title: Sample1

status: Public on Dec 02 2009

first: Johanna

middle: Cecilia

last: Andersson

address: Burlington Danes Building, Hammersmith Hospital, Du Cane Road

department: Division of Genetics of Common Disease

institute: Imperial College London

description: gene expression data from subcutaneous adipose tissue from an obese individual

hyb_protocol: Following fragmentation,15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline, the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: Gene expression levels were normalised using the Robust Multiarray Average (RMA) method.

source_name: subcutaneous adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen Lipid Tissue RNA extraction kit.

value: adbominal subcutaneous adipose tissue, collected via needle biopsy

tag: genome/variation

tag: disease status

value: obese


title: Lopez-Juez_1-10_Shoot-apex-72hr-light_Rep1_ATH1

status: Public on Dec 05 2009

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Imbibed (after sterilisation) in 0.1% agar for 3 days at 4 C in the dark. With ethanol, then dilute bleach, then rinses with sterile water. Growth chamber Agar 50-80 Murashige and Skoog basal salt mixture MES, pH 5.7

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Landsberg erecta, shoot apex, 72hr light

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: Seedlings were raised by exposing stratified seeds, sown on agar-solidified Murashige and Skoog medium (without sucrose), for 30 min to 100 micromol m-2 s-1 fluorescent cool white light, on horizontal plates as described (Vinti et al.; The Plant Journal 24(6), 883-894, 2000), to stimulate germination. The plates were placed in a dark incubator at 21 C for 3 days, at which time they were transfered back to white light for 72 h before harvesting.

extract_protocol: Seedlings were immersed in RNAlater (Ambion) for 1 h (the harvesting and immersion being under green safelight), and stored at 4°C. Within one week seedlings were dissected on a chilled platform under a stereomicroscope, by slicing below the meristem and at the base of each cotyledon ('meristem' or M samples) or near the base and tip of each cotyledon ('cotyledon' or C samples), before flash-freezing and storing at -80°C. Only one tissue was obtained per seedling and the number of seedlings per sample ranged from ca.1500 (72 h samples) to over 4000 (0 h samples). Each sample contained material from multiple plates and several separate experiments. RNA was extracted using an RiboPure kit (Ambion), essentially according to manufacturer's instructions.

tag: strain

value: Landsberg erecta

tag: developmental stage

tag: tissue

value: shoot apical meristem region and developing leaf primordia

tag: stock code

tag: treatment

value: 72hr light


title: sample 8b 30min 33--3, biological rep2, technical rep2

status: Public on Dec 04 2009

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

country: USA

institute: NCI/NIH

description: Mitogen stimulated Jurkat T-cells were harvest at 0, 30 min, 1hr, 2hr, 4hr, and 6hr and RNA was collected.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Homo sapiens

source_name: Jurkat T-cells were harvest at 30 min

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion MessageAmp II Biotin-enhanced protocol from 1 ug total RNA (Message Amp II Biotin-Enhanced Technical Manual, 2006, Ambion).

growth_protocol: Jurkat Cells were treated with P/I for 45 min.

extract_protocol: Human promoter microarray from NimbleGen Systems, Inc., was co-hybridized with either antibody precipitated and total imput control or an IgG-precipitated sample with the total imput control.

tag: Jurkat T-cells were harvest at 30 min


title: sample 3A 1hr 32--4, technical rep1

source_name: Jurkat T-cells were harvest at 1hr

tag: Jurkat T-cells were harvest at 1hr


title: Sample2

city: London


title: sample 8a 30min 33--3, biological rep2, technical rep1


title: sample 1A zero 32--2, technical rep1

source_name: Jurkat T-cells were harvest at 0

tag: Jurkat T-cells were harvest at 0


title: 33

status: Public on Dec 01 2009

city: New York

first: Dusan

last: Bogunovic

state: NY

address: 522 First Av. SML1307

department: Cancer Institute

institute: New York University Medical Center

description: gene expression data from melanoma tumor

hyb_protocol: 5 mcg of  biotin-labeled  fragmented cRNA was hybridized for 16 hrs onto the Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the PLIER algorithm.

source_name: Tumor

label_protocol: In-vitro transcription of biotin-labeled cRNA probes was done using an IVT labeling kit (Affymetrix)

extract_protocol: RNeasy Mini Kit, Qiagen was used for whole RNA extraction

treatment_protocol: Tumor samples were placed in RNA later

tag: stage at reccurence

value: IIIB

tag: days lived since metastasis

tag: days since initial diagnosis

tag: gender

value: male

tag: age

tag: staus dead or alive


title: sample 9a 1hr 33--4, biological rep2, technical rep1


title: sample 7b zero 33--1, biological rep2, technical rep2


title: 44


title: sample 2B 30min 32--3, technical rep2


title: 34

value: IIIC

value: female


title: 32


title: 39


title: 45


title: 37

value: IV


title: 46


title: 36


title: 43


title: 31

value: IIIA


title: 28


title: 29


title: 27


title: sample 2A 30min 32--3, technical rep1


title: 25B


title: 22B


title: 18


title: 19


title: 25


title: 10


title: 22


title: 07B


title: 9


title: 14


title: 26


title: 4


title: 16


title: 24


title: 7


title: 22D


title: 21


title: 8


title: 3


title: 12


title: 21B


title: 11


title: 6


title: 2


title: 17


title: 01B


title: 1


title: 5


title: EV_4

first: Ulf

last: Klein

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: Gene expression data from EV-transfected cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  U133_Plus2 Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: Stably transfected 13q14-/- CLL-I83E95 cell line

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

growth_protocol: CLL-I83U95 cells were cultured in 20% FCS-IMDM media at 0.5-1x10(6) cells/ml density.

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

treatment_protocol: Cells were harvested 48 hours after addition of doxycyclin that results in the induction of miR-expression.

tag: tumor/tissue type

value: CLL cell line

tag: cell line

tag: transfectant

value: empty vector


title: miR_1

description: Gene expression data from miR-15a/16-1-transfected cells

tag: genome/variation

value: doxycyclin-inducible expression vector containing miR-15a/16-1


title: miR_2


title: EV_1


title: miR_4


title: Cord Blood 20, biological replicate 6

first: Jeffery

middle: Lynn

last: Miller

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

description: Gene expression data of reticulocytes from umbilical cord blood.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Reticulocytes from umbilical cord blood

treatment_protocol: Reticulocytes-enriched pools were prepared from blood samples by removing plasma, platelets and nucleated cells using centrifugation and filtration methods.

value: umbilical cord blood

tag: cell type

value: reticulocytes


title: Cord Blood 18, biological replicate 4

tag: tissue


title: Cord Blood 16, biological replicate 2


title: EV_6


title: Cord Blood 19, biological replicate 5


title: Cord Blood 17, biological replicate 3


title: miR_5


title: EV_2


title: miR_3


title: miR_6


title: Cord Blood 15, biological replicate 1


title: EV_3


title: Adult Blood 15, biological replicate 1

description: Gene expression data of reticulocytes from adult periperal blood.

source_name: Reticulocytes from adult periperal blood

value: peripheral blood

tag: developmental stage

value: adult


title: 38


title: Adult Blood 20, biological replicate 6


title: Adult Blood 18, biological replicate 4


title: Adult Blood 16, biological replicate 2


title: Adult Blood 19, biological replicate 5


title: Adult Blood 17, biological replicate 3


title: CD34+ cells without fenretinide treatment from CML34

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

description: Untreated CD34+ cells isolated from the patient CML34, harvested after 48h in culture

hyb_protocol: The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.

data_processing: Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.

source_name: CD34+ cells from the patient (CML34)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).

treatment_protocol: CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.

tag: disease status

value: CML chronic phase (CP)

tag: cell source

value: bone marrow (BM)

value: CD34+ mononuclear cells


title: CD34+ cells without fenretinide treatment from CML35

description: Untreated CD34+ cells isolated from the patient CML35, harvested after 48h in culture

source_name: CD34+ cells from the patient (CML35)

value: leukapheresis products (LP)


title: CD34+ cells with fenretinide treatment from CML35

description: Fenretinide-treated CD34+ cells isolated from the patient CML35, harvested after 48h in culture


title: CD34+ cells with fenretinide treatment from CML34

description: Fenretinide-treated CD34+ cells isolated from the patient CML34, harvested after 48h in culture


title: CD34+ cells with fenretinide treatment from CML32

description: Fenretinide-treated CD34+ cells isolated from the patient CML32, harvested after 48h in culture

source_name: CD34+ cells from the patient (CML32)


title: CD34+ cells without fenretinide treatment from CML33

description: Untreated CD34+ cells isolated from the patient CML33, harvested after 48h in culture

source_name: CD34+ cells from the patient (CML33)


title: CD34+ cells without fenretinide treatment from CML32

description: Untreated CD34+ cells isolated from the patient CML32, harvested after 48h in culture


title: CD34+ cells with fenretinide treatment from CML33

description: Fenretinide-treated CD34+ cells isolated from the patient CML33, harvested after 48h in culture


title: C200 TOP-GFP low rep 2

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental Molecular Medicine

country: Netherlands

institute: Academic Medical Center Amsterdam

description: 10% lowest TOP-GFP fraction sorted by FACS

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: C200 CSC culture

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

value: colon cancer stem cells (CSC)

tag: expression

value: low Wnt


title: C100 TOP-GFP high rep 1

description: 10% highest TOP-GFP fraction sorted by FACS

source_name: C100 Colon CSC culture

value: high Wnt


title: C200 TOP-GFP high rep 2

description: 10% higest TOP-GFP fraction sorted by FACS


title: Tumor genes in the PDAC CAM model on day 6 (T6)

city: Talence

first: Martin

last: Hagedorn

address: Av des Facultes

department: Biology

country: France

institute: University Bordeaux 1

description: Human pancreatic adenocarcinoma cells (BxPC3) one day after grafting (T1) on the chick-chorio-allantoic membrane were compared to tumors after 6 days on the CAM (T6) to identify gene associated with tumor invasion and angiogenesis.

hyb_protocol: Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

label: Biotin

organism:
Gallus gallus
Homo sapiens

source_name: Human pancreatic adenocarcinoma cells (BxPC3) grown on the chick-chorio-allantoic membrane for 6 days (T6)

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol'

growth_protocol: Chick embryos were incubated at 37.8ºC and 75% humidity.

extract_protocol: CAMs were immediately snap-frozen in liquid nitrogen after excision. Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

treatment_protocol: 3-5 million BxPC3 cells were deposited on the surface of the intact CAM. CAMs were excised and snap-frozen in liquid nitrogen prior to mRNA isolation

tag: CAM was isolated from a chick embryo at developmental day 16


title: Tumor genes in the PDAC CAM model on day 1 (T1)

source_name: Human pancreatic adenocarcinoma cells (BxPC3) grown on the chick-chorio-allantoic membrane for 1 day (T1)

extract_protocol: CAMs were immediately snap-frozen in liquid nitrogen after excision. Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer

tag: CAM was isolated from a chick embryo at developmental day 11


title: RA01_anergic_CD21m_Bcells

first: Isabelle

last: Isnardi

address: 535E 70th Street

institute: Hospital for Special Surgery

description: The labelling, hybridizing, scanning and data processing steps were performed by the Cornell Microarray Core Facility, supervised by Dr. Jenny Xiang.

hyb_protocol: Targets were prepared for array hybridization according to Affymetrix Expression Analysis Technical manual except for some modifications. Hybridization conditions, array washing and staining (with GeneChip Fluidics Station 450) were carried out according to the Affymetrix Expression Analysis technical Manual.

scan_protocol: Scanning (with GeneChip Scanner 3000 7G) was carried out according to the Affymetrix Expression Analysis technical Manual.

data_processing: Affymetrix GeneChip Operating Software was used as the image acquisition software for the U133A 2.0 chips. The signal, which represents the intensity of each gene, was extracted from the image. The target intensity value from each chip was scaled to 500.

source_name: anergic naive B cells from RA01 patient, non stimulated

label_protocol: 50 ng of total RNA were amplified and labeled with biotin using the Ovation Biotin system (NuGEN Technologies, Inc., San Carlos, CA). Amplification of starting total RNA yielded on average 7 μg of amplified single stranded cDNA. This material was then fragmented and labeled with biotin.

extract_protocol: Total RNA was extracted from 200,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada). Enriched B cells were stained with FITC anti-human CD27, PE anti-human CD10, PECy7 anti-human CD19, and APC anti-human CD21. Single CD19+CD21-CD10-CD27- mature naive from the donor were sorted on a FACSVantage (Becton Deckinson).

value: Black female 60 y.o. suffering from Rheumatoid Arthritis

tag: CD19+CD21-CD10-CD27- anergic naive B cells.


title: CVID321_anergic_CD21m_Bcells

source_name: anergic naive B cells from CVID321 patient, non stimulated

extract_protocol: Total RNA was extracted from 175,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

value: Caucasian female 27 y.o. suffering from Common Variable Immunodeficiency Disease.


title: RA19_anergic_CD21m_Bcells

source_name: anergic naive B cells from RA19 patient, non stimulated

extract_protocol: Total RNA was extracted from 68,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

value: Hispanic female 52 y.o. suffering from Rheumatoid Arthritis


title: CVID214_conventional_CD21p_Bcells

source_name: conventional mature naive B cells from CVID214 patient, non stimulated

extract_protocol: Total RNA was extracted from 250,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

treatment_protocol: Peripheral B cells were purified from the blood of the donor by negative selection using RosetteSepTM procedure (StemCell Technologies, Vancouver, BC, Canada). Enriched B cells were stained with FITC anti-human CD27, PE anti-human CD10, PECy7 anti-human CD19, and APC anti-human CD21. Single CD19+CD21+CD10-CD27- mature naive from the donor were sorted on a FACSVantage (Becton Deckinson).

value: Caucasian male 46 y.o. suffering from Common Variable Immunodeficiency Disease.

tag: CD19+CD21+CD10-CD27- conventional mature naive B cells.


title: RA19_conventional_CD21p_Bcells

source_name: conventional mature naive B cells from RA19 patient, non stimulated

extract_protocol: Total RNA was extracted from 300,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.


title: RA01_conventional_CD21p_Bcells

source_name: conventional mature naive B cells from RA01 patient, non stimulated


title: C100 TOP-GFP low rep 1

source_name: C100 CSC culture


title: Col whole leaf amplified, 5 d UI, biological rep 1

city: Berkeley

first: Mary

middle: C

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from 5d uninfected wild type whole amplified leaves

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, functional genomics lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips. Quality assessment was done using the weights outputted from the linear model fitting function fitPLM() in the R package AffyExtensions.

source_name: Col whole leaf amplified uninfected 5d

label_protocol: Two-round and one-round target labeling was performed according to the protocols given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1. Quantity and quality of amplified RNA was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 9 plants per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 70% RH, 12 h photoperiod with photosynthetically active radiation=180 µE m-2 s-1.

extract_protocol: Total RNA was extracted using the Picopure kit from Arcturus according to the manufacturer's instructions from LMD, whole leaf and leaf section scrape samples.  Samples were subject to on-column DNase digestion using  DNase I from Qiagen. RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was infected with a light innoculum of G.orontii using a settling tower. Light innoculum is 2 half G.O.-infected leaves with conidia 10-14 dpi.  Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections were performed at 11:30 am to standardize experiments and minimize circadian effects. Samples were harvested at 5 dpi. An uninfected 5 d sample was also collected.  For each sample, four fully expanded mature leaves were excised per plant and transferred to Sorensen's buffer. Harvested leaves were microwave-fixed, dehydrated and embedded in paraffin. Embedded leaves were sectioned into 10 µm sections using a microtome prior to laser microdissection. Groups of epidermal and mesophyll cells surrounding G. orontii-infected cells were collected using the Leica AS LMD with 40XT objective from infected samples. In parallel, groups of epidermal and mesophyll cells were collected from uninfected samples. Whole leaves (3-4 fully expanded mature leaves) were also harvested for each sample and immediately frozen in liquid nitrogen. Two independent experiments were performed with triplicate samples collected within each experiment.  Two biological replicates were processed.

tag: genotype

value: wild type

value: 4 weeks old at time 0 (innoculation)

value: whole leaf


title: CVID214_anergic_CD21m_Bcells

source_name: anergic naive B cells from CVID214 patient, non stimulated

extract_protocol: Total RNA was extracted from 90,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.


title: Col leaf scrape, 5 dpi, biological rep 2

description: Gene expression data from 5d infected wild type scraped and amplified leaves

source_name: Col leaf scrape amplified infected with Golovinomyces orontii 5d

tag: age

value: leaf section scrapes


title: CVID321_conventional_CD21p_Bcells

source_name: conventional mature naive B cells from CVID321 patient, non stimulated


title: Col leaf scrape, 5 dpi, biological rep 1


title: CVID218_anergic_CD21m_Bcells

source_name: anergic naive B cells from CVID218 patient, non stimulated

extract_protocol: Total RNA was extracted from 110,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.

value: Caucasian female 46 y.o. suffering from Common Variable Immunodeficiency Disease.


title: Col whole leaf amplified, 5 d UI, biological rep 2


title: Col whole leaf amplified, 5 dpi, biological rep 1

description: Gene expression data from 5d infected wild type whole amplified leaves

source_name: Col whole leaf amplified infected with Golovinomyces orontii 5d


title: Col whole leaf amplified, 5 dpi, biological rep 2


title: Col whole leaf, 5 d UI, biological rep 2

description: Gene expression data from 5d uninfected wild type whole mature leaves

source_name: Col whole leaf uninfected 5d


title: Col laser microdissected, 5 dpi, biological rep 1

description: Gene expression data from 5d infected wild type laser-microdessected leaves around the infection site without vascular bundle cells and lower epidermis

source_name: Col laser-microdissected leaf amplified infected with Golovinomyces orontii 5d

value: LMD leaf epidermal and mesophyll cells


title: Col whole leaf, 5 dpi, biological rep 1

description: Gene expression data from 5d infected wild type whole mature leaves

source_name: Col whole leaf infected with Golovinomyces orontii 5d


title: Egr-3 siRNA #2, VEGF 4h #2

status: Public on Nov 30 2009

city: Mitaka

first: Jun-ichi

last: Suehiro

state: Tokyo

address: 6-20-2, Shinkawa

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyorin University School of Medicine

description: siRNA knockdown in VEGF-stimulated HUVEC

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: HUVEC, VEGF treatment for 4h

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Trizol (Invitrogen). 2 micrograms of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

tag: cell

value: HUVEC

tag: sirna type

value: Egr-3 siRNA #2

tag: stimulation

value: VEGF treatment for 4h


title: control, VEGF 4h #3

description: siRNA-mediated knockdown in VEGF-stimulated HUVEC

value: control


title: control, VEGF 1h #3

source_name: HUVEC, VEGF treatment for 1h

value: VEGF treatment for 1h


title: Spleen_WT_CD8_alphaplus denritic cells_rep2

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

country: Germany

institute: Munich University Hospital

description:
Strain: C57BL/6
Gender: Female
Age: 10 weeks
Tissue: spleen

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Data were normalized with quantile normalization. The expression values were computed using GC-RMA algorithm. All computations were performed with appropriate functions from the Affy package of the Bioconductor suite.

organism: Mus musculus

source_name: C57BL/6 WT spleen CD8 alpha plus dendritic cells

label_protocol: standard Affymetrix procedures

extract_protocol: ethanol extraction followed by Qiagen RNeasy total RNA cleanup protocol

tag: Strain

tag: Gender

value: Female

tag: Age

value: 10 weeks

tag: Tissue

value: spleen


title: Egr-3 siRNA #1, VEGF 4h #2

value: Egr-3 siRNA #1


title: Egr-3 siRNA #2, VEGF 1h #1


title: CVID218_conventional_CD21p_Bcells

source_name: conventional mature naive B cells from CVID218 patient, non stimulated

extract_protocol: Total RNA was extracted from 220,000 cells and purified using the AbsolutelyRNA microprep kit from Stratagene, by following the manufacturer’s protocol. Prior to use in amplification studies, the size integrity profile of all RNA samples was determined with an Agilent Bioanalyzer. All RNA preparation provided (A260/280) ratios greater than 1.8. RNA concentration was determined by Nanodrop spectrophotometry.


title: Spleen_WT_CD8_alphaminus denritic cells_rep2

source_name: C57BL/6 WT spleen CD8 alpha minus dendritic cells


title: control, VEGF 0h #3

source_name: HUVEC, VEGF treatment for 0h

value: VEGF treatment for 0h


title: Col laser microdissected, 5 d UI, biological rep 1

description: Gene expression data from 5d uninfected wild type laser-microdessected leaves around the infection site without vascular bundle cells and lower epidermis

source_name: Col laser-microdissected leaf uninfected 5d

tag: tissue


title: Egr-3 siRNA #2, VEGF 4h #1


title: Egr-3 siRNA #1, VEGF 1h #2


title: Egr-3 siRNA #1, VEGF 4h #1


title: Spleen_WT_CD8_alphaplus denritic cells_rep1


title: control, VEGF 4h #1


title: Spleen_WT_CD8_alphaminus denritic cells_rep1


title: control, VEGF 4h #2


title: Egr-3 siRNA #1, VEGF 1h #1


title: EV_5

description: Gene expression data from EV-transfected cells

source_name: Stably transfected 13q14-/- CLL-I83E95 cell line

tag: tumor/tissue type

value: CLL cell line

tag: cell line

tag: genome/variation

tag: transfectant

value: empty vector


title: 13

description: gene expression data from melanoma tumor

source_name: Tumor

tag: stage at reccurence

value: IIIB

tag: days lived since metastasis

tag: days since initial diagnosis

tag: gender

value: female

tag: staus dead or alive


title: Egr-3 siRNA #2, VEGF 0h #2

tag: cell


title: Egr-3 siRNA #1, VEGF 0h #1

tag: sirna type


title: control, VEGF 1h #1

tag: stimulation


title: Egr-3 siRNA #1, VEGF 0h #2

value: Egr-3 siRNA #1l


title: control, VEGF 1h #2


title: Egr-3 siRNA #2, VEGF 0h #1


title: control, VEGF 0h #1


title: Egr-3 siRNA #2, VEGF 1h #2


title: control, VEGF 0h #2


title: U937T:PR induced 48hr rep2

city: Chicago

first: Kim

middle: Lee

last: Rice

state: IL

address: 303E Superior Street

department: Hematology/Oncology

institute: Northwestern University

description: Gene expression data from U937T:PLZFRARa cells induced by tetracycline removal for 48hr

hyb_protocol: Following fragmentation, 10µg of cRNA was hybridized to U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Perkin-Elmer Scanarray HT

data_processing: Data was analyzed using ArrayAssistTM Version 5.2.2 (Stratagene, La Jolla, CA) and normalization was performed using the GC-RMA algorithm.

source_name: U937T cells after PLZFRARa induction

label_protocol: RNA was biotin labeled using the MessageAmpTMII kit (Ambion, Austin, TX).

growth_protocol: Cells were maintained in growth media: RPMI-1640 media supplemented with 10%(v/v) FBS, 1x Pen/Strep, puromycin (0.5ug/ml), G418 (1mg/ml) and tetracycline (0.1ug/ml)

extract_protocol: RNA was extracted using Qiagen Rneasy kit (Qiagen, Valencia, CA)

treatment_protocol: PLZF-RARα expression was induced by washing cells three times with PBS and culturing in growth media without tetracycline.

tag: protocol

value: PLZF-RARα expression induced by tetracycline removal for 48hr


title: U937T:PR induced 48hr rep3


title: U937T:PR no induction 48hr rep1

description: Gene expression data from uninduced U937T:PLZFRARa cells

source_name: U937T cells before induction


title: U937T:PR induced 48hr rep1


title: PBMC mRNA from Normal elder individual 2

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: This chip contains 47,000 transcripts and variants, including 38,500 well-characterized human genes.

hyb_protocol: The biotin labeled cRNA product (20 µg) was purified with a sample cleanup module (Qiagen) and samples were fragmented with the fragmentation buffer from Affymetrix at 94°C for 35 minutes. Fragmented and labeled targets (together with hybridization and oligo B2 controls) were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays at 45°C for 16 hours. Washing and staining of the arrays were performed on the Affymetrix fluidics station using the EukGE-WS2v5_450 protocol.

scan_protocol: Imaging of the arrays and signal quantification were performed with the Affymetrix GeneChip Scanner 3000 and GeneChip Operating Software.

data_processing: Gene expression analysis software was used for data analyses of differential expression profiles and RMA was used for normalization (GeneSpring GX software, version 7.3, Agilent Technologies, USA).

source_name: peripheral blood mononuclear cells, Normal elder individual

label_protocol: Trizol-purified RNA was quantified using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Palo Alto, CA, USA). High quality RNA (RIN>7) was transcribed into cDNA with a double reverse transcriptase-PCR technique, and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization on HG-U133 Plus2 GeneChips® (Affymetrix, CA, USA).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), according to the manufacturer's instructions. Briefly, the leukocyte pellet was lysed with 1-2 mL Trizol, and then 0.2 mL chloroform was added. Following centrifugation, the total RNA was precipitated from the aqueous phase by mixing with isopropyl alcohol. The RNA was pelleted by centrifugation; the pellet was washed with 75% ethanol, and centrifuged again. The RNA pellet was dried and dissolved in RNase-free water. RNA quality was determined using the RNA 6000 Pico LabChip kit and the Agilent 2100 bio-analyzer (Agilent Technologies Inc., USA).

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: disease status

value: Normal elder individual

tag: race/ethnicity = Taiwanese

tag: patient id(s)


title: U937T:PR no induction 48hr rep2


title: PBMC mRNA from mild cognitive impairment (MCI) patient 2

source_name: peripheral blood mononuclear cells, MCI patient

value: mild cognitive impairment (MCI) patient

tag: race/ethnicity

value: Taiwanese


title: Gliospheres_control_culture3

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: Manufacturer's protocol

scan_protocol: Manufacturer's protocol

data_processing: RMA, using the “affy” package from Bioconductor

source_name: Gliospheres, control, culture 3

label_protocol: Manufacturer's protocol

growth_protocol: Tumor samples of GBM from three patients undergoing surgical biopsies were obtained directly after surgical removal in accordance with local legislation (HUG protocol 04-113).  Single cell suspensions, freshly isolated from tumor samples, were cultivated in DMEM-F12 (Gibco), supplemented with 20% BIT (Stem Cell Technologies) or B27 (1/50 Invitrogen), 10ng/ml recombinant human EGF (Invitrogen), 10ng/ml recombinant human basic FGF (Invitrogen) and 1% Penicillin/Streptomycin (Gibco). As previously described (4, 5, 7, 21), non-adherent cellular spheroids derived from these serum-free cultures conditions were considered as enriched cancer stem cells cultures and were used for subsequent experiments.

extract_protocol: Total RNA was extracted from each of the three treated primary cultures and their respective controls, using the RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturer’s recommendations. The quality of total RNA was verified by an Agilent RNA 600 nanoassay and by measuring the 260/280 absorbance ratio.

tag: treatment

value: control

tag: culture

value: glioblastoma multiforme cancer stem cells


title: PBMC mRNA from mild cognitive impairment (MCI) patient 1


title: Gliospheres_DZNep_culture1

source_name: Gliospheres, DZNep treated, culture 1

treatment_protocol: 5uM DZNep was added to the cultures for 5 days

value: treated


title: PBMC mRNA from mild cognitive impairment (MCI) patient 3


title: Gliospheres_DZNep_culture3

source_name: Gliospheres, DZNep treated, culture 3


title: PBMC mRNA from Alzheimer's disease patient 2

source_name: peripheral blood mononuclear cells, Alzheimer's disease patient

value: Alzheimer's disease patient


title: PBMC mRNA from Normal elder individual 1


title: Gliospheres_control_culture1

source_name: Gliospheres, control, culture 1


title: U937T:PR no induction 48hr rep3

tag: cell line


title: Gliospheres_DZNep_culture2

source_name: Gliospheres, DZNep treated, culture 2


title: PBMC mRNA from Alzheimer's disease patient 3


title: PBMC mRNA from Normal elder individual 3


title: Gliospheres_control_culture2

source_name: Gliospheres, control, culture 2


title: PBMC mRNA from Alzheimer's disease patient 1


title: CBipS_4F_2

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

description: Gene expression of CBiPS, induced pluripotent stem cells obtained from human cord blood cells by reprogramming with two factors: Oct4 and Sox2.

hyb_protocol: For each sample, 3.75 ug ssDNA were labeled and hybridized to Affymetrix HG-U133 Plus 2.0 arrays.

scan_protocol: Default settings for the Affymetrix GeneChip Scanner (7G upgrade) were used.

data_processing: Data extraction was done using Affymetrix GCOS software v.1.4. Raw data were imported in R and normalized using the gcRMA algorithm.

source_name: CBiPS 4F 2 (iPS from Cord Blood cells reprogrammed with Oct4, Sox2, Klf4 and c-Myc - Sample 2)

label_protocol: The GeneChip microarray processing was performed by the Functional Genomics Core at the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer's protocols (Affymetrix, Santa Clara, CA) as described previously (Virtaneva et al., 2001). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75 ug ssDNA were labeled following the Nugen protocol FL-Ovation cDNA Biotin module V2.

growth_protocol: At day 3, the cells were harvested and transferred into 6 well-plates containing irradiated human fibroblasts and ES medium, consisting of KO-DMEM (Invitrogen) medium supplemented with 20% KO-Serum Replacement (GIBCO), non-essential amino acids (Lonza), 2-bmercaptoethanol (GIBCO), penicillin/Streptomycin (GIBCO), GlutaMAX (Invitrogene), and 10ng/ml bFGF (Peprotech). CBiPS cells were cultured on top of irradiated human fibroblasts and picked mechanically.

extract_protocol: Isolation of total RNA from CBiPS cells was performed using either Trizol reagent (Invitrogen, Carlsbad, CA) or RNAqueous-Micro kit (Ambion Inc., Austin TX) based on the cell number available. All samples were treated with TURBO DNase inhibitor (Ambion) to remove any residual genomic DNA.

treatment_protocol:
CD133+ cell purification:
Mononuclear cells (MNC) were isolated from CB using Lympholyte-H (Cederlane, Ontario, CA) density gradient centrifugation. CD133+ cells were positively selected using Mini-Macs immunomagnetic separation system (Miltenyi Biotec, Bergisch Gladbach, Germany). Purification efficiency was verified by flow cytometric analysis staining with CD133-phycoerythrin (PE; Miltenyi Biotec, Bergisch Gladbach, Germany) antibody (90%-94% CD133+).

Constructs and retroviral production:
Retroviruses for the two factors were independently produced after transfecting the cell line Phoenix Amphotropic using Fugene 6 reagent (Roche) according to manufacturer´s directions. After 24 hours, the medium was replaced, cells were incubated at 32°C, and viral supernatant was harvested every 12 hours.

Transduction of CD133+ cells:
CB CD133+ cells (1x105 cells per ml) were pre-stimulated for 24h in DMEM supplemented with 10% of FBS in the presence of SCF (50ng/ml) +FL (50ng/ml) +TPO (10ng/ml) +IL-6 (10ng/ml)(PeproTech). Multi-well non-tissue culture-treated plates were coated with retronectin (Takara, Otsu, Japan, www.takara-bio.com), a fibronectin fragment CH-296 (15mg/cm2), and preloaded by centrifuging the plates with a filtered 1:1:1:1 mix of retroviral supernatant for OCT4, SOX2, KLF4 and C-MYC factors at 2,500 RPM for 30 minutes. About 80,000 CD133+ cells were plated in the presence of DMEM+10% FBS and the cytokine cocktail mentioned above. Every 12h, half of the medium was replaced with fresh viral supernatant containing the cytokine cocktail and incubated at 32°C, 5% CO2; three infection cycles were performed.

value: human iPS from cord blood cells

tag: genetic modification

value: Oct4, Sox2, Klf4 and c-Myc


title: ES2_1

description: Gene expression of human ES2 cell line.

source_name: human ES2 cell line

growth_protocol: ES2 cells were cultured on top of irradiated human fibroblasts and picked manually. Knockout DMEM ES media was supplemented with 20% knockout serum replacement, non essential amino acids, 2-Mercaptoethanol, Penicillin/Streptomycin, GlutaMax, bFGF (all Gibco) and human albumin (Grifols).

extract_protocol: Isolation of total RNA from ES cells was performed using either Trizol extraction or using the RNAqueous-Micro kit (Ambion Inc., Austin TX), depending on the number of cells available. All samples were treated with TURBO DNase inhibitor (Ambion) to remove any residual genomic DNA.

value: human ES2 cell line


title: CBiPS_2F_2

source_name: CBiPS 2F 2 (iPS from Cord Blood cells reprogrammed with Oct4 and Sox2 - Sample 2)

treatment_protocol:
CD133+ cell purification:
Mononuclear cells (MNC) were isolated from CB using Lympholyte-H (Cederlane, Ontario, CA) density gradient centrifugation. CD133+ cells were positively selected using Mini-Macs immunomagnetic separation system (Miltenyi Biotec, Bergisch Gladbach, Germany). Purification efficiency was verified by flow cytometric analysis staining with CD133-phycoerythrin (PE; Miltenyi Biotec, Bergisch Gladbach, Germany) antibody (90%-94% CD133+).

Constructs and retroviral production:
Retroviruses for the two factors were independently produced after transfecting the cell line Phoenix Amphotropic using Fugene 6 reagent (Roche) according to manufacturer´s directions. After 24 hours, the medium was replaced, cells were incubated at 32°C, and viral supernatant was harvested every 12 hours.

Transduction of CD133+ cells:
CB CD133+ cells (1x105 cells per ml) were pre-stimulated for 24h in DMEM supplemented with 10% of FBS in the presence of SCF (50ng/ml) +FL (50ng/ml) +TPO (10ng/ml) +IL-6 (10ng/ml)(PeproTech). Multi-well non-tissue culture-treated plates were coated with retronectin (Takara, Otsu, Japan, www.takara-bio.com), a fibronectin fragment CH-296 (15mg/cm2), and preloaded by centrifuging the plates with a filtered 1:1:1:1 mix of retroviral supernatant for OCT4 and SOX2 factors at 2,500 RPM for 30 minutes. About 80,000 CD133+ cells were plated in the presence of DMEM+10% FBS and the cytokine cocktail mentioned above. Every 12h, half of the medium was replaced with fresh viral supernatant containing the cytokine cocktail and incubated at 32°C, 5% CO2; three infection cycles were performed.

value: Oct4 and Sox2.


title: WI38, biological replicate 2

city: Baltimore

first: Michael

middle: J

last: Betenbaugh

address: 3400 N. Charles St.

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

description: gene expression from WI38, biological replicate 2

hyb_protocol: cDNA fragmentation was done according to manufacturer's protocol (Affymetrix), 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on aGeneChip Human U133 Plus 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner G3000  and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.1 (GCOS) software from Affymetrix, using the standard default settings.

data_processing: The data was analyzed using dChip program developed by Li and Wong.  Data was normalized using the invariant set normalization method prior to analysis.

source_name: WI38 cells from ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix GeneChip® Expression Analysis Technical Manual, 701022 Rev. 2)

growth_protocol: All cells were grown at 37 degrees C, 5% CO2.  SDEC cells were were maintained on a matrix of type I bovine collagen (Collaborative Biomedical Products, Bedford, MA, 10 ug/cm2) in EGM2MV media (Clonetics) supplemented with 5% Fetal calf serum (FCS), hydrocortisone, human basic fibroblast growth factor (FGF-2), human vascular epidermal growth factor, R(3)-insulin-like growth factor I, ascorbic acid, human epidermal growth factor, heparin, gentamycin, and amphotericin. Detroit-551 (ATCC CCL-110) and WI-38 (ATCC CCL-75) cell lines were obtained from ATCC and maintained in DMEM media supplemented with 10% fetal bovine serum, 100U/ml Penicillin, 100 mg/ml streptomycin, 2 mM L-glutamine.

extract_protocol: RNeasy Total RNA purification kits (Qiagen) following manufacturor's protocol including the use of QIAshredder columns to homogenize samples

treatment_protocol: Cells were grown to confluence in their respective growth medias then the media was changed to huES media consisting of Knockout DMEM (Invitrogen), 10% knockout serum replacement (Invitrogen), 10% Plasmanate® (Bayer), 2 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), 0.1 mM 2-mercaptoethanol, 8 ng/ml FGF-2 (R&D systems).  The huES media was changed every 24 hours for 3 days and then the cell monolayers were used for mRNA extraction.

value: fibroblast


title: ES2_2

description: Gene expression of human ES2 cell line.

source_name: human ES2 cell line - sample 2


title: CD57 positive T cell from patient 1

status: Public on Nov 29 2009

city: Camperdown

first: Jennifer

middle: R

last: Gamble

state: New South Wales

address: Building 93, Royal Prince Alfred Hospital

department: Vascular Biology

country: Australia

institute: CENTENARY INSTITUTE

description: Gene expression data from cytotoxic T cell clone

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to the Affymetrix Human Genome U133Plus 2.0 gene chips

scan_protocol: The chips were further processed and scanned according to the manufacturer's protocol

data_processing: CEL files were normalized using RMA, and present/marginal/absent calls were generated using the affy library in R/Bioconductor. We deemed a probeset to be detected if it had at least one Present call. Differential expression due to CD57 pos/neg for non-control probeset that were determined in at least one sample was assessed.

source_name: PBMCs from patients with WM

label_protocol: Biotinylated cRNA were prepared after the two rounds of RNA amplification were conducted by using MessageAmpTM II aRNA Kit and MessageAmpTM II Biotin Enhanced Kit (Ambion, Austin, TX)

growth_protocol: peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll gradient centrifugation

extract_protocol: Total RNA was extracted using an RNeasy Micro Kit (Qiagen, Germany) from freshly purified CD3+CD4-TCRVβ+CD57+ and CD3+CD4-TCRVβ+CD57- T cells separately according to the manufacturer's instructions.

treatment_protocol: After stained with antibodies, cells were analyzed by a FACS ARIA II flow cytometry (BD Biosciences) and sorted to CD3+CD4-TCRVβ+CD57+ and CD3+CD4-TCRVβ+CD57-cells.

value: CD57 positive T cell

tag: tissue

value: PBMCs

tag: genotype

value: yellow white and Oregon R parents


title: CBiPS_4F_1

source_name: CBiPS 4F 1 (iPS from Cord Blood cells reprogrammed with Oct4, Sox2, Klf4 and C-Myc - Sample 1)

value: Oct4, Sox2, Klf4 and C-Myc


title: CD57 positive T cell from patient 3


title: CD57 negative T cell from patient 2

value: CD57 negative T cell


title: SDEC, biological replicate 2

description: gene expression from SDEC, biological replicate 2

source_name: SDEC cells derived from human embryonic germ cells

value: embryonic germ cell derived

value: SDEC


title: D551, biological replicate 1

description: gene expression from D551, biological replicate 1

source_name: D551 cells from ATCC


title: WI38, biological replicate 1

description: gene expression from WI38, biological replicate 1


title: CB_CD133+_2

description: Gene expression of human cord blood cells sorted with the antigen CD133+ to enrich for the more progenitor cells.

source_name: sorted Cord Blood cells CD133+ - sample 2

extract_protocol: Isolation of total RNA from CBiPS cells was performed using RNAqueous-Micro kit (Ambion Inc., Austin TX). All samples were treated with TURBO DNase inhibitor (Ambion) to remove any residual genomic DNA.

treatment_protocol:
CD133+ cell purification:
Mononuclear cells (MNC) were isolated from CB using Lympholyte-H (Cederlane, Ontario, CA) density gradient centrifugation. CD133+ cells were positively selected using Mini-Macs immunomagnetic separation system (Miltenyi Biotec, Bergisch Gladbach, Germany). Purification efficiency was verified by flow cytometric analysis staining with CD133-phycoerythrin (PE; Miltenyi Biotec, Bergisch Gladbach, Germany) antibody (90%-94% CD133+).

value: human cord blood cells sorted with the antigen CD133+.


title: WI38, biological replicate 3

description: gene expression from WI38, biological replicate 3


title: THRBL_spleen_case1

status: Public on Nov 27 2009

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: T cell/histiocyte rich B cell lymphoma affecting a spleen

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min.  The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

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

data_processing: Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)

molecule: cytoplasmic RNA

source_name: spleen affected by THRBL

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

growth_protocol: Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.

extract_protocol: Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations.  RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: tissue blocs were kept at -80° till use

tag: Gender

value: male, Age:40, Tissue:spleen taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVB, IPI prognostic score:low intermediate, follow-up:2 years; status at last follow-up:death with disease


title: D551, biological replicate 2

description: gene expression from D551, biological replicate 2


title: SDEC, biological replicate 1

description: gene expression from SDEC, biological replicate 1


title: THRBL_lymph_node_case9

description: T cell/histiocyte rich B cell lymphoma affecting a lymph node

source_name: lymph node affected by THRBL

value: male, Age:45, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:III, follow-up:<2 years; status at last follow-up:death with disease


title: Peripheral blood mononuclear cells (PBMC)-Patient HD4

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

description: We used the default settings of GCOS software to scan the chips

hyb_protocol: Affymetrix GeneChips Human Genome U133 PLUS 2.0 Array (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions

data_processing: We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

source_name: PBMC HD4

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: Before RNA extraction, cells were thaw, counted and their viability determined by Trypan Blue exclusion (>90% PBMC were viable). A minimum of 5 milion cryopreserved PBMC were centrifuged, and immediately lysed for RNA extraction.

extract_protocol: Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer’s instructions and resuspended in DEPC-treated Rnase-free distilled water. RNA concentration was determined by NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and its integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: The biological material was obtained at the beginning of the second hemodialysis session of the week. PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.

tag: patient

tag: disease

value: chronic kidney disease

value: undergoing hemodialysis

tag: group

value: Training


title: D551, biological replicate 3

description: gene expression from D551, biological replicate 3


title: CD57 negative T cell from patient 3


title: CBiPS_2F_1

source_name: CBiPS 2F 1 (iPS from Cord Blood cells reprogrammed with Oct4 and Sox2 - Sample 1)

value: human iPS from cord blood cells

value: Oct4 and Sox2


title: Peripheral blood mononuclear cells (PBMC)-Patient HD5

scan_protocol: We used the default settings of GCOS software to scan the chips

source_name: PBMC HD5


title: Peripheral blood mononuclear cells (PBMC)-Patient HD1

source_name: PBMC HD1


title: SDEC, biological replicate 3

description: gene expression from SDEC, biological replicate 3


title: CB_CD133+_1

source_name: sorted Cord Blood cells CD133+ - sample 1

extract_protocol: Isolation of total RNA from CD133+ cells was performed using RNAqueous-Micro kit (Ambion Inc., Austin TX). All samples were treated with TURBO DNase inhibitor (Ambion) to remove any residual genomic DNA.


title: CD57 positive T cell from patient 2


title: Peripheral blood mononuclear cells (PBMC)-Patient HD3

source_name: PBMC HD3


title: CD57 negative T cell from patient 1


title: Normal_reactive_lymph_node_pool

description: Reference sample, pool of 5 lymph nodes with follicular hyperplasia

tag: Tissue

value: lymph node with follicular hyperplasia, nr of pooled samples:5


title: NLPHL_lymph_node_case9

description: Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node

source_name: lymph node affected by NLPHL

value: male, Age:25, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IA, follow-up:11 years; status at last follow-up:alive without disease


title: THRBL_lymph_node_case7

value: male, Age:47, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVB, IPI prognostic score:high intermediate, follow-up:<1 year; status at last follow-up:death with disease


title: NLPHL_lymph_node_case8

value: male, Age:43, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, follow-up:lost for follow-up


title: NLPHL_lymph_node_case6

value: female, Age:22, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IIB, follow-up:10 years; status at last follow-up:alive without disease


title: Peripheral blood mononuclear cells (PBMC)-Patient HD2

source_name: PBMC HD2


title: THRBL_lymph_node_case5

value: male, Age:62, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IIIA, IPI prognostic score:low intermediate, follow-up:3 years; status at last follow-up:alive without disease


title: THRBL_lymph_node_case4

value: male, Age:52, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IV, IPI prognostic score:high, follow-up:3 years; status at last follow-up:alive with disease


title: THRBL_lymph_node_case8

value: male, Age:45, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVB, IPI prognostic score:high, follow-up:1 year; status at last follow-up:death with disease


title: THRBL_lymph_node_case3

value: male, Age:50, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVA, IPI prognostic score:low intermediate, follow-up:4 years; status at last follow-up:alive without disease


title: NLPHL_lymph_node_case7

value: male, Age:42, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IIA, follow-up:10 years; status at last follow-up:alive without disease


title: NLPHL_lymph_node_case10

value: male, Age:25, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IA, follow-up:12 years; status at last follow-up:alive without disease


title: THRBL_lymph_node_case6

value: female, Age:75, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IIIA, IPI prognostic score:low intermediate, follow-up:<1 year; status at last follow-up:death with disease


title: NLPHL_lymph_node_case5

value: male, Age:67, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IIA, follow-up:8 years; status at last follow-up:died of squamous cell carcinoma of the lung


title: NLPHL_lymph_node_case2

value: female, Age:71, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IIIB, follow-up:5 years; status at last follow-up:alive with disease


title: NLPHL_lymph_node_case4

value: male, Age:43, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IA, follow-up:6 years; status at last follow-up:alive without disease


title: THRBL_lymph_node_case1

value: female, Age:50, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVB, IPI prognostic score:low intermediate, follow-up:3 years; status at last follow-up:death with disease


title: ATRA treated NB4 cells, 72 hours

status: Public on Nov 26 2009

city: Shanghai

first: Jiantao

last: Shi

state: Shanghai

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)

description: gene expression of ATRA treated NB4 cells, 72 hours

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to Affymetrix HGU133plus2 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing: Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization.

source_name: ATRA treated NB4 cells, 72 hours

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using the RNeasy Protect Midi Kit (Qiagen, Valencia, CA).

treatment_protocol: NB4 cells were treated with E-6 M ATRA and harvested at 4, 12, 24, 48 and 72 hours, respectively.

value: ATRA

tag: time

value: 72 hours


title: THRBL_lymph_node_case2

value: male, Age:67, Tissue:lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage:IVB, IPI prognostic score:high intermediate, follow-up:2 years; status at last follow-up:death with disease


title: NLPHL_lymph_node_case3

value: male, Age:63, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:I, follow-up:lost for follow-up


title: ATRA treated NB4 cells, 4 hours

description: gene expression of ATRA treated NB4 cells, 4 hours

source_name: ATRA treated NB4 cells, 4 hours

value: 4 hours


title: ATRA treated NB4 cells, 24 hours

description: gene expression of ATRA treated NB4 cells, 24 hours

source_name: ATRA treated NB4 cells, 24 hours

value: 24 hours


title: WT seedlings in FN, biological rep2

status: Public on Nov 24 2009

city: Potsdam

first: Grit

last: Rubin

address: Am Mühlenberg 1

department: Stitt

institute: MPI-MP

description: grown in sterile liquid culture (Scheible et al., 2004) for nine days in N-replete conditions (FN, 4 mM KNO3)

hyb_protocol: All procedures including (i) quality control of RNA, (ii) biotin labeling of the cRNA target, (iii) hybridization, washing, staining, and scanning procedures, and (iv) processing of Affymetrix raw data (CEL files) were performed as outlined previously (Scheible et al., 2004).

data_processing: The data were analyzed with Robin and RMA-normalized

source_name: Arabidopsis wildtype (WT) seedlings in full nutrition (FN)

growth_protocol: Arabidopsis seedlings were grown in sterile liquid culture (Scheible et al., 2004) either for nine days in N-replete conditions (FN, 4 mM KNO3), or first during 7 days in FN and then for 2 days in N-deprivation conditions (no N added; noN).

extract_protocol: Total RNA was prepared using Quiagen RNeasy plant mini kit

treatment_protocol: Seedlings were pre-grown in 24 h light (150-180 µE, 20°C) on sterile 0.5% (w/v) agar plates (Falcon IntegridTM 100 mm square) containing 27 ml FN medium, and after 7 days seedlings were transferred individually to 24-well culture plates (Greiner Bio-one Cellstar #662160) containing 1 ml medium per well

tag: ecotype

value: whole seedling

tag: age

value: 9 days

value: full nutrition


title: WT seedlings in FN, biological rep1

scan_protocol: All procedures including (i) quality control of RNA, (ii) biotin labeling of the cRNA target, (iii) hybridization, washing, staining, and scanning procedures, and (iv) processing of Affymetrix raw data (CEL files) were performed as outlined previously (Scheible et al., 2004).


title: ATRA treated NB4 cells, 12 hours

description: gene expression of ATRA treated NB4 cells, 12 hours

source_name: ATRA treated NB4 cells, 12 hours

value: 12 hours


title: WT seedlings in FN, biological rep3

label_protocol: All procedures including (i) quality control of RNA, (ii) biotin labeling of the cRNA target, (iii) hybridization, washing, staining, and scanning procedures, and (iv) processing of Affymetrix raw data (CEL files) were performed as outlined previously (Scheible et al., 2004).


title: NLPHL_lymph_node_case1

value: male, Age:49, Tissue:lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage:IA, follow-up:10 years; status at last follow-up:died of squamous cell carcinoma of the larynx


title: Un-treated NB4 cells

description: gene expression of un-treated NB4 cells

source_name: Un-treated NB4 cells

value: 0 hour


title: T-DNA-insertion mutant of LBD38 seedling in FN, biological rep2

source_name: T-DNA-insertion mutant of LBD38 (KO38) seedling in full nutrition (FN)


title: T-DNA-insertion mutant of LBD38 seedling in FN, biological rep1


title: T-DNA-insertion mutant of LBD38 seedling in FN, biological rep3


title: ATRA treated NB4 cells, 48 hours

description: gene expression of ATRA treated NB4 cells, 48 hours

source_name: ATRA treated NB4 cells, 48 hours

value: 48 hours


title: T-DNA-insertion mutant of LBD37 seedling in FN, biological rep3

source_name: T-DNA-insertion mutant of LBD37 (KO37) seedling in full nutrition (FN)


title: T-DNA-insertion mutant of LBD37 seedling in FN, biological rep2


title: overexpresser of LBD37 seedlings in noN, biological rep3

description: grown first during 7 days in FN and then for 2 days in N-deplete conditions (no N added; noN)

source_name: overexpresser of LBD37 (OX37) seedling in nitrogen depletion (noN)

value: nitrogen depletion


title: overexpresser of LBD38 seedlings in noN, biological rep2

source_name: overexpresser of LBD38 (OX38) seedling in nitrogen depletion (noN)


title: overexpresser of LBD38 seedlings in noN, biological rep1


title: WT seedlings in noN, biological rep1

source_name: Arabidopsis wildtype (WT) seedlings in nitrogen depletion (noN)


title: overexpresser of LBD37 seedlings in noN, biological rep1


title: overexpresser of LBD37 seedlings in noN, biological rep2


title: WT seedlings in noN, biological rep2


title: Male post-meiotic cells, biological rep1

first: Maria

middle: D

last: Vibranovski

address: 1101 East 57th Street

department: Ecology and Evolution

institute: University of Chicago

description: Gene expression data from spermatogenic post-meiotic cells

hyb_protocol: Hybridization was done using Affymetrix default protocols.

scan_protocol: Scan were done using Affymetrix default protocols.

data_processing: Gene product expression was measured by hybridization intensity (log2) obtained using RMA background correction and quantile normalization (Bioconductor package in R)

organism: Drosophila melanogaster

source_name: Drosophila testis distal region

label_protocol: cDNAs were synthesized according to the Invitrogen SuperScript RNA Amplification System, except for a modified in vitro transcription step where Biotin-Labeled cRNA was produced

growth_protocol: Virgin males were collected and aged at room temperature (RT) for 6 to 10 days

extract_protocol: Total RNA was extracted from the apical, proximal and distal germ cell populations using PicoPure™ RNA Isolation Kit (Arcturus)

treatment_protocol: Testes without seminal vesicles were dissected in PBS. Cells enriched for mitotic, meiotic and post-meiotic phases were obtained by dissection of apical, proximal and distal regions of the testis, respectively. For each of three replicate experiments, 250-500 testis dissections were used for RNA isolation.

value: post-meiotic cells extracted from testes

value: wild-type TEMPE T strain

value: testes 6-10 days old


title: Male meiotic cells, biological rep1

description: Gene expression data from spermatogenic meiotic cells

source_name: Drosophila testis proximal region

value: meiotic cells extracted from testes


title: Male meiotic cells, biological rep2


title: Male meiotic cells, biological rep3


title: Male post-meiotic cells, biological rep3


title: Male post-meiotic cells, biological rep2


title: overexpresser of LBD38 seedlings in noN, biological rep3


title: Male mitotic cells, biological rep3

description: Gene expression data from spermatogenic mitotic cells

source_name: Drosophila testis apical region

value: mitotic cells extracted from testes


title: Male mitotic cells, biological rep1


title: Male mitotic cells, biological rep2


title: Andrographis treated PBMCs after 18 hours

status: Public on Nov 21 2009

city: Tempe

first: Robert

last: Waters

state: AZ

address: 1001 S. McAllister

department: Biodesign Institute

institute: Arizona State University

hyb_protocol: Total of 200 uL of each hybridization cocktail was hybridized to an Affymetrix Human Genome U133 Plus 2.0 array for 16 hours at 45 deg. C in the hybridization Oven 640.

scan_protocol: Affymetrix Genechip Scanner 3000 7G

data_processing: Data were analyzed using Affymetrix Genechip Operating System Version 1.4

label_protocol: Biotinylated cRNA was made using the Affymetrix One-Cycle Kit

growth_protocol: PBMCs were isolated from whole blood using Ficoll-Paque Plus system (Amersham Biosciences) and then resuspended in RPMI1640 with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated and purified as per manufacturers protocol using an Rneasy Kit (Qiagen)

treatment_protocol: 1 x 10^7 cells were treated with 5 ul herbal extract for the indicated times. Treatment of cells with phorbol-12-myristate-13-acetate (Calbiochem) was done at a final concentration of 50 nm.

tag: cell type

value: PBMC

tag: agent

value: Andrographis

tag: time point


title: Ethanol treated PBMCs after 18 hours, 2

description: Ethanol treated PBMCs after 18 hours

source_name: Ethanol treated PBMCs after 18 hours

value: Ethanol


title: Astragalus treated PBMCs after 18 hours

description: Astragalus treated PBMCs after 18 hours

source_name: Astragalus treated PBMCs after 18 hours

value: Astragalus


title: Astragalus treated PBMCs after 8 hours

description: Astragalus treated PBMCs after 8 hours

source_name: Astragalus treated PBMCs after 8 hours


title: Untreated PBMCs after 18 hours

description: Untreated PBMCs after 18 hours

source_name: Untreated PBMCs after 18 hours

value: mock


title: WT seedlings in noN, biological rep3

value: whole seedling

value: 9 days

tag: treatment


title: Sambucus treated PBMCs after 18 hours

description: Sambucus treated PBMCs after 18 hours

source_name: Sambucus treated PBMCs after 18 hours

value: Sambucus


title: Ethanol treated PBMCs after 18 hours, 3

description: Ethanol treated PBMCs after 18 hours


title: Astragalus treated PBMCs after 18 hours, 2

description: Astragalus treated PBMCs after 18 hours


title: Urtica treated PBMCs after 18 hours

description: Urtica treated PBMCs after 18 hours

source_name: Urtica treated PBMCs after 18 hours

value: Urtica


title: Mouse, Rapa 1-day-rep3

status: Public on Nov 20 2009

city: Houston

first: Funda

last: Meric-Bernstam

state: TX

address: 1515 Holcombe Boulevard

department: Surgical Oncology

institute: University of Texas M.D. Anderson Cancer Center

description: Gene expression data from MDA-MB-468 xenografts

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized overnight at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The probe intensities were processed using a position-dependent nearest neighbor (PDNN) model to estimate gene expression values.

source_name: breast tumor xenograft, Rapa-treated, 1-day

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (GeneChip Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Cells were cultured in DMEM/F12 medium supplemented with 10% FBS at 37C and humidified in 5% CO2, then injected to mammary fat pad of female nude mice.

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

treatment_protocol: Groups 1 and 2 received a single injection of DMSO or rapamycin (15 mg/kg) intraperitoneally and xenografts were harvested 24 h later. Groups 3 and 4 received weekly injections of DMSO and rapamycin (15 mg/kg) weekly and xenografts were harvested 24 h after the last injection (on day 22).

value: MDA-MB-468 xenograft

value: Rapamycin

value: 1 day


title: Mouse, Rapa 22-day-rep2

source_name: breast tumor xenograft, Rapa-treated, 22-day

value: 22 days


title: Mouse, Rapa 22-day-rep1


title: Mouse, Rapa 22-day-rep3


title: Ethanol treated PBMCs after 18 hours

description: Ethanol treated PBMCs after 18 hours


title: Astragalus treated PBMCs after 3 hours

description: Astragalus treated PBMCs after 3 hours

source_name: Astragalus treated PBMCs after 3 hours


title: Mouse, DMSO 1-day-rep3

source_name: breast tumor xenograft, DMSO-treated, 1-day

value: DMSO (vehicle)


title: Mouse, DMSO 22-day-rep1

source_name: breast tumor xenograft, DMSO-treated, 22-day


title: Mouse, DMSO 1-day-rep1


title: Mouse, DMSO 1-day-rep2


title: Mouse, Rapa 1-day-rep1


title: Mouse, Rapa 1-day-rep2


title: Mouse, DMSO 22-day-rep3


title: Mouse, DMSO 22-day-rep2


title: Cell line, Rapa 24 hr-rep3

description: Gene expression data from MDA-MB-468 cells

source_name: MDA-MB-468 cell line, Rapa-treated for 24 h

growth_protocol: Cells were cultured in DMEM/F12 medium supplemented with 10% FBS at 37C and humidified in 5% CO2.

treatment_protocol: DMSO (vehicle) or 100 nM rapamycin was added to cell culture medium. Cells were harvested 24 h later.

value: MDA-MB-468 breast cancer cell line


title: Cell line, DMSO 24 hr-rep2

source_name: MDA-MB-468 cell line, DMSO-treated for 24 h


title: Cell line, Rapa 24 hr-rep2


title: Cell line, DMSO 24 hr-rep3


title: Cell line, Rapa 24 hr-rep1


title: Cell line, DMSO 24 hr-rep1


title: mutant, Pst_48h, biological rep2

city: Saskatoon

first: Yangdou

last: Wei

state: SK

address: 112 Sceince Place

country: Canada

institute: University of Saskatchewan

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0721

hyb_protocol: Prehyb, hybridisation and wash were performed by Bio-Array Resource (BAR) center, University of Toronto (http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip).

scan_protocol: The scannings were performed by Bio-Array Resource (BAR) center, University of Toronto (http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip).

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

source_name: mutant, Pst-infiltrated leaves, 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6-10 ug total RNA. For the detailed protocol, please check the website http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip.

growth_protocol: The seedlings were grown in a growth chamber with a short day (8h light) illumination at 20C.

extract_protocol: Phenol/chloroform extraction and LiCl purification of total RNA were performed.

treatment_protocol: The leaves of wild type and mutant plants were or were not infiltrated with a Pst suspension at the concentration of 10-5 cfu ml-1.

value: lht1 mutant

value: leaf

value: three weeks

value: Pseudomonas syringae pv. tomato DC3000 (Pst) infection

tag: treatment time


title: mutant, untreated, biological rep2

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0717

source_name: mutant, untreated leaves

value: untreated


title: mutant, Pst_48h, biological rep3

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0819


title: mutant, Pst_48h, biological rep1

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0720


title: wild type, Pst_48h, biological rep1

description:
Gene expression data from 3-week-old wild type leaves.
bot0718

source_name: wild type, Pst-infiltrated leaves, 48h

value: wild type


title: mutant, untreated, biological rep3

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0817


title: wild type, untreated, biological rep2

description:
Gene expression data from 3-week-old wild type leaves.
bot0715

source_name: wild type, untreated leaves


title: wild type, untreated, biological rep3

description:
Gene expression data from 3-week-old wild type leaves.
bot0816


title: wild type, Pst_48h, biological rep2

description:
Gene expression data from 3-week-old wild type leaves.
bot0719


title: GV3101 3hpi 2

status: Public on Nov 19 2009

city: Wuerzburg

first: Rosalia

last: Deeken

address: Julius-von-Sachs-Platz 2

department: Botany I; Plant Molecular Physiology & Biophysics

institute: University of Wuerzburg, Julius-von-Sachs-Institute

description: Gene expression data of reference tissue were compared with those of inoculated tissue.

hyb_protocol: Affymetrix protocol.

scan_protocol: The GeneChip® Scanner 3000 7G is also controlled by GeneChip® Operating Software(GCOS).

data_processing: VSN (variance stabilization normalization, reference: Huber et al. (2002) Bioinformatics 18: suppl. 1, S96-S104)

source_name: wounded inflorescence stalk inoculated with GV3101

label_protocol: Affymetrix protocol.

growth_protocol: Arabidopsis thaliana plants were cultivated in a growth chamber under short-day conditions (8 h of light, 120 µE) at 22°C and 16°C during the dark period (16 h). Agrobacteria were grown on YEB plates over night.

extract_protocol: Total RNA was extracted, including digestion of DNA, from plant tissue samples by using the RNeasy Plant Mini Kit according to manufacturer’s protocol (Qiagen, Hilden, Germany).

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle and inoculated with A. tumefaciens strain GV3101. Agrobacteria were scratched from the surface of an agar plate with a bent pipette tip by preventing contamination with medium and evenly spread on the wounded inflorescence stalk area immediately after wounding. Inoculated plants were grown for another three hours.

value: wounded inflorescence stalk segments

tag: inoculant

value: inoculated with Agrobacterium tumefaciens strain GV3101, lacking the T-DNA but not virulence factors


title: C58 3hpi 5

source_name: wounded inflorescence stalk inoculated with C58

growth_protocol: Arabidopsis thaliana plants were cultivated in growth chambers under short-day conditions (8 h of light, 120 µE) at 22°C and 16°C during the dark period (16 h). Agrobacteria were grown on YEB plates over night.

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle and inoculated with A. tumefaciens strain C58. Agrobacteria were scratched from the surface of an agar plate with a bent pipette tip by preventing contamination with medium and evenly spread on the wounded inflorescence stalk area immediately after wounding. Inoculated plants were grown for another three hours.

value: inoculated with Agrobacterium tumefaciens strain C58


title: C58 3hpi 4


title: Reference 3hpi 6

source_name: wounded inflorescence stalk

growth_protocol: Arabidopsis thaliana plants were cultivated in a growth chamber under short-day conditions (8 h of light, 120 µE) at 22°C and 16°C during the dark period (16 h).

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle, mock-inoculated and grown for another three hours.

value: mock


title: mutant, untreated, biological rep1

description:
Gene expression data from 3-week-old lth1 mutant leaves.
bot0716


title: Reference 3hpi 5


title: Reference 3hpi 4


title: GV3101 3hpi 1


title: C58 3hpi 6


title: GV3101 6dpi 1

growth_protocol: Arabidopsis thaliana plants (ecotype WS-2) were cultivated in growth chambers under short-day conditions (8 h of light, 120 µE) at 22°C and 16°C during the dark period (16 h). Agrobacteria were grown on YEB plates over night.

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle and inoculated with A. tumefaciens strain GV3101. Agrobacteria were scratched from the surface of an agar plate with a bent pipette tip by preventing contamination with medium and evenly spread on the wounded inflorescence stalk area immediately after wounding. Inoculated plants were grown for another six days.


title: GV3101 6dpi 2


title: C58 6dpi 3

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle and inoculated with A. tumefaciens strain C58. Agrobacteria were scratched from the surface of an agar plate with a bent pipette tip by preventing contamination with medium and evenly spread on the wounded inflorescence stalk area immediately after wounding. Inoculated plants were grown for another six days.


title: wild type, untreated, biological rep1

description:
Gene expression data from 3-week-old wild type leaves.
bot0714


title: GV3101 3hpi 3


title: C58 6dpi 1


title: C58 6dpi 2


title: GV3101 6dpi 3


title: Reference 6dpi 1

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle, mock-inoculated, and grown for another six days.


title: Reference 6dpi 3


title: Reference 6dpi 2


title: Reference 3hpi 3


title: C58 3hpi 2


title: Reference 3hpi 2


title: C58 3hpi 1


title: Reference 3hpi 1


title: C58 35dpi 2

description: Gene expression data of reference tissue were compared with those of 35-day-old mature crown gall tissue.

source_name: wounded inflorescence stalk inoculated with C58 (Tumor)

treatment_protocol: The base of the first emerging main inflorescence stalk (3-5 cm) of intact plants was wounded with a syringe needle and inoculated with A. tumefaciens strain C58. Agrobacteria were scratched from the surface of an agar plate with a bent pipette tip by preventing contamination with medium and evenly spread on the wounded inflorescence stalk area immediately after wounding. Inoculated plants were grown for another 35 days to develop tumors.


title: Reference 35dpi 3

treatment_protocol: The base of the first emerging main inflorescence stalks (3-5 cm) of an intact plant was wounded with a syringe needle, mock-inoculated and grown for another 35 days.


title: C58 35dpi 1


title: C58 35dpi 3


title: Reference 35dpi 1


title: C58 3hpi 3


title: Reference 35dpi 4


title: Reference 35dpi 2


title: Gronlund_1-3_BR1+GA-30mins_Rep1_ATH1

status: Public on Nov 18 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description: After sterilisation, the seeds were incubated in water at 4ºC for 72 hours, in the dark. All seeds were placed in a 1.5ml eppendorf tube containing 70% ethanol with shaking for 3 minutes. The ethanol was removed and replaced with 10% bleach/0.1% Tween-20 for a further 3 minutes . The samples were washed by rinsing with sterile H2O for 2 minutes; this was repeated 4 times. GA2oxOE seeds were plated onto plates containing 0.7% Gelrite (Duchefa)0.05% MES (Sigma), 1x Murashige and Skoog (Duchefa), 1% Sucrose (Duchefa) at pH 5.8. The plates were stood at an angle of 70o from the horizontal. The plants were grown under continuous light (150umol-2.sec-1)at 22C. After six days seedlings were either treated with water or 5 uM GA4 for 0, 30, 60 and 180 min. Approximately 400 hypocotyls were harvested per timepoint using a razorblade and after excision the hypocotyls were frozen in liquid nitrogen. The hypocotyls were ground using a TissueLyser (Qiagen) and total RNA extracted using a Qiagen RNeasy kit. 22 ºC average, 22 ºC day, 22 ºC night 60 % average, 60 % day, 60 % night Murashige & Skoog basal salt mixture Constant light

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

extract_protocol: Qiagen RNeasy kit protocol

value: whole plant

tag: strain

tag: genome/variation

value: knock out mutation in Pcga2ox1


title: Gronlund_1-9_BR2-30mins_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

tag: tissue


title: Gronlund_1-7_BR1+GA-180mins_Rep1_ATH1


title: Gronlund_1-4_BR1-60mins_Rep1_ATH1


title: Gronlund_1-6_BR1-180mins_Rep1_ATH1


title: Gronlund_1-2_BR1-30mins_Rep1_ATH1


title: Gronlund_1-10_BR2+GA-30mins_Rep2_ATH1


title: Gronlund_1-15_BR3-0mins_Rep3_ATH1


title: Gronlund_1-14_BR2+GA-180mins_Rep2_ATH1


title: Gronlund_1-12_BR2+GA-60mins_Rep2_ATH1


title: Gronlund_1-5_BR1+GA-60mins_Rep1_ATH1


title: Gronlund_1-11_BR2-60mins_Rep2_ATH1


title: Gronlund_1-8_BR2-0mins_Rep2_ATH1


title: Gronlund_1-16_BR3-30mins_Rep3_ATH1


title: C58 35dpi 4


title: Gronlund_1-17_BR3+GA-30mins_Rep3_ATH1


title: Gronlund_1-19_BR3+GA-60mins_Rep3_ATH1


title: Gronlund_1-21_BR3+GA-180mins_Rep3_ATH1


title: Lager_1-10_8hr-pH6_Rep1_ATH1

description: Two days at 4C, 1 min 70% EtOH, 5 min 50% bleach, 0.5% Tween-20. Rinse with water 3 times. Seeds were germinated in tubes filled with 0.7% agarose, tubes, tubes were transferred to hydroponic cultures after germination.The hydroponic cultures were not kept sterile. The media used is a basic nutrient solution as previously described (Somerville and Ogren, 1982) but at half strength [2.5 mM KNO3, 1.25 mM KH2PO4 (pH5.6), 1 mM MgSO4, 1 mM Ca(NO3)2, 25 microM Fe-EDTA and the reported micronutrient mix at 1x concentration. 23 ðC average, 23 ðC day, 23 ðC night not controlled % average, not controlled % day, not controlled % night

source_name: Col-0 (Columbia)

tag: treatment group

value: 8hr, pH 6

value: Col-0 (Columbia)

tag: developmental stage

value: 3.90 weeks

value: roots

tag: stock code


title: Lager_1-7_8hr-pH4.5_Rep1_ATH1


title: Lager_1-11_8hr-pH6_Rep2_ATH1


title: Gronlund_1-1_BR1-0mins_Rep1_ATH1


title: Lager_1-4_1hr-pH6_Rep1_ATH1

value: 1hr, pH 6


title: Mitra_2-21_pad4-PsmES4326-24hpi_Rep3_ATH1

description: Seeds were stratified in 0.1 % Agar for 3 days at 4 degrees Celsius. Growth chamber BM-2 (Berger's) 75% 22oC 12 hr

growth_protocol: Seeds were planted in BM-2 soil (Berger's) at a density of 9 plants/pot. Flats of 8 pots/flat were placed in a growth chamber and grown at 22 degrees celsius, 75% humidity for a 12 hour day length

tag: strain/ecotype

value: 4 weeks

value: pad4 EMS induced mutation


title: Lager_1-12_8hr-pH6_Rep3_ATH1


title: Lager_1-6_1hr-pH6_Rep3_ATH1


title: Gronlund_1-13_BR2-180mins_Rep2_ATH1


title: Lager_1-9_8hr-pH4.5_Rep3_ATH1


title: Mitra_2-24_sid2-PsmES4326-24hpi_Rep3__ATH1

description: Seeds stratified in 0.1 % Agar for 2-3 days.. Growth chamber BM-2 (Berger's) 75% 22oC 12 hr

growth_protocol: Plants grown in BM-2 soil at 22 degrees celsius with 75% humidity and 12hr day length

value: leaf

value: sid2 Radiation induced mutation


title: Gronlund_1-18_BR3-60mins_Rep3_ATH1


title: Gronlund_1-20_BR3-180mins_Rep3_ATH1


title: Lager_1-5_1hr-pH6_Rep2_ATH1


title: Lager_1-2_1hr-pH4.5_Rep2_ATH1


title: Mitra_2-19_pad4-PsmES4326-24hpi_Rep1_ATH1


title: Mitra_2-22_sid2-PsmES4326-24hpi_Rep1_ATH1


title: Lager_1-3_1hr-pH4.5_Rep3_ATH1


title: Mitra_2-20_pad4-PsmES4326-24hpi_Rep2_ATH1


title: Lager_1-8_8hr-pH4.5_Rep2_ATH1


title: Mitra_2-15_npr1-PsmES4326-24hpi_Rep3_ATH1

value: npr1-1 EMS induced mutation


title: Mitra_2-18_pad2-PsmES4326-24hpi_Rep3_ATH1

value: pad2 EMS induced mutation


title: Mitra_2-16_pad2-PsmES4326-24hpi_Rep1_ATH1


title: Lager_1-1_1hr-pH4.5_Rep1_ATH1


title: Mitra_2-12_ein2-PsmES4326-24hpi_Rep3_ATH1

value: ein2 EMS induced mutation


title: Mitra_2-13_npr1-PsmES4326-24hpi_Rep1_ATH1


title: Mitra_2-23_sid2-PsmES4326-24hpi_Rep2_ATH1


title: Mitra_2-17_pad2-PsmES4326-24hpi_Rep2_ATH1


title: Mitra_2-14_npr1-PsmES4326-24hpi_Rep2_ATH1


title: Mitra_2-5_Col0-mock-24hpi_Rep2_ATH1


title: Mitra_2-8_Col0-PsmES4326-24hpi_Rep2_ATH1


title: Mitra_2-11_ein2-PsmES4326-24hpi_Rep2_ATH1


title: Mitra_2-10_ein2-PsmES4326-24hpi_Rep1_ATH1


title: Mitra_2-9_Col0-PsmES4326-24hpi_Rep3_ATH1


title: Quint_2-80_BI-1-1h_Rep2_ATH1

description:
After sterilization, seeds were incubated in sterile water in the dark for 5 days at 4Â°C prior to cultivation  Seed were washed briefly (4 min) in 70% ethanol followed by an 8 min treatment with bleach. Afterwards seeds were washed 3 times with sterile deionised water. After final wash, seeds were resuspended in sterile deionised water and subjected to stratification  Sterilized and stratified seeds were grown in 300 ml Erlenmeyer flasks containing 100 ml of sterile liquid ATS medium. Plants were cultivated on a shaker for 7 days at 90 rpm and 22 Â°C under constant white fluorescent light. For the last 24 hours of cultivation the light was filtered by yellow plexiglas (yellow 2208)to prevent photodegradation of IAA.  Reference for ATS medium:
Lincoln C, Britton JH, Estelle M (1990) Growth and Development of the axr1 Mutants of Arabidopsis. Plant Cell 2: 1071-1080  autoclaved  22 Â°C average, 22 Â°C day, 22 Â°C night 70 % average, 70 % day, 70 % night Own medium: ATS medium according to Lincoln et al. (1990)  Constant light


title: Mitra_2-2_coi1-PsmES4326-24hpi_Rep2_ATH1

value: coi1 induced_mutation


title: Mitra_2-3_coi1-PsmES4326-24hpi_Rep3_ATH1


title: Quint_2-84_BI-1-3h_Rep3_ATH1


title: Quint_2-83_BI-1-3h_Rep2_ATH1


title: Quint_2-75_BI-1-0h_Rep3_ATH1


title: Mitra_2-6_Col0-mock-24hpi_Rep3_ATH1


title: Quint_2-77_BI-1-30min_Rep2_ATH1


title: Mitra_2-1_coi1-PsmES4326-24hpi_Rep1_ATH1


title: Quint_2-78_BI-1-30min_Rep3_ATH1


title: Quint_2-79_BI-1-1h_Rep1_ATH1


title: Quint_2-81_BI-1-1h_Rep3_ATH1


title: Mitra_2-4_Col0-mock-24hpi_Rep1_ATH1


title: Quint_2-82_BI-1-3h_Rep1_ATH1


title: Mitra_2-7_Col0-PsmES4326-24hpi_Rep1_ATH1


title: Quint_2-74_BI-1-0h_Rep2_ATH1


title: Quint_2-73_BI-1-0h_Rep1_ATH1


title: Quint_2-76_BI-1-30min_Rep1_ATH1


title: Quint_2-1_Bay-0-0h_Rep1_ATH1

source_name: Bay-0 x Shahdara Core-Pop Bay-0 Parent

value: recombinant inbred line


title: Quint_2-71_Col-0-3h_Rep2_ATH1


title: Quint_2-4_Bay-0-30min_Rep1_ATH1


title: Quint_2-3_Bay-0-0h_Rep3_ATH1


title: Quint_2-72_Col-0-3h_Rep3_ATH1


title: Quint_2-2_Bay-0-0h_Rep2_ATH1


title: Quint_2-8_Bay-0-1h_Rep2_ATH1


title: Quint_2-7_Bay-0-1h_Rep1_ATH1


title: Quint_2-6_Bay-0-30min_Rep3_ATH1


title: Quint_2-11_Bay-0-3h_Rep2_ATH1


title: Quint_2-9_Bay-0-1h_Rep3_ATH1


title: Quint_2-17_Sha-30min_Rep2_ATH1

source_name: Shakdara (Sha)

value: Shakdara (Sha)


title: Quint_2-18_Sha-30min_Rep3_ATH1

value: whole plant


title: Quint_2-20_Sha-1h_Rep2_ATH1


title: Quint_2-19_Sha-1h_Rep1_ATH1


title: Quint_2-12_Bay-0-3h_Rep3_ATH1


title: Quint_2-15_Sha-0h_Rep3_ATH1


title: Quint_2-21_Sha-1h_Rep3_ATH1


title: Quint_2-5_Bay-0-30min_Rep2_ATH1


title: Quint_2-16_Sha-30min_Rep1_ATH1


title: Quint_2-14_Sha-0h_Rep2_ATH1


title: Quint_2-23_Sha-3h_Rep2_ATH1


title: Quint_2-24_Sha-3h_Rep3_ATH1


title: Quint_2-25_C24-0h_Rep1_ATH1


title: Quint_2-13_Sha-0h_Rep1_ATH1


title: Quint_2-10_Bay-0-3h_Rep1_ATH1


title: Quint_2-22_Sha-3h_Rep1_ATH1


title: Quint_2-26_C24-0h_Rep2_ATH1


title: Quint_2-27_C24-0h_Rep3_ATH1


title: Quint_2-28_C24-30min_Rep1_ATH1


title: Quint_2-29_C24-30min_Rep2_ATH1


title: Quint_2-34_C24-3h_Rep1_ATH1


title: Quint_2-30_C24-30min_Rep3_ATH1


title: Quint_2-33_C24-1h_Rep3_ATH1


title: Quint_2-32_C24-1h_Rep2_ATH1


title: Quint_2-31_C24-1h_Rep1_ATH1


title: Quint_2-36_C24-3h_Rep3_ATH1


title: Quint_2-39_Bur-0h_Rep3_ATH1


title: Quint_2-41_Bur-0-30min_Rep2_ATH1


title: Quint_2-45_Bur-0-1h_Rep3_ATH1


title: Quint_2-46_Bur-0-3h_Rep1_ATH1


title: Quint_2-47_Bur-0-3h_Rep2_ATH1


title: Quint_2-44_Bur-0-1h_Rep2_ATH1


title: Quint_2-49_Fei-0-0h_Rep1_ATH1


title: Quint_2-50_Fei-0-0h_Rep2_ATH1


title: Quint_2-38_Bur-0h_Rep2_ATH1


title: Quint_2-37_Bur-0h_Rep1_ATH1


title: Quint_2-43_Bur-0-1h_Rep1_ATH1


title: Quint_2-42_Bur-0-30min_Rep3_ATH1


title: Quint_2-40_Bur-0-30min_Rep1_ATH1


title: Quint_2-48_Bur-0-3h_Rep3_ATH1


title: Quint_2-35_C24-3h_Rep2_ATH1


title: Quint_2-53_Fei-0-30min_Rep2_ATH1


title: Quint_2-51_Fei-0-0h_Rep3_ATH1


title: Quint_2-57_Fei-0-1h_Rep3_ATH1


title: Quint_2-60_Fei-0-3h_Rep3_ATH1


title: Quint_2-62_Col-0-0h_Rep2_ATH1


title: Quint_2-52_Fei-0-30min_Rep1_ATH1


title: Quint_2-54_Fei-0-30min_Rep3_ATH1


title: Quint_2-59_Fei-0-3h_Rep2_ATH1


title: Quint_2-55_Fei-0-1h_Rep1_ATH1


title: Quint_2-56_Fei-0-1h_Rep2_ATH1


title: Quint_2-63_Col-0-0h_Rep3_ATH1


title: Quint_2-65_Col-0-30min_Rep2_ATH1


title: Quint_2-64_Col-0-30min_Rep1_ATH1


title: Quint_2-61_Col-0-0h_Rep1_ATH1


title: Quint_2-68_Col-0-1h_Rep2_ATH1