title: DBA to F1 Spleen 14d rep4

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

description:
CSV20
replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: Background subtraction and quantile normalization in Illumina GenomeStudio

source_name: Mouse spleen

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Labeling Kit kit for Illumina MouseRef-8 v2.0 Expression BeadChips

extract_protocol: Spleen tissue was stablized using Qiagen RNAlater Reagent before homogenization in QIAzol and isoltion using Qiagen Rneasy Mini Kit.  RNA integiry was assessed using Bio-Rad RNA HighSens Chips on an Experion Automated Electrophores Station.

tag: strain

value: Spleen

value: 10 weeks


title: DBA to F1 Spleen 14d rep3

status: Public on Sep 02 2015

type: RNA

country: USA

description:
CSV19
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age


title: DBA to F1 Spleen 14d rep2

description:
CSV18
replicate 2


title: S7_Normal

type: genomic

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

country: Spain

institute: IDIBAPS / Hospital Clinic

hyb_protocol: Standard Affymetrix Protocol. DNA digestion was done by using Sty I restriction enzyme.

scan_protocol: The chips were processed using fluidics station 450, high-resolution microarray scanner 3000, and GCOS workstation version 1,2

data_processing:
Allele call and signal intensity generated
Data were processed using Affymetrix Genotyping Console 3.0.2 software from CEL data. Genotype calling with BRLMM was performed on the Genotyping Console using default settings. Derived signal is computed using the two alleles using the formula (log2(A) +log2(B))/2.
Series-level supplementary file includes processed CNV and LOH calls.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Normal adjacent mucosa (Crc7N)

label_protocol: Standard Affymetrix Protocol

tag: gender

value: female

value: Normal adjacent mucosa

tag: tumor stage


title: S2_Normal

source_name: Normal adjacent mucosa (Crc2N)


title: S1_Normal

source_name: Normal adjacent mucosa (Crc1N)

value: male


title: 2D1-UV-3

city: Los Angeles

first: Andrea

middle: M

last: Kasko

state: CA

address: 410 Westwood Plaza, 4121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

hyb_protocol: RNA integrity analysis was performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource located at UCLA. Analysis was performed using the Agilent 2100 bioanalyzer. The bioanlayzer generated electropherograms and RNA integrity number (RIN). Samples used for microarray experiments need to have  RIN > 7. All our samples had distinct 18s and 28s RNA subunit peaks and average RIN > 9.40.  The Core then also performed the labeling, hybdridization, and scanning.

data_processing: Gene array processing and post-processing of data were performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource. We used the Affymetrix human genome U133 Plus 2.0 array. The Core used Partek Genomics Suite to identify differentially expressed genes (> 2-fold change, p < 0.05, unless otherwise noted). Gene lists were exported for functional annotation clustering and pathway analysis in two different programs, the Database for Annotation, Visualization, and Integrated Discovery (DAVID v6.7)5, 6_and Ingenuity Pathway Analysis (IPA, build version 242990, content version 17199142). When using DAVID for functional annotation clustering, default selections and medium stringency for filtering were used unless otherwise noted, and Benjamini-Hochberg multiple comparison correction p-values were used to determine significance in functional annotation clustering in DAVID.

source_name: bone marrow stromal cell

growth_protocol: Human mesenchymal stem cells (hMSCs) were obtained from Texas A&M Health Science Centre College of Medicine through a grant obtained from NCRR of the NIH (P40RR017447). The frozen cells were recovered overnight and passaged (seeding density: 60 cells/cm2) the next day. The cell culture medium used was MEM Richter's Modification medium with 20% Fetal Bovine Serum, 1% L-Glutamine and 1% Penicillin-Streptomycin. Media was changed once every 3 days. Once the cells reached ~80% confluency, they were trypsinized, counted and used for sample preparation (passage 2 hMSCs). For the scope of this project, we were interested in only analyzing the initial effects of free-radicals, UV exposure, and culture systems. Therefore, we did not test the effect of cell age (by using cells in different passage numbers) on free-radical sensitivity, UV exposure, and culture systems. All our sample sets had hMSCs in passage 2.

extract_protocol: Total RNA was extracted using the commercially available TRIzol® guanidinium-phenol based reagent followed by spin column purification using Ambion PureLink kit. For homogenization of samples: Homogenization  2D Samples: Plated cells were trypsinized and centrifuged at 0.5 rcf for 10 minutes. 1000 µL TRIzol® was added to the pellet and was pipette homogenized.  3D Samples: Gels were removed from the medium and washed with PBS. They were coarsely homogenized using a plastic tissue homogenizer and then flash frozen in liquid nitrogen. Each sample was thawed in 1000 µL TRIzol®. Fine homogenization was performed on ice using an electric tissue homogenizer (Tissue Tearor , Biospec Products, Inc) for 1 minute at speed 35.

treatment_protocol: Cells were plated or encapsulated on day 0. On day 1 samples were either irradiated with UVA light for 25 mintues at 3.5mW/cm^2 or not irradiated. On day 2 all samples were collected for total RNA extraction

value: bone marrow

tag: cell type

value: mesenchymal stem cells

tag: culture conditions

value: hmsc plated in T75 flask at 500,000 cells

tag: uva treatment at day 1

value: 5.25 J/cm^2 UVA radiation exposure at day 3


title: X20C.3

status: Public on Sep 01 2015

city: Austin

first: Brian

middle: D

last: Vaillant

state: TX

department: Neurology

institute: Seton Brain and Spine Institute

description: GSC 20 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #3

hyb_protocol: Performed by Expression Analysis (Durham, NC)

data_processing: Affymetrix data processed in R using a custom CDF from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp  ; package 'affy' from Bioconductor suite, robust multi-array average (rma) data processing

source_name: Glioma Stem Cells isolated from glioblastoma

growth_protocol: Neural basal media supplemented with bFGF and EGF OR long-term growth in fetal bovine serum

extract_protocol: Whole RNA extraction kit from ABI

value: brain

value: glioma stem cell

tag: host

value: mouse


title: X20S.3

description: GSC 20 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #3

scan_protocol: Performed by Expression Analysis (Durham, NC)


title: B10.D2 to F1 Spleen 14d rep3

description:
CSV15
replicate 3


title: 2D1-UV-2

scan_protocol: performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource

value: 5.25 J/cm^2 UVA radiation exposure at day 2


title: DBA to F1 Spleen 14d rep1

description:
CSV17
replicate 1


title: 3DR-noUV-1

label_protocol: performed by the UCLA Clinical Microarray Core/JCCC Genomics Shared Resource

value: hmsc encapsulated by radical polymerization at 3,000,000 cells/100uL


title: X23C.3

description: GSC 23 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #3

label_protocol: Performed by Expression Analysis (Durham, NC)


title: 2D1-UV-1

value: 5.25 J/cm^2 UVA radiation exposure at day 1


title: B10.D2 to F1 Spleen 14d rep4

description:
CSV16
replicate 4


title: X20C.1

description: GSC 20 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #1


title: X20S.1

description: GSC 20 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #1


title: 2D1-noUV3


title: B10.D2 to F1 Spleen 14d rep2

description:
CSV14
replicate 2


title: X20C.2

description: GSC 20 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #2


title: X23S.2

description: GSC 23 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #2


title: X20S.2

description: GSC 20 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #2


title: 2D1-noUV-1


title: 2D1-noUV-2


title: B10.D2 to F1 Spleen 14d rep1

description:
CSV13
replicate 1


title: X23S.1

description: GSC 23 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #1


title: X23S.3

description: GSC 23 grown in basal media +fetal bovine serum as per material and methods, then brain xenograft until harvest mouse #3


title: X23C.1

description: GSC 23 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #1


title: S-GSC23

description: Grown in fetal bovine serum long-term

growth_protocol: Grown in fetal bovine serum long-term as per materials and methods section

value: glioma stem cells


title: S-GSC11

description: Grown in fetal bovine serum long-term


title: X23C.2

description: GSC 23 grown in basal media +bFGF +EGF then brain xenograft until harvest mouse #2


title: S-GSC20

description: Grown in fetal bovine serum long-term


title: S-GSC2

description: Grown in fetal bovine serum long-term


title: 3DR-noUV-2


title: EC71

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: Endometrial Hyperplasias, Primary Cancers and Metastases

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Raw .idat files were processed using minfi (v1.11.0) Bioconductor package and beta-values defined according to the standard Illumina definition

source_name: genomic DNA from endometrial sample EC71

label_protocol: Standard Illumina Protocol for Infinium 450k Chip

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: sample id

tag: primary disease dx

value: Endometrial cancer

tag: sample type

value: Tumor

value: Metastasis

tag: tissue site

value: Vaginal tissue

tag: tumor percent

value: Female

tag: sentrix id


title: EC87

source_name: genomic DNA from endometrial sample EC87


title: EC72

source_name: genomic DNA from endometrial sample EC72


title: EC78

source_name: genomic DNA from endometrial sample EC78

value: Cervical tissue


title: EC95

source_name: genomic DNA from endometrial sample EC95

value: Endometrial hyperplasia

value: Hyperplasia

value: Corpus


title: EC96

source_name: genomic DNA from endometrial sample EC96

value: x


title: EC73

source_name: genomic DNA from endometrial sample EC73

value: Primary


title: EC69

source_name: genomic DNA from endometrial sample EC69


title: EC90

source_name: genomic DNA from endometrial sample EC90


title: EC91

source_name: genomic DNA from endometrial sample EC91


title: EC75

source_name: genomic DNA from endometrial sample EC75

value: Lymph node


title: EC74

source_name: genomic DNA from endometrial sample EC74

value: Abdomunal tissue


title: EC76

source_name: genomic DNA from endometrial sample EC76


title: EC84

source_name: genomic DNA from endometrial sample EC84


title: EC83

source_name: genomic DNA from endometrial sample EC83


title: EC92

source_name: genomic DNA from endometrial sample EC92

value: Endometrial carcinoma cell line

value: Cell-line

value: Cell line Hec-1-b

value: Endometrium


title: EC82

source_name: genomic DNA from endometrial sample EC82

value: Endometrial cancer


title: EC89

source_name: genomic DNA from endometrial sample EC89


title: EC88

source_name: genomic DNA from endometrial sample EC88


title: EC94

source_name: genomic DNA from endometrial sample EC94

value: Cell line ECC-1


title: EC79

source_name: genomic DNA from endometrial sample EC79

value: Tumor


title: EC86

source_name: genomic DNA from endometrial sample EC86


title: EC77

source_name: genomic DNA from endometrial sample EC77

value: Metastasis


title: EC81

source_name: genomic DNA from endometrial sample EC81

value: Vaginal tissue

value: Female


title: EC80

source_name: genomic DNA from endometrial sample EC80


title: EC67

source_name: genomic DNA from endometrial sample EC67


title: EC68

source_name: genomic DNA from endometrial sample EC68


title: EC66

source_name: genomic DNA from endometrial sample EC66

value: Ovarian tissue


title: EC65

source_name: genomic DNA from endometrial sample EC65


title: EC60

source_name: genomic DNA from endometrial sample EC60

value: Cervical tissue


title: EC54

source_name: genomic DNA from endometrial sample EC54


title: EC49

source_name: genomic DNA from endometrial sample EC49


title: EC61

source_name: genomic DNA from endometrial sample EC61

value: Corpus


title: EC63

source_name: genomic DNA from endometrial sample EC63


title: EC53

source_name: genomic DNA from endometrial sample EC53


title: EC58

source_name: genomic DNA from endometrial sample EC58


title: EC62

source_name: genomic DNA from endometrial sample EC62


title: EC45

source_name: genomic DNA from endometrial sample EC45


title: EC93

source_name: genomic DNA from endometrial sample EC93

value: Endometrial hyperplasia

value: Hyperplasia


title: EC59

source_name: genomic DNA from endometrial sample EC59

value: Primary


title: EC52

source_name: genomic DNA from endometrial sample EC52


title: EC57

source_name: genomic DNA from endometrial sample EC57


title: EC50

source_name: genomic DNA from endometrial sample EC50


title: EC46

source_name: genomic DNA from endometrial sample EC46

value: Uterine wall


title: EC55

source_name: genomic DNA from endometrial sample EC55


title: EC64

source_name: genomic DNA from endometrial sample EC64


title: EC48

source_name: genomic DNA from endometrial sample EC48

value: Lymph node


title: EC51

source_name: genomic DNA from endometrial sample EC51


title: EC85

source_name: genomic DNA from endometrial sample EC85

value: Omental tissue


title: EC47

source_name: genomic DNA from endometrial sample EC47


title: EC70

source_name: genomic DNA from endometrial sample EC70


title: HESC-parthenogenetic-SMA line

city: Jerusalem

first: Ephrat

last: Levy-Lahad

address: Shmu'el Bait 12

country: Israel

institute: Shaare Zedek Medical Center

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner7G.

data_processing:
The array image was acquired using GeneChip® Command Console® Software (AGCC) . Affymetrix Chromosome Analysis Suite (ChAS) was used to determine copy number, genotyping calls and LOH.
[primary data description] Copy number and LOH

label: Biotin

source_name: HESC cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions for HESC.

extract_protocol: Genomic DNA was extracted from HESC cell culture using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cell line

value: parthenogenetic Spinal muscular atrophy type 1 (SMA) HESC line


title: EC42

source_name: genomic DNA from endometrial sample EC42


title: EC41

source_name: genomic DNA from endometrial sample EC41


title: EC39

source_name: genomic DNA from endometrial sample EC39


title: EC32

source_name: genomic DNA from endometrial sample EC32


title: EC36

source_name: genomic DNA from endometrial sample EC36


title: EC37

source_name: genomic DNA from endometrial sample EC37


title: EC30

source_name: genomic DNA from endometrial sample EC30


title: EC43

source_name: genomic DNA from endometrial sample EC43


title: EC31

source_name: genomic DNA from endometrial sample EC31


title: EC27

source_name: genomic DNA from endometrial sample EC27


title: EC56

source_name: genomic DNA from endometrial sample EC56


title: EC40

source_name: genomic DNA from endometrial sample EC40


title: EC38

source_name: genomic DNA from endometrial sample EC38


title: EC28

source_name: genomic DNA from endometrial sample EC28


title: EC44

source_name: genomic DNA from endometrial sample EC44


title: EC29

source_name: genomic DNA from endometrial sample EC29


title: EC24

source_name: genomic DNA from endometrial sample EC24


title: EC21

source_name: genomic DNA from endometrial sample EC21

value: Abdomunal tissue


title: EC22

source_name: genomic DNA from endometrial sample EC22

value: Endometrial cancer


title: EC18

source_name: genomic DNA from endometrial sample EC18

value: Douglasi


title: EC33

source_name: genomic DNA from endometrial sample EC33

value: Tumor


title: EC19

source_name: genomic DNA from endometrial sample EC19

value: Metastasis


title: EC23

source_name: genomic DNA from endometrial sample EC23


title: EC26

source_name: genomic DNA from endometrial sample EC26


title: EC25

source_name: genomic DNA from endometrial sample EC25


title: EC20

source_name: genomic DNA from endometrial sample EC20


title: EC35

source_name: genomic DNA from endometrial sample EC35


title: EC34

source_name: genomic DNA from endometrial sample EC34


title: EC16

source_name: genomic DNA from endometrial sample EC16


title: TS-2 tofu + soy oil

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

country: Japan

institute: Akita Prefectural University

description: normalized by SuperNORM data service

hyb_protocol: GeneChip® Hybridization Oven 640（Affymetrix)

scan_protocol: GeneChip® Scanner 3000 7G（Affymetrix）

data_processing: The perfect match data were normalized by using the SuperNORM data service (Skylight Biotech Inc., Akita, Japan) according to a three-parameter lognormal distribution model.

organism: Rattus norvegicus

source_name: SD rat liver, male

label_protocol: One-Cycle Target Labeling and Control Reagents （Affymetrix), performed by Genetic Lab Inc., Sapporo, Japan

growth_protocol: Male Sprague Dawley rats were obtained from Charles River Japan (Kanagawa, Japan) at 4 weeks of age. The animals were housed individually in a room with controlled temperature and humidity and a 12 h light dark cycle.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: fed with the indicated diet for 3 weeks: 20% protein, 15% fat

tag: feeding

value: tofu + soy oil

value: liver

value: Male

value: Sprague-Dawley

value: 4 weeks


title: EC15

source_name: genomic DNA from endometrial sample EC15

value: Parametrial tissue

value: Female


title: 2DAP-2

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

description: Gene expression data from endosperm 2 DAP

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: Rice endosperm 2 DAP

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Rice plant of Zhonghua11(Japonica cultivars) was cultivated in a phytotron with a light (12h, 28℃)/dark(12h, 22℃) cycle.

extract_protocol: Total cellular RNA was isolated from the rice endosperm and using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.

treatment_protocol: Endosperm at 2 days after pollination(DAP) was manually selected under the dissecting scope. Selected endosperm was transferred to a eppendorf tube, rinsed with ethanoland placed on ice in the 100% ethanol.

value: Endosperm

tag: developmental stage

value: 2 DAP


title: CHO_Untr_24h PHx

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

description:
Untr_CHO_PHX
Pair-fed carbohydrate control liver 24h after 70% partial hepatectomy.

hyb_protocol: Rat Gene 2.0 ST Array were hybridized with 5 μg of fragmented and biotin-labeled cDNA in 220 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using GeneChip Fluidic Station 450, using Affymetrix GeneChip Hybridization, Wash & Stain Kit.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000 7G, using Command Console Software.

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

source_name: Pair-fed carbohydrate control liver, untreated, 24h after PHx

label_protocol: 50 ng of total RNA was reverse transcribed using a chimeric cDNA/mRNA primer, and a second complementary cDNA strand was synthesized. Purified cDNA was then amplified with ribo-SPIA enzyme and SPIA DNA/RNA primers (NuGEN Technologies, San Carlos, CA). Amplified cDNA was purified with Qiagen MinElute reaction cleanup kit. 5 μg of cDNAs were fragmented and chemically labeled with biotin to generate biotinylated cDNA using FL-Ovation cDNA biotin module (NuGen Technologies).

extract_protocol: Total RNA was isolated using Animal Tissue RNA Purification Kit (Norgen Biotek) and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. RNA from 3 (AM21 treated samples) or 4 (untreated samples) biological replicates were pooled.

treatment_protocol: Rats received i.p. injection of AM21 (7.5 mg/kg) in saline (1 ml) 72 h prior to PHx and the second injection immediately following PHx. Liver tissue was freeze-clamped in liquid nitrogen at the time of PHx and 24 h after PHx. Tissue was then stored at -80 degrees C.

tag: strain/background

value: male

tag: tissue

tag: diet

value: carbohydrate

tag: treatment

tag: timepoint

value: 24 hour after partial hepatectomy

tag: animal ids


title: TS-5 tofu + soy oil

description: normalized by SuperNORM data service

tag: gender

tag: strain

tag: age


title: EtOH_Untr_ctrl

description:
Untr_EtOH_LLM
Gene expression in chronic ethanol-fed liver prior to partial hepatectomy.

source_name: Chronic ethanol-fed liver, untreated, prior to PHx

value: ethanol

value: 0 (control)


title: CHO_AM21_ctrl

description:
AM21_CHO_LLM
Pair-fed carbohydrate control liver after treatment with locked nucleic acid (LNA)-modified oligo antisense to miR-21 and prior to partial hepatectomy.

source_name: Pair-fed carbohydrate control liver, AM21 treated, prior to PHx


title: TS-7 tofu + soy oil

description: normalized by SuperNORM data service


title: CHO_Untr_ctrl

description:
Untr_CHO_LLM
Pair-fed carbohydrate control liver prior to partial hepatectomy.

source_name: Pair-fed carbohydrate control liver, untreated, prior to PHx


title: EtOH_AM21_24h PHx

description:
AM21_EtOH_PHX
Gene expression in chronic ethanol-fed liver after treatment with locked nucleic acid (LNA)-modified oligo antisense to miR-21 and 24h after 70% partial hepatectomy.

source_name: Chronic ethanol-fed liver, AM21 treated, 24h after PHx


title: CHO_AM21_24h PHx

description:
AM21_CHO_PHX
Pair-fed carbohydrate control liver after treatment with locked nucleic acid (LNA)-modified oligo antisense to miR-21 and 24h after 70% partial hepatectomy.

source_name: Pair-fed carbohydrate control liver, AM21 treated, 24h after PHx


title: TS-4 tofu + soy oil

description: normalized by SuperNORM data service


title: 2DAP


title: EtOH_Untr_24h PHx

description:
Untr_EtOH_PHX
Gene expression in chronic ethanol-fed liver 24h after 70% partial hepatectomy.

source_name: Chronic ethanol-fed liver, untreated, 24h after PHx


title: EtOH_AM21_ctrl

description:
AM21_EtOH_LLM
Gene expression in chronic ethanol-fed liver after treatment with locked nucleic acid (LNA)-modified oligo antisense to miR-21 and prior to partial hepatectomy.

source_name: Chronic ethanol-fed liver, AM21 treated, prior to PHx


title: EC17

source_name: genomic DNA from endometrial sample EC17

tag: sample id

tag: primary disease dx

value: Endometrial cancer

value: Primary

value: Corpus


title: EC14

source_name: genomic DNA from endometrial sample EC14

tag: sample type

value: Tumor

value: Metastasis

tag: tissue site

value: Cervical tissue


title: TF-4 tofu + fish oil

description: normalized by SuperNORM data service

value: tofu + fish oil

value: liver

value: Male

value: Sprague-Dawley


title: EC13

source_name: genomic DNA from endometrial sample EC13

tag: tumor percent

value: Female

tag: sentrix id


title: EC5

source_name: genomic DNA from endometrial sample EC5


title: EC6

source_name: genomic DNA from endometrial sample EC6


title: TF-5 tofu + fish oil

description: normalized by SuperNORM data service

tag: feeding

value: 4 weeks


title: EC11

source_name: genomic DNA from endometrial sample EC11


title: EC7

source_name: genomic DNA from endometrial sample EC7

value: Vaginal tissue


title: EC2

source_name: genomic DNA from endometrial sample EC2

value: Omental tissue


title: CF-1 casein + fish oil

description: normalized by SuperNORM data service

source_name: SD rat liver, male

value: casein + fish oil


title: CS-6 casein + soy oil

description: normalized by SuperNORM data service

value: casein + soy oil


title: EC8

source_name: genomic DNA from endometrial sample EC8

value: Ovarian tissue


title: EC12

source_name: genomic DNA from endometrial sample EC12

value: Endometrial cancer

value: Spleen


title: TF-6 tofu + fish oil

description: normalized by SuperNORM data service


title: TS-1 tofu + soy oil

description: normalized by SuperNORM data service

value: tofu + soy oil


title: EC1

source_name: genomic DNA from endometrial sample EC1

value: Tumor

value: Primary

value: Corpus


title: CS-7 casein + soy oil

description: normalized by SuperNORM data service


title: EC10

source_name: genomic DNA from endometrial sample EC10


title: TF-7 tofu + fish oil

description: normalized by SuperNORM data service

value: tofu + fish oil


title: CF-5 casein + fish oil

description: normalized by SuperNORM data service

value: liver


title: CS-5 casein + soy oil

description: normalized by SuperNORM data service

value: Male


title: EC9

source_name: genomic DNA from endometrial sample EC9

value: Metastasis


title: CS-2 casein + soy oil

description: normalized by SuperNORM data service

value: Sprague-Dawley


title: TF-3 tofu + fish oil

description: normalized by SuperNORM data service

value: 4 weeks


title: CS-1 casein + soy oil

description: normalized by SuperNORM data service


title: CF-2 casein + fish oil

description: normalized by SuperNORM data service


title: EC4

source_name: genomic DNA from endometrial sample EC4

value: Gastrointertinal tissue

value: Female


title: CF-7 casein + fish oil

description: normalized by SuperNORM data service

value: casein + fish oil


title: EC3

source_name: genomic DNA from endometrial sample EC3

value: Omental tissue


title: 4th Passage, Uninfected age-matched Brain, 198dpi rep3

city: Edmonton

first: Allen

last: Herbst

state: AB

address: 114C BARB

country: Canada

institute: University of Alberta

hyb_protocol: Following fragmentation, cRNA was hybridized on Affymetrix Rat Genome 230 2.0 microarrays. GeneChips were washed and stained in the Affymetrix GC450.

scan_protocol: GeneChips were scanned using an Affymetrix GC3000 7G Scanner

data_processing: Data were processed using arraystar and robust multiarray averaging

source_name: Brain, Uninfected, 198 dpi, age-matched control

label_protocol: Biotinylated cRNA were prepared using the MessageAMP Premier RNA amplification kit according to the manufacturers instructions

growth_protocol: Sprague Dawley rats were housed 12 hour light cycle adlibitum food and water.

extract_protocol: RNA was isolated from whole brain halves using the Qiagen RNEASY tissue protocol and qiashredders. Because of the large mass of rat brains, 16.67% brain homogenates were first prepared in RLT lysis buffer. Subsequently, brain homogenate aliquots were diluted in additional RLT buffer to meet the manufacturers protocol.

treatment_protocol: Weanling rats were infected by intracranial inoculation of 50ul of a 10% brain homogenate prepared in water from clinically affected rats. In the case of the third passage, second passage rat adapted RML scrapie was used as inocula. For Fourth Passage, third passage brain homogenate was used.

value: Sprague Dawley

value: Brain

tag: passage

value: 4th Passage

tag: time point days post infection (dpi)

value: T3, 198 dpi, Clinical

tag: disease status

value: Uninfected age-matched control


title: 4th Passage, Uninfected age-matched Brain, 198dpi rep2

tag: tissue


title: 4th Passage, Uninfected age-matched Brain, 198dpi rep1


title: 4th Passage, Uninfected age-matched Brain, 150dpi rep2

source_name: Brain, Uninfected, 150 dpi, age-matched control


title: 4th Passage, Uninfected age-matched Brain, 150dpi rep3


title: 4th Passage, Uninfected age-matched Brain, 150dpi rep1


title: 4th Passage, Uninfected age-matched Brain, 113dpi rep2

source_name: Brain, Uninfected, 113 dpi, age-matched control


title: 4th Passage, Infected Brain, 198dpi rep3

source_name: Brain, Infected, Clinical, 198 days post infection

value: Infected


title: 4th Passage, Infected Brain, 150dpi rep1

source_name: Brain, Infected, 150 days post infection


title: 4th Passage, Infected Brain, 198dpi rep2


title: 4th Passage, Uninfected age-matched Brain, 113dpi rep3


title: 4th Passage, Infected Brain, 198dpi rep1


title: 4th Passage, Infected Brain, 150dpi rep3


title: 4th Passage, Infected Brain, 150dpi rep2


title: 4th Passage, Infected Brain, 113dpi rep2

source_name: Brain, Infected, 113 days post infection


title: 3rd Passage, Uninfected age-matched control brain, rep3

source_name: Brain, Uninfected, 215 dpi, age-matched control

value: 3rd Passage

value: 215 dpi, Clinical


title: 4th Passage, Infected Brain, 113dpi rep1


title: 3rd Passage, Infected Brain, Clinical, rep1

source_name: Brain, Infected, Clinical, 215 days post infection


title: 3th Passage, Infected Brain, Clinical, rep2


title: 4th Passage, Uninfected age-matched Brain, 113dpi rep1


title: 3th Passage, Infected Brain, Clinical, rep3


title: 3rd Passage, Uninfected age-matched control brain, rep2


title: 4th Passage, Infected Brain, 113dpi rep3


title: CF-6 casein + fish oil

description: normalized by SuperNORM data service

value: liver


title: MRT-contralateral-rat 11

city: LA TRONCHE

first: Michèle

last: EL ATIFI

address: Chemin fortuné ferrini

country: France

institute: INSERM

hyb_protocol: After fragmentation, biotinylated cRNA were hybridized for 16h at 45 °C on GeneChip® Rat 230_ 2 . Then arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were normalized using RMA algorithm with the Affymetrix software Expression Console Suite.

source_name: Normal brain , MRT irradiation

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 200 ng of total RNA using the GeneChip®  3’IVT Express Kit

growth_protocol: Rat glioblastoma cells 9L were cultured in complete medium (DMEM/Fetal bovin serum 10%/Penicillin and Streptavidin 1%) at 37°C in a humidified 5% CO2 incubator.

extract_protocol: 6 hours after MRT treatment, brain tumors were resected and total RNA were extracted with the MirVana TM isolation kit (AppliedBiosystems)

treatment_protocol: Brain tumors were developed in Fisher rats by injection of 100.000 9L cells into the right caudate nucleus. 10 days after tumor implantation, six rats were treated with MRT radiation (90 KeV, Microbeam dose : 400 Gy, valley dose : 18 Gy, dose rate 62 Gy.mA-1.s-1).

value: Normal brain tissue

tag: cell type

value: Normal brain


title: MRT-contralateral-rat 9


title: MRT-contralateral-rat 10


title: MRT-contralateral-rat 7


title: 3rd Passage, Uninfected age-matched control brain, rep1


title: MRT-contralateral-rat 8


title: MRT-contralateral-rat 6


title: MRT-treated-tumor-rat 10

source_name: Cerebral tumor, MRT irradiation

value: Orthotopic brain tumor

value: 9L rat cells (Glioblastoma)


title: Untreated-contralateral-rat 2

source_name: Normal brain , No irradiation


title: Untreated-contralateral-rat 1


title: Untreated-contralateral-rat 4


title: MRT-treated-tumor-rat 11


title: MRT-treated-tumor-rat 7


title: MRT-treated-tumor-rat 8


title: MRT-treated-tumor-rat 6


title: Untreated-tumor-rat 5

source_name: Cerebral tumor, No irradiation


title: Untreated-tumor-rat 4


title: MRT-treated-tumor-rat 9


title: Untreated-tumor-rat 2


title: Untreated-contralateral-rat 3


title: Untreated-contralateral-rat 5


title: Untreated-tumor-rat 3


title: Untreated-tumor-rat 1


title: E.coli W3110 cells (without induction) at 0 min, biological rep1

city: Hohhot

first: yao

last: yuan

state: Inner Mongolia

address: No. 235, Da xue West Road,

department: School of Life Sciences

institute: Inner Mongolia University

description: Gene expression data from synchronized grown W3110 derivatives at 0min.

hyb_protocol: Following fragmentation, 7 ug of cDNA were hybridized for 16 hr at 45oC and 60rpm onGeneChip E. coli Genome 2.0 Array. GeneChips were washedand stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000. GeneChips were imaged using Affymetrix® GeneChip® Command Console® Software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Using SAM （significance analysis of microarray）R procedure to analyze the   differential gene( q-value  ≤  5%  and  Fold Change  ≥2 or ≤0.5).

organism: Escherichia coli str. K-12 substr. W3110

source_name: synchronized grown E.coli W3110∆torRdnaC2/pTorR-GFP cells at 0 min (absent TorR-GFP)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

growth_protocol: Exponentially growing W3110∆torRdnaC2/pTorR-GFP cells in ABTGcasa medium with or without induction of TorR-GFP expression at the permissive temperature (30oC) were up-shifted to the nonpermissive temperature (42oC) for 2 hours to synchronize the cells. The synchronized cells were down-shifted to the permissive temperature.

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

tag: genotype


title: E.coli W3110 cells (with induction) at 0 min, biological rep2

source_name: synchronized grown E.coli W3110∆torRdnaC2/pTorR-GFP cells at 0 min (present TorR-GFP)


title: E.coli W3110 cells (without induction) at 0 min, biological rep2


title: E.coli W3110 cells (with induction) at 45 min, biological rep5

description: Gene expression data from synchronized grown W3110 derivatives at 45min.

source_name: synchronized grown E.coli W3110∆torRdnaC2/pTorR-GFP cells at 45 min (present TorR-GFP)


title: E.coli W3110 cells (with induction) at 45 min, biological rep2


title: E.coli W3110 cells (with induction) at 45 min, biological rep4


title: E.coli W3110 cells (without induction) at 45 min, biological rep1

source_name: synchronized grown E.coli W3110∆torRdnaC2/pTorR-GFP cells at 45 min (absent TorR-GFP)


title: E.coli W3110 cells (with induction) at 0 min, biological rep4


title: E.coli W3110 cells (without induction) at 45 min, biological rep2


title: E.coli W3110 cells (with induction) at 0 min, biological rep5


title: HEK293T CTRLpcDNA 24hr 3

city: Miami

first: Veronica

middle: J

last: Peschansky

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

hyb_protocol: Final yield was hybridized onto the array, washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit (cat# 900720).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G system.

data_processing: Background subtraction, normalization and quality control were performed using the Affymetrix GeneChip Command Console Software and R bioconductor. Data were normalized with GC-RMA.

source_name: HEK 293T cells, overexpression control, 24 hrs

label_protocol: At 6 or 24 hours post transfection, RNA was extracted and samples were submitted to the Hussman Institute for Human Genomics Center for Genome Technology for microarray analysis using Affymetrix Human Gene 1.0 ST Arrays. Total RNA samples were first prepared using the Ambion WT Expression Kit (cat# 4411974). Briefly, the kit generates sense-strand cDNA from total RNA using a reverse transcription priming method that specifically primes non-ribosomal RNA, including both poly(A) and non-poly(A) mRNA. Next, samples are fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit (cat# 902280).

extract_protocol: RNA was extracted using Trizol and the RNeasy Mini Kit columns from Qiagen.

treatment_protocol: CTLsiRNA & FMR4siRNA were transfected with Lipofectamine RNAiMAX and 40nM siRNA. CTRLpcDNA & FMR4pcDNA were transfected with Lipofectamine 2000CD and 0.5ug pcDNA 3.1 vector w/ or w/o FMR4, respectively.

tag: cell line

value: HEK 293T cells

tag: genotype/variation

value: overexpression control

tag: time

value: 24 hrs


title: HEK293T FMR4pcDNA 24hr 1

source_name: HEK 293T cells, FMR4 overexpression, 24 hrs

value: FMR4 overexpression


title: HEK293T FMR4pcDNA 24hr 3


title: HEK293T CTRLpcDNA 24hr 1


title: HEK293T FMR4pcDNA 24hr 2


title: HEK293T CTLsiRNA 24hr 3

source_name: HEK 293T cells, knockdown control, 24 hrs

value: knockdown control


title: HEK293T CTRLpcDNA 6hr 3

source_name: HEK 293T cells, overexpression control, 6 hrs

value: 6 hrs


title: HEK293T FMR4pcDNA 6hr 2

source_name: HEK 293T cells, FMR4 overexpression, 6 hrs


title: HEK293T CTRLpcDNA 24hr 2


title: HEK293T FMR4siRNA 6hr 2

source_name: HEK 293T cells, FMR4 knockdown, 6 hrs

value: FMR4 knockdown


title: HEK293T FMR4siRNA 24hr 1

source_name: HEK 293T cells, FMR4 knockdown, 24 hrs


title: HEK293T FMR4siRNA 24hr 3


title: HEK293T FMR4siRNA 24hr 2


title: HEK293T CTRLpcDNA 6hr 1


title: HEK293T CTRLpcDNA 6hr 2


title: HEK293T CTLsiRNA 24hr 2


title: HEK293T FMR4pcDNA 6hr 1


title: HEK293T FMR4pcDNA 6hr 3


title: HEK293T FMR4siRNA 6hr 3


title: HEK293T CTLsiRNA 6hr 2

source_name: HEK 293T cells, knockdown control, 6 hrs


title: HEK293T FMR4siRNA 6hr 1


title: DU145_siTET2

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

description: Gene expression data from DU145 cells  treated withsiTET2

hyb_protocol: The samples were hybridized to Human Gene 1.0 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: prostate cancer

label_protocol: Total RNA was labeled employing the Affymetrix GeneChip Whole Transcript (WT) Terminal Labeling kit according to the manufacturer’s instructions

growth_protocol: LNCaP and DU145 cells were cultured in RPMI 1640 containing 10% FBS.

extract_protocol: Total RNAs were extracted using ISOGEN (Nippon gene) according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with each siRNA or miRNA 72 h before RNA extraction.

value: prostate cancer

tag: transfection construct


title: DU145_nc

description: Gene expression data from DU145 cells treated with negative control miRNA

value: Negative control miR


title: LNCaP_siControl

description: Gene expression data from LNCaP cells treated with siControl

value: LNCaP

value: siControl


title: HEK293T CTLsiRNA 6hr 1


title: CLP from cord blood batch3

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description: Gene expression data from sorted human CLP cells

hyb_protocol: Samples were hybridised to the Affymetrix HuGene 1.0ST array accroding to Affymetrix protocols

scan_protocol: Scanning was performed according to Affymetrix protocols

data_processing: Signal intensities from the MAS5 suite were RMA summarised

source_name: Human cord blood

label_protocol: standard Affymetrix protocol

growth_protocol: Donated human cord blood (CB) samples from Lund, Malmö and Helsingborg hospitals were diluted in heparin immediately after delivery and processed within 24 hours

extract_protocol: At least 2,000 cells were sorted directly into RLT buffer (Qiagen) containing 2-β-Mercaptoethanol (Invitrogen) and the RNA extraction was performed with an RNA micro kit, according to manufacturer’s instructions (Qiagen).

treatment_protocol: The CD34+ fractions were obtain from human CB using CD34 positive selection (Miltenyi Biotec). After the staining with directly conjugated antibodies, cells were sorted on a BD FACSAria III (BD Biosciences) and the average purity of sorted cells in all experiments was 93%.

value: CLP cells

tag: immunophenotype


title: CLP from cord blood batch2


title: NK from Cord blood batch4

description: Gene expression data from sorted human NK cells

value: NK cells


title: NKP from Cord blood batch2

description: Gene expression data from sorted human NKP cells

value: NKP cells


title: NK from Cord blood batch2


title: DU145_miR-29b

description: Gene expression data from DU145 cells treated with miR-29b


title: NKP from Cord blood batch1


title: CLP from cord blood batch1


title: LMPP from Cord blood batch3

description: Gene expression data from sorted human LMPP cells

value: LMPP cells


title: LMPP from Cord blood batch4


title: LNCaP_miR-29b

description: Gene expression data from LNCaP cells treated with miR-29b


title: NK from Cord blood batch1


title: HEK293T CTLsiRNA 6hr 3


title: LMPP from Cord blood batch1


title: LNCaP_siTET2

description: Gene expression data from LNCaP cells  treated withsiTET2


title: NK from Cord blood batch3


title: NKP from Cord blood batch4


title: COG_170

city: Rovereto

first: Melissa

last: Morine

address: Via Manifattura 1

country: Italy

institute: The Microsoft Research - University of Trento Centre for Computational and Systems Biology

description: PBMC, fasting

hyb_protocol: Labeled cDNA was then hybridized to human whole-genome Gene ST 1.0 arrays encoding 28 869 genes (AffymetrixInc).

scan_protocol: Sample labeling, hybridization to chips, and image scanning were performed according to the manufacturer's GeneChip Expression Analysis Technical Manual (AffymetrixInc), using an Affymetrix Genechip Scanner 3000

data_processing: Data were normalized by RMA. All data processing and analysis were carried out in R.

source_name: PBMC, fasting

label_protocol: Synthesized cDNA was labeled using the GeneChip® WT Terminal Labeling and Hybridization kit (AffymetrixInc, Santa Clara, CA).

extract_protocol: cDNA was synthesized from total PBMC RNA using the Ambion WT Expression kit (Applied Biosystems, CA).

treatment_protocol: Participants consumed 100 mL Calogen (Nutricia, Ireland) combined with 50 mL Liquid Duocal (SHS Nutrition, Netherlands) for a total of 150 mL with a fat content of 54 g. PBMCs were collected at baseline and 240 minutes post-challenge

tag: age

tag: gender

value: F

tag: bmi


title: LMPP from Cord blood batch2


title: COG_171

description: PBMC, 60min post-OLTT

source_name: PBMC, 60min post-OLTT


title: NKP from Cord blood batch3


title: COG_174

description: PBMC, fasting

value: M


title: COG_175

description: PBMC, 60min post-OLTT


title: COG_158

description: PBMC, fasting


title: COG_139

description: PBMC, 60min post-OLTT


title: COG_130

description: PBMC, fasting


title: COG_138

description: PBMC, fasting


title: COG_118

description: PBMC, fasting


title: COG_154

description: PBMC, fasting


title: COG_123

description: PBMC, 60min post-OLTT


title: COG_127

description: PBMC, 60min post-OLTT


title: COG_151

description: PBMC, 60min post-OLTT


title: COG_155

description: PBMC, 60min post-OLTT


title: COG_115

description: PBMC, 60min post-OLTT


title: COG_126

description: PBMC, fasting


title: COG_159

description: PBMC, 60min post-OLTT


title: COG_131

description: PBMC, 60min post-OLTT


title: COG_114

description: PBMC, fasting


title: COG_150

description: PBMC, fasting


title: COG_122

description: PBMC, fasting


title: COG_119

description: PBMC, 60min post-OLTT


title: COG_105

description: PBMC, 60min post-OLTT


title: COG_104

description: PBMC, fasting


title: COG_110

description: PBMC, fasting


title: COG_039

description: PBMC, fasting


title: COG_040

description: PBMC, 60min post-OLTT


title: COG_103

description: PBMC, 60min post-OLTT


title: COG_111

description: PBMC, 60min post-OLTT


title: COG_032

description: PBMC, 60min post-OLTT


title: COG_102

description: PBMC, fasting


title: COG_031

description: PBMC, fasting


title: COG_023

description: PBMC, fasting


title: COG_024

description: PBMC, 60min post-OLTT


title: COG_027

description: PBMC, fasting


title: My/Tr P12 vs My/Tr dPAI  [1 hpi]

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: MyD88/Trif−/− double KO_H-pylori WT infected

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Bone marrow-derived macrophages (BMMs) were generated according to a standard protocol [Collins et al., 1997]. H. pylori P12 wildtype (strain collection no. 243) and its isogenic mutants P12ΔcagPAI (no. P387) as described previously (Koch et al., 2012) were plated from a glycerol stock and grown on GC agar plates containing 10% horse serum, 10 µg/ml vancomycin, 1 µg/ml nystatin and 5 µg/ml trimethoprim. They were kept under micro-aerophilic conditions (5% CO2, 4% O2) and replated after 3d on plate. Following another replating after 1d (maximum 3 times) bacteria were ready for infection.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Bacteria were washed two times with PBS prior to infection and added in a defined volume of PBS. All experiments were carried out at MOI 50. To determine MOI a calibration curve was generated for the bacteria via measuring the optical density at 550 nm (OD550). Mock infection is defined here as the non-infected control using the same volume of PBS or respective solvent. Before infection media was exchanged to RPMI medium containing no additional supplements. The number of BMMs was determined by the optical confluency using a standard curve.

tag: strain background

value: Balb/c

value: MyD88/Trif−/− double KO

value: Bone marrow-derived macrophages (BMMs)

tag: infected with

value: H-pylori wildtype

tag: time point

value: 60 min post infection

source_name: MyD88/Trif−/− double KO_H-pylori ΔcagPAI infected

value: H-pylori ΔcagPAI mutant


title: COG_028

description: PBMC, 60min post-OLTT


title: My/Tr ni vs My/Tr P12  [1 hpi]

source_name: MyD88/Trif−/− double KO_uninfected

value: none (uninfected)


title: COG_020

description: PBMC, 60min post-OLTT


title: My/Tr/Rip P12 vs My/Tr/Rip dPAI [3 hpi]

description:
144h experiment 1
251486828954_S01_GE2_1105_Oct12_1_3

source_name: MyD88/Trif/Rip2-/- triple KO_H-pylori wildtype

value: MyD88/Trif/Rip2-/- triple KO

source_name: MyD88/Trif/Rip2-/- triple KO_H-pylori ΔcagPAI mutant


title: My/Tr P12 vs My/Tr dPAI [3 hpi]

description:
24h experiment 3
251486828954_S01_GE2_1105_Oct12_1_1

source_name: MyD88/Trif-/- double KO_H-pylori wildtype

value: MyD88/Trif-/- double KO

source_name: MyD88/Trif-/- double KO_H-pylori ΔcagPAI mutant


title: My/Tr dPAI vs My/Tr P12 [3 hpi]

description:
24h experiment 3
251486828954_S01_GE2_1105_Oct12_1_2


title: COG_015

description: PBMC, fasting


title: COG_016

description: PBMC, 60min post-OLTT


title: My/Tr/Rip dPAI vs My/Tr/Rip P12 [3 hpi]

description:
144h experiment 1
251486828954_S01_GE2_1105_Oct12_1_4


title: COG_019

description: PBMC, fasting


title: Gene expression profiles of obese adipose tissue

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Gene expression data were obtained and statistically analyzed using Agilent Feature Extraction software, using defaults for all parameters except ratio terms, which were changed according to the Agilent protocol to fit the direct labeling procedure.
Files and images, including error values and P values, were exported from the Agilent Feature Extraction Program (version 9.5).

source_name: db/db (BKS.Cg-m+/+ Lepr db/J, 6 weeks old)

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: The mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNA of epididymal white adipose tissue were extracted using QIAzol following manufacturer's instructions.

value: db/db

value: male

source_name: db/+ (BKS.Cg-Dock7m +/+ Lepr db/J, 6 weeks old)

value: db/+


title: COG_012

description: PBMC, 60min post-OLTT


title: My/Tr/Rip ni vs My/Tr/Rip dPai [3 hpi]

description:
144h experiment 3
221486828952_S01_GE2_1010_Sep10_1_3

source_name: MyD88/Trif/Rip2-/- triple KO_uninfected


title: My/Tr P12 vs My/Tr ni  [1 hpi]


title: COG_011

description: PBMC, fasting


title: My/Tr/Rip P12 vs My/Tr/Rip ni [3 hpi]

description:
144h experiment 2
221486828952_S01_GE2_1010_Sep10_1_2


title: COG_007

description: PBMC, fasting


title: COG_002

description: PBMC, 60min post-OLTT


title: COG_169

description: PBMC, 60min post-OGTT

source_name: PBMC, 60min post-OGTT

treatment_protocol: Participants consumed 75 g glucose (anhydrous) in 150 mL of water. PBMCs were collected at baseline and 60 minutes post-challenge


title: My/Tr/Rip ni vs My/Tr/Rip P12 [3 hpi]

description:
144h experiment 2
221486828952_S01_GE2_1010_Sep10_1_1


title: DU145_siControl

description: Gene expression data from DU145 cells treated with siControl

value: prostate cancer

value: siControl


title: My/Tr/Rip dPai vs My/Tr/Rip ni [3 hpi]

description:
144h experiment 3
221486828952_S01_GE2_1010_Sep10_1_4


title: wt P12 vs wt ni [3 hpi]

description:
24h experiment 1
251486828951_S01_GE2_105_Dec08_1_2

source_name: wildtype_H-pylori wildtype

value: wildtype


title: wt ni vs wt P12 [3 hpi]

description:
24h experiment 1
251486828951_S01_GE2_105_Dec08_1_1


title: My/Tr P12 vs My/Tr ni [3 hpi]

description:
24h experiment 2
251486828951_S01_GE2_105_Dec08_1_4

source_name: MyD88/Trif-/- double KO_uninfected


title: HEK293T CTLsiRNA 24hr 1

source_name: HEK 293T cells, knockdown control, 24 hrs

value: HEK 293T cells

value: knockdown control

value: 24 hrs


title: COG_172

description: PBMC, fasting

value: M


title: COG_168

description: PBMC, fasting

value: F


title: COG_001

description: PBMC, fasting


title: COG_153

description: PBMC, 60min post-OGTT


title: My/Tr ni vs My/Tr P12 [3 hpi]

description:
24h experiment 2
251486828951_S01_GE2_105_Dec08_1_3

value: Balb/c

value: Bone marrow-derived macrophages (BMMs)

value: H-pylori wildtype


title: bovine mammary_SD_day-9_rep2

city: Columbia

first: Thomas

middle: B

last: McFadden

state: MO

address: S108 Animal Science Research Center

department: Animal Sciences

institute: University of Missouri

description: bovine mammary tissue obtained by biospy

hyb_protocol: The biotinylated cRNAs were fragmented into 50- to 200-base fragments and then hybridized to GeneChip® Bovine Genome Arrays (Affymetrix) for 16 h at 45°C in a rotating Affymetrix GeneChip® Hybridization Oven 320.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin on an automated Affymetrix GeneChip® Fluidic Station F450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip® Scanner 2700 and the images quantified using Affymetrix GeneChip® Operating Software.

data_processing: The signal intensity for each probe was calculated from scanned images using GeneChip® Operating Software (Affymetrix).  Signal intensities were analyzed using BioConductor (http://www.bioconductor.org), background corrected, normalized using the loess method, and summarized as robust multichip averages (RMA)

molecule: polyA RNA

organism: Bos taurus

source_name: mammary tissue, cows on SD photoperiod, day -9 relative to parturition

label_protocol: 2 μg of total RNA were reverse transcribed to single-stranded cDNA using T7-oligo (dT) primer.  T4 DNA polymerase was used to synthesize double-stranded cDNA, which served as a template for in vitro transcription using T7 RNA polymerase to produce biotinylated cRNA.

extract_protocol: RNA was isolated from biopsied mammary tissues as previously described using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.  Total RNA was further purified using the RNeasy Mini Kit (Qiagen).  Nucleic acid concentration was quantified using a NanoDrop ND1000 spectrophotometer and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).  Samples meeting the criteria of RIN > 7.0 were used for microarray analysis.

treatment_protocol: Holstein cows were dried-off approximately 60-days before their predicted parturition date, and randomly assigned to LD or SD photoperiod treatment for the duration of the dry period.  Lights were turned on at 0800 h for both groups, and off at 1600 h for SD or at 2400 h for LD.

tag: photoperiod

value: Short Day (8 h light:16 h dark)

tag: breed

value: Holstein

value: mammary

tag: day


title: LNCaP_nc

description: Gene expression data from LNCaP cells treated with negative control miRNA

source_name: prostate cancer

value: LNCaP

value: Negative control miR


title: COG_157

description: PBMC, 60min post-OGTT


title: COG_008

description: PBMC, 60min post-OLTT

source_name: PBMC, 60min post-OLTT


title: bovine mammary_SD_day-9_rep3

tag: tissue


title: COG_156

description: PBMC, fasting

source_name: PBMC, fasting


title: bovine mammary_SD_day-9_rep1


title: COG_149

description: PBMC, 60min post-OGTT


title: COG_152

description: PBMC, fasting


title: bovine mammary_SD_day-24_rep3

source_name: mammary tissue, cows on SD photoperiod, day -24 relative to parturition


title: bovine mammary_SD_day-24_rep2


title: bovine mammary_SD_day-9_rep4


title: bovine mammary_SD_day-24_rep1


title: COG_173

description: PBMC, 60min post-OGTT


title: bovine mammary_LD_day-9_rep4

source_name: mammary tissue, cows on LD photoperiod, day -9 relative to parturition

value: Long Day (16 h light:8 h dark)


title: COG_148

description: PBMC, fasting


title: COG_129

description: PBMC, 60min post-OGTT


title: bovine mammary_LD_day-24_rep3

source_name: mammary tissue, cows on LD photoperiod, day -24 relative to parturition


title: bovine mammary_LD_day-9_rep1


title: bovine mammary_LD_day-9_rep2


title: COG_128

description: PBMC, fasting


title: COG_121

description: PBMC, 60min post-OGTT


title: COG_136

description: PBMC, fasting


title: COG_120

description: PBMC, fasting


title: COG_112

description: PBMC, fasting


title: bovine mammary_LD_day-24_rep1


title: COG_113

description: PBMC, 60min post-OGTT


title: w1118_control_biological replicate 2

city: Chestnut Hill

first: Kimberly

last: Regna

state: Massachusetts

address: 140 Commonwealth Avenue

department: Biology

institute: Boston College

description:
Sample name: w1118_2
Gene expression data from control animals

hyb_protocol: EukGE-WS2v4 protocol was used for hybridization.

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

data_processing: Gene expression analysis was performed on the GeneChipR Drosophila genome array (DrosGenome1) using Affymetrix Gene Array technology, according to standard Affymetrix protocols.  Data were analyzed using the Microarray Suite program (Affymetrix, Santa Clara, CA), as well as Genespring array analysis software (Silicon Genetics).

organism: Drosophila melanogaster

source_name: Drosophila pale pupae (w1118;Act5C-Gal4/+)

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

growth_protocol: All crosses (Dop1R2 RNAi and w1118 control) were set up and maintained at 29C (retrictive conditions).

extract_protocol: RNA was extracted from 10-20 pooled Dop1R2 RNAi early/pale pupae and corresponding control pupae.  Total RNA was isolated using Trizol reagent (Invitrogen, Grand Island, NY), and purified using the RNeasy Kit with DNase treatment (Qiagen, Valencia, CA), according to the manufacturer’s recommendations.  double-strand cDNA was obtained using SuperScript Double Stranded cDNA Synthesis kit (Invitrogen, Grand Island, NY)

treatment_protocol: Pale/early pupae were picked from corresponding vials and processed using the extraction protocol (below).

value: whole organism

value: control

tag: developmental stage

value: pale pupae


title: COG_125

description: PBMC, 60min post-OGTT


title: COG_124

description: PBMC, fasting


title: COG_117

description: PBMC, 60min post-OGTT


title: Dop1R2_knockdown_biological replicate 1

description:
Sample name: Dop1R2_1
Gene expression data from Dop1R2 knockdown animals

source_name: Drosophila pale pupae (UAS-dsDop1R2/+;Act5C-Gal4/+)

value: Dop1R2 knockdown


title: COG_109

description: PBMC, 60min post-OGTT


title: CNOT3KD MEFs, Act.D 12h

city: Onna

first: Toru

last: Suzuki

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Instutue of Science and Technology Graduate University

description:
Sample name: CNOT3KD 12h
Gene expression data from CNOT3KD mouse embryonic fibroblasts which were treated actinomycin D for 12h.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CNOT3KD MEFs treated with actinomycin D for 12h

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

growth_protocol: Primary mouse embryonic fibroblasts were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at 37C, 5% CO2.

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

treatment_protocol: Primary mouse embryonic fibroblasts were infected with control retorvirus or Cre expression retrovirus, and were selected in puromycin-containing medium for 2 days.

tag: cell type

value: primary mouse embryonic fibroblasts

value: CNOT3 knock down

tag: agent

value: actinomycin D


title: w1118_control_biological replicate 1

description:
Sample name: w1118_1
Gene expression data from control animals

tag: genotype/variation


title: COG_137

description: PBMC, 60min post-OGTT

value: M


title: COG_116

description: PBMC, fasting


title: bovine mammary_LD_day-9_rep3


title: COG_108

description: PBMC, fasting

value: F


title: bovine mammary_LD_day-24_rep2


title: CNOT3KD MEFs

description:
Sample name: CNOT3KD 0h
Gene expression data from CNOT3KD mouse embryonic fibroblasts

source_name: CNOT3KD MEFs

value: untreated

tag: time


title: COG_107

description: PBMC, 60min post-OGTT


title: Control MEFs, Act.D 12h

description:
Sample name: Control 12h
Gene expression data from control mouse embryonic fibroblasts which were treated with actinomycin D for 12h.

source_name: Control MEFs treated with actinomycin D for 12h

value: wild type


title: COG_106

description: PBMC, fasting


title: COG_101

description: PBMC, 60min post-OGTT


title: CNOT3KD MEFs, Act.D 6h

description:
Sample name: CNOT3KD 6h
Gene expression data from CNOT3KD mouse embryonic fibroblasts which were treated actinomycin D for 6h.

source_name: CNOT3KD MEFs treated with actinomycin D for 6h


title: Control MEFs, Act.D 6h

description:
Sample name: Control 6h
Gene expression data from control mouse embryonic fibroblasts which were treated with actinomycin D for 6h

source_name: Control MEFs treated with actinomycin D for 6h


title: COG_021

description: PBMC, fasting


title: COG_038

description: PBMC, 60min post-OGTT

source_name: PBMC, 60min post-OGTT


title: My/Tr dPAI vs My/Tr P12  [1 hpi]

source_name: MyD88/Trif−/− double KO_H-pylori ΔcagPAI infected

value: Balb/c

value: MyD88/Trif−/− double KO

value: Bone marrow-derived macrophages (BMMs)

value: H-pylori ΔcagPAI mutant

value: 60 min post infection

source_name: MyD88/Trif−/− double KO_H-pylori WT infected

value: H-pylori wildtype


title: COG_026

description: PBMC, 60min post-OGTT


title: BDCA_Normal Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: 5 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: Non-tumor liver tissue.

label_protocol: Ten (10) ng of total RNA was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

growth_protocol: Not applicable since the tissue samples were collected at the end of the necropsy from the National Toxicology Program's bioassay on Ginkgo biloba extract in the B6C3F1 mouse.

extract_protocol: Frozen normal liver tissue and hepatocellular carcinomas (both spontaneously arising or due to chemical exposure) samples were lysed and homogenized in TRIzol reagent (Invitrogen) using a rotor-stator homogenizer. Isolation of RNA was performed according to the mini kit protocol. RNA samples were purified by On-column deoxyribonuclease (DNase) treatment using the Invitrogen PureLink DNase kit. RNA concentration and 260/280 ratio was measured using a bioanalyzer (Agilent Technologies, Santa Clara, CA), and RNA quality was checked on Embi Tec Precast RNA gels (Embec cat# GE-6010). Samples were aliquoted and stored at -80ºC.

treatment_protocol: The liver samples used in this study were collected from the National Toxicology Program's chronic bioassay on Ginkgo biloba extract (GBE). Male and female B6C3F1 mice were exposed to 0, 200, 600, and 2,000 mg/kg GBE by corn-oil gavage, 5 days a week for 2 years. At the end of 2 years, there was a dose dependent increase in the incidence of hepatocellular carcinomas. In addition, the background incidence of spontaneous hepatocellular carcinomas in the B6C3F1 mouse is around 15-30% (greater in males than females). Husbandry and experimental procedures were in compliance with requirements set forth by the Public Health Service’s Guide for the Care and Use of Laboratory Animals. At necropsy, tissue sections of normal liver and spontaneous HCC from vehicle control animals, and HCC from GBE-treated animals were collected and flash-frozen in liquid nitrogen at the time of necropsy for RNA isolation and subsequent microarray analysis and RTPCR validation.

value: liver

tag: strain

value: non-tumor liver


title: COG_030

description: PBMC, 60min post-OGTT


title: COG_014

description: PBMC, 60min post-OGTT


title: COG_025

description: PBMC, fasting


title: COG_013

description: PBMC, fasting


title: Dop1R2_knockdown_biological replicate 2

description:
Sample name: Dop1R2_2
Gene expression data from Dop1R2 knockdown animals

value: whole organism

value: pale pupae


title: Control MEFs

description:
Sample name: Control 0h
Gene expression data from control mouse embryonic fibroblasts

source_name: Control MEFs

value: primary mouse embryonic fibroblasts

value: control


title: Vehicle_Normal Replicate 3

source_name: Vehicle control normal liver tissue.

value: vehicle control normal liver


title: COG_018

description: PBMC, 60min post-OGTT

value: M


title: Vehicle_Normal Replicate 6


title: COG_037

description: PBMC, fasting

source_name: PBMC, fasting


title: COG_022

description: PBMC, 60min post-OGTT


title: BDCA_Normal Replicate 6


title: COG_029

description: PBMC, fasting


title: BDCA_Normal Replicate 4


title: BDCA_Normal Replicate 1


title: Vehicle_Normal Replicate 2


title: BDCA_Normal Replicate 5


title: BDCA_HCC Replicate 5

source_name: Hepatocellular carcinoma liver tissue.

value: hepatocellular carcinoma liver


title: COG_100

description: PBMC, fasting

value: F


title: Vehicle_Normal Replicate 4


title: COG_017

description: PBMC, fasting


title: Vehicle_Normal Replicate 5


title: Vehicle_Normal Replicate 1


title: BDCA_Normal Replicate 2


title: BDCA_HCC Replicate 6


title: COG_009

description: PBMC, fasting


title: COG_010

description: PBMC, 60min post-OGTT


title: BDCA_HCC Replicate 4


title: COG_004

description: PBMC, 60min post-OGTT


title: BDCA_HCC Replicate 1


title: COG_005

description: PBMC, fasting


title: BDCA_HCC Replicate 3


title: Allogeneic Rejected, Ly6C Low Expression,biological replicate 1

city: New York

first: Jordi

last: Ochando

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: 2.5ug of fragmented labeld ST cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays using standard Affymetrix protocols

scan_protocol: The arrays were washed, stained on a Affymetrix FS450 system and scanned on an GeneChip 3000 7G scanner using GeneChip® Command Console Software (AGCC)

data_processing: The summary expression scores were computed at the transcript meta-probeset level using annotation files supplied by the manufacturer. The data was imported into R. Since these arrays were run in different batches, the gene expression was batch corrected with Combat (Johnson et al., 2007). Gene expression was filtered based on IQR (0.25) filter using genefilter package. The log2 normalized and filtered data (adjusted P <0.05) was used for further analysis.

source_name: Genomic DNA

label_protocol: The isolated RNA was checked for quality using a nanodrop and a Bioanalyzer following which 15ng of total RNA was processed using WT Ovation Pico RNA Amplification System (NuGEN). Sense target cDNAs were generated using the standard NuGEN WT Ovation Exon protocol and biotinylated using the NuGEN Biotin module

extract_protocol: Total RNA was isolated from cells in trizol using standard protocol followed by cleanup and gDNA removal using a RNEasy Plus cleanup protocol

treatment_protocol: AT = treated with anti-CD40L mAb. AR = Untreated

tag: treatment

value: untreated

tag: ly6c expression

value: low

tag: allogeneic state

value: rejected


title: COG_003

description: PBMC, fasting

tag: age

tag: gender

tag: bmi


title: Allogeneic Rejected, Ly6G Expression,biological replicate 3

value: expressed


title: COG_006

description: PBMC, 60min post-OGTT


title: BDCA_HB Replicate 5

source_name: Hepatoblastoma liver tissue.

value: hepatoblastoma liver


title: BDCA_HB Replicate 6


title: Allogeneic Rejected, Ly6C High Expression,biological replicate 1

value: high


title: Allogeneic Rejected, Ly6C Low Expression,biological replicate 2


title: Allogeneic Rejected, Ly6C High Expression,biological replicate 3


title: Allogeneic Rejected, Ly6G Expression,biological replicate 1


title: Allogeneic Rejected, Ly6C Low Expression,biological replicate 3


title: Allogeneic Rejected, Ly6G Expression,biological replicate 2


title: BDCA_HB Replicate 4


title: 168h after NTHi injection 4205

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: RNA from middle ear infection model

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MU74Av2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using theAffymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: middle ear

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: All experiments were performed on naïve, young adult (60-90 days old) WBxB6 F1 hybrid mice from Jackson Labs during daylight hours

extract_protocol: ME mucosae from 20 mice were harvested at each of the following time points after inoculation with either NTHi or PBS: 3h, 6h, 24h (1d), 48h (2d), 72h (3d), 120h (5d), and 168h (7d). The tissue was homogenized in TRIzolTM reagent (Invitrogen) and total RNA extracted.  The mRNA was quantified and its integrity checked by agarose gel electrophoresis.

treatment_protocol: Haemophilus influenzae strain 3655 (non-typeable, biotype II; NTHi) was used at a concentration of 105 – 106/ml to induce an inflammatory response in the ME. WBxB6 F1 hybrid mice were inoculated bilaterally in the ME with NTHi in a laboratory setting under aseptic conditions. An identical number of control mice were injected with saline.  The mice were anesthetized with an intraperitoneal injection of 0.1-0.2 ml per 25-30 g bodyweight of rodent cocktail (13.3 mg/ml Ketamine HCl, 1.3 mg/ml Xylasine and 0.25 mg/ml Acepromazine), which produces deep anesthesia for the required period.  The ME bullae were exposed bilaterally by a ventral approach through a vertical midline incision on the neck. To access the ME cavity, the bulla was fenestrated using a 25 gauge syringe needle.  Approximately 3-5 µl of NTHi (105-106 NTHi/ml) or endotoxin-free PBS (sham) was injected into the ME cavity of mice.

value: middle ear

value: bacteria

value: WBxB6 F1 hybrid


title: BDCA_HCC Replicate 2

value: liver


title: BDCA_HB Replicate 2


title: 120h after NTHi injection 4201

description: RNA from middle ear infection model


title: Allogeneic Rejected, Ly6C High Expression,biological replicate 2


title: BDCA_HB Replicate 3


title: 72h after NTHi injection 3829

description: RNA from middle ear infection model


title: BDCA_HB Replicate 1


title: 120h after NTHi injection 4202

description: RNA from middle ear infection model


title: Control Embyro and LIF-siRNA-treated embryo Replicate 1

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

hyb_protocol: The labeled probes were hybridized to Agilent Mouse Oligo Microarrays, a commercial cDNA microarray (Agilent Technologies, Taipei, Taiwan) containing 9652 immobilized cDNA fragments.

scan_protocol: Fluorescence intensities of Cy3 and Cy5 targets were measured and scanned separately using a Dig Luminescent Detection Kit (Roche, Taipei, Taiwan) and Fluor-S MAZ Multi-Imager System (Bio-Rad, Hercules, CA).

data_processing:
Data analysis was performed using Agilent Feature extraction software Version A.6.1.1 (Agilent Technologies).
The normalized log ratio =LOG(SQRT( mean background light intensity of Cy3 channel*mean background light intensity of Cy5 channel),2). The criteria for determination of differentially expressed genes were that the absolute value of the ratio of Cy5 to Cy3 was greater than two-fold (up-regulated) or less than 0.5-fold (down-regulated), and the signal value of fluorescence intensity of either Cy3 or Cy5 was greater than 1,000 intensity.

source_name: The LIF-siRNA-treated embryo

label_protocol: Total RNA (1.5–3 μg) of LIF-siRNA injected embryo and scrambled-siRNA injected embryo were reverse transcribed with Superscript II RNase H- Reverse Transcriptase (Gibco BRL, Grand Island, NY, USA) to generate Cy5 (red) and Cy3 (green) fluorescent dye-labeled complementary DNA (cDNA) probes, respectively.

growth_protocol: Zygotes were collected from the oviducts of female mice successfully mated in the laboratory and placed into wells with fresh human tubal fluid medium. Embryos in the two-pronucleus (2PN) stage were obtained by incubating the zygotes in an atmosphere with 5% CO2 at 37℃ for 4 h.

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

treatment_protocol: The embryos were either injected with 1pl of 1.0 fmole siRNA into the cytoplasma. The embryos injected with scrambled siRNA (1pl of 1.0 fmole) act as a positive control. The embryos were then incubated in an atmosphere of 5% CO2 at 37℃ and monitored daily using an optical microscope.

value: 4 d

value: whole embryo

source_name: The scrambled siRNA-treated embryo


title: Control Embyro and LIF-siRNA-treated embryo Replicate 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.


title: 168h after NTHi injection 4206

description: RNA from middle ear infection model


title: Allogeneic Tolerant, Ly6G Expression,biological replicate 3

value: tolerant


title: Allogeneic Tolerant, Ly6C Low Expression,biological replicate 2


title: Allogeneic Tolerant, Ly6C Low Expression,biological replicate 3


title: Allogeneic Tolerant, Ly6G Expression,biological replicate 1


title: Allogeneic Tolerant, Ly6C High Expression,biological replicate 2


title: Allogeneic Tolerant, Ly6C High Expression,biological replicate 1


title: Allogeneic Tolerant, Ly6C High Expression,biological replicate 3


title: Allogeneic Tolerant, Ly6C Low Expression,biological replicate 1


title: 24h after NTHi injection 2634

description: RNA from middle ear infection model


title: 72h after NTHi injection 3384

description: RNA from middle ear infection model


title: 3h after NTHi injection 2553

description: RNA from middle ear infection model


title: 6h after NTHi injection 2558

description: RNA from middle ear infection model


title: Allogeneic Tolerant, Ly6G Expression,biological replicate 2


title: 24h after NTHi injection 2636

description: RNA from middle ear infection model


title: 3h after NTHi injection 2425

description: RNA from middle ear infection model


title: Day4_DOX_3

first: Dmitri

last: Papatsenko

state: NY

address: One Gustave L. Levy Place

institute: Mount Sinai School of Medicine

description: Doxycycline

hyb_protocol: The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132).

scan_protocol: Hybridized microarrays were scanned using standard procedures (Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132).

data_processing: Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day.  Spotfire(R) software was used for data management and filtering.

source_name: day4, Doxycycline, replica 3

label_protocol: The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5.

growth_protocol: Differentiating i-Mixl1 ES cells cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point).

extract_protocol: Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells) using RNeasy Mini columns (Qiagen).  RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA

value: mESC, i-Mixl1

value: Doxycycline

value: day 4


title: Day4_cntrl_2

description: No Doxycycline

source_name: day4, control, replica 2

value: No Doxycycline


title: 168h after saline injection 4203

description: RNA from middle ear infection model

value: saline


title: Day4_DOX_1

description: Doxycycline

source_name: day4, Doxycycline, replica 1


title: Day4_DOX_2

description: Doxycycline

source_name: day4, Doxycycline, replica 2


title: 6h after NTHi injection 2416

description: RNA from middle ear infection model


title: Day4_cntrl_3

description: No Doxycycline

source_name: day4, control, replica 3


title: 168h after saline injection 4204

description: RNA from middle ear infection model


title: 48h after NTHi injection 4462

description: RNA from middle ear infection model


title: Day4_cntrl_1

description: No Doxycycline

source_name: day4, control, replica 1


title: Day3_cntrl_3

description: No Doxycycline

source_name: day3, control, replica 3

value: day 3


title: 48h after NTHi injection 3827

description: RNA from middle ear infection model


title: Day3_cntrl_2

description: No Doxycycline

source_name: day3, control, replica 2


title: Day3_cntrl_1

description: No Doxycycline

source_name: day3, control, replica 1


title: KO6

city: Boston

first: Sarah

last: Morton

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: mRNA profiling

data_processing:
Microarray Core Facility at Boston Children's Hospital protocol
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Quadriceps, day 7

growth_protocol: Routine mouse care

extract_protocol: Rneasy fibrous tissue

value: cofilin-2 null

value: quadriceps


title: KO2

description: mRNA profiling

hyb_protocol: Microarray Core Facility at Boston Children's Hospital protocol


title: KO4

description: mRNA profiling

scan_protocol: Microarray Core Facility at Boston Children's Hospital protocol


title: KO5

description: mRNA profiling

label_protocol: Microarray Core Facility at Boston Children's Hospital protocol


title: Day3_DOX_2

description: Doxycycline

source_name: day3, Doxycycline, replica 2


title: WT4

description: mRNA profiling

value: wildtype


title: Day3_DOX_1

description: Doxycycline

source_name: day3, Doxycycline, replica 1


title: 120h after saline injection 4200

description: RNA from middle ear infection model


title: Day3_DOX_3

description: Doxycycline

source_name: day3, Doxycycline, replica 3


title: 72h after saline injection 3828

description: RNA from middle ear infection model


title: WT5

description: mRNA profiling


title: WT6

description: mRNA profiling


title: KO3

description: mRNA profiling


title: 120h after saline injection 4199

description: RNA from middle ear infection model


title: WT3

description: mRNA profiling


title: KO1

description: mRNA profiling


title: 48h after saline injection 3825

description: RNA from middle ear infection model


title: 72h after saline injection 3385

description: RNA from middle ear infection model


title: Day2_cntrl_2

description: No Doxycycline

source_name: day2, control, replica 2

value: day 2


title: 48h after saline injection 3256

description: RNA from middle ear infection model

source_name: middle ear

value: middle ear


title: 24h after saline injection 2635

description: RNA from middle ear infection model


title: WT2

description: mRNA profiling


title: 24h after saline injection 2633

description: RNA from middle ear infection model


title: Day2_cntrl_1

description: No Doxycycline

source_name: day2, control, replica 1


title: Day2_cntrl_3

description: No Doxycycline

source_name: day2, control, replica 3


title: Con A Treated MDSC - repeat 2 - mAdbID:120465

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 120465

hyb_protocol: Affymetrix Hybrization Protocol Other: Terminally labeled cDNA were hybridized to the Mouse Gene 1.0 ST array (Affymetrix) according to the manufacturers' instructions.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were then scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Affymetrix RMA Data Processing
Calculation Method: After Robust Multichip Average (RMA) normalization, the statistically significant gene expression changes were functionally analyzed using Partek Genomic Suite 6.6 (St. Louis, MO).

source_name: Con A Treated Sample

label_protocol:
Affymetrix Terminal Labeling Kit
Other: Affymetrix Terminal Labeling Kit according to manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: RNA extractions were performed using NucleoSpin RNA II (Macherey-Nagel) followed by whole transcriptome amplification using WT expression kit (Invitrogen).

treatment_protocol:
Agent: Type IV Concanavalin A (Con A)
Treatment dose: 12.5ug/kg
Treatment time: 3 hours

value: Liver

value: Hepatic CD11b+Gr-1+ Myeloid-derived suppressor cells (MDSC)

tag: other

value: EL4 tumors were established in C57BL/6 mice (n=3 per group), then mice were injected with 12.5mg/kg Con A. Three hours later mice were sacrificed, liver CD11b+Gr-1+ cells were sorted and samples were processed for gene expression.


title: Con A Treated MDSC - repeat 3 - mAdbID:120467

description: mAdb experiment ID: 120467


title: Untreated MDSC - repeat 2 - mAdbID:120464

description: mAdb experiment ID: 120464

source_name: Untreated Sample

treatment_protocol:
Agent: PBS
Treatment time: 3 hours

value: EL4 tumors were established in C57BL/6 mice (n=3 per group), then mice were injected with PBS. Three hours later mice were sacrificed, liver CD11b+Gr-1+ cells were sorted and samples were processed for gene expression analysis.


title: WT1

description: mRNA profiling


title: Untreated MDSC - repeat 3 - mAdbID:120466

description: mAdb experiment ID: 120466


title: Day2_DOX_1

description: Doxycycline

source_name: day2, Doxycycline, replica 1


title: Day2_DOX_3

description: Doxycycline

source_name: day2, Doxycycline, replica 3


title: 6h after saline injection 2555

description: RNA from middle ear infection model

value: WBxB6 F1 hybrid


title: untreated 2499

description: RNA from middle ear infection model


title: Day2_DOX_2

description: Doxycycline

source_name: day2, Doxycycline, replica 2


title: KO_4

city: Turku

first: Emmi

last: Rotgers

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description:
biological replicate 4
11/4821-/-

hyb_protocol: Labelled cRNA was then hybridized into the Illumina Sentrix Mouse WG-6 v2.0 Expression BeadChips at 58C overnight (17 h) following the standard Illumina hybridization protocol

scan_protocol: Arrays were scanned with Illumina’s Bead Array Scanner (Factor=1.5, PMT=552, Filter=100%) following the standard Illumina scanning protocol

data_processing:
The data set was normalized using quantile normalization with limma in R
non_normalized data: The numerical results were extracted with GenomeStudio Gene Expression Module v. 1.9.0 without any normalization or background subtraction.

label_protocol: To synthesize the biotinylated cRNA, 500 ng of total RNA was amplified using Ambion’s Illumina TotalPrep RNA Amplification kit (cat # AMIL1791)

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

tag: strain background

value: B6;129S4-E2f1tm1Meg/J in C57Bl/6J background

value: 20 dpp

value: testis


title: 3h after saline injection 2551

description: RNA from middle ear infection model


title: 3h after saline injection 2323

description: RNA from middle ear infection model


title: KO_3

description:
biological replicate 3
1/4816 -/-


title: Untreated MDSC - repeat 1 - mAdbID:120462

description: mAdb experiment ID: 120462


title: 6h after saline injection 2413

description: RNA from middle ear infection model


title: HZ_1

description:
biological replicate 1
1/4448 +/-


title: WT_4

description:
biological replicate 4
4/4820 +/+


title: 15-LNM2,Lymph node metastasis,N1

city: Anderlecht

first: Maxime

last: Tarabichi

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM

hyb_protocol: Genome wide mRNA profiles were obtained through hybridization of samples onto Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

scan_protocol: according to standard Affymetrix protocols

data_processing: Data analyses were performed in R v.3.1.0. The arrays used contain 54 613 probe sets representing 20 027 genes.CEL files, which contain the raw data, were normalized using the fRMA normalization method from the fRMA package v.1.6.0 (hgu133plus2frmavecs v.1.1.8) with default parameters.To annotate the probe sets, R packages annotate v1.32.3 and hgu133plus2.db v2.6.3 were used.

source_name: 15-LNM2,Lymph node metastasis,N1

extract_protocol: RNA extraction was performed using RNeasy Mini Kit columns (Qiagen, Hilden, Germany).

treatment_protocol: The samples used in this study were derived from 31 patients diagnosed for PTC and were chosen based on sample availability and RNA quality rather than clinical parameters. Thereby the samples consist of a variety of classical PTC and PTC variants with various pathological characteristics. Samples were obtained from the Jules Bordet Institute (Brussels, Belgium), and La Pitié-Salpêtrière Hospital (Paris, France).

tag: rqi

tag: Sex

value: F

tag: tnm

tag: Stage

value: I

value: Follicular

value: right

tag: multifocal

value: no

value: yes


title: HZ_4

description:
biological replicate 4
10/4445+/-

tag: tissue


title: HZ_3

description:
biological replicate 3
4/4446 +/-

tag: genotype/variation


title: HZ_2

description:
biological replicate 2
3/4444 +/-


title: KO_1

description:
biological replicate 1
11/4812-/-


title: 15-PT-N1,Papillary thyroid carcinoma,N1

source_name: 15-PT-N1,Papillary thyroid carcinoma,N1

label_protocol: according to standard Affymetrix protocols


title: untreated 2321

description: RNA from middle ear infection model

tag: time


title: KO_2

description:
biological replicate 2
10/4818 -/-


title: Con A Treated MDSC - repeat 1 - mAdbID:120463

description: mAdb experiment ID: 120463

tag: strain

tag: cell type


title: 14-PT-N1,Papillary thyroid carcinoma,N1

source_name: 14-PT-N1,Papillary thyroid carcinoma,N1

value: Diffuse sclerosis

value: both

value: BRAFmut


title: FH4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in striatum of adult female mouse

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Female_hetrozygous_Replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Heterozygous Brd2+/- females were mated to heterozygous Brd2+/- males. Mice of the 7th generation of backcrossing onto a C57Bl/6J background strain were used so that their genetic background could be considered on average 99% C57Bl/6J (Mouse Nomenclature, jaxmice.jax.org). Mice genotypes were assessed by PCR using primers that spanned the gene-trap vector junction inserted into the Brd2 gene.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: The striatum was disected and snap frozen.

value: Female

value: Prefrontal cortex striatum

tag: develomental stage

value: adult


title: WT_2

description:
biological replicate 2
1/4587 +/+


title: FH3

source_name: Female_hetrozygous_Replicate 3


title: 15-LNM1,Lymph node metastasis,N1

source_name: 15-LNM1,Lymph node metastasis,N1


title: 31-PT-N0,Papillary thyroid carcinoma,N0

source_name: 31-PT-N0,Papillary thyroid carcinoma,N0

value: Papillary

value: left


title: WT_3

description:
biological replicate 3
33/4815 +/+

value: B6;129S4-E2f1tm1Meg/J in C57Bl/6J background


title: C57BI6-72h post IR-rep2

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using Illumina HiScan

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.3

source_name: heart-72h post IR

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

growth_protocol: Mice were used in accordance with the Guide for the Use and Care of Laboratory Animals and experiments were approved by Emory University Standing Committee on Animals (IACUC). Male C57Bl/6 mice were used for experiments (Jackson Laboratory). Mice are kept on regular chow diet.

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: Group 1 is wild type C57Bl6 uninjured hearts. These mice were not undergone any surgery and used as controls.  Group 2 are wild type C57Bl6 72 h post-ischemia reperfusion (IR) injury hearts. These mice for subjected to ischemia reperfusion (IR) involving 90 min of left anterior descending coronary artery occlusion followed by reperfusion for 3 days or 72 h. In brief, prior to any surgical procedure, mice were anesthetized with intraperitoneal injections of ketamine (60 mg kg-1) and sodium pentobarbital (50 mg kg-1). The mice were then attached to a surgical board with their ventral side up and subjected to tracheal intubation with polyethylene-60 (PE-60) tubing connected via a loose junction to a rodent ventilator (MiniVent Type 845, Hugo-Sachs Elektronik) set at a tidal volume 240 µl of and a rate of 110 breaths/min and supplemented with 100% oxygen (at a flow rate of 0.1–0.2 l min-1) via a side port on the ventilator. Effective ventilation was visually confirmed by vapor condensation in the endotracheal tube and rhythmic rising of the chest. Mice were maintained at a constant temperature of 37°C with a heating pad. Temperature was monitored via a rectal probe connected to a Digisense K-Type digital thermometer. A median sternotomy was performed under aseptic conditions and the wound edges were cauterized. The left anterior descending coronary artery was visualized with the aid of an Olympus stereomicroscope and ligated with a 7-0 silk suture. A short segment of PE-10 tubing was placed between the left anterior descending coronary artery and the 7-0 silk suture to minimize damage to the coronary artery and to allow complete reperfusion following the ischemic period. During the ischemic period the incision was covered with Parafilm to prevent desiccation and dehydration. After 90 min of left anterior descending coronary artery occlusion, the ligature was removed, and reperfusion was confirmed visually. The chest wall and skin incision were carefully closed in layers and during recovery the animals were kept on a warming pad and received 100% oxygen. Buprenorphine at a dose of 0.05 mg kg-1 was administered after surgery and twice daily for two days postoperatively.

value: heart

value: male

tag: treatment

value: heart-72h post IR


title: 14-LNM,Lymph node metastasis,N1

source_name: 14-LNM,Lymph node metastasis,N1

value: F

value: I


title: C57BI6-72h post IR-rep3


title: FH1

source_name: Female_hetrozygous_Replicate 1


title: C57BI6-uninjured heart-rep3

source_name: uninjurted heart

value: uninjurted heart


title: C57BI6-uninjured heart-rep1


title: WT_1

description:
biological replicate 1
3/4459 +/+

tag: age

value: 20 dpp

value: testis


title: 15-N,Normal thyroid,N1

source_name: 15-N,Normal thyroid,N1

value: Follicular

value: right

value: no

value: yes


title: 14-N,Normal thyroid,N1

source_name: 14-N,Normal thyroid,N1

value: Diffuse sclerosis

value: both

value: BRAFmut


title: C57BI6-72h post IR-rep1

tag: gender


title: FW3

source_name: Female_wildtype_Replicate 3

value: Female

value: Prefrontal cortex striatum

value: adult


title: 30-PT-N0,Papillary thyroid carcinoma,N0

source_name: 30-PT-N0,Papillary thyroid carcinoma,N0

value: III

value: Papillary

value: left


title: C57BI6-uninjured heart-rep2

value: heart

value: male


title: MSC-64 rep 2

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol was used.

scan_protocol: Standard Illumina scanning protocol was used.

data_processing: Background correction and quantile normalization was performed by R/Bioconductor package limma (Linear Models for Microarray Data, version 3.14.4).

source_name: OP9 MSCs

label_protocol: Biotinylated cRNA was prepared as per standard protocol provided in Illumina TotalPrep RNA Amplification Kit .

extract_protocol: RNA was isolated from vehicle or imatinib treated MSCs with the TRI Reagent (Ambion). During RNA precipitation, 20 µg of linear polyacrylamide (Ambion) was added to isopropanol (Sigma), and precipitated RNA was gently washed once with n-butanol (Sigma) and twice with 70% alcohol before air-dried RNA pellets were dissolved in diethylpyrocarbonate-treated water (Fisher Scientific).

value: B6C3F1 op/op

tag: agent

value: imatinib

tag: time point (hrs)

value: Newborn Calvaria

value: MSCs


title: 30-N,Normal thyroid,N0

source_name: 30-N,Normal thyroid,N0

value: F

value: no


title: MSC-64 rep 3


title: FW4

source_name: Female_wildtype_Replicate 4


title: FH2

source_name: Female_hetrozygous_Replicate 2


title: 31-N,Normal thyroid,N0

source_name: 31-N,Normal thyroid,N0

value: yes


title: MSC-32 rep 1


title: FW2

source_name: Female_wildtype_Replicate 2


title: MSC-96 rep 2


title: MSC-32 rep 3


title: MSC-32 rep 2


title: MSC-64 rep 1


title: MSC-96 rep 3


title: MSC-96 rep 1


title: 17-N,Normal thyroid,N1

source_name: 17-N,Normal thyroid,N1

value: both

value: 1 on 6