title: 20130211_NC146_NC146_02


title: 20130211_NC144_NC144_05

status: Public on Aug 28 2014

type: RNA

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

hyb_protocol: Lysates in Qiagen RTL buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: NanoString nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins.

label: not provided

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: RosettaSep-purified CD4+ T cells were thawed and resuspended in RPMI-1640 supplemented with 10% FCS.

extract_protocol: After activation, cells were magnetically repurified with anti-CD4 Dynal beads, and lysed.

treatment_protocol: Thawed cells were activated with anti-CD3 and anti-CD28 beads, with or without IFNb (30U/ml) or with Th17 cocktail (anti-IFNg 10ng/ml, anti-IL4 10mg/ml, IL6 50ng/ml, IL23 20ng/ml, IL1b 10ng/ml, TGFb 5ng/ml).

tag: stimulation

value: Activated

tag: hours

tag: lane

tag: age

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: systolic

tag: diastolic

tag: ethnicity

value: Caucasian

tag: Sex

value: F

tag: individual id


title: 20130211_NC144_NC144_09

value: IFNb

value: M


title: 20130211_NC144_NC144_02

value: Asian


title: 20130210_NC143_NC143_12

value: African-American


title: 20130211_NC144_NC144_03


title: 20130210_NC143_NC143_10

value: Unstim


title: 20130210_NC143_NC143_09


title: 20130210_NC143_NC143_08


title: 20130210_NC143_NC143_04


title: 20130210_NC143_NC143_02


title: 20130211_NC144_NC144_08


title: 20130210_NC143_NC143_03


title: 20130210_NC143_NC143_01


title: 20130210_NC142_NC142_11


title: 20130210_NC142_NC142_09


title: 20130210_NC142_NC142_10


title: 20130210_NC143_NC143_05


title: 20130211_NC144_NC144_04


title: 20130210_NC142_NC142_08


title: 20130210_NC142_NC142_06


title: 20130210_NC142_NC142_07


title: 20130210_NC143_NC143_06


title: 20130210_NC142_NC142_04


title: 20130210_NC142_NC142_02


title: 20130210_NC142_NC142_01


title: 20130210_NC142_NC142_05


title: 20130210_NC142_NC142_03


title: 20130210_NC141_NC141_09


title: 20130210_NC141_NC141_11


title: 20130210_NC141_NC141_08


title: 20130210_NC141_NC141_10


title: 20130210_NC141_NC141_07


title: 20130210_NC141_NC141_06


title: 20130210_NC141_NC141_05


title: 20130210_NC142_NC142_12


title: 20130210_NC141_NC141_03


title: 20130210_NC141_NC141_04


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title: 20130210_NC141_NC141_01


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title: 20130210_NC140_NC140_04


title: 20130210_NC140_NC140_01


title: 20130210_NC139_NC139_12


title: 20130210_NC140_NC140_03


title: 20130210_NC140_NC140_06


title: 20130210_NC140_NC140_07


title: 20130210_NC139_NC139_10


title: 20130210_NC140_NC140_02


title: 20130210_NC139_NC139_09


title: 20130210_NC139_NC139_07


title: 20130210_NC139_NC139_04


title: 20130210_NC139_NC139_03


title: 20130210_NC139_NC139_05


title: 20130210_NC139_NC139_06


title: 20130210_NC139_NC139_02


title: 20130210_NC139_NC139_01


title: 20130210_NC141_NC141_02


title: 20130210_NC138_NC138_11


title: 20130210_NC138_NC138_10


title: 20130210_NC138_NC138_09


title: 20130210_NC138_NC138_12


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title: 20130210_NC138_NC138_03


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title: 20130210_NC137_NC137_08


title: 20130210_NC137_NC137_09


title: 20130210_NC137_NC137_07


title: 20130210_NC137_NC137_05

value: Asian Caucasian


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title: 20130204_NC96_NC96_04


title: 20130204_NC96_NC96_02


title: 20130204_NC102_NC102_12


title: 20130204_NC96_NC96_01


title: 20130204_NC102_NC102_11


title: 20130204_NC102_NC102_10


title: 20130204_NC102_NC102_08


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title: 20130204_NC102_NC102_05


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title: 20130204_NC102_NC102_03


title: 20130204_NC102_NC102_02


title: 20130204_NC101_NC101_12


title: 20130204_NC102_NC102_01


title: 20130204_NC101_NC101_11


title: 20130204_NC96_NC96_10


title: 20130204_NC101_NC101_07


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title: 20130204_NC100_NC100_05


title: 20130203_NC95_NC95_12


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title: 20130203_NC95_NC95_11


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title: 20130204_NC101_NC101_10


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title: 20120913_NC73_NC73_12

value: Batch control sample


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title: IGTB565 Activated 4hr

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner.

data_processing:
Data were processed using Affymetrix PowerTools, RMA package.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label: biotin

source_name: Anti-CD3/CD28 activated CD4+ T cells from individual IGTB565 profiled at 4hr

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit.

extract_protocol: Total RNA was isolated using Trizol extraction.

treatment_protocol: Thawed T cells were activated with anti-CD3 and anti-CD28 beads, with or without IFNb (30 U/ml) or with Th17 cocktail (anti-IFNg 10ng/ml, anti-IL4 10mg/ml, IL6 50ng/ml, IL23 20ng/ml, IL1b 10ng/ml, TGFb 5ng/ml).

tag: hour

tag: height

tag: weight

value: European


title: flavus at milk, rep1

status: Public on May 14 2014

city: Raleigh

first: Gary

last: Payne

address: 851 Main Campus Drive

institute: North Carolina State University

description:
Aflavus_2Milk_Rep1
Transcriptional changes in A. flavus-infected maize kernels.

hyb_protocol: Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip®.

scan_protocol: Standard Affymetrix protocols were followed to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: CEL files generated from the GeneChip DNA microarray scans were imported into JMP/Genomics and log2 transformed for each maize and A. flavus probe. Mismatch probe data were discarded. Log2 intensities were normalized separately for maize and A. flavus probes using the Loess normalization procedure implemented in JMP/Genomics. QC checks were performed before and after normalization. Final expression intensities for each probe set were generated by averaging across data from individual probes. Arrays for the mock-inoculated treatment that had moderate-to-strong A. flavus signal intensities were removed from further analysis. While these kernels visually did not appear infected, they were likely inadvertently contaminated with A. flavus.

organism: Zea mays

source_name: maize B73 kernels, milk stage, inoculated with A. flavus 3357

label_protocol: Standard Affymetrix protocol.

growth_protocol: Inbred maize genotype B73 was grown at the Central Crops Research Station in Clayton, NC. A. flavus NRRL 3357 was grown on potato dextrose agar (PDA) at 28°C for 7-10 days. Conidia were dislodged with 0.05% (v/v) Triton X-100 and diluted to a working solution of 1x10^6 spores mL-1.

extract_protocol: Eight kernels per rep were ground into a fine powder using a pestle in a mortar containing liquid nitrogen and glass beads (Sigma, St. Louis, MO). The ground kernel tissue was immediately transferred to an Oak Ridge centrifuge tube containing 5 ml phenol. The tube was vortexed, 5 ml of 2M Tris buffer solution pH 7 (Acros Organics, Geel, Belgium) was added, and the tube was vortexed again. The tubes were spun in a centrifuge at 10K rpm for 10 minutes at 4°C. The supernatant was transferred to another Oak Ridge centrifuge tube containing 5 ml of 5:1 Phenol: Chloroform at pH 4.5 (Ambion, Foster City, CA). The tubes were vortexed and spun in the centrifuge at 10K rpm for 10 minutes at 4°C. The supernatants were transferred to an additional Oak Ridge centrifuge tube and the Phenol: Chloroform extraction was repeated. The supernatant was transferred to another Oak Ridge centrifuge tube and two volumes of ice cold 95% ethanol were added. The tubes were incubated at -20ºC for 1 hour and then spun at 10K rpm for 30 minutes at 4°C. The liquid was decanted and the pellets were dried. 450 μl of buffer RLT was added as per the RNeasy RNA isolation kit instructions (Qiagen, Valencia, CA) and the rest of the protocol was performed, including DNase treatment.

treatment_protocol: Maize kernels were mock inoculated at the blister (R2) or dough (R4) stage or inoculated with A. flavus at the blister (R2), milk (R3), dough (R4), or dent (R5) stage, and harvested 4 days later.

tag: line

tag: tissue

value: kernels

tag: developmental stage

value: milk

tag: treatment

value: inoculated with Aspergillus flavus 3357


title: flavus at milk, rep3

description:
Aflavus_2Milk_Rep3
Transcriptional changes in A. flavus-infected maize kernels.


title: RUNX1 corrected clone F, Biological replicate 2

status: Public on Jul 01 2014

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: Gene expression data from Corrected RUNX1

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Gene 2.0 ST GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

label: Biotin

source_name: differentiated iPS clone

label_protocol: For RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

growth_protocol: Human iPSCs were derived using the Yamanaka episomal vector system1.  Briefly, patient fibroblasts were reprogrammed using three episomal vectors pCXCLE-hOCT3/4-shp53, pCXCLE-hSK, and pCXLE-hUL (all generous gifts from Dr. Yamanaka).  Cultured fibroblasts were nucleofected using the nucleofector II system with the NHDF solution (AMAXA, now part of Lonza).  Nucleofected fibroblasts were plated on an irradiated primary mouse embryonic fibroblast feeder layer and cultured as described previously1.   Once established, iPSC lines were adapted to a feeder free system, and cultured on Matrigel (BD Bioscience) in Nutristem (Stemgent), or the Essential 8 media (Life Technologies).

extract_protocol: Total RNA (including small and long RNAs) was extracted from cultured cells after 14 days of differentiation using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: No treatments were performed.

tag: genotype

value: RUNX1 corrected clone F


title: RUNX1 corrected clone F, Biological replicate 1


title: flavus at dent, rep1

description:
Aflavus_4Dent_Rep1
Transcriptional changes in A. flavus-infected maize kernels.

source_name: maize B73 kernels, dent stage, inoculated with A. flavus 3357

value: dent


title: flavus at dent, rep2

description:
Aflavus_4Dent_Rep2
Transcriptional changes in A. flavus-infected maize kernels.


title: flavus at milk, rep2

description:
Aflavus_2Milk_Rep2
Transcriptional changes in A. flavus-infected maize kernels.


title: RUNX1 corrected clone E, Biological replicate 2

value: RUNX1 corrected clone E


title: flavus at dent, rep3

description:
Aflavus_4Dent_Rep3
Transcriptional changes in A. flavus-infected maize kernels.


title: mock at dough, rep2

description:
Wounded_3Dough_Rep2
Transcriptional changes in mock-infected maize kernels.

source_name: maize B73 kernels, dough stage, mock inoculated

value: dough

value: mock inoculated


title: RUNX1 corrected clone F, Biological replicate 3


title: mock at blister, rep3

description:
Wounded_1Blister_Rep3
Transcriptional changes in mock-infected maize kernels.

source_name: maize B73 kernels, blister stage, mock inoculated

value: blister


title: RUNX1 mutant, Biological replicate 1

description: Gene expression data from mutant RUNX1

value: RUNX1 mutant


title: flavus at dough, rep3

description:
Aflavus_3Dough_Rep3
Transcriptional changes in A. flavus-infected maize kernels.

source_name: maize B73 kernels, dough stage, inoculated with A. flavus 3357


title: flavus at dough, rep2

description:
Aflavus_3Dough_Rep2
Transcriptional changes in A. flavus-infected maize kernels.


title: flavus at blister, rep1

description:
Aflavus_1Blister_Rep1
Transcriptional changes in A. flavus-infected maize kernels.

source_name: maize B73 kernels, blister stage, inoculated with A. flavus 3357


title: mock at dough, rep3

description:
Wounded_3Dough_Rep3
Transcriptional changes in mock-infected maize kernels.


title: RUNX1 corrected clone E, Biological replicate 1


title: flavus at blister, rep2

description:
Aflavus_1Blister_Rep2
Transcriptional changes in A. flavus-infected maize kernels.


title: mock at dough, rep1

description:
Wounded_3Dough_Rep1
Transcriptional changes in mock-infected maize kernels.


title: mock at blister, rep2

description:
Wounded_1Blister_Rep2
Transcriptional changes in mock-infected maize kernels.


title: RUNX1 mutant, Biological replicate 2

description: Gene expression data from mutant RUNX1


title: flavus at blister, rep3

description:
Aflavus_1Blister_Rep3
Transcriptional changes in A. flavus-infected maize kernels.


title: RUNX1 corrected clone E, Biological replicate 3


title: RUNX1 mutant, Biological replicate 3

description: Gene expression data from mutant RUNX1


title: flavus at dough, rep1

description:
Aflavus_3Dough_Rep1
Transcriptional changes in A. flavus-infected maize kernels.


title: mock at blister, rep1

description:
Wounded_1Blister_Rep1
Transcriptional changes in mock-infected maize kernels.


title: Wild type, biological rep 3

status: Public on May 09 2014

city: Cardiff

first: Philip

last: Taylor

address: Tenovus Building, Heath Park

department: School of Medicine

country: United Kingdom

institute: Cardiff University

description: Gene expression data from wild type myeloid cells

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

scan_protocol: Genechips were scanned using a GeneChip® Scanner 3000 7G

data_processing: The data were analyzed in the R/Bioconductor statistical programming environment. Summarization and MAS5.0 normalization were obtained via the affy package

organism: Mus musculus

source_name: Myeloid cells pooled from 2-3 7 week old wild type mice

label_protocol: RNA was extracted using RNeasy mini kit (QIAgen) according to the manufacturer's instructions.

extract_protocol: Peritoneal cells were recovered by lavage with 5ml of ice-cold 5 mM EDTA in PBS. Lavage from mice were pooled, stained and sorted on a FACSAria III (BD biosciences)

tag: cell

value: Peritoneal resident (CD11b-high, MHCII-low/negative) macrophages


title: Wild type, biological rep 2


title: GATA6 knockout, biological rep 2

description: Gene expression data from Gata6-knockout myeloid cells

source_name: Myeloid cells pooled from 2-3 7 week old knockout mice


title: Olfactory Placode, 12.5d, Dlx5 KO, replicate 3

status: Public on Jan 31 2014

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: We used Affymetrix hybridization kit materials • The procedure followed standard Affymetrix protocols. • Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA was applied separately to the samples involved in each pairwise comparison. The expression values reported are, for both epithelium and mesenchyme, the ones obtained from the following comparisons: OP_11.5 and OE_14.5 from the comparison between the two; OP_12.5 from the comparison with OP_11.5; VNO_14.5 from the comparison with OP_11.5
probe group file: MoEx-1_0-st-v1.na32.mm9.probeset.csv obtained from the website of the manufacturer
meta-probeset file: MoEx-1_0-st-v1.na32.mm9.transcript.csv obtained from the website of the manufacturer

source_name: Olfactory Placode_12.5d_Dlx5 KO

label_protocol: cDNAs were biotinylated using the Terminal Labeling Kit from Affymetrix

growth_protocol: Olfactory epithelia manually dissected from mouse embryos at the age E11.5,  E12.5 and  E14.5.

extract_protocol: Dlx5 mutant phenotypes were visually identified and easily distinguished from the wild-type. Tissues were individually collected in RNA-later, then frozen. Same genotype samples were pooled (at least 4 individuals each) and extracted using Trizol. Samples were treated with the RiobMinusâ„¢ rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using cDNA synthesis and amplification kits from Affymetrix.

treatment_protocol: not applicable

tag: strain background

value: F1 of a C57Black6 x DBA cross

tag: genotype/variation

value: Dlx5 KO

value: Olfactory Placode

tag: fraction


title: Wild type, biological rep 1


title: GATA6 knockout, biological rep 1


title: NR2 line 1 dpi B1R_2

status: Public on Feb 28 2014

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: -Aphanomyces euteiches (Ae), a soilborne oomycete, is the causal agent of pea root rot, a major disease on various cultivated legume species. To gain insight into the mechanism underlying partial resistance to this pathogen, a pathosystem has been developed using the model legume Medicago truncatula (Mt). Two Mt accessions A17 and F83005.5 have been shown to display differential responses upon infection with Ae (partially resistance and susceptibility, respectively). Genetic analyses using a RIL population derived from a cross between those two lines lead to the identification of, prAe1, a major QTL involved in the observed partial resistance. Near isogenic lines (NIL) NR2 and NS2 whose genomes are identical except at the prAe1 locus (resistant alleles for NR2, susceptible alleles for NS2) have been generated, and the same differential response toward Ae has been found. The aim of this experiment is to analyse and compare NR2 and NS2 transcriptomes at 1 and 6 days after Ae inoculation to identify gene networks that are regulated in a prAe1 dependent manner.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - -- In vitro conditions on M medium - 16h light 8h dark 22°C

treatment_protocol: see Djebali et al, MPMI, 2009

tag: strain

tag: infection

value: A. euteiches

tag: time

value: 1 dpi

value: root

tag: sample type

value: medicago truncatula (a17xf83005.5) - harvest date 23-02-11


title: NR2 line 1 dpi B1R_1


title: Olfactory Placode, 12.5d, Dlx5 KO, replicate 2


title: NS2 line 1 dpi D1R_2


title: Olfactory Placode, 12.5d, Dlx5 KO, replicate 1


title: NR2 line 6 dpi B6R_1

value: 6 dpi

value: medicago truncatula (a17xf83005.5) - harvest date 28-02-11


title: NR2 line 0 dpi BOR_1

value: 0 dpi

value: medicago truncatula (a17xf83005.5) - harvest date 22-02-11


title: NS2 line 0 dpi DOR_4

value: medicago truncatula (a17xf83005.5) - harvest date 01-03-11


title: NS2 line 6 dpi D6R_1


title: NS2 line 1 dpi D1R_1


title: NR2 line 0 dpi BOR_4


title: NS2 line 1 dpi D1R_4

value: medicago truncatula (a17xf83005.5) - harvest date 02-03-11


title: NS2 line 0 dpi DOR_1


title: NR2 line 6 dpi B6R_4

value: medicago truncatula (a17xf83005.5) - harvest date 07-03-11


title: GATA6 knockout, biological rep 3


title: NR2 line 6 dpi B6R_2


title: NS2 line 6 dpi D6R_4


title: NS2 line 6 dpi D6R_2


title: NR2 line 1 dpi B1R_4


title: NR2 line 0 dpi BOR_2


title: NS2 line 0 dpi DOR_2


title: Olfactory Placode, 12.5d, wild-type, replicate 3

source_name: Olfactory Placode_12.5d_wild-type

value: wild type


title: Vomeronasal Organ, 14.5d, mesenchymal fraction, replicate 3

source_name: Vomeronasal Organ_14.5d_mesenchymal

value: Vomeronasal Organ

value: mesenchymal


title: Olfactory Placode, 12.5d, wild-type, replicate 2

value: F1 of a C57Black6 x DBA cross


title: Olfactory Placode, 12.5d, mesenchymal fraction, replicate 1

source_name: Olfactory Placode_12.5d_mesenchymal


title: Olfactory Placode, 12.5d, mesenchymal fraction, replicate 2


title: Olfactory Epithelium, 14.5d, mesenchymal fraction, replicate 2

source_name: Olfactory Epithelium_14.5d_mesenchymal

value: Olfactory Epithelium


title: Olfactory Epithelium, 14.5d, mesenchymal fraction, replicate 1


title: Vomeronasal Organ, 14.5d, epithelial fraction, replicate 2

source_name: Vomeronasal Organ_14.5d_epithelial

value: epithelial


title: Vomeronasal Organ, 14.5d, mesenchymal fraction, replicate 1


title: Olfactory Placode, 11.5d, mesenchymal fraction, replicate 3

source_name: Olfactory Placode_11.5d_mesenchymal

value: Olfactory Placode


title: Vomeronasal Organ, 14.5d, mesenchymal fraction, replicate 2


title: Olfactory Placode, 11.5d, mesenchymal fraction, replicate 2


title: Vomeronasal Organ, 14.5d, epithelial fraction, replicate 3


title: Olfactory Epithelium, 14.5d, mesenchymal fraction, replicate 3


title: Olfactory Placode, 11.5d, mesenchymal fraction, replicate 1


title: Olfactory Placode, 12.5d, epithelial fraction, replicate 1

source_name: Olfactory Placode_12.5d_epithelial


title: Olfactory Placode, 11.5d, epithelial fraction, replicate 3

source_name: Olfactory Placode_11.5d_epithelial


title: Olfactory Placode, 12.5d, epithelial fraction, replicate 2


title: Olfactory Epithelium, 14.5d, epithelial fraction, replicate 1

source_name: Olfactory Epithelium_14.5d_epithelial


title: Olfactory Placode, 12.5d, epithelial fraction, replicate 3


title: Olfactory Placode, 11.5d, epithelial fraction, replicate 1


title: Olfactory Epithelium, 14.5d, epithelial fraction, replicate 2


title: Olfactory Placode, 12.5d, mesenchymal fraction, replicate 3


title: Olfactory Placode, 12.5d, wild-type, replicate 1


title: Vomeronasal Organ, 14.5d, epithelial fraction, replicate 1


title: Scramble for Mett3 at 0h, biological rep1 (YW-3-1)

status: Public on Jan 06 2014

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

description: Gene expression data from mouse embryos stem cell treated with scrambled control for 0 hour

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Microarray CEL files were imported and normalized using rma function from bioconductor package oligo.

source_name: mESC Scramble control for Mett3 at 0 hour

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: Mouse ES cells were maintained on feeder layers of irradiated mouse embryonic fibroblasts (MEFs) in DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 500 units/ml leukemia inhibiting factor (LIF, Chemicon). Lentiviral constructs including shRNA were purchased from Sigma. To produce lentivirus, lentiviral constructs and packaging constructs were transfected into 293ft cells by calcium phosphate reagent (Clontech). About 36 hours after transfection, viral supernatants were collected and supplemented with 6 μg/μl polybrene (Millipore). ES cells were incubated with virus-containing medium for 12 h. 3 days after infection, 2 μg/ml puromycin (Sigma) were added to medium for stable cell lines selection.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen).  RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination.  PolyA RNA was purified using GenElute™ mRNA Miniprep Kit (Sigma Aldrich) per manufacturer’s instruction.

treatment_protocol: ES cells J1 were seeded 2×105 per well in 6-well plate and transfected with siRNAs by lipofectamine RNAiMAX (Invitrogen) following manufacturer’s protocol. After 48 hours cells were reseeded and transfected with siRNA again. After another 48 hours cells were collected for analysis. Target sequences of siRNA:   Mettl3, GGACTGCGATGTGATTGTA, GACGAATTATCAATAAGCA;   Mettl14, CCGGATGTACAGAGGAAAT, GGGAACTCATCAGACTAAA, GCACCTCGGTCATTTATAT  Scramble

value: 0 hour

value: Wild type

tag: cell line

value: ES cells J1


title: Olfactory Epithelium, 14.5d, epithelial fraction, replicate 3


title: Mettl3 KD at 0h, biological rep1 (YW-4-1)

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl3 for 0 hour

source_name: mESC Mettl3 knockdown at 0 hour

value: Mettl3 KDMutant


title: Mettl3 KD at 0h, biological rep2 (YW-4)


title: Mettl14 KD at 0h, biological rep2 (YW-2)

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl14 for 0 hour

source_name: mESC Mettl14 knockdown at 0 hour

value: Mettl14 KDMutant


title: Scramble for Mett3 at 0h, biological rep2 (YW-3)

description: Gene expression data from mouse embryos stem cell treated with scrambled control for 4 hour


title: Mettl3 KD at 8h, biological rep1

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl3 for 8 hour

source_name: mESC Mettl3 knockdown at 8 hour

value: 8 hour

value: Mettl3 KD


title: Mettl14 KD at 0h, biological rep1 (YW-2-1)


title: Mettl14 KD at 4h, biological rep2

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl14 for 4 hour

source_name: mESC Mettl14 knockdown at 4 hour

value: 4 hour

value: Mettl14 KD


title: Mettl14 KD at 8h, biological rep2

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl14 for 8 hour

source_name: mESC Mettl14 knockdown at 8 hour


title: Mettl3 KD at 0h, biological rep2


title: Mettl3 KD at 4h, biological rep2

description: Gene expression data from mouse embryos stem cell treated with shRNA knockdown for Mettl3 for 4 hour

source_name: mESC Mettl3 knockdown at 4 hour


title: Mettl14 KD at 8h, biological rep1


title: Mettl3 KD at 8h, biological rep2


title: Scramble for Mett14 at 0h, biological rep1 (YW-1-1)

source_name: mESC Scramble control for Mett14 at 0 hour


title: Mettl3 KD at 0h, biological rep1


title: Mettl3 KD at 4h, biological rep1


title: Olfactory Placode, 11.5d, epithelial fraction, replicate 2


title: Mettl14 KD at 0h, biological rep2


title: Scramble for Mett14 at 0h, biological rep2 (YW-1)


title: Mettl14 KD at 4h, biological rep1


title: Scramble at 4h, biological rep2

source_name: mESC Scramble control at 4 hour


title: Scramble at 8h, biological rep2

description: Gene expression data from mouse embryos stem cell treated with scrambled control for 8 hour

source_name: mESC Scramble control at 8 hour


title: Mettl14 KD at 0h, biological rep1


title: Scramble at 0h, biological rep2

source_name: mESC Scramble control at 0 hour


title: Scramble at 0h, biological rep1


title: Control Non scratched C3

status: Public on Sep 01 2013

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: Normal human astrocytes (NHAs) isolated from cerebral neocortex of second trimester fetuses were grown to confluence over 6 weeks, passaged once and transferred to coated chamber slides.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Fetal NHAs derived from second trimester cerebral cortex were purchased cryopreserved after first passage (ScienCell Research Laboratories).  After thawing in a 37°C water bath, 1 x 106 cells were plated on poly-L-lysine coated 75 cm2 polystyrene tissue culture flasks in human astrocyte medium containing 2% serum and astrocyte growth factors (ScienCell).  Cells were grown to >90% confluence, trypsinized (trypsin-EDTA 0.5% w/v, Invitrogen), and replated for experiments.

value: Normal human astrocytes (NHAs)

value: linear monolyer no scratch


title: Scramble at 8h, biological rep1


title: Control Non scratched C2

source_name: cerebral neocortex of second trimester fetuses


title: scratched S1

value: linear monolyer scratch


title: Control Non scratched C4


title: GA_Base

status: Public on Aug 01 2013

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Summarization of bead-level data to gene-level signals was performed using the R package beadarray, after removal of outliers greater than 3 median absolute deviations (MADs). Between-sample quantile normalization was performed using Partek Genomics Suite (Partek, Inc., St. Louis, Missouri), followed by correction of experimental batch effects (i.e., related to differences in dates of RNA extraction and array processing) using the Partek Batch Remover TM tool. As a result, a total of 34,666 Expressed Genes with expression signals greater than 6 (in log2 scale) in at least one of the samples were retained for further analysis. The full Matrix table can be found on Series.

source_name: Spleen Cell Cultures

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

growth_protocol: Preparation of Mouse Spleen Cell Cultures: All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee (Protocols #506 and #512). To stimulate induction of GA-reactive T cells, eight female 8- to 12-week-old F1 hybrid (SJL X BALB/C) mice (purchased from Harlan Biotech Israel, Rehovot, Israel) were inoculated with 100 µL of a 2.5 mg/mL solution of GA reference standard (GA-RS) in PBS to achieve an immunization dose of 250 µg GA-RS per mouse. Mice were housed in individually ventilated cages for 3 days after immunization, and on the third day, were sacrificed by cervical dislocation. Mouse spleens (SPL) were excised via side incision using sterile procedures, placed in sterile 50-mL CellStar polypropylene tubes (2 spleens/tube) containing RPMI 1640 without glutamine (Biological Industries, Beit Haemek, Israel), and placed on ice to prevent tissue degradation. Primary cultures of pooled SPL cells were collected as follows: SPL tissue in RPMI was filtered (70 µm nylon) and centrifuged at 300xg for 10 minutes at room temperature (RT). The precipitate was resuspended in Ack lysing buffer (Invitrogen, Carlsbad, CA) incubated for 3 minutes at RT, diluted 1:10 with RPMI, and centrifuged again at 200xg for 10 minutes at RT. The pellet was re-washed (10 mL RPMI), re-centrifuged (200xg, 10 minutes at RT), and then resuspended in enriched defined cell culture media (DCCM1). DCMM1 (Biological Industries, Beit Haemek, Israel) (96.7% v/v) was enriched with L-glutamine 2mM (1% v/v), MEM 2mM (1% v/v), sodium pyruvate 1 mM (1% v/v), antibiotic/antimycotic solution (0.2% v/v), and 2-mercaptoethanol (0.1% v/v).  All SPL samples were pooled.  Cell density and viability were assessed using the Trypan Blue Exclusion method  (22) (hemacytometer, Sigma Z35,962-9). Viable cells were diluted with enriched DCCM1 to a concentration of 10 x 106 cells/mL.

extract_protocol: PerfectPure RNA Cultures CEKK kit 50 (5Prime GmbH, Hamburg, Germany) according to manufacturer’s instructions. RNA quality was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis (Experionä, Bio-Rad, Hercules, CA).

treatment_protocol: Aqueous activator samples (125 µL per well of 80 µg/mL solutions of Verified GA, DM-GA, Unverified Glatiramoid [TV-5010 concentration was 40 µg/mL since 80 µg/mL was cytotoxic], Unverified Generic GA, MBP, and mannitol [the non-active excipient in Copaxone]) and medium samples were added to 96-well tissue culture plates (3 wells per sample).Viable SPL cells (125 µL 10x106 SPL cell/mL suspension) were added to the activator solutions and incubated for 24 hours at 37°C in a humidified incubator with a 5% CO2 atmosphere. Incubated samples were then centrifuged at 3000g x 5 minutes at RT, washed, diluted RNA stabilization solution (RNAlaterÒ solution, Applied Biosystems), and stored at 4°C.

tag: group

value: Deliberately Modified GA


title: Scramble at 4h, biological rep1


title: Appo1.1

value: Unverified Glatiramoid


title: DM961


title: Appo2.2


title: DM962.2


title: Edan.1


title: TV5010.1


title: GA_Heat


title: TV5010.2


title: TV109


title: GA_Acid


title: scratched S3


title: Shira.2


title: Shira.1


title: Control Non scratched C1


title: N5.3

value: Unverified Generic GA


title: Appo2.1


title: N5.2


title: DM962.3


title: DM962.1


title: DM958


title: N4.3


title: Edan.2


title: N4.2


title: N2.2


title: N3.1


title: C1.1


title: N4.1


title: N2.1


title: DP-34

value: Verified GA


title: C1.2


title: DP-30


title: N1.1


title: DP-29


title: DP-18


title: DP-31


title: DP-24


title: DP-33


title: DP-17


title: DP-20


title: DP-23


title: DP-25


title: DP-16


title: DP-28


title: DP-27


title: DP-26


title: DP-21


title: DP-19


title: DP-32


title: DP-22


title: DP-15


title: DP-14


title: DP-09


title: N3.2


title: DP-08


title: DP-13


title: DP-10


title: DP-12


title: DP-11


title: DP-05


title: DP-07


title: DP-03


title: DP-06


title: DP-04


title: RS-19


title: RS-03


title: RS-16


title: RS-13


title: RS-18


title: RS-04


title: RS-01


title: DP-02


title: RS-12


title: RS-14


title: DP-01


title: RS-17


title: RS-15


title: RS-11


title: RS-10


title: RS-02


title: RS-08


title: RS-09


title: Medium-14

value: Background


title: RS_h-1

description:
RS_h-1
half dose


title: RS_h-2

description:
RS_h-2
half dose


title: RS-06


title: Medium-11


title: Medium-12


title: RS-05


title: Medium-02


title: RS-07


title: RS_h-3

description:
RS_h-3
half dose


title: Manitol

description: Manitol

value: other


title: Medium-04


title: Medium-09


title: TV-35


title: Medium-06


title: Medium-01


title: Medium-08


title: Medium-07


title: Medium-03


title: Medium-05


title: TV-66


title: Medium-13


title: Medium-10


title: CD47 null Endothelial Embryoid Bodies 2

status: Public on Jul 10 2013

description: CD47 null-C57Bl/6

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

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

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC version 3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (version 1.2.1) to generate an RMA normalized, log2 transformed and gene summarized matrix table.

source_name: CD47 null Lung Endothelial Embryoid Bodies

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: WT and CD47 null Mouse lung endothelial cells were cultured at 37 °C with 5% CO2 using Endothelial Growth Medium-2 (EGM2) (Lonza).V6.5  mES cells were cultured in DMEM medium containing 15% fetal bovine serum and 1000 IU/ml LIF (Leukemia Inhibitory Factor.

extract_protocol: total RNA  was extracted by TRIzol (Invitrogen) method.

treatment_protocol: CD47 null mouse lung endothelial cells passaged for 6 months were seeded into 6-well tissue culture plates using basal Endothelial Basal  Medium (Lonza) without serum . Embryoid bodies appeared after 24-36 h.

tag: cell type

value: CD47 null Endothelial Embryoid Bodies

value: CD47 null


title: CD47 null Endothelial Embryoid Bodies 3

description: CD47 null-C57Bl/6


title: CD47 null Endothelial cells 3

description: CD47 null-C57Bl/6

source_name: CD47 null lung Endothelial cells

value: CD47 null Endothelial cells


title: CD47 null Endothelial Embryoid Bodies 1

description: CD47 null-C57Bl/6


title: Established Embryonic Stem Cell line 3

description: V6.5 mouse ES

source_name: Established V6.5 Embryonic Stem Cell line

value: Established Embryonic Stem Cell line


title: Established Embryonic Stem Cell line 2

description: V6.5 mouse ES

source_name: Established V6.5  Embryonic Stem Cell line


title: Endothelial cells 2

description: CD47 WT-C57Bl/6

source_name: lung Endothelial cells

value: Endothelial cells

value: wild type


title: CD47 null Endothelial cells 2

description: CD47 null-C57Bl/6


title: CD47 null Endothelial cells 1

description: CD47 null-C57Bl/6


title: Established Embryonic Stem Cell line 1

description: V6.5 mouse ES


title: Endothelial cells 3

description: CD47 WT-C57Bl/6


title: Subject_AF0335_SR_T7

status: Public on Feb 27 2013

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

description:
Blood_25.5hrsAwake_at07:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 07:15 following 25.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37°C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Individual samples were filtered based on AgilentQC metrics of reproducibility statistics, minimum detection level estimates and feature flags. Samples with a median coefficient of variation of less than 10% in spike ins or non-control replicated probes (NCRPs) were retained and quantile-normalized using the R Bioconductor package limma. NCRPs along with their corresponding flags were averaged. Probes with more than 5 flagged samples within a subject in more than half of the total number of subjects were excluded. In addition, for time-series analyses, series with 2 consecutive or more than 2 missing time points were excluded.

label_protocol: cRNA was synthesized and fluorescently labelled with Cy3-CTP from 100 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit.

growth_protocol: Blood samples were collected via an indwelling venous cannula sited in the forearm for minimum discomfort and restriction of movement. Cannulae were kept patent by the use of sterile saline. Each sample tube was coded for subject and sample collection time (participant code/sample type/sequential number)

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: 2.5 ml of blood is drawn into the PAXGene tube at each sampling point. The tube is inverted 10 times to mix. The tube is then stored at room temperature for 4 hours in upright position. The tube is transferred to -50°C and placed lying down (never in upright position as this may cause the tube to crack) for storage at the university of Surrey Clinical Research Centre. The tube is transferred on ice to University of Surrey Faculty of Health and Medical Sciences for storage/processing

tag: subject

value: Blood

tag: sleepprotocol

value: Sleep Restriction

tag: hoursawake

tag: timesampletaken

tag: circadianphase


title: Subject_AF0335_SR_T9

description:
Blood_31.5hrsAwake_at13:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 13:15 following 31.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)

tag: tissue


title: Subject_AF0335_SR_T8

description:
Blood_28.5hrsAwake_at10:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 10:15 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: N5.1


title: Subject_AF0335_SR_T3

description:
Blood_13.5hrsAwake_at19:16afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 19:16 following 13.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SR_T10

description:
Blood_34.5hrsAwake_at16:17afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 16:17 following 34.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SR_T6

description:
Blood_22.5hrsAwake_at04:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 04:15 following 22.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T6

description:
Blood_22.5hrsAwake_at05:15afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 05:15 following 22.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)

value: Sleep Extension


title: Endothelial cells 1

description: CD47 WT-C57Bl/6


title: Subject_AF0335_SR_T5

description:
Blood_19.5hrsAwake_at01:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 01:15 following 19.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T5

description:
Blood_19.5hrsAwake_at02:15afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 02:15 following 19.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SR_T1

description:
Blood_ 7.5hrsAwake_at13:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 13:15 following  7.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SR_T2

description:
Blood_10.5hrsAwake_at16:17afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 16:17 following 10.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SR_T4

description:
Blood_16.5hrsAwake_at22:15afterSleepRestriction_Per3_5\5genotype_Subject_AF0335
Blood taken at 22:15 following 16.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T2

description:
Blood_10.5hrsAwake_at17:19afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 17:19 following 10.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T4

description:
Blood_16.5hrsAwake_at23:15afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 23:15 following 16.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0318_SR_T4

description:
Blood_16.5hrsAwake_at22:30afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 22:30 following 16.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0335_SE_T1

description:
Blood_ 7.5hrsAwake_at14:17afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 14:17 following  7.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T7

description:
Blood_25.5hrsAwake_at08:15afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 08:15 following 25.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0335_SE_T3

description:
Blood_13.5hrsAwake_at20:16afterSleepExtension_Per3_5\5genotype_Subject_AF0335
Blood taken at 20:16 following 13.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0335)


title: Subject_AF0318_SE_T9

description:
Blood_31.5hrsAwake_at14:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 14:30 following 31.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T8

description:
Blood_28.5hrsAwake_at10:32afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 10:32 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T9

description:
Blood_31.5hrsAwake_at13:30afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 13:30 following 31.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T10

description:
Blood_34.5hrsAwake_at16:30afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 16:30 following 34.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T10

description:
Blood_34.5hrsAwake_at18:10afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 18:10 following 34.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T1

description:
Blood_ 7.5hrsAwake_at13:30afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 13:30 following  7.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T3

description:
Blood_13.5hrsAwake_at19:29afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 19:29 following 13.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T7

description:
Blood_25.5hrsAwake_at07:30afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 07:30 following 25.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T4

description:
Blood_16.5hrsAwake_at23:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 23:30 following 16.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T8

description:
Blood_28.5hrsAwake_at11:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 11:30 following 28.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SR_T2

description:
Blood_10.5hrsAwake_at16:28afterSleepRestriction_Per3_5\5genotype_Subject_AF0318
Blood taken at 16:28 following 10.5 hours awake after following a Sleep Restriction protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T2

description:
Blood_10.5hrsAwake_at17:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 17:30 following 10.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T6

description:
Blood_22.5hrsAwake_at05:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 05:30 following 22.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0295_SE_T6

description:
Blood_22.5hrsAwake_at06:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 06:00 following 22.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0318_SE_T7

description:
Blood_25.5hrsAwake_at08:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 08:30 following 25.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0295_SE_T5

description:
Blood_19.5hrsAwake_at03:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 03:00 following 19.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0295_SE_T9

description:
Blood_31.5hrsAwake_at15:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 15:00 following 31.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0286_SR_T10

description:
Blood_34.5hrsAwake_at16:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 16:40 following 34.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0318_SE_T3

description:
Blood_13.5hrsAwake_at20:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 20:30 following 13.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0295_SE_T10

description:
Blood_34.5hrsAwake_at18:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 18:00 following 34.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0295_SE_T8

description:
Blood_28.5hrsAwake_at12:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 12:00 following 28.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0286_SR_T2

description:
Blood_10.5hrsAwake_at16:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 16:40 following 10.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0295_SE_T7

description:
Blood_25.5hrsAwake_at09:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 09:00 following 25.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0295_SE_T4

description:
Blood_16.5hrsAwake_at00:00afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 00:00 following 16.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0286_SR_T6

description:
Blood_22.5hrsAwake_at04:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 04:40 following 22.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0286_SR_T7

description:
Blood_25.5hrsAwake_at07:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 07:40 following 25.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0286_SR_T8

description:
Blood_28.5hrsAwake_at10:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 10:40 following 28.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0286_SR_T4

description:
Blood_16.5hrsAwake_at22:40afterSleepRestriction_Per3_4\4genotype_Subject_AF0286
Blood taken at 22:40 following 16.5 hours awake after following a Sleep Restriction protocol from a Per3 4\4 genotype subject (Subject AF0286)


title: Subject_AF0295_SE_T2

description:
Blood_10.5hrsAwake_at18:01afterSleepExtension_Per3_5\5genotype_Subject_AF0295
Blood taken at 18:01 following 10.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0295)


title: Subject_AF0318_SE_T1

description:
Blood_ 7.5hrsAwake_at14:34afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 14:34 following  7.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)


title: Subject_AF0318_SE_T5

description:
Blood_19.5hrsAwake_at02:30afterSleepExtension_Per3_5\5genotype_Subject_AF0318
Blood taken at 02:30 following 19.5 hours awake after following a Sleep Extension protocol from a Per3 5\5 genotype subject (Subject AF0318)