title: cDNA3 30ºC rpo21-4 on filter V8-L1-11

status: Public on Mar 31 2016

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling for YFN117 strain 30ºC. Replicate 3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: rpo21-4 at 30ºC

label_protocol: For cDNA labeling, about 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

growth_protocol: Cells were grown in YPD at 30ºC to 0.5 OD600. At that cells were spun-down or changed to 37ºC by adding hot YPD. These aliquots were cultured for 30 min and collected. Thus, wt and mutants have two samples: 30 and 37ºC. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: genotype/variation

tag: background strain


title: cDNA2 37ºC rpo21-4 on filter V8-L1-13

description: cDNA labelling for YFN117 strain 37ºC. Replicate 2

source_name: rpo21-4 at 37ºC


title: cDNA1 37ºC rpo21-4 on filter V8-L1-12

description: cDNA labelling for YFN117 strain 37ºC. Replicate 1


title: cDNA2 37ºC rpb1-84 on filter V8-L1-13

description: cDNA labelling for YFN104 strain 37ºC. Replicate 2

source_name: rpb1-84 at 37ºC


title: cDNA2 30ºC rpb1-84 on filter V8-L1-13

description: cDNA labelling for YFN104 strain 30ºC. Replicate 2

source_name: rpb1-84 at 30ºC


title: cDNA3 37ºC rpb1-84 on filter V8-L1-14

description: cDNA labelling for YFN104 strain 37ºC. Replicate 3


title: cDNA2 30ºC wt on filter V8-L1-10

description: cDNA labelling for WT strain 30ºC. Replicate 2

source_name: wt at 30ºC

value: YFN116 wild type


title: cDNA2 37ºC wt on filter V8-L1-14

description: cDNA labelling for WT strain 37ºC. Replicate 2

source_name: wt at 37ºC


title: cDNA3 37ºC rpo21-4 on filter V8-L1-14

description: cDNA labelling for YFN117 strain 37ºC. Replicate 3


title: cDNA1 37ºC rpb1-84 on filter V8-L1-12

description: cDNA labelling for YFN104 strain 37ºC. Replicate 1


title: cDNA1 37ºC wt on filter V8-L1-13

description: cDNA labelling for WT strain 37ºC. Replicate 1


title: cDNA3 30ºC rpb1-84 on filter V8-L1-14

description: cDNA labelling for YFN104 strain 30ºC. Replicate 3


title: cDNA3 37ºC wt on filter V8-L1-12

description: cDNA labelling for WT strain 37ºC. Replicate 3


title: cDNA3 30ºC wt on filter V8-L1-11

description: cDNA labelling for WT strain 30ºC. Replicate 3


title: cDNA1 30ºC rpb1-84 on filter V8-L1-12

description: cDNA labelling for YFN104 strain 30ºC. Replicate 1


title: cDNA1 30ºC wt on filter V8-L1-9

description: cDNA labelling for WT strain 30ºC. Replicate 1


title: cDNA1 30ºC rpo21-4 on filter V8-L1-10

description: cDNA labelling for YFN117 strain 30ºC. Replicate 1


title: cDNA2 30ºC rpo21-4 on filter V8-L1-8

description: cDNA labelling for YFN117 strain 30ºC. Replicate 2


title: Mfn1 AlbCre Mfn1 LKO High fat diet 638

city: Lausanne

first: Sameer

last: Kulkarni

address: EPFL Innovation Park

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: log2 transformed + quantile normalization

label: Biotin

organism: Mus musculus

source_name: Mouse liver

label_protocol: Illumina TotalPrep RNA amplification kit

extract_protocol: Total RNA extraction with RNAdvanced tissue kit ( Agencourt)

treatment_protocol: The mice were fed on high fat diet for 8 weeks

tag: strain

tag: tissue

value: liver

value: Mfn1 LKO


title: Mfn1 AlbCre Mfn1 LKO High fat diet 701


title: Mfn1 AlbCre Mfn1 LKO High fat diet 651


title: Mfn1 AlbCre Mfn1 LKO High fat diet 637


title: thyroid_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

country: Sweden

institute: Sahlgrenska Academy at University of Gothenburg

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

label: biotin

source_name: Mouse thyroid, 2 Gy, collum+thorax+abdomen irradiated

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Excised organs were flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Balb/c

value: Thyroid

tag: irradiated area

value: collum+thorax+abdomen

tag: absorbed dose

value: 2 Gy

tag: time point

tag: radiation quality

value: 4 MV (nominal) photon radiation


title: Mfn1 AlbCre Control High fat diet 663

value: Mfn1 Wildtype


title: thyroid_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse thyroid, 2 Gy, thorax+abdomen irradiated

value: thorax+abdomen


title: thyroid_control, not irradiated_excised after 24h_rep5_R_d1

source_name: Mouse thyroid, 0 Gy, not irradiation

value: 0 Gy


title: thyroid_control, not irradiated_excised after 24h_rep2


title: thyroid_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: thyroid_collum irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse thyroid, 2 Gy, collum irradiated

value: collum


title: thyroid_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: thyroid_collum irradiated with 2 Gy_excised after 24h_rep2


title: thyroid_control, not irradiated_excised after 24h_rep4


title: thyroid_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: thyroid_collum irradiated with 2 Gy_excised after 24h_rep1


title: Mfn1 AlbCre Control High fat diet 641


title: Mfn1 AlbCre Control High fat diet 658


title: Mfn1 AlbCre Control High fat diet 661


title: thyroid_control, not irradiated_excised after 24h_rep5


title: spleen_control, not irradiated_excised after 24h_rep5

source_name: Mouse spleen, 0 Gy, not irradiation

value: Spleen


title: spleen_control, not irradiated_excised after 24h_rep4


title: spleen_control, not irradiated_excised after 24h_rep3


title: thyroid_control, not irradiated_excised after 24h_rep5_R_d2


title: thyroid_control, not irradiated_excised after 24h_rep1


title: thyroid_control, not irradiated_excised after 24h_rep3


title: thyroid_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: Rosette leaves treated with IDL7 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 3)

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 825 ng cRNA from both mock-treated plants and IDL6 or IDL7 peptide-treated plants were used. The cRNA mixture was fragmented and hybridized on Arabidopsis (V4) Gene Expression Microarray 4x44K arrays in a rotary oven at 65°C in ~15 h. The slides were washed with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325), Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), acetonitrile (VWR International) and Stabilization and Drying Solution (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slides were scanned at 5 µm resolution on an Agilent DNA microarray scanner (Agilent Technologies).

data_processing: Prior to the statistical analysis spots from control spikes, landmarks and genes with low expression (absent) were filtered out. The data were analysed using the limma package (Smyth, 2004) and the R statistical data analysis program package (R 2.10.1). No background subtraction was performed and data were normalized by the global loess normalization method. The Benjamini and Hochberg’s method to control the false discovery rate was used to identify differentially regulated genes (Benjamini and Hochberg, 1995). Genes with dye bias effects were removed and genes with an adjusted p-value less than 0.05 were regarded as significantly differentially expressed.

organism: Arabidopsis thaliana

source_name: IDL7 peptide 2hr_rosette leaves

label_protocol: Total RNA (~0.2 µg) was reverse transcribed, amplified and labelled using the Low Input Quick Amp Labeling Kit, two-color, (Agilent p/n 5190-2306) (Agilent Technologies, USA). cRNA from the mock and IDL6 peptide treated plants (or IDL7 peptide treated plants) were alternately labelled with Cy3 or Cy5.

growth_protocol: Seeds of Col-0 ecotype were surface-sterilised and sown out on half-strength MS plates at a density of 20 seeds per Petri dish (14 cm diameter), and stratified for 3 days at 4°C. Plates were grown under a 16 h photoperiod (70 µmol m-2 s-1) at 22°C for two weeks.

extract_protocol: 100 mg frozen plant tissue each from four biological replicas were homogenised using TissueLyser II (Qiagen, Hilden, Germany) for 2 x 2 minutes at 25 Hz. Total RNA was extracted with the Spectrum Plant Total RNA kit (Sigma-Aldrich, Saint Louis, USA) as described by the supplier, but with lysis solution being added to the plant tissue between the two disruption cycles. An on-column DNase digestion was performed using the RNase-Free DNase Set (Qiagen, Hilden, Germany).

treatment_protocol: Seedlings were treated by spraying with an aqueous peptide solution (100 nM) supplemented with 0.02% silwet L-77 (Lehle Seeds, UK). Whole rosettes were collected 2 h after treatment, snap-frozen in liquid nitrogen, and stored at -80°C.

tag: ecotype

tag: age

value: 2 week stage

tag: treated with

value: IDL7 peptide for 2hrs

value: rosette leaves

source_name: Mock peptide 2hr_rosette leaves

value: Mock peptide for 2hrs


title: Rosette leaves treated with IDL6 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 3)

source_name: IDL6 peptide 2hr_rosette leaves

value: IDL6 peptide for 2hrs


title: spleen_control, not irradiated_excised after 24h_rep1


title: Rosette leaves treated with IDL7 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 4)


title: spleen_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse spleen, 2 Gy, collum+thorax+abdomen irradiated


title: Rosette leaves treated with IDL7 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 2)


title: Rosette leaves treated with IDL6 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 2)


title: PA_GW_UlkKD_2

city: Singapore

first: Paul

middle: Michael

last: Yen

address: 8 College Road

department: Cardiovascular & Metabolic disorder Program

country: Singapore

institute: Duke-NUS Graduate Medical School Singapore

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was quantile normalized in Partek Genomics Suite software (version 6.6)

source_name: AML-12 cells

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

growth_protocol: Aml-12 mose hepatocytes were culture in 1:1 DMEM/F12 Media with 10%FBS

extract_protocol: Total RNA was extracted using InviTrap Spin Cell RNA Mini Kit (Stratec) according to the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: AML-12 cells co-treated with 0.75mM PA+/- 10µM GW3965 for 24 h +/- Ulk1 SiRNA

value: Liver

tag: treatment

value: Palmitic acid and GW3965 and Ulk1 siRNA


title: Rosette leaves treated with IDL6 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 4)


title: spleen_control, not irradiated_excised after 24h_rep2

value: Balb/c


title: spleen_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse spleen, 2 Gy, thorax+abdomen irradiated


title: Rosette leaves treated with IDL6 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 1)


title: Rosette leaves treated with IDL7 peptide for 2 hours compared to rosette leaves treated with mock peptide (replica 1)


title: PA_GW_UlkKD_3

description: replicate 3


title: spleen_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: spleen_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: spleen_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: spleen_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: PA_GW_3

description: replicate 3

value: Palmitic acid and GW3965


title: SWEETMock2dpi4.txt:gProcessedSignal

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

country: Germany

hyb_protocol: following fragmentation, 600ng of Cy3-labeled cRNA were hybridisied for 17h at 65°C on Arabidopsis Agilent AthV4 arrays (Agilent Design ID 021169). Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 9.5.3.1 (Agilent Technologies Germany).

data_processing:
Data analysis was performed using GeneSpringXI (Agilent Technologies)
Signal intensities were normalized to the 75th percentile and normalized data were baseline transformed to the median using Gene Spring XI software.

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 400ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Arabidopsis plants were germinated for 10 days in short day conditions at 21°C and subsequently grown in a phytochamber in 12h (22°C)/ 12h (20°C) light-dark cycle for 25 days. At day 18 in the phytochamber, plants were fertilized with 40ml of a 0.2% Wuxal Super solution (Aglykon, Düsseldorf).

extract_protocol: Total leaf RNA was extracted using a guanidium isothiocyanate based method (as described by Chomczynski and Sacchi, 1987).

treatment_protocol: Five weeks old Arabidopsis plants were spray infected 1h before the end of the light period with 2 Mio. conidia/ ml of Colletotrichum higginsianum isolate MAFF 305635 harvested from 9d old OMA plates in a humid tray sealed with moist towel paper and covered with a dome. These high humidity conditions were released at 62 hours post treatment

tag: genotype

value: fully expanded leaves

tag: infection status

value: mock

tag: pathogen

value: 2.5 dpi


title: SWEETMock2dpi3.txt:gProcessedSignal


title: PA_GW_1

description: replicate 1


title: spleen_collum irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse spleen, 2 Gy, collum irradiated

value: 2 Gy

value: 4 MV (nominal) photon radiation


title: SWEETMock2dpi2.txt:gProcessedSignal


title: Ctrl_2

description: replicate 2


title: PA_1

description: replicate 1

value: Palmitic acid


title: SWEETInf2dpi2.txt:gProcessedSignal

value: infected

value: Colletotrichum higginsianum


title: spleen_collum irradiated with 2 Gy_excised after 24h_rep2

value: Spleen

value: collum


title: SWEETMock2dpi1.txt:gProcessedSignal


title: spleen_collum irradiated with 2 Gy_excised after 24h_rep1


title: PA_3

description: replicate 3


title: PA_2

description: replicate 2


title: lungs_control, not irradiated_excised after 24h_rep5

source_name: Mouse lungs, 0 Gy, not irradiation

value: Lungs

value: 0 Gy


title: PA_GW_2

description: replicate 2


title: Ctrl_3

description: replicate 3


title: SWEETInf2dpi1.txt:gProcessedSignal


title: lungs_control, not irradiated_excised after 24h_rep4


title: hindlimb muscle of aged mice, ZT 15, repeat 2

city: Berlin

middle: Florian

last: Thaben

state: Berlin

address: Philippstr. 13, Haus 4

department: Institute for Theoretical Biology

institute: Charite Universitätsmedizin Berlin

description:
Gene expression in aged mouse muscle at ZT 15
Mmu_Muscle_aged_ZT15_2

hyb_protocol: Labeled RNA was loaded on GeneChip Mouse Gene 2.0 ST Array chips following the manufacturer's instructions.

scan_protocol: Chips where scanned in Affymetrix GCS3000 high resolution scanner.

data_processing: Data where processed with R  (v3.2.2) using the package affy (v1.44.1). For normalization and summarization, the RMA procedure with custom made CDFs from the Brainarray project (mogene20st_Mm_ENTREZG; v18) were used.

source_name: hindlimb muscle of aged_ZT 15

label_protocol: RNA samples from 3 different animals sampled at the same time point were pooled and labeled as recommended by the manufacturer with the labeling kit for GeneChip Mouse Gene 2.0 ST Arrays.

growth_protocol: Mice of two different age groups (young = 8 weeks; aged = 80 weeks) where kept under 12 h light / 12 h dark conditions for 2 weeks to ensure stable circadian entrainment. Food and water where supplied ad libitum.

extract_protocol: Muscle samples where homogenized using the gentleMacs system following the manufacturer's instructions for frozen tissue. Extraction of total RNA was made with Trizol following manufacturers instructions. Purified RNA was redissolved in RNAse free water.

treatment_protocol: Beginning with ZT 0 and afterwards in intervals of 3 hours, 3 young and 3 aged mice where sacrificed. Hindlimb muscles where extracted, shock frozen in liquid nitrogen and stored at 193 K. Sample collection was done at 16 different time points over 2 sucsessive days.

tag: zt

tag: age (weeks)

value: hindlimb muscle

tag: repeat


title: SWEETInf0dpi4.txt:gProcessedSignal

value: 0 dpi


title: hindlimb muscle of aged mice, ZT 21, repeat 2

description:
Gene expression in aged mouse muscle at ZT 21
Mmu_Muscle_aged_ZT21_2

source_name: hindlimb muscle of aged_ZT 21


title: hindlimb muscle of aged mice, ZT 12, repeat 2

description:
Gene expression in aged mouse muscle at ZT 12
Mmu_Muscle_aged_ZT12_2

source_name: hindlimb muscle of aged_ZT 12


title: lungs_control, not irradiated_excised after 24h_rep3


title: Ctrl_1

description: replicate 1

value: Liver


title: hindlimb muscle of aged mice, ZT 18, repeat 2

description:
Gene expression in aged mouse muscle at ZT 18
Mmu_Muscle_aged_ZT18_2

source_name: hindlimb muscle of aged_ZT 18


title: lungs_control, not irradiated_excised after 24h_rep1

value: Balb/c


title: hindlimb muscle of aged mice, ZT 6, repeat 2

description:
Gene expression in aged mouse muscle at ZT 6
Mmu_Muscle_aged_ZT06_2

source_name: hindlimb muscle of aged_ZT 6


title: hindlimb muscle of aged mice, ZT 0, repeat 2

description:
Gene expression in aged mouse muscle at ZT 0
Mmu_Muscle_aged_ZT00_2

source_name: hindlimb muscle of aged_ZT 0


title: lungs_control, not irradiated_excised after 24h_rep2


title: hindlimb muscle of aged mice, ZT 21, repeat 1

description:
Gene expression in aged mouse muscle at ZT 21
Mmu_Muscle_aged_ZT21_1


title: hindlimb muscle of aged mice, ZT 3, repeat 2

description:
Gene expression in aged mouse muscle at ZT 3
Mmu_Muscle_aged_ZT03_2

source_name: hindlimb muscle of aged_ZT 3


title: SWEETInf0dpi1.txt:gProcessedSignal


title: ColMock2dpi3.txt:gProcessedSignal

source_name: fully expanded leaves_Col-0_mock_2.5


title: hindlimb muscle of aged mice, ZT 12, repeat 1

description:
Gene expression in aged mouse muscle at ZT 12
Mmu_Muscle_aged_ZT12_1


title: hindlimb muscle of aged mice, ZT 6, repeat 1

description:
Gene expression in aged mouse muscle at ZT 6
Mmu_Muscle_aged_ZT06_1


title: hindlimb muscle of aged mice, ZT 18, repeat 1

description:
Gene expression in aged mouse muscle at ZT 18
Mmu_Muscle_aged_ZT18_1


title: hindlimb muscle of aged mice, ZT 15, repeat 1

description:
Gene expression in aged mouse muscle at ZT 15
Mmu_Muscle_aged_ZT15_1


title: lungs_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse lungs, 2 Gy, collum+thorax+abdomen irradiated

value: collum+thorax+abdomen


title: hindlimb muscle of aged mice, ZT 3, repeat 1

description:
Gene expression in aged mouse muscle at ZT 3
Mmu_Muscle_aged_ZT03_1


title: lungs_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: hindlimb muscle of aged mice, ZT 9, repeat 1

description:
Gene expression in aged mouse muscle at ZT 9
Mmu_Muscle_aged_ZT09_1

source_name: hindlimb muscle of aged_ZT 9


title: ColMock2dpi1.txt:gProcessedSignal

value: fully expanded leaves


title: ColMock2dpi2.txt:gProcessedSignal

value: mock


title: SWEETInf0dpi3.txt:gProcessedSignal


title: ColInf2dpi3.txt:gProcessedSignal

value: 2.5 dpi


title: lungs_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1

value: 2 Gy


title: hindlimb muscle of aged mice, ZT 9, repeat 2

description:
Gene expression in aged mouse muscle at ZT 9
Mmu_Muscle_aged_ZT09_2


title: lungs_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse lungs, 2 Gy, thorax+abdomen irradiated

value: thorax+abdomen

value: 4 MV (nominal) photon radiation


title: hindlimb muscle of young mice, ZT 18, repeat 2

description:
Gene expression in young mouse muscle at ZT 18
Mmu_Muscle_young_ZT18_2

source_name: hindlimb muscle of young_ZT 18


title: hindlimb muscle of aged mice, ZT 0, repeat 1

description:
Gene expression in aged mouse muscle at ZT 0
Mmu_Muscle_aged_ZT00_1


title: hindlimb muscle of young mice, ZT 21, repeat 2

description:
Gene expression in young mouse muscle at ZT 21
Mmu_Muscle_young_ZT21_2

source_name: hindlimb muscle of young_ZT 21


title: lungs_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: hindlimb muscle of young mice, ZT 12, repeat 2

description:
Gene expression in young mouse muscle at ZT 12
Mmu_Muscle_young_ZT12_2

source_name: hindlimb muscle of young_ZT 12


title: lungs_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: ColInf2dpi2.txt:gProcessedSignal

value: infected


title: hindlimb muscle of young mice, ZT 9, repeat 2

description:
Gene expression in young mouse muscle at ZT 9
Mmu_Muscle_young_ZT09_2

source_name: hindlimb muscle of young_ZT 9


title: liver_control, not irradiated_excised after 24h_rep5

source_name: Mouse liver, 0 Gy, not irradiation


title: hindlimb muscle of young mice, ZT 12, repeat 1

description:
Gene expression in young mouse muscle at ZT 12
Mmu_Muscle_young_ZT12_1


title: hindlimb muscle of young mice, ZT 15, repeat 2

description:
Gene expression in young mouse muscle at ZT 15
Mmu_Muscle_young_ZT15_2

source_name: hindlimb muscle of young_ZT 15


title: ColInf2dpi1.txt:gProcessedSignal

value: Colletotrichum higginsianum


title: hindlimb muscle of young mice, ZT 6, repeat 2

description:
Gene expression in young mouse muscle at ZT 6
Mmu_Muscle_young_ZT06_2

source_name: hindlimb muscle of young_ZT 6


title: hindlimb muscle of young mice, ZT 6, repeat 1

description:
Gene expression in young mouse muscle at ZT 6
Mmu_Muscle_young_ZT06_1


title: hindlimb muscle of young mice, ZT 3, repeat 2

description:
Gene expression in young mouse muscle at ZT 3
Mmu_Muscle_young_ZT03_2

source_name: hindlimb muscle of young_ZT 3


title: hindlimb muscle of young mice, ZT 0, repeat 2

description:
Gene expression in young mouse muscle at ZT 0
Mmu_Muscle_young_ZT00_2

source_name: hindlimb muscle of young_ZT 0


title: hindlimb muscle of young mice, ZT 9, repeat 1

description:
Gene expression in young mouse muscle at ZT 9
Mmu_Muscle_young_ZT09_1


title: liver_control, not irradiated_excised after 24h_rep4


title: hindlimb muscle of young mice, ZT 18, repeat 1

description:
Gene expression in young mouse muscle at ZT 18
Mmu_Muscle_young_ZT18_1


title: lungs_collum irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse lungs, 2 Gy, collum irradiated


title: hindlimb muscle of young mice, ZT 15, repeat 1

description:
Gene expression in young mouse muscle at ZT 15
Mmu_Muscle_young_ZT15_1


title: hindlimb muscle of young mice, ZT 21, repeat 1

description:
Gene expression in young mouse muscle at ZT 21
Mmu_Muscle_young_ZT21_1


title: hindlimb muscle of young mice, ZT 0, repeat 1

description:
Gene expression in young mouse muscle at ZT 0
Mmu_Muscle_young_ZT00_1


title: liver_control, not irradiated_excised after 24h_rep2


title: hindlimb muscle of young mice, ZT 3, repeat 1

description:
Gene expression in young mouse muscle at ZT 3
Mmu_Muscle_young_ZT03_1


title: liver_control, not irradiated_excised after 24h_rep3


title: ColInf0dpi1.txt:gProcessedSignal

source_name: fully expanded leaves_Col-0_infected_0


title: lungs_collum irradiated with 2 Gy_excised after 24h_rep1


title: PA_GW_UlkKD_1

description: replicate 1

source_name: AML-12 cells

value: Palmitic acid and GW3965 and Ulk1 siRNA


title: lungs_collum irradiated with 2 Gy_excised after 24h_rep2

value: collum


title: liver_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse liver, 2 Gy, collum+thorax+abdomen irradiated


title: liver_collum irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse liver, 2 Gy, collum irradiated


title: liver_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse liver, 2 Gy, thorax+abdomen irradiated


title: liver_collum irradiated with 2 Gy_excised after 24h_rep2


title: liver_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: liver_control, not irradiated_excised after 24h_rep1


title: liver_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: kidney medulla_control, not irradiated_excised after 24h_rep5

source_name: Mouse kidney medulla, 0 Gy, not irradiation

value: Kidney medulla


title: ColInf0dpi2.txt:gProcessedSignal


title: liver_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: Hep_0877_NS

city: Shanghai

first: Jiming

last: Zhang

address: 12 Middle Wulumuqi Road

department: Department of Infectious Diseases

country: China

institute: Huashang Hospital, Fudan University

description: Gene expression data from chronic hepatitis B patients in immune tolerant phase

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The florescence intensity values were normalized using RMA (Robust Multichip Averaging) with GeneSpring10. The differentially expressed genes were identified by One-way ANOVA and t-Test unpaired unequal variance.

organism: Homo sapiens

source_name: Liver biopsy

label_protocol: Lableing was performed according to Affymetrix Gene Chip technical manual

extract_protocol: RNA extraction was performed as Affymetrix GeneChip expression technical manual (Affymetrix, Inc., Santa Clara, CA). Briefly, total RNA samples were extracted, followed by measurement of the A2260/a280 ratio with at least 1.8 for pure RNA. Quality of the RNA was checked by an Agilent 2100 Bioanalyzer.  The Bioanalyzer gel profile exhibited a 28S band that is 2 times more intense than 18S ribosomal RNA. The quality of RNA was assessed by agarose gel electrophoresis.

value: Liver biopsy in chronic hepatitis B patients in immune tolerant phase

tag: gender

value: Male


title: Hep_0863_NS


title: liver_collum irradiated with 2 Gy_excised after 24h_rep1_R_d1

tag: strain


title: liver_collum irradiated with 2 Gy_excised after 24h_rep1_R_d2

tag: tissue


title: liver_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2

tag: irradiated area


title: kidney medulla_control, not irradiated_excised after 24h_rep4

tag: absorbed dose

value: 0 Gy


title: liver_collum irradiated with 2 Gy_excised after 24h_rep1

value: Liver

tag: time point


title: Hep_0799_NS

value: Female


title: Hep_0816_NS


title: Hep_0284_NS


title: Hep_0858_NS


title: Hep_0859_NS


title: Hep_0782_NS


title: Hep_0759_NS


title: kidney medulla_control, not irradiated_excised after 24h_rep3

value: Balb/c

tag: radiation quality


title: Hep_0879_NS


title: Hep_0757_NS


title: Hep_0876_NS


title: Hep_0763_NS


title: hep_0211_NS


title: kidney medulla_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1

source_name: Mouse kidney medulla, 2 Gy, collum+thorax+abdomen irradiated

value: collum+thorax+abdomen


title: kidney medulla_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2

source_name: Mouse kidney medulla, 2 Gy, thorax+abdomen irradiated


title: Hep_0815_NS

description: Gene expression data from chronic hepatitis B patients in immune clearance phase

value: Liver biopsy in chronic hepatitis B patients in immune clearance phase


title: Hep_0068_NS


title: Hep_0272_NS


title: hep_0191_NS


title: kidney medulla_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2


title: Hep_0898_NS


title: kidney medulla_control, not irradiated_excised after 24h_rep2


title: hep_0024_NS


title: Hep_0784_NS


title: Hep_0783_NS


title: kidney medulla_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3


title: Hep_0758_NS


title: Hep_0067_NS


title: hep_0208_NS


title: Hep_0794_NS


title: kidney medulla_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: kidney medulla_collum irradiated with 2 Gy_excised after 24h_rep2

source_name: Mouse kidney medulla, 2 Gy, collum irradiated


title: kidney medulla_collum irradiated with 2 Gy_excised after 24h_rep3


title: kidney medulla_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3


title: Hep_0769_NS


title: hep_0030_NS


title: hep_0326_NS


title: kidney medulla_control, not irradiated_excised after 24h_rep1


title: hep_0321_NS


title: hep_0324_NS


title: kidney cortex_control, not irradiated_excised after 24h_rep5

source_name: Mouse kidney cortex, 0 Gy, not irradiation

value: Kidney cortex


title: hep_0309_NS


title: kidney medulla_collum irradiated with 2 Gy_excised after 24h_rep1

value: 2 Gy


title: kidney cortex_control, not irradiated_excised after 24h_rep1


title: Hep_0273_NS


title: hep_0319_NS


title: hep_0313_NS


title: hep_0213_NS


title: kidney cortex_control, not irradiated_excised after 24h_rep4


title: kidney cortex_control, not irradiated_excised after 24h_rep3


title: hep_0216_NS


title: hep_0220_NS


title: hep_0204_NS


title: hep_0112_NS


title: hep_0217_NS


title: Hep_0274_NS


title: kidney cortex_control, not irradiated_excised after 24h_rep2


title: hep_0126_NS


title: kidney cortex_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2

source_name: Mouse kidney cortex, 2 Gy, collum+thorax+abdomen irradiated


title: hep_0101_NS


title: hep_0214_NS


title: hep_0210_NS


title: hep_0086_NS


title: Hep_0762_NS


title: hep_0206_NS


title: hep_0076_NS


title: Hep_0073_NS


title: kidney cortex_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3


title: kidney cortex_collum+thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: hep_0111_NS


title: kidney cortex_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep3

source_name: Mouse kidney cortex, 2 Gy, thorax+abdomen irradiated

value: thorax+abdomen


title: kidney cortex_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep2

value: 4 MV (nominal) photon radiation


title: kidney cortex_collum irradiated with 2 Gy_excised after 24h_rep1

source_name: Mouse kidney cortex, 2 Gy, collum irradiated


title: Hep_0061_NS


title: kidney cortex_thorax+abdomen irradiated with 2 Gy_excised after 24h_rep1


title: kidney cortex_collum irradiated with 2 Gy_excised after 24h_rep2


title: hep_0039_NS


title: Hep_0072_NS


title: Hep_0775_NS


title: hep_0305_NS


title: Hep_0779_NS


title: hep_0040_NS


title: Thyroid_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3

scan_protocol: Standard Illumina iScan N240 scanning protocol; scan setting file: Direct Hyb

source_name: Mouse thyroid, 0 kBq 131I, 3 pm

value: female

value: Thyroid

tag: injected activity

value: 0 kBq

tag: time of day

tag: nuclide

value: none (physiol. saline)


title: hep_0025_NS

tag: age


title: Thyroid_physiol. saline i.v. injected at 3 pm, excised after 24h_rep1


title: Thyroid_physiol. saline i.v. injected at 3 pm, excised after 24h_rep2


title: Hep_0811_NS


title: hep_0323_NS


title: hep_0303_NS


title: hep_0110_NS


title: hep_0036_NS


title: Hep_0069_NS


title: hep_0754_NS


title: hep_0201_NS


title: Hep_0813_NS


title: Hep_0235_NS


title: Thyroid_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4

source_name: Mouse thyroid, 90 kBq 131I, 3 pm

value: 90 kBq


title: kidney cortex_collum irradiated with 2 Gy_excised after 24h_rep3

value: collum


title: hep_0102_NS


title: Thyroid_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3


title: Thyroid_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2

source_name: Mouse thyroid, 0 kBq 131I, 12 pm


title: Thyroid_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2


title: Hep_0006_NS


title: Thyroid_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1


title: Thyroid_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1


title: Thyroid_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3


title: Hep_0777_NS

description: Gene expression data from inactive carrier of chronic hepatitis B patients

value: Liver biopsy in inactive carrier of chronic hepatitis B patients

value: Male


title: Hep_0878_NS


title: Thyroid_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1

source_name: Mouse thyroid, 90 kBq 131I, 12 pm


title: Hep_0818_NS


title: Thyroid_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1_R


title: Hep_0846_NS


title: hep_0325_NS


title: Thyroid_physiol. saline i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse thyroid, 0 kBq 131I, 9 am


title: Thyroid_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3


title: Old p16-/-

city: Daejeon

first: Yee Sook

last: Cho

address: 125 Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Gene expression in reprogramming intermediates on D8 of TTFs from old p16-/- mice

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: TTFs were isolated from tail tips obtained from 2- and 22-month-old WT or p16-KO mice (NCI Mouse Repository, Frederick, MD, USA) and maintained in DMEM (Invitrogen, Grand Island, NY, USA) supplemented with 20% fetal bovine serum (FBS, Invitrogen), 1% non-essential amino acids (NEAA, Invitrogen), 0.1 mM β-mercaptoethanol (Sigma, St. Louis, MO, USA), and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: We collected TTFs from young WT, old WT, and old p16 KO mice and reprogrammed the cells by introducing four reprogramming factors, including Oct4, Sox2, Klf4, and c-Myc. Total RNA was isolated on D8 of reprogramming.

tag: genotype/variation

tag: cell type

value: tail-tip fibroblasts

tag: protocol


title: Hep_0773_NS


title: Thyroid_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2


title: Hep_0776_NS

value: Female


title: Thyroid_physiol. saline i.v. injected at 9 am, excised after 24h_rep3_R

value: Balb/c


title: Old

description: Gene expression in reprogramming intermediates on D8 of TTFs from old mice

value: WT

value: reprogrammed the cells by introducing four reprogramming factors


title: dentritic cells_63 day

city: Whuhan

first: Lin

last: Chen

address: 185 Donghu Road

institute: Whuhan

description: Gene expression of 63-day spleen dentritic cells in mice infected with Schistosoma japonicum

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μLcontaining 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μL of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole mouse Genome Oligo Microarrays (026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed  at room temperature with Gene Expression Wash Buffer 1(Agilent) and Gene Expression Wash Buffer 2  (Agilent), then dried immediately by removing 5-10s slide rack.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images(.tif) were extracted to Agilent Feature Extraction Feature(FE) project of FE Software. Then the properties of FE project was set and the  the Extraction Set Configuration was checked. In the end, save the FE Project (.fep) and export it.

source_name: spleen dentritic cells, 63 day

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using Quick Amp Labeling Kit, One-Color (Agilent, USA) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen, Canada) .  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C57BL/6 mice were kept in clean animal feeding room which have appropriate light and humidity.

extract_protocol: RNA was extracted from N day, 28-day, 63-day sorted dentrtic cells with Trizol reagent.

treatment_protocol: in N day, 28 day, 63 day the spleens of mice were removed to make single cell suspension, then the spleenocytes were maked with CD3e-PE-cy5, CD11c-FITC for flow cytometry.

value: whole spleen

value: dendritic cells

value: male


title: Hep_0293_NS


title: dentritic cells_N day

description: Gene expression of spleen dentritic cells in normal mice

source_name: spleen dentritic cells, N day


title: Young

description: Gene expression in reprogramming intermediates on D8 of TTFs from young mice


title: dentritic cells_28 day

description: Gene expression of 28-day spleen dentritic cells in mice infected with Schistosoma japonicum

source_name: spleen dentritic cells, 28 day


title: hep_0127_NS


title: Hep_0297_NS


title: WGA- 2

city: Stockholm

first: Kaneyasu

last: Nishimura

address: Scheeles väg 1

institute: Karolinska Institutet

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45˚C on GeneChip Mouse Gene-1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring version 13.0 using default analysis settings and global scaling as normalization method (PLIER16).

source_name: WGA- mouse striatal cells 2days after WGA-intranigral injection

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 50 ng total RNA (Ambion WT Expression Kit, 2011, Affymetrix).

extract_protocol: Total RNA was extracted by Rneasy mini Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: WGA protein was injected into adult mouse striatum. And 2 days after injection, WGA+ and WGA- striatal cells were separated by FACS.

tag: strain background

value: Striatum

value: Alexa Fluor 488- cells


title: WGA- 3


title: Thyroid_physiol. saline i.v. injected at 9 am, excised after 24h_rep3

value: female

value: Thyroid


title: WGA+ 3

source_name: WGA+ mouse striatal cells 2days after WGA-intranigral injection

value: Alexa Fluor 488+ cells


title: WGA- 1


title: Thyroid_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse thyroid, 90 kBq 131I, 9 am

value: 90 kBq


title: Thyroid_physiol. saline i.v. injected at 9 am, excised after 24h_rep2

value: 0 kBq

value: none (physiol. saline)


title: Thyroid_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: 2108-AK2

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Gene expression data from actinic keratosis skin two days after treatment

hyb_protocol: The labelled RNA was hybridized to Affymetrix GeneChip® HG-U133 Plus 2.0 microarrays (GPL570) according to the manufacturer’s protocol (two micrograms labelled cDNA per array).

scan_protocol: The microarrays were scanned in the Affymetrix GeneArray® 3000 scanner.

data_processing: The arrays were analysed in the Expression Console software (Affymetrix) using the default RMA normalization workflow to create CHP files.

source_name: skin biopsy-patient-2108-actinic keratosis skin-treatmentday2

label_protocol: 60 micrograms total RNA was amplified with the Ambion MessageAmp Premier RNA Amplification Kit and subsequently bioton labelled according to the manufacturer’s protocol (Affymetrix).

extract_protocol: Total-RNA was extracted with Ambion RecoverAll™ according to the manufacturer's protocol.

treatment_protocol: Ingenol mebutate 0.05% gel was applied on two consecutive days (day 1 and day 2) to both the AK treatment area and the US treatment area. 4 mm punch biopsies were taken from one AK lesion (AK0) and from uninvolved skin (US0) before treatment. On day 1, one 4 mm biopsy was obtained from one AK lesion (AK1) within the treatment area. On day 2, two 4 mm punch biopsies were taken: one from uninvolved skin (US2), and one from an AK lesion (AK2) within the treatment area. The biopsies were formalin fixed and paraffin embedded.

value: skin

tag: diagnosis

value: actinic keratosis (AK)


title: hep_0104_NS

source_name: Liver biopsy

value: Liver biopsy in inactive carrier of chronic hepatitis B patients

value: Male


title: WGA+ 2


title: WGA+ 1


title: Spleen_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3

source_name: Mouse spleen, 0 kBq 131I, 3 pm

value: Balb/c

value: Spleen


title: 2108-AK1

description: Gene expression data from actinic keratosis skin one day after treatment

source_name: skin biopsy-patient-2108-actinic keratosis skin-treatmentday1


title: 2108-US0

description: Gene expression data from uninvolved skin before treatment


title: 2108-US2

description: Gene expression data from uninvolved skin two days after treatment


title: Thyroid_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3


title: Spleen_physiol. saline i.v. injected at 3 pm, excised after 24h_rep2


title: 2107-AK0

description: Gene expression data from actinic keratosis skin before treatment

source_name: skin biopsy-patient-2107-actinic keratosis skin-pretreatment


title: Cy5 9 Og Vs Cy3 54 Yg

city: SASKATOON

first: Muhammad

middle: Irfan-ur-Rehman

last: Khan

state: SASKATCHEWAN

address: 52 Campus drive

department: Veterinary Biomedical Sciences

country: Canada

institute: University of Saskatchewan

hyb_protocol: Hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Images were scanned using Tecan scanning protocol.

data_processing: Arraypro software was used to extract target intensities. Background of a target was subtracted from the median signal intensity of the foreground of the target. If the difference was a negative value due to higher intensity of background vs. foreground signals, the negative value was replaced with a default value of 0.5. Flexarry software (1.6.1.1) was used to obtain the list of differentially expressed gene. The median pixel value for each target was transformed to the log2 and normalized “within array” for dye bias using nonparametric regression (locally weighted scatter plot smoothing; “lowess”), and subjected to “between-array” normalization to unify intensities across the arrays. Finally, a list of differentially expressed genes was obtained by running a simple linear model for microarray data; i.e., “simple limma algorithm”. A gene was considered to be differentially expressed when a ≥ 2-fold change in its expression at P-value of ≤ 0.05.

organism: Bos taurus

label_protocol: aRNA was labeled using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Aged (n=3) and young (n=3) Hereford beef cows were synchronized for ovualtion by giving a single intramuscular injection of PGF2α (Lutalyse® @ 25mg, Pfizer). Ovualtion and subsequent follicular dynamics were examined daily by transrectal ultrasonography using a 7.5 MHz linear-array transducer (Aloka SD 900, Tokyo, Japan). The day of ovulation was taken as the day of emergence of the first follicular wave (Day 0) [34, 35]. Granulosa cells were harvested on Day 3 (i.e., by ovariectomy or transvaginal aspiration). Follicular fluid was aliquoted into two RNase free 1.5 ml tubes after searching and removing the oocyte. Granulosa cells were obtained by centrifuging follicular fluid at 700g for 5 minutes. Follicular fluid was removed from both aliquots and granulosa cells were either snap frozen in liquid nitrogen or suspended in 300-700 µl of RNAlater® (Ambion Inc.) for 12 hours at 4°C. All samples were kept at -80°C until the extraction of RNA.

extract_protocol: PicoPure RNA Isolation Kit followed by RiboAmpb HSPlus RNA Amplification kit (Molecular devices).

tag: reproductive status (cattle)

value: Multiparous

value: Heifer


title: Thyroid_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2

tag: gender


title: Spleen_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4

source_name: Mouse spleen, 90 kBq 131I, 3 pm

tag: strain


title: Spleen_physiol. saline i.v. injected at 3 pm, excised after 24h_rep1

tag: tissue


title: 2107-AK1

source_name: skin biopsy-patient-2107-actinic keratosis skin-treatmentday1


title: Cy5 54 Yg Vs Cy3 9 Og

value: Heifer/nulliparous

value: Multiparity


title: Thyroid_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1


title: Cy5 184 Yg Vs Cy3 126 Og


title: 2107-US2


title: 2108-AK0

source_name: skin biopsy-patient-2108-actinic keratosis skin-pretreatment


title: 2107-US0


title: W62kd BTH+ 24h

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

description: SAMPLE 8

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and sofware G2565BA using default parameters.

data_processing: The scanned imags were analized with Feature Extraction software (version 9.1; Agilent Technologies) using default parameters. The measurements were normalized to their mean.

organism: Oryza sativa

source_name: WRKY62-kd rice+BTH

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies).

growth_protocol: Rice seeds were germinated on MS plates. Seedlings were grown in a plastic box containing 1/1000 hyponex culture medium.

extract_protocol: Total RNA was isolated using Trizol and cleand up with an RNeasy plant mini kit (Qiagen).

treatment_protocol: Rice plants at 3-leaf  stage were supplied with BTH solutin (30  µM at a final concentration) into the culture medium.

tag: developmental stage

value: 3-leaf stage

value: seedling

tag: treated with

value: 30 µM benzothiadiazole (BTH) for 24hrs


title: Spleen_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3

value: female

tag: time point


title: Cy5 62 Og Vs Cy3 158 Yg


title: W62-kd BTH+ 12h

description: SAMPLE 6

value: 30 µM benzothiadiazole (BTH) for 12hrs


title: NB BTH+ 24h

description: SAMPLE 7

source_name: Nipponbare rice+BTH

value: wild type


title: Cy5 126 Og Vs Cy3 184 Yg


title: Spleen_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2

value: 90 kBq


title: 2104-AK0

source_name: skin biopsy-patient-2104-actinic keratosis skin-pretreatment

value: skin


title: shRaly4

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young

department: Pathology

country: USA

institute: UCLA

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 11.5.1.11 version

source_name: Mouse Liver

label_protocol: Agilent standard protocol

growth_protocol: 12 weeks old bl6 mice on chow diet

extract_protocol: RNA was isolated from tissues on day#6 using TRIZOL followed by RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Mice transduced with 2.0 x 10^9 pblockITcontrol or pblockITshRaly

value: Liver

tag: treatment

value: adenoshRaly


title: Spleen_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1

source_name: Mouse spleen, 0 kBq 131I, 12 pm

tag: injected activity

value: 0 kBq

value: none (physiol. saline)


title: 2104-US2

value: actinic keratosis (AK)


title: Spleen_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3

value: Balb/c

value: Spleen

tag: time of day


title: Spleen_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1

tag: nuclide


title: Spleen_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep4

source_name: Mouse spleen, 90 kBq 131I, 12 pm


title: NB BTH- 12h

description: SAMPLE 3

source_name: Nipponbare rice

value: none for 12hr


title: NB BTH+ 12h

description: SAMPLE 5


title: W62-kd 0h

description: SAMPLE 2

source_name: WRKY62-kd rice

value: none for 0hr


title: 2104-AK2

source_name: skin biopsy-patient-2104-actinic keratosis skin-treatmentday2


title: shRaly3


title: 2103-AK2

source_name: skin biopsy-patient-2103-actinic keratosis skin-treatmentday2


title: 2104-US0


title: 2104-AK1

source_name: skin biopsy-patient-2104-actinic keratosis skin-treatmentday1


title: shRaly1


title: Spleen_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2


title: shRaly2


title: Control4

value: control


title: NB BTH- 24h

description: SAMPLE 4

value: 3-leaf stage

value: seedling

value: none for 24hr


title: 2107-AK2

source_name: skin biopsy-patient-2107-actinic keratosis skin-treatmentday2


title: Control3


title: Cy5 158 Yg Vs Cy3 62 Og

value: Heifer/nulliparous

value: Multiparity


title: 2103-AK0

source_name: skin biopsy-patient-2103-actinic keratosis skin-pretreatment


title: Spleen_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3

value: female

value: 90 kBq


title: Control2

value: Liver


title: NB 0h

description: SAMPLE 1

value: wild type


title: DV90_JQ1_135nM_24h_rep5

first: Ralf

last: Lesche

address: Muellerstr 178

institute: Bayer Pharma AG

description: gene expression data from DV90 cells treated, 135nM JQ1, 24h

hyb_protocol: An Affymetrix Human Gene 2.1 ST 96-array plate was hybridized with 3μg of fragmented and labeled ss cDNA, washed, stained, and scanned according to the protocol described in the User Manual GeneTitan®Instrument User Guide for Expression Array Plates  (P/N 702933 Rev.1) and Affymetrix® GeneChip® Command Console™ User’s Guide (P/N 702569 Rev.9)  using the Affymetrix GeneTitan instrument

scan_protocol: Array plates were scanned using Affymetrix GeneTitan, AGCC 4.2.0

data_processing: Genedata Refiner Array software was used to process the cel files. Antigenomic background probes were used for background subtraction before quantile normalization. RMA algorithm was used to aggregate the probe sets on a meta probe set level. Resulting values were shifted to mean value of 100 and further normalized using LOWESS normalization.

source_name: DV90 cells treated, 135nM JQ1, 24h

label_protocol: For each sample, 250ng of total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to the protocol described in User Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays (P/N 703174 Rev. 2)

growth_protocol: Human Lung Cell line , NSCLC adenocarcinoma, DV90 from Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) was cultured using RPMI1640 medium (Biochrom) supplemented with 10% fetal calve serum (Biochrom) and non-essential amino acids (Biochrom)

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

treatment_protocol: DV90 cells were seeded on the day before treatment and treated with 135 nM or 785 nM of JQ1 (BET inhibitor) or DMSO (vehicle control) for 4h or 24h.

value: lung

tag: cell line

tag: histologic subtype

value: NSCLC adenocarcinoma


title: Spleen_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2


title: 2102-AK1

source_name: skin biopsy-patient-2102-actinic keratosis skin-treatmentday1

value: skin

value: actinic keratosis (AK)


title: 2103-US2


title: Spleen_physiol. saline i.v. injected at 9 am, excised after 24h_rep3

source_name: Mouse spleen, 0 kBq 131I, 9 am

value: Balb/c

value: Spleen

value: 0 kBq

value: none (physiol. saline)


title: DV90_JQ1_785nM_24h_rep5

description: gene expression data from DV90 cells treated, 785nM JQ1, 24h

source_name: DV90 cells treated, 785nM JQ1, 24h


title: Spleen_physiol. saline i.v. injected at 9 am, excised after 24h_rep2


title: 2102-AK2

source_name: skin biopsy-patient-2102-actinic keratosis skin-treatmentday2


title: Spleen_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1


title: 2103-US0


title: Control1

value: control


title: LeXis3

value: AdLeXis


title: 2103-AK1

source_name: skin biopsy-patient-2103-actinic keratosis skin-treatmentday1


title: DV90_JQ1_135nM_4h_rep5

description: gene expression data from DV90 cells treated, 135nM JQ1, 4h

source_name: DV90 cells treated, 135nM JQ1, 4h


title: 2102-AK0

source_name: skin biopsy-patient-2102-actinic keratosis skin-pretreatment


title: 2102-US2


title: Spleen_physiol. saline i.v. injected at 9 am, excised after 24h_rep4


title: DV90_Vehicle_DMSO_4h_rep4

description: gene expression data from DV90 cells vehicle, DMSO, 4h

source_name: DV90 cells vehicle, DMSO, 4h


title: Spleen_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: DV90_JQ1_785nM_4h_rep5

description: gene expression data from DV90 cells treated, 785nM JQ1, 4h

source_name: DV90 cells treated, 785nM JQ1, 4h


title: LeXis4

source_name: Mouse Liver


title: DV90_Vehicle_DMSO_24h_rep4

description: gene expression data from DV90 cells vehicle, DMSO, 24h

source_name: DV90 cells vehicle, DMSO, 24h


title: LeXis2


title: Spleen_physiol. saline i.v. injected at 9 am, excised after 24h_rep2_R


title: LeXis1


title: 2102-US0


title: GFP4

value: AdGFP


title: 2101-AK1

source_name: skin biopsy-patient-2101-actinic keratosis skin-treatmentday1


title: DV90_JQ1_785nM_4h_rep4


title: DV90_JQ1_785nM_24h_rep4


title: Spleen_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2

source_name: Mouse spleen, 90 kBq 131I, 9 am


title: DV90_Vehicle_DMSO_24h_rep3


title: Spleen_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4


title: Medulla_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3

source_name: Mouse medulla, 0 kBq 131I, 3 pm

value: Kidney medulla


title: 2101-AK0

source_name: skin biopsy-patient-2101-actinic keratosis skin-pretreatment


title: DV90_JQ1_135nM_24h_rep4


title: Spleen_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3


title: Spleen_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1


title: GFP3


title: 2101-US0


title: DV90_Vehicle_DMSO_4h_rep3


title: DV90_JQ1_785nM_24h_rep3


title: GFP2


title: GW b

growth_protocol: Cells treated with DMEM, 10% FBS

extract_protocol: RNA was isolated from cells using TRIZOL followed by RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Cells were placed in DMEM containing 0.5% FBS, 5 μM simvastatin, 100 μM mevalonic acid and 1μM GW3965 or DMSO overnight

tag: cell type

value: primary hepatocytes

value: LXR against GW3965


title: DV90_JQ1_135nM_4h_rep4


title: GFP1


title: GW a


title: Medulla_physiol. saline i.v. injected at 3 pm, excised after 24h_rep2

value: female


title: Medulla_physiol. saline i.v. injected at 3 pm, excised after 24h_rep1


title: 2101-AK2

source_name: skin biopsy-patient-2101-actinic keratosis skin-treatmentday2


title: DMSO b

value: DMSO


title: DV90_JQ1_135nM_24h_rep3

source_name: DV90 cells treated, 135nM JQ1, 24h


title: DMSO a


title: Medulla_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2

source_name: Mouse medulla, 90 kBq 131I, 3 pm

value: 90 kBq


title: Medulla_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1


title: Medulla_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4


title: Medulla_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3


title: DV90_JQ1_785nM_4h_rep3

value: lung


title: DV90_JQ1_785nM_24h_rep2

value: NSCLC adenocarcinoma


title: 2101-US2

value: skin


title: DV90_JQ1_135nM_4h_rep3


title: DV90_Vehicle_DMSO_24h_rep2


title: adult primary neurospheres, offpspring of MG treated mothers_2

city: Toronto

first: Freda

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

institute: Hospital for Sick Children

description: Gene expression data from adult secondary neurospheres

hyb_protocol: 5.5ug of labeled cDNA was hybridized onto Mouse Gene ChIP 2.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: The data was analyzed using Partek Genomics Suite 6.6 using default settings

source_name: adult SVZ primary neurospheres

label_protocol: biotinylated cDNA was generated using standard Affymetrix protocol and Affymetrix WT PLUS kit from 250ng of total RNA.

growth_protocol: The subependymal region of adult (2 m.o.) brains was dissected and subjected to enzymatic digestion, and tritruated into single cells in serum-free medium with trypsin inhibitor. Viable cells were plated in 6-well ultra-low attachment dishes (Corning) at 2 cells/μl in serum- free medium containing 20 ng/ml EGF (Sigma), 10 ng/ml FGF2 (Sigma), 2% B27 supplement (Gibco) and 2 µg/ml heparin (Sigma). Cells were cultured for 7 days at 37° C to allow the formation of primary neurospheres for RNA extraction.

extract_protocol: Total RNA was extracted using E.Z.N.A. MicroElute Total RNA kit (Omega Biotek).

treatment_protocol: Pregnant CD1 mice were injected twice daily (intraperitoneal injections) with PBS or MG (0.5mg/kg) from gestational day 12 to delivery. 2-month-old offspring from these mothers were used for the experiment.

value: subventricular zone primary neurospheres

value: MG

tag: adult age

value: 2 month

tag: day in vitro


title: DV90_JQ1_785nM_4h_rep2


title: Medulla_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3

source_name: Mouse medulla, 0 kBq 131I, 12 pm

value: Balb/c

value: 0 kBq


title: DV90_JQ1_135nM_24h_rep2


title: adult primary neurospheres, offpspring of PBS treated mothers_3

value: PBS


title: adult primary neurospheres, offpspring of MG treated mothers_3


title: Medulla_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1

value: none (physiol. saline)


title: adult primary neurospheres, offpspring of MG treated mothers_1


title: adult primary neurospheres, offpspring of PBS treated mothers_2


title: Medulla_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3

source_name: Mouse medulla, 90 kBq 131I, 12 pm


title: DV90_Vehicle_DMSO_4h_rep1


title: DV90_JQ1_135nM_4h_rep2


title: Medulla_physiol. saline i.v. injected at 9 am, excised after 24h_rep2

source_name: Mouse medulla, 0 kBq 131I, 9 am


title: Medulla_physiol. saline i.v. injected at 9 am, excised after 24h_rep3


title: Medulla_physiol. saline i.v. injected at 9 am, excised after 24h_rep2_R


title: DV90_JQ1_785nM_24h_rep1

source_name: DV90 cells treated, 785nM JQ1, 24h


title: DV90_JQ1_135nM_24h_rep1


title: Medulla_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: DV90_JQ1_785nM_4h_rep1


title: DV90_JQ1_135nM_4h_rep1

source_name: DV90 cells treated, 135nM JQ1, 4h


title: Medulla_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3

source_name: Mouse medulla, 90 kBq 131I, 9 am


title: Medulla_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep4


title: Medulla_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2


title: Medulla_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2


title: DV90_Vehicle_DMSO_24h_rep1


title: DV90_Vehicle_DMSO_4h_rep2

source_name: DV90 cells vehicle, DMSO, 4h


title: adult primary neurospheres, offpspring of PBS treated mothers_1


title: Medulla_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3_R


title: Medulla_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4


title: Medulla_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2


title: Lung_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3

source_name: Mouse lung, 90 kBq 131I, 3 pm

value: Lung


title: Lung_physiol. saline i.v. injected at 3 pm, excised after 24h_rep1

source_name: Mouse lung, 0 kBq 131I, 3 pm


title: Lung_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3


title: Lung_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep4

source_name: Mouse lung, 90 kBq 131I, 12 pm


title: Lung_physiol. saline i.v. injected at 3 pm, excised after 24h_rep2


title: Lung_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3

source_name: Mouse lung, 0 kBq 131I, 12 pm


title: Lung_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4


title: Medulla_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1

value: Kidney medulla


title: Lung_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1


title: Lung_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2


title: Lung_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1


title: 20133452 Liver Low gain-high intake

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing: The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).

source_name: Liver of steer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Steers were fed a high-concentrate diet with WDGS for 78 days.

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform and the pellets were washed twice with 1 ml of 75% ethanol.  RNA pellets were centrifuged through RNeasy Plus Mini Kit columns (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions to remove genomic DNA.

treatment_protocol: Animals most divergent from the bivariate mean from in each of the four phenotypic Cartesian quadrants for gain x intake were selected and liver tissue samples were collected. The transcriptomes of the samples from the 16 animals selected were evaluated by microarray.

tag: Sex

value: Male

value: Liver

tag: phenotype

value: Low gain-high intake


title: Lung_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: gender

value: female


title: Lung_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2

tag: strain

value: 90 kBq


title: Lung_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1

tag: tissue


title: 20133403 Liver Low gain-low intake

value: Low gain-low intake


title: Lung_physiol. saline i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse lung, 0 kBq 131I, 9 am


title: Lung_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2


title: Lung_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: 20133697 Liver High gain-low intake

value: High gain-low intake


title: 20133356 Liver High gain-high intake

value: High gain-high intake


title: 20133337 Liver High gain-low intake


title: Lung_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse lung, 90 kBq 131I, 9 am


title: 20133412 Liver High gain-high intake


title: Lung_physiol. saline i.v. injected at 9 am, excised after 24h_rep3


title: 20133390 Liver High gain-high intake


title: Lung_physiol. saline i.v. injected at 9 am, excised after 24h_rep2


title: 20133173 Liver Low gain-high intake


title: Lung_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3


title: 20133327 Liver Low gain-high intake


title: Liver_physiol. saline i.v. injected at 3 pm, excised after 24h_rep2

source_name: Mouse liver, 0 kBq 131I, 3 pm


title: 20133179 Liver Low gain-low intake


title: 20133181 Liver Low gain-low intake


title: Lung_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2


title: 20133110 Liver High gain-low intake


title: 20133045 Liver High gain-low intake


title: Lung_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1


title: Liver_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4

source_name: Mouse liver, 90 kBq 131I, 3 pm


title: Liver_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3_R


title: Liver_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3


title: Liver_physiol. saline i.v. injected at 3 pm, excised after 24h_rep3


title: 20133101 Liver Low gain-low intake


title: 20133062 Liver Low gain-high intake


title: Liver_physiol. saline i.v. injected at 3 pm, excised after 24h_rep1


title: 20133015 Liver High gain-high intake


title: Liver_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2

source_name: Mouse liver, 0 kBq 131I, 12 pm


title: NHP_M982B_TBInfected_Week6_ReplicateArray3

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

description: Genisphere amplified Total RNA

hyb_protocol: Total amplified primate PBL mRNAs from each time-point were labelled with Cy3-labelled dCTP as described previously [50,51] and hybridised to replicate Operon Human Genome AROS V4.0 slides (n = 3/ sample/time point (http://www.microarrays.com/dna-arrays.php). This is a human oligonucleotide microarray comprising some 35,035 oligonucleotide probes, which represent approximately 25,100 unique genes and 39,600 transcripts. A subset of the total probe set (31,387 probes) is contained within the span of a single exon to provide the microarray detection precision at both the transcript and gene levels.  Microarray slides were pre-hybridized for 30 minutes at 42 °C in a hybridization solution containing 5 x standard saline citrate (SSC), 0.1% sodium dodecyl sulfate (SDS) and 4 x Denhardts solution, followed by a 1 minute wash in molecular reagent grade double distilled water then a brief rinse in isopropanol. The slides were then dried by centrifugation at 1500 rpm for 5 minutes. Prior to hybridization, 20 μg of Cy3-labelled mRNA was combined with 20 μg of Cot1 Human DNA (10 μg/μl) and 20 μg of polyA RNA (10 μg/μl) (Invitrogen) to a final volume of 40 μl in RNAase-free water and denatured at 95 oC for 2 minutes to denature the mRNA target. The mixture was then mixed 1:1 with 2 x concentrate hybridization solution (10 x SSC, 0.2% SDS, 8 x Denhardts solution) pre-warmed to 65 oC. The microarray slide was placed in the chamber of a Slidebooster microarray hybridisation platform (Olympus Advalytix, Germany) pre-heated to 42 oC and a lifterslip covering the area of the array affixed in place (http://www.thermoscientific.com/content/tfs/en/ product/lifterslips-cover-slips-microarray-slides.html). The prepared sample was applied to the array and drawn under the lifterslip by capillary action. This was then hybridised at 42 °C for 6 hours in the presence of proprietary formamide-free AdvaHum humidifying buffer (Olympus Advalytix, Germany) at maximum mixing power (M27). After completion of hybridisation lifterslips were removed and the slides were washed in two separate wash solutions for two minutes each at 42 oC - Buffer A (1x SSC 1% SDS) Buffer B1 (0.1x SSC 1% SDS), then a further wash in Buffer B2 (1% SSC) for two minutes at room temperature.

scan_protocol: The slides were air-dried and scanned using an Affymetrix 480 microarray scanner, at a gain of 65.

data_processing: Feature extraction was conducted using the microarray quantification package BlueFuseTM (BlueGnome; now a subsidiary of www.illumina.com). Raw data were exported and hybridisation fluorescence intensities quantified using default background subtraction and normalisation methods, to remove data generated from poor-quality spots and hybridisation artefacts. All raw data were then processed further using the microarray analysis package Genespring 12.5. Data output files from BlueFuse were imported into GeneSpring 12.5 (GX12.5) for differential gene expression and statistical analysis. Raw data was normalized to the 50th percentile followed by median baseline transformed to each animals corresponding pre-bleed sample. This was conducted to normalise data across all time points and assess differential gene expression of each gene entity, relative to a baseline i.e. pre-bleed level of expression prior to M. tuberculosis challenge. Mean values across three replicate sample slides were used for further ongoing analysis. Data were assessed for quality, then filtered on gene expression where entities in all samples and all conditions had normalised expression values within the cut-off -10.699 to 7.037. Statistically significant features were identified using one-way ANOVA analysis across all entities and time points, using either the Benjamini-Hochberg False Discovery Rate (BH-FDR), or the more parsimonious Bonferroni Family-Wise Error Rate (B-FWER), with multiple testing corrections at a cut-off p ≤ 0.05. To identify temporally, differentially expressed entities between time-points post-infection, fold-change cut-off analyses were conducted using the default cut-off setting ≥ 2.0 all referenced against the pre-bleed condition,  where the minimum number of pairs was equal to one out of the four condition pairs i.e. weeks one, two, four or six. These were further analysed and depicted graphically using the heat map, hierarchical cluster analysis and other functions in Genespring 12.5, using default settings.

organism: Macaca fascicularis

source_name: Total peripheral blood leukocytes Tuberculosis infected

label_protocol: Due to the small volumes of blood used in the study and consequently low yield of total RNA recovered, an enrichment step was then performed using the Genisphere SenseAmp RNA amplification kit according to manufactures instructions (http://genisphere.com/). The resulting amplified mRNA was purified using RNeasy Min-Elute Cleanup kit (Qiagen), again according to the manufacturers’ protocol. The mRNA concentration and purity (A260/A280 ratio ≥ 1.8) was then assessed by spectrophotometry using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: The samples analysed in this investigation were collected from six Cynomologus macaques (Macaca fascicularis) aged between 2 – 4 yrs in a pilot study set up  to characterise and compare the outcome of high dose M. tuberculosis aerosol challenge, using previously described methods [49]. None of the animals had been used previously for experimental procedures. They were confirmed as naïve in terms of prior exposure to mycobacterial antigens (M. tuberculosis infection or environmental mycobacteria),  by  negative tuberculin test while in their original breeding colony and prior to the start of the study using  the gamma interferon (IFN-γ)-based Primagam test kit (Biocor; CSL).  The animals were of two distinct genotypes; Chinese (diverse) and Mauritian (restricted). Following aerosol exposure animals were monitored for 12 weeks for changes in behaviour and clinical parameters such as body weight, temperature, anaemia and inflammation. Disease progressed to meet endpoint criteria in all three Cynomolgus macaques of the Mauritian genotype six weeks after challenge. The macaques of Chinese genotype controlled disease for the remainder of the study period and were euthanased twelve weeks after challenge.    The Cynomolgus macaques of Mauritian genotype were obtained from an established UK breeding colony, whilst the Cynomolgus macaques of Chinese genotype were obtained from a UK Home Office approved breeding facility in China.   Absence of previous exposure to mycobacterial antigens was confirmed by a tuberculin skin test and screening using an ex-vivo IFNγ ELISPOT (MabTech, Nacka. Sweden) to measure responses to PPD (SSI, Copenhagen, Denmark), and pooled 15-mer peptides of ESAT6 and CFP10 (Peptide Protein Research LTD, Fareham, U.K.). The animals were housed in compatible social groups, in accordance with the Home Office (UK) Code of Practice for the Housing and Care of Animals Used in Scientific Procedures (1989), (now updated to Code of Practice for the housing and Care of Animals Bred, Supplied or Used for Scientific Purposes, December 2014, and the National Committee for Refinement, Reduction and Replacement (NC3Rs), Guidelines on Primate Accommodation, Care and Use, August 2006 (NC3Rs, 2006)).  Animals were sedated by intramuscular (IM) injection with ketamine hydrochloride (Ketaset, 100mg/ml, Fort Dodge Animal Health Ltd, Southampton, UK; 10mg/kg) for procedures requiring removal from their housing. None of the animals had been used previously for experimental procedures. All animal procedures were approved by the Public Health England Ethical Review Committee, Porton Down, UK, and authorized under an appropriate UK Home Office project license.    The challenge was performed on sedated animals placed within a “head-out” plethysmography chamber (Buxco, Wilmington, NC), to enable the aerosol to be delivered simultaneously with the measurement of the respiration rate. This process has been shown previously to deliver a known number of viable M. tuberculosis bacilli in a target volume of inspired aerosol. Clinical assessment post-challenge; animal behaviour was observed daily throughout the study for contra-indicators such as depression, withdrawal from the group, aggression, food and water intake, changes in respiration rate, or cough. Animals were sedated every weeks to measure weight, body temperature, blood haemoglobin levels, and erythrocyte sedimentation rate (ESR) and to collect blood samples for immunology and RNA extraction.

extract_protocol: One ml of TRIzol® was added to the PBL pellet, then total RNA was extracted from the lysed PBL pellet according to the manufacturer’s instructions (www.Invitrogen.com) using aqueous-phase separation with chloroform isoamyl alcohol and the precipitation using 2-isopropanol. Recovered, dried RNA pellets were re-suspended in 10 μl of diethylpyrocarbonate (DECP) water (Invitrogen), then concentration and purity (A260/A280 ratio ≥ 1.8) assessed by spectrophotometry using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). Genomic DNA was removed prior to its use in further procedures using the DNase I kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Whole heparinised blood was obtained at three independent time points prior to challenge and at one, two, four and six weeks post M. tuberculosis challenge. Within one hour of collection, 1 ml of blood from each animal was mixed with 5 ml of Erythrocyte Lysis (EL) Buffer (Qiagen) followed by incubation on ice for 10-15 minutes. Peripheral blood leukocytes (PBLs) were recovered from erythrocyte-lysed blood by centrifugation at 400 x g for 10 minutes at 4 °C and re-suspended in a further 2 ml of EL buffer. PBLs were again recovered by centrifugation as described above and processed for recovery of total RNA.

value: Female

tag: origin

value: Mauritian Genotype

value: blood


title: Liver_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep4

last: Langen

address: Gula stråket 2B

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse liver, 90 kBq 131I, 12 pm

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

value: Balb/c


title: Liver_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1

value: 0 kBq


title: NHP_M982B_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2


title: NHP_M982B_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: Liver_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3


title: NHP_M982B_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1


title: NHP_M982B_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3


title: NHP_M982B_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1


title: NHP_M982B_TBInfected_Week1_ReplicateArray1

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2


title: NHP_M982B_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA


title: Liver_physiol. saline i.v. injected at 9 am, excised after 24h_rep2

source_name: Mouse liver, 0 kBq 131I, 9 am


title: NHP_M982B_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: Liver_physiol. saline i.v. injected at 9 am, excised after 24h_rep4


title: Liver_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: NHP_M982B_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA

source_name: Total peripheral blood leukocytes non-Tuberculosis infected


title: Liver_physiol. saline i.v. injected at 9 am, excised after 24h_rep3


title: Liver_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse liver, 90 kBq 131I, 9 am


title: NHP_M982B_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_M982B_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_M982B_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_M982B_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3


title: NHP_M982B_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA


title: Liver_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2


title: Kidney cortex_0 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3

source_name: Mouse kidney cortex, 0 kBq 131I, 3 pm

value: Kidney cortex


title: Liver_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1


title: NHP_M651A_TBInfected_Week6_ReplicateArray3

description: Genisphere amplified Total RNA


title: Kidney cortex_0 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2

value: none (physiol. saline)


title: Kidney cortex_0 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1


title: Kidney cortex_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep4

source_name: Mouse kidney cortex, 90 kBq 131I, 3 pm


title: NHP_M651A_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_M651A_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: Medulla_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1

source_name: Mouse medulla, 90 kBq 131I, 12 pm


title: Kidney cortex_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep3


title: NHP_M651A_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA


title: Kidney cortex_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep2


title: NHP_M651A_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA


title: Cited4-overexpressed cells at day 6.5 and Cited4-downregulated cells at day 6.5

city: Yonago

first: Junichiro

last: Miake

address: 36-1 Nishi-cho

department: Multidisciplinary Internal Medicine

institute: Tottori University Faculty of Medicine

description: embryoid body formed with mouse ES cells transfected with wild-type Cited4 gene or Cited4 siRNA

hyb_protocol: Hybridization for 20h at 50℃. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

scan_protocol: The arrays were scanned by FLA-8000 (Fuji Photo Film). Images were quantified using Array Gauge Ver2.0 (Fuji Photo Film).

data_processing: These data were analyzed by DNASIS array software (Hitachi Software Engineering Co., Ltd), which converted the signal intensity of each spot into text format. Data from microarray were normalized by Global normalization.

source_name: embryoid body

label_protocol: Amino Allyl aRNA was synthesed by Amino Allyl MessageAmp™ aRNA Amplification Kit (Amibion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

extract_protocol: Total RNA was extracted using RNeasy Mini Kit following manufacturer's instructions

value: embryoid body

value: transfected with wild-type Cited4 gene

value: transfected with Cited4 siRNA


title: Kidney cortex_90 kBq 131I i.v. injected at 3 pm, excised after 24h_rep1

city: Gothenburg

first: Britta

institute: Sahlgrenska Academy at University of Gothenburg


title: NHP_M651A_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA


title: Wild-type Cited4-transduced cells at day 6.5 and nontransduced cells at day 6.5

description: embryoid body formed with wild-type Cited4-transduced mouse ES cells and embryoid body formed with nontransduced mouse ES cells

tag: genotype/variation

value: nontransduced mouse ES cells


title: NHP_M651A_TBInfected_Week1_ReplicateArray1

description: Genisphere amplified Total RNA


title: Kidney cortex_physiol. saline i.v. injected at 12 pm, excised after 24h_rep2

source_name: Mouse kidney cortex, 0 kBq 131I, 12 pm

tag: time point


title: Nkx2.5-positive cardiac progenitor cells at day 7.5 and Bra-positive early mesodermal cells at day 4.5

description: Isolated lineage maker-positive cells

hyb_protocol: Hybridized for 20h at 50℃. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

data_processing: These data were analyzed by DNASIS array software (Hitachi Software Engineering Co., Ltd), which converted the signal intensity of each spot into text format. Data from each microarray were normalized by Global normalization. These data were analyzed by DNASIS® Stat version 2.0 (Hitachi Software Enguneering Co., Ltd).

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ aRNA Amplification Kit (Amibion). CyeDye Coupling and fragmentation were performed as the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc./AceGene)

tag: embryoid body


title: NHP_M651A_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA


title: Kidney cortex_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep4

source_name: Mouse kidney cortex, 90 kBq 131I, 12 pm

tag: injected activity


title: NHP_M651A_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: Kidney cortex_physiol. saline i.v. injected at 12 pm, excised after 24h_rep3

tag: time of day


title: NHP_M651A_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA


title: Nkx2.5-positive cardiac progenitor cells at day 7.5 and Flk1-positive cardiac mesodermal cells at day 4.5

description: Isolated lineage maker-positive cells


title: NHP_M651A_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_M651A_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: Nkx2.5-positive cardiac progenitor cells at day 7.5 and Rex1-positive undifferentiated stem cells at day 0

description: Isolated lineage maker-positive cells


title: Experiment, biological replicate3

city: Hyderabad

first: Utpal

last: Bhadra

state: TG

address: Uppal Road

department: UB group

country: India

institute: CCMB

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

scan_protocol: The gene chips were scanned on an Affymetrix Scanner

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1.1 - GX - PA   (Agilent Technology) for further analysis. The RMA and PLIER16 algorithms were used for data normalization

organism: Drosophila melanogaster

source_name: mle/mle homozygous

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mle/mle homozygous male larvae were segregated from heterozygous mle/ T(2-3)Tb and wild type cancon S genotypes.  The third instar larvae of each genotype were further processed

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

treatment_protocol: The larvae of each genotypes were collected based on the phenotype and washed throughly in the  wash buffer. The cleaned larvae of each gonotype were used for RNA extraction procedure.

tag: genotype

value: mle/mle homozygous

tag: developmental stage

value: third instar larvae


title: Kidney cortex_physiol. saline i.v. injected at 12 pm, excised after 24h_rep1

treatment_protocol: Excised organs were flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: female

tag: nuclide


title: NHP_M651A_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA


title: Flk1-positive cardiac mesodermal cells at day 4.5 and Rex1-positive undifferentiated stem cells at day 0

description: Isolated lineage maker-positive cells


title: Kidney cortex_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep2

value: 90 kBq


title: Experiment, biological replicate2


title: Bra-positive early mesodermal cells at day 4.5 and Rex1-positive undifferentiated stem cells at day 0

description: Isolated lineage maker-positive cells


title: Control, biological replicate3

source_name: wild type cancon S

value: wild type cancon S


title: NHP_M651A_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA


title: Control, biological replicate1


title: Kidney cortex_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep3


title: Kidney cortex_90 kBq 131I i.v. injected at 12 pm, excised after 24h_rep1


title: Kidney cortex_physiol. saline i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse kidney cortex, 0 kBq 131I, 9 am


title: Control, biological replicate2


title: Kidney cortex_physiol. saline i.v. injected at 9 am, excised after 24h_rep3


title: NHP_I131B_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_I131B_TBInfected_Week6_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_M651A_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA


title: Kidney cortex_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep4

source_name: Mouse kidney cortex, 90 kBq 131I, 9 am


title: NHP_I131B_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: Kidney cortex_physiol. saline i.v. injected at 9 am, excised after 24h_rep2


title: NHP_I131B_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: Kidney cortex_physiol. saline i.v. injected at 9 am, excised after 24h_rep1


title: untreated organoid at day6

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

institute: The JFCR-Cancer Institute

description:
Gene expression data from normal intestinal organoid
Apcfl/fl-day6-control

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on Mouse Geneome 430_2.0 array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GenePattern (Broad Institute) using default analysis setting and global scailing as normaization method.

source_name: Apc organoids untreated (day6)

label_protocol: Biotinylated cRNA were prepared from 100ng of total RNA using 3' IVT PLUS Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Organoids were treated with 4OHT for 24 hours and cultured for 4 or 6 days.

extract_protocol: Total RNA was isolated using a Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Organoids were recovered from Matrigel using Cell Recovery Sollution (Corning), washed with PBS once and collected by centrifugation.

value: mouse intestinal organoid


title: NHP_I131B_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA

value: Female


title: NHP_I131B_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA

value: Mauritian Genotype


title: NHP_I131B_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA

value: blood


title: 2i-treated Max-null ES Dox untreated

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: reference sample for 2i-treated Max-null ESCs Dox treated

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003).

data_processing: The data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.

source_name: 2i-treated Max-null ES Dox untreated

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

growth_protocol: Max-null ESCs (Hishida et al. Cell Stem Cell 9, 37-49, 2011) were cultured under conventional ESC medium with LIF and serum or cultured under 2i condition as indicated.

extract_protocol: Total RNAs were prepared using TRIzol reagent from Invitrogen (15596-026).

treatment_protocol: Max-null ESCs cultured under conventional ESC medium or 2i condition were treated with or without doxycycline.

value: male

tag: cell type

value: embryonic stem cells

value: Max-expression ablated (Max null)

tag: treated with

value: 2i for 6 days


title: NHP_I131B_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA

source_name: Total peripheral blood leukocytes Tuberculosis infected


title: NHP_I131B_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_I131B_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: R1 Myc-ER shEed Myc mESC

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

country: Italy

institute: National Institute of Molecular Genetics

description:
replicate 1
SAMPLE 13

hyb_protocol: Standard Illumina hybridization protocol to MouseRef-8 v2  BeadChip Arrays (Illumina, 1128893), following the Direct Hybridization Assay guideline.

scan_protocol: BeadChip Arrays were scanned with a HiScan Array Scanner (Illumina) using the iScan Control Software (Illumina).

data_processing: The data were normalised using quantile normalization and background subtraction implemented by the GenomeStudio Gene Expression Module v1.0 Software (Illumina).

source_name: Embryonic Stem Cell

label_protocol: 500 ng of each sample RNA were processed to generate biotinylated cRNAs following the Illumina TotalPrep RNA amplification Kit (Ambion, AMIL1791) protocol for Illumina Arrays.

growth_protocol: R1 mESC cells were cultured without feeders on plastic coated with 0.1% gelatin in the DMEM supplemented with 15% FCS (Hyclone Millipore, cat. ES-009-B), 100 mM 2‐mercaptoethanol (Sigma, cat. M7522), 1 × MEM non‐essential amino acids (Invitrogen, cat. 1140‐036), 2 mM l‐glutamine, 1 mM sodium pyruvate (both from Invitrogen). GOF18 EpiSCs were cultured in N2B27 medium supplemented with BSA 0,033%, Glutamax, b-Mercaptoethanol 0,1mM, bFGF 12ng/ml (Invitrogen, cat. 13256029) and Activin-A 20 ng/ml (R&D, cat. 338-AC). EpiSC were grown on fibronectin-coated plates and splitted every three days 1:20 by dissociation into small clumps with Collagenase Type IV 0,5 mg/ml (Gibco, cat. 17104-019).

extract_protocol: Total RNAs were isolated from cell cultures after 3 days growth in indicated conditions, using TRIzol® Reagent (Ambion, cat.15596-026), followed by clean up in accordance with the manifacturer's protocol provide with the kit.

treatment_protocol: ESC were treated with the following reagents as indicated above: 100 units/ml LIF (Millipore, cat. ESG1107); 50 nM 4-hydroxytamoxifen (OHT) (Sigma, cat. H6278); Dkk1 100ng/ml (R&D, cat. 5897-DK); Sfrp1 100ng/ml (R&D, cat. 1384-SF).

tag: age

value: day 3.5

value: Inner cell mass

tag: clone

tag: treatment

value: 50 nM 4-hydroxytamoxifen (OHT)


title: Kidney cortex_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep2

scan_protocol: Standard Illumina iScan N240 scanning protocol; scan setting file: Direct Hyb

value: Balb/c

tag: gender

value: Kidney cortex


title: Kidney cortex_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep3

tag: strain


title: 2i treated Max-null ES Dox treated

source_name: 2i treated Max-null ES Dox treated

value: 2i and Dox for 6 days


title: NHP_I131B_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA

tag: tissue


title: 4OHT treated organoid at day6

description:
Gene expression data from Apc-deficientl intestinal organoid
Apcfl/fl-day6-OHT

source_name: Apc organoids 4OHT treated (day6)