title: CD18hypo C57BL/6J

city: Shanghai

first: Yan

last: Sha

state: Shanghai

address: South Rd chongqing 280

department: Shanghai Institute of Immunology

institute: Shanghai jiao tong university

description: microRNA expression data from CD18hypo C57BL/6J mouse

hyb_protocol: 81.7ul Hybridization components were added into the labeled miRNA, following hybridized for 16 hr at 48C on GeneChips miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Affymetrix GeneChip Command Console1.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
The data were analyzed with Affymetrix miRNA-qc-tool

label_protocol: Biotinylated miRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (MiRNA expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were kept under specific pathogen-free(SPF) conditions and euthanized by CO2 inhalation.

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

treatment_protocol: Epidermis samples from affected ears derived from 3 CD18hypo PL/J mice or normal ears derived from 3 CD18hypo C57BL/6J mice were pooled together for RNA extraction.

tag: genotype

value: CD18hypo C57BL/6J

value: Female

value: ear epidermis


title: OsAPC6 mutant replicate 2

status: Public on Dec 31 2013

type: RNA

city: Roorkee

first: Anjali

last: Awasthi

state: Uttarakhand

address: Department of Biotechnology

department: Biotechnology

country: India

institute: Indian Institute of Technology Roorkee

description: Gene expression profile of mutant OsAPC6.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

label: biotin

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: Seedling 15 days after germination

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Grown under optimal rice growing conditions

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

tag: cultivar

value: Basmati 370

tag: genotype/variation

value: T-DNA insertional mutant OsAPC6


title: CD18hypo PL/J

country: China

description: microRNA expression data from CD18hypo PL/J mouse model of psoriasis

organism: Mus musculus

source_name: PL/J

value: CD18hypo PL/J

tag: gender

tag: tissue


title: B370 wild replicate 2

description: Gene expression profile of wild B370.

value: Wild type


title: Rice seedlings, control1, rep1

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

description: Gene expression data from control rice seedlings

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files were imported into Genespring software and probe summarization and normalization was performed using GCRMA algorithm

label: Biotin

organism: Oryza sativa

source_name: control rice seedlings

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

growth_protocol: Rice seedlings were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were incubated in water (control) or 50 µM solution of indole-3-acetic acid (auxin, IAA) and benzyl aminopurine (cytokinin, BAP) and 100 µM solution of abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ethylene derivative, ACC), salicylic acid (SA) and jasmonic acid (JA) for 3h

tag: subspecies

value: indica

tag: variety

value: Seedlings

tag: Stage


title: HeLa(Exp4_Rep2_shCDK6 clone_0h arrested_G0-G1)

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried out exactly as recommended in: “One-Color Microarray-Based Gene Expression Analysis Protocol V5.7” (Agilent Technologies, March 2008) except that 3 μg of each labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on an Agilent microarray scanner G2505B at two PMT settings (100 % and 5 %) to increase the dynamic range of the measurements according to the extended dynamic range mode (samples M2791-M2822). Microarray samples M3954-M4069 were scanned on the upgraded Agilent Micro ArrayScanner G2565 CA (pixel resolution 5 μm, bit depth 20).

data_processing: Data extraction was performed with the “Feature Extraction Software V9.5.3.1” by using the default extraction protocol file “GE1-v5_95_Feb07.xml” (M2791-M2822). For microarrays that were scanned with the upgraded Scanner (M3954-M4069) data extraction was performed with the “Feature Extraction Software V10.7.3.1” by using the extraction protocol file “GE1_107_Sep09.xml”. Resulting single channel raw data were further processed in GeneSpring GX software, version 12.0 (Agilent Technologies Inc., Santa Clara, CA). Raw data were imported and log2-transformed according to the recommended default procedure and were subsequently quantile normalized.

organism: Homo sapiens

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the “Quick Amp Labeling kit, one color” (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: HeLa cells were subjected to cell cycle arrest at G0-G1 by serum deprivation for 48 hs (arrested_G0-G1). Thereafter, cells were released for 6 hs by addition of 20% serum (released_G0-G1). In a different set of experiments HeLa cells were subjected for 48 hs to cell cycle arrest at late G1 by thymidine/aphidicoline treatment (arrested_G1-S). Thereafter, cells were released for 6 hs from the thymidine/aphidicoline block (released_G1-S).

extract_protocol: Total RNA was prepared with RNeasy Mini Kit (Qiagen).

treatment_protocol: HeLa cells were treated with Interleukin 1-alpha (10ng/ml) for 30 min or were left untreated.

tag: cell line

value: HeLa

tag: treatment

tag: cell cycle transition

tag: cell cycle state

value: arrested

tag: genotype state

value: CDK6 kd


title: HeLa(Exp4_Rep1_shCDK6 clone_6h released_G0-G1)

value: released


title: HeLa(Exp4_Rep2_shCDK6 clone_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp4_Rep2_shCDK6 clone_0h arrested_G0-G1) 0.5h IL1a


title: W45-ox-2

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and software G2565BA using default parameters

data_processing: The scanned images were analyzed with Feature Extraction software (version 9.1; Agilent Technologies)  using default parameters.

source_name: 4th leaves at 4-leaf stage

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies)

extract_protocol: Total RNA was isolated using Trizol and cleaned up with an RNeasy plant mini kit (Qiagen).

value: 4th leaves at 4-leaf stage


title: W45-ox-3


title: HeLa(Exp4_Rep1_shCDK6 clone_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp4_Rep1_shCDK6 clone_0h arrested_G0-G1)


title: HeLa(Exp4_Rep1_shCDK6 clone_6h released_G0-G1) 0.5h IL1a


title: Nipponbare-1

value: Nipponbare


title: Nipponbare-2


title: W45-ox-1


title: HeLa(Exp4_Rep1_control clone_6h released_G0-G1) 0.5h IL1a

value: WT


title: HeLa(Exp4_Rep2_shCDK6 clone_6h released_G0-G1)


title: Nipponbare-3


title: HeLa(Exp4_Rep1_control clone_6h released_G0-G1)


title: HeLa(Exp3_Rep2_shCDK4 clone_6h released_G0-G1) 0.5h IL1a

value: CDK4 kd


title: HeLa(Exp3_Rep2_shCDK4 clone_6h released_G0-G1)


title: HeLa(Exp3_Rep2_control clone_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp4_Rep1_control clone_0h arrested_G0-G1)


title: HeLa(Exp3_Rep2_shCDK4 clone_0h arrested_G0-G1)


title: HeLa(Exp3_Rep2_control clone_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp3_Rep2_control clone_6h released_G0-G1)


title: HeLa(Exp4_Rep1_control clone_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp3_Rep2_shCDK4 clone_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp3_Rep1_shCDK4 clone_6h released_G0-G1)


title: HeLa(Exp3_Rep1_shCDK4 clone_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp3_Rep1_shCDK4 clone_0h arrested_G0-G1)


title: HeLa(Exp3_Rep2_control clone_0h arrested_G0-G1)


title: HeLa(Exp3_Rep1_control clone_6h released_G0-G1)


title: HeLa(Exp3_Rep1_control clone_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp3_Rep1_shCDK4 clone_0h arrested_G0-G1) 0.5h IL1a


title: WRC-QRC

city: Stanford

first: Xiangqian

last: Guo

state: CA

address: 300 Pasteur Dr.

department: Department of Pathology

country: USA

institute: Stanford University

description: 6th day

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) with 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For the two colour experiments, the ratio of the two sets of detected signals (log2 transformed, balanced), one way ANOVA for different stage miRNA profiles, and the paired t-test between WJ and RJ were calculated.

organism: Apis mellifera

source_name: worker jelly

label_protocol: The total RNA sample was size fractionated using a YM-100 Microcon centrifugal filter (from 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, two   different   tags   were   used   for   the   two   RNA  samples   in   dual-sample   experiments.

growth_protocol: We prepared three healthy colonies of “Zhenongda No.1”- a royal jelly high-yielding breed of Apis mellifera ligustica at the Huajiachi campus, Zhejiang University. In each colony, worker jelly (WJ) and royal jelly (RJ) were collected at 4-days (73~90 hrs after hatch), 5-days (97~114 hrs after hatch) and 6-days (121~138 hrs after hatch).

extract_protocol: Total RNAs were extracted from the jellies with Trizol (Invitrogen) as per the manual.

treatment_protocol: The jelly samples were collected in 50ml tubes and immediately transferred to liquid nitrogen and thereafter stored at -80°C until total RNA extraction.

tag: sample

value: worker jelly

tag: sample type

value: Fresh Frozen

tag: developmental stage

value: 6th day

source_name: royal jelly

value: royal jelly


title: HeLa(Exp3_Rep1_control clone_0h arrested_G0-G1)


title: WRB-QRB

description: 5th day

value: 5th day


title: HeLa(Exp3_Rep1_control clone_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep2_shCDK6 pool_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep2_shCDK6 pool_6h released_G0-G1)


title: HeLa(Exp2_Rep2_control pool_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep2_shCDK6 pool_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep2_control pool_0h arrested_G0-G1)


title: HeLa(Exp2_Rep2_shCDK6 pool_0h arrested_G0-G1)


title: WRA-QRA

description: 4th day

value: 4th day


title: HeLa(Exp2_Rep2_control pool_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep2_control pool_6h released_G0-G1)


title: HeLa(Exp2_Rep1_shCDK6 pool_6h released_G0-G1)


title: HeLa(Exp2_Rep1_shCDK6 pool_0h arrested_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep1_shCDK6 pool_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep1_control pool_6h released_G0-G1) 0.5h IL1a


title: HeLa(Exp2_Rep1_shCDK6 pool_0h arrested_G0-G1)


title: HeLa(Exp1_Rep2_shCDK6 pool_0h arrested_G1-S)


title: HeLa(Exp2_Rep1_control pool_0h arrested_G0-G1) 0.5h IL1a


title: Gene expression change of Streptomyces coelicolor scbR2 mutation with jadomycin addition

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

hyb_protocol: Array hybridization, washing, scanning and data analysis were carried out according to NimbleGen Expression user’s guide and performed by CapitalBio Corporation (Beijing, China). The labeled samples were dried and resuspended according to hybridization kit manual (Roche NimbleGen). The transcription arrays were hybridized on a 12-bay Hybridization System (Roche NimbleGen) at 42°C for 14h, and then washed with NimbleGen wash buffers I, II and III supplied by NimbleGen, and finally dried in NimbleGen Microarray Dryer.

scan_protocol: The arrays were scanned using MS200 scanner (NimbleGen) with 2 µm resolution.

data_processing: The probe intensities were subjected to background correction, quantile normalization, and gene expression data were generated using Robust Multi-Array Analysis algorithm as implemented in the NimbleScan Software, version 2.6 (Roche NimbleGen, Inc.).

organism: Streptomyces coelicolor

source_name: Streptomyces coelicolor M145 deleting scbR2

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Streptomyces coelicolor were cultivated at 28°C and shaken in 250 Erlenmeyer flasks containing 100 ml liquid supplemented minimum medium at 250 rpm, add jadomycin with appropriate amount.

extract_protocol: RNA was isolated by using Ambion RiboPure bacteria kit (Life Technologies, USA) according to the manufacturer’s protocol. Total RNA was purified by NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany). RNA integrity and quantity were checked by denaturing agarose gel eletrophoresis and NanoDropND-1000 spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: Cell pellets were quickly harvested by fast filtration and flash frozen in liquid nitrogen, and then ground into powder.

value: scbR2 mutation

value: jadomycin

tag: strain


title: HeLa(Exp1_Rep2_shCDK6 pool_6h released_G1-S)


title: Gene expression change of Streptomyces coelicolor M145 with jadomycin addition

source_name: Streptomyces coelicolor M145, Wild-type

tag: genotype

value: Wild-type


title: Gene expression change of Streptomyces coelicolor scbR2 mutation


title: Gene expression change of Streptomyces coelicolor M145


title: HeLa(Exp1_Rep2_shCDK6 pool_0h arrested_G1-S) 0.5h IL1a

value: HeLa


title: Global gene expression profile of Streptomyces coelicolor M145 at 48 h

description: T5-48 h has 533435A06_2012-08-07_532.pair and 533435A06_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 48 h after fermentation

growth_protocol: Streptomyces coelicolor M145 were cultivated at 28°C and shaken in 250 Erlenmeyer flasks containing 100 ml liquid supplemented minimum medium at 250 rpm.

tag: time

value: Wild type

source_name: Cells of streptomyces coelicolor harvested at 18 h after fermentation


title: Global gene expression profile of Streptomyces coelicolor M145 at 60 h

description: T6-60 h has 533435A07_2012-08-07_532.pair and 533435A07_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 60 h after fermentation


title: HeLa(Exp2_Rep1_control pool_6h released_G0-G1)


title: Global gene expression profile of Streptomyces coelicolor M145 at 42 h

description: T4-42 h has 533435A05_2012-08-07_532.pair and 533435A05_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 42 h after fermentation


title: Global gene expression profile of Streptomyces coelicolor M145 at 36 h

description: T3-36 h has 533435A04_2012-08-07_532.pair and 533435A04_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 36 h after fermentation


title: HeLa(Exp1_Rep2_shCDK6 pool_6h released_G1-S) 0.5h IL1a

value: CDK6 kd


title: HeLa(Exp2_Rep1_control pool_0h arrested_G0-G1)

value: arrested


title: HeLa(Exp1_Rep2_control pool_0h arrested_G1-S)


title: HeLa(Exp1_Rep2_control pool_6h released_G1-S) 0.5h IL1a

value: released


title: HeLa(Exp1_Rep2_control pool_0h arrested_G1-S) 0.5h IL1a


title: HeLa(Exp1_Rep1_shCDK6 pool_6h released_G1-S) 0.5h IL1a


title: HeLa(Exp1_Rep2_control pool_6h released_G1-S)


title: HeLa(Exp1_Rep1_shCDK6 pool_0h arrested_G1-S) 0.5h IL1a


title: Global gene expression profile of Streptomyces coelicolor M145 at 30 h

description: T2-30 h has 533435A03_2012-08-07_532.pair and 533435A03_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 30 h after fermentation


title: HeLa(Exp1_Rep1_control pool_6h released_G1-S) 0.5h IL1a


title: HeLa(Exp1_Rep1_shCDK6 pool_0h arrested_G1-S)


title: Global gene expression profile of Streptomyces coelicolor M145 at 24 h

description: T1-24 h has 533435A02_2012-08-07_532.pair and 533435A02_2012-08-07_635.pair

source_name: Cells of streptomyces coelicolor harvested at 24 h after fermentation


title: HeLa(Exp1_Rep1_control pool_0h arrested_G1-S) 0.5h IL1a


title: HeLa(Exp1_Rep1_shCDK6 pool_6h released_G1-S)


title: HeLa(Exp1_Rep1_control pool_6h released_G1-S)


title: HeLa(Exp1_Rep1_control pool_0h arrested_G1-S)


title: Global gene expression profile of Streptomyces coelicolor M145 at 18 h

description: T0-18 h has 533435A01_2012-08-07_532.pair and 533435A01_2012-08-07_635.pair


title: IL4_plastic_rep3

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
SAM630169
treated with IL4 on plastic

hyb_protocol: cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray G4112F.

scan_protocol: Chips were scanned using the Agilent Surescan Microarray Scanner.

data_processing: The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.

source_name: IMR90, plastic, IL4

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

growth_protocol: IMR-90 cells (ATCC, Manassas, VA; Catalog # CCL-186) were cultured in DMEM medium supplemented with 10% FBS (Sigma, St. Louis, MO; Catalog # F2442) and Penicillin/Streptomycin (Invitrogen, Carlsbad, CA; Catalog # 15140) on a bed of growth factor reduced Matrigel (GFR Matrigel, BD Biosciences, Bedford, MA; Catalog No. 354230) or plastic.

extract_protocol: RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated for 24 hours with IL-4 (10 ng/ml), IL-13 (10ng/ml), or TNFa (10 ng/ml).

tag: cell type

value: lung fibroblasts

tag: substrate

value: plastic

tag: timepoint

extract_protocol: Stratagene Universal Human Reference RNA (catalog number 740000).

value: reference


title: TNFa_plastic_rep3

description:
SAM630171
treated with TNFa on plastic

source_name: IMR90, plastic, TNFa

value: TNFa

source_name: Stratagene Universal Human Reference RNA


title: unstim_matrigel_rep3

description:
SAM630172
treated with unstim on matrigel

source_name: IMR90, matrigel, unstimulated

value: matrigel

value: unstimulated


title: SATB1 silenced Mac-1 cells replicate 2

first: Yang

last: Wang

address: No.8 Xishiku Street

department: Department of Dermatology and Venerology

institute: Peking University First Hospital

description: Biological replicate 2 of 2, SATB1 silenced Mac-1 cells, treated with sh4

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Mac-1 cells were kept in RPMI 1640 culture media supplemented with 10% heat inactivated fetal bovine serum.The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2 before transduction.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-026, Life technologies, Carlsbad, CA,US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany)

treatment_protocol: 2X10^5 cells in 1mL culture media were treated with 10uL lentivirus media with lentivirus vector harboring shRNA against SATB1. Media was changed after 24 hours and cells were kept in culture for additional 72 hours before RNA extraction. Cells transduced with lenti-vector harboring scrambled shRNA were used as controls.

value: large cell lymphoma

tag: tumor stage

value: PCALCL


title: IL13_plastic_rep2

description:
SAM630165
treated with IL13 on plastic

source_name: IMR90, plastic, IL13


title: TNFa_plastic_rep2

description:
SAM630167
treated with TNFa on plastic


title: Control Mac-1 cells replicate 2

description: Biological replicate 2 of 2, Control Mac-1 cells, with sh0 shRNA

source_name: Control Mac-1 cells, with sh0 shRNA


title: TNFa_plastic_rep1

description:
SAM630166
treated with TNFa on plastic


title: Mutant_rep_2

city: Minden

first: Hokchai

last: Yam

state: Pulau Pinang

address: Jalan Batu Uban

department: School of Biological Sciences

country: Malaysia

institute: University Sains Malaysia

description: Gene expression of ∆BPSS1356 mutant strain

hyb_protocol: Manufacturer's protocol of Agilent One-colour Microarray hybridization protocol was strictly followed. Hybridization was performed at 65 ºC for 17 hours.

scan_protocol: Array slides were scanned using Agilent Technologies Scanner model G2505B according to Agilent One-colour microarray scanning protocol.

data_processing: The resultant high resolution images were then subjected to data extraction using Agilent Feature Extraction Software. The extracted gene expression data was later analyzed using GeneSpring GX software (Agilent Technologies, USA). The raw expression data of six samples were adjusted to a threshold value of 1, a median shift normalization value of 75 percentile and a baseline transformation using median of all samples.

organism: Burkholderia pseudomallei K96243

source_name: Type strain

label_protocol: The RNA samples were subjected to poly(A) polymerization using Poly(A) Tailing Kit obtained from Epicentre (USA). The A-tailed RNA was subjected to phenol/chloroform extraction and ethanol/ammonium acetate precipitation. The One-Color Microarray-Based Gene Expression Analysis (Low input Quick Amp Labelling Kit) provided by Agilent Technologies (USA) was used in this study. A total of 200 ng poly(A)-tailed RNA sample was used as the starting amount. The RNA was reverse transcribed to cDNA and it was then subjected to in vitro transcriptional amplification in which Cyanine 3-CTP was incorporated into the resultant cRNA. The resultant cRNA sample was purified using Absolute RNA Nanoprep Kit (Stratagene, USA).

growth_protocol: Both wild type and ∆BPSS1356 mutant strains were grown using Luria Bertani broth until exponential phase with OD600 value of 1.0. A total of 1 percent overnight grown culture was used to inoculate fresh medium.

extract_protocol: Total RNA was isolated using easy-BLUE™ Total RNA Extraction Kit (Intron, Korea) following strictly the manufacturer’s protocol. The isolated RNA samples were subjected to DNAase (Superase, Ambion) treatment. The DNAse treated RNA samples were then subjected to phenol/chloroform extraction and ethanol/ammonium acetate precipitation. The integrity of RNA was determined using Bioanalyzer (Algilent, USA). The RNA samples with RIN value of 10 were as of high quality and were chosen to proceed to the next step.

treatment_protocol: Not applicable.

value: ∆BPSS1356 mutant


title: Pinellia pedatisecta vs Pinellia ternata

city: hangzhou

first: miao

last: dong

address: No.2 street

institute: Zhejiang Sci-Tech University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).  using a micro-circulation pump (Atactic Technologies).

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

data_processing: Normalizing the signals using a LOWESS filter (Locally-weighted Regression). The ratio of the two sets of detected signals (log2 transformed,balanced) and p-values of the t-test were calculated.

organism: Pinellia pedatisecta

source_name: Pinellia pedatisecta leaves

label_protocol: 2 µg total RNA samples with a poly(A) tail. An oligonucleotide tag ligated to the poly(A) tail for later fluorescent dye staining; Two different tags were used for two RNA samples in dual-sample experiments.  RNA samples in dual-sample experiments.  later fluorescent dye staining; Two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA extracted using mirVana™ miRNA Kit (Ambion, Austin, TX, USA) following manufacturer's instructions

tag: tissue

value: Leaves

tag: development stage

value: After spathe, leaf stage

organism: Pinellia ternata

source_name: Pinellia ternata leaves


title: Mutant_rep_1


title: Mutant_rep_3


title: Mouse Mammary Gland FvB Rep2

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Mouse Gene 1.0 ST arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).  For the Mouse 430A v2.0 arrays, 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Affymetrix Expression Console 1.1 was used to compute Robust Multichip average (RMA) expression values.  For the Mouse Gene 1.0 ST microarrays. The core set of probe set clusters was used with annotation version na30, dated December 2009. The dataset was imported into Matlab version R2010b (The Mathworks, Natick, MA) and one-way ANOVA was used to evaluate the significance of differential expression between biological conditions. Genes with differential expression p-value ≤ 0.01 and absolute fold change ≥ 1.25 were clustered and visualized using a clustergram heatmap.

source_name: Mouse Mammary Gland

label_protocol: Labeling for Mouse Gene 1.0 ST arrays was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.).   For 430A v2.0 arrays, the double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA.Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: No specific growth protocol

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: rtTA/CCND1 KE mutant samples underwent 7 days of doxycycline treatment

value: FvB

value: Mammary gland

tag: transgenic mouse

value: WT


title: Wildtype_rep_3

description: Gene expression of wild type strain

value: Wild type


title: IL13_plastic_rep3

description:
SAM630170
treated with IL13 on plastic

tag: cell line

tag: treatment


title: Control Mac-1 cells replicate 1

description: Biological replicate 1 of 2, Control Mac-1 cells, untreated

source_name: Control Mac-1 cells, untreated


title: Mouse Mammary Gland FvB Rep3


title: SATB1 silenced Mac-1 cells replicate 1

description: Biological replicate 1 of 2, SATB1 silenced Mac-1 cells, treated with sh2


title: Mouse Mammary Gland FvB Rep1


title: unstim_plastic_rep3

description:
SAM630168
treated with unstim on plastic

source_name: IMR90, plastic, unstimulated


title: Mammary Tumor-Cyclin D1/KE Rep3

source_name: Mouse Mammary Tumor

value: FvB/N

value: Mammary Tumor

value: MMTV-CCND/KE


title: Mammary Tumor-Cyclin D1/KE Rep2


title: unstim_plastic_rep2

description:
SAM630161
treated with unstim on plastic

value: lung fibroblasts

value: plastic


title: IL13_plastic_rep1

description:
SAM630164
treated with IL13 on plastic

value: reference


title: Wildtype_rep_1

description: Gene expression of wild type strain


title: Wildtype_rep_2

description: Gene expression of wild type strain


title: IL4_plastic_rep2

description:
SAM630163
treated with IL4 on plastic


title: HB normal liver_508

first: Rui

last: Dong

address: 399 Wan Yuan Roa

department: Department of Pediatric Surgery

institute: Children’s Hospital of Fudan University

description: LncRNA expression in HB_508N

hyb_protocol: The labeled cDNA samples were used as probes to hybridize to microarrays for 17 h at 65 °C using an Agilent Gene Expression Hybridization Kit in hybridization chamber gasket slides (Agilent).

scan_protocol: After hybridization, the microarrays were washed with an Agilent Wash Buffer kit (Agilent) and scanned with an Agilent microarray scanner.

data_processing:
The microarrays were scanned at 5 μm/pixel resolutions using an Agilent microarray scanner piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into Agilent Feature Extraction software for grid alignment and expression data analysis.
Expression data were normalized by a quantile normalization and the Robust Multichip Average (RMA) algorithm that was included in the Agilent software. Probe-level files and mRNA-level files were generated after normalization. All gene-level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed lncRNAs and mRNAs were identiﬁed through fold change ﬁltering.

source_name: Normal liver_case 8

label_protocol: Total RNA (200 ng each) from these tissue samples was reversely transcribed into cDNA using an RNA Spike In Kit with one-color (Agilent) in the presence of 0.8 μL of Random Primer and 2 μL of Spike Mix. These cDNA samples were then cleaned and labeled in accordance with the Agilent Gene Expression Analysis protocol using Low Input Quick-Amp Labeling Kit, one-color (Agilent).

extract_protocol: Total cellular RNA was isolated from the fresh primary hepatoblastoma and paired distant noncancerous tissues using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.

treatment_protocol: Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients.

tag: gender

value: Female

tag: age


title: HB normal liver_509

description: LncRNA expression in HB_509N

source_name: Normal liver_case 9


title: Mammary Tumor-Cyclin D1/WT Rep2

value: MMTV-CCND/WT


title: Mammary Tumor-Cyclin D1/WT Rep3


title: TNFa_matrigel_rep1

description:
SAM630154
treated with TNFa on matrigel

source_name: IMR90, matrigel, TNFa

value: matrigel

value: TNFa


title: TNFa_matrigel_rep3

description:
SAM630159
treated with TNFa on matrigel


title: HB tumor_508

description: LncRNA expression in HB_508C

source_name: HB tumor_case 8


title: HB tumor_502

description: LncRNA expression in HB_502C

source_name: HB tumor_case 2


title: Cultured bacteria StrR49

type: genomic

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

hyb_protocol: Following the primer extension reaction, 80 µl of hybridization solution was added to each reaction. The total volume of 120 µl was then hybridized to a DNA microarray for 90 min at 42°C at high humidity. The tags on the extension primers hybridized to corresponding probes on the microarray. After hybridization, each chip was washed 5 times with 300 µl of 1X saline sodium citrate (SSC).

scan_protocol: Microarray were scanned using the confocal scanner integrated in the INFINITI analyzer

data_processing: Microarray results were controlled for background and negative control. For each probe a ratio between the mean of the background corrected signal of triplicate probes and background fluorescence was calculated. Positivity of the internal control probes (ratio > 3) confirmed the test validity for this sample. Serotypes were determined used the Pneumotyper software (https://github.com/fredericraymond/Pneumotyper)

molecule: genomic DNA

organism: Streptococcus pneumoniae

source_name: CRI

label_protocol: Multiplex PCR was performed in a T1plus thermocycler (Biometra, Montreal Biotech, Montreal, Canada). Multiplex PCR was performed for each sample. The amplification solution was composed of 1X Platinum Taq buffer, 0.2 µM dNTPs, 1.5 mM MgCl2, 1µl multiplex PCR primer mix, 0.5 units of Platinum Taq DNA polymerase (Invitrogen, Burlington, ON, Canada), and 2.5 µl of cDNA, in a final volume of 20 µl. Prior to PCR, 107 copies of phage M13amp18 RF1 DNA (New England Biolabs, Pickering, ON, Canada) was added to each reaction as an internal control. The PCR program consisted in the following steps: 60 s at 94°C followed by 39 cycles of 30 s at 94°C, 30 s at 55°C and 90 s at 72°C. Finally, the reaction was incubated at 72°C for 3 min. Then, 3 units of shrimp alkaline phosphatase (Clontech, Mountain View, CA), 7.5 units of exonuclease (Clontech) and 0.25 µl of 50X titanium DNA polymerase (Clontech) were added to the solution, which was incubated at 37°C for 20 min and at 94°C for 10 min. This step allows for the degradation of remaining dNTPs and PCR primers that were not used in the multiplex PCR. The subsequent steps were automated by the INFINITI analyzer (AutoGenomics Inc., Carlsbad, CA). The primer extension solution was composed of 1X Platinum Taq buffer, 2.5µM MgCl2, 156 µM d(A/G/T)TP, 10µM Cy5-dCTP, 2µl primer extension primer mix completed with water to 20µl per reaction. A volume of 20µl of primer extension solution was added to each reaction. Primer extension reaction consisted in the following steps: 60 s at 94°C followed by 39 cycles of 15 s at 94°C and 15 s at 50°C. Primer extension was done in the presence of Cy5-dCTP.

growth_protocol: One hundred and sixty-six (166) isolates of S. pneumoniae, which had been previously serotyped using the Quellung method, were provided by the Laboratoire de santé publique du Québec (LSPQ), the Swiss National Reference Laboratory for S. pneumoniae and the Centre de recherche en Infectiologie de l’Université Laval strain collection.

extract_protocol: DNA was extracted from clinical samples using the Purelink viral RNA/DNA minikit (Invitrogen, Burlington, ON, Canada). Reference bacterial strains were grown in the appropriate medium until a turbidity of 0.5 McFarland was obtained. Bacteria were centrifuged and resuspended in 5X TE buffer. DNA was extracted using the BD GeneOhm™ Lysis Kit (BD GeneOhm, San Diego, CA). Purified DNA was quantified on a agarose gel and diluted to a concentration of 100 ng/µl and then to a concentration of 1 ng/µl. Genomic DNA was kept at 4°C.

treatment_protocol: No treatment

tag: serotype (quellung)


title: HB tumor_509

description: LncRNA expression in HB_509C

source_name: HB tumor_case 9


title: IL4_matrigel_rep3

description:
SAM630157
treated with IL4 on matrigel

source_name: IMR90, matrigel, IL4

source_name: Stratagene Universal Human Reference RNA

tag: sample type


title: Cultured bacteria 8881


title: HB normal liver_501

description: LncRNA expression in HB_501N

source_name: Normal liver_case 1

value: Male


title: HB normal liver_502

description: LncRNA expression in HB_502N

source_name: Normal liver_case 2


title: unstim_plastic_rep1

description:
SAM630160
treated with unstim on plastic

value: unstimulated


title: unstim_matrigel_rep2

description:
SAM630156
treated with unstim on matrigel

source_name: IMR90, matrigel, unstimulated


title: TNFa_matrigel_rep2

description:
SAM630155
treated with TNFa on matrigel


title: IL13_matrigel_rep1

description:
SAM630152
treated with IL13 on matrigel

source_name: IMR90, matrigel, IL13


title: Mammary Tumor-Cyclin D1/WT Rep1


title: Cultured bacteria StrR42


title: HB tumor_501

description: LncRNA expression in HB_501C

source_name: HB tumor_case 1


title: Cultured bacteria StrR09


title: Cultured bacteria StrR01


title: Cultured bacteria 9063


title: IL4_matrigel_rep2

description:
SAM630151
treated with IL4 on matrigel


title: IL13_matrigel_rep2

description:
SAM630153
treated with IL13 on matrigel


title: IL13_matrigel_rep3

description:
SAM630158
treated with IL13 on matrigel


title: IL4_matrigel_rep1

description:
SAM630150
treated with IL4 on matrigel


title: Cultured bacteria Ser23f

source_name: Geneva


title: Cultured bacteria Ser20


title: Cultured bacteria Ser18c


title: Cultured bacteria Ser06b


title: Cultured bacteria Ser04


title: Cultured bacteria Ser02


title: Cultured bacteria Ser06a


title: Cultured bacteria Ser05


title: Cultured bacteria Ser01


title: Cultured bacteria Ser14


title: IMR90, IL13 + Mouse IgG, rep1

description:
SAM631228
IL13 + Mouse IgG

hyb_protocol: cRNA was hybridized on Agilent-014850 Whole Human Genome Microarray 4x44K.

source_name: IMR-90, IL13 + mouse IgG

growth_protocol: IMR-90 cells (ATCC, Manassas, VA; Catalog # CCL-186) were cultured in DMEM medium supplemented with 10% FBS (Sigma, St. Louis, MO; Catalog # F2442) and Penicillin/Streptomycin (Invitrogen, Carlsbad, CA; Catalog # 15140). Cells were plated on a bed of growth factor reduced Matrigel (GFR Matrigel, BD Biosciences, Bedford, MA; Catalog No. 354230).

treatment_protocol: Cells were treated for 24 hours with TNFa (10 ng/ml). After this 24 hour TNFa pre-treatment, cells were treated with IL-4 (10 ng/ml), IL-13 (10ng/ml), 228 B/C (which blocks signaling from IL13RA1), and/or 11H4 (which blocks signaling from IL13RA1 and IL13RA2).

tag: cytokine treatment

tag: antibody treatment

value: mouse IgG


title: unstim_matrigel_rep1

description:
SAM630149
treated with unstim on matrigel


title: IMR90, IL13 + Mouse IgG, rep3

description:
SAM631230
IL13 + Mouse IgG


title: Cultured bacteria Ser07f


title: IMR90, IL13 + IL4 + 228B/C + 11H4, rep1

description:
SAM631225
IL13 + IL4 + 228B/C + 11H4

value: IL13 + IL4


title: IMR90, IL13 + Mouse IgG, rep2

description:
SAM631229
IL13 + Mouse IgG


title: IMR90, IL13 + IL4 + 228B/C, rep3

description:
SAM631221
IL13 + IL4 + 228B/C


title: IMR90, IL13 + IL4 + 228B/C + 11H4, rep3

description:
SAM631227
IL13 + IL4 + 228B/C + 11H4


title: IMR90, IL13 + IL4 + 11H4, rep1

description:
SAM631222
IL13 + IL4 + 11H4


title: IMR90, IL13 + IL4 + 228B/C, rep2

description:
SAM631220
IL13 + IL4 + 228B/C


title: Cultured bacteria MA87707

source_name: LSPQ


title: IMR90, IL13 + IL4 + 11H4, rep3

description:
SAM631224
IL13 + IL4 + 11H4


title: Cultured bacteria MA87708


title: IMR90, IL13 + IL4 + 11H4, rep2

description:
SAM631223
IL13 + IL4 + 11H4


title: IMR90, IL13 + IL4 + 228B/C + 11H4, rep2

description:
SAM631226
IL13 + IL4 + 228B/C + 11H4


title: Cultured bacteria MA87701


title: Cultured bacteria MA87788


title: Cultured bacteria MA87627


title: Cultured bacteria MA87602


title: IMR90, IL4 + Mouse IgG, rep3

description:
SAM631218
IL4 + Mouse IgG

source_name: IMR-90, IL4 + mouse IgG


title: Cultured bacteria MA87496


title: Cultured bacteria MA87520


title: Cultured bacteria MA87470


title: Cultured bacteria MA87480


title: IMR90, IL4 + Mouse IgG, rep1

description:
SAM631216
IL4 + Mouse IgG


title: Cultured bacteria MA87492


title: IMR90, IL13 + IL4 + Mouse IgG, rep2

description:
SAM631214
IL13 + IL4 + Mouse IgG

source_name: IMR-90, IL13 + IL4 + mouse IgG


title: IMR90, IL13 + IL4 + Mouse IgG, rep1

description:
SAM631213
IL13 + IL4 + Mouse IgG


title: IMR90, IL13 + IL4 + 228B/C, rep1

description:
SAM631219
IL13 + IL4 + 228B/C


title: IMR90, IL4 + Mouse IgG, rep2

description:
SAM631217
IL4 + Mouse IgG


title: Cultured bacteria MA87455


title: IMR90, IL13 + IL4 + Mouse IgG, rep3

description:
SAM631215
IL13 + IL4 + Mouse IgG


title: IMR90, IL13 + 228B/C + 11H4, rep3

description:
SAM631212
IL13 + 228B/C + 11H4


title: Cultured bacteria MA87495


title: IMR90, IL13 + 228B/C, rep2

description:
SAM631205
IL13 + 228B/C


title: Cultured bacteria MA87417


title: IMR90, IL13 + 228B/C + 11H4, rep1

description:
SAM631210
IL13 + 228B/C + 11H4


title: IMR90, IL13 + 11H4, rep2

description:
SAM631209
IL13 + 11H4


title: IMR90, IL13 + 228B/C, rep3

description:
SAM631206
IL13 + 228B/C


title: (MEFs) by addition of serum from L/MDR-irradiated (20days) female C3H/HeN mice 3

city: Rokkasho

first: Takashi

last: Sugihara

state: Aomori

address: 2-121 Hacchazawa

department: Radiobiology

institute: Institute for Environmental Sciences

description: Gene expression after addition of serum derived 8Gy irrdiated mice for 20days

hyb_protocol: Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse embryonic fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol (Invitrogene) following the manufacturer's recommendations. The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Firstly, Female C3H/HeN mice were irradiated at 4 (10days) or 8 Gy (20days) at L/MDR, and MEFs were cultures with serum derived from these in incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: mouse embryonic fibroblasts

tag: co-culture

value: serum derived from L/MDR-irradiated female C3H/HeN

tag: irradiation dose


title: IMR90, IL13 + 228B/C + 11H4, rep2

description:
SAM631211
IL13 + 228B/C + 11H4

tag: cell type


title: (MEFs) by addition of serum from L/MDR-irradiated (20days) female C3H/HeN mice 4


title: Cultured bacteria MA87348


title: Cultured bacteria MA87346


title: IMR90, IL13 + 228B/C, rep1

description:
SAM631204
IL13 + 228B/C


title: IMR90, IL13 + 11H4, rep1

description:
SAM631207
IL13 + 11H4


title: (MEFs) by addition of serum from L/MDR-irradiated (20days) female C3H/HeN mice 5


title: (MEFs) by addition of serum from L/MDR-irradiated (20days) female C3H/HeN mice 1


title: IMR90, IL13, rep3

description:
SAM631203
IL13


title: (MEFs) by addition of serum from L/MDR-irradiated (20days) female C3H/HeN mice 2


title: Cultured bacteria MA87343


title: Mammary Tumor-Cyclin D1/KE Rep1

source_name: Mouse Mammary Tumor

tag: strain


title: (MEFs) by addition of serum from non-irradiated (20days) female C3H/HeN mice 4

description: Gene expression after addition of serum derived 0Gy mice for 20days

value: serum derived from non-irradiated female C3H/HeN


title: Cultured bacteria MA87389


title: IL4_plastic_rep1

description:
SAM630162
treated with IL4 on plastic

source_name: IMR90, plastic, IL4

tag: substrate

tag: timepoint


title: IMR90, IL13, rep2

description:
SAM631202
IL13


title: (MEFs) by addition of serum from non-irradiated (20days) female C3H/HeN mice 5


title: Cultured bacteria MA87230


title: IMR90, Mouse IgG, rep3

description:
SAM631200
Mouse IgG

source_name: IMR-90, mouse IgG


title: IMR90, Mouse IgG, rep2

description:
SAM631199
Mouse IgG


title: Cultured bacteria MA87006


title: Cultured bacteria MA87258


title: IMR90, IL13, rep1

description:
SAM631201
IL13


title: (MEFs) by addition of serum from non-irradiated (20days) female C3H/HeN mice 3


title: Cultured bacteria MA86891


title: Cultured bacteria MA86980


title: IMR90, Mouse IgG, rep1

description:
SAM631198
Mouse IgG


title: (MEFs) by addition of serum from non-irradiated (20days) female C3H/HeN mice 2


title: Cultured bacteria MA86880


title: (MEFs) by addition of serum from L/MDR-irradiated (10days) female C3H/HeN mice 5

description: Gene expression after addition of serum derived 4Gy irrdaiated mice for 10days


title: IMR90, untreated, rep3

description:
SAM631197
untreated

source_name: IMR-90, untreated


title: Cultured bacteria MA86867


title: IMR90, untreated, rep2

description:
SAM631196
untreated


title: (MEFs) by addition of serum from non-irradiated (20days) female C3H/HeN mice 1


title: (MEFs) by addition of serum from L/MDR-irradiated (10days) female C3H/HeN mice 3


title: Cultured bacteria MA86732


title: Cultured bacteria MA86758


title: Cultured bacteria MA86711


title: (MEFs) by addition of serum from L/MDR-irradiated (10days) female C3H/HeN mice 4


title: Cultured bacteria MA86575


title: Cultured bacteria MA86547


title: Cultured bacteria MA86538


title: Cultured bacteria MA87607


title: Cultured bacteria MA86507


title: Cultured bacteria MA86520


title: Cultured bacteria MA86428


title: Cultured bacteria MA86472


title: Cultured bacteria MA86399


title: M181S5

hyb_protocol: 250-350 pmol of dye per sample in a volume of 8µl for each sample were mixed with 1µl of pre-heated ssDNA (10mg/ml stock), 1µl tRNA (10mg/ml stock), 4.5µl Agilent 10X blocking agent and 22.5µl Agilent 2X hybridization buffer. The 45µl mix were heated at 95°C for 3 min then immediately transfered at 37°C for at least 30 min. The mix were loaded onto the micro-arrays and hybridization were performed during 24h at 65°C at 20 RPM.

scan_protocol: Detection of CY3 and CY5 signals were performed on a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA USA) at 5 µm resolution.

data_processing: The signal intensity data were extracted from the primary scanned images using GenePix Pro 6.0 software (Axon Instruments, Union City, CA, USA). Normalization and statistical analyses were performed in R 2.2.1 software using the LIMMA (Linear Models for Microarray Data) 3.12.0 package. Background correction was performed using the “edwards” method; within-array normalization was done by loess and between array normalization by the Aquantile method. Multiple testing corrections were done using the false discovery rate method with a threshold p value of 0.05. Only genes statistically significant with an absolute ratio greater than 1.5 were considered.

organism: Leishmania infantum

source_name: L. infantum 5FU500.4

label_protocol: 8 µg of purified PvuII + MseI digested genomic DNA were labeled by adding 9µg of random hexamers (Roche), 5µl 10X Klenow buffer (provided with the exo-klenow enzyme), 5µl 10X dNTP mix (2mM each dATP, dGTP, dTTP and 0.5 mM dCTP), 1.25µl 100µM DTT, 1.5µl Cy-dCTP (Amersham, 1mM stocks) and 1.5µl exo- Klenow (50U/µl stock, NEB). The reaction were incubated overnight at 37°C. The labeled probes were purified by using the Telechem purification kit and the probes were quantified by measuring the absorbance at 260nm, 280nm, 550nm (for Cy3) and 650nm (for Cy5).

growth_protocol: All cells were grown in SDM79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5µg/ml hemin at 25°C. The 5-fluorouracil (5-FU) resistant mutants were grown in the same condition but with 5-FU drug pressure at 500 µM.

extract_protocol: Cells are collected and washed in Hepes-NaCl and lysed in 500µl of DNAzol solution. The DNAs were precipitated by adding 500 µl of EtOH 99% and collected with a loop. The DNA were washed, once in 1 ml EtOH 70% and once in 1 ml EtOH 100% at room temperature. The DNAs were dissolved in 700 µl of nuclease-free water then sheared by passing successively through 22Gx1 (4-5 times) and 27G ½ needles (10-15 times). The sheared DNAs were digest with PvuII + MseI enzymes for 1h at 37. The digested DNAs were cleaned up by phenol/chloroforme extraction (Ambion, pH 7.9) and ethanol precipation, fellowed by resuspension in nuclease free water.

treatment_protocol: There is no treatment protocol.

value: L. infantum 5FU500.4

source_name: L. infantum 5FU500.3

value: L. infantum 5FU500.3


title: M181S6

source_name: L. infantum 5FU500.5

value: L. infantum 5FU500.5


title: (MEFs) by addition of serum from L/MDR-irradiated (10days) female C3H/HeN mice 2


title: (MEFs) by addition of serum from L/MDR-irradiated (10days) female C3H/HeN mice 1


title: M181S9

source_name: L. infantum 263 (Wt)

value: L. infantum 263 (Wt)

source_name: L. infantum 5FU5003

value: L. infantum 5FU5003


title: IMR90, untreated, rep1

description:
SAM631195
untreated

value: lung fibroblasts

source_name: Stratagene Universal Human Reference RNA

value: reference


title: M181S10


title: Cultured bacteria MA86300


title: M181S4

source_name: L. infantum 5FU500.2

value: L. infantum 5FU500.2


title: M181S8

source_name: L. infantum 5FU500.1

value: L. infantum 5FU500.1


title: M181S7


title: individual4_kerat_rep3

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Gene expression, individual 4, keratinocyte, rep2_2

hyb_protocol: The  hybridization, washing and staining protocols used in the study were those recomended by Agilent (USA). The One-color Microarray-based gene expression Analyisis protocol version 5.7.March 2008 were used in the study.

scan_protocol: The arrays were scanned using the DNA Microarray Scanner G2565CA (Agilent, US). Finally, Feature Extraction Software (FES, Agilent, USA) was used both to perform the quality control process and to extract the information.

data_processing: The Agilent Processed Signal returned by Agilent Feature Extraction Software, was standardized across arrays using quantile normalization

source_name: individual 4, keratinocyte, rep2_2

label_protocol: Overall, 50 ng of RNA were labeled using Low input Quickamp Labeling kit (Agilent, US).

extract_protocol: Total RNA isolation from primary cultures on passage 3-4 was performed using the Trizol extraction method (Invitrogen Life Technologies, Carlsbad, CA) followed by purification in commercial columns (Qiagen, Valencia, CA). Total isolated RNA was further purified using an RNeasy kit (Qiagen, Valencia, CA). RNA concentration was determined using a NanoDrop Spectrophotometer (Thermo Scientific) and integrity of the RNA was verified by Bioanalyzer 2100 (Agilent, USA). The RNA integrity number was in all cases higher than 8.

tag: subject

value: individual 4

tag: melanoma

value: wild type

tag: twins

value: keratinocyte

tag: disease state


title: M181S3


title: (MEFs) by addition of serum from non-irradiated (10days) female C3H/HeN mice 3

description: Gene expression after addition of serum derived 0Gy mice for 10days


title: individual4_kerat_rep1

description: Gene expression, individual 4, keratinocyte, rep1

source_name: individual 4, keratinocyte, rep1


title: (MEFs) by addition of serum from non-irradiated (10days) female C3H/HeN mice 4


title: individual2_kerat_rep3

description: Gene expression, individual 2, keratinocyte, rep3

source_name: individual 2, keratinocyte, rep3

value: individual 2

value: 2 variants

tag: genotype

value: MC1R variant


title: individual4_kerat_rep2

description: Gene expression, individual 4, keratinocyte, rep2_1

source_name: individual 4, keratinocyte, rep2_1


title: individual3_kerat_rep1

description: Gene expression, individual 3, keratinocyte, rep1

source_name: individual 3, keratinocyte, rep1

value: individual 3

value: mutant

value: CDKN2A mutant


title: (MEFs) by addition of serum from non-irradiated (10days) female C3H/HeN mice 1

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts

value: serum derived from non-irradiated female C3H/HeN


title: Cultured bacteria MA86178

source_name: LSPQ


title: M181S2

value: L. infantum 5FU500.5


title: individual1_kerat_rep3

description: Gene expression, individual 1, keratinocyte, rep3

source_name: individual 1, keratinocyte, rep3

value: individual 1

value: yes

value: melanoma

value: CDKN2A mutant and MC1R variant


title: individual2_kerat_rep1

description: Gene expression, individual 2, keratinocyte, rep1

source_name: individual 2, keratinocyte, rep1


title: (MEFs) by addition of serum from non-irradiated (10days) female C3H/HeN mice 2


title: individual2_kerat_rep2

description: Gene expression, individual 2, keratinocyte, rep2

source_name: individual 2, keratinocyte, rep2


title: Cultured bacteria MA86290


title: Cultured bacteria MA86115


title: individual1_kerat_rep1

description: Gene expression, individual 1, keratinocyte, rep1

source_name: individual 1, keratinocyte, rep1


title: individual3_kerat_rep2

description: Gene expression, individual 3, keratinocyte, rep2

source_name: individual 3, keratinocyte, rep2


title: individual1_kerat_rep2

description: Gene expression, individual 1, keratinocyte, rep2

source_name: individual 1, keratinocyte, rep2


title: (MEFs) by addition of serum from non-irradiated (10days) female C3H/HeN mice 5


title: Cultured bacteria MA85979


title: Cultured bacteria MA85975


title: M181S1

value: L. infantum 5FU500.1

value: L. infantum 5FU500.2


title: individual3_kerat_rep3

description: Gene expression, individual 3, keratinocyte, rep3

source_name: individual 3, keratinocyte, rep3

value: wild type


title: Cultured bacteria MA85874


title: Cultured bacteria MA85777


title: Cultured bacteria MA85705


title: Random melanoma patient 22

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Sporadic melanoma isolated from patient 22

hyb_protocol: After combining equal amounts of samples with the reference, DNA was prepared for hybridization with help of an Oligo aCGH Hybridization Kit (Agilent). Human Cot-1 DNA (Invitrogen), Blocking Agent (Agilent), and Agilent1s 2X Hi-RPM Buffer were added to all samples, and hybridized to 105K Human Genome CGH 105A Oligo Microarrays (Agilent). Hybridization was done for 40 hours at +65°C, 20 rpm in a Microarray Hybridization Oven (Agilent). Arrays were washed with Oligo aCGH Wash Buffers (Agilent).

scan_protocol: Arrays were scanned in a High-Resolution Microarray Scanner (Agilent). Raw data retrieval was performed using Agilent’s Feature Extraction software.

data_processing: Agilent aCGH data obtained from microarray analysis were imported into the Partek Genomics Suite software (Partek), quantile normalized, converted into copy number values and pre-processed using its built-in segmentation algorithm. Individual chromosomal segments were defined as continuous regions covered by at least 10 consecutive microarray probes, a significant (p<0.001) and considerable (>0.3 copies on average) difference between the copy number (CN) of the given segment and neighboring segments, accepting an error rate of  less than +/- 0.3 copies

source_name: PBMC

label_protocol: One ug of genomic DNA per sample was directly labeled with Cy5, while equal amounts of genomic DNA of a healthy donor were subjected to Cy3 labeling to serve as a common reference. Labeling reactions were performed using a Genomic DNA Enzymatic Labeling Kit (Agilent), according to the manufacturer’s recommendations. DNA was digested by AluI and RsaI in the presence of BSA for 2 hours at +37°C. After efficient fragmentation was confirmed by E-Gel® Agarose Gel Electrophoresis (Invitrogen), fragments were heat-denatured, random primers (Agilent) were annealed to them, and extended with help of the Exo-Klenow fragment in the presence of dNTP, Cyanine 5-dUTP and Cyanine 3-dUTP for samples and reference, respectively (all reagents from Agilent). Amplicons were purified on Amicon 30kDa filters (Agilent) and labeling efficiency was checked by assessing specific activity of Cy5 (A650) or Cy3 (A550) relative to the amount of DNA (A260) using a Nanodrop spectrophotometer (Nanodrop).

growth_protocol: After surgical removal, stable cell cultures were established and maintained in IMDM (Gibco) supplemented by 10% Human Serum AB (Gemini)

extract_protocol: Total genomic DNA was isolated from 2x106 cells per sample by automated sample processing using the QuickGene DNA whole blood kit S and a QuickGene-810 Nucleic Acid Isolation System (Fujifilm), following the manufacturer’s instructions. Sample purity and integrity was confirmed by > 1.8 A260/A280 ratio measured on a Nanodrop spectrophotometer (Nanodrop) and E-Gel® Agarose Gel Electrophoresis (Invitrogen), respectively.

value: PBMC

tag: disease course

value: Healthy control

source_name: Melanoma cells in culture

value: Random

tag: patient id

tag: lesion id

tag: date of isolation

tag: origin

value: Surgery Branch, NIH, Bethesda, USA

tag: originator's sample label


title: Cultured bacteria MA85666

tag: serotype (quellung)


title: Random melanoma patient 18

description: Sporadic melanoma isolated from patient 18

tag: sample type


title: Random melanoma patient 21

description: Sporadic melanoma isolated from patient 21

tag: cell type


title: Random melanoma patient 17

description: Sporadic melanoma isolated from patient 17


title: Cultured bacteria MA85528


title: Random melanoma patient 20

description: Sporadic melanoma isolated from patient 20


title: Random melanoma patient 19

description: Sporadic melanoma isolated from patient 19


title: Random melanoma patient 15

description: Sporadic melanoma isolated from patient 15


title: Random melanoma patient 16

description: Sporadic melanoma isolated from patient 16


title: Cultured bacteria MA85398


title: Cultured bacteria MA85394


title: Cultured bacteria MA85218


title: Cultured bacteria MA84968


title: Cultured bacteria MA84655


title: Random melanoma patient 12

description: Sporadic melanoma isolated from patient 12


title: Random melanoma patient 13

description: Sporadic melanoma isolated from patient 13


title: Scramble + PRDM14

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

institute: Kwansei Gakuin University

description: Gene expression of PRDM14-overexpressing ESCs

hyb_protocol: Labelled RNA were hybridised to an Affymetrix MG-430 PM array strip (Affymetrix)  according to the manufacturer’s instructions.

scan_protocol: Slide scan was performed by GeneAtlas (Affymetrix)

data_processing: The scan images were processed by expression console  (Affymetrix)

source_name: PRDM14-overexpressing ESCs

label_protocol: Total RNA (150 ng) was labelled using a GeneChip 3′ IVT Express Kit (Affymetrix)  according to the manufacturer’s instructions.

growth_protocol: ES cells were cultured in feeder-free conditions in Glasgow Minimum Essential Medium (GMEM) (WAKO) containing 10% FCS (Invitrogen), 1 mM glutamine (WAKO), nonessential amino acid (WAKO) and 0.1 mM mercaptoethanol (WAKO) and supplemented with LIF (WAKO).

extract_protocol: Total RNA from control and Tet1/Tet2 double knockdown (shTet1/Tet2) iP14 ESCs (-/+ Dox) was purified using the PureLinkTM RNA Mini Kit (Ambion).

tag: cell line


title: Random melanoma patient 10

description: Sporadic melanoma isolated from patient 10


title: Cultured bacteria MA84338


title: Tet1/Tet2 KD

description: Gene expression of Tet1/Tet2 KD ESCs

source_name: Tet1/Tet2 KD ESCs


title: Random melanoma patient 11

description: Sporadic melanoma isolated from patient 11


title: Tet1/Tet2 KD + PRDM14

description: Gene expression of Tet1/Tet2 KD and PRDM14-overexpressing ESCs


title: Random melanoma patient 14

description: Sporadic melanoma isolated from patient 14


title: Random melanoma patient 9

description: Sporadic melanoma isolated from patient 9


title: Scramble

description: Gene expression of wild type ESCs

source_name: Wild type ESCs


title: Cultured bacteria MA84314


title: Random melanoma patient 8

description: Sporadic melanoma isolated from patient 8


title: Random melanoma patient 5

description: Sporadic melanoma isolated from patient 5


title: Cultured bacteria MA84138


title: Random melanoma patient 7

description: Sporadic melanoma isolated from patient 7


title: Random melanoma patient 6

description: Sporadic melanoma isolated from patient 6


title: Random melanoma patient 4

description: Sporadic melanoma isolated from patient 4


title: Cultured bacteria MA83631


title: Cultured bacteria MA83684


title: Cultured bacteria MA83982


title: Cultured bacteria MA83584


title: Random melanoma patient 3

description: Sporadic melanoma isolated from patient 3


title: Cultured bacteria MA83443


title: Recurrent melanoma patient H, 3rd recurrence

description: Recurrent melanoma isolated from patient H, 3rd recurrence

value: Recurrent

value: H

value: barbaiotc 2297-1.2 p6 medi


title: Random melanoma patient 1

description: Sporadic melanoma isolated from patient 1


title: Cultured bacteria MA83284


title: Cultured bacteria MA83283


title: Random melanoma patient 2

description: Sporadic melanoma isolated from patient 2


title: Recurrent melanoma patient H, 2nd recurrence

description: Recurrent melanoma isolated from patient H, 2nd recurrence

value: barbaiotc 2195 medi p7


title: Recurrent melanoma patient H, 1st recurrence

description: Recurrent melanoma isolated from patient H, 1st recurrence

value: barbaiotc 2086 P9 frag


title: Cultured bacteria MA83193


title: 5mC, mucosa #14

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
MC.14N
5mC in colorectal mucosa, patient#14

hyb_protocol: According to NimbleGen Kit.

scan_protocol: Follow NimbleScan's default using Agilent Scanner.

data_processing: For each array, Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio. Quantile normalization was then applied across all the arrays.

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #14

label_protocol: According to standard NimbleGen Protocol.

extract_protocol: For analysis of genomic 5mC patterns, the methylated CpG island recovery assay (MIRA) was used. For this procedure, sonicated genomic DNA was incubated with MBD2b-GST and MBD3L1-HIS protein complex overnight at +4C with further capturing of methylated DNA fraction by GST-magnetic beads (Promega). After genome amplification, DNA was hybridized versus input on human CpG island/promoter microarrays (NimbleGen).

tag: disease status

value: colorectal cancer

tag: duke's stage

value: II

tag: tissue

value: matching normal colorectal mucosa

tag: enrichment procedure

value: 5mC (MIRA)

tag: kit information

value: In Lab purified His-MBD3L1 & GST-MBD2b

tag: patient identifier

source_name: Input DNA from colorectal mucosa matched to tumor from patient #14 with colorectal cancer Duke's stage II


title: 5mC, mucosa #15

description:
MC.15N
5mC in colorectal mucosa, patient#15

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #15

source_name: Input DNA from colorectal mucosa matched to tumor from patient #15 with colorectal cancer Duke's stage II


title: Cultured bacteria MA83042

source_name: LSPQ


title: Cultured bacteria MA83155


title: 5mC, mucosa #13

description:
MC.13N
5mC in colorectal mucosa, patient#13

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #13

source_name: Input DNA from colorectal mucosa matched to tumor from patient #13 with colorectal cancer Duke's stage II


title: 5mC, tumor #12

description:
MC.12T
5mC in colorectal tumor, patient#12

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #12

value: colorectal tumor

source_name: Input DNA from colorectal tumor from patient #12 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient G, 2nd recurrence

description: Recurrent melanoma isolated from patient G, 2nd recurrence

value: G

value: roman 2035 mel


title: Recurrent melanoma patient G, 3rd recurrence

description: Recurrent melanoma isolated from patient G, 3rd recurrence

value: PBMC

value: roman TC 2108 medi p6


title: Cultured bacteria MA82934


title: 5mC, mucosa #11

description:
MC.11N
5mC in colorectal mucosa, patient#11

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #11

source_name: Input DNA from colorectal mucosa matched to tumor from patient #11 with colorectal cancer Duke's stage II


title: 5mC, tumor #11

description:
MC.11T
5mC in colorectal tumor, patient#11

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #11

source_name: Input DNA from colorectal tumor from patient #11 with colorectal cancer Duke's stage II


title: 5mC, tumor #13

description:
MC.13T
5mC in colorectal tumor, patient#13

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #13

source_name: Input DNA from colorectal tumor from patient #13 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient F, 2nd recurrence

description: Recurrent melanoma isolated from patient F, 2nd recurrence

source_name: PBMC

value: Healthy control

source_name: Melanoma cells in culture

value: F

value: kilpatric 1937 frag P8


title: 5mC, tumor #15

description:
MC.15T
5mC in colorectal tumor, patient#15

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #15

source_name: Input DNA from colorectal tumor from patient #15 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient G, 1st recurrence

description: Recurrent melanoma isolated from patient G, 1st recurrence

value: Recurrent

value: Surgery Branch, NIH, Bethesda, USA

value: roman TC 1938 from sieve P7


title: Cultured bacteria MA82847


title: Cultured bacteria MA82551


title: Cultured bacteria MA82483


title: Cultured bacteria MA81885


title: Cultured bacteria MA82481


title: 5mC, tumor #14

description:
MC.14T
5mC in colorectal tumor, patient#14

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #14

source_name: Input DNA from colorectal tumor from patient #14 with colorectal cancer Duke's stage II


title: 5mC, mucosa #10

description:
MC.10N
5mC in colorectal mucosa, patient#10

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #10

source_name: Input DNA from colorectal mucosa matched to tumor from patient #10 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient D, 2nd recurrence

description: Recurrent melanoma isolated from patient D, 2nd recurrence

value: D

value: CRO, Aviano, Italy


title: Cultured bacteria MA81603

source_name: LSPQ


title: 5mC, tumor #10

description:
MC.10T
5mC in colorectal tumor, patient#10

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #10

value: colorectal cancer

value: II

source_name: Input DNA from colorectal tumor from patient #10 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient E, 3rd recurrence

description: Recurrent melanoma isolated from patient E, 3rd recurrence

value: E


title: 5mC, mucosa #9

description:
MC.9N
5mC in colorectal mucosa, patient#9

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #9

value: matching normal colorectal mucosa

value: 5mC (MIRA)

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: Input DNA from colorectal mucosa matched to tumor from patient #9 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient E, 2nd recurrence

description: Recurrent melanoma isolated from patient E, 2nd recurrence


title: Recurrent melanoma patient F, 3rd recurrence

description: Recurrent melanoma isolated from patient F, 3rd recurrence

value: kilpatric 2139 frag P8


title: Recurrent melanoma patient D, 1st recurrence

description: Recurrent melanoma isolated from patient D, 1st recurrence

value: PBMC


title: Recurrent melanoma patient C, 3rd recurrence

description: Recurrent melanoma isolated from patient C, 3rd recurrence

value: C

value: 146 III 6p


title: 5mC, tumor #7

description:
MC.7T
5mC in colorectal tumor, patient#7

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #7

value: colorectal tumor

source_name: Input DNA from colorectal tumor from patient #7 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient E, 1st recurrence

description: Recurrent melanoma isolated from patient E, 1st recurrence

value: Healthy control


title: Cultured bacteria MA81222


title: 5mC, mucosa #12

description:
MC.12N
5mC in colorectal mucosa, patient#12

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #12

source_name: Input DNA from colorectal mucosa matched to tumor from patient #12 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient F, 1st recurrence

description: Recurrent melanoma isolated from patient F, 1st recurrence

source_name: PBMC

value: Recurrent

value: F

value: kilpatric mel (1760)


title: Cultured bacteria MA80816


title: Cultured bacteria MA80812


title: Recurrent melanoma patient C, 2nd recurrence

description: Recurrent melanoma isolated from patient C, 2nd recurrence

source_name: Melanoma cells in culture


title: 5mC, mucosa #8

description:
MC.8N
5mC in colorectal mucosa, patient#8

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #8

source_name: Input DNA from colorectal mucosa matched to tumor from patient #8 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient C, 1st recurrence

description: Recurrent melanoma isolated from patient C, 1st recurrence


title: 5mC, tumor #9

description:
MC.9T
5mC in colorectal tumor, patient#9

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #9

source_name: Input DNA from colorectal tumor from patient #9 with colorectal cancer Duke's stage II


title: Cultured bacteria MA76483


title: Cultured bacteria MA75627


title: Cultured bacteria MA77832


title: 5mC, tumor #8

description:
MC.8T
5mC in colorectal tumor, patient#8

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #8

source_name: Input DNA from colorectal tumor from patient #8 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient A, 4th recurrence

description: Recurrent melanoma isolated from patient A, 4th recurrence

value: A

value: Surgery Branch, NIH, Bethesda, USA


title: Recurrent melanoma patient B, 1st recurrence

description: Recurrent melanoma isolated from patient B, 1st recurrence

value: B

value: CRO, Aviano, Italy


title: Cultured bacteria MA71886

source_name: LSPQ


title: 5mC, mucosa #6

description:
MC.6N
5mC in colorectal mucosa, patient#6

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #6

value: colorectal cancer

value: II

source_name: Input DNA from colorectal mucosa matched to tumor from patient #6 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient A, 3rd recurrence, 3rd synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 3rd synchronous lesion


title: Recurrent melanoma patient B, 2nd recurrence

description: Recurrent melanoma isolated from patient B, 2nd recurrence


title: 5mC, tumor #2

description:
MC.2T
5mC in colorectal tumor, patient#2

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #2

value: 5mC (MIRA)

source_name: Input DNA from colorectal tumor from patient #2 with colorectal cancer Duke's stage II


title: 5mC, tumor #5

description:
MC.5T
5mC in colorectal tumor, patient#5

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #5

value: In Lab purified His-MBD3L1 & GST-MBD2b

source_name: Input DNA from colorectal tumor from patient #5 with colorectal cancer Duke's stage II


title: 5mC, mucosa #5

description:
MC.5N
5mC in colorectal mucosa, patient#5

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #5

value: matching normal colorectal mucosa

source_name: Input DNA from colorectal mucosa matched to tumor from patient #5 with colorectal cancer Duke's stage II


title: 5mC, mucosa #2

description:
MC.2N
5mC in colorectal mucosa, patient#2

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #2

source_name: Input DNA from colorectal mucosa matched to tumor from patient #2 with colorectal cancer Duke's stage II


title: 5mC, tumor #1

description:
MC.1T
5mC in colorectal tumor, patient#1

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #1

source_name: Input DNA from colorectal tumor from patient #1 with colorectal cancer Duke's stage II


title: 5mC, mucosa #4

description:
MC.4N
5mC in colorectal mucosa, patient#4

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #4

source_name: Input DNA from colorectal mucosa matched to tumor from patient #4 with colorectal cancer Duke's stage II


title: 5mC, tumor #6

description:
MC.6T
5mC in colorectal tumor, patient#6

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #6

source_name: Input DNA from colorectal tumor from patient #6 with colorectal cancer Duke's stage II


title: Cultured bacteria MA73234

source_name: LSPQ


title: 5mC, mucosa #7

description:
MC.7N
5mC in colorectal mucosa, patient#7

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #7

source_name: Input DNA from colorectal mucosa matched to tumor from patient #7 with colorectal cancer Duke's stage II


title: Cultured bacteria MA66375


title: Recurrent melanoma patient A, 3rd recurrence, 1st synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 1st synchronous lesion

source_name: PBMC

value: PBMC

source_name: Melanoma cells in culture


title: 5mC, mucosa #3

description:
MC.3N
5mC in colorectal mucosa, patient#3

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #3

source_name: Input DNA from colorectal mucosa matched to tumor from patient #3 with colorectal cancer Duke's stage II


title: 5mC, tumor #4

description:
MC.4T
5mC in colorectal tumor, patient#4

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #4

source_name: Input DNA from colorectal tumor from patient #4 with colorectal cancer Duke's stage II


title: Cultured bacteria MA63936


title: Cultured bacteria MA085862


title: Recurrent melanoma patient A, 2nd recurrence, 2nd synchronous lesion

description: Recurrent melanoma isolated from patient A, 2nd recurrence, 2nd synchronous lesion


title: H3K4me3, mucosa #12,exp#2

description:
K4_2.12NR
H3K4me3 in colorectal mucosa, patient#12, experiment#2

source_name: H3K4me3 ChIP DNA from mucosa patient #12

extract_protocol: For chromatin immunoprecipitation, frozen tissues were homogenized in cold phosphate-buffered saline (PBS) and fixed for 10 min at room temperature in 1% formaldehyde. After adding of glycine to 0.125M final concentration, chromatin was sonicated and incubated with the following antibodies overnight: anti-H3K4me3 (39159, Active Motif), and anti-H3K27me3 (07-449, Millipore). For obtaining the H3K4me3 profile, the H3K4me3 antibodies were pre-blocked with an H3K9me3 peptide (Abcam) to remove minor cross-reactivity of this antibody. After genome amplification, immunoprecipitated DNA was hybridized versus input DNA on human CpG island/promoter microarrays (NimbleGen).

value: ChIP with H3K4me3 antibodies

tag: chip antibody

source_name: Input DNA from colorectal mucosa matched to tumor from patient #12 with colorectal cancer Duke's stage II


title: H3K4me3, mucosa #13

description:
K4_2.13N
H3K4me3 in colorectal mucosa, patient#13

source_name: H3K4me3 ChIP DNA from mucosa patient #13

source_name: Input DNA from colorectal mucosa matched to tumor from patient #13 with colorectal cancer Duke's stage II


title: Cultured bacteria MA66381


title: 5mC, mucosa #1

description:
MC.1N
5mC in colorectal mucosa, patient#1

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal mucosa from patient #1

source_name: Input DNA from colorectal mucosa matched to tumor from patient #1 with colorectal cancer Duke's stage II


title: Cultured bacteria MA085822


title: H3K4me3, tumor #13

description:
K4_2.13T
H3K4me3 in colorectal tumor, patient#13

source_name: H3K4me3 ChIP DNA from tumor patient #13

source_name: Input DNA from colorectal tumor from patient #13 with colorectal cancer Duke's stage II


title: H3K4me3, tumor #12,exp#2

description:
K4_2.12TR
H3K4me3 in colorectal tumor, patient#12, experiment#2

source_name: H3K4me3 ChIP DNA from tumor patient #12

source_name: Input DNA from colorectal tumor from patient #12 with colorectal cancer Duke's stage II


title: 5mC, tumor #3

description:
MC.3T
5mC in colorectal tumor, patient#3

source_name: methylated DNA fraction enriched by MIRA, DNA from colorectal tumor from patient #3

source_name: Input DNA from colorectal tumor from patient #3 with colorectal cancer Duke's stage II


title: Recurrent melanoma patient A, 3rd recurrence, 2nd synchronous lesion

description: Recurrent melanoma isolated from patient A, 3rd recurrence, 2nd synchronous lesion

source_name: PBMC

tag: disease course

source_name: Melanoma cells in culture


title: Cultured bacteria MA085699

source_name: LSPQ


title: H3K4me3, mucosa #12,exp#1

description:
K4_2.12N
H3K4me3 in colorectal mucosa, patient#12, experiment#1


title: H3K4me3, tumor #12,exp1

description:
K4_2.12T
H3K4me3 in colorectal tumor, patient#12, experiment#1


title: Cultured bacteria MA085611


title: Cultured bacteria MA085556


title: H3K4me3, tumor #8

description:
K4_2.8T
H3K4me3 in colorectal tumor, patient#8

source_name: H3K4me3 ChIP DNA from tumor patient #8

source_name: Input DNA from colorectal tumor from patient #8 with colorectal cancer Duke's stage II


title: oldDC -Fe_rep3

city: Tsukubashi

first: Yuko

last: Ogo

address: 3-1-3 Kannondai

institute: NARO

description: Gene expression of vascular bundle from old leaf at the lowest node grown under Fe-deficient condition

hyb_protocol: Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4 • 44K microarray RAP-DB (G2519F#15241; Agilent Technologies) at 65°C for 17 h. Hybridization and washing of the hybridized slide were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanne.

data_processing: The scanned images were analyzed with FEATURE EXTRACTION 10.5.1.1 (Agilent Technologies) to obtain background correction of the Cy3 raw signals.

label_protocol: One-color spikemix was added to the total RNA prior to the labeling reaction, and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP, according to the modified manufacturer’s protocol. The Cy3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen), and the quantity was examined with a NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop Technologies).

growth_protocol: Rice was grown hydroponically under 14-h/10-h light/dark cycles and at 30/25°C.

extract_protocol: The 0.5 cm to 1.5 cm of the root tip and DC were fixed in 75% ethanol/25% acetate and 100% acetone, respectively. Paraffin-embedding was followed by the microwave method. Serial paraffin sections were prepared at 10–20 μm in thickness, and they were put onto a glass slide. Laser Microdissection was performed using the Veritas Laser Microdissection System LCC1704 (Molecular Devices). Total RNA was extracted from cells prepared by Laser Microdissection with a Pico-PureTM RNA isolation kit (Molecular Devices) according to the manufacturer’s protocol. The extracted total RNA was quantified with a Quant-iTTM RiboGreen RNA reagent and kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The quality of total RNA was assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA integrity was judged by RNA Integrity Number (RIN), which was calculated with 2100 Expert Software (Agilent, version B.02.02, eukaryote total RNA pico mode).

treatment_protocol: Fe deficiency was initiated at day 27 after germination by omitting Fe(III)–EDTA from the culture medium, and plants were harvested after 7 days. For Cd stress, 10 μM CdCl2 was added to the hydroponic culture on day 33 after germination and plants were harvested after 24 h.

tag: growth condition

value: Fe-deficient


title: Cultured bacteria MA085521


title: Cultured bacteria MA65399


title: Cultured bacteria MA085490


title: Cultured bacteria MA085469


title: Recurrent melanoma patient A, 1st recurrence

description: Recurrent melanoma isolated from patient A, 1st recurrence

tag: patient id

tag: lesion id


title: oldDC Normal_rep2

description: Gene expression of vascular bundle from old leaf at the lowest node grown under normal condition

value: normal


title: oldDC Normal_rep3

source_name: vascular bundle from old leaf at the lowest node grown under normal condition


title: newDC -Fe_rep2

description: Gene expression of vascular bundle from new leaf at the lowest node grown under Fe-deficient condition


title: oldDC -Fe_rep2

source_name: vascular bundle from old leaf at the lowest node grown under Fe-deficient condition


title: oldDC -Fe_rep1

value: vascular bundle from old leaf at the lowest node


title: Recurrent melanoma patient A, 2nd recurrence, 1st synchronous lesion

description: Recurrent melanoma isolated from patient A, 2nd recurrence, 1st synchronous lesion

value: Healthy control

value: Recurrent

tag: date of isolation

tag: origin


title: newDC -Fe_rep3

source_name: vascular bundle from new leaf at the lowest node grown under Fe-deficient condition


title: SJTALL157

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710927

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases

extract_protocol: Trizol

tag: disease state

value: non-ETP T-lineage ALL


title: SJTALL159

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710929


title: oldDC Normal_rep1


title: SJTALL079

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710923


title: Cultured bacteria MA085416

tag: serotype (quellung)


title: newDC -Fe_rep1

value: vascular bundle from new leaf at the lowest node


title: H3K4me3, mucosa #8

description:
K4_2.8N
H3K4me3 in colorectal mucosa, patient#8

source_name: H3K4me3 ChIP DNA from mucosa patient #8

source_name: Input DNA from colorectal mucosa matched to tumor from patient #8 with colorectal cancer Duke's stage II


title: 13L peptide [SL12]

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

description: Gene expression data from C. elegans (strain N2) at young adult stage

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).

data_processing: GeneChip Operating Software supplied by Affymetrix was used to perform gene expression analysis. Four samples of control fed conditions and three samples of treated conditions were statistically analysed. Raw data obtained from Affymetrix arrays were background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. The difference between treated samples and controls was statistically tested using limma moderate t-statistic. Aiming to control the false disocvery rate, p-values were corrected for multiple testing using Benjamini and Hochberg method

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans at young adult stage

label_protocol: Gene expression analysis was performed according to the Affymetrix-recommended protocol using Affymetrix C.Elegans Genome Array. GeneChips containing probes for over 22,500 transcripts. Total RNA (300 ng per sample) was biotin- labeled using the Affymetrix GeneChip 3' IVT express protocol

growth_protocol: C. elegans was cultured in Nematode Growth Medium (NGM) as estándar diet. Nematodes were age-synchronized by isolating eggs from gravid adults. Embryos were incubated in the corresponding agar plates at 20ºC for 3 days (until reach young adult stage)

extract_protocol: Worms from each fed condition (NGM or 13L peptide) were collected with M9 buffer and disrupted by sonication (3 pulses at 10W, 20s/pulse). RNA was isolated with a comercial kit (RNAsy Kit, Qiagen)

treatment_protocol: Treated nematodes were cultured in NGM plates supplemented with 1 µg/mL of peptide 13L and incubated at 20ºC from egg to young adult stage.

tag: strin

tag: protocol

value: 1 µg/mL of 13L peptide


title: 13L peptide [SL8]


title: SJTALL077

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710919


title: newDC Normal_rep3

description: Gene expression of vascular bundle from new leaf at the lowest node grown under normal condition


title: SJTALL075

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710917


title: Cultured bacteria MA085415


title: SJTALL071

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710912


title: newDC Normal_rep2

source_name: vascular bundle from new leaf at the lowest node grown under normal condition


title: SJTALL072

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710914


title: Cultured bacteria MA085414


title: H3K4me3, tumor #6

description:
K4_2.6T
H3K4me3 in colorectal tumor, patient#6

source_name: H3K4me3 ChIP DNA from tumor patient #6

tag: disease status

value: colorectal tumor

source_name: Input DNA from colorectal tumor from patient #6 with colorectal cancer Duke's stage II


title: H3K4me3, mucosa #6

description:
K4_2.6N
H3K4me3 in colorectal mucosa, patient#6

source_name: H3K4me3 ChIP DNA from mucosa patient #6

tag: duke's stage

source_name: Input DNA from colorectal mucosa matched to tumor from patient #6 with colorectal cancer Duke's stage II


title: Cultured bacteria MA085285


title: 13L peptide [SL4]


title: Cultured bacteria MA085306


title: SJTALL069

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710909


title: Cultured bacteria MA085252


title: Cultured bacteria MA085278


title: NGM [SL69]

value: Nematode Growth medium, control


title: SJTALL056

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710901


title: SJTALL068

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710907


title: EP +Cd_rep2

description: Gene expression of epidermis plus exodermis of root grown under Cd-stressed condition

tag: tissue

value: epidermis plus exodermis of root

value: Cd-stressed


title: NGM [SL1]


title: SJTALL040

description:
RNA extracted from tumor cells obtained at diagnosis
Additional Array


title: NGM [SL5]


title: EP +Cd_rep1

source_name: epidermis plus exodermis of root grown under Cd-stressed condition


title: Cultured bacteria MA085243


title: EP +Cd_rep3


title: H3K27me3, tumor #12

description:
K27.12T
H3K27me3 in colorectal tumor, patient#12

source_name: H3K27me3 ChIP DNA from tumor patient #12

value: colorectal cancer

value: II

tag: enrichment procedure

value: ChIP with H3K27me3 antibodies

source_name: Input DNA from colorectal tumor from patient #12 with colorectal cancer Duke's stage II


title: SJTALL033

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710880


title: EP -Fe_rep3

description: Gene expression of epidermis plus exodermis of root grown under Fe-deficient condition


title: Cultured bacteria MA085126

source_name: LSPQ


title: EP -Fe_rep1

source_name: epidermis plus exodermis of root grown under Fe-deficient condition


title: Seedling_KUA1-IOX_est_rep1

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

institute: MPIMP-golm

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis

organism: Arabidopsis thaliana

source_name: 14-d-old seedling, overexpression of KUODA1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: T3 seeds were stratified on plate for 72 h in the dark at 4°C and then transferred to 22°C with a 16-h light (100 μE m−2 s−1)/8-h dark period.

extract_protocol: Total RNA was extracted with the Plant RNAeasy kit (Qiagen)

treatment_protocol: 14-day-old seedlings were transferred to liquid MS medium and subsequently estradiol disolved in ethanol (treatment) or ethanol alone (mock) was added to each well. After 4 hours seedlings were collected and directly frozen in liquid nitrogen for storage.

tag: ecotype

tag: age

value: 14 days

tag: developmental stage

value: Seedling

tag: genotype/variation

value: overexpression of KUODA1


title: Seedling_KUA1-IOX_est_rep2


title: Cultured bacteria MA085030


title: Cultured bacteria MA084920


title: H3K27me3, tumor #13

description:
K27.13T
H3K27me3 in colorectal tumor, patient#13

source_name: H3K27me3 ChIP DNA from tumor patient #13

tag: chip antibody

tag: patient identifier

source_name: Input DNA from colorectal tumor from patient #13 with colorectal cancer Duke's stage II


title: H3K27me3, mucosa #13

description:
K27.13N
H3K27me3 in colorectal mucosa, patient#13

source_name: H3K27me3 ChIP DNA from mucosa patient #13

value: matching normal colorectal mucosa

source_name: Input DNA from colorectal mucosa matched to tumor from patient #13 with colorectal cancer Duke's stage II


title: H3K27me3, mucosa #6

description:
K27.6N
H3K27me3 in colorectal mucosa, patient#6

source_name: H3K27me3 ChIP DNA from mucosa patient #6


title: Cultured bacteria MA084178


title: SJTALL030

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710874

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)


title: newDC Normal_rep1

description: Gene expression of vascular bundle from new leaf at the lowest node grown under normal condition

tag: growth condition

value: normal


title: Seedling_KUA1-IOX_mock_rep2

source_name: 14-d-old seedling, control

value: control


title: EP Normal_rep1

description: Gene expression of epidermis plus exodermis of root grown under normal condition


title: EP Normal_rep2

source_name: epidermis plus exodermis of root grown under normal condition


title: H3K27me3, tumor #6

description:
K27.6T
H3K27me3 in colorectal tumor, patient#6

source_name: H3K27me3 ChIP DNA from tumor patient #6

source_name: Input DNA from colorectal tumor from patient #6 with colorectal cancer Duke's stage II


title: SJTALL028

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710870


title: Cultured bacteria MA083962