title: RUNX1CGFPw_hESC_d7_34lo_41lo

city: Parkville

first: Andrew

last: Elefanty

state: Victoria

address: Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

description: CHIP 6747965016 SAMPLE G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Initial data analysis was performed using GenomeStudio Version 2010.2 (Illumina), using average normalization across all the samples. Further data analysis was performed in R/BioConductor using algorithms within the lumi package (function: bgAdjust.affy and quantile normalization)

source_name: hESC, differentiated, d7 sorted

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

growth_protocol: The parent cell line was maintained on mouse feeder cells in KOSR containing medium supplemented with 10 ng/ml FGF2. Differentiation was performed as spin EBs in APEL medium (Ng et al Nature Protocols 2008). For the first 4 days, medium was supplemented with BMP4, VEGF, SCF and Activin. Medium was changed at d4 to fresh APEL medium supplemented with BMP4, VEGF, SCF, FGF2 and IGF2.

extract_protocol: Total RNA was extracted from the collected cell fractions (High Pure RNA Isolation Kit, Roche Applied Science) and RNA quality was assessed using a NanoDrop 2000 analyzer (Thermo Scientific)

value: differentiated, d7 sorted

tag: cell line

value: hESC


title: E. coli incubated with GST protein for 10 min, biological rep2

status: Public on Jan 13 2015

type: RNA

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

hyb_protocol: Following fragmentation, 1.0-1.7 µg of cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip E. coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

label: biotin

molecule: total RNA

organism: Escherichia coli

source_name: E. coli incubated with GST protein alone for 10 min

label_protocol: The cDNA was purified using MinElute PCR Purification Kit (Qiagen), fragmented into 50~200 bp with DNase I (Takara-Bio, Kyoto, Japan) (0.06 units/μg DNA), labeled with biotin using terminal deoxynucleotidyl transferase (Promega KK, Tokyo, Japan) and GeneChip Labeling Reagent (Affymetrix, Santa Clara, CA, USA).

growth_protocol: E. coli BW25113 were maintained in Luria-Bertani medium at 37ºC for about 14 h until they reached the stationary phase of cell growth before treatment.

extract_protocol: Total RNA was purified with an RNeasy micro kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: The E. coli strain BW25113 (2 x 10^9) suspended with insect saline (0.13 M NaCl, 4.7 mM KCl, 1.9 mM CaCl2), was incubated with GST or GST-fused Drosophila immune proteins for 10 min at room temperature.

tag: strain

tag: genotype/variation

value: wild type

tag: incubated with

value: GST alone (3 μM; control)

tag: incubation duration

value: 10 min


title: 278_SM

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

description: Sample name: 278

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed at the UCLA Neuroscience Genomics Core (UNGC).

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value >0.05 in all samples) and normalizing with neqc using the control probes.

organism: Mus musculus

source_name: skeletal muscle

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX)

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks

extract_protocol: After sacrifice, an approximately 50-mg piece of the quadriceps muscle was excised and disrupted and homogenized using a TissueRupter.  Total RNA was isolated using Qiazol and Rneasy spin columns. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: tissue

value: skeletal muscle (quadriceps)

tag: gender

value: M

tag: age

value: 16 weeks


title: 296_SM

description: Sample name: 296


title: RUNX1CGFPw_hESC_d7_34hi_41-

description: CHIP 6747965016 SAMPLE F

organism: Homo sapiens

tag: treatment

tag: cell type


title: E. coli incubated with GST protein for 10 min, biological rep3


title: 254_SM

description: Sample name: 254

value: MA/MyJ


title: RUNX1CGFPw_hESC_d7_34lo_41-

description: CHIP 6747965016 SAMPLE E


title: E9.5Osr1-GFP-positive_Itga8-positive_Pdgfra-negative

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

institute: Kumamoto Univ.

description: Gene expression

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocolGE1_107_Sep09 and Grid: 028005_D_F_20100804) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E9.5 caudal half of the embryo

label_protocol: 10ng of total RNA was amplified using WT–Ovation Pico RNA　Amplification System (NuGEN Technologies, Inc., Cat.3300) according to the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Cat.5190-0449) according to the manufacturer's instructions, followed by Microcon YM-30 column purification (Millipore Corporation, Billerica, MA, USA). After amplification and labeling, cDNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophometer and an Agilent Bioanalyzer.

growth_protocol: nothing

extract_protocol: Each embryonic progenitor cells were sorted by a FACS Aria II (Becton Dickinson). Total RNA was extracted using "Rneasy Plus Micro Kit" purchased from QIAGEN following manufacture's protocol.

treatment_protocol: nothing

value: embryo

tag: developmental stage

tag: genotype

value: Osr1-GFP knock-in


title: E11.5MM_Osr1-GFP-positive_others

description: Gene expression

source_name: E11.5 metanephric mesenchyme


title: E11.5MM_Osr1-GFP-positive_Itga8-positive_Pdgfra-negative

description: Gene expression


title: E9.5Osr1-GFP-positive_others

description: Gene expression


title: RUNX1CGFPw_hESC_d7_34-_41-

description: CHIP 6747965016 SAMPLE D


title: E8.5Osr1-GFP-negative

description: Gene expression

source_name: E8.5 embryo


title: E9.5Osr1-GFP-negative

description: Gene expression


title: TCE_2mM(3)_8h

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

country: Netherlands

institute: Maastricht University

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(3)_8h

hyb_protocol: 12.5µg of cRNA was used. The GeneTitan arrays were hybridized, washed and stained using the GeneTitan hybridization, wash and stain kit for 3’ IVT Arrays and GeneTitan Operating Software and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008).

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing, or fresh medium containing a genotoxic of non-genotoxic carcinogen

value: hepatocellular carcinoma

value: liver

tag: compound and dose

value: 2mM tetrachloroethylene_8h_Biological replicate 3

tag: time (h)


title: 252_SM

description: Sample name: 252


title: E8.5Osr1-GFP-positive

description: Gene expression


title: TCE_2mM(3)-72h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(3)-72h

value: 2mM tetrachloroethylene_72h_Biological replicate 3


title: TCE_2mM(2)_4h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(2)_4h

value: 2mM tetrachloroethylene_4h_Biological replicate 2


title: TCE_2mM(2)_8h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(2)_8h

value: 2mM tetrachloroethylene_8h_Biological replicate 2


title: RUNX1CGFPw_hESC_d7

description: CHIP 5975034034 SAMPLE H

source_name: hESC, differentiated, d7

value: differentiated, d7


title: 225_SM

description: Sample name: 225


title: RUNX1CGFPw_hESC_d8

description: CHIP 5975034034 SAMPLE I

source_name: hESC, differentiated, d8

value: differentiated, d8

value: hESC


title: TCE_2mM(2)-72h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(2)-72h

value: 2mM tetrachloroethylene_72h_Biological replicate 2


title: 210_SM

description: Sample name: 210


title: TCE_2mM(1)_8h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(1)_8h

value: 2mM tetrachloroethylene_8h_Biological replicate 1


title: TCE_2mM(1)-72h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(1)-72h

value: 2mM tetrachloroethylene_72h_Biological replicate 1


title: RUNX1CGFPw_hESC_d4

description: CHIP 5975034034 SAMPLE E

source_name: hESC, differentiated, d4

value: differentiated, d4


title: TCE_2mM(3)_4h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(3)_4h

value: 2mM tetrachloroethylene_4h_Biological replicate 3


title: EtOH_Cont(3)-72h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(3)-72h

value: 0.5% ethanol control 72h_Biological replicate 3


title: 201_SM

description: Sample name: 201

value: skeletal muscle (quadriceps)

value: M

value: 16 weeks


title: EtOH_Cont(3)_8h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(3)_8h

value: hepatocellular carcinoma

value: liver

value: 0.5% ethanol control 8h_Biological replicate 3


title: RUNX1CGFPw_hESC_d5

description: CHIP 5975034034 SAMPLE F

source_name: hESC, differentiated, d5

value: differentiated, d5


title: 194_SM

description: Sample name: 194


title: RUNX1CGFPw_hESC_d6

description: CHIP 5975034034 SAMPLE G

source_name: hESC, differentiated, d6

value: differentiated, d6


title: EtOH_Cont(2)-72h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(2)-72h

value: 0.5% ethanol control 72h_Biological replicate 2


title: RUNX1CGFPw_hESC_d3

description: CHIP 5975034034 SAMPLE D

source_name: hESC, differentiated, d3

value: differentiated, d3


title: EtOH_Cont(2)_4h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(2)_4h

value: 0.5% ethanol control 4h_Biological replicate 2


title: 179_SM

description: Sample name: 179


title: TCE_2mM(1)_4h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
TCE_2mM(1)_4h

value: 2mM tetrachloroethylene_4h_Biological replicate 1


title: 221_SM

description: Sample name: 221


title: EtOH_Cont(1)-72h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(1)-72h

value: 0.5% ethanol control 72h_Biological replicate 1


title: 188_SM

description: Sample name: 188


title: RUNX1CGFPw_hESC_d2

description: CHIP 5975034034 SAMPLE C

source_name: hESC, differentiated, d2

value: differentiated, d2

value: hESC


title: 171_SM

description: Sample name: 171

value: SWR/J


title: 173_SM

description: Sample name: 173


title: HBSS_Cont(3)-72h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(3)-72h

value: 0.5% HBSS control 72h_Biological replicate 3


title: EtOH_Cont(2)_8h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(2)_8h

value: 0.5% ethanol control 8h_Biological replicate 2


title: 150_SM

description: Sample name: 150

value: skeletal muscle (quadriceps)

value: M


title: HBSS_Cont(3)_4h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(3)_4h

value: hepatocellular carcinoma

value: 0.5% HBSS control 4h_Biological replicate 3


title: 144_SM

description: Sample name: 144

value: 16 weeks


title: HBSS_Cont(2)-72h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(2)-72h

value: liver

value: 0.5% HBSS control 72h_Biological replicate 2


title: HBSS_Cont(2)_8h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(2)_8h

value: 0.5% HBSS control 8h_Biological replicate 2


title: HBSS_Cont(1)_4h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(1)_4h

value: 0.5% HBSS control 4h_Biological replicate 1


title: 143_SM

description: Sample name: 143

value: PL/J


title: HBSS_Cont(1)-72h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(1)-72h

value: 0.5% HBSS control 72h_Biological replicate 1


title: HBSS_Cont(1)_8h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(1)_8h

value: 0.5% HBSS control 8h_Biological replicate 1


title: EtOH_Cont(1)_4h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(1)_4h

value: 0.5% ethanol control 4h_Biological replicate 1


title: 138_SM

description: Sample name: 138


title: HBSS_Cont(3)_8h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(3)_8h

value: 0.5% HBSS control 8h_Biological replicate 3


title: Dman_250uM(2)-72h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(2)-72h

value: 250µM D-mannitol_72h_Biological replicate 2


title: Dman_250uM(3)_8h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(3)_8h

value: 250µM D-mannitol_8h_Biological replicate 3


title: 132_SM

description: Sample name: 132


title: RUNX1CGFPw_hESC_d1

description: CHIP 5975034034 SAMPLE B

source_name: hESC, differentiated, d1

value: differentiated, d1

value: hESC


title: Dman_250uM(3)_4h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(3)_4h

value: 250µM D-mannitol_4h_Biological replicate 3


title: Dman_250uM(2)_4h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(2)_4h

value: hepatocellular carcinoma

value: 250µM D-mannitol_4h_Biological replicate 2


title: 134_SM

description: Sample name: 134

value: skeletal muscle (quadriceps)

value: M

value: 16 weeks


title: 129_SM

description: Sample name: 129


title: Dman_250uM(1)_8h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(1)_8h

value: liver

value: 250µM D-mannitol_8h_Biological replicate 1


title: 85_SM

description: Sample name: 85


title: Dman_250uM(2)_8h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(2)_8h

value: 250µM D-mannitol_8h_Biological replicate 2


title: Dman_250uM(3)-72h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(3)-72h

value: 250µM D-mannitol_72h_Biological replicate 3


title: TPA_500nM(3)_8h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(3)_8h

value: 500nM Tetradecanoyl phorbol acetate_8h_Biological replicate 3


title: 111_SM

description: Sample name: 111

value: KK/HlJ


title: 71_SM

description: Sample name: 71

value: NON/ShiLtJ


title: TPA_500nM(3)_4h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(3)_4h

value: 500nM Tetradecanoyl phorbol acetate_4h_Biological replicate 3


title: RUNX1CGFPw_hESC_d0

description: CHIP 5975034034 SAMPLE A

source_name: hESC, differentiated, d0

value: differentiated, d0


title: TPA_500nM(2)-72h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(2)-72h

value: 500nM Tetradecanoyl phorbol acetate_72h_Biological replicate 2


title: Dman_250uM(1)_4h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(1)_4h

value: 250µM D-mannitol_4h_Biological replicate 1


title: TPA_500nM(2)_8h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(2)_8h

value: 500nM Tetradecanoyl phorbol acetate_8h_Biological replicate 2


title: TPA_500nM(1)_4h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(1)_4h

value: hepatocellular carcinoma

value: 500nM Tetradecanoyl phorbol acetate_4h_Biological replicate 1


title: Dman_250uM(1)-72h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
Dman_250uM(1)-72h

value: 250µM D-mannitol_72h_Biological replicate 1


title: 58_SM

description: Sample name: 58

value: skeletal muscle (quadriceps)

value: M

value: FVB/NJ


title: TPA_500nM(3)-72h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(3)-72h

value: liver

value: 500nM Tetradecanoyl phorbol acetate_72h_Biological replicate 3


title: HBSS_Cont(2)_4h

description:
Effect of HBBS solvent control on mRNA levels in HepG2 cells
HBSS_Cont(2)_4h

value: 0.5% HBSS control 4h_Biological replicate 2


title: TPA_500nM(1)-72h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(1)-72h

value: 500nM Tetradecanoyl phorbol acetate_72h_Biological replicate 1


title: Fu_2mM(3)-72h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(3)-72h

value: 2mM Furan_72h_Biological replicate 3


title: Fu_2mM(3)_8h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(3)_8h

value: 2mM Furan_8h_Biological replicate 3


title: Fu_2mM(3)_4h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(3)_4h

value: 2mM Furan_4h_Biological replicate 3


title: 47_SM

description: Sample name: 47

value: 16 weeks

value: AKR/J


title: 31_SM

description: Sample name: 31

value: A/J


title: Fu_2mM(2)-72h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(2)-72h

value: 2mM Furan_72h_Biological replicate 2


title: TPA_500nM(2)_4h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(2)_4h

value: hepatocellular carcinoma

value: 500nM Tetradecanoyl phorbol acetate_4h_Biological replicate 2


title: 43_SM

description: Sample name: 43

value: SJL/J


title: TPA_500nM(1)_8h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
TPA_500nM(1)_8h

value: 500nM Tetradecanoyl phorbol acetate_8h_Biological replicate 1


title: Fu_2mM(2)_8h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(2)_8h

value: 2mM Furan_8h_Biological replicate 2


title: 64_SM

description: Sample name: 64

value: skeletal muscle (quadriceps)

value: M


title: Fu_2mM(1)-72h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(1)-72h

value: liver

value: 2mM Furan_72h_Biological replicate 1


title: atf1Δ H2O2 exp3

city: Seoul

first: Dong-Hoon

last: Yang

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University

description: Ctr vs atf1Δ H2O2 exp3

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (1000 rpm, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific).  The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides.  To prevent slides from drying, 5 ml of 3x SSC buffer was applied into the hybridization chamber, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100A scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity (Axon) by employing Lowess normalization (Lowess M log ratio (F532 Mean - B532, F635 Mean - B635)), reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans

source_name: atf1Δ H2O2 exp3

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min. Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.3 µl RNase inhibitor (iNtRON), 1.2 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM). 40 µl DEPC-treated water), 1.5 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas), 6 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase buffer, 3 µl DEPC-treated water) was added and incubated at 42°C for 2 hrs. Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPC-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr. For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1 µl of each dye was aliquoted into separate tubes. The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min. The cDNAs prepared from pooled reference RNAs were mixed with Cy5 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy3. Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: The wild-type H99 strain and atf1Δ (YSB676) mutant strain were grown in 50 ml YPD medium at 30°C for 16 h. Then 5 ml of the overnight culture was inoculated into 100 ml of fresh YPD medium and further incubated for 4 h at 30°C  to an optical density at 600 nm (OD600 =1.0)

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of easy-BLUE reagent (easy-BLUE reagent, iNtRON), and allowed to incubate at room temperature for 5 min. Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor). Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature. Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min. The pellet was dried and resuspended with 400 µl DEPC-treated water. Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT and atf1Δ mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: The inoculated 100 ml YPD medium was divided into two 50 ml flasks. One is treated with 2.5 mM of hydrogen peroxide and incubated for 30 min at 30°C. Another 50 ml culture has no hydrogen peroxide treatment and was grown under the same condition.

tag: hydrogen peroxide treatment

value: treated

source_name: pooled total RNA from all strain all treatment


title: atf1Δ H2O2 exp2

description: Ctr vs atf1Δ H2O2 exp2

source_name: atf1Δ H2O2 exp2


title: atf1Δ H2O2 exp1

description: Ctr vs atf1Δ H2O2 exp1

source_name: atf1Δ H2O2 exp1


title: DZN_250uM(3)-72h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(3)-72h

value: 250µM Diazinon_72h_Biological replicate 3


title: DZN_250uM(3)_8h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(3)_8h

value: 250µM Diazinon_8h_Biological replicate 3


title: Fu_2mM(1)_8h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(1)_8h

value: 2mM Furan_8h_Biological replicate 1


title: Fu_2mM(1)_4h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(1)_4h

value: 2mM Furan_4h_Biological replicate 1


title: DZN_250uM(3)_4h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(3)_4h

value: 250µM Diazinon_4h_Biological replicate 3


title: DZN_250uM(2)-72h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(2)-72h

value: 250µM Diazinon_72h_Biological replicate 2


title: atf1Δ_exp3

description: Ctr vs atf1Δ_exp3

value: not treated


title: WT H2O2 exp1

description: Ctr vs WT H2O2 exp1

source_name: WT H2O2 exp1

value: wild type H99


title: DZN_250uM(2)_8h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(2)_8h

value: hepatocellular carcinoma

value: 250µM Diazinon_8h_Biological replicate 2


title: DZN_250uM(2)_4h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(2)_4h

value: 250µM Diazinon_4h_Biological replicate 2


title: DMSO_Cont(3)_4h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(3)_4h

value: 0.5% DMSO control 4h_Biological replicate 3


title: WT H2O2 exp3

description: Ctr vs WT H2O2 exp3

source_name: WT H2O2 exp3


title: DMSO_Cont(3)-72h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(3)-72h

value: 0.5% DMSO control 72h_Biological replicate 3


title: DZN_250uM(1)_8h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(1)_8h

value: 250µM Diazinon_8h_Biological replicate 1


title: DZN_250uM(1)-72h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(1)-72h

value: liver

value: 250µM Diazinon_72h_Biological replicate 1


title: WT_exp2

description: Ctr vs WT_exp2


title: Fu_2mM(2)_4h

description:
Effect of Furan on mRNA levels in HepG2 cells
Fu_2mM(2)_4h

value: 2mM Furan_4h_Biological replicate 2


title: DMSO_Cont(2)-72h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(2)-72h

value: 0.5% DMSO control 72h_Biological replicate 2


title: atf1Δ_exp1

description: Ctr vs atf1Δ_exp1


title: WT H2O2 exp2

description: Ctr vs WT H2O2 exp2

source_name: WT H2O2 exp2

value: treated


title: WT_exp1

description: Ctr vs WT_exp1


title: atf1Δ_exp2

description: Ctr vs atf1Δ_exp2


title: DZN_250uM(1)_4h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
DZN_250uM(1)_4h

source_name: hepatocellular carcinoma cell line

value: 250µM Diazinon_4h_Biological replicate 1


title: DMSO_Cont(2)_8h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(2)_8h

value: 0.5% DMSO control 8h_Biological replicate 2


title: DMSO_Cont(2)_4h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(2)_4h

value: 0.5% DMSO control 4h_Biological replicate 2


title: DMSO_Cont(3)_8h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(3)_8h

value: 0.5% DMSO control 8h_Biological replicate 3


title: DMSO_Cont(1)-72h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(1)-72h

value: 0.5% DMSO control 72h_Biological replicate 1


title: fluorescent schizonts, biological rep1

city: Boston

first: Matthias

last: Marti

state: MA

address: 665 Huntington Avenue

institute: Harvard School of Public Health

hyb_protocol: RNA quality was assessed by Bioanalyzer (Agilent 2100 Bioanalyser RNA 60000 Nano), and high quality RNA samples were hybridized to GPL8604, an oligonucleotide array (Affymetrix) custom-designed for the P. falciparum 3D7 genome.

scan_protocol: Arrays were scanned with an emission wavelength of 560nm at 3um resolution using a confocal scanner(Affymetrix), and the signal intensity for each sequence feature on the array was determined using the Microarray Suite 5 (Affymetrix)

data_processing: The raw CEL files were condensed into GCT expression files using RMA and the default parameter settings in ExpressionFileCreator in GenePattern.

organism: Plasmodium falciparum

source_name: FACSAria II flow sorted fluorescent cells

label_protocol: Eight micrograms of total RNA was used for cDNA synthesis. An oligodT primer containing a phage T7 promoter at its 5’ end was used to prime the cDNA synthesis reaction following the manufacturer’s protocol (Invitrogen). The second strand of cDNA was then synthesized and double strand cDNA were purified using QIAquick purification kit (Qiagen). The faction of double strand cDNA was used for the synthesis of Biotin-Labeled cRNA (using ENZO BioArray High Yield RNA Transcript Labeling Kit) – IVT Reaction. The collected cRNA was cleaned up using the QIAGEN RNeasy mini kit following the manufacturer’s instruction.

growth_protocol: Parasites were maintained in O+ blood at 4% hematocrit in RPMI-1640 media supplemented with 10% human serum.  Cultures were kept at 37°C in a chamber containing mixed gas (5% CO2, 5% O2, 90% N2).

extract_protocol: Flow sorted cells were transferred directly into RNA lysis buffer (RNAeasy Micro Kit, Qiagen, Hildesheim, Germany) and subsequent RNA preparation was carried out according to the Manufacturer’s instructions. The eluted RNA was subjected to DNAse treatment using RQ1 RNAse-free DNAse (Promega, Madison, WI, USA), followed by another round of purification and elution into water.

treatment_protocol: Prior to induction of sexual commitment, asexual parasite cultures were synchronized for two cycles with 5% D-sorbitol. To induce a maximal number of sexually committed schizonts, highly synchronous ring stage parasites (0-2 h post invasion) were seeded into multiple T75 flasks 5 days prior to flow sorting, at a starting parasitemia of 0.1-0.25%. P2G12 wild-type (WT) and fluorescent 164/TdTom parasite lines were cultured alongside, in order to be able to properly gate the non-fluorescent population in preparation of flow sorting. To induce sexual commitment half of the medium was changed daily and 17h prior to sorting (at around 28h post invasion) parasites were stressed by doubling the medium volume. For flow sorting late schizont stage parasites were separated from uninfected RBCs using a Percoll gradient. P. falciparum infected RBCs were washed and resuspended in RPMI medium without Phenol-red. Cells were subsequently stained for 30 minutes with 0.5 μM Vvbrant DyeCycle Violet stain (Invitrogen, Eugene, OR, USA), which has fluorescence excitation and emission maxima of 369/437 nm, respectively, in complex with DNA. A FACSAria II flow cytometer (BD Biosciences, San Jose, CA, USA) equipped with a combination of 407 nm, 488 nm, 561 nm, 640 nm lasers was used for flow cytometry analysis and cell sorting. All experimental procedures with live cells were performed according to biosafety BL2+ level practice. To avoid the sorting of cell doublets or cell aggregates; single cells were sequentially gated based on FSC-H/FSC-W and SSC-H/SSC-W. Gating of fluorescent versus non-fluorescent schizonts was then done based on nuclear content using Vybrant dye violet and TdTom fluorescence, with the WT parasite as a negative control.


title: DMSO_Cont(1)_4h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(1)_4h

value: 0.5% DMSO control 4h_Biological replicate 1


title: DMSO_Cont(1)_8h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
DMSO_Cont(1)_8h

value: hepatocellular carcinoma

value: 0.5% DMSO control 8h_Biological replicate 1


title: AZA_250uM(3)-72h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(3)-72h

value: 250µM Azathriopine_72h_Biological replicate 3


title: fluorescent schizonts, biological rep2

value: FACSAria II flow sorted fluorescent cells


title: Peripheral_NK_3rd_rep4

city: Bunkyo

first: Yoichi

last: Ishida

state: Tokyo

address: Nippon Medical School

department: Molecular Anatomy

institute: Nippon Medical School

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 55 μl containing 2.2 μl of 25x Agilent fragmentation buffer, 11 μl of 10x Agilent blocking agent and 41.8 μl Nuclease-free water following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human GE 4×44 K, v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44 K array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20110325).

source_name: Peripheral blood NK cells, 3rd-trimester

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20 ng total RNA using a Low-Input QuickAmp Labeling Kit, One-Color (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification(QIAGEN,Valencia, CA). Dye incorporation, quality and cRNA yield were checked with the NanoDrop 2000 (Thermo Scientific).

extract_protocol: Total RNA was extracted with RNAiso reagent (TaKaRa, Shiga, Japan) according to the manufacturer’s instructions. The integrity of the total RNA was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Peripheral blood NK cells in pregnancy

tag: trimester


title: AZA_250uM(3)_8h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(3)_8h

value: 250µM Azathriopine_8h_Biological replicate 3


title: Peripheral_NK_3rd_rep5


title: Peripheral_NK_1st_rep4

source_name: Peripheral blood NK cells, 1st-trimester


title: AZA_250uM(2)-72h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(2)-72h

value: liver

value: 250µM Azathriopine_72h_Biological replicate 2


title: Peripheral_NK_1st_rep5


title: AZA_250uM(2)_8h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(2)_8h

value: 250µM Azathriopine_8h_Biological replicate 2


title: AZA_250uM(2)_4h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(2)_4h

value: 250µM Azathriopine_4h_Biological replicate 2


title: Peripheral_NK_1st_rep3


title: non-fluorescent schizonts, biological rep2

source_name: FACSAria II flow sorted non-fluorescent cells


title: Peripheral_NK_1st_rep1


title: Peripheral_NK_3rd_rep2


title: liver_treatment_rep2

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description:
replicate 2
SAMPLE 6

data_processing: The data were normalized with the rank invariant normalization in the Illumina GenomeStudio 2011.1 software, which comes with the Gene Expression 1.9.0 and Illumina Genome Viewer 1.9.0 modules

organism: Arvicanthis niloticus

source_name: liver, treatment

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Young Nile rats (Arvicanthis niloticus) were given a high carbohydrate diet (percentage energy from carbohydrate:fat:protein = 70:10:20, 16.7 kJ/g) for four weeks

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plus Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer

treatment_protocol: Control group was given the high carbohydrate diet only while treatment group was given PFJ supplemented in the high carbohydrate diet (415 ml of 13000 ppm gallic acid equivalent (GAE) for a final concentration of 5.4 g GAE per kg diet or 2.7 g per 2000 kcal)

value: 3 weeks

value: male

tag: diet

value: high card diet with PFJ


title: OSU12-hisI, histidine depleted, >10 hrs, rep 2

status: Public on Jan 12 2015

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009). The log10 mRNA concentration (pM) data are provided as a supplementary file on the SERIES record.

source_name: OSU12-hisI, histidine depleted, >10 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in the minimal media, modified M63. The final cell concentrations were controlled ~ 10^8 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

value: DH1 ΔhisI::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5

tag: condition

value: histidine depleted


title: OSU12-hisI, histidine depleted, >10 hrs, rep 3

tag: strain


title: AZA_250uM(3)_4h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(3)_4h

tag: cell line

value: 250µM Azathriopine_4h_Biological replicate 3


title: non-fluorescent schizonts, biological rep1

value: FACSAria II flow sorted non-fluorescent cells


title: liver_treatment_rep3

description:
replicate 3
SAMPLE 7


title: Peripheral_NK_3rd_rep1


title: AZA_250uM(1)_8h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(1)_8h

value: hepatocellular carcinoma

value: 250µM Azathriopine_8h_Biological replicate 1


title: Peripheral_NK_3rd_rep3


title: EtOH_Cont(3)_4h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(3)_4h

value: 0.5% ethanol control 4h_Biological replicate 3


title: OSU12-hisI, histidine depleted, 10 min, rep 3

source_name: OSU12-hisI, histidine depleted, 10 min


title: OSU12-hisI, histidine depleted, 2 hrs, rep 1

source_name: OSU12-hisI, histidine depleted, 2 hrs


title: OSU12-hisI, histidine depleted, >10 hrs, rep 1


title: OSU12-hisI, histidine depleted, 2 hrs, rep 3


title: OSU12-hisI, histidine depleted, 10 min, rep 2


title: OSU12-hisI, histidine depleted, 10 min, rep 1


title: liver_control_rep1

description:
replicate 1
SAMPLE 1

source_name: liver, control

value: high carb diet


title: OSU12-hisI, histidine supplied, 1 mM, rep 3

source_name: OSU12-hisI, histidine supplied, 1 mM

value: histidine supplied, 1 mM


title: liver_control_rep2

description:
replicate 2
SAMPLE 2


title: OSU12-hisI, histidine supplied, 1 mM, rep 2


title: OSU12-hisG, histidine depleted, 10 min, rep 3

source_name: OSU12-hisG, histidine depleted, 10 min

value: DH1 ΔhisG::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU12-hisI, histidine supplied, 1 mM, rep 1


title: OSU12-hisG, histidine depleted, 2 hrs, rep 1

source_name: OSU12-hisG, histidine depleted, 2 hrs


title: OSU12-hisG, histidine depleted, 2 hrs, rep 3


title: OSU12-hisG, histidine depleted, 2 hrs, rep 2


title: OSU12-hisG, histidine depleted, 10 min, rep 2


title: liver_control_rep3

description:
replicate 3
SAMPLE 3

value: liver


title: liver_treatment_rep1

description:
replicate 1
SAMPLE 5


title: liver_control_rep4

description:
replicate 4
SAMPLE 4


title: OSU12-hisG, histidine depleted, 10 min, rep 1


title: OSU12-hisG, histidine supplied, 1 mM, rep 3

source_name: OSU12-hisG, histidine supplied, 1 mM


title: OSU12-hisG, histidine supplied, 1 mM, rep 2


title: Cell lines stably transfected with vector [mRNA]

city: Shanghai

first: Hui

middle: zhen

last: Nie

address: 800 Dongchuan Road

country: China

institute: Shanghai Cancer Institute

description: Gene expression data from SMMC-7721 Cell line transfected with vector

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: SMMC-7721 Cell lines

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cell lines were grown under standard cell culture conditions in a 5% CO2-humidified chamber

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: shRNA-interference

value: transfected with vector


title: AZA_250uM(1)-72h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(1)-72h

value: 250µM Azathriopine_72h_Biological replicate 1


title: OSU12-hisG, histidine supplied, 1 mM, rep 1


title: Peripheral_NK_1st_rep2

value: Peripheral blood NK cells in pregnancy


title: OSU12-hisF, histidine depleted, >10 hrs, rep 3

source_name: OSU12-hisF, histidine depleted, >10 hrs

value: DH1 ΔhisF::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU12-hisF, histidine depleted, >10 hrs, rep 2


title: OSU12-hisF, histidine depleted, >10 hrs, rep 1


title: OSU12-hisF, histidine depleted, 2 hrs, rep 2

source_name: OSU12-hisF, histidine depleted, 2 hrs


title: OSU12-hisF, histidine depleted, 10 min, rep 2

source_name: OSU12-hisF, histidine depleted, 10 min


title: OSU12-hisF, histidine depleted, 2 hrs, rep 1


title: OSU12-hisF, histidine depleted, 10 min, rep 3


title: EtOH_Cont(1)_8h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
EtOH_Cont(1)_8h

source_name: hepatocellular carcinoma cell line

value: 0.5% ethanol control 8h_Biological replicate 1


title: OSU12-hisF, histidine supplied, 1 mM, rep 3

source_name: OSU12-hisF, histidine supplied, 1 mM


title: OSU12-hisF, histidine depleted, 10 min, rep 1


title: Cell lines stably transfected with shRNA-MR [mRNA]

description: Gene expression data from SMMC-7721 Cell line transfected with shRNA-MR

value: transfected with shRNA-MR


title: OSU12-hisF, histidine supplied, 1 mM, rep 2


title: AZA_250uM(1)_4h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
AZA_250uM(1)_4h

value: 250µM Azathriopine_4h_Biological replicate 1


title: OSU12-hisF, histidine supplied, 1 mM, rep 1


title: OSU12-hisD, histidine depleted, 2 hrs, rep 2

source_name: OSU12-hisD, histidine depleted, 2 hrs

value: DH1 ΔhisD::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5

value: histidine depleted


title: OSU12-hisD, histidine depleted, 2 hrs, rep 1


title: OSU12-hisD, histidine depleted, 2 hrs, rep 3


title: OSU12-hisD, histidine depleted, 10 min, rep 3

source_name: OSU12-hisD, histidine depleted, 10 min


title: OSU12-hisD, histidine depleted, 10 min, rep 2


title: OSU12-hisD, histidine depleted, 10 min, rep 1


title: OSU12-hisD, histidine supplied, 1 mM, rep 3

source_name: OSU12-hisD, histidine supplied, 1 mM


title: OSU12-hisD, histidine supplied, 1 mM, rep 2


title: OSU12-hisC, histidine depleted, >10 hrs, rep 3

source_name: OSU12-hisC, histidine depleted, >10 hrs

value: DH1 ΔhisC::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU12-hisC, histidine depleted, >10 hrs, rep 2


title: OSU12-hisC, histidine depleted, 2 hrs, rep 3

source_name: OSU12-hisC, histidine depleted, 2 hrs


title: OSU12-hisF, histidine depleted, 2 hrs, rep 3


title: OSU12-hisC, histidine depleted, >10 hrs, rep 1


title: OSU12-hisC, histidine depleted, 2 hrs, rep 2


title: OSU12-hisC, histidine depleted, 10 min, rep 2

source_name: OSU12-hisC, histidine depleted, 10 min


title: OSU12-hisC, histidine depleted, 10 min, rep 1


title: OSU12-hisC, histidine supplied, 1 mM, rep 2

source_name: OSU12-hisC, histidine supplied, 1 mM


title: OSU12-hisC, histidine supplied, 1 mM, rep 3


title: OSU12-hisC, histidine supplied, 1 mM, rep 1


title: OSU12-hisB, histidine depleted, 2 hrs, rep 3

source_name: OSU12-hisB, histidine depleted, 2 hrs

value: DH1 ΔhisB::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU12-hisB, histidine depleted, >10 hrs, rep 3

source_name: OSU12-hisB, histidine depleted, >10 hrs


title: OSU12-hisB, histidine depleted, >10 hrs, rep 2


title: OSU12-hisB, histidine depleted, >10 hrs, rep 1


title: OSU12-hisB, histidine depleted, 10 min, rep 3

source_name: OSU12-hisB, histidine depleted, 10 min


title: OSU12-hisB, histidine depleted, 10 min, rep 1


title: OSU12-hisB, histidine depleted, 2 hrs, rep 1


title: OSU12-hisA, histidine depleted, >10 hrs, rep 2

source_name: OSU12-hisA, histidine depleted, >10 hrs

value: DH1 ΔhisA::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU12-hisB, histidine supplied, 1 mM, rep 1

source_name: OSU12-hisB, histidine supplied, 1 mM


title: OSU12-hisB, histidine depleted, 2 hrs, rep 2


title: OSU12-hisB, histidine supplied, 1 mM, rep 3


title: OSU12-hisB, histidine depleted, 10 min, rep 2


title: OSU12-hisB, histidine supplied, 1 mM, rep 2


title: OSU12-hisA, histidine depleted, >10 hrs, rep 3


title: OSU12-hisD, histidine supplied, 1 mM, rep 1


title: OSU12-hisA, histidine depleted, 2 hrs, rep 3

source_name: OSU12-hisA, histidine depleted, 2 hrs


title: OSU12-hisA, histidine depleted, 2 hrs, rep 1


title: OSU12-hisA, histidine depleted, 10 min, rep 3

source_name: OSU12-hisA, histidine depleted, 10 min


title: OSU12-hisC, histidine depleted, 10 min, rep 3


title: OSU12-hisA, histidine depleted, 2 hrs, rep 2


title: OSU12-hisA, histidine depleted, 10 min, rep 2


title: OSU12-hisA, histidine depleted, 10 min, rep 1


title: OSU11, histidine depleted, >10 hrs, rep 2

source_name: OSU11, histidine depleted, >10 hrs


title: OSU11, histidine depleted, >10 hrs, rep 3


title: OSU12-hisA, histidine supplied, 1 mM, rep 2

source_name: OSU12-hisA, histidine supplied, 1 mM


title: OSU12-hisA, histidine supplied, 1 mM, rep 1


title: OSU12-hisA, histidine supplied, 1 mM, rep 3


title: OSU11, histidine depleted, 2 hrs, rep 3

source_name: OSU11, histidine depleted, 2 hrs


title: OSU11, histidine depleted, >10 hrs, rep 1


title: OSU11, histidine depleted, 2 hrs, rep 1


title: OSU11, histidine depleted, 2 hrs, rep 2


title: OSU11, histidine depleted, 10 min, rep 2

source_name: OSU11, histidine depleted, 10 min


title: OSU11, histidine supplied, 1 mM, rep 3

source_name: OSU11, histidine supplied, 1 mM


title: OSU11, histidine supplied, 1 mM, rep 2


title: OSU11, histidine supplied, 1 mM, rep 1


title: OSU11, histidine depleted, 10 min, rep 1


title: OSU12-hisA, histidine depleted, >10 hrs, rep 1


title: OSU12-hisI, histidine depleted, 2 hrs, rep 2

source_name: OSU12-hisI, histidine depleted, 2 hrs

value: DH1 ΔhisI::cat ΔintC::Ptrc-dsred.t4-tetR-PEM7-zeo ΔgalK::PtetA-gfpuv5


title: OSU11, histidine depleted, 10 min, rep 3


title: Tim-Fbl_ZT3

city: Jerusalem

first: Sebastian

last: Kadener

address: The Alexander Silberman Inst. of Life Sciences, Edmond J. Safra Campus

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene expression from Tim-Fbl flies collected at ZT3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. 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 R suite using RMA

organism: Drosophila melanogaster

source_name: Tim-Fbl collected at ZT3

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

growth_protocol: Fly head collections of control and tim-fbl flies growth at 25C and collected at two different circadian timepoints.

extract_protocol: Zymo RNA purification kit  was performed according to the manufacturer's instructions.

treatment_protocol: Female fly heads were collected and RNA prepared using zymo RNA purification kit

value: head

tag: RNAi

value: Tim-Fbl

tag: circadian timepoint


title: Control_ZT3(1)

description: Gene expression from control flies collected at ZT3

source_name: Control Flies collected at ZT3

tag: tissue

value: control


title: Control_ZT15(2)

description: Gene expression from control flies collected at ZT15

source_name: Control Flies collected at ZT15


title: Control_ZT3(2)


title: Tim-Fbl_ZT15

description: Gene expression from Tim-Fbl flies collected at ZT15

source_name: Tim-Fbl Flies collected at ZT15


title: Control_ZT15(1)


title: LLC125 class1_cohort2

city: Padova

first: Barbara

last: Di Camillo

address: via Gradenigo 6B

department: Information Engineering Department

country: Italy

institute: University of Padova

description:
class1_cohort2
LLC125

hyb_protocol: Hybridization was performed using protocols described in the Affymetrix GeneChip expression analysis technical manual.

scan_protocol: Image quantification was performed using GeneChip (Affymetrix) scanner and software.

data_processing: Preprocessing steps such as background substraction, probe cell normalization and expression level calculations, were performed using quantile normalization and Robust Microarray Analysis (RMA) software.

source_name: CD19+ cells purified from fresh peripheral blood mononuclear cells

label_protocol: A first cohort of 62 subjects was analyzed using GeneChip Expression 3' Amplification One-Cycle Target Labeling Kit, while a second cohort of 50 subjects using GeneChip 3'IVT Express Kit, according to manufacturer’s protocol (Affymetrix), respectively.

extract_protocol: Total RNA was extracted using using RNeasy minikit including a DNAse treatment step (Quiagen), and QIAshredder following the supplier’s instructions. Afterwards, total RNA was repurified and concentrated with RNeasy MinElute Cleanup Kit (Quiagen) as per the manufacturer’s instructions.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) from all samples were isolated by Ficoll density gradient centrifugation (Invitrogen), and soon after CD19+ cells were purified using MACS CD19 Microbeads (Miltenyi Biotech) from fresh PBMCs. CD19+ cells were resuspended in RNA later (Ambion) and stored in a CLL cell bank at -20°C until RNA extraction was performed.

tag: disease state

value: Chronic lymphocytic leukemia

tag: igvh mutation status

value: IgVHMT

tag: zap-70 expression

tag: Sex

value: M


title: LLC110 class1_cohort2

description:
class1_cohort2
LLC110

tag: age


title: LLC112 class2_cohort2

description:
class2_cohort2
LLC112

value: IgVHUM


title: LLC114 class3_cohort2

description:
class3_cohort2
LLC114

value: IgVHMT or IgVHUM

value: - or +

value: F


title: LLC102 class3_cohort2

description:
class3_cohort2
LLC102


title: LLC109 class1_cohort2

description:
class1_cohort2
LLC109


title: LLC115 class1_cohort2

description:
class1_cohort2
LLC115


title: LLC104 class3_cohort2

description:
class3_cohort2
LLC104


title: LLC123 class3_cohort2

description:
class3_cohort2
LLC123


title: LLC105 class3_cohort2

description:
class3_cohort2
LLC105


title: OSU12-hisC, histidine depleted, 2 hrs, rep 1

source_name: OSU12-hisC, histidine depleted, 2 hrs


title: LLC100 class2_cohort2

description:
class2_cohort2
LLC100


title: LLC101 class2_cohort2

description:
class2_cohort2
LLC101


title: LLC098 class1_cohort2

description:
class1_cohort2
LLC98


title: LLC103 class1_cohort2

description:
class1_cohort2
LLC103


title: LLC113 class2_cohort2

description:
class2_cohort2
LLC113


title: LLC111 class1_cohort2

description:
class1_cohort2
LLC111


title: LLC121 class2_cohort2

description:
class2_cohort2
LLC121


title: LLC108 class1_cohort2

description:
class1_cohort2
LLC108


title: LLC120 class2_cohort2

description:
class2_cohort2
LLC120


title: LLC107 class3_cohort2

description:
class3_cohort2
LLC107


title: LLC097 class1_cohort2

description:
class1_cohort2
LLC97


title: LLC126 class3_cohort2

description:
class3_cohort2
LLC126


title: LLC128 class1_cohort2

description:
class1_cohort2
LLC128


title: LLC091 class2_cohort2

description:
class2_cohort2
LLC91


title: LLC092 class1_cohort2

description:
class1_cohort2
LLC92


title: LLC096 class2_cohort2

description:
class2_cohort2
LLC96


title: LLC095 class3_cohort2

description:
class3_cohort2
LLC95


title: LLC088 class2_cohort2

description:
class2_cohort2
LLC88


title: LLC093 class2_cohort2

description:
class2_cohort2
LLC93


title: LLC083 class1_cohort2

description:
class1_cohort2
LLC83


title: LLC084 class3_cohort2

description:
class3_cohort2
LLC84


title: LLC090 class3_cohort2

description:
class3_cohort2
LLC90


title: LLC089 class2_cohort2

description:
class2_cohort2
LLC89


title: LLC081 class3_cohort2

description:
class3_cohort2
LLC81


title: LLC087 class3_cohort2

description:
class3_cohort2
LLC87


title: LLC080 class1_cohort2

description:
class1_cohort2
LLC80


title: LLC086 class1_cohort2

description:
class1_cohort2
LLC86


title: LLC079 class1_cohort2

description:
class1_cohort2
LLC79


title: LLC075 class2_cohort1

description:
class2_cohort1
LLC75


title: LLC068 class1_cohort2

description:
class1_cohort2
LLC68


title: LLC072 class2_cohort2

description:
class2_cohort2
LLC72


title: LLC078 class1_cohort2

description:
class1_cohort2
LLC78


title: LLC064 class1_cohort2

description:
class1_cohort2
LLC64


title: LLC067 class3_cohort2

description:
class3_cohort2
LLC67


title: LLC071 class1_cohort2

description:
class1_cohort2
LLC71


title: LLC065 class1_cohort1

description:
class1_cohort1
LLC65


title: LLC066 class2_cohort1

description:
class2_cohort1
LLC66


title: LLC073 class1_cohort2

description:
class1_cohort2
LLC73


title: LLC074 class1_cohort2

description:
class1_cohort2
LLC74


title: LLC070 class1_cohort2

description:
class1_cohort2
LLC70


title: LLC082 class1_cohort2

description:
class1_cohort2
LLC82


title: LLC057 class1_cohort1

description:
class1_cohort1
LLC57


title: LLC054 class3_cohort1

description:
class3_cohort1
LLC54


title: LLC051 class2_cohort1

description:
class2_cohort1
LLC51


title: LLC055 class1_cohort2

description:
class1_cohort2
LLC55


title: LLC062 class3_cohort1

description:
class3_cohort1
LLC62


title: LLC052 class1_cohort1

description:
class1_cohort1
LLC52


title: LLC060 class1_cohort1

description:
class1_cohort1
LLC60


title: LLC056 class2_cohort1

description:
class2_cohort1
LLC56


title: LLC063 class1_cohort1

description:
class1_cohort1
LLC63


title: LLC049 class2_cohort1

description:
class2_cohort1
LLC49


title: LLC050 class2_cohort1

description:
class2_cohort1
LLC50


title: LLC061 class1_cohort2

description:
class1_cohort2
LLC61


title: LLC048 class3_cohort1

description:
class3_cohort1
LLC48


title: LLC059 class3_cohort1

description:
class3_cohort1
LLC59


title: LLC053 class1_cohort1

description:
class1_cohort1
LLC53


title: PCOS ovarian tissue vs. normal control ovarian tissue

city: Guangzhou

first: Lin

last: Lin

state: Guangdong

address: No. 107, Yanjiang Road

department: Ob/Gyn

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

hyb_protocol: The samples are hybridized on the miRCURY™ LNA Array (v.11.0).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: ovarian cortical tissue obtained by laparoscopy

label_protocol: The samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer's instructions.

value: ovary

tag: serial number

tag: disease status

value: Polycystic ovary syndrome (PCOS)

value: non-PCOS (healthy control)


title: locus-coeruleus_control_7

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from locus coeruleus

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014850_D__F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: brain, locus_coeruleus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Brain tissue explants from locus coeruleus (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen).

treatment_protocol: Post-mortem locus coeruleus explants from patients were obtained and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: gender

value: Female

tag: disease stage


title: LLC045 class3_cohort1

description:
class3_cohort1
LLC45


title: locus-coeruleus_control_6

description: Gene expression from locus coeruleus

value: Male


title: LLC047 class3_cohort1

description:
class3_cohort1
LLC47


title: LLC046 class1_cohort1

description:
class1_cohort1
LLC46


title: LLC043 class1_cohort1

description:
class1_cohort1
LLC43


title: locus-coeruleus_control_3

description: Gene expression from locus coeruleus


title: locus-coeruleus_control_1

description: Gene expression from locus coeruleus


title: locus-coeruleus_control_4

description: Gene expression from locus coeruleus


title: LLC042 class1_cohort1

description:
class1_cohort1
LLC42


title: LLC041 class2_cohort1

description:
class2_cohort1
LLC41


title: locus-coeruleus_control_5

description: Gene expression from locus coeruleus


title: LLC040 class1_cohort1

description:
class1_cohort1
LLC40


title: LLC038 class2_cohort1

description:
class2_cohort1
LLC38


title: LLC044 class1_cohort1

description:
class1_cohort1
LLC44


title: locus-coeruleus_Braak5_2

description: Gene expression from locus coeruleus

value: Parkinson's disease

value: Braak 5


title: locus-coeruleus_Braak5_1

description: Gene expression from locus coeruleus


title: locus-coeruleus_Braak4_4

description: Gene expression from locus coeruleus

value: Braak 4


title: locus-coeruleus_control_2

description: Gene expression from locus coeruleus


title: LLC034 class1_cohort1

description:
class1_cohort1
LLC34


title: locus-coeruleus_Braak5_3

description: Gene expression from locus coeruleus


title: LLC037 class2_cohort1

description:
class2_cohort1
LLC37


title: locus-coeruleus_Braak4_2

description: Gene expression from locus coeruleus


title: LLC036 class1_cohort1

description:
class1_cohort1
LLC36


title: locus-coeruleus_Braak4_3

description: Gene expression from locus coeruleus


title: LLC035 class1_cohort1

description:
class1_cohort1
LLC35


title: locus-coeruleus_Braak4_1

description: Gene expression from locus coeruleus


title: LLC033 class2_cohort1

description:
class2_cohort1
LLC33


title: substantia-nigra_control_4

description: Gene expression from substantia nigra

source_name: brain, substantia_nigra

extract_protocol: Brain tissue explants from substantia nigra (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen).

treatment_protocol: Post-mortem substrantia nigra explants from patients were obtained and immediately preserved with 600 uL of RNAlater (Qiagen).


title: LLC031 class1_cohort1

description:
class1_cohort1
LLC31


title: LLC032 class1_cohort1

description:
class1_cohort1
LLC32


title: substantia-nigra_control_5

description: Gene expression from substantia nigra


title: substantia-nigra_control_3

description: Gene expression from substantia nigra


title: LLC029 class1_cohort1

description:
class1_cohort1
LLC29


title: LLC030 class3_cohort1

description:
class3_cohort1
LLC30


title: substantia-nigra_Braak5_3

description: Gene expression from substantia nigra


title: substantia-nigra_control_1

description: Gene expression from substantia nigra


title: LLC027 class2_cohort1

description:
class2_cohort1
LLC27


title: substantia-nigra_control_2

description: Gene expression from substantia nigra


title: substantia-nigra_Braak5_1

description: Gene expression from substantia nigra


title: LLC026 class1_cohort1

description:
class1_cohort1
LLC26


title: LLC028 class1_cohort1

description:
class1_cohort1
LLC28


title: substantia-nigra_Braak5_2

description: Gene expression from substantia nigra


title: Silver Russell patient 19

type: genomic

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

description: Silver Russell patient 19

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 450k Human Methylation Beadchip using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an iScan instrument with standard recommended Illumina scanner settings.

data_processing: Bioconductor packages minfi v1.6.0 and IlluminaHumanMethylation450kmanifest v0.4.0

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood samples of Silver Russell patients using a standard phenol-chloroform kit (Sigma), and from PBMC samples of healthy controls using a Ficoll-density gradient.

value: male

value: whole blood

value: SRS


title: LLC025 class1_cohort1

description:
class1_cohort1
LLC25

value: Chronic lymphocytic leukemia

value: IgVHMT


title: Silver Russell patient 4

description: Silver Russell patient 4


title: Silver Russell patient 22

description: Silver Russell patient 22

value: female


title: substantia-nigra_Braak4_5

description: Gene expression from substantia nigra


title: LLC024 class1_cohort1

description:
class1_cohort1
LLC24

value: M


title: substantia-nigra_Braak4_4

description: Gene expression from substantia nigra


title: LLC023 class3_cohort1

description:
class3_cohort1
LLC23

value: IgVHMT or IgVHUM

value: - or +


title: substantia-nigra_Braak4_3

description: Gene expression from substantia nigra


title: Silver Russell patient 17

description: Silver Russell patient 17


title: substantia-nigra_Braak4_2

description: Gene expression from substantia nigra


title: Silver Russell patient 12

description: Silver Russell patient 12


title: LLC022 class1_cohort1

description:
class1_cohort1
LLC22


title: Silver Russell patient 29

description: Silver Russell patient 29


title: substantia-nigra_Braak4_1

description: Gene expression from substantia nigra


title: LLC020 class3_cohort1

description:
class3_cohort1
LLC20


title: LLC021 class1_cohort1

description:
class1_cohort1
LLC21

value: F


title: Silver Russell patient 26

description: Silver Russell patient 26


title: dorsal-nucleus-of-vagus-nerve_control_6

description: Gene expression from dorsal nucleus of vagus nerve

source_name: brain, dorsal_nucleus_of_vagus_nerve

extract_protocol: Brain tissue explants from dorsal nucleus of vagus nerve (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Post-mortem dorsal nucleus of vagus nerve explants from patients were obtained and immediately preserved with 600 uL of RNAlater (Qiagen).

value: control


title: Silver Russell patient 39

description: Silver Russell patient 39


title: Silver Russell patient 44

description: Silver Russell patient 44


title: Silver Russell patient 31

description: Silver Russell patient 31


title: LLC019 class1_cohort1

description:
class1_cohort1
LLC19


title: Silver Russell patient 6

description: Silver Russell patient 6


title: dorsal-nucleus-of-vagus-nerve_control_5


title: Silver Russell patient 30

description: Silver Russell patient 30


title: LLC017 class3_cohort1

description:
class3_cohort1
LLC17


title: LLC018 class1_cohort1

description:
class1_cohort1
LLC18


title: dorsal-nucleus-of-vagus-nerve_control_4


title: Silver Russell patient 5

description: Silver Russell patient 5


title: dorsal-nucleus-of-vagus-nerve_control_2


title: dorsal-nucleus-of-vagus-nerve_control_3


title: LLC016 class2_cohort1

description:
class2_cohort1
LLC16

value: IgVHUM


title: LLC015 class2_cohort1

description:
class2_cohort1
LLC15


title: normal control 6

description: normal control 6

value: PBMC

value: normal


title: Silver Russell patient 94

description: Silver Russell patient 94


title: LLC012 class1_cohort1

description:
class1_cohort1
LLC12


title: dorsal-nucleus-of-vagus-nerve_control_1

value: Female


title: LLC014 class1_cohort1

description:
class1_cohort1
LLC14


title: LLC011_B class1_cohort1

description:
class1_cohort1
LLC11_B


title: dorsal-nucleus-of-vagus-nerve_Braak5_3

value: Male

value: Parkinson's disease

value: Braak 5


title: dorsal-nucleus-of-vagus-nerve_Braak5_1


title: Silver Russell patient 62

description: Silver Russell patient 62

value: whole blood


title: normal control 16911

description: normal control 16911

value: male


title: LLC010 class1_cohort1

description:
class1_cohort1
LLC10

value: Chronic lymphocytic leukemia


title: dorsal-nucleus-of-vagus-nerve_Braak4_4

value: Braak 4


title: normal control 9

description: normal control 9


title: LLC009 class1_cohort1

description:
class1_cohort1
LLC09

value: IgVHMT


title: dorsal-nucleus-of-vagus-nerve_Braak4_5


title: normal control 5

description: normal control 5


title: dorsal-nucleus-of-vagus-nerve_Braak4_2


title: Snail-ER ESC 24h

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

hyb_protocol: Direct Hybridization of RNA library was performed using Standard Operating Procedures in Whole-Genome Gene Expression Direct Hybridization Assay Guide (Illumina)

scan_protocol: Chips were scanned using Illumina HiScan software

data_processing: data were normalized using quantile normalization and background subtraction by default parameters in Genome Studio (Illumina)

molecule: polyA RNA

source_name: Embryonic Stem Cells

label_protocol: RNA library were performed using Illumina Total Prep RNA Amplification Kit following the manufacturing protocol

growth_protocol: Embryonic stem cells were cultured in DMEM high glucose medium (Invitrogen) supplemented with 15% FBS (Millipore), 0.1mM nonessential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen), 0.1mM 2-mercaptoethanol, 1500U/ml LIF (Millipore), 25 U of penicillin/ml, and 25 µg of streptomycin/ml.

extract_protocol: RNA was extracted using TRIzol reagent from Invitrogen.

treatment_protocol: Cells were induced with 4-OHT at the indicated times for SNAIL-ER nuclear localization before RNA extraction

tag: cell type

value: Embryonic stem cells


title: dorsal-nucleus-of-vagus-nerve_Braak4_1


title: LLC013 class1_cohort1

description:
class1_cohort1
LLC13


title: Snail-ER ESC 12h


title: LLC007 class1_cohort1

description:
class1_cohort1
LLC07

value: M


title: LLC003 class2_cohort1

description:
class2_cohort1
LLC03


title: Snail-ER ESC 8h


title: dorsal-nucleus-of-vagus-nerve_Braak4_3


title: LLC008 class1_cohort1

description:
class1_cohort1
LLC08


title: LLC006 class1_cohort1

description:
class1_cohort1
LLC06


title: Silver Russell patient 96

description: Silver Russell patient 96

value: female

value: SRS


title: Silver Russell patient 50

description: Silver Russell patient 50


title: dorsal-nucleus-of-vagus-nerve_Braak5_2


title: LLC002 class1_cohort1

description:
class1_cohort1
LLC02


title: Silver Russell patient 23

description: Silver Russell patient 23


title: Snail-ER ESC 0h


title: Snail-ER ESC 2h


title: Snail-ER ESC 4h


title: Patient #5, passage IV xenograft, treated (1) (HTHuGene11_061412H_GL113_220)

status: Public on Jan 11 2015

city: Toronto

first: Maud

middle: HW

last: Starmans

state: Ontario

address: 661 University Avenue

department: Informatics and Biocomputing Program

country: Canada

institute: Ontario Institute for Cancer Research (OICR)

hyb_protocol: Subsequently samples were hybridized to the Human Gene 1.1 ST arrays.

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

data_processing: Microarray processing was performed in R (version2.15.2)

source_name: Xenograft

label_protocol: Samples were labaled according the GeneChip WT Terminal Labeling and Hybridization manual.

extract_protocol: RNA was extracted using the Rneasy Mini kit from Qiagen.

tag: passage

value: IV

tag: engraft

tag: size


title: Patient #5, passage III xenograft, large tumour (HTHuGene11_061412H_GL108_79)

value: III

value: Large


title: Patient #1, passage XII xenograft, treated (2) (HTHuGene11_061412H_GL105_19)

value: XII


title: LLC001 class2_cohort1

description:
class2_cohort1
LLC01

value: IgVHUM


title: Patient #1, passage XII xenograft, large tumour (HTHuGene11_061412H_GL103_23)


title: Patient #5, passage III xenograft, treated (3) (HTHuGene11_061412H_GL111_83)


title: Patient #5, passage IV xenograft, small tumour (HTHuGene11_061412H_GL112_219)

value: Small


title: normal control 8

description: normal control 8

value: PBMC

value: normal


title: R-1h-BPS

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

hyb_protocol: In each experiment a G1 control sample and an S phase sample (R-1h-BPS or R-1h+BPS) were paired and the DNA cohybridized to Agilent G4493A Yeast Whole Genome ChIP-on-Chip 4x44k microarrays.

scan_protocol: Scanned on an Agilent G2565B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.  Chromosome coordinates (kb) for each probe were extracted.

organism: Saccharomyces cerevisiae

label_protocol: Agarose-embedded chromosomal DNA samples were differentially labeled for DSBs by End-Repair reaction (Epicentre) with Cy5- or Cy3-conjugated dUTP.  All procedures were performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).

growth_protocol: Log phase cells were synchronized by alpha factor in G1 and released into S phase in the presence of 200 mM HU for 1h. Cells were then filtered to remove HU and allowed to recover in fresh media with or without 0.8 micromolar BPS for 1h.

extract_protocol: DSB-labeled chromosomal DNA was extracted from agarose plugs by beta-agarase digestion and sonicated in a Bioruptor to reduce DNA fragment size to an average of 500 bp.

tag: strain

tag: genotype


title: Patient #1, passage XI xenograft, treated (2) (HTHuGene11_061412H_GL102_14)

value: XI


title: Patient #5, passage IV xenograft, treated (2) (HTHuGene11_061412H_GL115_222)


title: LLC005 class1_cohort1

description:
class1_cohort1
LLC05


title: Patient, tumour sample (HTHuGene11_061412H_GL116_74)

source_name: Patient

value: P

value: No


title: Patient #5, passage III xenograft, treated (1) (HTHuGene11_061412H_GL109_125)


title: Patient #5, tumour sample (HTHuGene11_061412H_GL106_76)

value: Yes


title: Patient #5, passage III xenograft, treated (2) (HTHuGene11_061412H_GL110_81)


title: Patient #5, passage I xenograft (HTHuGene11_061412H_GL107_77)

value: I


title: Patient, tumour sample (HTHuGene11_061412Hl_GL117_112)


title: Patient #5, passage IV xenograft, large tumour (HTHuGene11_061412Hl_GL114_221)


title: R-1h+BPS


title: Patient #1, passage XII xenograft, treated (1) (HTHuGene11_061412H_GL104_17)


title: normal control 7

description: normal control 7

value: male


title: Patient #1, passage XI xenograft, large tumour (HTHuGene11_061412H_GL101_10)


title: Patient, tumour sample (HTHuGene11_061112Hl_GL94_42)


title: Patient #1, passage XI xenograft, small tumour (HTHuGene11_061412H_GL99_308)


title: Patient #1, passage XI xenograft, treated (1) (HTHuGene11_061412H_GL100_12)


title: Patient #1, passage VI xenograft (HTHuGene11_061412H_GL98_2)

value: VI


title: Patient #9, passage III xenograft, large tumour (HTHuGene11_060612H_GL69_256)


title: Patient, tumour sample (HTHuGene11_061112H_GL95_123)


title: Patient #9, passage III xenograft, treated (3) (HTHuGene11_060612H_GL71_258)


title: Patient #9, passage III xenograft, treated (2) (HTHuGene11_060612H_GL70_278)


title: Patient #7, passage IV xenograft, treated (4) (HTHuGene11_060612H_GL64_237)


title: Patient, tumour sample (HTHuGene11_061112Hl_GL96_316)


title: 3flc/SVP.LD.Apex.r3

city: Cologne

first: Julieta

last: Mateos

address: Carl-von-Linné-Weg 10

department: Department of Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: Biotinylated cRNA samples were mixed in 250 μL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.

data_processing: The raw data (CEL files) were subjected to RMA.

organism: Arabidopsis thaliana

source_name: flc-/SVP+ 2 weeks Short Days + 2 Long days-ZT8-Apex

label_protocol: Total RNA samples (150 ng) were reverse transcribed into double-stranded cDNA and then in vitro transcribed in the presence of biotin-labeled nucleotides using the GeneChip 3′ IVT Express kit (Affymetrix; 901229) including poly(A) controls as recommended by the manufacturer. The quality and quantity of the biotinylated cRNA were determined using NanoDrop ND 1000 and Bioanalyzer 2100. Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35 min. at 94°C in fragmentation buffer (Affymetrix).

growth_protocol: Plants were grown on soil in short days at 22°C.

extract_protocol: RNA was extracted using the RNA Plant Mini kit, QIAGEN  from leaves and apices.

treatment_protocol: Plants were collected either after two weeks growing in short days or transfered to two days to long days. All genotypes were collected at ZT8.

tag: developmental stage

value: 2 weeks old short days

tag: treatment

value: additional 2 long days

value: Apex

tag: cultivar

value: Columbia


title: Patient #1, tumour sample (HTHuGene11_061412Hb_GL97_1)


title: Patient #9, passage III xenograft, treated (1) (HTHuGene11_060612H_GL68_255)

value: III


title: Patient #9, passage III xenograft, treated (4) (HTHuGene11_060612H_GL72_279)


title: 4flc/svp.LD.Apex.r3

source_name: flc-/svp- 2 weeks Short Days + 2 Long days-ZT8-Apex

tag: tissue


title: 4flc/svp.LD.Apex.r2


title: Patient #9, passage III xenograft, small tumour (HTHuGene11_060612H_GL67_254)


title: Patient #7, passage IV xenograft, treated (2) (HTHuGene11_060612H_GL62_238)

value: IV


title: 1FLC/SVP.LD.Apex.r3

source_name: FLC+/SVP+ 2 weeks Short Days + 2 Long days-ZT8-Apex


title: 3flc/SVP.LD.Apex.r2


title: 4flc/svp.LD.Apex.r1


title: 2FLC/svp.LD.Apex.r3

source_name: FLC+/svp- 2 weeks Short Days + 2 Long days-ZT8-Apex


title: Patient #9, passage I xenograft (HTHuGene11_060612H_GL66_236)


title: 2FLC/svp.LD.Apex.r2


title: Patient #7, passage IV xenograft, treated (3) (HTHuGene11_060612H_GL63_239)


title: Patient #9, tumour sample (HTHuGene11_060612Hl_GL65_321)


title: Patient #7, passage I xenograft (HTHuGene11_060612H_GL58_87)


title: Patient #7, passage IV xenograft, small tumour (HTHuGene11_060612H_GL59_223)


title: 3flc/SVP.LD.Apex.r1


title: 3flc/SVP._SD.Apex.r3

source_name: flc-/SVP+ 2 weeks Short Days - ZT8-Apex

value: additional 2 short days


title: Patient #7, tumour sample (HTHuGene11_060612Hl_GL57_324)


title: 4flc/svp._SD.Apex.r3

source_name: flc-/svp- 2 weeks Short Days - ZT8-Apex


title: Patient #6, passage III xenograft, large tumour (HTHuGene11_060612H_GL53_229)

value: Large


title: Patient #6, passage III xenograft, treated (3) (HTHuGene11_060612H_GL55_231)


title: 2FLC/svp._SD.Apex.r3

source_name: FLC+/svp- 2 weeks Short Days - ZT8-Apex


title: Patient #7, passage IV xenograft, treated (1) (HTHuGene11_060612H_GL60_224)


title: Patient #6, passage III xenograft, treated (1) (HTHuGene11_060612H_GL52_311)


title: Patient #7, passage IV xenograft, large tumour (HTHuGene11_060612H_GL61_240)


title: 1FLC/SVP.LD.Apex.r2


title: Patient #6, passage I xenograft (HTHuGene11_060612H_GL50_108)


title: 3flc/SVP._SD.Apex.r2


title: 2FLC/svp.LD.Apex.r1


title: 1FLC/SVP.LD.Apex.r1


title: 2FLC/svp._SD.Apex.r2


title: Patient #6, passage III xenograft, treated (2) (HTHuGene11_060612H_GL54_230)


title: 1FLC/SVP._SD.Apex.r2

source_name: FLC+/SVP+ 2 weeks Short Days - ZT8-Apex


title: Patient #6, passage III xenograft, treated (4) (HTHuGene11_060612Hb_GL56_232)


title: 1FLC/SVP._SD.Apex.r3


title: Patient, tumour sample (HTHuGene11_060412H_GL47_111)


title: 4flc/svp._SD.Apex.r1


title: Patient #6, tumour sample (HTHuGene11_060612H_GL49_107)

value: O


title: Patient, tumour sample (HTHuGene11_060412H_GL46_109)


title: 2FLC/svp._SD.Apex.r1


title: Patient #3, passage III xenograft, large tumour (HTHuGene11_060412H_GL40_93)


title: 3flc/SVP._SD.Apex.r1


title: Patient #3, passage IV xenograft, large tumour (HTHuGene11_060412H_GL44_313)


title: Patient #3, passage IV xenograft, small tumour (HTHuGene11_060412H_GL43_243)

value: Small


title: Patient #3, passage III xenograft, treated (1) (HTHuGene11_060412H_GL41_94)


title: LLC004 class2_cohort1

description:
class2_cohort1
LLC04

source_name: CD19+ cells purified from fresh peripheral blood mononuclear cells

tag: disease state

value: Chronic lymphocytic leukemia

tag: igvh mutation status

value: IgVHUM

tag: zap-70 expression

value: M


title: 2FLC/svp.LD._Leaf.r3

source_name: FLC+/svp- 2 weeks Short Days + 2 Long days-ZT8-Leaf

value: Leaf


title: 4flc/svp.LD._Leaf.r3

source_name: flc-/svp- 2 weeks Short Days + 2 Long days-ZT8-Leaf


title: Patient #8, tumour sample (HTHuGene11_052212H_GL21_105)

value: P

value: Yes


title: 4flc/svp._SD.Apex.r2


title: 3flc/SVP.LD._Leaf.r3

source_name: flc-/SVP+ 2 weeks Short Days + 2 Long days-ZT8-Leaf


title: Patient #3, passage III xenograft, treated (2) (HTHuGene11_060412H_GL42_309)


title: 2FLC/svp.LD._Leaf.r2


title: 1FLC/SVP._SD.Apex.r1


title: Patient #3, passage IV xenograft, treated (HTHuGene11_060412H_GL45_248)


title: 1FLC/SVP.LD._Leaf.r3

source_name: FLC+/SVP+ 2 weeks Short Days + 2 Long days-ZT8-Leaf


title: Patient #3, passage I xenograft (HTHuGene11_060412H_GL39_92)

value: I


title: 1FLC/SVP.LD._Leaf.r2

value: 2 weeks old short days


title: 3flc/SVP.LD._Leaf.r1

value: additional 2 long days


title: 4flc/svp.LD._Leaf.r1


title: Patient #6, passage III xenograft, small tumour (HTHuGene11_060612H_GL51_227)


title: Patient, tumour sample (HTHuGene11_052212H_GL20_352)

value: No


title: 3flc/SVP.LD._Leaf.r2

value: Columbia


title: Patient, tumour sample (HTHuGene11_052212H_GL18_85)


title: Patient #8, passage I xenograft (HTHuGene11_052212H_GL22_106)


title: Patient, tumour sample (HTHuGene11_052212H_GL17_209)


title: 2FLC/svp.LD._Leaf.r1


title: 1FLC/SVP.LD._Leaf.r1


title: Patient #4, passage V xenograft, treated (2) (HTHuGene11_052212H_GL14_68)

value: V


title: Patient, tumour sample (HTHuGene11_052212Hl_GL19_166)


title: Patient, tumour sample (HTHuGene11_052212H_GL16_211)


title: Patient #4, passage V xenograft, treated (3) (HTHuGene11_052212H_GL15_277)


title: 4flc/svp._SD._Leaf.r3

source_name: flc-/svp- 2 weeks Short Days - ZT8-Leaf


title: Patient #4, passage V xenograft, large tumour (HTHuGene11_052212H_GL12_65)


title: 2FLC/svp._SD._Leaf.r3

source_name: FLC+/svp- 2 weeks Short Days - ZT8-Leaf


title: Patient #4, passage I xenograft (HTHuGene11_052212H_GL9_49)

source_name: Xenograft


title: Patient #4, passage V xenograft, small tumour (HTHuGene11_052212H_GL10_61)


title: 2FLC/svp._SD._Leaf.r2


title: Patient #4, tumour sample (HTHuGene11_052212Hl_GL8_323)

source_name: Patient


title: Patient #2, passage X xenograft, treated (HTHuGene11_052212H_GL7_157)

value: X


title: 1FLC/SVP._SD._Leaf.r3

source_name: FLC+/SVP+ 2 weeks Short Days - ZT8-Leaf

value: additional 2 short days


title: 1FLC/SVP._SD._Leaf.r2


title: Patient #3, tumour sample (HTHuGene11_060412H_GL38_91)


title: 4flc/svp._SD._Leaf.r2


title: Patient #4, passage V xenograft, treated (1) (HTHuGene11_052212H_GL13_52)


title: 4flc/svp._SD._Leaf.r1


title: Patient #4, passage V xenograft, treated (HTHuGene11_052212H_GL11_62)


title: AdiposeDerivedStemCells7_osteo_rep1

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

description: Gene expression in osteogenically differentiated ADSCs from donor 7

hyb_protocol: All amount of labeled cRNA was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human Gene Expression (v2) 8×60K microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09, grid 039494_D_F_20120628 for ADSC4 and 039494_D_F_20140228 for ADSC6 and ADSC7). Background subtracted and spatially detrended signals were obtained.

source_name: Adipose-derived stem cells, donor 7, passage 3, osteogenic differentiation

label_protocol: Cyanine-3 labeled cRNA was prepared from 200 ng of purified RNA using Low Input Quick Amp Labeling Kit, One Color and RNA Spike-In Kit, One Color acording to manufacturer's protocol (Agilent Technologies), followed by purification with RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield was measured with NanoDrop 2000.

growth_protocol: Sections of adipose tissue were digested with 0.2% collagenase type I in DMEM at 37°C and filtered through 100 μm filter. Cells were grown in DMEM, supplemented with 10% FCS and antibiotics, in a humidified atmosphere with 5% CO2 at 37°C and passaged when reached subconfluence of 75-90%.

extract_protocol: Total RNA was extracted from 2 mln. cells on average with mirVana miRNA Isolation Kit according to manufacturer’s protocol (Life Technologies). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were treated with osteogenic-induction medium, prepared from DMEM-high glucose plus osteogenic stimulatory supplement, dexamethasone (final concentration 10^-8 M) and ascorbic acid (50 μg/ml). When formation of cell multilayers became evident, β-glycerophosphate was added to the osteogenic-induction medium (10^-6 M) and differentiation was performed for another 2 weeks. Control cells were simultaneously cultured in the complete proliferation medium.

tag: differentiation status

value: osteogenic differentiation

tag: original cell type

value: Adipose-derived stem cells


title: AdiposeDerivedStemCells6_osteo_rep1

description: Gene expression in osteogenically differentiated ADSCs from donor 6

source_name: Adipose-derived stem cells, donor 6, passage 3, osteogenic differentiation


title: 3flc/SVP._SD._Leaf.r2

source_name: flc-/SVP+ 2 weeks Short Days - ZT8-Leaf


title: Patient #2, passage X xenograft, small tumour (HTHuGene11_052212H_GL5_148)

value: Small


title: Patient #2, passage X xenograft, large tumour (HTHuGene11_052212H_GL6_154)

value: Large


title: 3flc/SVP._SD._Leaf.r1


title: Patient #2, tumour sample (HTHuGene11_052212H_GL1_26)


title: Patient #2, passage V xenograft, treated (HTHuGene11_052212H_GL4_29)


title: Patient #2, passage I xenograft (HTHuGene11_052212H_GL2_218)


title: Patient #2, passage V xenograft (HTHuGene11_081512H2p_GL3_27)


title: AdiposeDerivedStemCells7_control_rep1

description: Gene expression in undifferentiated ADSCs from donor 7

source_name: Adipose-derived stem cells, donor 7, passage 3, control

value: undifferentiated


title: 2FLC/svp._SD._Leaf.r1


title: AdiposeDerivedStemCells6_control_rep1

description: Gene expression in undifferentiated ADSCs from donor 6

source_name: Adipose-derived stem cells, donor 6, passage 3, control


title: ExVivoTonsil_11_rep16

status: Public on Jan 10 2015

city: Canberra

first: Monika

last: Srivastava

state: ACT

address: Building 131, Garran Road

department: Pathogen and Immunity

institute: JCSMR, ANU

description:
microRNA expression in Naïve T cells
The provided raw data has been summarized at the miRNA level. Probe-level raw data are not available.

hyb_protocol: not provided

scan_protocol: In association with the Peter Wills Bioinformatics Centre (PWBC) at the Garvan Institute, NSW,  the data was scanned on the Ramaciotti Centre's Affymetrix scanner

data_processing: Following scanning of the arrays, the raw images are processed by “Feature Extractor” which produces raw (‘TXT’), and summarised (‘Gene View’) data for each array, as well a QC report. On this array, there are 13,737 probes, representing 821 miR’s. Of these, there are 723 human miR’s, with the remaining 98 miR’s being derived from other species, or controls. The summarised data was imported into GeneSpring. Since this processed data contains negative values, it was ensured that all measurements are above 1.0, and then further normalise the data, by normalising each miR to the median of the measurements for that miR. That is, expression level of each miR into was converted in to an expression ratio.

source_name: Tonsil11-CD4+CD45ROneg Naïve T cells

label_protocol: not provided

extract_protocol: Total RNA was extracted using miRVANA mRNA isolation kit (Ambion) according to the manufacturer's protocol

treatment_protocol: Tonsils are cut in small pieces  with cleaned surgical scissors on an agar plate in a small volume of culture media. They are then minced  through a cell strainer sitting on an agar plate, using the handle-end of a 5 mL syringe.  • The resulting suspension on the floor of the agar plate is pipetted (via sterile transfer pipette) through another cell strainer. The cell suspension is layered onto room-temperature FicollPaque PLUS (‘Ficoll’): typically, 3 mL cell suspension is layered onto 9-10 mL Ficoll in a 15 mL (red-top) Falcon tube.    • These tubes are centrifuged (2000 rpm / 20°C / 20 minutes, without braking on deceleration). The lymphocyte layer (often somewhat adherent to the Falcon tube wall, and generally less well-defined than with density gradient separation of blood) is removed by pipetting, and lymphocytes are washed twice in cold culture media.  • After resuspension (e.g. in 10 mL WM), cells are passed through a cell strainer before counting. Cells are then stained for surface markers and FACS sorted for different T cell population.

value: Tonsils


title: ExVivoTonsil_8_rep15

description:
microRNA expression in CD57neg Tfh cells
The provided raw data has been summarized at the miRNA level. Probe-level raw data are not available.

source_name: Tonsil8-CD4+CD57neg Tfh cells


title: ExVivoTonsil_3_rep14

description:
microRNA expression in CD57+ Tfh cells
The provided raw data has been summarized at the miRNA level. Probe-level raw data are not available.

source_name: Tonsil3-CD4+CD57+ Tfh cells


title: Wild type (N-60000), biological rep 2

city: Darmstadt

first: Anastassia

last: Boudichevskaia

state: Hessen

address: Schnittspahnstrasse 10

department: FB Biologie

institute: TU Darmstadt

description: Wildtype (N60000) #2

hyb_protocol: According to the Hybridization, Wash and Stain Kit manual (Affymetrix, USA). The resulting target was hybridized to the GeneChip AraGene-1.0 ST arrays (Affymetrix, USA) for 17 hrs at 45 °C (3 plants from each line)

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

data_processing: Images were processed using Partek’s Genomic Suite’s workflow designed for Exon-Arrays. Chp-files were generated applying quantile normalization and the RMA summarization algorithm (Irizarry et al. 2003).

label: Biotin

source_name: 3 weeks old leaves

label_protocol: GeneChip WT Terminal Labelling Kit (Affymetrix, USA) and WT Expression Kit (Ambion, USA)

growth_protocol: plants  were grown in the greenhouse 3 weeks. 12-h photoperiod (24°C day/20°C night), 60% relative humidity; a photon flux density at plant level of about 70 to 80 µmol m-2s-1 and an ambient CO2 concentration of 370 µmol mol-1

extract_protocol: Total RNA was isolated from 5 individual plants for each microarray (15 plants from each line in total) using the Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA)

tag: genotype/variation

value: Wildtype (N60000)

value: leaf material


title: AdiposeDerivedStemCells4_control_rep1

description: Gene expression in undifferentiated ADSCs from donor 4

source_name: Adipose-derived stem cells, donor 4, passage 3, control


title: T-DNA insertion line atpip1;2-1, biological rep 3

description: atpip1_2-1 #3


title: ExVivoTonsil_2_rep9

source_name: Tonsil2-CD4+CD57+ Tfh cells


title: ExVivoTonsil_6_rep10

source_name: Tonsil6-CD4+CD57neg Tfh cells


title: T-DNA insertion line atpip1;2-1, biological rep 2

description: atpip1_2-1 #2


title: AdiposeDerivedStemCells4_osteo_rep1

description: Gene expression in osteogenically differentiated ADSCs from donor 4

source_name: Adipose-derived stem cells, donor 4, passage 3, osteogenic differentiation


title: Wild type (N-60000), biological rep 3

description: Wildtype (N60000) #3


title: ExVivoTonsil_5_rep7

source_name: Tonsil5-CD4+CD57neg Tfh cells


title: 1FLC/SVP._SD._Leaf.r1

value: Leaf


title: ExVivoTonsil_12_rep13

source_name: Tonsil12-CD4+CD45ROneg Naïve T cells


title: T-DNA insertion line atpip1;2-1, biological rep 1

description: atpip1_2-1 #1


title: ExVivoTonsil_10_rep11

source_name: Tonsil10-CD4+CD45ROneg Naïve T cells


title: ExVivoTonsil_15_rep12

description:
microRNA expression in Memory T cells
The provided raw data has been summarized at the miRNA level. Probe-level raw data are not available.

source_name: Tonsil15-CD4+CD45RO+PD1negCXCR5neg  Memory T cells


title: ExVivoTonsil_16_rep8

source_name: Tonsil16-CD4+CD45RO+PD1negCXCR5neg  Memory T cells


title: ExVivoTonsil_7_rep6

source_name: Tonsil7-CD4+CD57neg Tfh cells


title: ExVivoTonsil_14_rep5

source_name: Tonsil14-CD4+CD45RO+PD1negCXCR5_neg  Memory T cells


title: ExVivoTonsil_13_rep4

source_name: Tonsil13-CD4+CD45ROneg Naïve T cells


title: Wild type (N-60000), biological rep 1

description: Wildtype (N60000) #1


title: ExVivoTonsil_9_rep3

source_name: Tonsil9-CD4+CD45ROneg Naïve T cells


title: ExVivoTonsil_1_rep1

source_name: Tonsil1-CD4+CD57+ Tfh cells


title: ExVivoTonsil_4_rep2

source_name: Tonsil4-CD4+CD57neg Tfh cells