title: HB3 - SJ140722

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ140722


title: mor.4_b9

status: Public on Dec 01 2015

type: RNA

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing:
The raw Ct were first subtracted from the global threshold value (30-Ct) and then normalized by subtracting the average signal for Ssu72, Hnrnpr and Ube2e1.
Excluded genes:
Gene-by-gene QC was performed by Fluidigm's qPCR Analysis software. In the Matrix normalized worksheet, the column Gene_QC indicates which whether a gene passed or failed QC.

molecule: total RNA

organism: Mus musculus

source_name: morual blastocyst, rep13

label_protocol: CellsDirect (Invitrogen), Fluidigm qPCR

growth_protocol: Preimplantation embryos were cultured in KSOMaa medium under low oxygen conditions.

extract_protocol: single cells, obtained from preimplantation embryos, were directly transferred in RT-qPCR reaction mix.

tag: developmental stage

value: morula (16-cell)


title: mor.4_b8

source_name: morual blastocyst, rep12


title: mor.5_b1

source_name: morual blastocyst, rep14


title: mor.4_b6

source_name: morual blastocyst, rep10


title: Dd2 - SJ194935

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

country: USA

institute: University of Notre Dame

hyb_protocol: Hybridizations were performed for 22 hrs followed by washing of the arrays as described according to standard protocols (Roche NimbleGen Inc., Madison, WI).

scan_protocol: The microarray image was obtained using a 2uM scanner and probe intensity values extracted using NimbleScan software (Roche NimbleGen Inc., Madison, WI).

data_processing: Probe intensities were normalized using robust multichip average (RMA) method (Irizarry, Hobbs et al. Biostatistics. 2003; 4(2):249-264). This normalization was performed across all samples hybridized on a single chip. Transcript level for each gene was obtained by averaging the processed signal intensity of all the probes across its exons as follows. Exon signal intensity for each gene was obtained by averaging the intensities of all probes within each exon. To determine a significance threshold for exon expression levels, a background distribution of signal intensities from a set of 10,000 negative control probes with no sequence matches to the P. falciparum genome was generated.  A threshold corresponding to the 95th percentile (5% FDR) of the signal distribution of the negative control probes was then applied (Clark, Schweitzer et al. Genome Biol. 2007; 8(4):R64).  To determine gene expression levels, exons that passed the 5% significance threshold were subjected to an additional threshold derived from intensities of 1000 simulated exons each consisting of 20 randomly sampled negative control probes. Intensities of exons that passed a 5% FDR threshold based on this background distribution were averaged to obtain an average transcript level for each gene.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with SJ194935

label_protocol: 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: Parasite clones Dd2 and HB3 were cultured using standard methods in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2.

extract_protocol: Total RNA was extracted from 20mls of culture using TriZol reagent (Invitrogen, Carlsbad, CA) as described previously (Bozdech, Llinas et al. PLoS Biol, 2003; 1(1):E5).

treatment_protocol: Sorbitol double-synchronized cultures of HB3 and Dd2 were exposed briefly for 2 hrs to each compound at a single developmental stage (24 hr trophozoites) at a concentration (IC50) obtained from literature sources or determined by our laboratory.

tag: strain

tag: small molecule


title: mor.4_b7

source_name: morual blastocyst, rep11


title: mor.4_b5

source_name: morual blastocyst, rep9


title: Dd2 - SJ140722


title: HB3 - JQ1

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with JQ1


title: KO52 GNF-7 (-) biological rep1

city: Boston

first: Atsushi

last: Nonami

state: MA

address: 450 Brookline Ave

institute: DFCI

description: Gene expression data of KO52 without treatment with GNF-7

hyb_protocol: Following fragmentation,  cRNA were hybridized  onto Affymetrix Human Gene 1.0ST arrays.The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: Fluorescence intensities were normalized according to the RMA algorithm using the affymetrix Bioconductor package

label: biotin

organism: Homo sapiens

source_name: KO52 without treatment with GNF-7

label_protocol: Biotinylated cRNA were prepared with Ambion WT Expression Kit followed by labeling with Affymetrix GeneChip WT Terminal Labeling and Hybridization

growth_protocol: cultured in RPMI1640 media with 10% of FBS

extract_protocol: used RNeasy kit of Qiagen

treatment_protocol: treat cells with GNF-7 for 8 hours

tag: tissue

value: AML

tag: genotype

value: NRAS G13R

tag: age


title: Dd2 - JQ1


title: Dd2 - Nelfinavir

description: 2012-08-17_D100813_522474_Dd2_Nelfinavir

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Nelfinavir

value: Nelfinavir


title: mor.4_b4

source_name: morual blastocyst, rep8


title: NOR1, biological rep 1

city: Wuhan

first: Yuchao

last: LU

state: Hubei

address: 1095# Jiefang Avenue

department: Urology

country: China

institute: Tongji Hospital of Tongji medical college, Huazhong University of Science &Technology

description: Male SD rats with a body weight of 250-280g, and fed with 13 g/d of a normal calcium diet (1.2% calcium, 0.65% phosphorus, 0.43% chloride, 0.4% sodium, and 0.24% magnesium per 1 g of food)

hyb_protocol: The labled RNA were hybridized for 16 hr at 60 rpm at 48C on Affymetrix miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data files were analyzed by using Affymetrix Expression Console with the default miRNA array settings. Raw data were processed and normalized on basis of organism rat using RMA-DABG algorithm.

organism: Rattus norvegicus

source_name: Non-coding RNA profiling data from the kidney of SD rat fed with 13 g/d of a normal calcium diet.

label_protocol: About 1ug total RNA were polyA tailed and labled with FlashTag™ Biotin HSR Labeling Kit(Affymetrix, Santa Clara, CA, USA).

growth_protocol: all rats were acclimated at 23℃ on a 12 h light/dark and fed with 13 g/d of a normal calcium diet in the SPF level animal house.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The colony of GHS rats were created by the selective breeding of male and female SD rats with the highest 24 hour urine excretions (doi: 10.3390/ijms160716313). By the 28th generation, GHS rats stably excreted significantly higher levels of urine calcium than wild-type normal SD rats.

value: Sprague-Dawley

tag: gender

value: male

tag: disease state

value: control

tag: diet

value: normal calcium diet

value: kidney


title: mor.4_b2

source_name: morual blastocyst, rep7


title: Dd2 - DMSO (Control) (2)

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with DMSO (Control)

value: DMSO (Control)


title: Cisplatin-sensitive, biological rep3

city: Stillwater

first: Winyoo

last: Chowanadisai

state: OK

address: 301 Human Sciences

institute: Oklahoma State University

description: Parental cell line without step-wide exposure to cisplatin

hyb_protocol: Standard Affymetrix protocol for Gene ST Array

data_processing:
Data were processed using Affymetrix Expression Console software. Default (RMA) for Gene ST Array
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Spheroids, cultured in vitro

growth_protocol: Both cell lines were maintained in DMEM containing 10% FBS and penicillin/streptomycin and 300 μm spheroids were grown in 2% agarose molds.

extract_protocol: Total RNA from spheroids were prepared using Trizol extraction.

treatment_protocol: Human ovarian adenocarcinoma cancer cell line OVCAR-8 was made resistant to cisplatin in vitro by continuous stepwise exposure to cisplatin up to 5 μM, producing the corresponding cisplatin-resistant cell line OVCAR8-C.

tag: cell line

value: ovarian adenocarcinoma

value: wild-type (OVCAR-8)


title: D5 Endoderm, Bio Rep2

city: Milwaukee

first: Kirk

last: Twaroski

state: WI

address: 8701 W Watertown Plank Rd

department: CBNA

institute: Medical College of Wisconsin

description: Gene expression data from endoderm

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite Statistical Analysis Software version 6.6 using Affymetrix default analysis settings

source_name: hiPS cell derived endoderm cells

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3' IVT Express kit from 100ng total RNA

growth_protocol: Pluripotent Cells were differentiated for 2 Days with 50ng/ml Activin A, 10ng/ml BMP4, and 20ng/ml FGF2 followed by 3 Days of 50ng/ml Activin A to Definitive Endoderm

extract_protocol: Qiagen RNeasy Total RNA Kit According to Manufacturer's Protocol

treatment_protocol: Cells were scraped and pelleted, flash frozen, and suspended in RLT Buffer with BME from the Qiagen RNeasy Total RNA Kit

tag: inhibitor

tag: cycloheximide


title: Dd2 - Apicidin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Apicidin

value: Apicidin


title: Cisplatin-resistant, biological rep4

description: Stably resistant to cisplatin even after withdrawl of cisplatin

scan_protocol: Standard Affymetrix protocol for Gene ST Array

value: resistant (OVCAR-8C)


title: Cisplatin-resistant, biological rep3

label_protocol: Standard Affymetrix protocol for Gene ST Array


title: Cisplatin-sensitive, biological rep4


title: Cisplatin-sensitive, biological rep2


title: mor.4_b18-20

source_name: morual blastocyst, rep6


title: D5 Endoderm, Bio Rep1

description: Gene expression data from endoderm


title: Cisplatin-sensitive, biological rep1


title: 2hrs BMP/FGF, No Inhibitor, No Cycloheximide, Bio Rep3

description: Gene expression data from endoderm after 2hrs BMP/FGF

source_name: hiPS cell derived endoderm cells treated with BMP/FGF for 2 hours


title: D5 Endoderm, Bio Rep3

description: Gene expression data from endoderm


title: Cisplatin-resistant, biological rep2


title: 2hrs BMP/FGF, 2.5uM PD173074, No Cycloheximide, Bio Rep3

description: Gene expression data from endoderm after 2hrs BMP/FGF with FGFR inhibitor PD173074

source_name: hiPS cell derived endoderm cells treated with BMP/FGF and the FGFR Inhibitor PD173074 for 2 hours


title: 2hrs BMP/FGF, No Inhibitor, No Cycloheximide, Bio Rep2


title: mor.4_b15-17

source_name: morual blastocyst, rep5


title: mor.4_b13-14

source_name: morual blastocyst, rep4


title: Dd2 - Atovaquone

description: 2012-02-02_D100813_522339_D8_Dd2_Atovaquone

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Atovaquone

value: Atovaquone


title: Dd2 - Doxycycline

description: 2012-02-02_D100813_522339_D6_Dd2_Doxycycline

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Doxycycline

value: Doxycycline


title: Dd2 - Water control

description: 2012-02-02_D100813_522339_D6_Dd2_Control

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Water control

value: Water control


title: Dd2 - Chloramphenicol

description: 2012-02-02_D100813_522339_D7_Dd2_Chloramphenicol

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Chloramphenicol

value: Chloramphenicol


title: mor.4_b11

source_name: morual blastocyst, rep3

value: morula (16-cell)


title: 2hrs BMP/FGF, 2.5uM PD173074, No Cycloheximide, Bio Rep2


title: 2hrs BMP/FGF, No Inhibitor, No Cycloheximide, Bio Rep1


title: Cisplatin-resistant, biological rep1


title: 2hrs BMP/FGF, 2.5uM PD173074, No Cycloheximide, Bio Rep1


title: Line14_rep1

city: miki

first: kenji

last: gomi

state: kagawa

country: Japan

institute: Kagawa University

description: gene expression in OsMYC2-overexpressing transgenic rice

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays for 17 hours at 65 ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

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

organism: Oryza sativa

source_name: Rice leaf blades of OsMYC2-overexpressing transgenic rice, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rice plants were grown from seed in growthchamber [25 ºC, 60 - 80% relative humidity (RH)].

extract_protocol: Total RNA from rice was extracted from leaf blades using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: No treatment.

tag: cultivar

value: a Japonica cultivar Nipponbare

value: four- leaf-stage

value: fourth-leaf blade

tag: genotype/variation

value: OsMYC2-overexpressing transgenic rice


title: Line14_rep3

source_name: Rice leaf blades of OsMYC2-overexpressing transgenic rice, replicate3


title: 2hrs BMP/FGF, 2.5uM PD161570, No Cycloheximide, Bio Rep2

description: Gene expression data from endoderm after 2hrs BMP/FGF with FGFR inhibitor PD161570

source_name: hiPS cell derived endoderm cells treated with BMP/FGF and the FGFR Inhibitor PD161570 for 2 hours


title: mor.4_b10

source_name: morual blastocyst, rep2


title: mor.4_b1

source_name: morual blastocyst, rep1


title: mor.3

source_name: morula embryo, rep3


title: Dd2 - Artemisinin

description: 2012-02-02_D100813_522339_D2_Dd2_Artemisinin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Artemisinin

value: Artemisinin


title: Dd2 - DMSO (Control)

description: 2012-02-02_D100813_522339_D11_Dd2_DMSOcontrol

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with DMSO (Control)


title: MII.9

source_name: MII oocyte, rep12

value: MII oocyte


title: mor.2

source_name: morula embryo, rep2


title: mor.1

source_name: morula embryo, rep1


title: HB3 - Atovaquone

description: 2012-02-02_D100813_522206_H9_HB3_Atovaquone


title: HB3 - Proguanil

description: 2012-02-02_D100813_522206_H4_HB3_Proguanil

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Proguanil

value: Proguanil


title: 2hrs BMP/FGF, 2.5uM PD161570, No Cycloheximide, Bio Rep1


title: Wildtype_rep3

description: gene expression in WT rice

source_name: Rice leaf blades of wild type rice, replicate3

value: WT


title: HB3 - Methyl methane sulfonate

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Methyl methane sulfonate

value: Methyl methane sulfonate


title: MII.7

source_name: MII oocyte, rep10


title: HB3 - Chloramphenicol

description: 2012-02-02_D100813_522206_H6_HB3_Chloramphenicol

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Chloramphenicol


title: Wildtype_rep1

description: gene expression in WT rice

source_name: Rice leaf blades of wild type rice, replicate1


title: Wildtype_rep2

description: gene expression in WT rice

source_name: Rice leaf blades of wild type rice, replicate2


title: 2hrs BMP/FGF, No Inhibitor, 100uM Cycloheximide, Bio Rep3

description: Gene expression data from endoderm after 2hrs BMP/FGF and CHX

source_name: hiPS cell derived endoderm cells treated with BMP/FGF and CHX for 2 hours


title: MII.8

source_name: MII oocyte, rep11


title: CD110+TICs untreated 24h rep2 [FAK7_C2]

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

institute: fudan university

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Colon tumor Fapbl-Cre;Apc2lox14/+;tet-KrasLSL-G12D/+(FAK) mice#7

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

growth_protocol: When magnetic-activated cell sorting (MACS) was used to sort for CD110+ cells, dissociated tumor cells from FAK1,FAK5,FAK7 mice were incubated with a monoclonal CD110 antibody labeled with MicroBeads (Miltenyi Biotec) for 30 min at 4℃, followed by cleavage of the MicroBeads.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: CD110+ cells isolated from primary FAK#1, FAK#5 and FAK#7 tumors were maintained with Dox and treated with or without U73122(1μM) for 24h

tag: agent

value: 17 weeks

value: Colon


title: HB3 - Methotrexate

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Methotrexate

value: Methotrexate


title: 2hrs BMP/FGF, 2.5uM PD161570, No Cycloheximide, Bio Rep3

source_name: hiPS cell derived endoderm cells treated with BMP/FGF and the FGFR Inhibitor PD161570 for 2 hours


title: MII.6

source_name: MII oocyte, rep9


title: CD110+TICs untreated 24h rep1 [FAK7_C1]

description: replicate 1


title: 2hrs BMP/FGF, No Inhibitor, 100uM Cycloheximide, Bio Rep1


title: HB3 - Artemisinin

description: 2012-02-02_D100813_522206_H3_HB3_Artemisinin

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Artemisinin


title: Line14_rep2

source_name: Rice leaf blades of OsMYC2-overexpressing transgenic rice, replicate2


title: CD110+TICs untreated 24h rep3 [FAK7_C3]

description: replicate 3


title: MII.5

source_name: MII oocyte, rep8


title: CD110+TICs treated 24h rep3 [FAK7_T3]

description: replicate 3


title: 2hrs BMP/FGF, 2.5uM PD173074, 100uM Cycloheximide, Bio Rep3

description: Gene expression data from endoderm after 2hrs BMP/FGF with FGFR inhibitor PD173074 and CHX

source_name: hiPS cell derived endoderm cells treated with BMP/FGF, CHX, and the FGFR Inhibitor PD173074 for 2 hours


title: MII.4

source_name: MII oocyte, rep7


title: HB3 - DMSO (Control)

description: 2012-02-02_D100813_522206_H2_HB3_DMSOcontrol

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with DMSO (Control)

value: DMSO (Control)


title: HB3 - Tafenoquine

description: 2012-02-02_D100813_522206_H11_HB3_Tafenoquine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Tafenoquine

value: Tafenoquine


title: HB3 - Chloroquine

description: 2012-02-02_D100813_522206_H12_HB3_Chloroquine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Chloroquine

value: Chloroquine


title: 2hrs BMP/FGF, No Inhibitor, 100uM Cycloheximide, Bio Rep2


title: 2hrs BMP/FGF, 2.5uM PD161570, 100uM Cycloheximide, Bio Rep3

description: Gene expression data from endoderm after 2hrs BMP/FGF with FGFR inhibitor PD161570 and CHX

source_name: hiPS cell derived endoderm cells treated with BMP/FGF, CHX, and the FGFR Inhibitor PD161570 for 2 hours


title: CD110+TICs treated 24h rep1 [FAK7_T1]

description: replicate 1


title: CD110+TICs treated 24h rep2 [FAK7_T2]

description: replicate 2


title: HB3 - Water control

description: 2012-02-02_D100813_522206_H8_HB3_Control

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Water control

value: Water control


title: 2hrs BMP/FGF, 2.5uM PD173074, 100uM Cycloheximide, Bio Rep1


title: 2hrs BMP/FGF, 2.5uM PD173074, 100uM Cycloheximide, Bio Rep2


title: CD110+TICs untreated 24h rep3 [FAK5_C3]

description: replicate 3

source_name: Colon tumor Fapbl-Cre;Apc2lox14/+;tet-KrasLSL-G12D/+(FAK) mice#5


title: MII.3

source_name: MII oocyte, rep6


title: MII.2

source_name: MII oocyte, rep5


title: 2hrs BMP/FGF, 2.5uM PD161570, 100uM Cycloheximide, Bio Rep2


title: HB3 - 5-Fluorouracil

description: 2012-02-02_D100813_522206_H1_HB3_5-Fluorouracil

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with 5-Fluorouracil


title: HB3 - Doxycycline

description: 2012-02-02_D100813_522206_H10_HB3_Doxycycline

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Doxycycline

value: Doxycycline


title: LAN-1_fr_th_nolympho_rep3

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Enriched LAN-1 cells after thawing but without lymphoprep

hyb_protocol: Hybridization was performed according to manufacture's instructions (Affymetrix GeneChip 3' IVT expression analysis)

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the RMA algorithm

source_name: LAN-1 cell line with freezing/thawing (-lymphoprep)

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip 3' IVT expression analysis, 100ng total RNA was processed according to manufacture's instructions

growth_protocol: Cells were kept in tumor-free bone marrow

extract_protocol: Total RNA was extrated using Trizol according to the manufacturer's instructions.

treatment_protocol: Cells were spiked into bone marrow and frozen in 20% DMSO at -80°C. After thawing, LAN-1 cells were isolated by magnetic bead-based enrichment

value: Human neuroblastoma cell line LAN-1


title: MII.11

source_name: MII oocyte, rep3


title: LAN-1_fr_th_lympho_rep3

description: Enriched LAN-1 cells after thawing and lymphoprep

source_name: LAN-1 cell line with freezing/thawing

treatment_protocol: Cells were spiked into bone marrow and frozen in 20% DMSO at -80°C. After thawing, an additional lymphoprep step was done and LAN-1 cells were isolated by magnetic bead-based enrichment


title: CD110+TICs untreated 24h rep1 [FAK5_C1]

description: replicate 1


title: MII.12

source_name: MII oocyte, rep4


title: CD110+TICs treated 24h rep3 [FAK5_T3]

description: replicate 3


title: MII.10

source_name: MII oocyte, rep2


title: 2hrs BMP/FGF, 2.5uM PD161570, 100uM Cycloheximide, Bio Rep1


title: CD110+TICs untreated 24h rep2 [FAK5_C2]

description: replicate 2


title: LAN-1_fresh_rep3

description: Enriched LAN-1 cells prior freezing

source_name: LAN-1 cell line without freezing/thawing

treatment_protocol: Cells were spiked into bone marrow and isolated by magnetic bead-based enrichment


title: MII.1

source_name: MII oocyte, rep1


title: ESC2_800

source_name: ESC standard RNA, 800pg, rep10

value: ESC standard RNA


title: CD110+TICs treated 24h rep2 [FAK5_T2]

description: replicate 2


title: Dd2 - Chloroquine

description: 2011-09-23_D100813_453299_D2_Dd2_Chloroquine


title: CD110+TICs untreated 24h rep3 [FAK1_C3]

description: replicate 3

source_name: Colon tumor from Fapbl-Cre;Apc2lox14/+;tet-KrasLSL-G12D/+(FAK) mice#1


title: ESC2_32

source_name: ESC standard RNA, 32pg, rep9


title: ESC2_160

source_name: ESC standard RNA, 160pg, rep8


title: ESC.b.50pg

source_name: ESC standard RNA, 50pg, rep7


title: ESC.b.25pg

source_name: ESC standard RNA, 25pg, rep6


title: ESC.b.200pg

source_name: ESC standard RNA, 200pg, rep5


title: ESC.b.100pg

source_name: ESC standard RNA, 100pg, rep4


title: Dd2 - Methyl methane sulfonate

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Methyl methane sulfonate


title: ESC.a.200_3

source_name: ESC standard RNA, 200pg, rep3


title: ESC.a.200_2

source_name: ESC standard RNA, 200pg, rep2


title: GIST_high-grade_9 loss (GIST016_HG)

city: Taipei

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University Hospital

data_processing: NanoStriDE normalization; Nat Biotechnol 2008; 26: 317-325 (PubMed ID 18278033). BMC Bioinformatics 2011; 12: 479-2105-12-479 (PubMed ID 22177214).

label: color-coded digital barcodes

source_name: GIST, stomach

extract_protocol: RNA was extracted with the RecoverAll™ Total Nucleic Acid Isolation Kit FFPE, as the manufacturer's instruction.

value: female

value: gastrointestinal stromal tumor

tag: location

value: stomach

tag: mutation

value: KIT E11 M552_W557del

tag: chromosome 9 status

value: 9 loss, homozygous


title: GIST_low-grade (GIST013_LG)

source_name: GIST, jejunum

value: jejunum

value: KIT E11 D572_P573dup


title: GIST_low-grade (GIST016_LG)


title: GIST_low-grade (GIST017_LG)

source_name: GIST, ileum

value: ileum

value: KIT E11 D579del


title: GIST_high-grade_9p loss (GIST017_HG)

value: 9p loss, homozygous


title: CD110+TICs treated 24h rep1 [FAK5_T1]

description: replicate 1

source_name: Colon tumor Fapbl-Cre;Apc2lox14/+;tet-KrasLSL-G12D/+(FAK) mice#5

tag: strain

value: 17 weeks

value: Colon


title: GIST_high-grade_9 loss (GIST012_HG)

value: male

value: KIT E11 L576P

value: 9 loss, heterozygous


title: GIST_high-grade_9 loss (GIST013_HG)


title: GIST_low-grade (GIST012_LG)


title: blast.13_b5.6.7

source_name: blastocyst blastomere, rep51

tag: developmental stage

value: blastocyst (32-cell)


title: Dd2 - Proguanil

description: 2011-09-23_D100813_453299_D1_Dd2_Proguanil

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Proguanil

tag: small molecule

value: Proguanil


title: CD110+TICs untreated 24h rep1 [FAK1_C1]

description: replicate 1

tag: tissue


title: CD110+TICs untreated 24h rep2 [FAK1_C2]

description: replicate 2

tag: age


title: Dd2 - Tafenoquine

description: 2011-09-23_D100813_453299_D9_Dd2_Tafenoquine

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Tafenoquine

value: Tafenoquine


title: Dd2 - Methotrexate

description: 2011-09-23_D100813_453299_D4_Dd2_Methotrexate

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with Methotrexate

value: Methotrexate


title: CD110+TICs treated 24h rep2 [FAK1_T2]

description: replicate 2

source_name: Colon tumor from Fapbl-Cre;Apc2lox14/+;tet-KrasLSL-G12D/+(FAK) mice#1


title: GIST_low-grade (GIST007_LG)

tag: gender

value: gastrointestinal stromal tumor

value: stomach

value: KIT E11 W557_K558del


title: Dd2 - 5-Fluorouracil

description: 2011-09-23_D100813_453299_D5_Dd2_5-Fluorouracil

source_name: Plasmodium falciparum blood stage parasites at 24 hpi perturbed with 5-Fluorouracil


title: ESC.a.200_1

source_name: ESC standard RNA, 200pg, rep1

value: ESC standard RNA


title: blast.13_b8.9

source_name: blastocyst blastomere, rep52


title: CD110+TICs treated 24h rep1 [FAK1_T1]

description: replicate 1


title: CD110+TICs treated 24h rep3 [FAK1_T3]

description: replicate 3


title: blast.13_b3.4

source_name: blastocyst blastomere, rep50


title: GIST_low-grade (GIST003_LG)

value: female

value: KIT E11 T574_S590dup


title: blast.13_b1

source_name: blastocyst blastomere, rep47


title: blast.12_bb4-10

source_name: blastocyst blastomere, rep46


title: GIST_high-grade_9 loss (GIST007_HG)

value: 9 loss, homozygous


title: BrafV600E-CDK4R24C_MPNSTlike (9965580082_D)

city: Bonn

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

data_processing: Variance stabilization and normalization using vsn package from bioconductor in R without background correction

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase

growth_protocol: Animals were kept according to the institutional and national  guidelines for the care and use of laboratory animals with approval by the local government authorities (LANUV, NRW, Germany)

extract_protocol: Total RNA was isolated using TRI Reagent and purified using Rneasy columns (Quiagen).  RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: Tamoxifen was applied on 4 consecutive days on the skin of BrafV600E-CDK4R24C  mice to activate the BRAF(V600E) allele followed by a single topical dose of DMBA to synchronize tumor formation.

tag: genotype

tag: phenotype

value: MPNST-like (amelanotic)

tag: material

value: melanoma


title: blast.13_b2

source_name: blastocyst blastomere, rep49


title: blast.13_b10.11

source_name: blastocyst blastomere, rep48


title: GIST_high-grade_9p loss (GIST003_HG)

source_name: GIST, stomach

value: 9p loss, heterozygous


title: BrafV600E-CDK4R24C_MPNSTlike (9965580082_C)


title: LAN-1_fr_th_nolympho_rep2

source_name: LAN-1 cell line with freezing/thawing (-lymphoprep)

tag: cell line

value: Human neuroblastoma cell line LAN-1


title: LAN-1_fresh_rep2

description: Enriched LAN-1 cells prior freezing

source_name: LAN-1 cell line without freezing/thawing


title: LAN-1_fr_th_lympho_rep2

source_name: LAN-1 cell line with freezing/thawing


title: 1412023098_E

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

description: WT epithalamus rep1

data_processing: Summary of raw data was exported from the BeadStudio/GenomeStudio software and processed in the R software environment. Background correction, variance stabilizing transformation and normalization were performed using the background correction, VST and quantile methods implemented in the lumi package. To combine the array data from two generations of BeadChip used in our experiments, we resolved the inconsistency of Illumina identifiers through nuID. Batch effects were corrected using ComBat. Two samples, 4370236008_D and 4370236008_D, were treated as outliers and excluded from differential expression analysis.

source_name: WT epithalamus rep1

extract_protocol: Total RNA was extracted with TRIzol® (Invitrogen) and purified with RNeasy column (QIAGEN) following manufacturer’s instructions. Quality and quantity of the extracted RNA was determined by Bioanalyzer (Agilent Technologies).

value: thalamus


title: LAN-1_fresh_rep1

description: Enriched LAN-1 cells prior freezing


title: BrafV600E-CDK4R24C_pigmented (9703881154_C)

value: pigmented


title: 1412023098_D

description: WT thalamus rep2

source_name: WT thalamus rep2


title: BrafV600E-CDK4R24C_MPNSTlike (9703881154_F)


title: BrafV600E-CDK4R24C_pigmented (9703881154_A)


title: BrafV600E-CDK4R24C_pigmented (9965580082_A)


title: 254706910087_b3 - col0_BR2 vs mur1_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are genes involved in lignin modifications in mur1 stems?

hyb_protocol: mur1_BR2 Cy5 / col0_BR2 Cy3 : 20pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 200 nmol.

growth_protocol: stem - Media=soil  hygrometry=relative humidity (60%)  Temperature= 22C day/16C night, 150 umol/m2/s  Light=16h light/8h dark

extract_protocol: mur1_BR2:5ug. (Qiagenv1_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: mutant (mur1)

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

value: boyes 6.10

extract_protocol: col0_BR2:5ug. (Qiagenv1_RNeasy.pdf)

value: wild type


title: BrafV600E-CDK4R24C_pigmented (9965580082_B)


title: BrafV600E-CDK4R24C_MPNSTlike (9703881154_D)


title: 1412023098_F

description: WT prethalamus rep1

source_name: WT prethalamus rep1


title: LAN-1_fr_th_lympho_rep1


title: BrafV600E-CDK4R24C_pigmented (9703881154_B)


title: BrafV600E-CDK4R24C_MPNSTlike (9703881154_E)


title: 254706910087_b4 - mur1_BR2 vs col0_BR2

hyb_protocol: col0_BR2 Cy5 / mur1_BR2 Cy3 : 20pmol.

tag: genotype/variation


title: blast.11_b4.b5

source_name: blastocyst blastomere, rep41

value: blastocyst (32-cell)


title: blast.12_b2

source_name: blastocyst blastomere, rep45


title: 1412023098_C

description: KO thalamus rep2

source_name: KO thalamus rep2


title: blast.11_b3

source_name: blastocyst blastomere, rep40


title: blast.12_b1

source_name: blastocyst blastomere, rep42


title: blast.11_b2

source_name: blastocyst blastomere, rep39


title: 254706910087_b2 - mur1_BR1 vs col0_BR1

hyb_protocol: col0_BR1 Cy5 / mur1_BR1 Cy3 : 20pmol.

extract_protocol: col0_BR1:5ug. (Qiagenv1_RNeasy.pdf)

extract_protocol: mur1_BR1:5ug. (Qiagenv1_RNeasy.pdf)


title: HL-23 OSA

city: Toronto

first: Yuning

middle: Jackie

last: Tang

state: Ontario

address: 686 Bay Street

department: Program in Developmental Biology

country: Canada

institute: Hospital for Sick Children

description:
fresh frozen
Replicate 2

source_name: Osteosarcoma

growth_protocol: Transgenic mice bearing p53 mutation were monitored until tumors were readily observable and/or limb paralysis symptoms appeared

extract_protocol: RNA was extracted using standard Trizol method

treatment_protocol: No treatment was used

value: Osteosarcoma

value: p53 flow/flox


title: HL-68 OSA

description:
fresh frozen
Replicate 4


title: blast.11_b1

source_name: blastocyst blastomere, rep38

extract_protocol: single cells, obtained from preimplantation embryos, were directly transferred in RT-qPCR reaction mix.


title: blast.12_b11

source_name: blastocyst blastomere, rep43


title: oocyte samples collected from female 59 sampled in Ria de Aveiro (bad quality)

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description:
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal
Gonads RNA of Ruditapes decussatus

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Quantile normalization always outperformed cyclic loess and quantile-normalized data were further adjusted for the known between-experiments batch effects by implementing the parametric Combat in R (Johnson et al., 2007).

label: Cyanine 3

organism: Ruditapes decussatus

source_name: oocytes of R.decussatus

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Total RNA was isolated using Extract-all (Eurobio) procedure.

value: oocytes

tag: d-larval rate (%)


title: 254706910087_b1 - col0_BR1 vs mur1_BR1

hyb_protocol: mur1_BR1 Cy5 / col0_BR1 Cy3 : 20pmol.


title: oocyte samples collected from female 44 sampled in Ria de Aveiro (bad quality)


title: 254706910088_b2 - mur1_BR3 vs col0_BR3

hyb_protocol: col0_BR3 Cy5 / mur1_BR3 Cy3 : 20pmol.

extract_protocol: col0_BR3:5ug. (Qiagenv1_RNeasy.pdf)

extract_protocol: mur1_BR3:5ug. (Qiagenv1_RNeasy.pdf)


title: oocyte samples collected from female 37 sampled in Ria de Aveiro (bad quality)


title: LAN-1_fr_th_nolympho_rep1


title: blast.12_b12

source_name: blastocyst blastomere, rep44


title: 1412023098_B

description: KO thalamus rep1

source_name: KO thalamus rep1


title: 540121A12_(12)Col 0 (NO) 60 min Rep 3

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC-UPV)

description: It is the third of three independent wild-type biological replicates treated with NO for 60 min.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: A. thaliana Col-0 60 min after NO

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

growth_protocol: Samples were harvested 12 h after dawn of day 12 after sowing and seedlings were grown under long days (16 h light / 8 h darkness) photoperiodic conditions.

extract_protocol: Total RNA from wild type and NO-deficient plants was isolated and purified by the Micro-to-Midi Total RNA Purification System from Invitrogen (Carlsbad, CA, USA).

treatment_protocol: The pulse of NO was performed by incubating plants in a tightly sealed transparent box after injection of 300 ppm of pure NO gas (Linde AG, Germany) during 5 min.

value: seedling


title: oocyte samples collected from female 32 sampled in Ria de Aveiro (good quality)


title: 540121A08_(8)Col 0 (NO) 60 min Rep 2

description: It is the second of three independent wild-type biological replicates treated with NO for 60 min.


title: HL-60 OSA

description:
fresh frozen
Replicate 3


title: oocyte samples collected from female 26 sampled in Ria de Aveiro (intermediate quality)


title: blast.10_b3

source_name: blastocyst blastomere, rep35


title: blast.10_b4.b5

source_name: blastocyst blastomere, rep36


title: blast.10_b1

source_name: blastocyst blastomere, rep33


title: blast.10_b6

source_name: blastocyst blastomere, rep37


title: blast.10_b2

source_name: blastocyst blastomere, rep34


title: HL-50 STS

description:
fresh frozen
Replicate 4

source_name: Leiomyosarcoma

value: Leiomyosarcoma


title: HL-3 STS

description:
fresh frozen
Replicate 2


title: 540121A10_(10)Col 0 (NO) 15 min Rep 3

description: It is the third of three independent wild-type biological replicates treated with NO for 15 min.

source_name: A. thaliana Col-0 15 min after NO


title: HL-27 STS

description:
fresh frozen
Replicate 3


title: HL53-A Bone Marrow

description:
fresh frozen
Replicate 2

source_name: Bone Marrow tissue

value: Bone Marrow


title: HL-6 OSA

description:
fresh frozen
Replicate 1


title: 540121A09_(9)Col 0 Rep 3

description: It is the third of three independent wild-type biological replicates not treated with NO.

source_name: A. thaliana Col-0 untreated


title: oocyte samples collected from female 27 sampled in Ria de Aveiro (good quality)


title: 540121A07_(7)Col 0 (NO) 30 min Rep 2

description: It is the second of three independent wild-type biological replicates treated with NO for 30 min.

source_name: A. thaliana Col-0 30 min after NO


title: 540121A06_(6)Col 0 (NO) 15 min Rep 2

description: It is the second of three independent wild-type biological replicates treated with NO for 15 min.


title: HL-1 STS

description:
fresh frozen
Replicate 1


title: blast.09_b9.10

source_name: blastocyst blastomere, rep32


title: 540121A05_(5)Col 0 Rep 2

description: It is the second of three independent wild-type biological replicates not treated with NO.


title: oocyte samples collected from female 24 sampled in Ria de Aveiro (good quality)


title: 540121A11_(11)Col 0 (NO) 30 min Rep 3

description: It is the third of three independent wild-type biological replicates treated with NO for 30 min.


title: 540121A04_(4)Col 0 (NO) 60 min Rep 1

description: It is the first of three independent wild-type biological replicates treated with NO for 60 min.


title: oocyte samples collected from female 25 sampled in Ria de Aveiro (intermediate quality)


title: 540121A03_(3)Col 0 (NO) 30 min Rep 1

description: It is the first of three independent wild-type biological replicates treated with NO for 30 min.


title: oocyte samples collected from female 30 sampled in Ria de Aveiro (intermediate quality)


title: 254706910088_b1 - col0_BR3 vs mur1_BR3

hyb_protocol: mur1_BR3 Cy5 / col0_BR3 Cy3 : 20pmol.


title: oocyte samples collected from female 18 sampled in Ria de Aveiro (bad quality)


title: oocyte samples collected from female 12 sampled in Ria de Aveiro (good quality)


title: PG-KS_061 mouse ESC cell line R1 exposed to 1 mM VPA/0.1% DMSO

city: stockholm

first: ying

last: sun

address: Tomtebodavagen 23

department: Personalized Healthcare and biomarkers

country: Sweden

institute: AstraZeneca

hyb_protocol: fragmented and biotin-labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip® Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with R software (3.0.0 version), Expression values were log2 transformed and normalized by RMA method.

source_name: embryonic stem cell

label_protocol: Biotinylated single-stranded cDNA  (ss-cDNA) were prepared according to the standard Affymetrix protocol from total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: R1 mouse ES cells were grown on feeder cells in complete ES cell medium, and feeder depleted and seeded for experiments, as previously described by Jergil et al. (Toxicol Sci. 2011;121:328-42. PMID: 21427059).

extract_protocol: Total RNA was extracted using RNeasy mini spin columns (Qiagen), DNase treated according to manufac, concentration determined using a NanoDrop ND-1000 Spectrophotometer, and quality determined using RNA6000 LabChips in the Agilent 2100 Bioanalyzer.

treatment_protocol: R1 mouse embryonic stem cells in the attached undifferentiated stem-cell state were exposed for 6h in complete ES medium at the IC10 (the 10% inhibitory concentration as determined in a cell viability assay), the maximum concentration of 1 mM, or at the concentration of maximum solubility, whichever was found to be lower for each compound.

tag: compound

value: teratogen

tag: treatment

value: 1 mM VPA/0.1% DMSO


title: blast.09_b17.18.19.20.21

city: Basel

last: Peters

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

source_name: blastocyst blastomere, rep26


title: oocyte samples collected from female 14 sampled in Ria de Aveiro (bad quality)

source_name: oocytes of R.decussatus


title: blast.09_b2

source_name: blastocyst blastomere, rep27


title: blast.09_b3.4

source_name: blastocyst blastomere, rep29


title: blast.09_b5.6.7

source_name: blastocyst blastomere, rep30


title: blast.09_b22.23.24.25.26

source_name: blastocyst blastomere, rep28


title: blast.09_b8

source_name: blastocyst blastomere, rep31


title: oocyte samples collected from female 10 sampled in Ria de Aveiro (good quality)


title: oocyte samples collected from female 15 sampled in Ria de Aveiro (bad quality)


title: PG-KS_060 mouse ESC cell line R1 exposed to 1 mM Sulfasalazine/0.1% DMSO

value: non-teratogen

value: 1 mM Sulfasalazine/0.1% DMSO


title: 540121A01_(1)Col 0 Rep 1

description: It is the first of three independent wild-type biological replicates not treated with NO.


title: PG-KS_059 mouse ESC cell line R1 exposed to 1 mM Sulfasalazine/0.1% DMSO


title: PG-KS_056 mouse ESC cell line R1 exposed to 0.028 µM Methotrexate/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.028 µM Methotrexate/0.1% DMSO

value: 0.028 µM Methotrexate/0.1% DMSO


title: blast.09_b11.12.13.14

source_name: blastocyst blastomere, rep24


title: blast.09_b15.16

source_name: blastocyst blastomere, rep25


title: PG-KS_063 mouse ESC cell line R1 exposed to 1 mM VPA/0.1% DMSO


title: PG-KS_058 mouse ESC cell line R1 exposed to 1 mM Sulfasalazine/0.1% DMSO


title: blast.08_b9

source_name: blastocyst blastomere, rep22


title: PG-KS_055 mouse ESC cell line R1 exposed to 0.028 µM Methotrexate/0.1% DMSO


title: blast.09_b1

source_name: blastocyst blastomere, rep23


title: blast.08_b4

source_name: blastocyst blastomere, rep20


title: blast.08_b5.6.7.8

source_name: blastocyst blastomere, rep21


title: HL53-2 Muscle

description:
fresh frozen
Replicate 1

source_name: Muscle tissue

value: Muscle


title: HL49-A Bone Marrow

description:
fresh frozen
Replicate 1

source_name: Bone Marrow tissue


title: oocyte samples collected from female 16 sampled in Ria de Aveiro (intermediate quality)


title: 1412023098_A

description: WT thalamus rep1

source_name: WT thalamus rep1

value: thalamus


title: oocyte samples collected from female 19 sampled in Ria de Aveiro (intermediate quality)


title: oocyte samples collected from female 20 sampled in Ria de Aveiro (bad quality)


title: oocyte samples collected from female 9 sampled in Ria de Aveiro (good quality)


title: PG-KS_062 mouse ESC cell line R1 exposed to 1 mM VPA/0.1% DMSO

source_name: embryonic stem cell


title: blast.08_b3

source_name: blastocyst blastomere, rep19


title: PG-KS_054 mouse ESC cell line R1 exposed to 1 mM Paracetamol/0.1% DMSO

value: 1 mM Paracetamol/0.1% DMSO


title: 540121A02_(2)Col 0 (NO) 15 min Rep 1

description: It is the first of three independent wild-type biological replicates treated with NO for 15 min.

source_name: A. thaliana Col-0 15 min after NO


title: oocyte samples collected from female 6 sampled in Ria de Aveiro (intermediate quality)

source_name: oocytes of R.decussatus


title: PG-KS_053 mouse ESC cell line R1 exposed to 1 mM Paracetamol/0.1% DMSO


title: oocyte samples collected from female 5 sampled in Ria de Aveiro (good quality)


title: PG-KS_057 mouse ESC cell line R1 exposed to 0.028 µM Methotrexate/0.1% DMSO


title: oocyte samples collected from female 7 sampled in Ria de Aveiro (intermediate quality)


title: oocyte samples collected from female 4 sampled in Ria de Aveiro (bad quality)


title: HL94-2 Muscle

description:
fresh frozen
Replicate 2


title: blast.08_b2

source_name: blastocyst blastomere, rep18


title: oocyte samples collected from female 2 sampled in Ria de Aveiro (good quality)


title: blast.08_b12.13

source_name: blastocyst blastomere, rep16


title: blast.08_b14

source_name: blastocyst blastomere, rep17


title: oocyte samples collected from female 3 sampled in Ria de Aveiro (good quality)


title: blast.08_b12

source_name: blastocyst blastomere, rep15


title: blast.08_b1

source_name: blastocyst blastomere, rep13


title: PG-KS_052 mouse ESC cell line R1 exposed to 1 mM Paracetamol/0.1% DMSO


title: oocyte samples collected from female 1 sampled in Ria de Aveiro (bad quality)


title: PG-KS_049 mouse ESC cell line R1 exposed to 1 mM Topiramate/0.1% DMSO

value: 1 mM Topiramate/0.1% DMSO


title: PG-KS_050 mouse ESC cell line R1 exposed to 1 mM Topiramate/0.1% DMSO


title: PG-KS_051 mouse ESC cell line R1 exposed to 1 mM Topiramate/0.1% DMSO


title: blast.07_TE

source_name: blastocyst trophectoderm, rep1


title: PG-KS_048 mouse ESC cell line R1 exposed to 0.054 mM Ondansetron/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.054 mM Ondansetron/0.1% DMSO

value: 0.054 mM Ondansetron/0.1% DMSO


title: blast.06

source_name: blastocyst embryo, rep3

value: blastocyst (32-cell)


title: PG-KS_046 mouse ESC cell line R1 exposed to 0.054 mM Ondansetron/0.1% DMSO


title: PG-KS_047 mouse ESC cell line R1 exposed to 0.054 mM Ondansetron/0.1% DMSO


title: blast.05

source_name: blastocyst embryo, rep2


title: blast.08_b10

source_name: blastocyst blastomere, rep14


title: PG-KS_045b mouse ESC cell line R1 exposed to 1 mM Fluconazole/0.1% DMSO

value: 1 mM Fluconazole/0.1% DMSO


title: PG-KS_044 mouse ESC cell line R1 exposed to 1 mM Fluconazole/0.1% DMSO


title: blast.02_ICM

source_name: blastocyst inner cell mass, rep1


title: blast.04

source_name: blastocyst embryo, rep1


title: PG-KS_043b mouse ESC cell line R1 exposed to 1 mM Fluconazole/0.1% DMSO


title: blast.01_b9

source_name: blastocyst blastomere, rep12


title: PG-KS_042 mouse ESC cell line R1 exposed to 0.17 mM Metoclopramide/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.17 mM Metoclopramide/0.1% DMSO

value: 0.17 mM Metoclopramide/0.1% DMSO


title: blast.01_b8

source_name: blastocyst blastomere, rep11


title: genomic DNA from adipose tissue sample 69 [Twin34_2]

type: genomic

city: Helsinki

first: Khadeeja

last: Ismail

state: Helsinki

address: Mannerheimintie 172

department: Department of Public Health

country: Finland

institute: University of Helsinki

description: normal adipose tissue sample

hyb_protocol: DNA was bisulfite converted by using the EZ-96 DNA Methylation-Gold Kit according to the manufacturer’s instructions  and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Quantile and BMIQ normalized using Bioconductor 2.13 packages
SIgnalIntensityMatrix.txt: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA from adipose tissue samples was extracted and purified  using the QIAamp DNA Mini kit according to standard instructions

tag: twin id

value: Male

tag: bmi

value: low

tag: disease state

tag: tissue type

value: adipose tissue


title: genomic DNA from adipose tissue sample 66 [Twin31_2]

description: normal adipose tissue sample

value: Female


title: PG-KS_041 mouse ESC cell line R1 exposed to 0.17 mM Metoclopramide/0.1% DMSO

source_name: embryonic stem cell


title: PG-KS_040 mouse ESC cell line R1 exposed to 0.17 mM Metoclopramide/0.1% DMSO


title: blast.01_b7

first: Antoine

address: Maulbeerstrasse 66

data_processing:
The raw Ct were first subtracted from the global threshold value (30-Ct) and then normalized by subtracting the average signal for Ssu72, Hnrnpr and Ube2e1.
Excluded genes:
Gene-by-gene QC was performed by Fluidigm's qPCR Analysis software. In the Matrix normalized worksheet, the column Gene_QC indicates which whether a gene passed or failed QC.

source_name: blastocyst blastomere, rep10

tag: developmental stage


title: genomic DNA from adipose tissue sample 67 [Twin32_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 68 [Twin33_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 70 [Twin35_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 62 [Twin27_2]

description: normal adipose tissue sample


title: blast.01_b6

source_name: blastocyst blastomere, rep9


title: blast.01_b4

source_name: blastocyst blastomere, rep7


title: blast.01_b5

source_name: blastocyst blastomere, rep8


title: genomic DNA from adipose tissue sample 60 [Twin25_2]

description: normal adipose tissue sample


title: PG-KS_035 mouse ESC cell line R1 exposed to 0.043 mM Loratadine/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.043 mM Loratadine/0.1% DMSO

value: 0.043 mM Loratadine/0.1% DMSO


title: genomic DNA from adipose tissue sample 59 [Twin24_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 64 [Twin29_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 56 [Twin21_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 61 [Twin26_2]

description: normal adipose tissue sample


title: PG-KS_039 mouse ESC cell line R1 exposed to 1 mM Dimethadione/0.1% DMSO

value: teratogen

value: 1 mM Dimethadione/0.1% DMSO


title: PG-KS_037 mouse ESC cell line R1 exposed to 1 mM Dimethadione/0.1% DMSO


title: genomic DNA from adipose tissue sample 54 [Twin19_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 58 [Twin23_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 65 [Twin30_2]

description: normal adipose tissue sample


title: PG-KS_038 mouse ESC cell line R1 exposed to 1 mM Dimethadione/0.1% DMSO


title: blast.01_b3

source_name: blastocyst blastomere, rep6


title: genomic DNA from adipose tissue sample 55 [Twin20_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 53 [Twin18_2]

description: normal adipose tissue sample


title: PG-KS_036 mouse ESC cell line R1 exposed to 0.043 mM Loratadine/0.1% DMSO

value: non-teratogen


title: PG-KS_033b mouse ESC cell line R1 exposed to 0.1 mM Dexamethazone/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.1 mM Dexamethazone/0.1% DMSO

value: 0.1 mM Dexamethazone/0.1% DMSO


title: PG-KS_032 mouse ESC cell line R1 exposed to 0.1 mM Dexamethazone/0.1% DMSO


title: blast.01_b13

source_name: blastocyst blastomere, rep3


title: genomic DNA from adipose tissue sample 50 [Twin15_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 51 [Twin16_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 52 [Twin17_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 63 [Twin28_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 49 [Twin14_2]

description: normal adipose tissue sample


title: blast.01_b10.11

source_name: blastocyst blastomere, rep2


title: genomic DNA from adipose tissue sample 46 [Twin11_2]

description: normal adipose tissue sample


title: 8c.e7_b3

source_name: 8-cell blastomere, rep24


title: genomic DNA from adipose tissue sample 57 [Twin22_2]

description: normal adipose tissue sample


title: 8c.e7_b2

source_name: 8-cell blastomere, rep23


title: genomic DNA from adipose tissue sample 45 [Twin10_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 47 [Twin12_2]

description: normal adipose tissue sample


title: PG-KS_029 mouse ESC cell line R1 exposed to 1 mM Hydrochlorothiazide/0.1% DMSO

value: 1 mM Hydrochlorothiazide/0.1% DMSO


title: blast.01_b2

source_name: blastocyst blastomere, rep5


title: genomic DNA from adipose tissue sample 44 [Twin9_2]

description: normal adipose tissue sample


title: PG-KS_030 mouse ESC cell line R1 exposed to 1 mM Hydrochlorothiazide/0.1% DMSO


title: PG-KS_028 mouse ESC cell line R1 exposed to 1 mM Hydrochlorothiazide/0.1% DMSO


title: 8c.e6_b5

source_name: 8-cell blastomere, rep21


title: 8c.e7_b1

source_name: 8-cell blastomere, rep22


title: blast.01_b1

source_name: blastocyst blastomere, rep1


title: PG-KS_031 mouse ESC cell line R1 exposed to 0.1 mM Dexamethazone/0.1% DMSO


title: PG-KS_026b mouse ESC cell line R1 exposed to 0.024 mM All trans retinoic acid/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.024 mM All trans retinoic acid/0.1% DMSO


title: blast.01_b15.16.17.18

source_name: blastocyst blastomere, rep4


title: PG-KS_024 mouse ESC cell line R1 exposed to 0.37 mM Glybenclamide/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.37 mM Glybenclamide/0.1% DMSO

value: 0.37 mM Glybenclamide/0.1% DMSO


title: PG-KS_027 mouse ESC cell line R1 exposed to 0.024 mM All trans retinoic acid/0.1% DMSO


title: 8c.e6_b1

source_name: 8-cell blastomere, rep17


title: 8c.e5_b8

source_name: 8-cell blastomere, rep16


title: 8c.e6_b3

source_name: 8-cell blastomere, rep19


title: 8c.e6_b2

source_name: 8-cell blastomere, rep18


title: 8c.e6_b4

source_name: 8-cell blastomere, rep20


title: PG-KS_023 mouse ESC cell line R1 exposed to 0.37 mM Glybenclamide/0.1% DMSO

source_name: embryonic stem cell


title: PG-KS_022 mouse ESC cell line R1 exposed to 0.37 mM Glybenclamide/0.1% DMSO


title: genomic DNA from adipose tissue sample 43 [Twin8_2]

description: normal adipose tissue sample


title: PG-KS_025 mouse ESC cell line R1 exposed to 0.024 mM All trans retinoic acid/0.1% DMSO


title: 8c.e5_b7

source_name: 8-cell blastomere, rep15


title: PG-KS_034b mouse ESC cell line R1 exposed to 0.043 mM Loratadine/0.1% DMSO


title: PG-KS_021 mouse ESC cell line R1 exposed to 0.23 µM 5-azacytidine  (azacitidine)/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.23 µM 5-azacytidine  (azacitidine)/0.1% DMSO


title: PG-KS_020 mouse ESC cell line R1 exposed to 0.23 µM 5-azacytidine  (azacitidine)/0.1% DMSO


title: 8c.e5_b5

source_name: 8-cell blastomere, rep13


title: 8c.e5_b4

source_name: 8-cell blastomere, rep12


title: 8c.e5_b6

source_name: 8-cell blastomere, rep14


title: genomic DNA from adipose tissue sample 42 [Twin7_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 38 [Twin3_2]

description: normal adipose tissue sample


title: 8c.e5_b3

source_name: 8-cell blastomere, rep11


title: PG-KS_019b mouse ESC cell line R1 exposed to 0.23 µM 5-azacytidine  (azacitidine)/0.1% DMSO


title: genomic DNA from adipose tissue sample 48 [Twin13_2]

description: normal adipose tissue sample


title: 4370236008_E

description: WT thalamus rep4

source_name: WT thalamus rep4

tag: strain

tag: age

tag: tissue

value: thalamus


title: PG-KS_016 mouse ESC cell line R1 exposed to 0.028 mM Clozapine/0.1% DMSO

description:
IC10 determined from the dose-response curve in a 24-h cell viability assay, using CellTiter-Glo® (Promega)
mouse ESC cell line R1 exposed to 0.028 mM Clozapine/0.1% DMSO

value: 0.028 mM Clozapine/0.1% DMSO


title: PG-KS_018 mouse ESC cell line R1 exposed to 0.028 mM Clozapine/0.1% DMSO


title: PG-KS_017 mouse ESC cell line R1 exposed to 0.028 mM Clozapine/0.1% DMSO


title: 8c.e5_b2

source_name: 8-cell blastomere, rep10


title: 4370236008_F

description: WT thalamus rep5 (excluded outlier)

source_name: WT thalamus rep5


title: genomic DNA from adipose tissue sample 40 [Twin5_2]

description: normal adipose tissue sample

tag: gender


title: 8c.e5_b1

source_name: 8-cell blastomere, rep9


title: 4370236008_C

description: WT thalamus rep3

source_name: WT thalamus rep3


title: PG-KS_014 mouse ESC cell line R1 exposed to 0.35 mM (+/-)-Thalidomide/0.1% DMSO

value: 0.35 mM (+/-)-Thalidomide/0.1% DMSO


title: PG-KS_015b mouse ESC cell line R1 exposed to 0.35 mM (+/-)-Thalidomide/0.1% DMSO


title: 4370236008_D

description: KO thalamus rep5 (excluded outliner)

source_name: KO thalamus rep5


title: 8c.e4_b8

source_name: 8-cell blastomere, rep8


title: 8c.e4_b7

source_name: 8-cell blastomere, rep7


title: genomic DNA from adipose tissue sample 39 [Twin4_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 32 [Twin32_1]

description: normal adipose tissue sample

value: high


title: genomic DNA from adipose tissue sample 33 [Twin33_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 37 [Twin2_2]

description: normal adipose tissue sample


title: 4370236008_A

description: KO thalamus rep3

source_name: KO thalamus rep3


title: PG-KS_012 mouse ESC cell line R1 exposed to 1 mM Chlorthalidone/0.1% DMSO

value: 1 mM Chlorthalidone/0.1% DMSO


title: 8c.e4_b6

source_name: 8-cell blastomere, rep6


title: Peg(-1.0)_2

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

institute: University of Lausanne

description: Hot-phenol extraccion

hyb_protocol: The volume of the different samples was adjusted for the hybridization in order to add 60 ng of labelled Cy3-cDNA per array on the slide. Hybridization was performed at 65°C for 17 hours, after which slides were washed according to Agilent procedures and scanned. The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%). The AGILENT FEATURE EXTRACTION SOFTWARE was used to extract the signal intensities of the probes from the scanned images.

data_processing: The text data file was used as input in GeneSpring GX v12. Expression data were quantile normalized by GeneSpring and baseline transformed. All genes were filtered by expression and were retained when the signal intensity was above the 20th percentile in at least one of the samples.

label: Cyanine 3-dCTP

organism: Pseudarthrobacter chlorophenolicus A6

source_name: Matric stress -1.0Mpa

label_protocol: Labelled cDNAs were produced in a reverse transcription reaction using cyanine-3-labeled dCTP. The labelled cDNA was purified with a MinElute PCR purification kit (Qiagen 28004). The percentage of incorporation of Cy-3-dCTP was calculated by the MICROARRAY function of the Nanodrop spectrophotometer.

growth_protocol: Arthrobacter chlorophenolicus (A6) was cultured in GM minimal medium with 0.1% yeast extract as carbon source at 28°C and 180 rpm until exponential phase (OD600= 0.2)

extract_protocol: After 30 min incubation culture samples were immediately filtered over a 0.2 µm membrane filter by vacuum suction. The filter with the cells was removed and frozen in liquid nitrogen. The filters were stored at -80°C until RNA isolation. RNA was extracted from frozen cells on filters with an acid-phenol method.

treatment_protocol: 10 ml of culture sample was added to 10 ml of GM containing PEG8000 so as to obtain a final matric potential of -1.0 Mpa  or 10ml  of GM containing NaCl to obtain a final solute potential of -1.5Mpa and incubated for 30 min. Each treatment or control was run in four independent replicates.

tag: media

value: GM yeast extract 0.1% and PEG8000 at -1.0Mpa


title: PG-KS_013b mouse ESC cell line R1 exposed to 0.35 mM (+/-)-Thalidomide/0.1% DMSO

source_name: embryonic stem cell

tag: cell line


title: 8c.e4_b5

source_name: 8-cell blastomere, rep5


title: 4370236008_B

description: KO thalamus rep4

source_name: KO thalamus rep4


title: Peg(-1.0)_1

description: Hot-phenol extraccion


title: PG-KS_011 mouse ESC cell line R1 exposed to 1 mM Chlorthalidone/0.1% DMSO


title: genomic DNA from adipose tissue sample 41 [Twin6_2]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 36 [Twin1_2]

description: normal adipose tissue sample

value: Male


title: genomic DNA from adipose tissue sample 35 [Twin35_1]

description: normal adipose tissue sample


title: 8c.e4_b4

source_name: 8-cell blastomere, rep4


title: Control-M4

description: Hot-phenol extraccion

source_name: Control culutre for matric stress

value: GM yeast extract 0.1%


title: Control-M3

description: Hot-phenol extraccion


title: genomic DNA from adipose tissue sample 34 [Twin34_1]

description: normal adipose tissue sample

value: adipose tissue


title: PG-KS_009 mouse ESC cell line R1 exposed to 1 mM (-)-d-penicillamine/0.1% DMSO

value: 1 mM (-)-d-penicillamine/0.1% DMSO


title: PG-KS_010 mouse ESC cell line R1 exposed to 1 mM Chlorthalidone/0.1% DMSO


title: PG-KS_008 mouse ESC cell line R1 exposed to 1 mM (-)-d-penicillamine/0.1% DMSO


title: genomic DNA from adipose tissue sample 29 [Twin29_1]

description: normal adipose tissue sample

value: Female


title: 8c.e4_b2

source_name: 8-cell blastomere, rep2


title: 8c.e4_b1

source_name: 8-cell blastomere, rep1


title: 8c.e4_b3

source_name: 8-cell blastomere, rep3


title: Control-M1

description: Hot-phenol extraccion


title: genomic DNA from adipose tissue sample 27 [Twin27_1]

description: normal adipose tissue sample


title: 8c.e3

source_name: 8-cell embryo, rep3


title: PG-KS_006 mouse ESC cell line R1 exposed to 0.1% DMSO

value: solvent

value: 0.1% DMSO


title: genomic DNA from adipose tissue sample 22 [Twin22_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 25 [Twin25_1]

description: normal adipose tissue sample


title: 8c.e2

source_name: 8-cell embryo, rep2


title: genomic DNA from adipose tissue sample 31 [Twin31_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 28 [Twin28_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 30 [Twin30_1]

description: normal adipose tissue sample


title: PG-KS_005 mouse ESC cell line R1 exposed to 0.1% DMSO


title: PG-KS_004 mouse ESC cell line R1 exposed to 0.1% DMSO


title: NaCl(-1.5)_4

description: Hot-phenol extraccion

source_name: Solute stress -1.5Mpa

value: GM yeast extract 0.1% and Nacl at -1.5Mpa


title: NaCl(-1.5)_3

description: Hot-phenol extraccion


title: NaCl(-1.5)_2

description: Hot-phenol extraccion


title: genomic DNA from adipose tissue sample 24 [Twin24_1]

description: normal adipose tissue sample


title: NaCl(-1.5)_1

description: Hot-phenol extraccion


title: 4c.e6_b4

source_name: 4-cell blastomere, rep9


title: genomic DNA from adipose tissue sample 23 [Twin23_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 26 [Twin26_1]

description: normal adipose tissue sample


title: 4c.e6_b3

source_name: 4-cell blastomere, rep8


title: 4c.e6_b2

source_name: 4-cell blastomere, rep7


title: Control-M2

description: Hot-phenol extraccion


title: Control-S4

description: Hot-phenol extraccion

source_name: Control culutre for solute stress


title: Control-S3

description: Hot-phenol extraccion


title: genomic DNA from adipose tissue sample 20 [Twin20_1]

description: normal adipose tissue sample


title: 8c.e1

source_name: 8-cell embryo, rep1


title: Control-S2

description: Hot-phenol extraccion


title: 4c.e6_b1

source_name: 4-cell blastomere, rep6


title: genomic DNA from adipose tissue sample 19 [Twin19_1]

description: normal adipose tissue sample


title: 4c.e5_b3

source_name: 4-cell blastomere, rep5


title: PG-KS_007 mouse ESC cell line R1 exposed to 1 mM (-)-d-penicillamine/0.1% DMSO

source_name: embryonic stem cell

value: teratogen


title: Control-S1

description: Hot-phenol extraccion


title: genomic DNA from adipose tissue sample 17 [Twin17_1]

description: normal adipose tissue sample


title: 4c.e5_b1

source_name: 4-cell blastomere, rep3


title: 4c.e5_b2

source_name: 4-cell blastomere, rep4


title: 4c.e4_b2

source_name: 4-cell blastomere, rep2


title: genomic DNA from adipose tissue sample 21 [Twin21_1]

description: normal adipose tissue sample


title: 4c.e4_b1

source_name: 4-cell blastomere, rep1


title: 4c.e3

source_name: 4-cell embryo, rep3


title: genomic DNA from adipose tissue sample 18 [Twin18_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 15 [Twin15_1]

description: normal adipose tissue sample


title: IMR90 CB20903630 replicate 2

city: Glasgow

first: W. Nicol

last: Keith

address: Wolfson Wohl Translational Cancer Research Centre

department: Institute of Cancer Science

country: United Kingdom

institute: University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm and washed as as per manufacturers instructions for one colour arrays (Agilent Technologies)

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: Normalisation performed in GeneSpring GX (Agilent Technologies).  Feature extraction data normalised to the 75th percentile with intensities below 0.01 set to 0.01.

source_name: IMR90 diploid fibroblasts DMSO treated with 10mM CB20903630, replicate 2

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) following manufacturers instructions

growth_protocol: IMR90 human diploid fibroblasts were cultured in phenol-red free DMEM containing 10% feotal bovine serum under 5% oxygen

extract_protocol: Total RNA was extracted from trypsinised cell pellets using the Nucleospin II kit (Macherey-Nagel) following manufacturers instructions

treatment_protocol: 1,000,000 cells were seeded in T75 flasks.  After 24hrs medium was changed to contain CB20903630 or DMSO control and cells were cultured for a further 2 days in the presence of drug, followed by RNA extraction at day 3.

tag: cell type

value: fibroblast


title: IMR90 DMSO (CB control) replicate 2

source_name: IMR90 diploid fibroblasts DMSO control for CB20903630 treatments, replicate 2


title: HCT116 CB20903630 replicate 2

source_name: HCT116 colorectal cancer cells treated with 10mM CB20903630, replicate 2

value: colorectal cancer


title: IMR90 DMSO (CB control) replicate 1

source_name: IMR90 diploid fibroblasts DMSO control for CB20903630 treatments, replicate 1


title: IMR90 CB20903630 replicate 1

source_name: IMR90 diploid fibroblasts DMSO treated with 10mM CB20903630, replicate 1


title: HCT116 DMSO replicate 3

source_name: HCT116 colorectal cancer cells DMSO control, replicate 3


title: 4c.e2

source_name: 4-cell embryo, rep2

label_protocol: CellsDirect (Invitrogen), Fluidigm qPCR


title: HCT116 CB20903630 replicate 1

source_name: HCT116 colorectal cancer cells treated with 10mM CB20903630, replicate 1


title: HCT116 CB20903630 replicate 3

source_name: HCT116 colorectal cancer cells treated with 10mM CB20903630, replicate 3


title: genomic DNA from adipose tissue sample 14 [Twin14_1]

description: normal adipose tissue sample


title: 4c.e1

source_name: 4-cell embryo, rep1


title: genomic DNA from adipose tissue sample 9 [Twin9_1]

description: normal adipose tissue sample


title: 3c.e3_b1

source_name: 3-cell blastomere, rep7


title: HCT116 DMSO replicate 2

source_name: HCT116 colorectal cancer cells DMSO control, replicate 2


title: T-47D BMP4

city: Tampere

first: Emma-Leena

last: Alarmo

address: Biokatu 6

institute: Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere

hyb_protocol: The hybridization of the samples were executed using Agilent miRNA Complete Labeling and Hyb Kit to the Agilent Unrestricted Human miRNA v14 Rev.2 microarray (Human miRBase 14.0 probe group) according to manufacturer’s instructions.

scan_protocol: After hybridization, the arrays were scanned using an Agilent DNA microarray scanner and data were extracted using the Feature Extraction software, version 10.7.1.1 (Agilent Technologies).

data_processing: Background corrected probe intensities were quantile normalized between samples.

source_name: T-47D human breast cancer cell line, treated with BMP4, 4h

label_protocol: The labeling of the samples were executed using Agilent miRNA Complete Labeling and Hyb Kit according to manufacturer’s instructions. Shortly, 100 ng of total RNA was dephosphorylated, denatured, and labeled with pCp-Cy3 dye. Labeled RNA was purified using the Micro BioSpin 6 columns.

growth_protocol: All the cell lines were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the recommended conditions.

extract_protocol: Total RNA was extracted with Agilent Absolutely RNA miRNA Kit (Agilent Technologies) according the manufacturer’s instructions. The quality of the RNA samples was confirmed with Agilent 2100 Bioanalyzer.

value: breast cancer


title: 3c.e2_b2-3-2

source_name: 3-cell blastomere, rep6

growth_protocol: Preimplantation embryos were cultured in KSOMaa medium under low oxygen conditions.


title: MDA-MB-436 BMP4

source_name: MDA-MB-436 human breast cancer cell line, treated with BMP4, 4h


title: MDA-MB-436 vehicle

source_name: MDA-MB-436 human breast cancer cell line, treated with vehicle, 4h


title: 3c.e2_b2-3-1

source_name: 3-cell blastomere, rep5


title: HCT116 DMSO replicate 1

source_name: HCT116 colorectal cancer cells DMSO control, replicate 1


title: genomic DNA from adipose tissue sample 12 [Twin12_1]

description: normal adipose tissue sample


title: MDA-MB-361 vehicle

source_name: MDA-MB-361 human breast cancer cell line, treated with vehicle, 4h


title: genomic DNA from adipose tissue sample 16 [Twin16_1]

description: normal adipose tissue sample


title: IMR90 ZM1 replicate 2

source_name: IMR90 diploid fibroblasts treated with 2µM Aurora kinase inhibitor ZM1, replicate 2

treatment_protocol: 500,000 cells were seeded in 10cm dishes.  After 24hrs (day 1) medium was changed to contain specific kinase inhibitors or DMSO control and cells were cultured for a further 4 days in the presence of drug. Cells were re-plated once on day 3. The cells were then harvested for RNA extraction on day 5.


title: genomic DNA from adipose tissue sample 13 [Twin13_1]

description: normal adipose tissue sample


title: IMR90 ZM1 replicate 1

source_name: IMR90 diploid fibroblasts treated with 2µM Aurora kinase inhibitor ZM1, replicate 1


title: genomic DNA from adipose tissue sample 10 [Twin10_1]

description: normal adipose tissue sample


title: IMR90 SU6656 replicate 2

source_name: IMR90 diploid fibroblasts treated with 10µM Src kinase inhibitor SU6656, replicate 2


title: genomic DNA from adipose tissue sample 11 [Twin11_1]

description: normal adipose tissue sample


title: 3c.e2_b1

source_name: 3-cell blastomere, rep4


title: MDA-MB-361 BMP4

source_name: MDA-MB-361 human breast cancer cell line, treated with BMP4, 4h


title: 3c.e1_b3

source_name: 3-cell blastomere, rep3


title: 3c.e1_b2

source_name: 3-cell blastomere, rep2


title: MDA-MB-231 vehicle

source_name: MDA-MB-231 human breast cancer cell line, treated with vehicle, 4h


title: IMR90 SU6656 replicate 1

source_name: IMR90 diploid fibroblasts treated with 10µM Src kinase inhibitor SU6656, replicate 1


title: 3c.e1_b1

source_name: 3-cell blastomere, rep1


title: T-47D vehicle

source_name: T-47D human breast cancer cell line, treated with vehicle, 4h


title: MCF-7 vehicle

source_name: MCF-7 human breast cancer cell line, treated with vehicle, 4h


title: IMR90 RHOK IV replicate 2

source_name: IMR90 diploid fibroblasts treated with 10µM Rho kinase inhibitor IV, replicate 2


title: IMR90 RHOK IV replicate 1

source_name: IMR90 diploid fibroblasts treated with 10µM Rho kinase inhibitor IV, replicate 1


title: IMR90 PI 103 replicate 2

source_name: IMR90 diploid fibroblasts treated with 1µM PI3K/mTOR inhibitor PI-103, replicate 2


title: MDA-MB-231 BMP4

source_name: MDA-MB-231 human breast cancer cell line, treated with BMP4, 4h


title: genomic DNA from fibroblasts FIB-SP-13-L2PD

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

institute: Fundacio Clinic/IDIBAPS

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using the standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan reader using standard recommended Illumina scanner setting

data_processing: Using the minfi R package available through Bioconductor

source_name: IPSC-PD  LRRK2 G2019S mutation carrier

growth_protocol: Keratinocytes or dermal fibroblasts were cultured using standard protocols from skin biopsy obtained from participating subjects [Sanchez-Danes et al., 2012]. Briefly, keratinocytes and/ or fibroblasts were transformed to induced pluripotent stem cells (iPSC) by retroviral transduction of three transcription factors (OTC4, SOX2 and KLF4). Subsequently, iPSC were differentiated into DAn specific growth factor medium supplementation (bFGF, FGF-8 and SHH) and lentiviral LMX1A delivery.Described in Sanchez-Danes et al., EMBO Mol Med. 2012 ;4(5):380-95. doi: 10.1002/emmm.201200215.

extract_protocol: DNA extracted according to AllPrep DNA/RNA/Protein Mini Kit - Qiagen

treatment_protocol: No specific treatment of cells

tag: patient id

tag: patient id2

value: female

value: Parkinson's disease

tag: number of ipsc obtained to generate neurons

tag: family history of pd

value: yes

tag: age at onset (years)

tag: age at tissue collection (years)

tag: l-dopa response

value: good

tag: initial symptoms

value: tremor

value: fibroblasts


title: genomic DNA from adipose tissue sample 5 [Twin5_1]

description: normal adipose tissue sample

tag: twin id

tag: bmi

value: high

tag: disease state

tag: tissue type


title: 2c.e2

source_name: 2-cell embryo, rep2

tag: developmental stage


title: genomic DNA from adipose tissue sample 7 [Twin7_1]

description: normal adipose tissue sample

tag: gender

value: Male

value: adipose tissue


title: IMR90 PI 103 replicate 1

source_name: IMR90 diploid fibroblasts treated with 1µM PI3K/mTOR inhibitor PI-103, replicate 1


title: MCF-10A vehicle

source_name: MCF-10A human mammary epithelial cell line, treated with vehicle, 4h

value: mammary epithelial cells


title: MCF-7 BMP4

source_name: MCF-7 human breast cancer cell line, treated with BMP4, 4h


title: genomic DNA from adipose tissue sample 6 [Twin6_1]

description: normal adipose tissue sample

value: Female


title: genomic DNA from fibroblasts FIB-SP-06-L2PD

value: male


title: 2c.e1

source_name: 2-cell embryo, rep1


title: genomic DNA from adipose tissue sample 3 [Twin3_1]

description: normal adipose tissue sample


title: genomic DNA from adipose tissue sample 1 [Twin1_1]

description: normal adipose tissue sample


title: genomic DNA from fibroblasts FIB-SP-16-sPD

source_name: IPSC-idiopathic PD

value: no

value: Bradykinesia


title: MCF-10A BMP4

source_name: MCF-10A human mammary epithelial cell line, treated with BMP4, 4h


title: genomic DNA from adipose tissue sample 8 [Twin8_1]

description: normal adipose tissue sample


title: HCC1954 vehicle

source_name: HCC1954 human breast cancer cell line, treated with vehicle, 4h


title: 2c.A.e5b1

source_name: 2-cell blastomere, rep17


title: genomic DNA from fibroblasts FIB-SP-04-sPD


title: IMR90 MK2a replicate 2

source_name: IMR90 diploid fibroblasts treated with 0.7µM MK2a inhibitor, replicate 2

value: fibroblast


title: IMR90 PDGFR replicate 1

source_name: IMR90 diploid fibroblasts treated with 8µM PDGFR inhibitor, replicate 1


title: 2c.A.e3

source_name: 2-cell blastomere, rep16


title: HCC1954 BMP4

source_name: HCC1954 human breast cancer cell line, treated with BMP4, 4h


title: BT-474 vehicle

source_name: BT-474 human breast cancer cell line, treated with vehicle, 4h


title: 2c.A.e2

source_name: 2-cell blastomere, rep15


title: genomic DNA from fibroblasts FIB-SP-11-CON

source_name: IPSC-control

value: Healthy

value: control


title: 2c.A.e1b2

source_name: 2-cell blastomere, rep14


title: genomic DNA from IPSC IPSC.SP-13-L2PD

source_name: IPSC-PD  LRRK2 G2019S mutation carrier

value: female

value: IPSC


title: BT-474 BMP4

source_name: BT-474 human breast cancer cell line, treated with BMP4, 4h

value: breast cancer


title: 2c.A.e5b2

source_name: 2-cell blastomere, rep18


title: genomic DNA from adipose tissue sample 2 [Twin2_1]

description: normal adipose tissue sample


title: IMR90 MK2a replicate 1

source_name: IMR90 diploid fibroblasts treated with 0.7µM MK2a inhibitor, replicate 1


title: IMR90 JNK IX replicate 2

source_name: IMR90 diploid fibroblasts treated with 0.5µM JNK inhibitor IX, replicate 2


title: 2c.A.e1b1

source_name: 2-cell blastomere, rep13


title: IMR90 JNK IX replicate 1

source_name: IMR90 diploid fibroblasts treated with 0.5µM JNK inhibitor IX, replicate 1


title: genomic DNA from adipose tissue sample 4 [Twin4_1]

description: normal adipose tissue sample


title: IMR90 PDGFR replicate 2

source_name: IMR90 diploid fibroblasts treated with 8µM PDGFR inhibitor, replicate 2


title: IMR90 GDC-0941 replicate 2

source_name: IMR90 diploid fibroblasts treated with 1µM PI3K inhibitor GDC-0941, replicate 2


title: KLF15_MTg_rep3

city: San Francisco

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

hyb_protocol: Labeled, fragmented DNA was hybridized to Mouse 430A 2.0 arrays (Affymetrix, Santa Clara, CA) for 16-18 hours in a GeneChip Hybridization oven 645 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: Genechip arrays were scanned immediately after staining on an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Arrays were corrected for background, normalized and log2-transformed using the rma function of the affy Bioconductor package.

source_name: KLF15 Mtg quadriceps

label_protocol: cDNA was generated using the Ambion WT Expression Kit and labeled using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol.

extract_protocol: Samples were collected directly into lysis buffer and amplified cDNA was made using the WT-Ovation one-direct amplification system kits following the manufacturer's protocol (NuGen Technologies, Inc., San Carlos, CA)

tag: genotype

value: KLF15 transgenic

tag: tissue

value: quadriceps


title: 2c.A.e1

source_name: 2-cell blastomere, rep12


title: IMR90 GDC-0941 replicate 1

source_name: IMR90 diploid fibroblasts treated with 1µM PI3K inhibitor GDC-0941, replicate 1

tag: cell line

tag: cell type


title: genomic DNA from fibroblasts FIB-SP-09-CON

tag: patient id

tag: patient id2

value: fibroblasts


title: genomic DNA from fibroblasts FIB-SP-17-CON

tag: number of ipsc obtained to generate neurons

tag: family history of pd


title: KLF15_MTg_rep4


title: genomic DNA from IPSC IPSC.SP-04-sPD

source_name: IPSC-idiopathic PD

value: Parkinson's disease

tag: age at onset (years)

tag: age at tissue collection (years)

value: good


title: 2c.A.bX9

source_name: 2-cell blastomere, rep11


title: IMR90 EGFR replicate 2

source_name: IMR90 diploid fibroblasts treated with 0.5µM EGFR inhibitor, replicate 2


title: genomic DNA from IPSC IPSC.SP-06-L2PD

value: yes

tag: l-dopa response

tag: initial symptoms

value: tremor


title: 2c.A.bX8

source_name: 2-cell blastomere, rep10


title: IMR90 EGFR replicate 1

source_name: IMR90 diploid fibroblasts treated with 0.5µM EGFR inhibitor, replicate 1


title: KLF15_MTg_rep1


title: 2c.A.bX7

source_name: 2-cell blastomere, rep9


title: 2c.A.bX6

source_name: 2-cell blastomere, rep8


title: nonTg_rep4

source_name: non-Tg quadriceps

value: non-transgenic


title: genomic DNA from IPSC IPSC.SP-11-CON

source_name: IPSC-control


title: 2c.A.bX5

source_name: 2-cell blastomere, rep7


title: nonTg_rep3


title: IMR90 CDK2 IV replicate 2

source_name: IMR90 diploid fibroblasts treated with 4µM CDK2 inhibitor IV, replicate 2


title: genomic DNA from IPSC-derived DAn SP-13-L2PD

source_name: 30-days neuron-PD  LRRK2 G2019S mutation carrier

value: IPSC-derived DAn


title: 2c.A.bX4

source_name: 2-cell blastomere, rep6


title: nonTg_rep1


title: IMR90 CDK2 IV replicate 1

source_name: IMR90 diploid fibroblasts treated with 4µM CDK2 inhibitor IV, replicate 1


title: genomic DNA from IPSC IPSC.SP-09-CON

value: male

value: no


title: IMR90 AURORA II replicate 2

source_name: IMR90 diploid fibroblasts treated with 8µM Aurora kinase inhibitor II, replicate 2

value: fibroblast


title: nonTg_rep2


title: 2c.A.bX3

source_name: 2-cell blastomere, rep5


title: 2c.e3

source_name: 2-cell embryo, rep3


title: IMR90 AURORA II replicate 1

source_name: IMR90 diploid fibroblasts treated with 8µM Aurora kinase inhibitor II, replicate 1


title: 2c.A.bX2

source_name: 2-cell blastomere, rep4


title: genomic DNA from IPSC-derived DAn SP-06-L2PD


title: 2c.A.bX11

source_name: 2-cell blastomere, rep3


title: 2c.A.bX10

source_name: 2-cell blastomere, rep2


title: IMR90 AKT VIII replicate 2

source_name: IMR90 diploid fibroblasts treated with 15µM AKT inhibitor VIII, replicate 2


title: 2c.A.bX1

source_name: 2-cell blastomere, rep1


title: IMR90 AKT VIII replicate 1

source_name: IMR90 diploid fibroblasts treated with 15µM AKT inhibitor VIII, replicate 1


title: genomic DNA from IPSC-derived DAn SP-16-IPD

source_name: 30-days neuron-idiopathic PD

value: Bradykinesia


title: genomic DNA from IPSC-derived DAn SP-05-L2PD


title: genomic DNA from IPSC IPSC.SP-17-CON

source_name: IPSC-control

value: Healthy

value: control


title: IMR90 AKT V replicate 1

source_name: IMR90 diploid fibroblasts treated with 15µM AKT inhibitor V, replicate 1


title: IMR90 AKT V replicate 2

source_name: IMR90 diploid fibroblasts treated with 15µM AKT inhibitor V, replicate 2


title: IMR90 DMSO replicate 2

source_name: IMR90 diploid fibroblast, DMSO control, replicate 2


title: KLF15_MTg_rep2

source_name: KLF15 Mtg quadriceps


title: SAMPLE 11_NPC_A

status: Public on Nov 30 2015

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

hyb_protocol: The labeled material was then hybridized to Human Gene 1.0 ST Array (Affymetrix) for 16 hours at 45ºC and 60 rpm in a GeneChip® Hybridization Oven 640.

scan_protocol: The stained array was scanned using an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
Samples were normalized and log transformed and then filtered using a variance filter (σ/σ max) of 0.2. Sample7 was considered an outlier sample and was removed from further analysis.
Microarray analysis is done in R (version 2.15) with Bioconductor packages i.e. affy and limma. After quality control of raw data, it was background corrected, quantile-normalized and log2 transformed.

source_name: iPSC-derived human Neural Progenitor Cell

label_protocol: 200 ng of total RNA were amplified using the Ambion® WT Expression Kit (Ambion/Applied Biosystems) and labeled using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Neurobasal media (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), and FGF2 (10 ng/ml; preprotech)

extract_protocol: RNA was purified using the RNeasy Plus mini kit (74134, Qiagen). Purity and integrity of the RNA samples were assessed by spectrophotometry and nanoelectrophoresis using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the Nano lab-on-a-chip assay for total eukaryotic RNA using Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

value: Neural Progenitor Cell

tag: treatment

value: No Treatment

value: iPSC derived


title: genomic DNA from IPSC-derived DAn SP-04-IPD

tag: disease state


title: IMR90 DMSO replicate 1

source_name: IMR90 diploid fibroblast, DMSO control, replicate 1


title: SAMPLE 9_NPC_4F_A

source_name: iPSC-derived human Neural Progenitor Cell, inhibition of the PI3K and MAPK signaling pathways

value: Inhibitionition of PI3K and MAPK signaling pathways


title: genomic DNA from IPSC-derived DAn SP-10-IPD

value: foot distonia


title: SAMPLE 7_NPC P53_5_4F

source_name: iPSC-derived human Neural Progenitor Cell, P53 knockdown and inhibition of the PI3K and MAPK signaling pathways

value: Inhibition of P53 and PI3K and MAPK signaling pathways


title: SAMPLE 8_NPC wt_B


title: SAMPLE 3_GNS_c

source_name: human Glioma Tumor Initiating Cells

value: Glioma Stem Cell

value: Derived by Pollard et al., 2009 Cell Stem Cell, GNS G179. Deposited by Steve Pollard, Austin Smith, Peter Dirks and Ian Clarke at the biorep S.r.l. Catalog number NS00011*B


title: SAMPLE 10_NPC_4F_B


title: SAMPLE 4_NPC P53_1

source_name: iPSC-derived human Neural Progenitor Cell with P53 knockdown

value: Inhibition of P53


title: genomic DNA from IPSC-derived DAn SP-12-L2PD

source_name: 30-days neuron-PD  LRRK2 G2019S mutation carrier

value: female

value: Parkinson's disease

value: yes

value: good

value: tremor


title: PCLS_subject 3_Wy14643

status: Public on Nov 23 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

label: Biotin

source_name: precision-cut liver slices, after 24h incubation with Wy14643 (100 μM)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Liver biopsies were collected from obese patients undergoing bariatric surgery. After collection, biopsies were immediately placed in ice-cold oxygenated Belzer UW Cold Storage Solution and quickly transferred to the laboratory for further processing. 5 mm cylindrical liver cores were prepared with a surgical biopsy punch and sectioned to 200 μm slices using a Krumdieck tissue slicer.

extract_protocol: Total RNA was prepared from the liver slices using TRIzol reagent and purified using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Liver slices were incubated in William's E Medium in 6-well plates at 37°C/5% CO2/80% O2 under continuous shaking (70 rpm). Duplicate wells were used per donor with 3 liver slices per well. After 1 hour the media was replaced with fresh William's E Medium in the presence or absence of Wy14643 (100 μM) dissolved in dimethyl sulfoxide (DMSO, final concentration 0.1%). After 24 h incubation, liver slices were snap-frozen in liquid nitrogen and stored in -80°C for RNA isolation.

value: liver

tag: time point

tag: age (yr)

tag: bmi


title: SAMPLE 5_NPC P53_1_4F


title: PCLS_subject 2_Wy14643

tag: gender


title: SAMPLE 6_NPC P53_5


title: SAMPLE 2_GNS_b


title: PCLS_subject 4_DMSO

source_name: precision-cut liver slices, after 24h incubation with vehicle (0.1% DMSO)

tag: tissue

value: vehicle (0.1% DMSO)


title: PCLS_subject 4_Wy14643


title: SAMPLE 1_ES4p15

source_name: IVF-derived Human Embryonic Stem-Cell

value: Human Embryonic Stem Cell

tag: cell line

value: IVF derived


title: genomic DNA from IPSC-derived DAn SP-02-IPD

value: male

value: no

tag: cell type

value: IPSC-derived DAn


title: PCLS_subject 3_DMSO


title: PCLS_subject 1_DMSO


title: genomic DNA from IPSC-derived DAn SP-08-IPD

tag: patient id


title: genomic DNA from IPSC IPSC.SP-16-sPD

source_name: IPSC-idiopathic PD

tag: patient id2

value: Bradykinesia

value: IPSC


title: genomic DNA from IPSC-derived DAn SP-15-CON

source_name: 30 days-neuron control

value: Healthy

tag: number of ipsc obtained to generate neurons

value: control


title: genomic DNA from IPSC-derived DAn SP-17-CON

tag: family history of pd


title: MLL5-overexpressing cells, biological rep 3

status: Public on Nov 11 2015

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

description:
HTA2_091814H_PD6_M3.CEL.pimg
Cells grown in NS media

hyb_protocol: Hybridization was performed at 45°C for 16 h.

scan_protocol: Scanning was performed with Affymetrix GeneChip Scanner 3000.

data_processing:
Normalization was performed with Partek Genomic Suite v. 6.6, applying RMA. All steps were performed according the Partek users  manual.
the fold_change.txt contains p<0.05 >|1.2|fold data

source_name: GBM primary culture G514NS_MLL5

label_protocol: Fragmented ss-cDNA was lebelled with biotin allonamide triphosphate.

growth_protocol: Cells derived from an adult GBM patient and mantained in neural stem-like conditions according to a paper by Pollard et al (2009) Cell Stem Cell.

extract_protocol: 72 h post-transfection, total RNA was extracted with an RNA extraction kit (RNeasy Mini Kit, QIAGEN).

treatment_protocol: One million cells were transfected with plasmids for the expression of either EGFP or the N-terminal isoform of MLL5. Plasmid backbone was pcDNA-DEST40. Selection for transfected cells was performed with puromycin 24 h after transfection.

value: glioblastoma (GBM) primary culture

tag: genotype/variation

value: 72 h post-transfection


title: PCLS_subject 1_Wy14643

value: female


title: EGFP-expressing cells, biological rep 3

description:
HTA2_091814H_PD3_E3.CEL.pimg
Cells grown in NS media

source_name: GBM primary culture G514NS_EGFP

value: EGFP-expressing


title: genomic DNA from IPSC-derived DAn SP-01-IPD

source_name: 30-days neuron-idiopathic PD

value: Parkinson's disease

tag: age at onset (years)

tag: age at tissue collection (years)

value: Tremor-Badykinesia


title: genomic DNA from IPSC-derived DAn SP-09-CON

tag: l-dopa response

tag: initial symptoms


title: EGFP-expressing cells, biological rep 2

description:
HTA2_091814H_PD2_E2.CEL.pimg
Cells grown in NS media


title: EGFP-expressing cells, biological rep 1

description:
HTA2_091814H_PD1_E1.CEL.pimg
Cells grown in NS media


title: genomic DNA from IPSC-derived DAn SP-11-CON

tag: disease state


title: MLL5-overexpressing cells, biological rep 2

description:
HTA2_091814H_PD5_M2.CEL.pimg
Cells grown in NS media

tag: time point


title: MLL5-overexpressing cells, biological rep 1

description:
HTA2_091814H_PD4_M1.CEL.pimg
Cells grown in NS media