title: EPC, apoptotic bodies (24h), biological rep3

description: miRNA expression data from EPC apoptotic bodies.

source_name: apoptotic bodies collected 24h after CHX treatment, EPCs

value: primary endothelial progenitor cells (EPCs)


title: Non infected MDM at T0h, donor 3

status: Public on Dec 31 2015

type: RNA

city: Tunis-Belvedere

first: Dhafer

last: Laouini

address: 13, place Pasteur. BP74

country: Tunisia

institute: Institut Pasteur de Tunis

description: Gene expression data from MDM at 0h

hyb_protocol: The fragmented and labeled ssDNA was hybridized to Affymetrix/HuGene-1_0-st-v1 for human analyses (Affymetrix, Santa Clara, CA), washed with the Fluidics station 450

scan_protocol: Samples were scanned using the Affymetrix Scanner 30007G.

data_processing:
Data processing entailed: (i) an intrachip normalisation step which corrects for the GC content of the probes; (ii) the interchip normalisation step which reduces non- biological differences between chips; and (iii) the summarisation step which combines the probe intensities into single gene expression values.For the intrachip normalisation the 'Model-based Analysis of Tiling-arrays' (MAT) was implemented (Kapur et al. 2007) as this method provides the most advanced GC correction for whole-transcript prepared samples by combining content and position dependency of probe sequences in a unified linear model. The parameters of the model are estimated from the control probes and subsequently the probe affinities are calculated for the perfect matches. On linear intensity scale, the probe intensities are divided by an estimated probe affinity. Interchip normalisation was applied as a quantile normalisation to adjust the intensity distributions over the arrays to reduce unwanted effects between 3' expression arrays (Irizarry et al. 2003). Finally, probe intensities were summarised to a probe set expression by computing a median over the intensities in two replicate dimensions: a) The different probe intensities within the probe set; b) The arrays with the same biological condition. This provides very robust summarised expression values also for low-replicate settings.
Detection call p-values were computed for each probeset with a paired Wilcoxon signed rank test that compares probe intensity to control probes of similar GC content. More precisely, each probe is compared to the 75% quantile of the set of control probes with similar GC content. A gene probeset was called present when the corresponding FDR corrected p-value was below 5%. The sole threshold in this approach is the height of the quantile (75%) in the GC bin. The same probe-Entrez gene assignment and subsequent mapping was used as in the summarisation process.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MDM at 0h

label_protocol: 100ng of RNA from each biological condition were amplified and labelled with biotin according to the GeneChip whole transcript sense target labeling assay manual and using the GeneChip WT cDNA Synthesis and amplification Kit and WT terminal labeling Kit. The fragmented ssDNA was checked on Agilent RNA Pico LabChips.

growth_protocol:
Human donors were selected as negative for any recent infection and with no history of Leishmaniasis. Their peripheral blood mononuclear cells (PBMC) do not proliferate in vitro in response to soluble Leishmania antigens and they were not taking medication at the time of the study. For intial transcriptomics and proteomics, three human donors were used.
Human PBMC were isolated from cytapheresis leukopacks peripheral blood mononuclear cells using Ficoll-Paque (Pharmacia, Uppsala, Sweden) density gradient centrifugation. Cells were washed and resuspended at 107 cells/ml in RPMI 1640 medium supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 /ml  streptomycin and 5% heat inactivated fetal calf serum. Monocytes were purified by fibronectin-mediated adhesion using gelatin (Sigma) and autologous heat inactivated serum substratum. Monocyte cell purity was assessed by flow cytometry (FACSVantage; Becton Dickinson, Sunnyvale, CA) using directly conjugated anti-CD3, anti-CD19 and anti-CD14 antibodies (Becton-Dickinson, San Jose, CA) and was routinely greater than 85% of CD14+ cells. Macrophages (MDM) were derived from monocytes cultured for 8 days at 37°C, 5% CO2 in endotoxin-free RPMI 1640 medium supplemented with 5% heat-inactivated normal human AB serum and 10% heat-inactivated fetal calf serum (HyClone Laboratories, Logan, UT), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine at 2 x 106 cells/ml, in 6-well tissue-culture plates.

extract_protocol: Human macrophages were lysed directly in 3 ml Trizol reagent (Invitrogen). Total RNA from uninfected and infected macrophages were prepared using the RNeasy mini kit (Qiagen) and treated with DNase according to the manufacturer’s protocol. Extracted RNAs were stored at -80°C. RNAs were quantified using NanoDrop ND-1000 micro-spectrophotometer and RNA quality was monitored on Agilent RNA Pico LabChips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: L. major GLC94 isolate (MHOM/TN/95/GLC94) was obtained from the field and cultured at 26°C in RPMI medium supplemented with 2mM L-glutamine 100 U/ml of penicillin, 10mg/ml of streptomycin, 10% heat-inactivated fetal calf serum (HyClone ) was used to prepare metacyclic promastigotes using Ficoll density gradients centrifugation (Sigma) as previously described (Spath and Beverley 2001). MDM were exposed to metacyclic parasites of L. major at a ratio of 5 parasites per cell; for 3, 6, 12 and 24hr at 37°C/5% CO2, washed to remove extracellular parasites, and then harvested. Non-infected MDM were used as controls for the same conditions.

tag: cell type

value: Monocyte-derived Macrophages purified from Peripheral Blood Leucocytes

tag: age

value: Adult

tag: infection

value: non-infected

tag: time

tag: individual

value: donor 3


title: EPC, apoptotic bodies (24h), biological rep2

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

hyb_protocol: Hybridization was performed for 16 hr at 48°C and 60 rpm on GeneChip miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450-0002.

scan_protocol: GeneChip miRNA 3.0 Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The image data were analyzed with the miRNA QC Tool software for quality control. The expression values were summarized and normalized with robust multi-array average (RMA) using RMA package in Bioconductor 2.5 under R2.10.  Only miRNAs that were detectable in all three arrays for each group and whose expression levels were found to have changed significantly (P<0.05), at least by twofold, were considered to be differentially expressed.

label_protocol: Labelling was prepared according to the standard FlashTag (Genisphere) protocol.

growth_protocol: Cells were cultured in endothelial growth medium (PromoCell) to confluency before starting apoptosis.

extract_protocol: Total RNA was isolated from apoptotic bodies with the ZR RNA MicroPrep kit (Zymo Research) according to the manufacturer's instructions.

treatment_protocol: To induce apoptosis, the cells were incubated with cycloheximide (5µg/ml) in hypoxia (2% O2) for 24 hours. Afterwards, the apoptotic bodies were collected.

tag: cell source

value: apoptotic bodies


title: HK-2 cells, Ota, hd and ld, t72h, control sample, biological rep 1, Tox3

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

hyb_protocol: 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.

scan_protocol: Fluorescence was read with an Affymetrix 3000 Scanner.

data_processing: Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.

source_name: Human renal proximal tubular epithelial cells, control for Ota, t72h

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

growth_protocol: HK-2 cells were maintained in a 1-1 mixture of DMEM and Ham'sF12 containing 5 mM glucose supplemented with 10 ng/ml human recombinant EGF, 36 ng/ml hydrocortisone, 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 5 ng/ml sodium selenite, 2 mM Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit.

treatment_protocol: Cells were seeded 24 hours before treatment on Greiner 6-well plates at a density of 7x10^5 cells per well with 2mls of medium per well. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

tag: cell line

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: control

tag: treatment duration

value: 72 hrs


title: Non infected MDM at T0h, donor 2

description: Gene expression data from MDM at 0h

value: donor 2


title: HK-2 cells, Ota, ld, t24h, biological rep 1, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t24h

value: Ota

tag: treatment dosage

value: low

value: 24 hrs


title: Non infected MDM at T3h, donor 2

description: Gene expression data from MDM at 3h

source_name: MDM at 3h


title: HK-2 cells, Ota, hd, t24h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t24h

value: high


title: EPC, apoptotic bodies (24h), biological rep1


title: AD-specific iPSC7-3

city: Sydney

first: Henry

last: Chung

state: NSW

address: High St

department: Clinical Sciences Bld

country: Australia

institute: Prince of Wales Hospital

description: Biological replicate 3 of 3.

hyb_protocol: Following fragmentation, cRNA was processed through second-cycle single-stranded cDNA. Fragmented and labelled cDNA was then hybridized onto Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual).

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

data_processing: Gene array data is processed by Partek GenomeSuite software in which mean probeset signals for all probesets were analysed. A receiver operating curve (ROC) is generated by thresholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

label: Biotin

source_name: AD-specific iPSC7

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual).

growth_protocol: Human induced pluripotent stem cells were cultured under feeder-free conditions using Matrigel and mTeSR1 media as per the manufacturer's protocol.

extract_protocol: Total RNA was extracted from cell cultures using TRIZOL (Invitrogen) as per the manufacturer's instructions.

tag: disease state of patient

value: non-familial Alzheimer's disease

value: human induced pluripotent stem cell (hiPSC)

tag: clone

tag: culture type

value: feeder-free


title: HK-2 cells, Ota, hd, t24h, biological rep 1, Tox3


title: AD-specific fibroblast-3

description: Biological replicate 3 of 3.

source_name: AD-specific fibroblast

value: fibroblast


title: HK-2 cells, Ota, hd, t24h, biological rep 2, Tox3


title: AD-specific iPSC7-2

description: Biological replicate 2 of 3.


title: HK-2 cells, Aa, ld, t48h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t48h

value: Aa

value: 48 hrs


title: Non infected MDM at T0h, donor 1

description: Gene expression data from MDM at 0h

value: Monocyte-derived Macrophages purified from Peripheral Blood Leucocytes

value: Adult

value: non-infected

value: donor 1


title: stimulated GASH:Sal hamster, biological rep3

city: Salamanca

first: Raquel

middle: E.

last: Rodriguez

state: Salamanca

address: C/ Pintor Fernando Gallego, 1

country: Spain

institute: Institute of Neurosciences of Castilla y León

description: GASH est 102_rep3

hyb_protocol: Following fragmentation, cRNA were hybridized to GeneChip® Zebrafish Genome Array (Affymetrix). Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

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

data_processing: The RMA (Robust Multi-array Analysis) algorithm was used for background correction and normalization of fluorescent hybridization signals of the microarrays, both at internal (intra-microarrays) and comparative (inter-microarrays) levels. We used Bioconductor and R as computational tools (www.bioconductor.org), to apply RMA to the data set of 12 microarray hybridizations including six different biological replicas corresponding to each of the different experimental groups under study (Control and Morphine). After quantitation of expression level of each probe set in all microarrays analyzed, the SAM algorithm was used to identify probe sets displaying significant differential expression when comparing the treat samples to it controls, using a False Discovery Rate (FDR) of 10% or less as significant.

organism: Mesocricetus auratus

source_name: GASH:Sal hamsters exposed to auditory stimulation

label_protocol: Microarray analysis was performed in the Cancer Research Center (CIC) of Salamanca according to standard procedures. Label protocol was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was purified using TRIZOL (Gibco BRL, Gaithersburg, MD, USA) following further RNA purification using an RNeasy Mini Kit for RNA clean-up (Qiagen Sicences, Maryland, USA). RNA quantification and quality was then assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), to test the integrity of the 18S and 28S rRNA bands, and samples with an RNA integrity number (RIN) > 8.0 were used.

treatment_protocol: The animals were free of ear infection. To rapidly confirm normal hearing, we used the bilateral finger friction test in all cases. The animals in both models were exposed to auditory stimulation, and 60 min after the seizures, we harvested the IC for all gene expression analyses. As controls, normal Wistar rats and Syrian hamsters were exposed to the same stimulation according to the identical procedure.

tag: genotype/variation

value: genetic audiogenic seizure hamster (GASH:Sal), University of Salamanca

value: 16 weeks

tag: body weight

tag: exposed to

value: auditory stimulation

tag: tissue

value: inferior colliculus (IC)


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 2, Tox3

source_name: Human renal proximal tubular epithelial cells, control for Ota, t24h

tag: cell type

value: immortalized human renal proximal tubular epithelial cells

value: control


title: stimulated GASH:Sal hamster, biological rep6

description: 4a GASH est_rep6

tag: age


title: stimulated GASH:Sal hamster, biological rep4

description: 2a GASH est_rep4


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 1, Tox3

value: 24 hrs


title: stimulated GASH:Sal hamster, biological rep5

description: 3a GASH est_rep5


title: GASH:Sal hamster, biological rep3

description: GASH sin est 125_rep3

source_name: GASH:Sal hamsters

value: none (control)


title: GASH:Sal hamster, biological rep4

description: GASH sin est_1b_rep4


title: stimulated GASH:Sal hamster, biological rep1

description: GASH est 100_rep1


title: AD-specific iPSC7-1

description: Biological replicate 1 of 3.

value: non-familial Alzheimer's disease

value: human induced pluripotent stem cell (hiPSC)


title: GASH:Sal hamster, biological rep6

description: GASH sin est_4c_rep6


title: GASH:Sal hamster, biological rep2

description: GASH sin est 124_rep2


title: HK-2 cells, Ota, hd and ld, t24h, control sample, biological rep 3, Tox3


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, control for Aa, t48h


title: AD-specific fibroblast-2

description: Biological replicate 2 of 3.

value: fibroblast

value: feeder-free


title: AD-specific iPSC1-2

description: Biological replicate 2 of 2.

source_name: AD-specific iPSC1


title: HK-2 cells, Aa, hd, t48h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t48h

value: Aa

value: high

value: 48 hrs


title: AD-specific iPSC1-1

description: Biological replicate 1 of 2.


title: AD-specific fibroblast-1

description: Biological replicate 1 of 3.


title: stimulated GASH:Sal hamster, biological rep2

description: GASH est 101_rep2


title: GASH:Sal hamster, biological rep5

description: GASH sin est_3c_rep5


title: stimulated Syrian control hamster, biological rep6

description: 4c Control est_rep6

source_name: Syrian control hamster exposed to auditory stimulation

value: control Syrian hamster


title: stimulated Syrian control hamster, biological rep5

description: 3c Control est_rep5


title: stimulated Syrian control hamster, biological rep1

description: Control est 103_rep1


title: HK-2 cells, Aa, hd, t24h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Aa, t24h


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, control for Aa, t24h


title: stimulated Syrian control hamster, biological rep2

description: Control est 104_rep2


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 2, Tox3


title: HK-2 cells, Aa, hd, t48h, biological rep 2, Tox3


title: HK-2 cells, Aa, ld, t24h, biological rep 3, Tox3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Aa, t24h

value: low


title: GASH:Sal hamster, biological rep1

description: GASH sin est 123_rep1

value: genetic audiogenic seizure hamster (GASH:Sal), University of Salamanca


title: stimulated Syrian control hamster, biological rep3

description: Control est 105_rep3

value: 16 weeks


title: Syrian control hamster, biological rep6

description: Control sin est_3d_rep6

source_name: Syrian control hamster


title: Syrian control hamster, biological rep4

description: Control sin est_1d_rep4


title: stimulated Syrian control hamster, biological rep4

description: 2c Control est_rep4

value: auditory stimulation


title: Syrian control hamster, biological rep1

description: Control sin est 127_rep1

value: inferior colliculus (IC)


title: HK-2 cells, Aa, ld, t24h, biological rep 2, Tox3

value: immortalized human renal proximal tubular epithelial cells


title: Syrian control hamster, biological rep3

description: Control sin est 129_rep3


title: OCpp_3

city: Paris

first: Sedigheh

last: Delmaghani

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

hyb_protocol: Following fragmentation, 2,5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were summarized with Affymetrix Expression Console software using Affymetrix default analysis settings for Mouse Gene 1.0 ST array

organism: Mus musculus

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix Genechip Mouse ST Array KIT)

extract_protocol: RNA Extraction with TRIzol reagent (Invitrogen). Extracted RNA was further purified and concentrated using the Qiagen RNeasy Mini Kit (Qiagen, CA) according to the manufacturer's protocol

tag: strain background

value: Pjvk-+/+

value: Organ of Corti (OC)


title: OCmm_3

value: Pjvk-/-


title: OCmm_2


title: OCpp_1


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 2, Tox3

value: control

value: 24 hrs


title: HK-2 cells, Aa, ld, t48h, biological rep 2, Tox3


title: Syrian control hamster, biological rep5

description: Control sin est_2d_rep5

value: none (control)


title: HK-2 cells, Aa, hd, t24h, biological rep 2, Tox3


title: HK-2 cells, Aa, ld, t48h, biological rep 1, Tox3


title: OCpp_2


title: OCmm_1


title: Syrian control hamster, biological rep2

description: Control sin est 128_rep2


title: B419 Mutant 15 month

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description: Replicate 3

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

source_name: Liver

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: The animals were maitained in 24 hour light and temperature controlled facilities in USC

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: Animals were fasted overnight before tissue extraction

tag: strain

value: mutant

tag: time point

value: 15 months


title: B417 Mutant 15 Month

description: Replicate 1


title: B418 Mutant 15 Month

description: Replicate 2


title: HK-2 cells, Aa, hd and ld, t48h, control sample, biological rep 1, Tox3


title: HK-2 cells, Aa, hd, t48h, biological rep 1, Tox3

value: Aa

value: high


title: B306 Mutant 3Month

description: Replicate 5

value: 3 months


title: B412 WT 15 month

description: Replicate 1

value: wild type


title: B416 WT 15 month

description: Replicate 5


title: B414 WT 15 month

description: Replicate 3


title: B415 WT 15 month

description: Replicate 4


title: B413 WT 15 month

description: Replicate 2


title: HK-2 cells, Aa, hd, t24h, biological rep 1, Tox3


title: B303 Mutant 3Month

description: Replicate 2


title: B298 WT 3Month

description: Replicate 2


title: HK-2 cells, Aa, hd and ld, t24h, control sample, biological rep 1, Tox3


title: B300 WT 3Month

description: Replicate 4


title: B304 Mutant 3Month

description: Replicate 3


title: B301 WT 3Month

description: Replicate 5


title: B297 WT 3Month

description: Replicate 1


title: HK-2 cells, Kbr, ld, t48h, biological rep 2, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t48h

value: Kbr

value: low

value: 48 hrs


title: HK-2 cells, Kbr, ld, t48h, biological rep 1, Tox2


title: HK-2 cells, Aa, ld, t24h, biological rep 1, Tox3


title: HK-2 cells, Kbr, ld, t24h, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t24h


title: HK-2 cells, Kbr, ld, t48h, biological rep 3, Tox2


title: B305 Mutant 3Month

description: Replicate 4


title: B299 WT 3Month

description: Replicate 3


title: B302 Mutant 3Month

description: Replicate 1


title: HK-2 cells, Kbr, ld, t24h, biological rep 2, Tox2


title: SCN_CT62

city: Philadelphia

first: Heather

last: Ballance

state: PA

address: 3400 Civic Center Blvd. Building 421

institute: University of Pennsylvania

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: GeneChip 3000 7G scanner

data_processing: Expression Console, RMA, 1.3.1.187

source_name: suprachiasmatic nucleus

label_protocol: Amplification and labeling: Pico WTA V2 (NuGen, 3302) and Encore Biotin Module (Nugen, 4200)

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for three weeks. Mice were then transferred to complete darkness prior to collection. Collection began at CT18.

extract_protocol: SCN samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, with the modification that 1.5 volumes of 100% ethanol were added to the aqueous phase following centrifugation. Samples were resuspended in 25 uL of RNase free H2O. RNA was quantified by QUBIT (Invitrogen). Equal amounts of SCN RNA from three mice were pooled for each time point.

value: suprachiasmatic nucleus


title: SCN_CT64


title: SCN_CT60


title: HK-2 cells, Kbr, hd, t48h, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t48h

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, Kbr, ld, t24h, biological rep 1, Tox2


title: SCN_CT50


title: SCN_CT44


title: HK-2 cells, Kbr, hd, t48h, biological rep 1, Tox2


title: SCN_CT52


title: SCN_CT40


title: SCN_CT54


title: SCN_CT48


title: SCN_CT58


title: SCN_CT38


title: HK-2 cells, Kbr, hd, t24h, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t24h


title: SCN_CT28


title: SCN_CT30


title: SCN_CT32


title: HK-2 cells, Kbr, hd, t48h, biological rep 2, Tox2


title: HK-2 cells, Kbr, hd, t24h, biological rep 2, Tox2


title: SCN_CT42


title: SCN_CT46


title: SCN_CT36


title: HK-2 cells, Kbr, hd and ld, t48h, control sample, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, control for Kbr, hd and ld, t48h


title: SCN_CT56


title: SCN_CT24


title: SCN_CT34


title: SCN_CT26


title: HK-2 cells, Kbr, hd and ld, t48h, control sample, biological rep 2, Tox2


title: SCN_CT18


title: HK-2 cells, Kbr, hd, t24h, biological rep 1, Tox2


title: SCN_CT20


title: pancreas-FVFpositive-E15.5-rep2

city: Neuherberg

first: Nikola

last: Müller

address: Ingostädter Landstr. 1

institute: Helmholtz Zentrum München

hyb_protocol: Affymetrix Mouse Gene 1.0 ST array according to the Affymetrix expression protocol

scan_protocol: Array Scanner 3000 7G, according to the Affymetrix expression protocol

data_processing:
The probesets were filtered for annotated gene symbols using R/Bioconductor package mogene10sttranscriptcluster.db (version 8.0.1) annotations.
Data were RMA normalized using R/Bioconductor package affy (version 1.44.0).

label_protocol: WT Expression kit (Ambion) and the WT Terminal Labeling and Fragmentation kit (Affymetrix)

extract_protocol: Rneasy Mini kit (Qiagen)

value: mixed (C57-Bl6/SV129/CD1)

tag: developmental stage

value: pancreas

tag: sorting

value: FVF+


title: pancreas-FVFnegative-E15.5-rep2

value: FVF-


title: pancreas-FVFnegative-E15.5-rep3


title: HK-2 cells, Kbr, hd and ld, t24h, control sample, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, control for Kbr, hd and ld, t24h

tag: cell line

tag: treatment

value: control

value: 24 hrs


title: pancreas-FVFpositive-E15.5-rep3


title: HK-2 cells, Kbr, hd and ld, t48h, control sample, biological rep 1, Tox2

tag: treatment duration


title: HK-2 cells, Kbr, hd and ld, t24h, control sample, biological rep 2, Tox2


title: HK-2 cells, Kbr, hd and ld, t24h, control sample, biological rep 1, Tox2


title: pancreas-FVFpositive-E14.5-rep2


title: pancreas-FVFpositive-E14.5-rep1


title: pancreas-FVFnegative-E14.5-rep2


title: SCN_CT22


title: pancreas-FVFpositive-E14.5-rep3


title: HK-2 cells, Di, t48h, biological rep 2, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with Di, t48h

value: Di


title: pancreas-FVFnegative-E14.5-rep1


title: HK-2 cells, Di, t48h, biological rep 3, Tox2


title: pancreas-FVFpositive-E13.5-rep1


title: pancreas-FVFpositive-E15.5-rep1


title: HK-2 cells, Di, t48h, biological rep 1, Tox2


title: pancreas-FVFnegative-E15.5-rep1


title: pancreas-FVFnegative-E13.5-rep2


title: pancreas-FVFnegative-E14.5-rep3


title: HK-2 cells, Di, t12h, biological rep 2, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with Di, t12h

value: 12 hrs


title: pancreas-FVFnegative-E13.5-rep1


title: HK-2 cells, Di, t12h, biological rep 3, Tox2


title: HK-2 cells, Di, t12h, biological rep 1, Tox2


title: pancreas-FVFpositive-E13.5-rep2


title: HK-2 cells, CdCl, t48h, biological rep 2, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t48h

value: CdCl


title: pancreas-FVFpositive-E12.5-rep3


title: pancreas-FVFnegative-E12.5-rep1


title: pancreas-FVFpositive-E12.5-rep1


title: pancreas-FVFpositive-E12.5-rep2


title: pancreas-FVFnegative-E12.5-rep2


title: HK-2 cells, CdCl, t12h, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, treated with CdCl, t12h


title: Follicles female 3_1

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

description: Biological replicate 3_Cy3Cy5

hyb_protocol: Overnight hybridization (17 hrs, 65ºC and 10 rpm rotation) was performed in a Microrarray Hybridization Oven (Agilent Technologies). After hybridization, microrarrays were washed with Gene Expression Wash Buffers 1 and 2 (Agilent Technologies).

scan_protocol: Microrarrays were scanned using the High-Resolution Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction Software 10.7.3.1 (Agilent Technologies) was used for spot to grid alignment, feature extraction and quantification. Processed data were subsequently imported into GeneSpring GX 11.5 (Agilent Technologies).

organism: Salmo trutta

source_name: Follicles female 3_control

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

growth_protocol: Preovulatory brown trout (Salmo trutta) females were raised in a local goverment hatchery (Piscifactoria de Bagà, Barcelona, Spain), staged and sacrificed according to approved local animal welfare regulations.

extract_protocol: Total RNA from brown trout preovulatory follicles was isolated with TRIzol (Invitrogen, Spain) according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Preovulatory follicles were isolated and incubated in the absence or presence of salmon LH for 18 h at 15 ºC.

value: Preovulatory follicles

source_name: Follicles female 3_LH


title: HK-2 cells, CdCl, t12h, biological rep 2, Tox2


title: HK-2 cells, CdCl, t48h, biological rep 1, Tox2


title: Mouse EF CR85, biological rep 1

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

description: Gene expression data from epidydimal fat of wild type C57BL/6 mouse responsed by 15% caloric restriction

hyb_protocol: Following fragmentation, ss-cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Gene 1.0 ST Array. 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 quantile normalization using Partek genomics Suite 6.6.

source_name: Mouse epidydimal fat under 15% caloric restriction

label_protocol: Biotinylated single-stranded cDNA (ss-cDNA) were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2009, Affymetrix).

growth_protocol: Six-week old male mice (C57BL/6N) were fed ad libitum and adapted for two weeks before the conditioned diets were treated.

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

treatment_protocol: The mice were grouped and raised under four different CR conditions including a control group (85% of the control diet, CR85, 70%, CR70, and 55%, CR55) for 10 weeks. We reduced cornstarch, dextrose and sucrose by maintaining their relative contents in the CR diets. The control group (CD) was set as 95% calories (17.11 kcal/day) of the average amount of feed during the first two weeks for adaptation. The CR85, CR70 and CR55 groups were fed 14.51 kcal/day, 11.91 kcal/day and 9.32 kcal/day, respectively.

tag: gender

value: male

value: Epidydimal fat

value: 18 weeks

tag: diet

value: 15% caloric restriction


title: Mouse EF CR70, biological rep 3

description: Gene expression data from epidydimal fat of wild type C57BL/6 mouse responsed by 30% caloric restriction

source_name: Mouse epidydimal fat under 30% caloric restriction

value: 30% caloric restriction


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 3, Tox2

source_name: Human renal proximal tubular epithelial cells, control for CdCl and Di, t48h

value: 48 hrs


title: HK-2 cells, CdCl, t48h, biological rep 3, Tox2

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 2, Tox2


title: Mouse EF CR55, biological rep 1

description: Gene expression data from epidydimal fat of wild type C57BL/6 mouse responsed by 45% caloric restriction

source_name: Mouse epidydimal fat under 45% caloric restriction

value: 45% caloric restriction


title: HK-2 cells, CdCl, t12h, biological rep 1, Tox2


title: Mouse EF CD, biological rep 3

description: Gene expression data from epidydimal fat of wild type C57BL/6 mouse responsed by control diet

source_name: Mouse epidydimal fat under control diet

value: control diet


title: Mouse EF CR85, biological rep 3


title: Mouse EF CR70, biological rep 2


title: Mouse EF CR85, biological rep 2


title: Mouse EF CD, biological rep 2


title: Follicles female 3_2

description: Biological replicate 3_C5Cy3


title: Follicles female 2_2

description: Biological replicate 2_C5Cy3

source_name: Follicles female 2_control

source_name: Follicles female 2_LH


title: Follicles female 4_2

description: Biological replicate 4_C5Cy3

source_name: Follicles female 4_control

source_name: Follicles female 4_LH


title: Mouse EF CR55, biological rep 2


title: Mouse EF CR70, biological rep 1


title: Mouse EF CR55, biological rep 3


title: Follicles female 4_1

description: Biological replicate 4_Cy3Cy5


title: Follicles female 2_1

description: Biological replicate 2_Cy3Cy5


title: BHL - BRAF(+) - M_958

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: Data was acquired using GeneChip Command Console Software 1.1 (Affymetrix). The preprocessing was performed by Robust Multi-Array expression measure (RMA).

source_name: BHL, BRAF(+)

label_protocol: Total RNA (100 ng) was used for synthesis of double stranded cDNA and aRNA labeling according to manufacturer's instructions (GeneChip 3' IVT Express Kit, Affymetrix).

extract_protocol: The RNA was extracted from mice thyroids with the RNeasy Micro Kit (Qiagen GmbH, Hilden, Niemcy) according to the protocol. The quantity and quality of RNA were analyzed with NanoDrop ND-1000 and Bioanalyzer 2100 (Agilent Technologies) respectively.

treatment_protocol: The mice were sacrificed after 4-24 months. The thyroids were resected and from the half of the gland (comprising of fragments of both lobes) RNA was isolated and the remaining half was subjected to histopathological evaluation.

tag: type of thyroid tissue

value: benign hyperplastic lesion

tag: brafv600e mutation

value: positive

tag: Sex

tag: age (months)


title: AT - BRAF(-) - M_956

source_name: AT, BRAF(-)

value: asymptomatic thyroid

value: not present

value: female


title: AT - BRAF(+) - M_948

source_name: AT, BRAF(+)


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 2, Tox2

source_name: Human renal proximal tubular epithelial cells, control for CdCl and Di, t12h

value: control

value: 12 hrs


title: Follicles female 1_1

description: Biological replicate 1_Cy3Cy5

source_name: Follicles female 1_control

tag: tissue

value: Preovulatory follicles

source_name: Follicles female 1_LH


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 3, Tox2

tag: cell type


title: Follicles female 1_2

description: Biological replicate 1_C5Cy3


title: BHL - BRAF(+) - M_997


title: AT - BRAF(+) - M_945


title: BHL - BRAF(-) - M_946

source_name: BHL, BRAF(-)


title: PTC - M_884

source_name: PTC

value: papillary thyroid carcinoma


title: BHL - BRAF(-) - M_930


title: BHL - BRAF(+) - M_942


title: HK-2 cells, CdCl and Di, t12h, control sample, biological rep 1, Tox2


title: HK-2 cells, Ra, t48h, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t48h

value: Ra


title: AT - BRAF(-) - M_940


title: HK-2 cells, CdCl and Di, t48h, control sample, biological rep 1, Tox2


title: BHL - BRAF(+) - M_943


title: BL - M_80

source_name: BL

value: borderline lesion

value: male


title: Adipocytes_Dhet.mice_Chow.diet_16weeks, rep5

city: Charlottesville

first: Annamalai

last: Muthiah

state: VA

address: 857, Swan Ridge Road

institute: University of Virginia

description: Gene.Expression.Data from adipose tissue of mice fed chow diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array (Affymetrix MG430-2.0 GeneChips). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw intensity values of hybridization were scanned and stored as .CEL files using Affymetrix Microarray suite software with global scaling option. Gene expression values were obtained by reading and normalizing the .CEL files with Robust Multi Average (RMA) express software using the cdf file Mouse430_2.cdf

source_name: Adipocytes obtained from Dhet mice fed Chow diet for 16 weeks

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol starting with 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Adipocytes were isolated from parametrial and periovarian adipose tissues and total RNA was extracted from the adipocytes using TRIzol (Life Technologies Corporation).

tag: background strain

value: Female

tag: genotype


title: Mouse EF CD, biological rep 1

tag: strain

value: Epidydimal fat

tag: age

value: 18 weeks


title: Adipocytes_ApoE.mice_Chow.diet_16weeks, rep4

source_name: Adipocytes obtained from ApoE null mice fed Chow diet for 16 weeks

value: ApoE -/-

value: parametrial and periovarian adipose tissues


title: Adipocytes_ApoE.mice_Chow.diet_16weeks, rep3


title: HK-2 cells, Ra, t48h, biological rep 3, Tox1

value: immortalized human renal proximal tubular epithelial cells

value: 48 hrs


title: Adipocytes_ApoE.mice_Chow.diet_16weeks, rep1


title: AT - BRAF(-) - M_957

value: asymptomatic thyroid


title: Adipocytes_ApoE.mice_Chow.diet_16weeks, rep5


title: AT - BRAF(+) - M_779

value: positive


title: HK-2 cells, Ra, t48h, biological rep 1, Tox1


title: Adipocytes_ApoE.mice_Chow.diet_16weeks, rep2


title: Adipocytes_Dhet.mice_Chow.diet_16weeks, rep4


title: BHL - BRAF(-) - M_764

value: benign hyperplastic lesion

value: not present

value: female


title: AT - BRAF(-) - M_771


title: HK-2 cells, Fk, t48h, biological rep 1, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t48h

value: Fk


title: HK-2 cells, Fk, t48h, biological rep 3, Tox1


title: BHL - BRAF(-) - M_701


title: HK-2 cells, Fk, t48h, biological rep 2, Tox1


title: BL - M_649


title: Adipocytes_Dhet.mice_Chow.diet_16weeks, rep2


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Fk and Ra, t48h

value: control


title: Adipocytes_Dhet.mice_Chow.diet_16weeks, rep3


title: Adipocytes_Dhet.mice_Chow.diet_16weeks, rep1


title: PTC - M_686

value: papillary thyroid carcinoma


title: BL - M_772

value: borderline lesion


title: BL - M_530


title: BL - M_416


title: BL - M_528


title: AT - BRAF(-) - M_524

value: male


title: PTC - M_700


title: BL - M_527


title: PTC - M_415


title: AT - BRAF(+) - M_523


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep8

description: Gene.Expression.Data from adipose tissue of mice fed western diet

source_name: Adipocytes obtained from ApoE null mice fed Western diet for 16 weeks

value: Female


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep6


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 2, Tox1


title: HK-2 cells, Ra, t12h, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t12h

value: Ra

value: 12 hrs


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep7

value: ApoE -/-


title: PTC - M_364


title: HK-2 cells, Fk and Ra, t48h, control sample, biological rep 1, Tox1


title: HK-2 cells, Fk, t12h, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t12h


title: PTC - M_358


title: AT - BRAF(+) - M_1003


title: HK-2 cells, Ra, t12h, biological rep 3, Tox1


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep2

value: parametrial and periovarian adipose tissues


title: HK-2 cells, Ra, t12h, biological rep 1, Tox1

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, Fk, t12h, biological rep 1, Tox1


title: PTC - M_347


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep4


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep3


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep5


title: BL - M_360


title: PTC - M_348


title: PTC - M_359


title: BL - M_1005


title: PTC - M_1002


title: BL - M_414


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Fk and Ra, t12h


title: HK-2 cells, Fk, t12h, biological rep 2, Tox1


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep9

source_name: Adipocytes obtained from Dhet mice fed Western diet for 16 weeks


title: PTC-209 in Vehicle control (0.5% DMSO), rep1

city: Singapore

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: Gene expression data from embryos in slow phase of cellularisation.

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

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

data_processing: The data were analyzed using RMA in the bioconducter and normalized using cross correlation.  The trimmed mean target intensity of each array was set to 3.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A316 cebp alpha knock out primary adenocarcinoma line cells were cultured at standard conditions.

treatment_protocol: A316 cebp alpha knock out primary adenocarcinoma line cells treated with Bmi inhibition through compound PTC-209 in Vehicle control (0.5% DMSO) compared to the corresponding the control treatment (0.5% DMSO).

value: primary adenocarcinoma line

value: cebp alpha knock out


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 1, Tox1


title: Control Footshock C57BL/6J rep5

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

institute: Institute of Pharmacology PAS

description:
3999936016_F
C-FC5_C57

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with preprocessCore in R.

source_name: C57BL/6J_control footshock

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

value: 8-10 weeks

tag: sample group

value: control footshock

value: amygdala


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep8


title: PTC-209 in Vehicle control (0.5% DMSO), rep3

source_name: A316 cebp alpha knock out primary adenocarcinoma line

value: Bmi inhibition through compound PTC-209 in Vehicle control (0.5% DMSO)


title: Adipocytes_ApoE.mice_Western.diet_16weeks, rep1


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep4


title: PTC-209 in Vehicle control (0.5% DMSO), rep2


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep6


title: HK-2 cells, Fk and Ra, t12h, control sample, biological rep 2, Tox1


title: control treatment with 0.5% DMSO, rep3

value: control treatment (0.5% DMSO)


title: HK-2 cells, Nnm, hd and ld, t48h, control sample, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Nnm, hd and ld, t48h

value: control

value: 48 hrs


title: control treatment with 0.5% DMSO, rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: Control Control SWR/J rep2

description:
3999936016_E
C2_SWR

source_name: SWR/J_control control

value: SWR/J

value: control control


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep5

value: Female


title: HK-2 cells, Nnm, hd, t48h, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h

value: Nnm

tag: treatment dosage

value: high


title: HK-2 cells, Nnm, ld, t24h, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t24h

tag: cell line

value: low

value: 24 hrs


title: HK-2 cells, Nnm, ld, t48h, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h

value: immortalized human renal proximal tubular epithelial cells

tag: treatment


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep3

value: parametrial and periovarian adipose tissues


title: Control Context C57BL/6J rep3

description:
3999936016_B
C-CTX3_C57

source_name: C57BL/6J_control context

value: control context


title: Control Restraint C57BL/6J rep4

description:
3999936002_E
R4_C57

source_name: C57BL/6J_control restaint

value: 8-10 weeks

value: control restaint


title: Control Context SWR/J rep7

description:
3999936016_D
C-CTX7_SWR

source_name: SWR/J_control context

value: amygdala


title: HK-2 cells, Nnm, hd, t24h, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h

tag: treatment duration


title: Control Context C57BL/6J rep6

description:
3999936002_D
C-CTX6_C57


title: Control Footshock C57BL/6J rep1

description:
3999936016_A
C-FC1_C57

value: control footshock


title: control treatment with 0.5% DMSO, rep1

value: primary adenocarcinoma line

value: cebp alpha knock out

value: control treatment (0.5% DMSO)


title: Restraint Footshock SWR/J rep4

description:
3999936016_C
R-FC4_SWR

source_name: SWR/J_restraint footshock

value: SWR/J

value: restraint footshock


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep7

tag: gender

value: Female


title: Control Footshock SWR/J rep4

description:
3999936002_F
C-FC4_SWR

source_name: SWR/J_control footshock


title: HK-2 cells, Nnm, hd and ld, t24h, control sample, biological rep 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Nnm, hd and ld, t24h

value: control


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep2


title: Restraint Context C57BL/6J rep5

description:
3999936002_C
R-CTX5_C57

source_name: C57BL/6J_restraint context

value: restraint context


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep7

source_name: Adipocytes obtained from Dhet mice fed Chow diet for 8 weeks


title: Control Control C57BL/6J rep4

description:
3999926071_D
C4_C57

source_name: C57BL/6J_control control

value: control control


title: Control Context SWR/J rep6

description:
3999936002_A
C-CTX6_SWR


title: Control Control SWR/J rep1

description:
3999936002_B
C1_SWR


title: Restraint Context C57BL/6J rep1

description:
3999926071_C
R-CTX1_C57


title: Adipocytes_Dhet.mice_Western.diet_16weeks, rep1

source_name: Adipocytes obtained from Dhet mice fed Western diet for 16 weeks


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep6


title: Restraint Context C57BL/6J rep3

description:
3999926064_F
R-CTX3_C57


title: Restraint Context SWR/J rep6

description:
3999926071_E
R-CTX6_SWR

source_name: SWR/J_restraint context


title: Restraint Footshock C57BL/6J rep4

description:
3999926064_E
R-FC4_C57

source_name: C57BL/6J_restraint footshock


title: Control Context SWR/J rep2

description:
3999926071_A
C-CTX2_SWR


title: HK-2 cells, Nnm, hd and ld, t48h, control sample, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Nnm, hd and ld, t48h

value: 48 hrs


title: Control Restraint SWR/J rep3

description:
3999926071_F
R3_SWR

source_name: SWR/J_control restaint


title: Control Context SWR/J rep4

description:
3999926064_D
C-CTX4_SWR


title: HK-2 cells, Nnm, hd, t48h, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h

value: immortalized human renal proximal tubular epithelial cells

value: Nnm

value: high


title: HK-2 cells, Nnm, ld, t24h, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t24h

value: low

value: 24 hrs


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep5

value: parametrial and periovarian adipose tissues


title: Restraint Footshock C57BL/6J rep2

description:
3999926071_B
R-FC2_C57

value: 8-10 weeks

value: amygdala


title: HK-2 cells, Nnm, hd, t24h, biological rep 2, Tox1


title: HK-2 cells, Nnm, ld, t48h, biological rep 2, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep3


title: Restraint Context C57BL/6J rep7

description:
3999926064_A
R-CTX7_C57


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep4


title: Control Restraint C57BL/6J rep5

description:
3999926064_B
R5_C57

source_name: C57BL/6J_control restaint

value: control restaint


title: HK-2 cells, Nnm, hd and ld, t24h, control sample, biological rep 2, Tox1


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep2


title: Restraint Footshock SWR/J rep1

description:
3999926064_C
R-FC1_SWR


title: Adipocytes_Dhet.mice_Chow.diet_8weeks, rep1


title: Control Footshock C57BL/6J rep4

description:
3999926053_A
C-FC4_C57

source_name: C57BL/6J_control footshock

value: control footshock


title: Control Context C57BL/6J rep7

description:
3999926053_C
C-CTX7_C57

source_name: C57BL/6J_control context

value: control context


title: Control Restraint SWR/J rep1

description:
3999926053_F
R1_SWR

value: SWR/J


title: Control Control C57BL/6J rep2

description:
3999926053_D
C2_C57


title: Restraint Context C57BL/6J rep6

description:
3999926053_B
R-CTX6_C57


title: Restraint Context SWR/J rep4

description:
3999926053_E
R-CTX4_SWR


title: HK-2 cells, Nnm, ld, t48h, biological rep 1, Tox1


title: HK-2 cells, Nnm, hd, t48h, biological rep 1, Tox1


title: Control Control C57BL/6J rep5

description:
3999926050_D
C5_C57


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep5

source_name: Adipocytes obtained from ApoE null mice fed Western diet for 8 weeks

value: Female

value: ApoE -/-


title: Control Restraint SWR/J rep4

description:
3999926050_F
R4_SWR


title: Restraint Context SWR/J rep7

description:
3999926050_E
R-CTX7_SWR

value: restraint context


title: HK-2 cells, Nnm, hd, t24h, biological rep 1, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep4


title: HK-2 cells, Nnm, hd and ld, t48h, control sample, biological rep 1, Tox1

value: control


title: Restraint Context C57BL/6J rep2

description:
3999926050_C
R-CTX2_C57


title: Restraint Footshock C57BL/6J rep3

description:
3999926050_B
R-FC3_C57

value: restraint footshock


title: HK-2 cells, Nnm, ld, t24h, biological rep 1, Tox1

value: immortalized human renal proximal tubular epithelial cells


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep2


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep3


title: Control Context SWR/J rep3

description:
3999926050_A
C-CTX3_SWR

source_name: SWR/J_control context


title: Control Footshock SWR/J rep3

description:
3999483081_D
C-FC3_SWR

source_name: SWR/J_control footshock


title: HK-2 cells, CsA, t48h, control sample, biological rep 3, lab 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for CsA, t48h

value: 48 hrs


title: HK-2 cells, Nnm, hd and ld, t24h, control sample, biological rep 1, Tox1

source_name: Human renal proximal tubular epithelial cells, control for Nnm, hd and ld, t24h


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep1


title: Control Restraint C57BL/6J rep3

description:
3999483081_C
R3_C57


title: Control Context C57BL/6J rep5

description:
3999483081_B
C-CTX5_C57


title: HK-2 cells, CsA, t48h, control sample, biological rep 2, lab 3, Tox1


title: Control Restraint C57BL/6J rep2

description:
10012449064_D
R2_C57


title: Control Footshock SWR/J rep2

description:
10012449064_E
C-FC2_SWR


title: HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 3, Tox1


title: Control Context SWR/J rep5

description:
10012449064_A
C-CTX5_SWR


title: Adipocytes_Dhet.mice_Western.diet_8weeks, rep5

source_name: Adipocytes obtained from Dhet mice fed Western diet for 8 weeks


title: Adipocytes_Dhet.mice_Western.diet_8weeks, rep4


title: Restraint Footshock SWR/J rep2

description:
10012449052_F
R-FC2_SWR

source_name: SWR/J_restraint footshock


title: HK-2 cells, CsA, t48h, biological rep 3, lab 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t48h

value: CsA


title: Restraint Context SWR/J rep2

description:
10012449064_F
R-CTX2_SWR

source_name: SWR/J_restraint context


title: Restraint Context C57BL/6J rep4

description:
10012449064_C
R-CTX4_C57

source_name: C57BL/6J_restraint context


title: HK-2 cells, CsA, t48h, biological rep 1, lab 3, Tox1


title: Control Control SWR/J rep4

description:
10012449052_C
C4_SWR

source_name: SWR/J_control control

value: control control


title: Adipocytes_Dhet.mice_Western.diet_8weeks, rep2


title: Restraint Context C57BL/6J rep8

description:
10012449052_D
R-CTX8_C57


title: Adipocytes_Dhet.mice_Western.diet_8weeks, rep1


title: HK-2 cells, CsA, t48h, biological rep 2, lab 3, Tox1


title: cell line IPEC‑J2_3

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

description: I1EC J2  K 22.10.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and PLIER algorithm.

organism: Sus scrofa

source_name: polarized intestinal porcine epithelial cell line IPEC‑J2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: IPEC 1 (ACC 701, DSMZ) and IPEC‑J2 cells (ACC701, DSMZ) were cultured in Dulbecco’s modified eagle medium (DMEM/Ham’s F-12 (1:1)) supplemented with 5 % fetal calf serum (FCS), 1 % insulin-transferrin-selenium (ITS), 16 mmol/L HEPES (all PAN-Biotech, Germany) and 5 ng/mL epidermal growth factor (EGF; BD Biosciences, Germany) and incubated at 39°C and 5 % CO2. The cells were routinely seeded at a density of 0.5*105/mL with 7.5 mL in plastic tissue culture flasks (25 cm2 Nunc, Denmark) and passaged every 3‑4 d for a maximum of 20 times (passages 78‑98). For the use in experiments, cells were seeded at a density of 2.0 x 105/ well in uncoated 6‑well 1 µm pore-sized ThinCert™ membrane inserts (Greiner bio-one, Germany) and cultured for 7 d.

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: intestinal epithelial cell line

value: spontaneously immortalised cell lines from the porcine intestine


title: cell line IPEC‑J2_1

description: I1EC J2 K 19.10.


title: Control Context C57BL/6J rep1

description:
10012449052_E
C-CTX1_C57

source_name: C57BL/6J_control control

value: 8-10 weeks


title: Control Footshock C57BL/6J rep3

description:
3999483081_A
C-FC3_C57

value: amygdala


title: Adipocytes_Dhet.mice_Western.diet_8weeks, rep3

value: parametrial and periovarian adipose tissues


title: Control Context SWR/J rep1

description:
10012449052_B
C-CTX1_SWR


title: Restraint Footshock SWR/J rep3

description:
10012449049_F
R-FC3_SWR


title: HK-2 cells, CsA, t12h, control sample, biological rep 3, lab 3, Tox1

source_name: Human renal proximal tubular epithelial cells, control for CsA, t12h

value: 12 hrs


title: Restraint Footshock C57BL/6J rep5

description:
10012449064_B
R-FC5_C57

source_name: C57BL/6J_restraint footshock


title: cell line IPEC‑J2_2

description: I1EC J2 K17


title: Restraint Context SWR/J rep1

description:
10012449052_A
R-CTX1_SWR


title: HK-2 cells, CsA, t12h, control sample, biological rep 1, lab 3, Tox1


title: HK-2 cells, CsA, t12h, control sample, biological rep 2, lab 3, Tox1


title: Control Context C57BL/6J rep2

description:
10012449049_E
C-CTX2_C57

source_name: C57BL/6J_control context

value: control context


title: HK-2 cells, CsA, t12h, biological rep 2, lab 3, Tox1

source_name: Human renal proximal tubular epithelial cells, treated with CsA, t12h


title: HK-2 cells, CsA, t12h, biological rep 3, lab 3, Tox1


title: Control Control SWR/J rep5

description:
10012449049_C
C5_SWR

value: SWR/J


title: cell line IPEC‑1_2

description: I1EC 1 K 19.10.

source_name: polarized intestinal porcine epithelial cell line IPEC‑1


title: Control Control C57BL/6J rep1

description:
10012449049_A
C1_C57


title: Restraint Context SWR/J rep3

description:
10012449049_B
R-CTX3_SWR


title: Restraint Context C57BL/6J rep9

description:
10012449049_D
R-CTX9_C57


title: Control Context C57BL/6J rep4

description:
10012449037_E
C-CTX4_C57


title: cell line IPEC‑1_3

description: I1EC 1 K1


title: cell line IPEC‑1_1

description: I1EC 1  K 22.10.


title: Restraint Footshock SWR/J rep5

description:
10012449037_F
R-FC5_SWR


title: Control Footshock C57BL/6J rep2

description:
10012449037_D
C-FC2_C57

source_name: C57BL/6J_control footshock

value: control footshock


title: HK-2 cells, Ra, t48h, control sample, biological rep 1

source_name: Human renal proximal tubular epithelial cells, control for Ra, t48h


title: Control Control SWR/J rep3

description:
10012449034_D
C3_SWR


title: Y50-3

city: wuhan

first: Jiangnan

last: Huang

state: Hubei

address: Shizishan Street

country: China

institute: Huazhong (Central China) Agricultural University

description: Gene expression data from the endometrium of Yorkshire pigs on gestation 50

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip® Fluidics Station 400. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the fluidics station 400.

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

data_processing: The raw data intensity files were read into R (http://www.r-project.org/) and preprocessed using functions of the Affymetrix and Gene Chip Robust Multi-array Average (GCRMA) packages of the BioConductor project (http://www.bioconductor.org/) (Gentleman et al Genome Biology 2004).For quality control, normalized data were analyzed with a distance matrix and a heatmap based on pair-wise distances (BioConducter package geneplotter).

label_protocol: Total RNA (1 μg to 15 μg) or mRNA (0.2 μg to 2 μg) is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays.

treatment_protocol: Two different areas of endometrial tissue were removed from the middle portion of each uterine horn, snap-frozen in liquid nitrogen immediately and stored at -80℃ until extraction of RNA.

tag: breed

value: Yorkshire

value: gestational day 50

value: endometrium


title: Control Restraint SWR/J rep2

description:
10012449037_C
R2_SWR

source_name: SWR/J_control restaint

value: control restaint


title: HK-2 cells, CsA, t12h, biological rep 1, lab 3, Tox1

value: immortalized human renal proximal tubular epithelial cells


title: Control Context C57BL/6J rep8

description:
10012449034_F
C-CTX8_C57


title: Control Restraint SWR/J rep5

description:
10012449034_C
R5_SWR


title: Restraint Context SWR/J rep5

description:
10012449037_B
R-CTX5_SWR

value: restraint context


title: Control Control C57BL/6J rep3

description:
10012449037_A
C3_C57


title: HK-2 cells, Ra, t48h, control sample, biological rep 3

value: control

value: 48 hrs


title: HK-2 cells, Ra, t48h, control sample, biological rep 2


title: Y26-3

description: Gene expression data from the endometrium of Yorkshire pigs on gestation 26

value: gestational day 26


title: Y50-2

source_name: the endometrium of Yorkshire pigs on gestation 50


title: HK-2 cells, Ra, t12h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Ra, t12h


title: Y50-1


title: Restraint Footshock C57BL/6J rep1

description:
10012449034_E
R-FC1_C57

value: restraint footshock


title: HK-2 cells, Ra, t12h, control sample, biological rep 2


title: Adipocytes_ApoE.mice_Western.diet_8weeks, rep6

source_name: Adipocytes obtained from ApoE null mice fed Western diet for 8 weeks

value: Female

value: ApoE -/-


title: HK-2 cells, Ra, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t48h

value: Ra


title: Control Footshock SWR/J rep1

description:
10012449034_B
C-FC1_SWR

source_name: SWR/J_control footshock

value: 8-10 weeks

value: amygdala


title: Y26-1

source_name: the endometrium of Yorkshire pigs on gestation 26


title: Control Restraint C57BL/6J rep1

description:
10012449034_A
R1_C57

source_name: C57BL/6J_control restaint


title: HK-2 cells, Ra, t12h, control sample, biological rep 1

value: 12 hrs


title: Y26-2


title: STR_PHE_8_2

source_name: Striatum Phencyclidyne 8h rep2

value: Striatum

value: 8-10 week old

tag: timepoint

tag: drug

value: Phencyclidyne


title: STR_PHE_1_1

source_name: Striatum Phencyclidyne 1h rep1


title: STR_NAI_1_3

source_name: Striatum Naive 1h rep3

value: Naive


title: Y15-2

description: Gene expression data from the endometrium of Yorkshire pigs on gestation 15

value: Yorkshire

value: gestational day 15

value: endometrium


title: STR_KET_4_1

source_name: Striatum Ketamine 4h rep1

value: Ketamine


title: STR_SAL_4_3

source_name: Striatum Saline 4h rep3

value: Saline


title: STR_SAL_4_1

source_name: Striatum Saline 4h rep1


title: STR_NAI_8_2

source_name: Striatum Naive 8h rep2


title: HK-2 cells, Ra, t12h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with Ra, t12h

value: immortalized human renal proximal tubular epithelial cells


title: Y15-1

source_name: the endometrium of Yorkshire pigs on gestation 15


title: HK-2 cells, Ra, t48h, biological rep 1

value: 48 hrs


title: M50-3

description: Gene expression data from the endometrium of meishan pigs on gestation 50

value: Meishan

value: gestational day 50


title: STR_PHE_4_3

source_name: Striatum Phencyclidyne 4h rep3


title: STR_MEM_2_2

source_name: Striatum Memantine 2h rep2

value: Memantine


title: Y15-3


title: HK-2 cells, Ra, t48h, biological rep 2

value: Ra


title: STR_KET_2_2

source_name: Striatum Ketamine 2h rep2


title: STR_NAI_1_1

source_name: Striatum Naive 1h rep1


title: HK-2 cells, Ra, t12h, biological rep 2


title: STR_MEM_1_3

source_name: Striatum Memantine 1h rep3


title: M50-1

source_name: the endometrium of meishan pigs on gestation 50


title: M50-2


title: HK-2 cells, Ra, t12h, biological rep 1


title: STR_MEM_8_1

source_name: Striatum Memantine 8h rep1


title: STR_PHE_2_3

source_name: Striatum Phencyclidyne 2h rep3


title: STR_SAL_2_1

source_name: Striatum Saline 2h rep1


title: HK-2 cells, Ota, ld, t72h, control sample, biological rep 1

source_name: Human renal proximal tubular epithelial cells, control for Ota, t72h

value: control

value: 72 hrs


title: HK-2 cells, Ota, ld, t72h, control sample, biological rep 3


title: STR_NAI_4_2

source_name: Striatum Naive 4h rep2

value: Striatum


title: M26-3

description: Gene expression data from the endometrium of meishan pigs on gestation 26

value: gestational day 26


title: STR_KET_8_3

source_name: Striatum Ketamine 8h rep3

value: 8-10 week old


title: M26-1

source_name: the endometrium of meishan pigs on gestation 26


title: HK-2 cells, Ota, ld, t24h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Ota, t24h

value: 24 hrs


title: HK-2 cells, Ota, ld, t72h, control sample, biological rep 2


title: HK-2 cells, Ota, ld, t24h, control sample, biological rep 2


title: M26-2


title: STR_NAI_2_2

source_name: Striatum Naive 2h rep2

value: Naive


title: M15-3

description: Gene expression data from the endometrium of meishan pigs on gestation 15

value: gestational day 15


title: STR_MEM_4_1

source_name: Striatum Memantine 4h rep1


title: M15-2

source_name: the endometrium of meishan pigs on gestation 15

value: endometrium


title: STR_SAL_8_2

source_name: Striatum Saline 8h rep2


title: STR_PHE_1_3

source_name: Striatum Phencyclidyne 1h rep3

value: Phencyclidyne


title: STR_SAL_1_1

source_name: Striatum Saline 1h rep1

value: Saline


title: STR_SAL_4_2

source_name: Striatum Saline 4h rep2


title: STR_KET_1_2

source_name: Striatum Ketamine 1h rep2

value: Ketamine


title: HK-2 cells, Ota, ld, t72h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t72h

value: immortalized human renal proximal tubular epithelial cells

value: Ota

value: low


title: STR_PHE_8_1

source_name: Striatum Phencyclidyne 8h rep1


title: HK-2 cells, Ota, ld, t24h, control sample, biological rep 1


title: STR_NAI_1_2

source_name: Striatum Naive 1h rep2


title: STR_KET_4_3

source_name: Striatum Ketamine 4h rep3


title: STR_NAI_8_3

source_name: Striatum Naive 8h rep3


title: M15-1

value: Meishan


title: HK-2 cells, Ota, ld, t72h, biological rep 1


title: HK-2 cells, Ota, ld, t72h, biological rep 2


title: STR_MEM_2_1

source_name: Striatum Memantine 2h rep1

value: Memantine


title: STR_NAI_8_1

source_name: Striatum Naive 8h rep1


title: STR_MEM_8_3

source_name: Striatum Memantine 8h rep3


title: STR_SAL_2_3

source_name: Striatum Saline 2h rep3


title: HK-2 cells, Ota, ld, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Ota, t24h


title: STR_KET_2_3

source_name: Striatum Ketamine 2h rep3


title: CR13

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: Cumulative low doses of the organic pesticide rotenone in the adult rat substantia nigra pars compacta

hyb_protocol: Fragmented aRNA was added to Amersham hybridization solution (Amersham) (final volume 260 uL) and injected onto CodeLink Uniset mouse 35K bioarrays containing 35,000 mouse oligonucleotide gene probes (Amersham). The arrays were hybridized overnight at 37-C at 300 rpm on a rotary mixer in an incubator, washed at 46-C for 1 hour in stringent TNT buffer (100 mM Tris, 150 mM NaCl, 0.02% Tween 20; all from Sigma- Aldrich, Saint Quentin-Fallavier, France), incubated in 3.4 mL of streptavidin-Cy5 (Amersham) solution for 30 minutes, washed 4 times in 240 mL of TNT buffer, rinsed twice in 240 mL of water containing 0.2% Triton X-100, and dried by centrifugation at 600 rpm.

scan_protocol: The arrays were scanned with a Genepix 4000B scanner (Axon Instruments, Dipsi Industrie, Chatillon, France) using Genepix software with the laser set at 635 nm, the power at 100%, and the photomultiplier tube voltage at 60%. The scanned image files were analyzed using CodeLink expression software version 4.0, which produces both raw and normalized hybridization signals for each spot on the array.

data_processing: The CodeLink software (version 4) normalizes the overall raw hybridization signal intensity on each array to the median of the array (median intensity is one after normalization).

organism: Rattus norvegicus

label_protocol: Biotin-labeled aRNA (10 ug) was fragmented with 5 uL of fragmentation buffer (GE Healthcare, Amersham, Saclay, France) in a final volume of 20 uL.

growth_protocol: Male Sprague Dawley rats aged of 5 months were housed with ad libitum access to food and water in a temperature- (24 + 1°C) and humidity- (60%) controlled room under a 12 h / 12 h light-dark schedule (lights on at 08.00 h).

extract_protocol: Total RNA was prepared from laser-capture microdissected rat substantia nigra pars compacta (SNpc) using the RNeasy mini-kit (QIAGEN, Courtaboeuf, France) according to manufacturer’s instructions, including the additional step of DNase treatment. Total RNA (2 ug) was amplified and labeled by a round of in vitro transcription using a MessageAmp aRNA kit (Ambion, Cambridgeshire, U.K.) following the manufacturers protocol. Before amplification, spikes of different concentrations of synthetic mRNA were added to all tubes. These positive controls were used to verify the quality of the process. Amplified RNA (aRNA) was measured with an ultraviolet spectrophotometer and the quality verified on picochips using the Agilent bioanalyzer.

treatment_protocol: Rotenone (Sigma, Lyon, France) was dissolved in a solution of dimethylsulfoxide (DMSO) / polyethylene glycol (PEG) (1/1) containing the non-ionic surfactant polyol Pluronic® F-127 (Interchim, Montluçon, France) used as a dispersing reagent at the final concentration of 0.05%. Prior to the implantation, Alzet® osmotic mini-pumps (2ML4, Charles River Laboratories, Saint Germain sur l’Arbresle, France) were filled with the solvent or rotenone and incubated overnight at 37°C in a sterile saline solution (NaCl 0.9%, wt/vol) according to manufacturer’s instructions. Rats were anaesthetized by an intraperitoneal injection of ketamine (75 mg/kg) and xylazine (10 mg/kg). Osmotic pumps were implanted subcutaneously and diffused either the solvent (SOLV, control group, n = 3) or 0.5 mg/kg/day rotenone (ROT group, n = 3) for 28 days. The final delivery of rotenone was calculated with respect to average body weight at the time of the implantation. In order to monitor potential side effects of pesticide exposure, body weight was recorded daily for each rat throughout the experimentation.

value: Sprague Dawley

tag: developmental stage

value: adult

tag: sex

value: male

tag: treatment group

value: rotenone

value: substantia nigra pars compacta


title: CR9

tag: tissue


title: STR_MEM_1_2

source_name: Striatum Memantine 1h rep2

value: Striatum

value: 8-10 week old


title: HK-2 cells, Ota, ld, t24h, biological rep 2

tag: cell type

value: 24 hrs


title: CS1

value: solvent


title: STR_PHE_4_2

source_name: Striatum Phencyclidyne 4h rep2

value: Phencyclidyne


title: CR16


title: STR_KET_2_1

source_name: Striatum Ketamine 2h rep1


title: STR_PHE_4_1

source_name: Striatum Phencyclidyne 4h rep1


title: STR_SAL_2_2

source_name: Striatum Saline 2h rep2

value: Saline


title: HK-2 cells, Ota, hd, t72h, control sample, biological rep 2

source_name: Human renal proximal tubular epithelial cells, control for Ota, t72h

value: control

value: 72 hrs


title: STR_MEM_1_1

source_name: Striatum Memantine 1h rep1


title: STR_NAI_4_3

source_name: Striatum Naive 4h rep3

value: Naive


title: CS7


title: STR_MEM_8_2

source_name: Striatum Memantine 8h rep2


title: CS11


title: HK-2 cells, Ota, hd, t72h, control sample, biological rep 3

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, Ota, ld, t24h, biological rep 1

value: Ota

value: low


title: STR_KET_1_3

source_name: Striatum Ketamine 1h rep3

value: Ketamine


title: HK-2 cells, Ota, hd, t24h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Ota, t24h


title: HK-2 cells, Ota, hd, t72h, control sample, biological rep 1


title: STR_NAI_2_3

source_name: Striatum Naive 2h rep3


title: STR_SAL_1_2

source_name: Striatum Saline 1h rep2


title: STR_SAL_8_3

source_name: Striatum Saline 8h rep3


title: STR_MEM_4_2

source_name: Striatum Memantine 4h rep2

value: Memantine


title: STR_PHE_2_2

source_name: Striatum Phencyclidyne 2h rep2


title: STR_KET_8_2

source_name: Striatum Ketamine 8h rep2


title: STR_KET_8_1

source_name: Striatum Ketamine 8h rep1


title: STR_NAI_4_1

source_name: Striatum Naive 4h rep1


title: STR_SAL_1_3

source_name: Striatum Sailne 1h rep3


title: STR_MEM_4_3

source_name: Striatum Memantine 4h rep3


title: STR_PHE_2_1

source_name: Striatum Phencyclidyne 2h rep1


title: HK-2 cells, Ota, hd, t72h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t72h

value: high


title: HK-2 cells, Ota, hd, t72h, biological rep 1


title: STR_SAL_8_1

source_name: Striatum Saline 8h rep1


title: STR_PHE_8_3

source_name: Striatum Phencyclidyne 8h rep3


title: HK-2 cells, Ota, hd, t24h, control sample, biological rep 1


title: HK-2 cells, Ota, hd, t24h, control sample, biological rep 2


title: STR_KET_1_1

source_name: Striatum Ketamine 1h rep1


title: HK-2 cells, Ota, hd, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Ota, t24h


title: STR_KET_4_2

source_name: Striatum Ketamine 4h rep2


title: STR_MEM_2_3

source_name: Striatum Memantine 2h rep3


title: STR_NAI_2_1

source_name: Striatum Naive 2h rep1


title: HK-2 cells, Ota, hd, t72h, biological rep 3


title: HK-2 cells, Ota, hd, t24h, biological rep 2


title: HIP_PHE_4_3

source_name: Hippocampus Phencyclidyne 4h rep3

value: Hippocampus


title: HIP_SAL_4_1

source_name: Hippocampus Saline 4h rep1


title: HIP_NAI_8_2

source_name: Hippocampus Naive 8h rep2


title: HK-2 cells, Nnm, ld, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t48h

value: 48 hrs


title: STR_PHE_1_2

source_name: Striatum Phencyclidyne 1h rep2

value: Striatum


title: HK-2 cells, Ota, hd, t24h, biological rep 1


title: HIP_NAI_1_1

source_name: Hippocampus Naive 1h rep1

value: 8-10 week old


title: HK-2 cells, Nnm, ld, t48h, control sample, biological rep 2


title: HIP_MEM_1_3

source_name: Hippocampus Memantine 1h rep3


title: HK-2 cells, Nnm, ld, t48h, control sample, biological rep 1


title: HIP_SAL_8_2

source_name: Hippocampus Saline 8h rep2


title: HIP_NAI_4_2

source_name: Hippocampus Naive 4h rep2


title: HIP_KET_8_3

source_name: Hippocampus Ketamine 8h rep3


title: HIP_SAL_2_1

source_name: Hippocampus Saline 2h rep1


title: HIP_KET_2_2

source_name: Hippocampus Ketamine 2h rep2


title: HIP_PHE_2_3

source_name: Hippocampus Phencyclidyne 2h rep3


title: HK-2 cells, Nnm, ld, t24h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t24h

value: 24 hrs


title: HIP_KET_1_2

source_name: Hippocampus Ketamine 1h rep2


title: HK-2 cells, Nnm, ld, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t48h

value: Nnm


title: HIP_NAI_2_2

source_name: Hippocampus Naive 2h rep2


title: HIP_SAL_1_1

source_name: Hippocampus Saline 1h rep1


title: HIP_MEM_8_1

source_name: Hippocampus Memantine 8h rep1


title: HIP_MEM_4_1

source_name: Hippocampus Memantine 4h rep1


title: HIP_NAI_8_3

source_name: Hippocampus Naive 8h rep3


title: HIP_PHE_8_1

source_name: Hippocampus Phencyclidyne 8h rep1

value: Phencyclidyne


title: HIP_KET_4_3

source_name: Hippocampus Ketamine 4h rep3


title: HIP_SAL_4_2

source_name: Hippocampus Saline 4h rep2

value: Saline


title: HK-2 cells, Nnm, ld, t24h, control sample, biological rep 2

value: control


title: HIP_NAI_1_2

source_name: Hippocampus Naive 1h rep2


title: HK-2 cells, Nnm, ld, t24h, control sample, biological rep 1


title: HK-2 cells, Nnm, ld, t24h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with low dose Nnm, t24h


title: HIP_PHE_1_3

source_name: Hippocampus Phencyclidyne 1h rep3


title: HK-2 cells, Nnm, ld, t48h, biological rep 1


title: HK-2 cells, Nnm, ld, t48h, biological rep 2


title: HK-2 cells, Nnm, ld, t24h, biological rep 3


title: HK-2 cells, Nnm, ld, t24h, biological rep 1


title: HIP_SAL_4_3

source_name: Hippocampus Saline 4h rep3


title: HIP_KET_2_3

source_name: Hippocampus Ketamine 2h rep3


title: HIP_MEM_2_1

source_name: Hippocampus Memantine 2h rep1


title: HK-2 cells, Nnm, hd, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t48h


title: HIP_PHE_1_1

source_name: Hippocampus Phencyclidyne 1h rep1


title: HK-2 cells, Nnm, hd, t48h, control sample, biological rep 2


title: HIP_PHE_8_2

source_name: Hippocampus Phencyclidyne 8h rep2


title: HIP_NAI_1_3

source_name: Hippocampus Naive 1h rep3


title: HK-2 cells, Nnm, hd, t48h, control sample, biological rep 1


title: HIP_SAL_1_2

source_name: Hippocampus Saline 1h rep2


title: HIP_SAL_8_3

source_name: Hippocampus Saline 8h rep3


title: HIP_MEM_2_2

source_name: Hippocampus Memantine 2h rep2


title: HIP_NAI_2_3

source_name: Hippocampus Naive 2h rep3


title: HIP_PHE_2_1

source_name: Hippocampus Phencyclidyne 2h rep1


title: HIP_KET_4_1

source_name: Hippocampus Ketamine 4h rep1


title: HK-2 cells, Nnm, hd, t24h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Nnm, t24h


title: HK-2 cells, Nnm, hd, t24h, control sample, biological rep 2


title: HIP_NAI_8_1

source_name: Hippocampus Naive 8h rep1


title: HIP_KET_8_1

source_name: Hippocampus Ketamine 8h rep1


title: HIP_MEM_4_2

source_name: Hippocampus Memantine 4h rep2


title: HIP_SAL_2_3

source_name: Hippocampus Saline 2h rep3


title: HIP_MEM_1_2

source_name: Hippocampus Memantine 1h rep2


title: HIP_PHE_4_2

source_name: Hippocampus Phencyclidyne 4h rep2


title: HK-2 cells, Nnm, hd, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t48h


title: HK-2 cells, Nnm, hd, t48h, biological rep 2


title: HIP_MEM_8_3

source_name: Hippocampus Memantine 8h rep3


title: HK-2 cells, Nnm, hd, t24h, control sample, biological rep 1


title: HK-2 cells, Nnm, hd, t48h, biological rep 1


title: HIP_SAL_2_2

source_name: Hippocampus Saline 2h rep2


title: HIP_KET_2_1

source_name: Hippocampus Ketamine 2h rep1


title: HIP_PHE_4_1

source_name: Hippocampus Phencyclidyne 4h rep1


title: HK-2 cells, Nnm, hd, t24h, biological rep 1

source_name: Human renal proximal tubular epithelial cells, treated with high dose Nnm, t24h


title: HIP_NAI_4_3

source_name: Hippocampus Naive 4h rep3


title: HK-2 cells, Nnm, hd, t24h, biological rep 3


title: HIP_SAL_8_1

source_name: Hippocampus Sailne 8h rep1

value: Sailne


title: HIP_MEM_1_1

source_name: Hippocampus Memantine 1h rep1


title: HK-2 cells, Nnm, hd, t24h, biological rep 2


title: HIP_KET_1_3

source_name: Hippocampus Ketamine 1h rep3


title: HIP_PHE_8_3

source_name: Hippocampus Phencyclidyne 8h rep3


title: HK-2 cells, Kbr, ld, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Kbr, t48h


title: HIP_MEM_8_2

source_name: Hippocampus Memantine 8h rep2


title: HIP_SAL_1_3

source_name: Hippocampus Saline 1h rep3


title: HIP_MEM_4_3

source_name: Hippocampus Memantine 4h rep3


title: HIP_PHE_2_2

source_name: Hippocampus Phencyclidyne 2h rep2


title: HIP_NAI_2_1

source_name: Hippocampus Naive 2h rep1

value: Naive


title: HK-2 cells, Kbr, ld, t48h, control sample, biological rep 1

value: immortalized human renal proximal tubular epithelial cells


title: HK-2 cells, Kbr, ld, t24h, control sample, biological rep 2

source_name: Human renal proximal tubular epithelial cells, control for Kbr, t24h


title: HIP_KET_4_2

source_name: Hippocampus Ketamine 4h rep2


title: HIP_KET_1_1

source_name: Hippocampus Ketamine 1h rep1


title: HIP_PHE_1_2

source_name: Hippocampus Phencyclidyne 1h rep2


title: HIP_KET_8_2

source_name: Hippocampus Ketamine 8h rep2


title: HIP_NAI_4_1

source_name: Hippocampus Naive 4h rep1


title: HK-2 cells, Kbr, ld, t24h, control sample, biological rep 3


title: HK-2 cells, Kbr, ld, t24h, control sample, biological rep 1


title: BcorFl/Y BM cells transduced with control empty retrovirus, repeat 3

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 24 based on detection p value of 0.05.

source_name: mononuclear cells after Ficoll purification

label_protocol: Standard Illumina protocol.

growth_protocol: BcorFl/Y BM cells were cultured in Iscove's Modified Dulbecco's Media (Invitrogen, CA) with 20% fetal bovine serum (FBS) plus 50 ng/ml stem cell factor (SCF), 25 ng/ml IL6 and 10 ng/ml IL-3.

extract_protocol: Total RNA from BM cells or CD34+ cells with or without Bcor mutation was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cultured cells were infected either a control empty retrovirus or a retrovirus expressing CRE recombinase and selected with puromycin. And CD34+ cells were then sorted by Flow cytometry.

value: 3-months old

tag: growth protocol

value: BM cells cultured under myeloid stem/progenitor conditions

tag: genotype/variation

value: BM cells


title: BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase, repeat 2

tag: age


title: BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase, repeat 1


title: HK-2 cells, Kbr, ld, t48h, biological rep 1

hyb_protocol: 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.

scan_protocol: Fluorescence was read with an Affymetrix 3000 Scanner.

data_processing: Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t48h

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

value: Kbr

value: low


title: HK-2 cells, Kbr, ld, t48h, control sample, biological rep 2


title: BcorFl/Y BM cells transduced with control empty retrovirus, repeat 1


title: BcorFl/Y BM cells transduced with control empty retrovirus, repeat 2


title: CD34+ cells sorted from #2 BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase, repeat 2

description: F2 KO 2

source_name: CD34+ mononuclear cells after Ficoll purification

value: CD34+ cells sorted from BM cells


title: BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase, repeat 3


title: CD34+ cells sorted from #2 BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase, repeat 1

description: F2 KO 1


title: CD34+ cells sorted from #4 BcorFl/Y BM cells transduced with control empty retrovirus

description: F4 WT


title: CD34+ cells sorted from #4 BcorFl/Y BM cells transduced with retrovirus expressing CRE recombinase

description: F4 KO


title: HIP_MEM_2_3

source_name: Hippocampus Memantine 2h rep3

tag: strain

value: Hippocampus

value: Memantine


title: HK-2 cells, Kbr, ld, t48h, biological rep 2

tag: treatment dosage

value: 48 hrs


title: HK-2 cells, Kbr, ld, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with low dose Kbr, t24h

tag: cell line

value: 24 hrs


title: HK-2 cells, Kbr, ld, t24h, biological rep 2

tag: treatment


title: CD34+ cells sorted from #2 BcorFl/Y BM cells transduced with control empty retrovirus, repeat 2

description: F2 WT 2


title: HK-2 cells, Kbr, ld, t48h, biological rep 3

tag: treatment duration


title: HK-2 cells, Kbr, hd, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Kbr, t48h


title: CD34+ cells sorted from #2 BcorFl/Y BM cells transduced with control empty retrovirus, repeat 1

description: F2 WT 1


title: rudhira mutant yolk sac_exon 6 deletion_2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
Sample_8YS669(YS)
growth retarded, abnormal vascularization

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring GX v 10.0.2. Quantile normalization was performed for each sample individually and baseline was corrected to each probe across the samples in the experiment.

source_name: Yolk Sac 9.5 dpc

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

growth_protocol: Mouse colony were bred and expanded in the transgenic facility (temperature- 22 degC+/-2; relative humidity-42-45%) prior to the extraction of the sample. Matings were set up between rudhira heterzygotes (+/-) . Pregnant females were dissected at 9.5 dpc, embryo and yolk sac collected in separate tubes. Embryonic tail was used for genotyping. Samples with genotype +/+ were used as control and -/- were used as mutant.

extract_protocol: Implantations of pregnant female mice at E 9.5 were obtained; embryos and yolk sacs were separated, control (+/+) and mutant (-/-) were identified by genotyping.   and subjected for further analysis. Total RNA extracted from each by Trizol method. RNA integrity and quality were analysed by 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: yolk sac

tag: genotype

value: rudhira mutant


title: HK-2 cells, Kbr, ld, t24h, biological rep 1

city: Dublin

last: O'Gaora

address: Belfield

institute: UCD


title: rudhira mutant yolk sac_exon 6 deletion_1

description:
Sample_7YS676(YS)
growth retarded, abnormal vascularization


title: rudhira mutant yolk sac_exon 6 deletion_1_rep2

description:
Sample_7YS676_REP(YS)
growth retarded, abnormal vascularization


title: rudhira mutant embryo_ exon 6 deletion_2_rep2

description:
Sample_6E669_REP(Emb)
growth retarded, abnormal vascularization

source_name: Embryo 9.5 dpc

value: embryo


title: rudhira mutant embryo_ exon 6 deletion_1_rep2

description:
Sample_5E676_REP(Emb)
growth retarded, abnormal vascularization


title: HK-2 cells, Kbr, hd, t48h, control sample, biological rep 2

value: control


title: wild type yolk sac_2_rep2

description:
Sample_4YS682_REP(YS)
growth normal, tissue vascularized

value: wildtype


title: rudhira mutant embryo_ exon 6 deletion_1

description:
Sample_5E676(Emb)
growth retarded, abnormal vascularization


title: rudhira mutant embryo_ exon 6 deletion_2

description:
Sample_6E669(Emb)
growth retarded, abnormal vascularization


title: wild type yolk sac_1

description:
Sample_3YS679(YS)
growth normal, tissue vascularized


title: wild type embryo 2

description:
Sample_2E682(Emb)
growth normal, tissue vascularized


title: wild type embryo 2_rep2

description:
Sample_2E682_REP(Emb)
growth normal, tissue vascularized


title: HK-2 cells, Kbr, hd, t24h, control sample, biological rep 3


title: HK-2 cells, Kbr, hd, t24h, control sample, biological rep 2


title: wild type yolk sac_1_rep2

description:
Sample_3YS679_REP(YS)
growth normal, tissue vascularized


title: HK-2 cells, Kbr, hd, t48h, control sample, biological rep 1


title: wild type yolk sac_2

description:
Sample_4YS682(YS)
growth normal, tissue vascularized


title: wild type embryo 1

description:
Sample_1E679(Emb)
growth normal, tissue vascularized


title: HK-2 cells, Kbr, hd, t48h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t48h

value: high


title: HK-2 cells, Kbr, hd, t24h, control sample, biological rep 1

value: immortalized human renal proximal tubular epithelial cells


title: wild type embryo 1_rep2

description:
Sample_1E679_REP(Emb)
growth normal, tissue vascularized


title: HK-2 cells, Kbr, hd, t48h, biological rep 1


title: HK-2 cells, Kbr, hd, t24h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with high dose Kbr, t24h


title: HK-2 cells, Kbr, hd, t48h, biological rep 3


title: HK-2 cells, Kbr, hd, t24h, biological rep 1


title: HK-2 cells, Kbr, hd, t24h, biological rep 2


title: HK-2 cells, Fk, t48h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Fk, t48h


title: Ts2Yah WT 34925

city: Strasbourg

first: Veronique

last: BRAULT

address: 1 rue Laurent Fries

institute: IGBMC

description: SAMPLE 23

data_processing: Quantile normalization

source_name: gastrocnemius muscle

label_protocol: Biotinylated cDNA were prepared from total RNAs

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.

value: Ts2Yah WT (diploid control)

value: gastrocnemius muscle


title: Ts2Yah WT 34723

description: SAMPLE 21


title: HK-2 cells, Fk, t48h, control sample, biological rep 2

first: Peadar


title: HK-2 cells, Fk, t48h, control sample, biological rep 1


title: Ts2Yah WT 34561

description: SAMPLE 19


title: HK-2 cells, Fk, t12h, control sample, biological rep 3

source_name: Human renal proximal tubular epithelial cells, control for Fk, t12h

value: 12 hrs


title: Ts2Yah Dup 34661

description: SAMPLE 17

value: Ts2Yah Dup (trisomic)


title: Ms3Yah WT 37075

description: SAMPLE 12

value: Ms3Yah WT (diploid control)


title: Ts2Yah Dup 34725

description: SAMPLE 18


title: Ts2Yah Dup 34662

description: SAMPLE 14


title: HK-2 cells, Fk, t12h, control sample, biological rep 2


title: Ts2Yah Dup 34558

description: SAMPLE 16


title: Ts2Yah Dup 34730

description: SAMPLE 15


title: HK-2 cells, Fk, t48h, biological rep 2

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t48h

value: Fk


title: Ts2Yah WT 34923

description: SAMPLE 22


title: HK-2 cells, Fk, t48h, biological rep 3


title: HK-2 cells, Fk, t12h, control sample, biological rep 1


title: HK-2 cells, Fk, t48h, biological rep 1


title: Ts2Yah WT 34731

description: SAMPLE 20


title: Ms3Yah Del 37074

description: SAMPLE 6

value: Ms3Yah Del (monosomic)


title: Ms3Yah WT 37040

description: SAMPLE 10


title: Ms3Yah WT 37145

description: SAMPLE 8


title: Ms3Yah WT 37041

description: SAMPLE 11


title: Ts2Yah Dup 34498

description: SAMPLE 13


title: HK-2 cells, Fk, t12h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with Fk, t12h


title: rudhira mutant yolk sac_exon 6 deletion_2_rep2

description:
Sample_8YS669_REP(YS)
growth retarded, abnormal vascularization


title: HK-2 cells, Fk, t12h, biological rep 2


title: Ms3Yah WT 37146

description: SAMPLE 9


title: Ms3Yah WT 37094

description: SAMPLE 7


title: Ms3Yah Del 37072

description: SAMPLE 5


title: Ms3Yah Del 37039

description: SAMPLE 4


title: Ms3Yah Del 37448

description: SAMPLE 3


title: Ms3Yah Del 37148

description: SAMPLE 2


title: Ms3Yah Del 37038

description: SAMPLE 1


title: HK-2 cells, Di, t12h, control sample, biological rep 2

source_name: Human renal proximal tubular epithelial cells, control for Di, t12h


title: HK-2 cells, Di, t48h, control sample, biological rep 1

source_name: Human renal proximal tubular epithelial cells, control for Di, t48h


title: HK-2 cells, Di, t48h, control sample, biological rep 2


title: wild type 2996

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

description: 2996, wild type

scan_protocol: Standard Illumina scan protocol

data_processing: Data extraction was done for all beads individually, and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. The data was quantile normalized using R (function normalize.quantiles from library preprocessCore).

source_name: brain SVZ

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies) for Illumina arrays.

growth_protocol: In vivo mice primary tissue

extract_protocol: Laser microdissection  of mouse SVZ

value: wild type

value: 8 weeks

value: SVZ, Brain


title: HK-2 cells, Di, t12h, control sample, biological rep 1

extract_protocol: Total RNA was isolated using the Qiagen RNeasy mini kit.


title: wild type c1 repeat 2

description: c1, repeat2, wild type


title: wild type 3164

description: 3164, wild type


title: HK-2 cells, Fk, t12h, biological rep 1


title: Tlx overexpressed 3155

description: 3155,TLX overexpress

value: Tlx overexpressing


title: HK-2 cells, Di, t48h, control sample, biological rep 3

value: 48 hrs


title: wild type 2989

description: 2989, wild type


title: Tlx overexpressed 3157

description: 3157,TLX overexpress


title: Tlx overexpressed 3163

description: 3163,TLX overexpress


title: Tlx overexpressed 2995

description: 2995,TLX overexpress


title: wild type c2

description: c2, wild type


title: HK-2 cells, Di, t48h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with Di, t48h

value: Di


title: noninducible_0drug_nomif_rep1_total

city: Minneaplois

first: Matthew

last: Parker

state: MINNESOTA

address: 420 Delaware St. SE

department: Department of Medicine

institute: University of Minnesota

description: total RNA

data_processing: The data was normalized using the robust spline normalization (RSN) and log2 transformed in the statistical R package

source_name: noninducible 0 drug nomif  total

label_protocol: Illumina Total Pre-96 RNA Amp. Kit

extract_protocol: Cells were treated with cycloheximide to immobilize ribosomes on RNA. Total RNA was isolated using Tri Reagent. Polysome-associated RNA was obtained by centrifuging samples on sucrose gradient, fractionating, and isolating using Tri Reagent.

value: NIH 3T3

value: non-inducible

tag: fraction

value: total

tag: dose 4ei-1

tag: dose 4ei-4

tag: mifepristone treatment

value: FALSE

tag: replicate

tag: processing batch


title: HK-2 cells, Di, t48h, biological rep 2

value: immortalized human renal proximal tubular epithelial cells


title: noninducible_0drug_mif_rep3_total

description: total RNA

source_name: noninducible 0 drug mif  total

value: TRUE


title: HK-2 cells, Di, t48h, biological rep 1


title: wild type c1 repeat 1

description: c1, repeat1, wild type

tag: tissue


title: noninducible_0drug_nomif_rep1_heavy

description: polysome-associated RNA

source_name: noninducible 0 drug nomif  heavy

tag: cell type

value: heavy


title: noninducible_0drug_mif_rep1_total

description: total RNA


title: HK-2 cells, Di, t12h, control sample, biological rep 3

value: control

value: 12 hrs


title: HK-2 cells, Di, t12h, biological rep 3

source_name: Human renal proximal tubular epithelial cells, treated with Di, t12h


title: noninducible_0drug_mif_rep1_heavy

description: polysome-associated RNA

source_name: noninducible 0 drug mif  heavy


title: noninducible_0drug_mif_rep2_heavy

description: polysome-associated RNA


title: noninducible_0drug_mif_rep2_total

description: total RNA


title: HK-2 cells, Di, t12h, biological rep 1


title: inducible_200druganalog_mif_rep3_heavy

description: polysome-associated RNA

source_name: inducible 200 druganalog mif  heavy


title: inducible_200druganalog_mif_rep1_total

description: total RNA

source_name: inducible 200 druganalog mif  total