title: islets of non-pregant PRLR+/+ mice, biological rep 3

description: Gene expression data from islets of PRLR+/+ mice that were non-pregnant

source_name: mouse islets, PRLR+/+, 129Sv, NP


title: High (162 ug) Day 28 Sample 158

status: Public on Mar 31 2015

type: RNA

city: Ottawa

first: Mainul

last: Husain

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

description: Biological replicate Day 28, Treated

hyb_protocol: Each experimental cRNA sample was mixed with an equimolar amount of reference cRNA and was hybridized to Agilent mouse 4×44 oligonucleotide microarrays (Agilent Technologies Inc., Mississauga, ON, Canada) for 17 h in a hybridization chamber at 60C with a rotation speed of 10 rpm.

scan_protocol: Arrays were washed according to manufacturer’s protocols (Agilent Technologies Inc., Mississauga, ON, Canada) and scanned on an Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1.). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

molecule: total RNA

organism: Mus musculus

source_name: Heart

label_protocol: Total RNA (250 ng) samples from individual mice (n = 5-6 per experimental and control group) and from universal reference total RNA (Agilent Technologies, Inc., Mississauga, ON, Canada) were used to synthesize double-stranded cDNA and cyanine labelled cRNA using Quick Amp Labeling Kit (Agilent Technologies Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Control and nano-TiO2 treated cRNAs were labelled with Cyanine 5-CTP, and reference RNAs were labelled with Cyanine 3-CTP using a T7 RNA polymerase in vitro transcription kit (Agilent Technologies Inc., Mississauga, ON, Canada) and purified using RNeasy Mini kits (Qiagen, Mississauga, ON, Canada).

growth_protocol: Five-to-seven week old female C57BL/6 mice were purchased from Taconic (Ry, Denmark) and were acclimatized for 1-3 weeks prior to the commencement of the experiment. Mice were maintained in groups in polypropylene cages with sawdust bedding and enrichment, at 20-22°C room temperature and relative humidity of 40-60% with a 12 h light-to-dark cycle. All mice received food and water ad libitum throughout the experiment. All animal experiments were approved by the Danish “Animal Experiments Inspectorate” and performed according to their guidelines for ethical conduct and care of animals in research.

extract_protocol: Total RNA was isolated from random sections of the left lungs (n = 5-6 per group) using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Plus Mini kits (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instruction. Total RNA concentration was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and RNA quality and integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Mississauga, ON, Canada) according to the manufacturer’s instruction. Samples with RNA integrity numbers of 7 and above were used to conduct microarray and qPCR experiments.

treatment_protocol: Naïve C57BL/6 mice were flushed twice with 0.6 ml of 0.9% NaCl to obtain approximately 1 ml of bronchoalveolar lavage fluid (BAL). BAL was centrifuged at 400 g for 10 min at 4°C to remove cells. The supernatant was used in the dispersant liquid. A total of 4.05 mg of nano-TiO2 was suspended in 1 ml of MilliQ water containing 0.9% NaCl and 10% v/v acellular BAL. Particle suspensions were prepared by sonicating the samples using a S-450D sonifier (Branson Ultrasonics Corp., Danbury, CT, USA) at 10% amplitude for a total of 16 minutes on ice with alternating 10 s pulses and pauses. One dilution of nano-TiO2 were prepared and used in this experiment: 162 µg. Control vehicle solutions were prepared without the nano-TiO2 (MilliQ water containing 90% of 0.9% NaCl and 10% acellular BAL fluid). The dose162 μg/mouse equals 15 working days at the Danish occupational exposure level for TiO2 (6.0 mg Ti/m3 ~ 9.75 mg TiO2/m3), respectively. Each treatment group consisted of a minimum of 5 animals. Mice in the experimental groups received a single intratracheal instillation of 162 µg of nano-TiO2 in a 40 µl suspension, followed by 150 μl air with a 250 µl SGE glass syringe (250F-LT-GT, MicroLab, Aarhus, Denmark). Intratracheal instillation was performed at 37 ºC on heating plates, under anesthesia using Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml from Janssen Pharma) and Dormicum® (Midazolam 5 mg/mL from Roche). Control mice received 40 µl of dispersant vehicle only. Following instillation, mice were under observation until they recovered from anaesthesia. Mice were allowed to recover for 24 hours and 28 days following instillation before sacrificing under anaesthesia (Hypnorm/Dormicum). Blood, BAL fluid and tissues were collected. Heart tissues from each experimental and control mice were cut into small pieces, and stored in cryogenic vials and snap frozen immediately in liquid nitrogen. All tissues were stored at -80°C until analysis.

tag: strain

tag: tissue

value: heart

tag: treatment

tag: sampleID

tag: treatment type

value: High

tag: dose

tag: time point (day)

source_name: Agilent Universal Mouse Reference RNA (UMRR)

tag: sample type

value: Reference 11 mouse cell lines


title: High (162 ug) Day 1 Sample 126

description: Biological replicate Day 1, Treated


title: High (162 ug) Day 28 Sample 159

description: Biological replicate Day 28, Treated


title: islets of  PRLR+/+ mice day 9.5 of pregnancy, biological rep 2

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

description: Gene expression data from islets of PRLR+/+ mice that were pregnant (day 9.5)

hyb_protocol: Labeled DNA was hybridized to the array during 16h at 45°C

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: All image files were generated using the Affymetrix GeneChip command console (AGCC). The raw data (.CEL files) were preprocessed with robust multichip analysis using the implementation in the aroma.affymetrix R package.

label: biotin

source_name: mouse islets, PRLR+/+, 129Sv, P9.5

label_protocol: according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA). Briefly, in the first cycle, double stranded cDNA was prepared with random hexamers tagged with a T7 promoter sequence followed by the generation of cRNA using the GeneChip WT Synthesis and Amplification kit (Affymetrix). cRNA concentration after cleanup was measured with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW). In the second cycle, sense oriented single-stranded DNA containing dUTP is generated and the concentration is, after cleanup, measured using the nanodrop. The cRNA is hydrolysed and the single stranded DNA is fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) (GeneChip WT terminal Labeling kit, Affymetrix). The quality of fragmentation (fragments should be between 40 and 70 nucleotides) is checked on the bioanalyzer (Agilent, Waldbronn, Germany). The fragmented DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix).

extract_protocol: The absolute RNA microprep kit of Strategene was used to extract total RNA according to the manufacturer's instructions. The total RNA quantity and quality was determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DW) and the 2100 Bioanalyzer (Agilent, Waldbronn, Germany), respectively. Total RNA profiles of all tested samples were similar with sharp 18S and 28S rRNA peaks on a flat baseline.

tag: pregnancy day

value: pancreatic islets

tag: genetic background

tag: genotype

value: PRLR WT


title: High (162 ug) Day 28 Sample 157

description: Biological replicate Day 28, Treated


title: islets of  PRLR-/- mice day 9.5 of pregnancy, biological rep 1

description: Gene expression data from islets of PRLR-/- mice that were pregnant (day 9.5)

source_name: mouse islets, PRLR-/-, 129Sv, P9.5

value: PRLR KO


title: islets of  PRLR-/- mice day 9.5 of pregnancy, biological rep 3


title: islets of  PRLR-/- mice day 9.5 of pregnancy, biological rep 2


title: High (162 ug) Day 1 Sample 121

description: Biological replicate Day 1, Treated


title: islets of non-pregant PRLR-/- mice, biological rep 2

description: Gene expression data from islets of PRLR-/- mice that were non-pregnant

source_name: mouse islets, PRLR-/-, 129Sv, NP

value: NP


title: High (162 ug) Day 1 Sample 122

description: Biological replicate Day 1, Treated


title: Control Day 28 Sample 589

description: Biological replicate Day 28, Control

value: Control


title: Control Day 28 Sample 590

description: Biological replicate Day 28, Control


title: Control Day 28 Sample 587

description: Biological replicate Day 28, Control


title: Control Day 28 Sample 586

description: Biological replicate Day 28, Control


title: islets of non-pregant PRLR+/+ mice, biological rep 1


title: High (162 ug) Day 1 Sample 123

description: Biological replicate Day 1, Treated


title: High (162 ug) Day 28 Sample 160

description: Biological replicate Day 28, Treated


title: islets of non-pregant PRLR-/- mice, biological rep 3


title: Control Day 1 Sample 552

description: Biological replicate Day 1, Control


title: islets of non-pregant PRLR-/- mice, biological rep 1


title: Control Day 28 Sample 585

description: Biological replicate Day 28, Control


title: Control Day 1 Sample 550

description: Biological replicate Day 1, Control


title: Control Day 1 Sample 548

description: Biological replicate Day 1, Control


title: High (162 ug) Day 1 Sample 124

description: Biological replicate Day 1, Treated


title: HBE_HLA_1

city: Greifswald

first: Joerg

last: Mostertz

address: F.-L.-Jahnstr 15

department: Competence Center Functional Genomics

country: Germany

institute: Greifswald University

description: Gene expression data from 16HBE14o- cells treated with alpha-toxin.

hyb_protocol: Biotinylated sense-strand DNA was then hybridized onto the Affymetrix GeneChip Human Gene 1.0 ST arrays for 16 h. Arrays were washed and stained using the Fluidics Station 450.

scan_protocol: Scanning was performed by GeneChip Scanner 3000 7G (Affymetrix); raw CEL files were generated using the GCOS software. Quality assessment of all hybridizations was carried out by inspecting scan images and by reviewing external and endogenous controls using the Expression Console software (Affymetrix).

data_processing:
Data analysis was carried out using Rosetta Resolver system for gene expression data analysis (Rosetta Bio software). In brief, the raw signals of the gene-specific probes were summarized using the Robust Multi-array Average algorithm and data transformation for array comparability was achieved by performing quantile normalization. Genes exhibiting significantly different expression on the RNA level were identified using the following cut-off criteria: one-way analysis of variance with subsequent Benjamini and Hochberg false discovery rate multiple-testing correction on pair-wise comparisons (ANOVA, p≤0.05), signal correction statistics (Ratio Builder, p≤0.05) and fold-change≥1.5-fold. Probe-set transformation into genes was performed by using the Rosetta Resolver transformation tool based on the Entrez Genes/Unigenes search engine (NCBI).
processed_data.txt: Columns A to C: Gene Identification; Columns D to J: Summarized Intensity signals; Column L & O: Fold Change, Column M,N and P, Q: p-value and post hoc p-value, respectively

organism: Homo sapiens

source_name: cell line 16HBE14o-

label_protocol: For each sample, 200 ng of total RNA was reverse transcribed into cDNA, amplified, and in vitro transcribed to cRNA. Sense-strand cDNA was generated from 10 µg of purified cRNA using random primers, followed by fragmentation and labelling using 5.5 µg of purified sense-strand DNA.

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen). RNA was purified using the RNA Clean-Up and Concentration Micro Kit (Norgen) and concentrations were measured using a ND-1000 spectrophotometer (Thermo Fisher Scientific Inc). RNA integrity was validated by means of the lab-on-chip capillary electrophoresis technology (Bioanalyzer 2100, Agilent Technologies). Only RNA samples with an RNA integrity number (RIN)>9.5 [34], 260/280 nm≥1.8, 260/230 nm≥1.9 were used for microarray analyses.

tag: origin

value: human bronchium

tag: cell line

tag: condition

value: alpha-toxin treatment


title: islets of non-pregant PRLR+/+ mice, biological rep 2


title: Control Day 28 Sample 588

description: Biological replicate Day 28, Control


title: Control Day 1 Sample 549

description: Biological replicate Day 1, Control


title: HBE_KO_2

description: Gene expression data from 16HBE14o- cells treated as control.

value: control


title: Sc1 vs Sc2

status: Public on Mar 30 2015

type: genomic

city: Paterna (Valencia)

first: Laura

last: Pérez Través

address: Avda Catedrático Agustín Escardino

country: Spain

institute: IATA

description: Duplicate arrays and Cy5-dCTP and Cy3-dCTP dye-swap assays

hyb_protocol: Array competitive genomic hybridization (aCGH) was performed using a double-spotted array containing 6,240 ORFs of Saccharomyces cerevisiae plus control spots totaling 6.4 K (Microarray Centre, University Health Network, Toronto, Canada). New microarrays were pre-treated for one hour at 65°C with pre-hybridization solution (7.5 ml 20× SSC, 0.5 ml 10% SDS, 0.5 ml 10 mg/ml bovine serum albumin in 50 ml final volume). Pre-hybridization solution was washed during 15 s in mili-Q H2O, 2 s in 2-propanol, 2 s in milli-Q H2O and dried by centrifugation at 1200 rpm, 10 min. Microarrays were treated with hybridization solution (15μl SSC, 0.6μl 10% SDS, 6μl 1 mg/ml salmon DNA and DNA labelled in 60μl final volume) at 95°C for 1 min and at room temperature for 5 min before DNA hybridization. Hybridization was performed for 18 h in chamber at 65°C.

scan_protocol: Microarray scanning was carried out using a GenePix Personal 4100A scanner (Axon Instruments/Molecular Devices Corp., USA).

data_processing: Microarray images and raw data were produced using the GenePix Pro 6.1 software (Axon Instruments/Molecular Devices Corp.) and the background was subtracted by applying the local feature background median option. M-A plots (M = Log2 ratios; A = log2 of the product of intensities) were represented in order to evaluate if the ratio data were intensity-dependent.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: 2μg was labelled using BioPrime Array CGH Genomic Labelling System (Invitrogen, California,USA). Unincorporated label was removed using MinElute PCR Purification Kit (Qiagen, Germany). Equal amounts of labelled DNA from the strains to be compared were used as probes for microarray hybridization.

extract_protocol: Total DNA, extracted as described in Querol et al. [15], was resuspended in 50μl of de-ionized water and digested with endonuclease Hinf I (Roche Applied Science, Germany), according to the manufacturer’s instructions, to fragments of an average length of 0.25 to 8 kbp. Each sample was purified using High pure PCR Product Purification Kit (Roche Applied Science, Germany)

treatment_protocol: Industrial cultivation and drying were performed according to the Laboratory of Research and Development (Lallemand S.A.S.) standard protocols.

value: Parental strain 1

value: Parental strain 2


title: S9_HLA_2

description: Gene expression data from S9 cells treated with alpha-toxin.

source_name: cell line S9


title: S9_KO_2

description: Gene expression data from S9 cells treated as control.


title: wt vs. scl15-1, Rep 3

city: Saskatoon

first: Dwayne

last: Hegedus

address: 107 Science Place

institute: Agriculture Canada

description: dyeswap 3

hyb_protocol: After fragmentation of the labelled antisense RNA with Ambion's fragmentation buffer (Applied Biosystems, Foster City, CA, USA), 45 µl of DIG Easy Hyb solution (Roche, USA) and 3 µl of liquid block buffer (GE Healthcare, Little Chalfont, Buckinghamshire, UK) were added and heated to 65°C for 2 min. Samples were hybridized at 37°C for 16-18 h using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Image analysis and feature extraction were performed with ArrayPro Analyzer software (Media Cybernetics, Bethesda, MD, USA).

data_processing:
Background that surrounded each spot was subtracted from the data for each spot. Data were imported into the Limma (Linear Models for Microarray data) package in R version 3.1.3 for normalization.
For statistical analysis, gene expression data had to pass the false discovery rate (FDR) multiple testing corrections. An FDR-adjusted P-value cutoff of 0.05 was chosen, and differentially expressed genes were selected if they exhibited at least a two-fold difference in normalized signals across all replicate experiments.

organism: Arabidopsis thaliana

source_name: wild type seedlings

label_protocol: cDNA probes were synthesized and labelled with Cy3- or Cy5-dCTP (GE Healthcare, Life Sciences) using CyDye Post-Labelling Reactive Dye Packs (GE Healthcare, Little Chalfont, Buckinghamshire, UK).

growth_protocol: Seeds sterilized and germinated on plates with half-strength MS medium. Seedlings harvested after 14 days.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen).

tag: cultivar

value: Columbia

tag: genotype/variation

value: wild type

tag: age

value: 14 days

value: seedlings

source_name: scl15-1 mutant seedlings

value: SALK_110871 mutant


title: scl15-1 vs. wt, Rep 1

description: biorep 1


title: S9_HLA_1


title: R2 IVo vs R2 IVo LSA

hyb_protocol: Array competitive genomic hybridization (aCGH) was performed using a stable hybrid strain before and after processing as ADY. Array competitive genomic hybridization (aCGH) was performed using a double-spotted array containing 6,240 ORFs of S. cerevisiae plus control spots totaling 6.4 K (Microarray Centre, University Health Network, Toronto, Canada). New microarrays were pre-treated for one hour at 65°C with pre-hybridization solution (7.5 ml 20× SSC, 0.5 ml 10% SDS, 0.5 ml 10 mg/ml bovine serum albumin in 50 ml final volume). Pre-hybridization solution was washed during 15 s in mili-Q H2O, 2 s in 2-propanol, 2 s in milli-Q H2O and dried by centrifugation at 1200 rpm, 10 min. Microarrays were treated with hybridization solution (15μl SSC, 0.6μl 10% SDS, 6μl 1 mg/ml salmon DNA and DNA labelled in 60μl final volume) at 95°C for 1 min and at room temperature for 5 min before DNA hybridization. Hybridization was performed for 18 h in chamber at 65°C.

data_processing: Microarray images and raw data were produced using the GenePix Pro 6.1 software (Axon Instruments/Molecular Devices Corp.) and the background was subtracted by applying the local feature background median option. M-A plots (M = Log2 ratios; A = log2 of the product of intensities) were represented in order to evaluate if the ratio data were intensity-dependent. The normalization process and filtering were done with Acuity 4.0 (Axon Instruments/Molecular Devices Corp.). Raw data were normalized by the ratio-based option. Features with artifacts or flagged as bad were removed from the analysis. Replicates were averaged after filtering.

source_name: R2 IVo hybrid before ADY production

tag: strain

value: Intraspecific hybrid

source_name: R2 IVo hybrid after ADY production (R2 IVo LSA)


title: HBE_KO_1


title: Control Day 1 Sample 547

description: Biological replicate Day 1, Control

tag: tissue

value: heart

value: Reference 11 mouse cell lines


title: R2 IVo vs Sc2

source_name: R2 IVo


title: scl15-1 vs. wt, Rep 2

description: biorep 2


title: R2 IVo vs Sc1


title: wt vs. scl15-1, Rep 2

description: dyeswap 2


title: HBE_HLA_2


title: wt vs. scl15-1, Rep 1

description: dyeswap 1


title: S9_KO_1


title: tFL-48

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

country: USA

institute: UNMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping console software. Log2 intensities were generated from genotyping console were exported for further processing using the DNAcopy package for R.

source_name: tumor biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from FL and tFL tissue using the Qiagen AllPrep DNA/RNA kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: tumor type

value: transformed follicular lymphoma


title: scl15-1 vs. wt, Rep 3

description: biorep 3


title: tFL-43


title: tFL-62


title: tFL-55


title: tFL-60


title: tFL-13


title: tFL-53


title: tFL-44


title: tFL-14


title: tFL-224


title: tFL-57


title: tFL-42


title: tFL-41


title: tFL-46


title: tFL-219


title: tFL-49


title: tFL-50


title: tFL-56


title: tFL-47


title: tFL-221


title: tFL-15


title: tFL-54


title: tFL-52


title: tFL-223


title: tFL-51


title: tFL-59


title: tFL-218


title: tFL-58


title: tFL-179


title: tFL-177


title: tFL-176


title: tFL-175


title: tFL-45


title: tFL-174


title: tFL-172


title: tFL-173


title: tFL-164


title: tFL-165


title: tFL-166


title: tFL-168


title: tFL-40


title: tFL-171


title: tFL-167


title: tFL-34


title: tFL-170


title: tFL-33


title: tFL-25


title: tFL-24


title: tFL-37


title: tFL-36


title: tFL-61


title: tFL-39


title: tFL-23


title: tFL-20


title: tFL-28


title: tFL-38


title: tFL-29


title: tFL-35


title: tFL-32


title: tFL-27


title: tFL-19


title: tFL-16


title: tFL-30


title: tFL-18


title: tFL-7


title: tFL-21


title: tFL-12


title: tFL-5


title: tFL-6


title: tFL-10


title: tFL-26


title: tFL-8


title: tFL-9


title: tFL-11


title: tFL-17


title: FL-1

value: follicular lymphoma


title: FL-9


title: FL-220


title: tFL-4


title: tFL-3


title: FL-218


title: FL-29


title: FL-3


title: FL-217


title: FL-222


title: FL-6


title: FL-216


title: tFL-1


title: FL-214


title: DLD-1/DKK1 cells treated with DOX, DKK1-2

city: Madrid

first: beatriz

last: Morte

address: C/arturo Duperier 4

institute: CIBERER

description: DLD-1/DKK1 cells treated with DOX (10mg/ml)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is Fluidics  Station 450.

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Data were processed using the R platform and several packages from the Bioconductor project.

source_name: colon cancer cell line

label_protocol: Double-stranded cDNA synthesis and in vitro  transcription to generated cRNA was carried out using a commercial kit of Affymetrix (Sense Target Labeling kit).

growth_protocol: All cell lines used in this study were maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum and 2 mM L-glutamine (Invitrogen, Paisley, UK).

extract_protocol: Total cellular RNA was isolated using the Rneasy Kit (Qiagen).

treatment_protocol: For transduction of DLD1 cells, lentiviruses at a multiplicity of infection of 10-60 were added to the culture medium in the presence of 8  g/ml polybrene (Sigma) for 8 h, typically yielding more than 95% transduced (GFP-positive) cells.

tag: treatment

value: colon cancer cells transfected with DKK1


title: DLD-1/DKK1 cells treated with DOX, DKK1-1


title: FL-4


title: FL-219


title: FL-224


title: tFL-2


title: FL-7


title: DLD-1/DKK1 cells treated with DOX, DKK1-3


title: FL-23


title: FL-10


title: FL-221


title: FL-215


title: FL-223


title: DLD-1/Mock cells treated with DOX, control-2

description: DLD-1/Mock cells treated with DOX (10mg/ml)

value: colon cancer cells mock


title: DLD-1/Mock cells treated with DOX, control-3


title: FL-212


title: FL-203


title: FL-213


title: FL-211


title: DLD-1/Mock cells treated with DOX, control 1


title: FL-205


title: FL-210


title: FL-208


title: FL-207


title: FL-209


title: FL-206


title: FL-192


title: FL-202


title: FL-204


title: FL-200


title: FL-191


title: FL-197


title: FL-190


title: FL-194


title: FL-196


title: FL-201


title: FL-193


title: FL-188


title: FL-199


title: FL-195


title: FL-184


title: FL-189


title: FL-185


title: FL-182


title: FL-186


title: FL-187


title: FL-183


title: FL-179


title: FL-178


title: FL-180


title: FL-198


title: FL-174


title: FL-176


title: FL-177


title: FL-30


title: FL-173


title: FL-25


title: FL-181


title: siCtrl treated cells 0h rep 3 (basal)

city: New York

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: siCtrl 0h-3

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Data was analysed using Genespring GX12.5 . To analyze gene expression changes during stimulation, raw data were subject to quantile normalization and baseline transformation was performed to the median of all 9 samples

source_name: A549 cells

label_protocol: Biotin-labeled RNA was prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems)

growth_protocol: Standard culture techniques

extract_protocol: QIAGEN Rneasy mini kit

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or Xrn2 siRNA (L-017622-01-0010, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions and cells were used for further experiments 48 hours post intransfection.RNA and protein levels of Xrn2 were quantified to determine knockdown efficiency. Note: This experiment was done in parallel with the experiments described in GSE52933 and GSE52932 and share the same Untransfected and siCtrl treated control cells.

value: Control siRNA

tag: infection

value: no infection


title: siXrn2 treated cells 0h rep 3 (basal)

description: siXrn2 0h-3

value: Xrn2 siRNA


title: siXrn2 treated cells 0h rep 1 (basal)

description: siXrn2 0h-1


title: FL-171


title: siCtrl treated cells 0h rep 2 (basal)

description: siCtrl 0h-2


title: siCtrl treated cells 4h rep 3

description: siCtrl 4h-3

data_processing: Data was analysed using Genespring GX12.5 . To analyze gene expression changes during stimulation, raw data were subject to quantile normalization and baseline transformation was performed to the median of unstimulated samples of the corresponding siRNA treatment.

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or Xrn2 siRNA (L-017622-01-0010, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions. 48 hours post transfection, the cells were infected with the Influenza A/Puerto Rico/8/34(ΔNS1) strain at an multiplicity of infection of 3. Wells of uninfected cells were used as controls for infection. Cells were collected for further processing 4 hours post infection. RNA and protein levels of Xrn2 were quantified to determine knockdown efficiency. Note: This experiment was done in parallel with the experiments described in GSE52933 and GSE52932 share the same UT and siCtrl treated controls, and hence share the same raw values for those two conditions

value: A/PR/8/34(ΔNS6) Infection


title: siXrn2 treated cells 4h rep 2

description: siXrn2 4h-2

value: A/PR/8/34(ΔNS8) Infection


title: siCtrl treated cells 4h rep 2

description: siCtrl 4h-2

value: A/PR/8/34(ΔNS5) Infection


title: siXrn2 treated cells 4h rep 1

description: siXrn2 4h-1

value: A/PR/8/34(ΔNS7) Infection


title: siXrn2 treated cells 0h rep 2 (basal)

description: siXrn2 0h-2


title: Untransfected cells 0h rep 2 (basal)

description: UT 0h-2

value: no siRNA


title: FL-175


title: siXrn2 treated cells 4h rep 3

description: siXrn2 4h-3

value: A/PR/8/34(ΔNS9) Infection


title: siCtrl treated cells 0h rep 1 (basal)

description: siCtrl 0h-1


title: Untransfected cells 0h rep 1 (basal)

description: UT 0h-1


title: Untransfected cells 4h rep 3

description: UT 4h-3

value: A/PR/8/34(ΔNS3) Infection


title: Untransfected cells 0h rep 3 (basal)

description: UT 0h-3


title: siCtrl treated cells 4h rep 1

description: siCtrl 4h-1

value: A/PR/8/34(ΔNS4) Infection


title: FL-170


title: FL-167


title: FL-172


title: FL-24


title: siXrn2 treated cells 0h rep 2

description: siXrn2 0h-2


title: FL-169


title: Untransfected cells 4h rep 2

description: UT 4h-2

value: A/PR/8/34(ΔNS2) Infection


title: FL-168


title: FL-165


title: FL-166


title: siXrn2 treated cells 0h rep 1

description: siXrn2 0h-1


title: Untransfected cells 0h rep 3

description: UT 0h-3


title: siCtrl treated cells 0h rep 2

description: siCtrl 0h-2


title: siCtrl treated cells 0h rep 3

description: siCtrl 0h-3


title: siXrn2 treated cells 0h rep 3

description: siXrn2 0h-3


title: Untransfected cells 4h rep 1

description: UT 4h-1

value: A/PR/8/34(ΔNS1) Infection


title: Untransfected cells 0h rep 2

description: UT 0h-2


title: FL-160


title: siCtrl treated cells 0h rep 1

description: siCtrl 0h-1


title: FL-164


title: Untransfected cells 0h rep 1

description: UT 0h-1


title: FL-162


title: FL-27


title: FL-157


title: FL-163


title: 5786057034_E

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

hyb_protocol: 750 ng biotinylated cRNA was used for hybridization using the Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring

source_name: CD14+ cells

label_protocol: Biotinylated cRNA were prepared with the Illumina®TotalPrep™ RNA amplification kit (Ambion)for Illumina arrays

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were freshly isolated from heparinized venous blood using Ficoll-Hypaque

extract_protocol: For gene expression analyses total RNA was extracted from monocytes by with RNeasy Mini kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: CD14+ cells were obtained immuno-labelling PBMCs with CD14positive selection kits following the manufacturer’s specifications

tag: disease status

value: Healthy Blood Donor

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)


title: FL-159

value: follicular lymphoma


title: 5786057034_G


title: 5786057034_C


title: 5786057034_I


title: 5786057034_B


title: FL-26


title: 5786057055_L


title: FL-161


title: FL-158


title: 5786057055_H


title: 5786057055_I


title: FL-155


title: WT_2nd_neurosphere _24h_DMSO_rep2

city: Berkeley

first: Chenyan

last: Ma

state: CA

address: 230E Li Ka Shing Center

institute: UC Berkeley

description: Gene expression profile of 2nd neurospheres from wildtype mice hippocampus treated with DMSO for 24 hours

hyb_protocol: Each slide was hybridized with 1.65 mg Cy3-labeled cRNA using Gen Expression Hybridization Kit (Cat#5188-5242, Agilent technologies)in Hybridization Oven (Cat#G2545A, Agilent technologies) at 65°C, 10rpm for 17 hours. Then slides were washed in staining dishes (Cat#121, Thermo Shandon) with Gene expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies) with default settings. Dye channel: Green, scan resolution=5 mm, PMT 100%, 10%, 16 bit.

data_processing: The scanned images were analysed with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm using Gene Spring Software 11.0 (Agilent technologies)

source_name: 2nd neurosphere from WT adult mice, treated with DMSO for 24h

label_protocol: Total RNA was amplified and labeled by Low input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies), followed the manufacturer's instructions.

growth_protocol: Adult hippocampal neural stem cells were isolated by gradient centrifugation, seeded low adhension 6-well plate with Neurobasal A supplemented with B27 minus retinyl acetate, glutamax, penicillin/streptomycin, bFGF (10ng/ml), EGF(10ng/ml), PDGFbb(10ng/ml) and heparin (2 mg/ml). 7 to 9 days after seeding, primary neurospheres are dissociated and seeded again into low adhension 6-well plate at 5*10^4 cells/ml with NeurobasalA supplemented with B27 minus retinyl acetate, glutamax, penicillin/streptomycin, bFGF (20ng/ml), EGF(20ng/ml), and heparin (2 mg/ml).

extract_protocol: Total RNA was prepared with Trizol reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: WT and KO neurospheres were cultured for 6 days before harvest. DMSO- and resveratrol- treated neurospheres were cultured for 5 days followed by 24 hours DMSO and 10 mm resveratrol treatment.

value: WT

value: hippocampus

tag: developmental stage

value: 7 to 9 weeks

tag: gender

value: male

tag: agent

value: DMSO

value: secondary neurospheres


title: WT_2nd_neurosphere _24h_resveratrol_rep2

description: Gene expression profile of 2nd neurospheres from wildtype mice hippocampus treated with 10 mm resveratrol for 24 hours

source_name: 2nd neurosphere from WT adult mice, treated with 10 mm resveratrol for 24 hours

value: resveratrol


title: FL-156


title: FL-154


title: 5786057055_G


title: FL-153


title: WT_2nd_neurosphere _24h_resveratrol_rep1


title: FL-146


title: 5786057055_K

value: Affected IgAN


title: FL-149


title: FL-151


title: FL-148


title: FL-152


title: FL-145


title: 5786057055_D


title: sirt1_KO 2nd_neurosphere _6DIV_rep2

description: Gene expression profile of 2nd neurospheres from sirt1 KO mice hippocampus

source_name: 2nd neurosphere from sirt1 KO adult mice,cultured for 6 days

value: sirt1 KO


title: WT_2nd_neurosphere _24h_DMSO_rep1


title: FL-143


title: sirt1_KO 2nd_neurosphere _6DIV_rep1

value: female


title: FL-142


title: 5786057055_F


title: 5786057055_E


title: FL-147


title: FL-150


title: 5786057055_J


title: WT_2nd_neurosphere _6DIV_rep1

description: Gene expression profile of 2nd neurospheres from wildtype mice hippocampus

source_name: 2nd neurosphere from WT adult mice, cultured for 6 days


title: FL-138


title: FL-140


title: FL-144


title: 5786057055_C


title: FL-141


title: FL-137


title: 5786057055_A


title: FL-135


title: FL-136


title: FL-134


title: HCC_363T_CGH

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

country: China

institute: astrazeneca

hyb_protocol: Scanned on an Agilent  scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (v 9.1)

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

source_name: hepatocyte

label_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: Tumor tissues were collected after surgical resection and frozed for DNA extraction

extract_protocol: 2 µg of genomic DNA were primed with 5µl random DNA primer at 96°C for 5 min

treatment_protocol: Genomic DNA was extracted using Gentra Puregene Cell Kit (Qiagen)  following manufacturer’s instructions. QC process was performed using 1% agarose gel at 120V for 45min and single clear band with its size ~4000bp was defined as QC pass.

value: M

value: Tumor

value: hepatocyte

source_name: standard reference genomic DNA


title: FL-133


title: FL-132


title: 5786057055_B


title: FL-131


title: HCC_361T_CGH


title: FL-128


title: HCC_362T_CGH


title: siSetx treated cells 0h rep 1 (SETX reanalysis)

description: Replicate 1

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or SETX siRNA (23064, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions and cells were used for further experiments 48 hours post intransfection.RNA and protein levels of SETX were quantified to determine knockdown efficiency.

value: Setx siRNA

value: no infection


title: siSetx treated cells 0h rep 3 (SETX reanalysis)

description: Replicate 3


title: HCC_359T_CGH

value: F


title: HCC_360T_CGH


title: WT_2nd_neurosphere _6DIV_rep2

source_name: 2nd neurosphere from WT adult mice,cultured for 6 days


title: siSetx treated cells 0h rep 2 (SETX reanalysis)

description: Replicate 2


title: FL-129

value: follicular lymphoma


title: FL-127


title: siCtrl treated cells 0h rep 2 (SETX reanalysis)

description: Replicate 2

value: Control siRNA


title: FL-139


title: FL-126


title: FL-124


title: FL-130


title: Untransfected cells 0h rep 3 (SETX reanalysis)

description: Replicate 3

value: no siRNA


title: siCtrl treated cells 0h rep 3 (SETX reanalysis)

description: Replicate 3


title: HCC_358T_CGH


title: FL-125


title: HCC_357T_CGH


title: HCC_356T_CGH


title: FL-122


title: siCtrl treated cells 0h rep 1 (SETX reanalysis)

description: Replicate 1


title: HCC_355T_CGH


title: Untransfected cells 0h rep 2 (SETX reanalysis)

description: Replicate 2


title: FL-120


title: FL-119


title: Untransfected cells 0h rep 1 (SETX reanalysis)

description: Replicate 1


title: FL-121


title: FL-117


title: HCC_354T_CGH


title: HCC_353T_CGH


title: siSetx treated cells 4h rep 3 (SETX)

description: Replicate 3

treatment_protocol: A549 cells were transfected with either control siRNA (D-001810-10-05, Dharmacon) or SETX siRNA (23064, Dharmacon) pools using the Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen). Transfections were performed according to the manufacturer’s instructions. 48 hours post transfection, the cells were infected with the Influenza A/Puerto Rico/8/34(ΔNS1) strain at an multiplicity of infection of 3. Wells of uninfected cells were used as controls for infection. Cells were collected for further processing 4 hours post infection. RNA and protein levels of SETX were quantified to determine knockdown efficiency.

value: SETX siRNA

value: A/PR/8/34(ΔNS9) Infection


title: FL-118


title: HCC_353N_CGH

value: Adjacent normal


title: FL-123


title: FL-115


title: siSetx treated cells 4h rep 2 (SETX)

description: Replicate 2

value: A/PR/8/34(ΔNS8) Infection


title: FL-116


title: FL-113


title: FL-114


title: FL-111


title: Untransfected cells 4h rep 3 (SETX)

description: Replicate 3

value: A/PR/8/34(ΔNS3) Infection


title: siSetx treated cells 4h rep 1 (SETX)

description: Replicate 1

value: A/PR/8/34(ΔNS7) Infection


title: FL-108


title: FL-107


title: FL-109


title: FL-110


title: HCC_352T_CGH


title: siCtrl treated cells 4h rep 3 (SETX)

description: Replicate 3

value: A/PR/8/34(ΔNS6) Infection


title: HCC_350T_CGH


title: HCC_351N_CGH


title: siCtrl treated cells 4h rep 2 (SETX)

description: Replicate 2

value: A/PR/8/34(ΔNS5) Infection


title: siCtrl treated cells 4h rep 1 (SETX)

description: Replicate 1

value: A/PR/8/34(ΔNS4) Infection


title: FL-106


title: Untransfected cells 4h rep 2 (SETX)

description: Replicate 2

value: A/PR/8/34(ΔNS2) Infection


title: FL-105


title: HCC_351T_CGH

value: M

value: Tumor

value: hepatocyte


title: FL-112


title: HCC_349T_CGH


title: HCC_358N_CGH

value: F


title: FL-104

value: follicular lymphoma


title: FL-101


title: HCC_348T_CGH


title: FL-99


title: FL-97


title: FL-103


title: FL-102


title: FL-100


title: Untransfected cells 4h rep 1 (SETX)

description: Replicate 1

value: A/PR/8/34(ΔNS1) Infection


title: siSetx treated cells 0h rep 3 (SETX)

description: Replicate 3

value: no infection


title: HCC_348N_CGH


title: siSetx treated cells 0h rep 2 (SETX)

description: Replicate 2

value: SETX siRNA


title: siSetx treated cells 0h rep 1 (SETX)

description: Replicate 1


title: FL-96


title: siCtrl treated cells 0h rep 3 (SETX)

description: Replicate 3

value: Control siRNA


title: FL-98


title: HCC_345T_CGH


title: HCC_346T_CGH


title: HCC_347T_CGH


title: FL-91


title: FL-95


title: FL-92


title: FL-93


title: FL-88


title: Untransfected cells 0h rep 3 (SETX)

description: Replicate 3

value: no siRNA


title: siCtrl treated cells 0h rep 1 (SETX)

description: Replicate 1


title: FL-90


title: Untransfected cells 0h rep 2 (SETX)

description: Replicate 2


title: siCtrl treated cells 0h rep 2 (SETX)

description: Replicate 2


title: FL-94


title: FL-86


title: HCC_336T_CGH


title: FL-89


title: FL-87


title: HCC_339T_CGH


title: FL-85


title: HCC_337T_CGH


title: HCC_342T_CGH


title: FL-84


title: Untransfected cells 0h rep 1 (SETX)

description: Replicate 1


title: FL-83


title: FL-81


title: FL-80


title: FL-82


title: Cow_based_formula

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

data_processing:
The HTqPCR software was provides biostatistical methods for the analysis of Ct values from TaqMan OpenArray (OA) assays. The software package handles data loading, quality assessment, normalisation, visualisation and parametric or non-parametric testing for statistical significance in Ct values between features (the individual microRNAs).
For the normalisation, RNU48, RNU44 and U6 rRNA as endogenous controls (miRNA) were used.
The primary experimental data were loaded into the software according to the authors’ recommendations, where Ct≤29 is considered as detectable microRNA. Also, in each sample group, miRNAs that was identified in 4 or more samples of each group with Ct value between 5 and 29 were considered as reliable microRNAs. Highly expressed miRNAs were also determined at more strict conditions, where the miRNA Ct value must have been between 8 and 12, and present in at least 4 samples in each sample group.
Complete raw data were normalised using the deltaCt method, which scales the individual samples while retaining the distribution of Ct values.
Normalised miRNAs were done in R without generating deltaCT values, thus only the list of normalized miRNA with Ct vlaue between 8 and 29 and that detected in at least 4 samples out of 10 analysed in each group is provided ('normalized_miRNAs_list.txt').
The 'fold_change.txt' contains only differentially expressed miRNAs between milk lipid and milk cell samples.

label: FAM

organism: Bos taurus

label_protocol: Reverse transcription was performed from 200 ng total RNA using RT kit (life technologies), megaplex RT primer pool was used. Cycler parameters for RT reaction was 40 cycles of 16C for 2 min, 42C for 1 min, and 50C for 1 sec. Then 85C hold for 5 min. All cDNA were preamplified using Taqman PreAmp master mix and megaplex PreAmp Primers. Cycler parameters for PreAmp reaction, 95C for 10 min, 55C for 2 min, 72C for 2 min, 12 cycles of 95C for 15 sec and 60C for 4 min. then hold at 99.9C for 10 min. All samples were applied into 14 OpenArray panels (3 samples per one panel) suing openarray loader. Then OpenArray real time PCR cycler was used to run all panels.

growth_protocol: Milk samples were taken under sterilization conditions using pumps and sterile bottles, shields, etc. Blood was taken into EDTA to obtain plasma and PBMCs.

extract_protocol: All cells and macromolecules were lysed, and then washed three times using different reagents, then resoluble using RNase free water. These four miRNA extraction kits are all filter column-based methods. All the extractions were done according to the manufacturer’s protocol except the amount of lipid and lysis reagent in the miRCURY RNA Isolation-Biofluids Kit, where 400 μL of lipid in 120 μL of lysis reagent was used.

treatment_protocol: All samples were fractionated and milk extracted immediately.

tag: tissue type

value: bovine milk


title: Soy_based_formula

organism: Glycine max

value: soy milk


title: FL-77


title: FL-79


title: FL-78


title: HCC_335T_CGH


title: HCC_333T_CGH


title: HCC_334T_CGH


title: FL-76


title: 14084_plasma

source_name: plasma

tag: subject id

tag: subject status

value: exclusively breastfeeding female

value: whole blood

value: plasma


title: 14090_plasma


title: FL-75


title: FL-74


title: HCC_329T_CGH


title: HCC_330T_CGH


title: FL-71


title: 14012_plasma


title: 13184_plasma


title: HCC_328T_CGH


title: FL-69


title: FL-72


title: FL-70


title: 13332_plasma


title: HCC_332T_CGH


title: 13331_plasma


title: FL-68


title: FL-73


title: HCC_328N_CGH

value: Adjacent normal


title: 13297_plasma


title: FL-67


title: 13286_plasma


title: HCC_327T_CGH


title: 14123_plasma


title: FL-66


title: FL-64


title: 13156_plasma


title: HCC_326T_CGH


title: HCC_325T_CGH


title: 14123_PBMCs

source_name: PBMCs

value: peripheral blood mononuclear cell (PBMC)


title: FL-65


title: FL-62


title: 14090_PBMCs


title: FL-63


title: HCC_323T_CGH

value: M


title: FL-61


title: FL-58


title: FL-57


title: FL-59


title: 14084_PBMCs


title: FL-60


title: FL-54


title: HCC_321T_CGH

value: Tumor


title: FL-55


title: HCC_320T_CGH

value: hepatocyte


title: FL-56


title: HCC_322T_CGH


title: 13184_PBMCs


title: FL-50


title: 14012_PBMCs


title: FL-51


title: 13332_PBMCs


title: 13331_PBMCs


title: FL-47


title: FL-49


title: FL-53


title: 13297_PBMCs


title: HCC_319T_CGH

value: F


title: HCC_323N_CGH


title: FL-48

value: follicular lymphoma


title: Testis of Ccnyl1 KO mice,biological rep2

city: Dallas

first: Richard

middle: Chih-Chien

last: Wang

state: Texas

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern Medical Center

description: Sample name: Ccnyl1 KO-2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene array Scanner3000.

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

source_name: Mouse testis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: All mice were housed under specific pathogen-free conditions

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

treatment_protocol: Testis were quickly obtained from two month old mice, and froze in liquid nitrogen, and then put into the Trizol solution (GibcoBRL).

value: testis

value: Ccnyl1 knockout

value: Two months old

value: adult


title: 13286_PBMCs


title: FL-45


title: HCC_320N_CGH


title: HCC_316N_CGH


title: HCC_317T_CGH


title: FL-46


title: Testis of WT mice,biological rep2

description: Sample name: WT-2

value: WT


title: FL-41


title: FL-42


title: 14123_milk_lipid

source_name: milk lipids

value: whole milk

value: milk lipids


title: 13156_PBMCs

value: exclusively breastfeeding female


title: FL-43


title: HCC_315T_CGH


title: Testis of Ccnyl1 KO mice,biological rep1

description: Sample name: Ccnyl1 KO-1


title: 14090_milk_lipid


title: Testis of WT mice,biological rep1

description: Sample name: WT-1


title: HCC_315N_CGH


title: Forskolin+BMP4,biological replicate 2

city: Boston

first: Peter

middle: Geon

last: Kim

state: MA

address: 360 Longwood Ave, Lc8202

department: Hematology/Oncology

institute: Dana Farber Cancer Institute

description:
Forskolin+BMP4_rep_2
8_021014.CEL

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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 filtered using nsFilter from the genefilter package and Multi-array Average-summarized, quantile normalized using R (v.2.15)/Bioconductor v.2.11 (BiocInstaller 1.8.3).
After nsFilter (backup, var.filter=FALSE, require.entrez=FALSE, require.symbol=FALSE, remove.dupEntrez=TRUE) removing duplicate Entrez entries, the reduced data set of 20,757 rows was obtained.

source_name: AGM VE-cadherin+ cells_Forskolin+BMP4

label_protocol: NuGen amplified, biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: E11.5 aorta-gonad-mesonephros region was microdissected, dissociated using DNase I, Collagenase IV and Hyaluronidase, then sorted for VE-cadherin+ cells. Cells were cultured in serum-free media containing 2% BSA / IMDM (vol/vol) supplemented with Insulin-Transferrin-Selenium (ITS-G; Life Technologies), 25 μg/ml ascorbic acid, 450 μM monothioglycerol, 2 mM penicillin/streptomycin/glutamate and of 20 ng/ml VEGF (R&D), 50 ng/ml IL3 (R&D), 50 ng/ml IL6 (R&D), 50 ng/ml SCF (R&D), 50 ng/ml FLT3L (R&D), 50 ng/ml TPO (R&D), 50 ng/ml IL6R (SBH Sciences)

extract_protocol: RNA was extracted with RNeasy Micro Kit (Qiagen)

treatment_protocol: Cells were treated with BMP4 (4ng/ml) or forskolin (25uM) or both for 8 hours.

value: E11.5 embryo

value: aorta-gonad-mesonephros (AGM) region

value: VE-cadherin+ cells

tag: treated with

value: Forskolin+BMP4 for 8hrs


title: 14084_milk_lipid


title: HCC_314T_CGH

value: M


title: 13184_milk_lipid


title: FL-44


title: Forskolin,biological replicate 2

description:
Forskolin_rep_2
6_021014.CEL

source_name: AGM VE-cadherin+ cells_Forskolin

value: forskolin (25uM) for 8 hrs


title: BMP4,biological replicate 2

description:
BMP4_rep_2
7_021014.CEL

source_name: AGM VE-cadherin+ cells_BMP4

value: BMP4 (4ng/ml) for 8 hrs


title: HCC_312T_CGH

value: F

value: Tumor

value: hepatocyte


title: FL-52

source_name: tumor biopsy

value: follicular lymphoma


title: DMSO,biological replicate 2

description:
DMSO_rep_2
5_021014.CEL

source_name: AGM VE-cadherin+ cells_DMSO

value: DMSO for 8hrs


title: Forskolin+BMP4,biological replicate 1

description:
Forskolin+BMP4_rep_1
4_021014.CEL


title: HCC_311T_CGH


title: 13297_milk_lipid


title: 13331_milk_lipid


title: 14012_milk_lipid


title: 13332_milk_lipid


title: HCC_311N_CGH

value: Adjacent normal


title: BMP4,biological replicate 1

description:
BMP4_rep_1
3_021014.CEL


title: Dox+Sca1-

city: Palo Alto

first: Shang

last: Cai

address: 915 Campus Dr.

institute: Stanford University

description: gene expression data from  sca1- comma D beta cells treated with 100ng/ml Doxycycline

hyb_protocol: The fragmented and labeled cRNA was hybridized to mouse genome array MOE430 2.0 with 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G. Scanned microarray images were imported into Gene Chip Operating Software (GCOS, Affymetrix) to generate signal values

data_processing: Data were processed using BRB-ArrayTools (Biometric Research Branch) using default settings

source_name: Sca1- cell treated with 100ng/ml Doxycycline

label_protocol: Affymetrix 3'IVT Express protocol was used to generate biotinylated cRNA from 50-500ngs of total RNA

growth_protocol: Comma D beta cell line was cultured in DMEM F12+2% FBS+1% PSA+5ug/ml insulin+10ng/ml EGF in 175 cm2 culture flask overnight

extract_protocol: RNA was extracted using Qiagen Microplus RNeasy.

treatment_protocol: The next day, 100ng/ml Doxycycline was added to cells and treated for 1day. Untreated and treated cells were then trypsinized and stained with Sca1. 200k Sca1+ and Sca- were sorted on BD FacsAria

tag: cell line

value: Comma D beta


title: 13156_milk_lipid

value: whole milk


title: 13286_milk_lipid

value: milk lipids


title: HCC_310T_CGH


title: Forskolin,biological replicate 1

description:
Forskolin_rep_1
2_021014.CEL


title: HCC_309T_CGH


title: DMSO,biological replicate 1

description:
DMSO_rep_1
1_021014.CEL


title: HCC_309N_CGH


title: 14090_milk_cells

source_name: milk cell

value: exclusively breastfeeding female

value: milk cell


title: Dox+Sca1+

description: gene expression data from  sca1+ comma D beta cells treated with 100ng/ml Doxycycline

source_name: Sca1+ cell treated by 100ng/ml Doxycycline


title: HCC_308N_CGH


title: 14084_milk_cells


title: HCC_308T_CGH


title: Dox- Sca1-

description: gene expression data from untreated sca1- comma D beta cells

source_name: Sca1- cell in the absence of Doxycycline


title: HCC_307T_CGH


title: HCC_316T_CGH


title: 14123_milk_cells


title: 14012_milk_cells


title: 13184_milk_cells


title: Dox- Sca1+

description: gene expression data from untreated sca1+ comma D beta cells

source_name: Sca1+ cells in the absence of Doxycycline


title: HCC_305T_CGH

source_name: hepatocyte


title: HCC_305N_CGH

source_name: standard reference genomic DNA


title: 13332_milk_cells


title: 13297_milk_cells


title: HCC_304T_CGH


title: sh-Sirt1-A5-EPZ4777_21d

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were Robust Multi-Array Average (RMA) and quantile normalized using GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/).

label: Biotin

source_name: Murine MLL-AF9 leukemic cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Murine MLL-AF9 leukemic cells were cultured in IMDM plus 15% FBS supplemented with 20 ng/ml murine SCF, 10 ng/ml murine IL-3 and 10 ng/ml murine IL-6.

treatment_protocol: Cells were incubated with EPZ4777 (3uM) or DMSO in standard culture medium for indicated time point.

value: MLL-AF9 transformed leukemic cells

value: shSirt1 RNA interference

tag: time


title: 13286_milk_cells


title: PEDF KNOCKOUT 5

city: West Haven

first: Petr

last: Protiva

address: 950 Campbell Avenue

institute: Yale University and VA CT Healthcare System

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using 75 percentile shift normalisation using Genespring GX 12.6.1

source_name: Liver tissue

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

growth_protocol: mice were fed high fat diet for 7 months

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: mice were fed high fat diet, liver tissue were collected and immediately flash frozen for subsequent RNA extraction

tag: genotype/variation

value: pedf knockout

value: male

tag: age

value: 7 months old


title: HCC_304N_CGH

value: M

tag: tissue


title: 13331_milk_cells


title: sh-Sirt1-A5-DMSO

description: Gene expression data

value: DMSO

value: control


title: 13156_milk_cells


title: sh-Sirt1-A1-DMSO

description: Gene expression data


title: PEDF KNOCKOUT 4

tag: strain


title: sh-LUC-D11-EPZ4777_6d

description: Gene expression data

tag: treatment

value: shLUC RNA interference


title: PEDF KNOCKOUT 2


title: sh-Sirt1-A1-EPZ4777_21d

description: Gene expression data


title: sh-LUC-A4-EPZ4777_6d

description: Gene expression data


title: PEDF KNOCKOUT 3


title: WILD TYPE 5

value: wild type


title: WILD TYPE 4


title: WILD TYPE 2


title: sh-LUC-A4-DMSO

description: Gene expression data


title: WILD TYPE 1


title: WILD TYPE 3


title: sh-LUC-D11-DMSO

description: Gene expression data


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 total DNA methylation RepA

status: Public on Mar 29 2015

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

description: Biological replicate A

data_processing: The data were filtered for detection pValue < 0.01 and background subtraction was applied using Genome Studio

label: biotin and dinitrophenyl

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl labeled

growth_protocol: Human Embryonic Stem Cells grew in different subtrates (Feeder Layer and extracellular matrix) and were passaged with different methods (mechanically and enzymatically)

extract_protocol: Total DNA was extracted using Quiagen DNeasy Blood & Tissue Kit

value: female

tag: growth condition

value: hESCs cultured on extacellular matrix  and enzymatically passagged P5

tag: passage


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on extacellular matrix  and mechanically passagged P41


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 total DNA methylation RepA

description: Biological replicate A

value: hESCs cultured on extacellular matrix  and enzymatically passagged P41


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on mouse feeder layer and enzymatically passagged P104


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 total DNA methylation RepB

description: Biological replicate B

value: hESCs cultured on extacellular matrix  and enzymatically passagged P161


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 total DNA methylation RepC

description: Biological replicate C


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 total DNA methylation RepC

description: Biological replicate C


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on extacellular matrix  and mechanically passagged P147


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 total DNA methylation RepB

description: Biological replicate B

value: hESCs cultured on extacellular matrix  and mechanically passagged P6


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 total DNA methylation RepC

description: Biological replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on mouse feeder layer and mechanically passagged P103


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 total DNA methylation RepC

description: Biological replicate C


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on mouse feeder layer and enzymatically passagged P41


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA methylation RepD

description: Biological replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on mouse feeder layer and enzymatically passagged P6


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepF

description: Biological Replicate F

data_processing: The data were filtered for detection pValue <= 0.05 and normalised using robust spline normalisation with lumi in R. Filtering in Genome Studio using the OR clause (it means that even only a sample has a p-value lower  than 0.05 for one specific probe, this probe will be selected).

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion), quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: extacellular matrix  and enzymatically passagged P161


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 total DNA methylation RepB

description: Biological replicate B


title: HDF51iPS11_ECMENZ_P25

description: Retro-Virus Derived

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing:
Genotyping calls were made with GenomeStudio (Illumina, Inc.) via the cluster files provided by the manufacturer. The GenCall (v. 6.3.0) threshold was set to 0.15, and the call rates were greater than 0.998. Reproducibility and heritability were calculated in GenomeStudio (Illumina, Inc.).
Header definitions of Series supplementary files: Name is the SNP ID, Chr (Chromosome), Position (location on Chr), Genotype: AA,AB,BB,or NC (No Call), Score, Theta, R, B Allele, Log R Ratio

label: C-Bio and A-DNP

source_name: induced Pluripotent Stem Cell

label_protocol: Standard Illumina Protocol

growth_protocol: The HDF51iPS1, HDF51iPS7, and HDF51iPS11 lines were three independent hiPSC clones reprogrammed from human fetal dermal fibroblasts using the standard reprogramming factors (OCT4/POU5F1, SOX2, KLF4, and MYC) carried by retroviral vectors.

extract_protocol: All DNA was isolated (QIAGEN Gentra Puregene Cell Kit) except the sperm sample (PicoPure DNA Extraction Kit, Life Technologies, Inc.), and quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) according to the manufacturer’s protocol.

treatment_protocol: HDF51iPS1, HDF51iPS7, and HDF51iPS11 cells were cultured at 37ºC and 5% CO2 on extracellular matrix (GeltrexTM ; Life Technologies) or irradiated mouse embryonic fibroblasts (MEFs).  Cells on feeder layers were cultured in standard hPSC medium, consisting of DMEM/F12 with 20% Knockout Serum Replacement, 1 mM GlutaMAXTM, 0.1 mM non-essential amino acids (NEAA), and 12 ng/ml basic FGF (all from Life Technologies) and passaged mechanically enzymatically dissociated (MefEnz)  with Accutase® (Life Technologies).  Cells cultured on Geltrex in StemPro® hESC SFM (Life Technologies) with 0.1 mM β-mercaptoethanol and 12 ng/ml basic FGF, were passaged mechanically (EcmMech) or enzymatically (EcmEnz) with Accutase.

tag: cell type

value: induced Pluripotent Stem Cell

tag: passage number

tag: condition

value: enzymatic passaging,


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepD

description: Biological Replicate D

value: extacellular matrix  and enzymatically passagged P41

tag: gender


title: HDF51iPS7_ECMENZ_P25

description: Retro-Virus Derived


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepA

description: Biological Replicate A

value: extacellular matrix  and enzymatically passagged P5


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepF

description: Biological Replicate F


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepE

description: Biological Replicate E


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 total DNA methylation RepA

description: Biological replicate A


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA methylation RepC

description: Biological replicate C

value: hESCs cultured on mouse feeder layer and mechanically passagged P42


title: HDF51iPS1_ECMENZ_P25

description: Retro-Virus Derived


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepD

description: Biological Replicate D

value: female


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepE

description: Biological Replicate E


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepC

description: Biological Replicate C


title: HDF51IPS11_MEFMECH_P35

description: Retro-Virus Derived

value: mechanical passaging


title: hESCs cultured on extacellular matrix  and enzymatically passaged P161 mRNA RepD

description: Biological Replicate D


title: hESCs cultured on extacellular matrix  and enzymatically passaged P41 mRNA RepE

description: Biological Replicate E


title: HDF51IPS7_MEFMECH_P33

description: Retro-Virus Derived


title: hESCs cultured on extacellular matrix  and enzymatically passaged P5 mRNA RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and mechanically passaged P6 total DNA methylation RepD

description: Biological replicate D

value: hESCs cultured on mouse feeder layer and mechanically passagged P6


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepF

description: Biological Replicate F

value: extacellular matrix  and mechanically passagged P147


title: HDF51IPS1_MEFMECH_P25

description: Retro-Virus Derived


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA methylation RepD

description: Biological replicate D


title: HDF51IPS11_MEFMECH_P8

description: Retro-Virus Derived


title: hESCs cultured on mouse feeder layer and mechanically passaged P6 total DNA methylation RepC

description: Biological replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA methylation RepB

description: Biological replicate B


title: HDF51IPS7_MEFMECH_P5

description: Retro-Virus Derived


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepD

description: Biological Replicate D


title: HDF51IPS1_MEFMECH_P6

description: Retro-Virus Derived


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepE

description: Biological Replicate E


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on extacellular matrix  and mechanically passaged P147 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepC

description: Biological Replicate C

value: extacellular matrix  and mechanically passagged P41


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and mechanically passaged P6 total DNA methylation RepB

description: Biological replicate B


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepE

description: Biological Replicate E


title: PBMCs, 17-061

city: Stanford

first: Aaron

middle: M

last: Newman

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine & Division of Oncology, Stanford School of Medicine

description: Expression data of PBMCs (~1×106 viable cells per mL) collected from a healthy adult receiving influenza immunization.

hyb_protocol: 750 ng of labeled cRNA was hybridized overnight to Human HT-12 V4 BeadChip arrays (Illumina).

scan_protocol: The arrays were then washed, blocked, stained and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing: BeadStudio/GenomeStudio software version 1.9.0 (Illumina) was used to generate signal intensity values from the scans. Expression data were then normalized with limma v3.20.8 (R/Bioconductor) using normexp background correction with negative controls (neqc function).

source_name: PBMCs

label_protocol: Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200 to 250 ng of total RNA using the Illumina RNA amplification kit (Applied Biosystems/Ambion).

extract_protocol: PBMCs (~1×106 viable cells per mL) were collected in 1 mL TRIzol (Invitrogen) and stored at -80 °C until use. Total RNA was isolated according to the TRIzol protocol (Invitrogen). Total RNA yield was assessed using the Thermo Scientific NanoDrop 1000 micro-volume spectrophotometer (absorbance at 260 nm and the ratio of 260/280 and 260/230). RNA integrity was assessed using a Bioanalyzer NANO Lab-on-a-Chip instrument (Agilent).

value: PBMC

tag: disease status

value: Normal

tag: flow cytometry cell subset proportions

value: Naïve B cells = 5.14%; Memory B cells = 1%; CD8 T cells = 12.89%; Naïve CD4 T cells = 26.48%; Resting memory CD4 T cells = 23.27%; Activated memory CD4 T cells = 6.77%; Gamma delta T cells = 1.81%; NK cells = 7.84%; Monocytes = 14.79%


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepD

description: Biological Replicate D


title: PBMCs, 17-060

value: Naïve B cells = 2.17%; Memory B cells = 0.39%; CD8 T cells = 24.82%; Naïve CD4 T cells = 20.8%; Resting memory CD4 T cells = 26.15%; Activated memory CD4 T cells = 3.03%; Gamma delta T cells = 6.29%; NK cells = 6.6%; Monocytes = 9.76%


title: PBMCs, 17-058

value: Naïve B cells = 4.51%; Memory B cells = 0.83%; CD8 T cells = 33.13%; Naïve CD4 T cells = 32.66%; Resting memory CD4 T cells = 11.66%; Activated memory CD4 T cells = 1.82%; Gamma delta T cells = 4.63%; NK cells = 6.79%; Monocytes = 3.97%


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA genotyping RepE

description: Biological Replicate E

data_processing: Standard Illumina protocol

label_protocol: C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled  nucleotides are dinitrophenyl labeled

extract_protocol: genomic DNA was extracted using Quiagen DNeasy Blood & Tissue Kit

value: hESCs cultured on mouse feeder layer and mechanically passagged P103


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepB

description: Biological Replicate B


title: PBMCs, 17-057

value: Naïve B cells = 4.58%; Memory B cells = 0.77%; CD8 T cells = 36.11%; Naïve CD4 T cells = 30.61%; Resting memory CD4 T cells = 9.99%; Activated memory CD4 T cells = 2.3%; Gamma delta T cells = 4.14%; NK cells = 7.43%; Monocytes = 4.09%


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA genotyping RepC

description: Biological Replicate C


title: PBMCs, 17-055

value: Naïve B cells = 2.54%; Memory B cells = 1%; CD8 T cells = 14.67%; Naïve CD4 T cells = 28.3%; Resting memory CD4 T cells = 16.45%; Activated memory CD4 T cells = 3.43%; Gamma delta T cells = 0.49%; NK cells = 12.8%; Monocytes = 20.34%


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepF

description: Biological Replicate F

value: extacellular matrix  and mechanically passagged P6


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA genotyping RepF

description: Biological Replicate F


title: hESCs cultured on extacellular matrix  and mechanically passaged P41 mRNA RepA

description: Biological Replicate A


title: PBMCs, 17-054

value: Naïve B cells = 4.26%; Memory B cells = 1.96%; CD8 T cells = 19.55%; Naïve CD4 T cells = 36.23%; Resting memory CD4 T cells = 14.34%; Activated memory CD4 T cells = 2.25%; Gamma delta T cells = 6.58%; NK cells = 4.24%; Monocytes = 10.6%


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepE

description: Biological Replicate E


title: hESCs cultured on mouse feeder layer and mechanically passaged P85 total DNA genotyping RepC

description: Biological Replicate C

value: hESCs cultured on mouse feeder layer and mechanically passagged P85


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepD

description: Biological Replicate D

value: hESCs cultured on mouse feeder layer and mechanically passagged P42


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepE

description: Biological Replicate E

value: female


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and mechanically passaged P119 total DNA genotyping RepC

description: Biological Replicate C

value: hESCs cultured on extracellular matrix and mechanically passagged P119


title: PBMCs, 17-045

value: Naïve B cells = 3.82%; Memory B cells = 0.7%; CD8 T cells = 19.1%; Naïve CD4 T cells = 31.41%; Resting memory CD4 T cells = 9.42%; Activated memory CD4 T cells = 1.74%; Gamma delta T cells = 8.67%; NK cells = 9.56%; Monocytes = 15.58%


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and mechanically passaged P85 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepB

description: Biological Replicate B

value: hESCs cultured on extracellular matrix and mechanically passagged P147


title: hESCs cultured on extracellular matrix and mechanically passaged P119 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and mechanically passaged P85 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepF

description: Biological Replicate F

value: hESCs cultured on extracellular matrix and mechanically passagged P41


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepE

description: Biological Replicate E


title: PBMCs, 17-043

value: PBMC

value: Naïve B cells = 2.43%; Memory B cells = 1.61%; CD8 T cells = 10.05%; Naïve CD4 T cells = 29.4%; Resting memory CD4 T cells = 20.35%; Activated memory CD4 T cells = 2.96%; Gamma delta T cells = 0.43%; NK cells = 15.51%; Monocytes = 17.27%


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and mechanically passaged P119 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepF

description: Biological Replicate F

value: mouse feeder layer and enzymatically passagged P104


title: PBMCs, 17-042

value: Normal

value: Naïve B cells = 0.33%; Memory B cells = 0.21%; CD8 T cells = 8.89%; Naïve CD4 T cells = 10.42%; Resting memory CD4 T cells = 5.06%; Activated memory CD4 T cells = 3.23%; Gamma delta T cells = 3.64%; NK cells = 23.7%; Monocytes = 44.52%


title: PBMCs, 17-041

value: Naïve B cells = 5.65%; Memory B cells = 1.44%; CD8 T cells = 6.89%; Naïve CD4 T cells = 39.57%; Resting memory CD4 T cells = 15.21%; Activated memory CD4 T cells = 7.19%; Gamma delta T cells = 0.48%; NK cells = 14.71%; Monocytes = 8.86%


title: hESCs cultured on extacellular matrix  and mechanically passaged P6 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepE

description: Biological Replicate E


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepD

description: Biological Replicate D


title: PBMCs, 17-034

value: Naïve B cells = 7.43%; Memory B cells = 0.89%; CD8 T cells = 9.84%; Naïve CD4 T cells = 34.52%; Resting memory CD4 T cells = 10.86%; Activated memory CD4 T cells = 2.12%; Gamma delta T cells = 1.75%; NK cells = 13.93%; Monocytes = 18.67%


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepE

description: Biological Replicate E


title: PBMCs, 17-047

value: Naïve B cells = 3.29%; Memory B cells = 1.29%; CD8 T cells = 19.99%; Naïve CD4 T cells = 24.17%; Resting memory CD4 T cells = 14.29%; Activated memory CD4 T cells = 1.81%; Gamma delta T cells = 1.62%; NK cells = 18.87%; Monocytes = 14.67%


title: PBMCs, 17-040

value: Naïve B cells = 9.69%; Memory B cells = 1.9%; CD8 T cells = 6.87%; Naïve CD4 T cells = 20.56%; Resting memory CD4 T cells = 17.08%; Activated memory CD4 T cells = 5.63%; Gamma delta T cells = 1.12%; NK cells = 10.06%; Monocytes = 27.11%


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepB

description: Biological Replicate B


title: PBMCs, 17-030

value: Naïve B cells = 3.31%; Memory B cells = 3.55%; CD8 T cells = 24.22%; Naïve CD4 T cells = 25.48%; Resting memory CD4 T cells = 0.02%; Activated memory CD4 T cells = 1.8%; Gamma delta T cells = 14.94%; NK cells = 10.81%; Monocytes = 15.87%


title: hESCs cultured on extracellular matrix and mechanically passaged P147 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepB

description: Biological Replicate B


title: PBMCs, 17-026

value: Naïve B cells = 8.4%; Memory B cells = 4.69%; CD8 T cells = 27.98%; Naïve CD4 T cells = 8.98%; Resting memory CD4 T cells = 21.17%; Activated memory CD4 T cells = 1.92%; Gamma delta T cells = 5.59%; NK cells = 7.88%; Monocytes = 13.38%


title: PBMCs, 17-027

value: Naïve B cells = 11.62%; Memory B cells = 4.16%; CD8 T cells = 20.37%; Naïve CD4 T cells = 17.89%; Resting memory CD4 T cells = 11.39%; Activated memory CD4 T cells = 2.36%; Gamma delta T cells = 7.55%; NK cells = 14.18%; Monocytes = 10.47%


title: Normal tonsil T cells, 6

description: Gene expression data from normal tonsil T cells (CD5+), which were collected as part of routine tonsilectomy procedures at Lucile Packard Children’s Hospital at Stanford University

hyb_protocol: cRNA was hybridized to HGU133 Plus 2.0 microarrays (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: standard Affymetrix protocol

data_processing: MAS5 normalized using the affy package in R/Bioconductor.

source_name: Normal tonsil T cells, 6

label_protocol: standard Affymetrix protocol

extract_protocol: Nucleic acids were extracted from tonsil specimens and PBMCs using AllPrep DNA/RNA Mini kits (Qiagen). For FL lymph node biopsies, total RNA and genomic DNA were prepared and stored using TRIzol and RNeasy Midi Kits (Qiagen, Valencia, CA). Total cellular RNA (at least 300 ng) was assessed for yield (NanoDrop 2000, Thermo Scientific) and quality (2100 Bioanalyzer, Agilent).

value: Tonsil T cells

tag: disease state

value: Healthy


title: hESCs cultured on extracellular matrix and mechanically passaged P41 total DNA genotyping RepA

description: Biological Replicate A

value: female


title: Normal tonsil T cells, 5

source_name: Normal tonsil T cells, 5


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepF

description: Biological Replicate F

value: mouse feeder layer and enzymatically passagged P41


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 mRNA RepA

description: Biological Replicate A


title: PBMCs, 17-023

value: Naïve B cells = 16.77%; Memory B cells = 2.95%; CD8 T cells = 8.69%; Naïve CD4 T cells = 7.53%; Resting memory CD4 T cells = 27.54%; Activated memory CD4 T cells = 1.7%; Gamma delta T cells = 0.64%; NK cells = 17.11%; Monocytes = 17.08%


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepC

description: Biological Replicate C

value: hESCs cultured on extracellular matrix and enzymatically passagged P161


title: PBMCs, 17-019

value: PBMC

value: Naïve B cells = 15.09%; Memory B cells = 4.07%; CD8 T cells = 17.86%; Naïve CD4 T cells = 4.53%; Resting memory CD4 T cells = 6.63%; Activated memory CD4 T cells = 1.69%; Gamma delta T cells = 12.49%; NK cells = 29.64%; Monocytes = 7.99%


title: Normal tonsil T cells, 4

source_name: Normal tonsil T cells, 4


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepE

description: Biological Replicate E


title: Normal tonsil T cells, 3

source_name: Normal tonsil T cells, 3


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepE

description: Biological Replicate E


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepD

description: Biological Replicate D


title: PBMCs, 17-006

value: Normal

value: Naïve B cells = 3.33%; Memory B cells = 1.83%; CD8 T cells = 32.05%; Naïve CD4 T cells = 32.57%; Resting memory CD4 T cells = 11.67%; Activated memory CD4 T cells = 1.68%; Gamma delta T cells = 2.28%; NK cells = 8.9%; Monocytes = 5.7%


title: Normal tonsil T cells, 1

source_name: Normal tonsil T cells, 1


title: PBMCs, 17-002

value: Naïve B cells = 12.36%; Memory B cells = 2.96%; CD8 T cells = 22.36%; Naïve CD4 T cells = 10.96%; Resting memory CD4 T cells = 9.43%; Activated memory CD4 T cells = 2.81%; Gamma delta T cells = 5.44%; NK cells = 16.58%; Monocytes = 17.1%


title: hESCs cultured on extracellular matrix and enzymatically passaged P130 total DNA genotyping RepB

description: Biological Replicate B

value: hESCs cultured on extracellular matrix and enzymatically passagged P130


title: hESCs cultured on extracellular matrix and enzymatically passaged P130 total DNA genotyping RepC

description: Biological Replicate C


title: Normal tonsil B cells, 6

description: Gene expression data from normal tonsil B cells (CD19+), which were collected as part of routine tonsilectomy procedures at Lucile Packard Children’s Hospital at Stanford University

source_name: Normal tonsil B cells, 6

value: Tonsil B cells


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepF

description: Biological Replicate F

value: hESCs cultured on extracellular matrix and enzymatically passagged P41


title: hippocampal formation recovery of PS rats biological rep2

city: LYON

first: leslie

last: renouard

address: 7 rue Guillaume Paradin

country: France

institute: Inserm U1028 - CNRS UMR5292

description: pool of 6 rats

hyb_protocol: RNAc biotinylated is hybridized on GeneChip rat 230 2.0 with the standard Affymetrix protocol (Expression 10 Analysis Technical Manual, ref 701021 rev.5, Affymetrix, GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 and analyzed with Affymetrix GeneChip Operating software (GCOS) version 1.2 using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

data_processing:
For each intergroup comparison, significant expression changes were determined with paired nonparametric test (Microarray Suite 5.0, Affymetrix) using Affymetrix default analysis settings and global scaling. Transcript expression level was considered as modified in the hippocampal formation between two experimental conditions when the three comparisons between the replicas designed them as decreased or increased. Relative measure of the expression level, was computed for each assayed gene.
A weighted mean of probe fluorescence is the signal value (Signal intensity), a relative measure of the expression level, computed for each assayed gene. Global, probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold was used to assign a call of absent present or marginal for each assayed gene (Signal detection). A p-value was calculated to reflect confidence in the detection call (Signal detection p-value).

organism: Rattus norvegicus

source_name: hippocampal formation of rats deprived during 72h of paradoxical sleep permitted to recover during 6h

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

growth_protocol: Sprague-Dawley rats were housed individually and placed under a constant light/dark cycle (light on from 7:00 AM to 7:00 PM).

extract_protocol: Total RNA was isolated from right neocortex and hippocampal formation of each animal by using RNeasy Lipid Tissue Mini Kit (Qiagen) and RNase-free DNase set (Qiagen) to eliminate DNA contamination according to the manufacturer's instructions. An equal mass amount of total RNA from the right neocortex and hippocampal formation was pooled from two sets of 6 rats for each experimental group (PSC, PSD, PSR; 36 μg/pool).

treatment_protocol: Rats were implanted with electroencephalographic (EEG) and electromyographic (EMG) electrodes. PS deprivation was performed using the flowerpot method. Rats were divided in 3 groups: control, deprived of PS for 78 h and rats allowed to recover for 6 h after such deprivation. After anesthesia, rats were decapitated and the whole brain was removed, right neocortex and hippocampal formation were dissected and stored at -80°C.

tag: group

value: PS hypersomniac rat

value: male

tag: number

value: Sprague Dawley (Charles River, L'Arbresle France)

value: hippocampal formation

tag: weight


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepE

description: Biological Replicate E

tag: cell line


title: hESCs cultured on extracellular matrix and enzymatically passaged P161 total DNA genotyping RepF

description: Biological Replicate F


title: Normal tonsil B cells, 5

source_name: Normal tonsil B cells, 5

value: Healthy


title: hESCs cultured on extracellular matrix and enzymatically passaged P130 total DNA genotyping RepA

description: Biological Replicate A

value: female


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepB

description: Biological Replicate B


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepC

description: Biological Replicate C


title: hippocampal formation recovery of PS rats biological rep1, technical rep2

description: pool of 6 rats


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepE

description: Biological Replicate E

value: hESCs cultured on mouse feeder layer and enzymatically passagged P104


title: hippocampal formation deprived of PS rats biological rep2

description: pool of 6 rats

source_name: hippocampal formation of rats deprived during 78h of paradoxical sleep

value: PS deprived rat


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepC

description: Biological Replicate C


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepD

description: Biological Replicate D

value: mouse feeder layer and enzymatically passagged P6


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 mRNA RepA

description: Biological Replicate A

value: mouse feeder layer and enzymatically passagged P41


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepE

description: Biological Replicate E


title: Normal tonsil B cells, 4

source_name: Normal tonsil B cells, 4


title: Normal tonsil B cells, 1

source_name: Normal tonsil B cells, 1


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepF

description: Biological Replicate F


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepF

description: Biological Replicate F


title: hESCs cultured on extracellular matrix and enzymatically passaged P41 total DNA genotyping RepA

description: Biological Replicate A


title: hippocampal formation recovery of PS rats biological rep1, technical rep1

description: pool of 6 rats


title: hippocampal formation deprived of PS rats biological rep1, technical rep2

description: pool of 6 rats


title: Normal tonsil B cells, 3

source_name: Normal tonsil B cells, 3


title: hippocampal formation deprived of PS rats biological rep1, technical rep1

description: pool of 6 rats


title: FL lymph node biopsy, untreated, 944

description: Gene expression data from a surgical lymph node biopsy obtained from an untreated FL patient enrolled in a Phase III clinical trial (NCT00017290)

source_name: FL lymph node biopsy, untreated, 944

value: Lymph node

value: FL


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepC

description: Biological Replicate C


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepD

description: Biological Replicate D


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepB

description: Biological Replicate B


title: hippocampal formation control rats biological rep2

description: pool of 6 rats

source_name: hippocampal formation of rats staying in standard condition

value: control rat


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and enzymatically passaged P104 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 mRNA RepF

description: Biological Replicate F

value: mouse feeder layer and mechanically passagged P103


title: FL lymph node biopsy, untreated, 726

source_name: FL lymph node biopsy, untreated, 726


title: FL lymph node biopsy, untreated, 959

source_name: FL lymph node biopsy, untreated, 959


title: neocortex recovery of PS rats biological rep2

description: pool of 6 rats

source_name: neocortices of rats deprived during 72h of paradoxical sleep permitted to recover during 6h

value: neocortex


title: FL lymph node biopsy, untreated, 706

source_name: FL lymph node biopsy, untreated, 706


title: hESCs cultured on mouse feeder layer and enzymatically passaged P85 total DNA genotyping RepC

description: Biological Replicate C

value: hESCs cultured on mouse feeder layer and enzymatically passagged P85


title: hESCs cultured on mouse feeder layer and enzymatically passaged P6 mRNA RepB

description: Biological Replicate B


title: neocortex recovery of PS rats biological rep1, technical rep1

description: pool of 6 rats


title: neocortex recovery of PS rats biological rep1, technical rep2

description: pool of 6 rats


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 mRNA RepD

description: Biological Replicate D


title: hippocampal formation control rats biological rep1, technical rep2

description: pool of 6 rats


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 mRNA RepC

description: Biological Replicate C


title: FL lymph node biopsy, untreated, 666

source_name: FL lymph node biopsy, untreated, 666


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepF

description: Biological Replicate F

value: hESCs cultured on mouse feeder layer and enzymatically passagged P41


title: FL lymph node biopsy, untreated, 664

source_name: FL lymph node biopsy, untreated, 664


title: neocortex deprived of PS rats biological rep2

description: pool of 6 rats

source_name: neocortices of rats deprived during 78h of paradoxical sleep


title: hESCs cultured on mouse feeder layer and enzymatically passaged P85 total DNA genotyping RepA

description: Biological Replicate A


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepF

description: Biological Replicate F

value: mouse feeder layer and mechanically passagged P42


title: FL lymph node biopsy, untreated, 639

source_name: FL lymph node biopsy, untreated, 639


title: hESCs cultured on mouse feeder layer and mechanically passaged P103 mRNA RepB

description: Biological Replicate B


title: neocortex deprived of PS rats biological rep1, technical rep2

description: pool of 6 rats

value: male


title: neocortex deprived of PS rats biological rep1, technical rep1

description: pool of 6 rats

value: Sprague Dawley (Charles River, L'Arbresle France)


title: hippocampal formation control rats biological rep1, technical rep1

description: pool of 6 rats

value: hippocampal formation


title: hESCs cultured on mouse feeder layer and enzymatically passaged P41 total DNA genotyping RepC

description: Biological Replicate C


title: FL lymph node biopsy, untreated, 598

source_name: FL lymph node biopsy, untreated, 598


title: hESCs cultured on mouse feeder layer and mechanically passaged P42 mRNA RepE

description: Biological Replicate E