC3 control VPA 4 days versus PC3 control VPA 2 days


title: PC3 control SAHA 4 days versus PC3 SAHA treated 4 days

growth_protocol: PC3 control SAHA 4 days


title: DU-145 control SAHA 4 days versus DU-145 control SAHA 2 days

growth_protocol: DU-145 control SAHA 4 days


title: DU-145 SAHA treated 2 days versus PC3 SAHA treated 2 days


title: PC3 control SAHA 2 days versus PC3 control SAHA 4 days


title: MIXED_MMTV_T121_WAPCre_p53coco_113291_SIMIN

city: Worcester

first: Karl

last: Simin

state: MA

address: 364 Plantation St.

institute: UMass Medical School

hyb_protocol: The amplified sample and reference were co-hybridized overnight to Agilent Mouse Oligo Microarrays (G4121A) according the manufacturer's protocol.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner.

data_processing: Image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software. Data for both channels were Lowess-normalized and then log(2) ratio was taken.

source_name: Mouse reference

label_protocol: Two micrograms of total RNA was reverse transcribed, amplified and labeled using the Low RNA Input Amplification kit (Agilent).

extract_protocol: Total RNA was purified from 20-30 mg tissue of end-stage tumors using the Qiagen RNeasy Mini Kit according to the manufacturer’s protoco.

tag: reference

value: Whole mouse total RNA

tag: test

value: mammary tumor


title: DU-145 SAHA treated 4 days versus DU-145 control SAHA 4 days


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_144543_SIMIN


title: MIXED_WAPCre_p53coco_Brca1coco_130619_SIMIN


title: S.LEW(10)x12x2x3x5  2

city: Toledo

first: Bina

last: Joe

state: OH

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array.

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

data_processing: The data were analyzed with R statistical package (version 2.8.1).

organism: Rattus norvegicus

source_name: S.LEW(10)x12x2x3x5 Congenic Rat  fed with Low-salt (0.3%) diet

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

growth_protocol: All rats born on the same day were selected and weaned at 30 days of age.

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

treatment_protocol: After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).

tag: genetic background

value: S.LEW(10)x12x2x3x5 Congenic

tag: tissue

value: Kidney

tag: genotype

value: Congenic rat with Dahl S background

value: 53 days old

value: low salt diet

value: male


title: MIXED_MMTV_T121_WAPCre_p53coco_690_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_144532_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_135537_SIMIN


title: Dahl S Rat 1

source_name: Dahl S Rat fed with Low-salt (0.3%) diet

value: Dahl S

value: Dahl salt sensitive rat


title: Dahl S Rat 3


title: S.LEW(10)x12x2x3x5  3


title: S.LEW(10)x12x2x3x5  1


title: Dahl S Rat 2


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_144542_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_130370_SIMIN


title: Th17 ex vivo day 15, replicate 2, 2hr stim

city: Bethesda

first: Steven

last: Kern

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

description: Expression data from TRP1 Th17 cells recovered 15 days after adoptive cell transfer, restimulated for 2 hours.

hyb_protocol: 1.8 ug of labeled and fragmented SS DNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST arrays , following the Affymetrix protocol. GeneChips arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console using default settings for median polish RMA summarization and Sketch-Quantile as the normalization method.

label: Biotin

source_name: TRP1 Th17 cells ex vivo day 15 2hr stim

label_protocol: The Ambion WT  Expression kit was used for the synthesis of cDNA. 150 ng of total RNA were utilized as starting material following the manufacturer's protocol.  cDNA was labeled with the Affymetrix GeneChip® WT Terminal Labeling Kit.

growth_protocol: TRP1 cells were stimulated with irradiated (30 Gy) C57/B6 splenocytes pulsed with TRP1 peptide  (1µM) added at a 10:1 ratio. Th1 polarization was performed in the presence of 3.33 ng/ml of IL-12 (Peprotech) and 10µg/ml of anti-IL-4 (eBioscience).  Th17 polarization was performed in the presence of IL-1 (10ng/ml, Peprotech), IL-6 (30ng/ml, R&D or Peprotech), IL-21 (100ng/ml), TGFβ2 (5ng/ml, R&D), anti-IL-2 (10µg/ml), anti-IL-4 (10µg/ml), anti-IFN-γ (10µg/ml). All antibodies were purchased from eBioscience. After 72 hours, media containing IL-2 was added and the polarizing cytokines were repleted. Th17 cultures were also supplemented with IL-23 (5ng/ml, R&D).

extract_protocol: Total RNA was obtained using the RNeasy kit (Qiagen) following the manufacturer's protocols. Total RNA concentration was measured by nanodrop and total RNA quality was evaluated by Bioanalyzer.

treatment_protocol: Th1 and Th17 polarized cells (Thy1.2+) were transferred into sublethaly irradiated (5Gy) B6.PL (Thy1.1+) mice. On indicated days, spleens and inguinal lymph nodes were harvested. TRP1 cells were recovered by CD4 enrichment (Millteny) and sorted by FACS for the expression of Thy1.2. Samples were divided in half and one part was stimulated in vitro with aCD3/aCD28 for 2 hours.

tag: strain

value: BwTRP1 Rag1-/-

tag: polarization

tag: growth condition

value: ex vivo

tag: time after adoptive transfer

value: day 15

value: spleen,inguinal lymph node

value: TRP1 CD4+ T cells

value: 2hr stimulation with CD3/aCD28


title: mesothelium (plaura and pericardium) rep3

description:
mesothelium (plaura and pericardium)-3
replicate 3

tag: Sex

tag: age

value: 7 weeks

value: mesothelium (plaura and pericardium)


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_133574_SIMIN

value: Whole mouse total RNA

value: mammary tumor


title: Th17 ex vivo day 15, replicate 3, 2hr stim

tag: cell type


title: Th17 ex vivo day 15, replicate 1, 2hr stim


title: MIXED_MMTV_T121_WAPCre_p53coco_81728_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_130615_SIMIN


title: Th17 ex vivo day 15, replicate 4, 2hr stim


title: blpr-2

value: whole splenocytes

value: female


title: MIXED_MMTV_T121_MMTVCre_p53cohet_89747_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53cohet_85152_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53cococ_101371_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_130381_SIMIN


title: MIXED_MMTV_T121_WAPCre_p53coco_Brca1coco_130371_SIMIN


title: Th17 ex vivo day 15, replicate 3

description: Expression data from TRP1 Th17 cells recovered 15 days after adoptive cell transfer.

source_name: TRP1 Th17 cells ex vivo day 15


title: Th17 ex vivo day 15, replicate 4


title: Th1 ex vivo day 15, replicate 2, 2hr stim

description: Expression data from TRP1 Th1 cells recovered 15 days after adoptive cell transfer, restimulated for 2 hours.

source_name: TRP1 Th1 cells ex vivo day 15 2hr stim


title: Th17 day 0 in vitro, 2hr stim

description: Expression data from TRP1 Th17 cells polarized in vitro for 7 days, restimulated fro 2 hours.

source_name: TRP1 Th17 cells polarized in vitro 2hr stim

value: in vitro

value: day 0


title: Th1 ex vivo day 5, replicate 3, 2hr stim

description: Expression data from TRP1 Th1 cells recovered 5 days after adoptive cell transfer, restimulated for 2 hours.

source_name: TRP1 Th1 cells ex vivo day 5 2hr stim

value: day 5


title: Th1 ex vivo day 5, replicate 2, 2hr stim


title: Th17 ex vivo day 15, replicate 2


title: Th17 ex vivo day 5, replicate 2, 2hr stim

description: Expression data from TRP1 Th17 cells recovered 5 days after adoptive cell transfer, restimulated for 2 hours.

source_name: TRP1 Th17 cells ex vivo day 5 2hr stim


title: Th1 ex vivo day 5, replicate 1, 2hr stim


title: Control 2 H02-1060906073

city: Houston

first: Margarita

last: Bonilla

state: TX

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

hyb_protocol: Phalanx Hybridization Protocol (http://www.phalanxbiotech.com/)

scan_protocol: Scanned by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  Normalized intensities were computed using One-Array(V2.5)-software.

source_name: Control

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

extract_protocol: Dissected E11.5 mandibles were placed in RNAlater for tissue stabilization. Total RNA was then extracted using the RNeasy Micro Kit (Qiagen) and optical density was measured by NanoDrop ND-1000, Agilent RNA 6000 Nano Assay and agarose electrophoresis.

tag: background strain

tag: genotype/variation

value: wild-type

tag: developmental stage

value: whole embryonic mandible


title: Th1 ex vivo day 15, replicate 1, 2hr stim

value: BwTRP1 Rag1-/-

tag: treatment


title: Mixed_TgMFT121_TgWAPCRE_p53coco_749_678_Malini


title: B6D2F1_WAP_T121_p53null_KS50_SIMIN


title: Th17 ex vivo day 5, replicate 3, 2hr stim

value: ex vivo


title: Mixed_TgMFT21_TgWAPCre_p53coco_750_79661_Malini


title: Bmp4 OE 1 H03-1060906061

source_name: Bmp4 OE

value: conditional Bmp4 overexpression


title: Th17 ex vivo day 5, replicate 3

description: Expression data from TRP1 Th17 cells recovered 5 days after adoptive cell transfer.

source_name: TRP1 Th17 cells ex vivo day 5

value: spleen,inguinal lymph node


title: B6D2F1_WAP_T121_p53het_KS601_SIMIN


title: Th1 ex vivo day 15, replicate 1

description: Expression data from TRP1 Th1 cells recovered 15 days after adoptive cell transfer.

source_name: TRP1 Th1 cells ex vivo day 15

value: day 15

value: TRP1 CD4+ T cells


title: BALBc_WAP_T121_KS592_SIMIN


title: Bmp4 OE 2 H04-1060906062


title: untreated pool vs LY-364947 replicate 2

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

state: MO

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

description: Biological replicate 2 of 3, 48 hpf embryos treated with 40 microM LY-364947 vs untreated pool, dye swap.

hyb_protocol: The paired and balanced aRNAs were suspended in Agilent Gene Expression buffer, Agilent Blocking agent, and Kreablock.  The hybridization solutions were applied to Agilent Zebrafishv2 4x44K microarrays.  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Arrays were scanned on a Molecular Devices-Axon 4000B scanner to detect Cy3 and Cy5 fluorescence.

data_processing:
Images were quantitated using Genepix v6.1.
Data was imported into Partek Genomoics Suite. Missing data was set to a constant of 27RFU.  M-values were generated by Loess normalization.  Dye swap effects was removed using Remove Batch Effect function.

organism: Danio rerio

label_protocol: 3ug of aRNA was labeled with Kreatech ULS cy3 or cy5.  Following column cleanup, labeled aRNAs were quantified, paired (2ug each sample), and fragmented with Ambion Fragmentation reagent.

growth_protocol: Wild type (strain Ab) fertilized eggs were obtained by timed mating.

extract_protocol: 10-15 embryos for each biological replicate were homogenized at 48 hpf in Trizol and total RNA was extracted, quantified, and qualified on Agilent Bioanalyzer.  Control total RNA samples were pooled, then all samples were subjected to T7 linear amplification (Ambion MessageAmp).

treatment_protocol: Embryos were treated with 40 microM LY-364947 in chemical screening medium starting 8 hpf through 48 hpf. Untreated embryos served as controls.

value: whole embryo

source_name: untreated pool

value: untreated pool


title: Th17 ex vivo day 5, replicate 1, 2hr stim

value: 2hr stimulation with CD3/aCD28


title: Th1 day 0 in vitro, 2hr stim

description: Expression data from TRP1 Th1 cells polarized in vitro for 7 days, restimulated for 2 hours.

source_name: TRP1 Th1 cells polarized in vitro 2hr stim


title: Control 1 H01-1060906072


title: U19/EAF2 knockout ventral prostates

first: Fei

last: Su

address: 3605 Cullen Blvd

institute: university of houston

description: Gene expression data from ventral prostate

hyb_protocol: Following fragmentation, 15-20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the HP ChipScanner (Affymetrix).

data_processing: The data were analyzed with GeneChip Operating Software, GCOS v1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 3-month-old male mouse, ventral prostate

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

extract_protocol: Trizol extraction of total RNA was performed following RNeasy Mini Kit QIAGEN Cat # 74104 according to the manufacturer's instructions. RNA quality and quantity were measured with spectrophotometry.

value: ventral prostate


title: Th1 ex vivo day 5, replicate 1

description: Expression data from TRP1 Th1 cells recovered 5 days after adoptive cell transfer.

source_name: TRP1 Th1 cells ex vivo day 5


title: B6D2F1_WAP_T121_p53null_KS593_SIMIN

source_name: Mouse reference

value: Whole mouse total RNA

value: mammary tumor


title: Th17 ex vivo day 5, replicate 2


title: control MO pool vs slc2a10 MO replicate 2

description: Biological replicate 2 of 3, 48 hpf embryos treated with 7.5ng of slc2a10 MO vs 5ng of control MO pool, dye swap.

source_name: slc2a10 MO

growth_protocol: Wild type (strain Ab) fertilized eggs were used for MO injections.

treatment_protocol: 7.5 ng of MO directed against the donor splice site of exon 2 (CAAATAAAGTCCACTTACTTGGT) of slc2a10 was injected into each embryo. 5 ng of control MO (CCTCTTACCTCAGTTACAATTTATA) was injected into a different set of embryos. Embryos were maintained at 28 degrees C up to 48 hours post fertilization, slc2a10 MO treated embryos were sorted for the presence of a recognizable (Class 1) phenotype.

value: slc2a10 MO

source_name: control MO pool

value: control MO pool


title: Th17 ex vivo day 5, replicate 1

value: day 5


title: Th17 ex vivo day 15, replicate 1


title: Th1 ex vivo day 5, replicate 2


title: Wild-type ventral prostates


title: Th1 ex vivo day 5, replicate 3


title: Normal sample, 413

status: Public on Dec 16 2011

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was performed in a rotating oven overnight at 57 degrees C. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Data were Lowess normalized.

source_name: endoscopic biopsy, normal healthy

label_protocol: The total RNAs containing the microRNAs were labeled using the miRCURY™ LNA microRNA Array Power Labeling kit (Exiqon Inc, Woburn, MA).  The 3’-end of the total RNA was enzymatically labeled with the Hy3 and/or Hy5 fluorescent dye (Exiqon) by incubation with T4 RNA ligase for 1 hr, and the labeled RNA was hybridized onto the microarrays without the need for column purification.

growth_protocol: Endoscopic biopsies.

extract_protocol: Total RNA was extracted using TRIzol. Tissues were homogenized in 1ml of TRIzol reagent per 100 mg tissue using Qiagen Tissuelyzer. 0.2 ml of chloroform was added to 1 ml TRIzol. Sample was vortexed for 15 secs, and centrifuged for 15 minutes at 10,000 rpm to separate the aqueous phase from the organic phase. The aqueous phase was transferred to a fresh tube and precipitated with 0.5 ml of isopropanol per 1.0ml TRIzol added to tissue. Sample was incubated at room temperature for 10 minutes and centrifuged at 10,000 rpm for 10 minutes. The pellet was washed with 75% ethanol once, and air-dried. The dry pellet was resuspended in water prior to analysis by the Agilent Bioanalyzer for RNA integrity.

treatment_protocol: Pre- and post-cisplatin/fluorouracil treatment.

value: normal stomach

source_name: Pooled gastric cell lines

tag: sample type

value: reference RNA


title: Th1 ex vivo day 15, replicate 2

value: BwTRP1 Rag1-/-


title: Normal sample, 416


title: Normal sample, 423


title: Normal sample, 409


title: Normal sample, 434


title: Normal sample, 404


title: Normal sample, 435


title: LY-364947 replicate 1 vs untreated pool

description: Biological replicate 1 of 3, 48 hpf embryos treated with 40 microM LY-364947 vs untreated pool.


title: Normal sample, 433


title: Normal sample, 455


title: slc2a10 MO replicate 1 vs control MO pool

description: Biological replicate 1 of 3, 48 hpf embryos treated with 7.5ng of slc2a10 MO vs 5ng of control MO pool.


title: LY-364947 replicate 3 vs untreated pool

description: Biological replicate 3 of 3, 48 hpf embryos treated with 40 microM LY-364947 vs untreated pool.


title: Normal sample, 401


title: Normal sample, 436


title: slc2a10 MO replicate 3 vs control MO pool

description: Biological replicate 3 of 3, 48 hpf embryos treated with 7.5ng of slc2a10 MO vs 5ng of control MO pool.


title: Th17 day 0 in vitro

description: Expression data from TRP1 Th17 cells polarized in vitro for 7 days.

source_name: TRP1 Th17 cells polarized in vitro

value: in vitro

value: day 0


title: Normal sample, N6


title: Normal sample, N5


title: Normal sample, N467


title: Normal sample, N459


title: Normal sample, N25


title: Normal sample, N453


title: Normal sample, N21


title: Normal sample, N3


title: Normal sample, 454


title: Normal sample, N24


title: Normal sample, N8


title: Normal sample, N9


title: Normal sample, N7


title: Th1 day 0 in vitro

description: Expression data from TRP1 Th1 cells polarized in vitro for 7 days.

source_name: TRP1 Th1 cells polarized in vitro


title: Normal sample, N20


title: Normal sample, N17


title: Normal sample, N19


title: Normal sample, N11


title: Normal sample, N16


title: Normal sample, N10


title: Normal sample, N022


title: Normal sample, N14


title: Normal sample, N018


title: Posttreatment sample, R225

source_name: endoscopic biopsy, post-treatment

value: gastric cancer

value: cisplatin/fluorouracil chemotherapy


title: Normal sample, N13


title: Posttreatment sample, R219


title: Posttreatment sample, R197


title: Mo17 endosperm rep 2

type: genomic

city: St. Paul

first: Steve

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description:
Sample 5
processed data : fit.Mo17_endo_c.05-12-11.txt

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the 2.1M arrays according to the array manufacturer protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix4000B Scanner (Axon/Molecular Devices) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent MeDIP enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Smyth, 2004). The following contrasts were then fit: B73 IP vs B73 input and  Mo17 IP vs (Mo17 input vs B73 input). Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05.

molecule: genomic DNA

organism: Zea mays

source_name: Mo17 Rep 2 Endosperm input

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the 2.1M feature array and washed according to the array manufacturers protocol.  Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

extract_protocol: Genomic DNAs were extracted using the Qiagen DNeasy Plant Mini Kit.  10ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps).  Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

treatment_protocol: genomic DNAs were sonicated, amplified, and fluorophore-labeled

tag: cross date

value: Endosperm

source_name: Mo17 Rep 2 Endosperm methylated DNA IP

treatment_protocol: genomic DNAs were sonicated, methylated DNAs were isolated, amplified and fluorophore-labeled

tag: ip antibody vendor

tag: ip antibody

value: Zymo Research


title: Mo17 endosperm rep 1

description:
Sample 4
processed data : fit.Mo17_endo_c.05-12-11.txt

source_name: Mo17 Rep 1 Endosperm input

tag: tissue

source_name: Mo17 Rep 1 Endosperm methylated DNA IP


title: Mo17 endosperm rep 3

description:
Sample 6
processed data : fit.Mo17_endo_c.05-12-11.txt

source_name: Mo17 Rep 3 Endosperm input

tag: genotype

source_name: Mo17 Rep 3 Endosperm methylated DNA IP


title: Pretreatment gastric cancer sample, 630

source_name: endoscopic biopsy, cancer


title: Pretreatment gastric cancer sample, 604


title: Posttreatment sample, R138


title: Posttreatment sample, R91


title: Pretreatment gastric cancer sample, 601


title: Pretreatment gastric cancer sample, 614


title: Posttreatment sample, R63


title: Posttreatment sample, R67


title: Posttreatment sample, R43


title: Pretreatment gastric cancer sample, 613


title: Pretreatment gastric cancer sample, 368


title: Pretreatment gastric cancer sample, 238


title: Pretreatment gastric cancer sample, 237_0


title: Pretreatment gastric cancer sample, 383


title: Pretreatment gastric cancer sample, 10


title: Pretreatment gastric cancer sample, 37


title: Pretreatment gastric cancer sample, 188_0


title: Pretreatment gastric cancer sample, 3_0


title: Pretreatment gastric cancer sample, 220_0


title: Pretreatment gastric cancer sample, 179_0


title: Pretreatment gastric cancer sample, 129_0


title: WBC sample 133 (anti-acetyl Histone H3)

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

hyb_protocol: Hybridizations were performed for 18h.

scan_protocol: Slides were scanned using an Axon 4000B scanner. Images were quantified using the SpotReader software.

data_processing: Background intensities given by the SpotReader software were subtracted from foreground intensities. The vsn method (W. Huber et al.; Bioinformatics 2002;18 Suppl 1:S96-104) was then applied for single color normalization of the green (ChIP) channel across all arrays. A model with 48 strata per array according to the print-tips was used. Probes that were flagged by the Spotreader software in more than 25% of the samples as well as empty/blank probes were excluded from the estimation of the model’s parameters. The quantile that is used for the least trimmed sum of squares regression was set to 0.75. After parameter estimation, vsn transformation was applied to all probes. All computations were done within the R-package vsn (ver. 3.18.0).

source_name: pooled AML blasts

label_protocol: DNA was amplified in 2 steps, including a T7 sequenase extension using random primer with a fixed sequence linker and a second step of amplification using the fixed sequence primer and Taq polymerase. The products were purified and labeled with amino-allyl-conjugated dUTP using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) and random primer. Products were purified and crosslinked with monofunctional NHS-ester Cy3 or Cy5 dye.

extract_protocol: DNA was extracted and sonicated to an average DNA length of 500 bp.

value: pooled AML blasts

source_name: white blood cells

extract_protocol: 2.0E+07 cells were fixed with formaldehyde, neutralized with glycine, and rinsed with cold phosphatate-buffered saline. After lysis of the cells, samples were sonicated to an average DNA length of 500 bp. Immunoprecipitation of 0.5 mg precleared chromatin was carried out by addition of 3 ug of the following antibodies: anti-acetylated Histone H3, anti-HDAC1 and anti-H3K9me3 (all antibodies obtained from Upstate Biotechnology). Only the anti-acetylated Histone H3 data is presented here. At least 2 independent ChIPs were performed for each cell line and antibody.

value: white blood cells

tag: diagnosis

value: WBC

tag: antibody

value: anti-acetylated Histone H3 (Upstate Biotechnology)


title: CD34+ sample 135 (anti-acetyl Histone H3)

source_name: CD34+ progenitor cells

value: CD34+ progenitor cells


title: WBC sample 134 (anti-acetyl Histone H3)


title: CD34+ sample 128 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 69_0


title: Pretreatment gastric cancer sample, 85_0


title: Pretreatment gastric cancer sample, 98


title: CD34+ sample 130 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 80_0


title: WBC sample 127 (anti-acetyl Histone H3)


title: CD34+ sample 131 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 66_0


title: CD34+ sample 122 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 211


title: WBC sample 132 (anti-acetyl Histone H3)


title: WBC sample 123 (anti-acetyl Histone H3)


title: AML sample 108 (anti-acetyl Histone H3)

source_name: AML blasts

value: AML blasts

value: AML

tag: gender

value: female


title: WBC sample 112 (anti-acetyl Histone H3)


title: CD34+ sample 111 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 65_0


title: Pretreatment gastric cancer sample, 121_0


title: Pretreatment gastric cancer sample, 44_0


title: CD34+ sample 124 (anti-acetyl Histone H3)


title: WBC sample 125 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 34_0


title: Pretreatment gastric cancer sample, 28


title: AML sample 121 (anti-acetyl Histone H3)


title: AML sample 107 (anti-acetyl Histone H3)

value: male


title: Pretreatment gastric cancer sample, 23_0

value: reference RNA


title: Pretreatment gastric cancer sample, 56_0


title: WBC sample 104 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 29_0


title: AML sample 105 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 132_0


title: WBC sample 103 (anti-acetyl Histone H3)


title: AML sample 102 (anti-acetyl Histone H3)


title: WBC sample 099 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 208_0


title: Pretreatment gastric cancer sample, 242_0


title: Pretreatment gastric cancer sample, 251_0


title: Pretreatment gastric cancer sample, 26


title: AML sample 101 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 187


title: Pretreatment gastric cancer sample, 260_0


title: AML sample 096 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 262_0


title: Pretreatment gastric cancer sample, 173_0


title: AML sample 097 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 162_0


title: Pretreatment gastric cancer sample, 74


title: AML sample 094 (anti-acetyl Histone H3)


title: AML sample 095 (anti-acetyl Histone H3)


title: CD34+ sample 098 (anti-acetyl Histone H3)


title: AML sample 093 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 45


title: AML sample 091 (anti-acetyl Histone H3)


title: AML sample 092 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 47_0


title: Pretreatment gastric cancer sample, 393


title: AML sample 089 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 399


title: AML sample 085 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 391s


title: WBC sample 088 (anti-acetyl Histone H3)


title: AML sample 090 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 12


title: Pretreatment gastric cancer sample, 49_0


title: Pretreatment gastric cancer sample, 6


title: Pretreatment gastric cancer sample, 361r


title: CD34+ sample 083 (anti-acetyl Histone H3)


title: WBC sample 078 (anti-acetyl Histone H3)


title: AML sample 082 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 35


title: WBC sample 084 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 341


title: CD34+ sample 077 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 309


title: AML sample 081 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 308


title: Pretreatment gastric cancer sample, 310


title: AML sample 080 (anti-acetyl Histone H3)


title: AML sample 079 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 307s


title: Pretreatment gastric cancer sample, 267c


title: WBC sample 076 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 268s


title: AML sample 072 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 265c


title: AML sample 086 (anti-acetyl Histone H3)


title: AML sample 073 (anti-acetyl Histone H3)


title: AML sample 074 (anti-acetyl Histone H3)


title: AML sample 071 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 256


title: Pretreatment gastric cancer sample, 266c


title: WBC sample 070 (anti-acetyl Histone H3)


title: WBC sample 068 (anti-acetyl Histone H3)


title: CD34+ sample 067 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 243


title: AML sample 066 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 230


title: Pretreatment gastric cancer sample, 236


title: Pretreatment gastric cancer sample, 250


title: AML sample 064 (anti-acetyl Histone H3)


title: AML sample 062 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 244


title: CD34+ sample 069 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 249


title: CD34+ sample 061 (anti-acetyl Histone H3)


title: AML sample 059 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 191


title: AML sample 065 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 229


title: Pretreatment gastric cancer sample, 197_0


title: Pretreatment gastric cancer sample, 222


title: Pretreatment gastric cancer sample, 221


title: Pretreatment gastric cancer sample, 225c


title: Pretreatment gastric cancer sample, 181


title: CD34+ sample 063 (anti-acetyl Histone H3)


title: AML sample 050 (anti-acetyl Histone H3)


title: AML sample 052 (anti-acetyl Histone H3)


title: AML sample 056 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 138s


title: AML sample 057 (anti-acetyl Histone H3)


title: AML sample 054 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 145_0


title: Pretreatment gastric cancer sample, 160


title: AML sample 060 (anti-acetyl Histone H3)


title: AML sample 053 (anti-acetyl Histone H3)


title: AML sample 045 (anti-acetyl Histone H3)


title: AML sample 049 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 70_0


title: Pretreatment gastric cancer sample, 79


title: Pretreatment gastric cancer sample, 50_0


title: Pretreatment gastric cancer sample, 54_0


title: AML sample 046 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 91_0


title: AML sample 044 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 67


title: Pretreatment gastric cancer sample, 43_ob


title: Pretreatment gastric cancer sample, 41_0


title: Pretreatment gastric cancer sample, 33_0


title: AML sample 041 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 30_0


title: Pretreatment gastric cancer sample, 219c


title: Pretreatment gastric cancer sample, 24_0


title: AML sample 043 (anti-acetyl Histone H3)


title: AML sample 038 (anti-acetyl Histone H3)


title: AML sample 032 (anti-acetyl Histone H3)


title: AML sample 035 (anti-acetyl Histone H3)


title: AML sample 042 (anti-acetyl Histone H3)


title: AML sample 037 (anti-acetyl Histone H3)


title: Pretreatment gastric cancer sample, 63


title: AML sample 039 (anti-acetyl Histone H3)


title: AML sample 028 (anti-acetyl Histone H3)


title: AML sample 034 (anti-acetyl Histone H3)


title: AML sample 036 (anti-acetyl Histone H3)


title: AML sample 030 (anti-acetyl Histone H3)


title: AML sample 027 (anti-acetyl Histone H3)


title: AML sample 024 (anti-acetyl Histone H3)


title: TS cell, 50 nM TSA, rep2

city: Rockland

first: Benjamin

middle: L

last: Kidder

address: 1 Technology Place

department: Reproductive Health

institute: EMD Serono Research Institute

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 50 nM Trichostatin A, biological rep-2

hyb_protocol: 13 µg of aRNA were hybridized for 16 hr at 45 deg C on Affymetrix mouse 430 v2.0 microarrays. GeneChips were washed and stained using an Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000 7G

data_processing: CEL files were loaded into ArrayAssist (Stratagene, La Jolla, CA) and probes were normalized using the GC-RMA algorithm.  ANOVA was performed on all groups using a Benjamini and Hochberg FDR correction.  Genes whose expression differed by at least 2-fold between any two groups with a P-value less than 5 % were considered differentially expressed.

source_name: RNA from TS cells

label_protocol: 13 µg biotinylated aRNA were prepared using a MessageAmpTM Premier RNA Amplification kit (Ambion) protocol from 100 ng total RNA.

growth_protocol: ES cells and TS cells were grown on feeder-free dishes for 2 passages to remove iMEFs

extract_protocol: Total RNA was isolated from ES cells and TS cells cultured in the presence of 0 nM, 10 nM, 50 nM, or 100 nM Trichostatin A for 24 hours using an RNeasy Mini Kit (Qiagen, Valencia, CA).  For each duplicate biological replicate, 100 ng of RNA was amplified using a MessageAmpTM Premier RNA Amplification kit (Ambion), and 13 µg of fragmented aRNA was hybridized to Affymetrix mouse 430 v2.0 microarrays.

treatment_protocol: ES cells and TS cells were cultured in the presence of 0 nM, 10 nM, 50 nM, or 100 nM Trichostatin A (TSA) for 24 hours.

value: trophoblast stem cell

tag: cell origin

value: E3.5 blastocyst

tag: genetic background

value: 50 nM TSA


title: AML sample 031 (anti-acetyl Histone H3)

tag: age


title: AML sample 026 (anti-acetyl Histone H3)


title: TS cell, 100 nM TSA, rep2

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 100 nM Trichostatin A, biological rep-2

tag: cell type

value: 100 nM TSA


title: CD34+ sample 025 (anti-acetyl Histone H3)


title: AML sample 023 (anti-acetyl Histone H3)


title: AML sample 022 (anti-acetyl Histone H3)


title: AML sample 019 (anti-acetyl Histone H3)


title: TS cell, 50 nM TSA, rep1

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 50 nM Trichostatin A, biological rep-1


title: TS cell, 100 nM TSA, rep1

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 100 nM Trichostatin A, biological rep-1


title: TS cell, 0 nM TSA, rep2

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 0 nM Trichostatin A, biological rep-2

value: 0 nM TSA


title: TS cell, 10 nM TSA, rep2

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 10 nM Trichostatin A, biological rep-2

value: 10 nM TSA


title: AML sample 012 (anti-acetyl Histone H3)


title: ES cell, 100 nM TSA, rep2

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 100 nM Trichostatin A, biological rep-2

source_name: RNA from ES cells

value: embryonic stem cell


title: AML sample 021 (anti-acetyl Histone H3)

value: pooled AML blasts


title: TS cell, 0 nM TSA, rep1

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 0 nM Trichostatin A, biological rep-1


title: AML sample 018 (anti-acetyl Histone H3)


title: AML sample 016 (anti-acetyl Histone H3)


title: ES cell, 100 nM TSA, rep1

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 100 nM Trichostatin A, biological rep-1


title: AML sample 011 (anti-acetyl Histone H3)


title: AML sample 013 (anti-acetyl Histone H3)


title: ES cell, 50 nM TSA, rep2

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 50 nM Trichostatin A, biological rep-2


title: ES cell, 10 nM TSA, rep1

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 10 nM Trichostatin A, biological rep-1


title: AML sample 007 (anti-acetyl Histone H3)


title: TS cell, 10 nM TSA, rep1

description: Gene expression data from undifferentiated TS cells treated for 24 hrs with 10 nM Trichostatin A, biological rep-1


title: ES cell, 10 nM TSA, rep2

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 10 nM Trichostatin A, biological rep-2


title: AML sample 017 (anti-acetyl Histone H3)


title: AML sample 006 (anti-acetyl Histone H3)


title: ES cell, 0 nM TSA, rep2

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 0 nM Trichostatin A, biological rep-2


title: AML sample 010 (anti-acetyl Histone H3)


title: AML sample 009 (anti-acetyl Histone H3)


title: ES cell, 50 nM TSA, rep1

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 50 nM Trichostatin A, biological rep-1


title: AML sample 003 (anti-acetyl Histone H3)


title: CD34+ sample 002 (anti-acetyl Histone H3)


title: ES cell, 0 nM TSA, rep1

description: Gene expression data from undifferentiated ES cells treated for 24 hrs with 0 nM Trichostatin A, biological rep-1


title: CD34+ sample 004 (anti-acetyl Histone H3)


title: MLL_00134

description: AML with normal karyotype, molecular analyses performed for BCOR mutations

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: mononuclear cells after Ficoll purification

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: untreated samples

tag: disease

tag: bcor mutation

value: BCOR mutation

tag: karyotype

value: normal karyotype


title: Sv.1

city: Stockholm

first: Therese

last: Hogfeldt

address: Cancer Centre Karolinska, R:8

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Hybridization to Affymetrix Human GeneChip U133 Plus 2.0 (Affymetrix, Santa Clara, CA, USA) was performed according to Affymetrix manuals with some modifications recommended by Nugen Technologies. The hybridization cocktail was heated at 99°C for 2 minutes and the hybridization time was 18 hours. The arrays were washed and stained with Streptavidin-Phycoerythrin (SAPE) (Molecular Probes Inc., Eugene, OR, USA) in an Affymetrix fluidics station.

scan_protocol: The arrays were scanned in an Affymetrix scanner and the expression values for each probe set were estimated using the Affymetrix Microarray Suite Software (MAS v5.0).

data_processing: The MAS5.0 signal values were imported into the GeneSpring 7.0 software tool (Silicon Genetics, Redwood City, CA, USA) to determine genes with significant differential expression.

source_name: Diffuse Large B-cell Lymphoma, Swedish

label_protocol: Fragmentation and labeling of amplified cDNA (4μg) was performed using FL-ovation cDNA biotin module V2 (Nugen Technologies, Inc.). All incubations were made using the thermal cycler: #1294, Techne Progene Peltier Thermal cycler (Scientific Support, Inc.). In brief, the cDNA was fragmented using fragmentation buffer and fragmentation enzyme mix during incubation at 37°C for 30 minutes followed by 95°C for 2 minutes. The fragments were labeled using labeling buffer mix, labeling reagent and labeling enzyme mix. The reaction was carried out at 37°C for 60 minutes followed by 70°C for 10 minutes.

extract_protocol: Extraction of RNA from FFPE material with Ambion RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems/Ambion, Austin, TX, USA) was successfully performed following the manufacturer’s instructions. RNA samples were stored at -80°C until amplification. The RNA was eluted in 30µl RNase free water. Yield and quality was measured using Nanodrop Technologies ND 1000 (Wilmington, Delaware, USA). Amplification of extracted RNA (100ng) was performed using WT-ovation FFPE RNA amplification system V2 (Nugen Technologies, Inc., San Carlos, CA, USA). All incubations were made using the thermal cycler: #1294, Techne Progene Peltier Thermal cycler (Scientific Support, Inc, Hayward, CA, USA). The purification step was made using Beckman Coulter’s Agencourt RNA Clean purification beads (Beckman Coulter, Fullerton, CA, USA). The amplified cDNA was purified using Zymo research DNA Clean & Concentrator kit (Orange, CA, USA). The yield and quality was measured using Nanodrop.

tag: disease state

value: Activated B-cell-like Diffuse Large B-cell Lymphoma (ABC DLBCL)

value: formalin-fixed and paraffin-embedded (FFPE) ABC DLBCL

tag: geographic region

value: Sweden


title: Sv.2


title: MLL_00124

value: AML


title: Eg.3

source_name: Diffuse Large B-cell Lymphoma, Egyptian

value: Egypt


title: MLL_00127


title: MLL_00133


title: Sv.3


title: Eg.1


title: MLL_00128


title: MLL_00126


title: MLL_00125


title: MLL_00131


title: Eg.2


title: MLL_00129


title: MLL_00123


title: MLL_00135

value: wild-type


title: MLL_00122


title: TP30-1

city: Huntsville

first: Devin

last: Absher

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Genomic DNA extracted from blood was genotyped using Infinium Human660W Quad Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genotypes and other intensity data were called and exported with Illumina GenomeStudio software

label: C-Bio and A-DNP

source_name: Blood DNA

label_protocol: 500ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA was extracted from peripheral blood with QIAGEN kits

value: female


title: MLL_00119


title: MLL_00120


title: TP12-2

value: male


title: MLL_00117


title: MLL_00116


title: MLL_00112


title: MLL_00113


title: MLL_00114


title: MLL_00118


title: LM2-miR126-B

first: Nils

last: Halberg

address: 1230 York Avenue

institute: Rockefeller University

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: The data were normalized to the median

source_name: Breast Cancer Cell Line

label_protocol: Standard Affymetrix Protocol

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extraced using the miRVana Kit (Ambion)

tag: cell line

tag: expression

value: miR-126 Over-expression


title: MLL_00115


title: LM2 control-B

value: Control


title: MLL_00110


title: MLL_00107


title: HDAC1_ESC_Genome_mm8_1

description: HDAC1 ESC ChIP biological replicates 1-3

hyb_protocol: 5 μg of DNA was hybridzed to Affymetrix mouse 1.0R tiling arrays array using the Affymetrix hybridization kit.  Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

data_processing:
Data was quantile normalized and analyzed using TileMap. Log2 (IP/Input) fold change values (fc) and TileMap moving average (ma) statistics were reported in BAR files.
fc.bar and ma.bar files were generated using CisGenome software. fc.bar files contain log2 (IP/Input) fold change values for each probe. ma.bar files contain a moving average statistic for each probe.

source_name: ChIP DNA from ES cells

label_protocol: Samples were enzymatically fragmented using DNase and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol: ChIP-chip experiments were performed as previously described with minor modifications (Kidder and Palmer 2010).  The polyclonal HDAC1 (ab7028) antibody was obtained from Abcam.  Briefly, 1 X 10^8 mouse ES cells (R1) and TS cells (TSC-BK12) (all feeder-free) were harvested and chemically crosslinked with 1 % formaldehyde (Sigma) for 20 hours at 4oC and subsequently sonicated.  Sonicated cell extracts equivalent to 2 X 10^6 cells were used for immunoprecipitation assays.  5 μg amplified ChIP-enriched DNA (ES cell HDAC1-ChIP and TS cell HDAC1-ChIP, and corresponding Input whole cell extracts for ES cells and TS cells) was DNase treated, labeled, and hybridized to Affymetrix mouse promoter 1.0R tiling arrays.  Mouse promoter 1.0R DNA tiling arrays contain 4.6 million 25-mer oligonucleotide probes spanning a distance of -6kb to +2.5kb relative to the transcriptional start site for 28,000 mouse promoter regions, providing a resolution of 35 bp with 10 bp gaps between probes.  At least three biological replicates were used for each ChIP-chip analysis.  Quantile normalization, including probe intensity computation and log2 adjustment, was applied to the tiling array data using CisGenome.  Peak detection and gene annotation were performed as previously described (Kidder et al. 2009).  Briefly, peak detection was performed using the TileMap application in CisGenome.  MA statistics was applied to analyze the tiling array data.  Post filtering included discarding peaks if the total length was less than 100 bp, or if there were less than 3 continuous probes passing the cutoff, and merging two adjacent peaks if the gap between the two peaks was less than 300 bp and if there were less than 5 probes that did not pass the cutoff between the two peaks.  Peaks with an FDR less than 0.10 were also discarded.  Enrichment peaks were annotated with the closest gene using build 36 of the mouse genome.

value: ES cell

tag: source

value: E3.5 blastocyst

tag: strain

tag: antibody catalog #

tag: antibody manufacturer

value: Abcam

source_name: Input DNA from ES cells


title: MCF-7 cells with miR-9 transfection

city: Columbus

first: Pei-Yin

last: Hsu

address: BRT836, 460W 12th Ave

institute: OSU

description: Gene expression data from the miR-9 transfectant

hyb_protocol: cRNA were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays

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

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

source_name: MCF-7 cells

tag: tissue

value: breast cancer cell line

tag: genotype

value: ERa-positive

tag: treatment

value: miR-9 transfection


title: MCF-7 cells with miR-9* transfection

description: Gene expression data from the miR-9* transfectant

value: miR-9* transfection


title: HDAC1_TSC_Genome_mm8_1

description: HDAC1 TSC ChIP biological replicates 1-3

source_name: ChIP DNA from TS cells

value: TS cell

tag: antibody

source_name: Input DNA from TS cells


title: LM2-miR126-A


title: MLL_00111

value: normal karyotype


title: Bifidobacterium breve UCC2003 1 hr exposure to 0.15 % ox-gall

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing:
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 ratios from a single array experiment.
Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

organism: Bifidobacterium breve UCC2003

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 1. Sterile water was added with the same volume as the ox-gall in the target sample and growth was continued for 1 hr.

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: growth stage

value: exponential

source_name: Bifidobacterium breve UCC2003 grown in MRS exposed to 0.15 % ox-gall for 1hr

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.06 % cholic acid. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 1. Ox-gall was added at a concentration of 0.15 % and growth was continued for 1 hr.


title: TP25-2

tag: gender

tag: age


title: B. breve UCC2003 0.3 % ox-gall stress

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

source_name: Bifidobacterium breve UCC2003 grown in MRS with 0.3 % ox-gall

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.3% ox-gall. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5


title: LM2 control-A


title: B. breve UCC2003 0.06 % cholic acid growth stress

source_name: Bifidobacterium breve UCC2003 grown in MRS with 0.06 % cholic acid

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.06 % cholic acid. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5


title: Bifidobacterium breve UCC2003 1 hr exposure to 0.06 % cholic acid

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 1. Sterile water was added with the same volume as the cholate in the target sample and growth was continued for 1 hr.

source_name: Bifidobacterium breve UCC2003 grown in MRS exposed to 0.06% cholic acid for 1hr

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.06 % cholic acid. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 1. Cholic acid was added at a concentration of 0.06 % and growth was continued for 1 hr.


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat maternally nutrient restricted_9073

city: Baton Rouge

first: Yourka

last: Tchoukalova

state: LA

address: 6400 Perkins Road

institute: Penninton BioMedical Research Center

description: pooled RNA from triplicate wells

hyb_protocol: Hybridization to the Sentrix HumanRef-6 Expression BeadChip version 2 (Illumina, Inc., San Diego, CA) using IntelliHyb Seal system was performed.  However, the 'Sentrix HumanRef-6 Expression BeadChip version 2' is discontinued and embedded in the new and currently only one available version GPL6947 "Illumina HumanHT-12 V3.0 expression beadchip".

scan_protocol: Scanning was performed at the intensity of factor 1 using Illumina® BeadStation Scanner. The raw intensity values obtained for the scanned array images were compiled using the proprietary BeadStudio version 2.0 software provided by Illumina.

data_processing: Signal intensities across microarrays were normalized using the quantile method (www.bioconductor.org). Detection Pval = likelihood that probe quantile signal is greater than negative controls; values less than 0.05 deemed present.

organism: Papio

label_protocol: Biotinylated cRNA was prepared using the Illumina® Total Prep RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer's directions starting with ~100 ng total RNA.

growth_protocol: Fetal baboon adipose-derived stem cells were isolated after collagenase digestion, cultured in 10% fetal bovine serum in αMEM until they reach confluence, and frozen. Cells were thawed, seeded in triplicate in 6-well plates, grown to confluence, and harvested for RNA. The RNA from the three wells were pooled into 1 sample.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA)  and cleaned using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA).  Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Adipose tissue samples were collected from baboon fetuses from mothers fed ad libitum or 30% nutrient restricted diet theoughout all pregnancy at 165dG (term - 184dG).

tag: developmental stage

value: fetus

tag: cells

value: Adipose-derived stem cells

value: subcutaneous femoral fat

tag: diet

value: maternally nutrient restricted condition-mother was nutrient globally restricted throughout all pregnancy by 30%


title: DU145N 24h withHGF

city: Rotterdam

first: Guido

last: Jenster

department: Urology

institute: Erasmus MC

description: expression data of HGF/cMET pathway in prostate cancer DU145 cell line

hyb_protocol: Hybridization to Affymetrix Human U133plus2.0 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were performed as described by Affymetrix (Affymetrix, Santa Clara, CA, USA), and performed by Erasmus MC Center for Biomics.

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

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

source_name: DU145 cells 24 hours with 25 ng/ml HGF

label_protocol: 5 μg of total RNA from stimulated and control samples was used to prepare antisense biotinylated RNA according to manufacturer’s one-cycle protocol (Affymetrix, Santa Clara, CA, USA)

growth_protocol: DU145 were seeded overnight in RPMI/ FCS medium. After 1 day, medium was replaced by RPMI medium containing 5% Dextran Charcoal treated (DCC).

extract_protocol: RNA was isolated using RNAzol B reagent. After standard RNA isolation with chloroform, isopropanol and ethanol, DNA was digested using DNA-free kit. RNA quality and quantity was measured with the RNA 6000 Nano kit on a 2100 Bioanalyzer. Samples with RNA integrity numbers of >8.5 were selected.

treatment_protocol: One day after medium replacement, DU145 prostate cancer cells were treated with 25 ng/ml hepatocyte growth factor (HGF) or vehicle for 2, 8, or 24 hours.

tag: time point

value: 24 hours

tag: agent

value: 25 ng/ml HGF

value: In vitro prostate cancer DU145 cell line


title: DU145N 8h withHGF

source_name: DU145 cells 8 hours with 25 ng/ml HGF

value: 8 hours

tag: cell line


title: DU145N 2h withHGF

source_name: DU145 cells 2 hours with 25 ng/ml HGF

value: 2 hours


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat maternally nutrient restricted_9073

description: pooled RNA from triplicate wells

value: female

value: subcutaneous abdominal fat


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat maternally nutrient restricted_9075

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal omenal fat maternally nutrient restricted_9073

description: pooled RNA from triplicate wells

value: omental fat


title: DU145N 24h noHGF

source_name: DU145 cells 24 hours with vehicle

value: vehicle


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat control_8009

description: pooled RNA from triplicate wells

source_name: subcutaneous femoral fat control

value: control condition-mother was fed ad libitum


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat control_8009

description: pooled RNA from triplicate wells

source_name: subcutaneous abdominal fat control


title: DU145N 8h noHGF

source_name: DU145 cells 8 hours with vehicle


title: DU145N 2h noHGF

source_name: DU145 cells 2 hours with vehicle


title: Adipose-derived stem cells from baboon fetal omenal fat control_8009

description: pooled RNA from triplicate wells

source_name: omenal fat control


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat maternally nutrient restricted_9075

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal omenal fat maternally nutrient restricted_9075

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal omenal fat control_8011

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal omenal fat maternally nutrient restricted_2820

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat control_8011

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat control_8011

description: pooled RNA from triplicate wells


title: Preimmune_2

type: protein

description: Serum for ProtoArray hybridization was derived from an immuno-competent male nude (nu/+) BALB/c mouse before immunization (annotated as preimmune_2)

hyb_protocol: ProtoArrays were developed according to the protocol of the manufacturer. In short, after blocking, arrays were incubated with serum 1:500 diluted in PBS with 1% BSA and 0.1% Tween. After 90 minutes at 4ºC, arrays were washed and incubated with Alexa Fluor 647 rabbit anti-mouse IgG (H+L) (Invitrogen) 1:2000 diluted in PBS-Tween with 1% BSA for 90 minutes at 4ºC.

scan_protocol: After washing, arrays were dried and immediately scanned in a ScanArray Express HT (Perkin Elmer, The Netherlands). Laser power was set at 60%.

data_processing: Spot intensities were quantified using Prospector Imager (version 4.0, Invitrogen) and ProtoArray Prospector (version 4.0.0, Invitrogen). Spot background was subtracted from spot signal to calculate the Value.

label: Alexa Fluor 647

molecule: protein

source_name: Pre-Immunization

label_protocol: Alexa Fluor 647 rabbit anti-mouse or rabbit anti-human IgG (H+L)  were purchased from Invitrogen.

extract_protocol:
Prior to tumor inoculation, control serum was collected by retro-orbital punction.
After immunization, mice were sacrificed and serum was collected.

treatment_protocol: For immunization, mice were subcutaneously injected with 100 µl of a mixture of 10 µg serum and 50 µl complete Freund’s adjuvant. After 3 weeks a boost-immunization was performed with a mixture of 10 µg serum and 50 µl incomplete Freund’s adjuvant. Four weeks after the last boost-immunization, mice were sacrificed and serum was collected. The protocol was approved by the Animal Experiments Committee under the national Experiments on Animals Act and adhered to the rules laid down in this national law that serves the implementation of “Guidelines on the protection of experimental animals” by the council of Europe under Directive 86/609/EC.

value: male

value: nude (nu/+) BALB/c

tag: immunization

value: Pre-Immunization


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat maternally nutrient restricted_2820

description: pooled RNA from triplicate wells

value: fetus


title: Adipose-derived stem cells from baboon fetal omenal fat control_9087

description: pooled RNA from triplicate wells

value: Adipose-derived stem cells


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat control_9087

description: pooled RNA from triplicate wells

value: subcutaneous femoral fat


title: PC346_immunized_full

description: Serum for ProtoArray hybridization was derived from a immuno-competent male nude (nu/+) BALB/c mouse that was immunized with full serum from a PC346 xenografted mice (annotated as PC346_immunized_full)

source_name: Immunization with full serum from PC346 xenografted mice


title: Control_immunized

description: Serum for ProtoArray hybridization was derived from an immuno-competent male nude (nu/+) BALB/c mouse that was immunized with a pool (n=2) of serum depleted for abundant proteins from nude mice and boosted with serum from the same animals (annotated as preimmune_1)

source_name: Immunization with serum from nude mice

value: Immunization with serum from nude mice


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat maternally nutrient restricted_2820

description: pooled RNA from triplicate wells

value: maternally nutrient restricted condition-mother was nutrient globally restricted throughout all pregnancy by 30%


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat control_9087

description: pooled RNA from triplicate wells


title: PC346_immunized_depleted_full

description: Serum for ProtoArray hybridization was derived from an immuno-competent male nude (nu/+) BALB/c mouse that was immunized with a pool (n=3) of serum depleted for abundant proteins from PC346 xenografted mice and boosted with full serum from the same xenografted animals (annotated as PC346_immunized_depleted_full).

source_name: Immunization with serum depleted for abundant proteins and full serum from PC346 xenografted mice

treatment_protocol: For immunization, mice were subcutaneously injected with 100 µl of a mixture of 10 µg serum and 50 µl complete Freund’s adjuvant. After 3 weeks a boost-immunization was performed with a mixture of 10 µg serum and 50 µl incomplete Freund’s adjuvant. After 6 weeks a second boost-immunization with full serum derived from PC346 bearing mice was performed. Four weeks after the last boost-immunization, mice were sacrificed and serum was collected. The protocol was approved by the Animal Experiments Committee under the national Experiments on Animals Act and adhered to the rules laid down in this national law that serves the implementation of “Guidelines on the protection of experimental animals” by the council of Europe under Directive 86/609/EC.


title: Preimmune_1

description: Serum for ProtoArray hybridization was derived from an immuno-competent male nude (nu/+) BALB/c mouse before immunization (annotated as preimmune_1)


title: Adipose-derived stem cells from baboon fetal omenal fat maternally nutrient restricted_9085

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat maternally nutrient restricted_9085

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal subcutaneous femoral fat control_9017

description: pooled RNA from triplicate wells


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat maternally nutrient restricted_9085

description: pooled RNA from triplicate wells


title: MDS, 5q- Syndrome

hyb_protocol: according to the standard Affymetrix SNP 6.0 method protocol

data_processing: Using Genotyping Console version 3.0.1 (Affymetrix) according to the default settings for the "Copy Number / LOH Configuration" except for "Smoothing Gaussian Window". It was set to 5000 instead of 50000 and the "Smooth Log2 ratio" was selected instead of "Calibrate Smooth Log2 ratio to CN".

source_name: untreated patient at diagnosis

extract_protocol: Qiagen DNA extraction kit (QIAamp DNA Mini Kit; 51306); elution buffer was 10mM Tris, 0.1mM EDTA, pH 8.0

treatment_protocol: none; samples were obtained from untreated patients at diagnosis

tag: disease

value: MDS, 5q- Syndrome

value: bone marrow

value: small 12p deletions


title: PC346_immunized_depleted

description: Serum for ProtoArray hybridization was derived from a immuno-competent male nude (nu/+) BALB/c mouse that was immunized with a pool (n=3) of serum depleted for abundant proteins from PC346 xenografted mice (annotated as PC346_immunized_depleted).

source_name: Immunization with serum depleted for abundant proteins from PC346 xenografted mice


title: Adipose-derived stem cells from baboon fetal omenal fat control_9017

description: pooled RNA from triplicate wells


title: PC339_immunized_depleted_full

description: Serum for ProtoArray hybridization was derived from an immuno-competent male nude (nu/+) BALB/c mouse that was immunized with a pool (n=3) of serum depleted for abundant proteins from PC339 xenografted mice and boosted with full serum from the same xenografted animals (annotated as PC339_immunized_depleted_full).

source_name: Immunization with serum depleted for abundant proteins and full serum from PC339 xenografted mice

treatment_protocol: For immunization, mice were subcutaneously injected with 100 µl of a mixture of 10 µg serum and 50 µl complete Freund’s adjuvant. After 3 weeks a boost-immunization was performed with a mixture of 10 µg serum and 50 µl incomplete Freund’s adjuvant. After 6 weeks a second boost-immunization with full serum derived from PC339 bearing mice was performed. Four weeks after the last boost-immunization, mice were sacrificed and serum was collected. The protocol was approved by the Animal Experiments Committee under the national Experiments on Animals Act and adhered to the rules laid down in this national law that serves the implementation of “Guidelines on the protection of experimental animals” by the council of Europe under Directive 86/609/EC.


title: MDAtr-A

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

source_name: Breast Cancer Cell line

label_protocol: Standard Illumina Protocol

extract_protocol: Total RNA was extracted using the Mirvana kit from Ambion.  Quality control was performed with Agilent Bioanalyser

tag: tumor type

value: Poorly Metastatic


title: MDAtr-B


title: PC339_immunized_depleted

description: Serum for ProtoArray hybridization was derived from a immuno-competent male nude (nu/+) BALB/c mouse that was immunized with a pool (n=3) of serum depleted for abundant proteins from PC339 xenografted mice (annotated as PC339_immunized_depleted).

source_name: Immunization with serum depleted for abundant proteins from PC339 xenografted mice


title: LM2tr-B

value: Highly Metastatic


title: PC339_immunized_full

description: Serum for ProtoArray hybridization was derived from a immuno-competent male nude (nu/+) BALB/c mouse that was immunized with full serum from a PC339 xenografted mice (annotated as PC339_immunized_full)

source_name: Immunization with full serum from PC339 xenografted mice


title: Osteomyelofibrosis

scan_protocol: according to the standard Affymetrix SNP 6.0 method protocol

value: Osteomyelofibrosis

value: peripheral blood


title: s-AML

label_protocol: according to the standard Affymetrix SNP 6.0 method protocol

value: s-AML


title: Adipose-derived stem cells from baboon fetal subcutaneous abdominal fat control_9017

description: pooled RNA from triplicate wells

value: subcutaneous abdominal fat

value: control condition-mother was fed ad libitum


title: Striatum_T1D_rep3

status: Public on Dec 15 2011

city: Budapest

first: Omar

last: Abdul-Rahman

address: Tüzoltó utca 37-47

department: Department of Medical Chemistry, Molecular Biology and Pathobiochemistry

country: Hungary

institute: Semmelweis University

description: Gene expression after 4 weeks treatment with streptozotocin (65mg/kg iv.)

hyb_protocol: 1650 ng of cRNA were hybridized to Agilent’s Rat Whole GenomeCustom Arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Hybridized arrays were imaged with Agilent’s Microarray Scanner in the extended dynamic range at 100% and 10% laser beam intensities at a resolutionof 5 μm.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters protocol GE1-v5_91_0806.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1000 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions. Dye incorporation was controlled by a Nanodrop spectrophotometer; all samples were labeled with an efficiency of 10.2 – 17.5 pmol Cy3/μg cRNA.

growth_protocol: Experiments were performed on ten-week old male rats (weighing 286±60g). Rats were kept in a room with constant temperature (20°C), humidity and a 12-hour light-dark cycle, and were allowed to free access to standard chow and water.

extract_protocol: Excised tissue samples were immediately fixed in RNA later RNA stabilization reagent (Qiagen, Valencia, CA). Total RNA was extracted from samples by homogenization using the RNeasy Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. RNA integrity and purity were checked both by agarose gel electrophoresis and with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo scientific, Wilmington, DE). Samples of acceptable quality fulfilled the following criteria: OD260/280>1.8, OD260/230>1.8 and RIN>7.

treatment_protocol: 10 week old male Wistar rats (n=9) served as control animals in our experiments.  6 weeks old male Wistar rats were rendered diabetic via tail vein injection of STZ (n=9)  (65 mg/kg iv, Sigma Chemical Co.) dissolved in 0.1M citrate buffer (pH 4.5)and served as models of type 1 diabetes mellitus. Only STZ-treated animals with plasma glucose concentrations above 15 mmol/L were considered diabetic and included in the study. 10 week old Goto Kakizaki rats (n=9)  were used as a model of type 2 diabetes mellitus. Animals were anaesthetized by an intraperitoneal injection of pentobarbital sodium (5 mg /100 g body weight), then killed by decapitation.

value: male

value: 10 week

tag: brain region

value: Striatum

tag: strain

value: Wistar

tag: average blood sugar [mmol/l]

tag: disease state

value: type 1 diabetes


title: Striatum_T1D_rep2


title: AML (2)

value: AML

tag: tissue

tag: genotype


title: MDS CMML-1

value: MDS CMML-1


title: PrefrontalCortex_T1D_rep2

tag: gender

value: Prefrontal cortex


title: LM2tr-A


title: Striatum_T1D_rep1

tag: age


title: Panc05.04

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: CA

address: 555 MISSION BAY SOUTH BLVD RM 282 # 3118

department: Pathology and Dermatology

institute: University of California San Francisco

description: Common reference pool consists of genomic DNA from 8 normal individuals.

hyb_protocol: Agilent factory protocols.

scan_protocol: Agilent G2505C Microarray Scanner.

data_processing: Lowess normalization using Agilent Feature Extraction Software.

source_name: Tumor DNA, cell line

label_protocol: Genomic DNA was digested with DpnII, randomly primed, and labeled with direct Cy dye-incorporated molecules.

growth_protocol: Xenografts were established as described: B. Rubio-Viqueira et al., Clin Cancer Res 12, 4652-61, Aug 1, 2006 (PMID: 16899615). Cell lines were grown under the recommended conditions of ATCC.

extract_protocol: DNA/RNA Allprep Kit (Qiagen 80204).

tag: sample source

value: cell line

tag: tissue derivation

value: pancreatic tumor

value: pancreatic ductal adenocarcinoma (PDAC)

source_name: Common reference

value: normal


title: 472

source_name: Tumor DNA, xenograft

value: xenograft


title: 443


title: JH102


title: PrefrontalCortex_T1D_rep3


title: 302


title: JH82


title: Hippocampus_T1D_rep3

value: Hippocampus


title: JH39


title: JH131


title: Hippocampus_T1D_rep2


title: Striatum_Control_rep3

source_name: Striatum_Wistar rat_replicate3


title: Striatum_Control_rep1

source_name: Striatum_Wistar rat_replicate1


title: Hippocampus_T1D_rep1


title: PrefrontalCortex_T1D_rep1


title: Striatum_Control_rep2

source_name: Striatum_Wistar rat_replicate2


title: 480


title: JH166


title: PrefrontalCortex_Control_rep2

source_name: PrefrontalCortex_Wistar rat_replicate2


title: PrefrontalCortex_Control_rep3

source_name: PrefrontalCortex_Wistar rat_replicate3


title: Hippocampus_Control_rep3

source_name: Hippocampus_Wistar rat_replicate3


title: 486


title: JH161


title: JH51


title: Hippocampus_Control_rep1

source_name: Hippocampus_Wistar rat_replicate1


title: Hippocampus_Control_rep2

source_name: Hippocampus_Wistar rat_replicate2


title: JH127


title: 475


title: Striatum_T2D_rep2

source_name: Striatum_Goto-Kakizaki rat_replicate2

value: Goto-Kakizaki

value: type 2 diabetes


title: AML M6a

source_name: untreated patient at diagnosis

value: AML M6a

value: bone marrow

value: small 12p deletions


title: JH171


title: PrefrontalCortex_T2D_rep3

value: male

value: 10 week


title: Striatum_T2D_rep3

source_name: Striatum_Goto-Kakizaki rat_replicate3

value: Striatum


title: Hs766T


title: PrefrontalCortex_Control_rep1

source_name: PrefrontalCortex_Wistar rat_replicate1

value: Wistar


title: 440


title: PrefrontalCortex_T2D_rep2


title: 235


title: PrefrontalCortex_T2D_rep1


title: Striatum_T2D_rep1

source_name: Striatum_Goto-Kakizaki rat_replicate1


title: JH29


title: Hippocampus_T2D_rep3


title: Hippocampus_T2D_rep2


title: 479


title: AML (1)

value: AML

value: peripheral blood


title: 340/USLAM

description: Genomic DNA extracted from blood was genotyped using Infinium Human1MDuo Genotyping BeadChips (Illumina).

source_name: Blood DNA


title: 470


title: 102/USLAM


title: Hippocampus_T2D_rep1


title: Aspc1

source_name: Tumor DNA, cell line

value: cell line


title: Panc8.13

value: pancreatic tumor

source_name: Common reference


title: 341

source_name: Tumor DNA, xenograft

value: pancreatic ductal adenocarcinoma (PDAC)


title: Panc3.27

value: normal


title: Capan1


title: CFPAC1