title: saliva_lowstress_biorep16

value: never


title: CAM explants infected with DvirB2 B. abortus: Replicate 3

status: Public on Sep 04 2014

type: RNA

city: Belo Horizonte

first: Alex

middle: FIORINI

last: Carvalho

state: MG

address: Avenida Antonio Carlos 6627

department: DMVP

country: Brazil

institute: UFMG

description:
Biological replicate 3 of 4. Chorioallantoic membrane explant culture (CAM) infected-DvirB2 B. abortus 2308
Sample V6

hyb_protocol: 825 ng of Cy3-labelled cRNA and 825 ng of Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5/ug cRNA) were mixed and fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ull of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Bovine Oligo Microarrays design ID 023647 - GPL11648 (4x44K ) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C  GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Bos taurus

source_name: bovine trophoblastic cells [test]

label_protocol: Labeled cRNA was prepared from 0.5 ug RNA using the Two-Color Quick amp Iabelink kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seven intact pregnant bovine uteruses at the final third of gestation were obtained at local slaughterhouses. All fetuses were serologically negative for Brucella spp. by using the Acidified Antigen Buffered test with fetal amniotic fluid. Prior to obtaining the CAM, the perimetrium was thoroughly decontaminated with iodinated alcohol, the uterus was then opened and CAM removed and placed in sterile medium containing antibiotics. Snapwell plates were used for culturing CAM explants. Sterile rings and detachable supports were positioned over the intercotyledonary portion of the CAM explants. Excess tissue was removed from CAM explants, which were placed in 6 well culture plates containing supplemented sterile culture medium and incubated at 37°C in a humidified atmosphere with 5% CO2.

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

treatment_protocol: The trophoblastic surface of the CAM explants was inoculated with 2.0 x 107 CFU, in a multiplicity of infection of approximately 1000 (MOI 1000:1). CAM explants were inoculated in triplicates with wild type, ΔvirB2, or ΔbtpB B. abortus 2308. Plates were incubated at 37°C with 5% CO2 for 4 h, the medium was then replaced with medium supplemented with 50 µg gentamicin/mL (Invitrogen, São Paulo, Brazil) to inactivate extracellular bacteria. Plates were maintained at 37°C with an atmosphere containing 5% CO2 for 1 h followed by washing three times with with PBS (phosphate buffered saline - pH 7.4) to eliminate the antibiotic. Uninfected CAM controls were inoculated with sterile medium and kept under the same conditions

tag: source tissue

tag: tissue

tag: cell type

value: trophoblastic cells

tag: infection

value: DvirB2 B. abortus 2308

tag: infection time

value: 4 hours

source_name: bovine trophoblastic cells [reference]

value: Non-infected

tag: sample type

value: reference


title: CAM explants infected with DvirB2 B. abortus: Replicate 1

description:
Biological replicate 1 of 4. Chorioallantoic membrane explant culture (CAM) infected-DvirB2 B. abortus 2308
Sample V8

value: intact pregnant bovine uteruses at the final third of gestation


title: CAM explants infected with DvirB2 B. abortus: Replicate 2

description:
Biological replicate 2 of 4. Chorioallantoic membrane explant culture (CAM) infected-DvirB2 B. abortus 2308
Sample V5


title: Control CAM explants without infection: Replicate 2

description:
Biological replicate 2 of 4. Control Chorioallantoic membrane explant culture (CAM), non-infected
Sample C5

value: control


title: CAM explants infected with wild type B. abortus 2308: Replicate 1

description:
Biological replicate 1 of 4. Chorioallantoic membrane explant culture (CAM) infected-wild type B. abortus 2308
Sample W8

value: wild type B. abortus 2308


title: saliva_highstress_biorep20

city: Menlo Park

first: Aaron

last: Wacholder

state: CA

address: 333 Ravenswood Ave

department: Molecular Genetics Program

country: USA

institute: SRI International

hyb_protocol: The biotin-dscDNA was hybridized for 18h at 47C to Affymetrix® Whole-Transcript Expression Arrays. Washing and Staining were done with the GeneChip(R) Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip Scanner and Affymetrix GeneChip Command Console Version 3.0.

data_processing: Probe data was generated using the RMA function in the Oligo R package from Bioconductor.

label: biotin

organism: Homo sapiens

source_name: whole saliva, high chronic stress exposure

label_protocol: Fragmented dscDNA samples were end-labeled with terminal deoxynucleotidyl transferase and an Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

extract_protocol: RNA was extracted using the Genotek Expression Analysis Self-Collection Kit according to the manufacturer's protocol.

value: whole saliva

tag: gender

value: male

tag: age

tag: race

value: white

tag: smoking status

value: former

tag: chronic stress level

value: high


title: saliva_highstress_biorep19


title: CAM explants infected with wild type B. abortus 2308: Replicate 2

description:
Biological replicate 2 of 4. Chorioallantoic membrane explant culture (CAM) infected-wild type B. abortus 2308
Sample W5


title: CAM explants infected with DbtpB B. abortus: Replicate 1

description:
Biological replicate 1 of 4. Chorioallantoic membrane explant culture (CAM) infected-DbtpB B. abortus 2308
Sample 108

value: DbtpB B. abortus 2308


title: MKN45 pre-miR-210 rep2

city: Tokyo

first: Kotaro

last: Kiga

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: University of Tokyo

description: Gene expression data from MKN45 cells transfected with pre-miR-210

hyb_protocol: 12.5μg of aRNA was hybridized for 16 hrs.

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

data_processing: The data were analyzed by using the Affymetrix Expression Console.

source_name: MKN45 cells pre-miR-210 transfected

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

growth_protocol: AGS and MKN45 cells were maintained in RPMI-1640 containing 10% FBS.

extract_protocol: Total RNA was purified using an RNeasy Kit according to the manufacturer’s instructions.

treatment_protocol: 50nM of pre-miR-Nega or pre-miR-210 were transfected into the cells for 36 hrs using Lipofectamine RNAiMAX.

tag: cell line

tag: transfection


title: MKN45 pre-miR-Nega rep2

description: Gene expression data from MKN45 cells transfected with pre-miR-Nega

source_name: MKN45 cells pre-miR-Nega transfected

value: pre-miR-Nega


title: Control CAM explants without infection: Replicate 1

description:
Biological replicate 1 of 4. Control Chorioallantoic membrane explant culture (CAM), non-infected
Sample C8


title: saliva_lowstress_biorep15

source_name: whole saliva, low chronic stress exposure

value: low


title: saliva_highstress_biorep16

value: female

value: current


title: saliva_highstress_biorep17

value: never


title: saliva_lowstress_biorep14


title: MKN45 pre-miR-210 rep1


title: MKN45 pre-miR-Nega rep1


title: AGS pre-miR-210 rep1

description: Gene expression data from AGS cells transfected with pre-miR-210

source_name: AGS cells pre-miR-210 transfected

value: AGS


title: saliva_lowstress_biorep13


title: saliva_highstress_biorep14


title: saliva_highstress_biorep15

value: native american


title: AGS pre-miR-210 rep2


title: saliva_highstress_biorep11


title: saliva_lowstress_biorep12


title: saliva_highstress_biorep13


title: saliva_lowstress_biorep11


title: AGS pre-miR-Nega rep1

description: Gene expression data from AGS cells transfected with pre-miR-Nega

source_name: AGS cells pre-miR-Nega transfected


title: AGS pre-miR-Nega rep2


title: Bipolar disorder patient manic phase, 23

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
DE56AAAZIMR103619
Gene expression data.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: CEL files were imported with the Expression Console from Affymetrix. The raw data were processed with the RMA procedure (Exon Level - Core RMA Sketch). Differential gene expression was analyzed using ANOVA and the commercial software package SAS JMP7 Genomics, version 4 from SAS (SAS Institute, Cary, NC, USA).

source_name: Bipolar disorder patient, manic phase

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

growth_protocol: Blood samples were collected in RNA stabilizing PAXgene tubes in accordance with the recommendations of the manufacturer (PreAnalytix, BD), and stored at -80°C until processing.

extract_protocol: RNA was isolated with the PAXgene Blood RNA Kit 50 (PreAnalytix, Qiagen) according to standard protocols.

value: blood

tag: disease status

value: bipolar disorder (BD)

tag: bd phase

value: mania

tag: patient identifier


title: saliva_lowstress_biorep10


title: Bipolar disorder patient euthymic phase, 30

description:
DE96AABZIMR103622
Gene expression data.

source_name: Bipolar disorder patient, euthymic phase

value: euthymia


title: saliva_lowstress_biorep8

value: whole saliva


title: saliva_highstress_biorep10


title: saliva_highstress_biorep12

value: male


title: Bipolar disorder patient euthymic phase, 19

description:
DE78AABZIMR102394
Gene expression data.


title: saliva_lowstress_biorep9

value: white


title: Control, 9

description:
DE47AAAZIMR101647
Gene expression data.

source_name: Control

value: control


title: saliva_lowstress_biorep6


title: Bipolar disorder patient euthymic phase, 24

description:
DE80AABZIMR103619
Gene expression data.


title: Bipolar disorder patient manic phase, 21

description:
DE83AAAZIMR103618
Gene expression data.


title: Control, 2_DE40

description:
DE40AAAZIMR100124
Gene expression data.


title: Control, 8

description:
DE74AAAZIMR101646
Gene expression data.


title: saliva_highstress_biorep9

value: high


title: Bipolar disorder patient euthymic phase, 22

description:
DE10AABZIMR103618
Gene expression data.


title: saliva_lowstress_biorep4


title: saliva_lowstress_biorep5


title: saliva_lowstress_biorep7

value: former


title: Bipolar disorder patient euthymic phase, 17

description:
DE62AABZIMR102391
Gene expression data.


title: Bipolar disorder patient manic phase, 29

description:
DE72AAAZIMR103622
Gene expression data.


title: Bipolar disorder patient manic phase, 16

description:
DE38AAAZIMR102391
Gene expression data.


title: Bipolar disorder patient manic phase, 18

description:
DE54AAAZIMR102394
Gene expression data.


title: saliva_highstress_biorep8


title: Bipolar disorder patient euthymic phase, 11

description:
DE68AABZIMR101701
Gene expression data.


title: Control, 12

description:
DE80AAAZIMR101732
Gene expression data.


title: saliva_lowstress_biorep3


title: Control, 15

description:
DE04AAAZIMR102130
Gene expression data.


title: saliva_highstress_biorep7


title: saliva_highstress_biorep6


title: saliva_lowstress_biorep2


title: saliva_highstress_biorep4


title: Bipolar disorder patient manic phase, 10

description:
DE44AAAZIMR101701
Gene expression data.


title: Control, 1_DE62

description:
DE62AAAZIMR100116
Gene expression data.


title: saliva_highstress_biorep5


title: Control, 4

description:
DE55AAAZIMR103540
Gene expression data.


title: 3-month-old male rat, biological replicate 4

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

hyb_protocol: hybridization was performed according to microRNA Labeling & Hybridization Kit (Agilent)

scan_protocol: microarrays were scanned with Agilent High-Resolution Microarray Scanner

data_processing: Data were imported into GeneSpringGX (Agilent Technologies) and quantile normalized. Values are in log2. Detection = ability to detect miRNA (1 = present; 0 = not present)

organism: Rattus norvegicus

source_name: islets of control 3-month male rat

label_protocol: 100ng of total RNA was submitted to microRNA Labeling & Hybridization Kit (Agilent)

extract_protocol: total RNA was extracted with miRNeasy kit QIAGEN following manufacturer's instructions

tag: strain

value: Sprague Dawley

value: islets

value: 3 months


title: 3-month-old male rat, biological replicate 2


title: 3-month-old male rat, biological replicate 3


title: saliva_highstress_biorep2

value: current


title: Bipolar disorder patient manic phase, 5

description:
DE29AAAZIMR103620
Gene expression data.


title: Control, 2_DE23

description:
DE23AAAZIMR101788
Gene expression data.


title: Bipolar disorder patient euthymic phase, 6

description:
DE53AABZIMR103620
Gene expression data.


title: 10-day-old rat, biological replicate 2

source_name: islets of control 10-day-old rat

value: 10 day


title: Control, 1_DE50

description:
DE50AAAZIMR101787
Gene expression data.


title: 10-day-old rat, biological replicate 3


title: Bipolar disorder patient euthymic phase, 36

description:
DE85AABZIMR103626
Gene expression data.


title: 10-day-old rat, biological replicate 4


title: Hippocampus at E18, EtOH

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

description: Gene expression data of mouse embryo hippocampus at E18 fetus from maternal bindge alcohol consumption

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix 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. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

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

growth_protocol: Breeder mice (C57BL/6J) were individually housed and maintained under a 12 hour light-dark cycle.

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

treatment_protocol: Pregnant mice were randomly divided into two experimental groups: one receiving distilled phosphate-buffered saline (PBS) treatment and the other receiving ethanol treatment. Pregnant mice received either PBS or ethanol (2.9 g/kg/day, 15% v/v ethanol solution) via intragastric injection for 5 days from ED8 to 12. On ED18, the dams were sacrificed via cervical vertebra dislocation. The litter of each dam was delivered through Cesarean section.

value: Hippocampus


title: Bipolar disorder patient manic phase, 37

description:
DE34AAAZIMR103627
Gene expression data.


title: saliva_highstress_biorep1


title: Forebrain at E18, PBS

description: Gene expression data of mouse embryo forebrain at E18 fetus from maternal PBS treatment

value: Forebrain


title: Forebrain at E18, EtOH

description: Gene expression data of mouse embryo forebrain at E18 fetus from maternal bindge alcohol consumption


title: DIO+LFD: 58 kcal% HFD (D12331) for 8 wks to induce obesity, then 10.5 kcal% LFD (D 12329) for additional 4 wks rep2

status: Public on Sep 03 2014

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: DIO+LFD: the mice fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks rep2

hyb_protocol: The pre-hybridization of MRmiOA v3 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v3 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1). We fltered out probes that flag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method. Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: serum

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy3, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

growth_protocol: C57BL/6 mice were purchased from BioLasco (Taipei, Taiwan). All housing conditions were maintained, and surgical procedures, including analgesia, were performed in an Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC)-accredited SPF facility according to national and institutional guidelines.

extract_protocol: After the end of experiment at 12w, all mice were killed. The abdominal WAT of each mice was removed and weighted. Paraffin-embedded abdominal WAT was sectioned at 5 μm and stained with hematoxylin and eosin to measure mean adipocyte area. A volume of 1 mL of whole blood was collected into a plain tube and allowed to clot for 1 hour. The sera samples were aliquoted after centrifugation at 3,000 × g for 10 minutes and stored at −80°C until further analysis.  Total RNA was extracted from the serum using the mirVana™ miRNA Isolation Kit (Life Technologies, NY). Samples of purified RNAs were evaluated for quantity by absorbance at 260 nm using an SSP-3000 Nanodrop spectrophotometer (Infinigen Biotechnology, Inc., City of Industry, CA) and for quality using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). Total RNA (10 ng) was reverse transcribed to cDNA using the TaqMan miRNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA). Target miRNAs were reverse transcribed using sequence-specific stem-loop primers, and cDNA was used for quantitative real-time polymerase chain reaction (qPCR).

treatment_protocol: In this experiment, eighteen C57BL/6 wild type male mice were randomly grouped into three subgroups (n=6 in each group): (1) Control: the control mice were fed ad libitum a standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks; (2) DIO: the mice were fed ad libitum a 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity; (3) DIO+LFD: the mice fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks.

tag: treatment

value: serum


title: Hippocampus at E18, PBS

description: Gene expression data of mouse embryo hippocampus at E18 fetus from maternal PBS treatment

tag: tissue


title: DIO+LFD: 58 kcal% HFD (D12331) for 8 wks to induce obesity, then 10.5 kcal% LFD (D 12329) for additional 4 wks rep3

description: DIO+LFD: the mice fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks rep3

value: fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks.


title: DIO+LFD: 58 kcal% HFD (D12331) for 8 wks to induce obesity, then 10.5 kcal% LFD (D 12329) for additional 4 wks rep1

description: DIO+LFD: the mice fed ad libitum a 58 kcal% HFD (D12331) for 8 wks to induce obesity, then continued the feeding of 10.5 kcal% LFD (D 12329; Research Diets Inc.) for additional 4 wks rep1


title: DIO: 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep2

description: DIO: the mice were fed ad libitum a 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep2


title: Bipolar disorder patient manic phase, 35

description:
DE61AAAZIMR103626
Gene expression data.

value: blood

value: bipolar disorder (BD)

value: mania


title: Bipolar disorder patient euthymic phase, 34

description:
DE15AABZIMR103625
Gene expression data.

value: euthymia


city: Guangzhou

first: Hong-Ling

last: Jia

state: Guangdong

address: Huangpu Road

country: China

institute: Jinan University

description: human miRNA expression after Kawasaki disease after Intravenous immunoglobulin (IVIG) therapy human serum samples

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent miRNA Spike- In kit and miRNA Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

label_protocol: 100 ng of total RNA(including miRNA) were dephosphorylated and denaturated,then ligated with Cyanine 3-pCp at 16℃ for 2 hours using T4 RNA Ligase.

extract_protocol: We isolated exosomes of sera from all participants by using ExoQuick precipitation following manufacturer's instructions, Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Blood samples from 5 KD patients and 5 KD patients after IVIG therapy were randomly selected according to the American Heart Association and the Japanese Ministry of Health and Welfare criteria.Blood samples from 5 healthy children were used as control group. All the diagnoses of these patients were confirmed by more than two pediatric cardiologists and other diseases were excluded. Serum were separated by centrifugation at 1,000 ×g for 10 min. Serum aliquots were collected and stored at -80°C. The serum obtained was further processed for exosome isolation.

tag: disease


title: Control, 3

description:
DE23AAAZIMR103534
Gene expression data.


title: Kawasaki disease

description: human miRNA expression after Kawasaki disease human serum samples

source_name: Kawasaki disease

value: Kawasaki disease


title: Bipolar disorder patient manic phase, 33

description:
DE88AAAZIMR103625
Gene expression data.


title: Control N1

description: human miRNA expression after control human serum samples

value: Control


title: DIO: 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep1

description: DIO: the mice were fed ad libitum a 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep1


title: Bipolar disorder patient euthymic phase, 38

description:
DE58AABZIMR103627
Gene expression data.


title: DIO: 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep3

description: DIO: the mice were fed ad libitum a 58 kcal% HFD (D12331; Research Diets Inc., New Brunswick, NJ) for 12 wks to induce obesity rep3


title: Control: standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep2

description: Control: the control mice were fed ad libitum a standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep2

value: fed ad libitum a standard AIN-76A (fat:11.5 kcal%) diet for 12 wks


title: Control: standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep3

description: Control: the control mice were fed ad libitum a standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep3


title: 3-month-old male rat, biological replicate 1


title: Control: standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep1

description: Control: the control mice were fed ad libitum a standard AIN-76A (fat: 11.5 kcal%) diet for 12 wks rep1


title: BH13707-2_5D7M

city: Shanghai

first: Weidong

last: Le

address: #197 Ruijin No.2 Road

institute: Institute of Health Sciences

description:
Gene expression data from  H9 cells after 7 days of neural differentiation with MGCD treatment
D7M

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

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

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

source_name: H9 on day 7 of differentiation with MGCD treatment

growth_protocol: Undifferentiated H9 cells were cultured in mTeSR1 medium (STEMCELL Technologies, Vancouver, BC, Canada), whereas differentiated cells were cultured in mTeSR1 medium containing 10 μM all-trans-retinoic acid (Sigma, St.Louis, MO, USA).

treatment_protocol: Control cells (D3C and D7C) were differentiated in nomal condition of neural differentiation, while cells of D3M and D7M were treated with 0.5 μM MGCD during neural differentiation.

value: H9 embryonic stem cells

tag: agent

value: MGCD

tag: time

value: day 7

tag: differentiation state

value: differentiated embryonic stem cells


title: BH13707-2_4D7C

description:
Gene expression data from  H9 cells after 7 days of neural differentiation without MGCD treatment
D7C

source_name: H9 on day 7 of differentiation without MGCD treatment

value: control


title: H2-2

first: Fang

last: Tingting

state: Shanghai

address: 180 Fenglin Road, Xuhui

department: Liver Cancer Institute

institute: Zhongshan Hospital

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) between two groups were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

source_name: HCC cell

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum.

tag: metastatic potential

value: high lymphatic metastatic potential

tag: cell type

value: hepatocellular carcinoma cell line


title: H2-3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)


title: H2-1


title: BH13707-2_2D3C

description:
Gene expression data from  H9 cells after 3 days of neural differentiation without MGCD treatment
D3C

source_name: H9 on day 3 of differentiation without MGCD treatment

value: day 3


title: LM3-3

value: high lung metastatic potential


title: BH13707-2_5D3M

description:
Gene expression data from  H9 cells after 3 days of neural differentiation with MGCD treatment
D3M

source_name: H9 on day 3 of differentiation with MGCD treatment


title: Bipolar disorder patient manic phase, 31

description:
DE45AAAZIMR103623
Gene expression data.


title: Bipolar disorder patient euthymic phase, 32

description:
DE69AABZIMR103623
Gene expression data.


title: liver_NEMO_TNFR_DOUBLE_KO_replicate3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: A202_12_TW61_452_HTNF_(MOGENE-1_0-ST-V1).CEL

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.14.0).

label_protocol: The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

growth_protocol: We generated mice carrying the loxP-site-flanked NEMO gene as described before (Beraza et al., 2009, J Exp Med; PMID: 19635861). From NemoΔhepa, we generated double knockout animals by crossing NemoΔhepa with constitutive TRAIL-/- and TNFR1-/- animals.

extract_protocol: Total RNA was purified from liver tissue using Trizol reagent (Invitrogen, Karlsruhe, Germany) andpurified using RNeasy microkit (Qiagen, Venlo, The Netherlands). RNA quality was assessed on a Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice were kept on standard laboratory chow diet and had free access to water. Hepatic expression profiles of the four genotypes (wild type, and the three knockouts) was performed on male mice, that were all aged between 8-9 weeks.

tag: genotype/variation

value: NEMO-TNFR1 double knockout (NemoΔhepa/TNFR1-/-)

tag: gender

value: male

tag: age

value: 8-9 weeks

value: liver


title: saliva_lowstress_biorep1

value: whole saliva

tag: race

value: white

tag: smoking status

value: never

tag: chronic stress level

value: low


title: LM3-2

tag: cell line


title: LM3-1


title: liver_NEMO_TNFR_DOUBLE_KO_replicate2

description: A202_11_TW61_404_HTNF_(MOGENE-1_0-ST-V1).CEL


title: AN01570 BA10

type: genomic

city: Safed

first: Evan

last: Elliott

state: Israel

address: Hanrietta Sold 8

department: Faculty of Medicine

country: Israel

institute: Bar Ilan University

hyb_protocol: bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

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

value: Female

tag: sample type

value: frontal cortex (BA10)

tag: disease state

value: autism


title: liver_NEMO_TNFR_DOUBLE_KO_replicate1

description: A202_10_TW61_407_HTNF_(MOGENE-1_0-ST-V1).CEL

tag: strain


title: BH13707-2_1D0

description:
Gene expression data from undifferentiated H9 cells
D0

source_name: Undifferentiated H9

value: H9 embryonic stem cells

value: undifferentiated embryonic stem cells


title: liver_NEMO_TRAIL_DOUBLE_KO_replicate2

description: A202_09_TW100_378_HTR_(MOGENE-1_0-ST-V1).CEL

value: NEMO-TRAIL double knockout (NemoΔhepa/TRAIL-/-)

tag: tissue


title: CAL1R-VRB

city: Montpellier

first: Laure-Anais

last: Vincent

address: 15 Avenue Charles Flahault

country: France

institute: IBMM

description: gene expression data from vinorelbine CAL1 resistant cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA (bioconductor)

source_name: Malignant melanoma cell line

label_protocol: standard Affymetrix protocol

growth_protocol: long time exposure to CAL1 CI50 to vinka-alkaloids ( 4nM, 6-12 months)

extract_protocol: Rneasy (Quiagen)

tag: cell line origin

value: melanoma metastasis

tag: phenotype

value: vinorelbine resistant


title: 10-day-old rat, biological replicate 1

value: Sprague Dawley

value: islets

value: 10 day


title: AN11989 BA10

value: Male


title: AN09730 BA10


title: AN04166 BA10


title: CAL1R-VDS

description: gene expression data from vindesine CAL1 resistant cells

value: vindesine resistant


title: AN08166 BA10


title: ECC1 stably transfected with retroviral vector carying WWOX cDNA, replicate 4

city: Lodz

first: Magdalena

last: Nowakowska

address: Zeligowskiego 7/9

department: Department of Molecular Cancerogenesis

country: Poland

institute: Medical University of Lodz

hyb_protocol: Before pre-hybridization microarrays were pre-heated at 60˚C for 10 min., followed by 99% ethanol wash. Residual ethanol was removed by thorough rinse in deionized water. Hybridization was carried out in a humidity chamber filled with 2X SSPE buffer at 42°C for 16 – 18 h. Post-hybridization washings comprised 1 X SSPE / 0.03% SDS for 2 min. at 42°C, then in 1 X SSPE for 2 min. RT, and  0.1 X SSPE, RT.

scan_protocol: Microarray scanning was done by means of ProScanArray (Perkin Elmer, USA).

data_processing:
Preliminary analysis using ScanArrayExpress software (Perkin Elmer, USA). Further analysis procedures were carried out on freeware TM4 software suite, which is provided by The Institute for Genomic Research on http://www.tm4.org/ site. Normalization and transformation was performed using MIDAS (v2.22). Data from dye-swap experiments were merged, lowess normalized with a smoothing parameter of 0.33  and then standard deviation regularized. Pairs of flip-dye data were then subjected to a flip-dye consistency check.
Statistical analysis were performed in MeV software (v.4.6.1; MultiExperiment Viewer, TM4 software suite)

source_name: endometrial  cancer cell line

label_protocol: Labeling with Cy3 and Cy5 was performed according to the ULS™ Labelling Kit manufacturer's instructions (Kreatech Diagnostics, Netherlands)

growth_protocol: ECC1 cells, derived from a human endometrial cancer were grown in RMPI 1640 medium (Gibco) supplemented with 2 mM L-glutamine (Gibco), 0.1 mM NEAA (Gibco), 10% heat inactivated FBS (Gibco), 0.05 mg/ml penicillin (Gibco), 0.05 mg/ml streptomycin (Gibco) and 0.1 mg/ml neomycin (Gibco) in a humified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Life Technologies). The cDNA synthesis was performed from 10 µg of total RNA  using ImProm RT-IITM reverse transcriptase (Promega)

treatment_protocol: The WWOX gene cDNA was introduced into ECC1 cells by a retroviral transduction. The pLNCX2 retroviral vector with cloned WWOX was produced in the PT67 packaging line. Target cells were grown to 30% confluence and infected with the viruses (approximately 1E+06 CFU/ml) suspended in culture medium with Polybrene as vehicle (8 μg/ml, Sigma Aldrich). After 24 h, medium was replaced, and stable transfectants were selected with 400 μg/ml G418 (Sigma Aldrich) in seven doses, added every 48 hours. Pool of stable transfectants was used for a microarray study of global gene expression and biological experiments. Transfection efficiency was confirmed by real-time RT-PCR and Western Blot.

value: endometrial cancer cell line ECC1

tag: treatment

value: WWOX transfection

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: Universal Human Reference RNA composed of total RNA from 10 human cell lines


title: liver_NEMO_KO_replicate3

description: A202_06_TW51_939_H_(MOGENE-1_0-ST-V1).CEL

value: NEMO knockout (NemoΔhepa)

value: male

value: 8-9 weeks

value: liver


title: AN17425 BA24

value: cingulate cortex (BA24)

value: normal


title: AN06420 BA10

value: frontal cortex (BA10)

value: autism


title: liver_NEMO_TRAIL_DOUBLE_KO_replicate1

description: A202_07_TW100_420_HTR_(MOGENE-1_0-ST-V1).CEL

value: NEMO-TRAIL double knockout (NemoΔhepa/TRAIL-/-)


title: liver_NEMO_KO_replicate2

description: A202_05_TW51_937_H_(MOGENE-1_0-ST-V1).CEL


title: CAL1R-VCR

description: gene expression data from vincristine CAL1 resistant cells

value: melanoma metastasis

value: vincristine resistant


title: CAL1-WT

description: gene expression data from CAL1 cells

value: control


title: AN08792 BA10

value: Male


title: AN01971 BA10


title: AN12457 BA10

value: Female


title: AN10028 BA24


title: AN00142 BA24


title: ECC1 stably transfected with retroviral vector carying WWOX cDNA, replicate 3

value: endometrial cancer cell line ECC1


title: liver_NEMO_KO_replicate1

description: A202_04_TW51_936_H_(MOGENE-1_0-ST-V1).CEL


title: ECC1 stably transfected with retroviral vector carying WWOX cDNA, replicate 2

value: WWOX transfection


title: AN04479 BA24


title: UK20119 BA10


title: 8226_LR5_control5

city: Trondheim

first: Animesh

last: Sharma

state: Trondelag

address: Erlingskjallsons gate 1

department: Cancer Research

country: Norway

institute: NTNU

description: resistant control_biological replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were exported from the Illumina GenomeStudio software to R using the Bioconductor package `lumi`. The data were quantile normalized and log2 transformed. The groups were compared using a t-test with empirical Bayes correction from the Bioconductor package `limma`. The fold change was used to demonstrate rate of changes in average gene expressions between studied groups. Statistical analyses were performed using the false discovery rate (FDR) with a significance threshold of 0.01.

label: control

source_name: 8226-LR5 control

label_protocol: not provided

extract_protocol: The Illumina TotalPrep RNA amplification Kit (Ambion Inc., Austin, TX) was used to amplify RNA for hybridization on Illumina BeadChips. To synthesize first strand cDNA by reverse transcription, we used totalRNA from each sample collected above. Following the second strand cDNA synthesis and cDNA purification steps, the in vitro transcription to synthesize cRNA was prepared overnight for 12 hours.

value: melphalan resistant

tag: cells

tag: date


title: 8226_LR5_treated5

description: resistant treated_biological replicate 6

label: treated-melphalan

source_name: 8226-LR5 treated


title: AN17254 BA10


title: UK28768 BA10


title: saliva_highstress_biorep3

source_name: whole saliva, high chronic stress exposure

value: whole saliva

value: white

value: never

value: high


title: ECC1 stably transfected with retroviral vector carying WWOX cDNA, replicate 1

value: Universal Human Reference RNA composed of total RNA from 10 human cell lines


title: Control ECC1 cells transfected with an empty vector, replicate 4

value: control empty vector transfection


title: Control ECC1 cells transfected with an empty vector, replicate 3


title: Control ECC1 cells transfected with an empty vector, replicate 2


title: 8226_control5

description: sensitive control_biological replicate 6

source_name: 8226 control

value: melphalan sensitive


title: liver_WT_replicate1

description: A202_01_TW51_963_WT_(MOGENE-1_0-ST-V1).CEL

tag: genotype/variation

value: wild type

value: male

value: 8-9 weeks

value: liver


title: 8226_treated4

description: sensitive treated_biological replicate 5

source_name: 8226 treated


title: liver_WT_replicate3

description: A202_03_TW51_938_WT_(MOGENE-1_0-ST-V1).CEL

tag: gender


title: 8226_LR5_control4

description: resistant control_biological replicate 5


title: Control ECC1 cells transfected with an empty vector, replicate 1

source_name: endometrial cancer cell line


title: 8226_LR5_treated4

description: resistant treated_biological replicate 5


title: AN14757 BA24

value: cingulate cortex (BA24)

value: normal


title: AN15566 BA24

value: Female


title: 8226_control4

description: sensitive control_biological replicate 5


title: liver_WT_replicate2

description: A202_02_TW51_935_WT_(MOGENE-1_0-ST-V1).CEL

tag: age


title: 8226_LR5_control3

description: resistant control_biological replicate 4


title: 8226_LR5_treated3

description: resistant treated_biological replicate 4


title: Tra2β-IP

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

description: RNAs in Tra2β-IP materials

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA).

data_processing: Data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA). Raw data output was imported into Genespring GX11 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: After washing with NT2 buffer, the beads were incubated with 20 U of RNase-free DNase I (Invitrogen) in NT2 buffer for 15 min at 37°C and further incubated in NT2 buffer containing 0.1% SDS and 0.5 mg/ml proteinase K for 20 min at 55°C. The bound RNAs were extracted by acid phenol-chloroform.

treatment_protocol: HCT116 cells were lysed with 25 mM Tris-HCl buffer (pH 7.5) containing 150 mM NaCl, 1 mM EDTA, 1% (v/v) Nonidet P-40, 5% (v/v) glycerol, and 100 U/ml RNase inhibitor, and then whole-cell extracts were incubated with protein-A Sepharose beads precoated with 3 μg anti-Tra2β antibody or control rabbit IgG for 2 h at 4°C.


title: 8226_treated3

description: sensitive treated_biological replicate 4


title: AN07176 BA24

value: Male


title: AN07444 BA24


title: AN12137 BA24


title: AN17254 BA24

value: autism


title: 8226_LR5_treated2

description: resistant treated_biological replicate 3

value: melphalan resistant


title: 8226_treated5

description: sensitive treated_biological replicate 6


title: AN11989 BA24


title: AN08166 BA24


title: AN03217 BA24


title: AN12457 BA24


title: AN06420 BA24


title: AN09730 BA24


title: 8226_treated2

description: sensitive treated_biological replicate 3


title: 8226_control3

description: sensitive control_biological replicate 4


title: IRF9TG mice arteries, biological rep2

city: Wuhan

first: Hongliang

last: Li

state: Hubei

address: JieFang Road 238, Wuhan

department: Department of Cardiology

institute: Renmin Hospital of Wuhan University

description:
Gene expression data from IRF9 TG mice artery sufferd from wire injury
vascu-IRF9 TG2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Scanner 7G.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. RMA analysis was employed to evaluate the gene expression

source_name: mice artery sufferd from wire injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA

growth_protocol: The mice were exposed to a 12-h light/dark cycle with controlled temperature and humidity. Food and water were provided ad libitum.

treatment_protocol: Mice were treated with wire-injury operation, and the arteries were collected at 14 days post-injury and were immediately put in RNAlatter reagent.

value: IRF9 TG

tag: stress

value: wire-injury

value: carotid artery


title: NTG mice arteries, biological rep2

description:
Gene expression data from NTG mice artery sufferd from wire injury
vascu-NTG2

value: control


title: AN08792 BA24


title: IgG-IP

description: control


title: 8226_control2

description: sensitive control_biological replicate 3


title: IRF9TG mice arteries, biological rep3

description:
Gene expression data from IRF9 TG mice artery sufferd from wire injury
vascu-IRF9 TG3


title: AN01971 BA24


title: 8226_control1

description: sensitive control_biological replicate 2


title: NTG mice arteries, biological rep1

description:
Gene expression data from NTG mice artery sufferd from wire injury
vascu-NTG1


title: AN19760 BA24


title: 8226_LR5_treated1

description: resistant treated_biological replicate 2


title: NTG mice arteries, biological rep3

description:
Gene expression data from NTG mice artery sufferd from wire injury
vascu-NTG3


title: H9 HOXA9 EBD15 PFVs Rep 2

city: Granada

first: Pedro

middle: Jose

last: Real

state: Granada

address: Avda. Ilustracion 114

department: Molecular Oncology

country: Spain

institute: GENyO

description: Gene expression D15 purified PFVs from hESCs H9 HOXA9

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent  Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.  Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).

source_name: H9 HOXA9 Purified EB D15 PFVs Replicate 2

label_protocol: For the linear T7-based amplification step, 70 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000  Spectrophotometer (NanoDrop Technologies).

growth_protocol: Undifferentiated hESCs at confluence were treated with collagenase IV and scraped off of the Matrigel attachments. To allow human embryoid body (hEB) formation, hESC clumps were transferred to low-attachment plates (Corning) and incubated overnight in differentiation medium [DM; Knock-out-Dulbecco’s modified Eagle’s medium (KO-DMEM) supplemented with 20% non-heat-inactivated fetal bovine serum (FBS), 1% nonessential amino acids (NEAA), 1 mmol/L l-glutamine, and 0.1 mM β-mercaptoethanol]. The medium was changed the next day (day 1) with the same DM supplemented with hematopoietic cytokines: 300 ng/mL stem cell factor (SCF), 300 ng/mL Flt3L, 10 ng/mL interleukin (IL)-3, 10 ng/mL IL-6, 50 ng/mL granulocyte-colony stimulating factor (G-CSF) and 25 ng/mL bone morphogenetic protein 4 (BMP-4)19, 54. hEBs were dissociated using collagenase B (Roche Diagnostic) for 2 h at 37ºC followed by 10min incubation at 37ºC with enzyme-free Cell Dissociation Buffer (Invitrogen). A single-cell suspension was obtained by gentle pipetting and passage through a 70-µm cell strainer. The dissociated cells were stained with anti-CD34-PE-Cy7(BD Biosciences), anti-CD31-PE, anti-CD45-APC or -FITC and DLL4-APC or -PE antibodies (all from Miltenyi) and 7-actinomycinD (7-AAD, BD Biosciences). CD31+CD34+CD45- PFVs, and CD45+ were isolated using a FACSAria sorter (Becton Dickinson).

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin® RNA II). The RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies)

value: female

tag: cell type

value: human embryonic stem cell

value: HOXA9 overexpression


title: 8226_treated1

description: sensitive treated_biological replicate 2

value: melphalan sensitive


title: 8226_LR5_control2

description: resistant control_biological replicate 3


title: 8226_LR5_control1

description: resistant control_biological replicate 2


title: IRF9TG mice arteries, biological rep1

description:
Gene expression data from IRF9 TG mice artery sufferd from wire injury
vascu-IRF9 TG1


title: 8226_LR5_heavy_treated_6h

description: resistant treated_biological replicate 1

source_name: 8226-LR5 heavy treated 6 h


title: AN06597 BA10

value: frontal cortex (BA10)


title: H9 GFP EBD15 PFVs

description: Gene expression D15 purified PFVs from hESCs H9 GFP (Control)

source_name: H9 GFP Purified EB D15 PFVs


title: AN00764 BA24


title: NF90-NF45 dbTg mouse, quadriceps

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: Each array was hybritized with 100 ng Cy3-labeled RNA using miRNA Labeling and Hyb Kit (Agilent Technologies) according to the manufacture's instructions.

scan_protocol: The array was scanned using Microarray Scanner (Agilent Technologies).

data_processing: RAW data were normalized by GeneSpring GX.

source_name: NF90-NF45 dbTg mouse, quadriceps

label_protocol: Total RNA was labeled with Cy3 by an miRNA Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacture's instructions.

extract_protocol: Total RNA isolated from the quadriceps of WT and NF90-NF45 dbTg mice using miRNeasy Mini Kit (Qiagen).

tag: genotype

value: NF90-NF45 double transgenic (dbTg)

value: Quadriceps muscle

value: 15-16 weeks of age


title: Hep3B_FIR_siRNA_3

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Hugene-1_0-st-v1-type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA Background correction and Probe-Summary with Medianpolish

growth_protocol: Hep3B cells were grwon under full media conditions for 24 hours. After transfection with siRNAs cells were cultivated for further 24 hours.

extract_protocol: Nucleospin RNAII II (Macherey-Nagel) was used for total RNA extraction.

treatment_protocol: Transfection of siRNAs was performed according to the Oligofectamine protocol provided by the company (Invitrogen).

tag: cell line

value: human hepatoma cells

tag: transfected with

value: FIR-specific siRNA


title: 8226_LR5_light_heavy_control_0_6h

description: resistant control_biological replicate 1

source_name: 8226-LR5 heavy control 0 h


title: Hep3B_nonsense_2

source_name: Hep3B_nonsense siRNA

value: nonsense siRNA


title: Hep3B_nonsense_3


title: Hep3B_FIR_siRNA_1


title: H9 HOXA9 EBD15 PFVs Rep 1

source_name: H9 HOXA9 Purified EB D15 PFVs Replicate 1


title: 8226_light_control_0_6h

description: sensitive control_biological replicate 1

source_name: 8226 light control 0 h


title: 8226_heavy_treated_6h

description: sensitive treated_biological replicate 1

source_name: 8226 heavy treated 6 h


title: Hep3B_FIR_siRNA_2


title: WT mouse, quadriceps

source_name: WT mouse, quadriceps

value: wild-type


title: AN00142 BA10

value: Male

tag: sample type

tag: disease state

value: normal


title: AN01570 BA24

value: Female

value: cingulate cortex (BA24)

value: autism


title: brain CCNC-KO, biological rep3

status: Public on Sep 02 2014

city: Boston

first: Tobias

last: Otto

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: not provided

data_processing: RMA normalized using the 'RMA' package in R

source_name: embryonic brain E18.5 CCNC knockout

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: standard

extract_protocol: Invitrogen TRIzol, Qiagen RNeasy Mini kit

tag: tissue

value: brain

tag: developmental stage

value: embryonic E18.5

value: CCNC-/-


title: brain CCNC-KO, biological rep2


title: MEF CCNC-KO, biological rep2

source_name: primary embryonic fibroblasts CCNC knockout

value: primary embryonic fibroblasts


title: brain control, biological rep3

source_name: embryonic brain E18.5 wild-type


title: brain control, biological rep1


title: brain CCNC-KO, biological rep1


title: MEF CCNC-KO, biological rep3


title: MEF control, biological rep2

source_name: primary embryonic fibroblasts wild-type


title: ESC CCNC-KO, biological rep1

source_name: embryonic stem cells CCNC knockout

value: embryonic stem cells


title: ESC CCNC-KO, biological rep2


title: MEF control, biological rep1


title: brain control, biological rep2


title: ESC control, biological rep3

source_name: embryonic stem cells wild-type


title: ESC CCNC-KO, biological rep3


title: MEF control, biological rep3


title: AN14757 BA10

value: frontal cortex (BA10)


title: ESC control, biological rep2


title: AN19760 BA10


title: ESC control, biological rep1


title: MEF CCNC-KO, biological rep1


title: EA_Colon_2

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

description: Total RNAs were extracted from tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

hyb_protocol: Fluorescent targets were hybridized to Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

source_name: EA treatment/TNBS-induced colitis

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

treatment_protocol: Mice were intrarectally administered 250 mg/kg TNBS and electroacupunctured at Quze (PC3) and Neiguan (PC6) acupoints, which have been applied for gastrointestinal disorders. Gene expression profiles in colons and spleens were analyzed by microarray for the elucidation of mechanism of EA.

tag: strain

value: FVB

value: Colon


title: AN07176 BA10


title: AN10028 BA10


title: AN04479 BA10


title: AN17425 BA10


title: AN15566 BA10


title: AN12137 BA10


title: EA_Colon_1

extract_protocol: Total RNAs were extracted from tissues using RNeasy Mini kit (Qiagen, Valencia, CA, USA).


title: Mock_Colon_1

source_name: Mock


title: EA_Spleen_2

value: Spleen


title: TNBS_Colon_1

source_name: TNBS-induced colitis


title: AN03217 BA10


title: EA_Spleen_1


title: AN07444 BA10


title: Mock_Colon_2


title: TNBS_Colon_2


title: Mock_Spleen_1


title: TNBS_Spleen_2


title: Mock_Spleen_2


title: TNBS_Spleen_1


title: Healthy control blood, 124

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

description: Blood gene expression data from healthy control

hyb_protocol: cRNA were hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by GC-RMA algorithm

source_name: Healthy Control Blood

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

extract_protocol: Total RNA was isolated from whole blood using the Tempus Spin RNA isolation kit

tag: diagnosis

value: Healthy

value: blood

value: M

tag: ethnicity

value: Not available

tag: virus genotype


title: Healthy control blood, 123


title: Healthy control blood, 121

value: F


title: Healthy control blood, 117


title: Healthy control blood, 120


title: Healthy control blood, 095


title: Healthy control blood, 113


title: Healthy control blood, 111


title: Healthy control blood, 093


title: Healthy control blood, 119


title: Healthy control blood, 112


title: Healthy control blood, 094


title: Healthy control blood, 122


title: Healthy control blood, 084


title: Healthy control blood, 085


title: Healthy control blood, 087


title: Healthy control blood, 082


title: Hep3B_nonsense_1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

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

value: human hepatoma cells

value: nonsense siRNA


title: Healthy control blood, 070


title: HCV blood, 277

description: Blood gene expression data from chronic HCV infection

source_name: HCV Blood

value: HCV

value: Caucasian


title: Healthy control blood, 074


title: HCV blood, 280

value: Other


title: HCV blood, 276


title: HCV blood, 274


title: HCV blood, 260


title: HCV blood, 266


title: HCV blood, 263


title: HCV blood, 258


title: HCV blood, 284


title: HCV blood, 270


title: HCV blood, 281


title: HCV blood, 269


title: HCV blood, 272


title: HCV blood, 265

value: Asian

value: UN


title: HCV blood, 262


title: Healthy control blood, 073


title: HCV blood, 282


title: HCV blood, 264


title: HCV blood, 251


title: HCV blood, 278


title: HCV blood, 252


title: HCV blood, 271


title: HCV blood, 249


title: HCV blood, 256


title: HCV blood, 254


title: HCV blood, 257


title: HCV blood, 275


title: HCV blood, 261


title: HCV blood, 268


title: HCV blood, 253


title: HCV blood, 180


title: HCV blood, 250


title: HCV blood, 179


title: HCV blood, 163


title: HCV blood, 165


title: HCV blood, 178


title: HCV blood, 166


title: HCV blood, 177


title: HCV blood, 160


title: HCV blood, 181


title: HCV blood, 154


title: HCV blood, 157


title: HCV blood, 167


title: HCV blood, 161


title: HCV blood, 164


title: HCV blood, 158


title: HCV blood, 155


title: HCV blood, 153


title: HCV blood, 159


title: HCV blood, 152


title: HCV blood, 156


title: HCV blood, 176


title: HCV blood, 175


title: HCV blood, 162


title: HCV blood, 174


title: HCV blood, 172


title: HCV blood, 170


title: HCV blood, 171


title: BLOOD_Cardioembolic_STROKE_Rep64

city: Sacramento

first: Boryana

last: Stamova

state: California

address: 2805 50th Street

department: Neurology; MIND Institute

institute: University of California, Davis Medical Center

hyb_protocol: Hybridization, washing and laser scanning of Whole Genome U133 Affymetrix Arrays were performed according to protocol (Affymetrix, Santa Clara, CA).

data_processing: Raw CEL file data was uploaded in Partek Genomics Suite and was internal gene normalized (Stamova et al, BMC Medical Genomics, 2009).

source_name: Homo sapiens Blood

label_protocol: 50 ng RNA samples were amplified using the RNA Amplification System V2 (Catalogue #3100) (NuGEN, San Carlos, CA); Ovation WB Reagent (Catalogue #1300); Encore ® Biotin Module (Catalogue #4200) (NuGEN, San Carlos, CA).

extract_protocol: Whole blood  was collected from each subject via antecubital fossa venipuncture into PAXgene Vacutainer tubes (Qiagen, Valencia, CA, USA). These tubes contain a solution that immediately lyses all of the cells in whole blood and stabilizes the RNA without measurable degradation. Blood was collected in PaxGen tubes. RNA Amplification System V2 (Catalogue #3100) (NuGEN, San Carlos, CA); using the Encore ®  Biotin Module (Catalogue #4200)(NuGEN, San Carlos, CA).

tag: group

value: Cardioembolic Stroke

tag: time after stroke (h)

tag: subject id


title: BLOOD_Cardioembolic_STROKE_Rep66

scan_protocol: Hybridization, washing and laser scanning of Whole Genome U133 Affymetrix Arrays were performed according to protocol (Affymetrix, Santa Clara, CA).


title: HCV blood, 168

tag: gender


title: BLOOD_Cardioembolic_STROKE_Rep67


title: BLOOD_Cardioembolic_STROKE_Rep69


title: HCV blood, 169


title: BLOOD_Cardioembolic_STROKE_Rep68


title: BLOOD_Cardioembolic_STROKE_Rep65


title: BLOOD_Cardioembolic_STROKE_Rep63


title: BLOOD_Cardioembolic_STROKE_Rep62


title: MDT_MB_0726

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Methylation data from a medulloblastoma tumor sample

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Data analysis has been carried out using the minfi Bioconductor package (version 1.4.0), performing background correction and normalization to internal controls.

label: biotin/DNP

source_name: Primary medulloblastoma tumor tissue

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Allprep DNA/RNA/Protein Mini Kit.

tag: age

tag: histology

value: classic


title: ICGC_MB171

value: desmoplastic


title: MDT_MB_0706

value: medulloblastoma, NOS


title: ICGC_MB180


title: BLOOD_Cardioembolic_STROKE_Rep60


title: ICGC_MB178


title: BLOOD_Cardioembolic_STROKE_Rep61


title: BLOOD_Cardioembolic_STROKE_Rep59


title: BLOOD_Cardioembolic_STROKE_Rep57


title: BLOOD_Cardioembolic_STROKE_Rep58


title: BLOOD_Cardioembolic_STROKE_Rep56


title: Broad_MD_320


title: ICGC_MB181


title: BLOOD_Cardioembolic_STROKE_Rep55


title: BLOOD_Cardioembolic_STROKE_Rep54


title: Broad_MD_335


title: BLOOD_Cardioembolic_STROKE_Rep53


title: BLOOD_Cardioembolic_STROKE_Rep52


title: Broad_MD_286


title: Broad_MD_332


title: Broad_MD_325


title: BLOOD_Cardioembolic_STROKE_Rep51


title: Broad_MD_330


title: Broad_MD_282

value: LCA


title: BLOOD_Cardioembolic_STROKE_Rep50


title: BLOOD_Cardioembolic_STROKE_Rep49


title: Broad_MD_294


title: Broad_MD_241


title: ICGC_MB155


title: Broad_MD_237


title: Broad_MD_057


title: BLOOD_Cardioembolic_STROKE_Rep47


title: Broad_MD_085


title: BLOOD_Cardioembolic_STROKE_Rep45


title: BLOOD_Cardioembolic_STROKE_Rep48


title: BLOOD_Cardioembolic_STROKE_Rep44


title: Broad_MD_133


title: MB137


title: Broad_MD_050


title: BLOOD_Cardioembolic_STROKE_Rep46


title: MBRep-T13


title: MB_FB_428


title: BLOOD_Cardioembolic_STROKE_Rep43


title: ICGC_MB159


title: BLOOD_Cardioembolic_STROKE_Rep42


title: BLOOD_Cardioembolic_STROKE_Rep37


title: BLOOD_Cardioembolic_STROKE_Rep40


title: BLOOD_Cardioembolic_STROKE_Rep36


title: MB69


title: BLOOD_Cardioembolic_STROKE_Rep39


title: MB66


title: BLOOD_Cardioembolic_STROKE_Rep38


title: BLOOD_Cardioembolic_STROKE_Rep41


title: MB142


title: MB67


title: MB88


title: MB132


title: Ad-REP105


title: BLOOD_Cardioembolic_STROKE_Rep34


title: BLOOD_Cardioembolic_STROKE_Rep31


title: Broad_MD_042


title: BLOOD_Cardioembolic_STROKE_Rep32


title: LFS_MB4


title: BLOOD_Cardioembolic_STROKE_Rep35


title: MB_FB_081a


title: MB_FB_146


title: BLOOD_Cardioembolic_STROKE_Rep30


title: BLOOD_Cardioembolic_STROKE_Rep28


title: BLOOD_Cardioembolic_STROKE_Rep29


title: BLOOD_Cardioembolic_STROKE_Rep33


title: MB_FB_310


title: MB_FB_270


title: BLOOD_Cardioembolic_STROKE_Rep25


title: BLOOD_Cardioembolic_STROKE_Rep27


title: BLOOD_Cardioembolic_STROKE_Rep26


title: MB59


title: MB136


title: MB104


title: LFS_MB1


title: BLOOD_Cardioembolic_STROKE_Rep23


title: BLOOD_Cardioembolic_STROKE_Rep24


title: MB101


title: BLOOD_Cardioembolic_STROKE_Rep21


title: BLOOD_Cardioembolic_STROKE_Rep22


title: BLOOD_Cardioembolic_STROKE_Rep18


title: BLOOD_Cardioembolic_STROKE_Rep20


title: t01-11423


title: BLOOD_Cardioembolic_STROKE_Rep16


title: BLOOD_Cardioembolic_STROKE_Rep17


title: MBRep_T78


title: MB81


title: BLOOD_Cardioembolic_STROKE_Rep15


title: BLOOD_Cardioembolic_STROKE_Rep19


title: MB82


title: MB79


title: 4m21


title: MB74


title: MB63


title: BLOOD_Cardioembolic_STROKE_Rep14


title: MB1


title: t07-03091


title: BLOOD_Cardioembolic_STROKE_Rep11


title: BLOOD_Cardioembolic_STROKE_Rep13


title: BLOOD_Cardioembolic_STROKE_Rep12


title: MB72


title: MB68


title: MB102


title: BLOOD_Cardioembolic_STROKE_Rep9


title: MB56


title: BLOOD_Cardioembolic_STROKE_Rep10


title: BLOOD_Cardioembolic_STROKE_Rep7


title: MB53


title: BLOOD_Cardioembolic_STROKE_Rep8


title: BLOOD_Cardioembolic_STROKE_Rep6


title: BLOOD_Cardioembolic_STROKE_Rep5


title: MB60


title: MB37


title: MB34


title: BLOOD_Cardioembolic_STROKE_Rep3


title: BLOOD_Cardioembolic_STROKE_Rep1


title: BLOOD_Cardioembolic_STROKE_Rep2


title: BLOOD_Control_Rep22

value: Control


title: BLOOD_Control_Rep23

value: blood


title: BLOOD_Cardioembolic_STROKE_Rep4


title: MB143


title: 5m6

value: M


title: MB21


title: BLOOD_Control_Rep20


title: MB28


title: MB35


title: 5m18


title: 5m9


title: 5m8


title: 5m17


title: BLOOD_Control_Rep21


title: BLOOD_Control_Rep18


title: BLOOD_Control_Rep17


title: 5m16


title: MB61


title: 2m17


title: BLOOD_Control_Rep15


title: BLOOD_Control_Rep13


title: BLOOD_Control_Rep19


title: BLOOD_Control_Rep16


title: BLOOD_Control_Rep14


title: BLOOD_Control_Rep11


title: 2m8


title: 2m20


title: BLOOD_Control_Rep12


title: 1m5


title: 1m31


title: 1m12


title: BLOOD_Control_Rep7


title: BLOOD_Control_Rep8


title: BLOOD_Control_Rep9


title: BLOOD_Control_Rep10


title: MDT-MB-1234

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

description: Methylation data from a glioblastoma tumor sample


title: MDT-MB-755


title: 2m21


title: 2m9


title: BLOOD_Control_Rep6


title: BLOOD_Control_Rep3


title: 2m16


title: 1m9


title: MDT-MB-452


title: MDT-MB-1201


title: rdr6 dry, rep1

city: Yokohama

first: Akihiro

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

description: WT flower buds under 1-week-drought stress condition.

hyb_protocol: 1650ng of cRNAs were hybridized to Agilent-021169 microarrays at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarrays were scanned by Agilent DNA Microarray Scanner G2539A ver. C and extracted to raw data, using Feature Extraction program ver 9.1.

data_processing: 75 percentile normalization was performed for signals of microarray probes according to Agilent data analysis protocol.

organism: Arabidopsis thaliana

source_name: rdr6 plant, drought condition

label_protocol: 200ng of total RNA was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: 2-week-old rdr6-15 and wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 30g of vermiculite soil of plastic pot.

extract_protocol: Total RNA was extracted from flower buds using Plant RNA Isolation Reagent (Life Technologies).

treatment_protocol: Water supply was depleted for 1 week. Water content of the soil was decreased to less than 20% after the treatment.

tag: ecotype

value: Columbia

tag: genotype/variation

value: flower buds

tag: condition

value: drought stress

tag: treatment duration

value: 1 week


title: MDT-MB-1200

value: F


title: MB3


title: BLOOD_Control_Rep5


title: BLOOD_Control_Rep2


title: MDT-MB-516


title: rdr6 dry, rep3


title: BLOOD_Control_Rep1


title: rdr6 dry, rep2


title: MDT-MB-826


title: rdr6 control, rep2

description: WT flower bud under unstressed condition.

source_name: rdr6 plant, control condition

value: unstressed


title: BLOOD_Control_Rep4


title: rdr6 control, rep3


title: spleen 28 days [S28_28]

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

description: The signal#1 and signal#2 (i.e. SIGNAL_MEAN*.1 and SIGNAL_MEAN*.2) columns in .ftr files correspond to 'test/Cy3' and 'reference/Cy5' channels, respectively.

hyb_protocol: Each hybridization mixture was made up from 1.1 µg Test (Cy3) and 1.1 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of the appropriate sample tracking control (STC, Roche Nimblegen) was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 95°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto a 12x135k Mus musculus microarray (Catalog no. 05543797001, Design 090901 MM9 EXP HX12) containing 44,170 genes with 3 probes per target gene. Microarrays were hybridized for 20 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen). Afterwards, the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0

scan_protocol: Slides were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

data_processing: Raw microarray signal data were normalised in R (www.r-project.org), using a four step approach: (1) natural log-transformation, (2) quantile normalisation of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate oligo spots. Normalised data for the resulting 44170 oligonucleotides were further analysed in R and Microsoft Excel. As the actual calculations for this experiment are done on ratios infected vs uninfected (t=0), the sample data table contains log2-ratios per sample vs average control. Further calculations were based on logratios compared to uninfected animals.

source_name: spleen 28 days

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: Female BALB/c mice (Harlan, The Netherlands), 8-week-old, were divided in groups of three animals and housed in cages (macrolon III including filter top).

extract_protocol: RNA isolation was performed using a miRNeasy Mini Kit with DNAse treatment (Qiagen). RNA concentrations were determined using UV spectroscopy (Tech3 module, Synergy Mx, BioTek). RNA quality was determined using electrophoresis (RNA nano 6000 kit, 2100 Bioanalyzer, Agilent).

treatment_protocol: Three healthy mice were euthanized at day 0 and considered as naïve group. Other mice were intranasally infected under anesthesia (isoflurane/oxygen), with 2x10^5 cfu Bordetella pertussis B1917 in 40 µl Verweij medium at day 0. Groups of animals (n=3) were euthanized after 2, 4, 6 hours, and after 1, 2, 4, 7, 10, 14, 21 and 28 days of infection, respectively. Please note that some  timepoints were not used for microarray analysis, but were included to compare bacterial counts.

value: BALB/c

value: female

value: 8 weeks

tag: infected with

value: 2x10^5 cfu Bordetella pertussis B1917

value: spleen

tag: time after infection

value: 28 days

source_name: spleen 28 days (reference pool)


title: MDT-MB-1329

value: desmoplastic


title: spleen 28 days [S28_29]

tag: tissue


title: MDT-MB-194

value: classic


title: spleen 21 days [S21_51]

source_name: spleen 21 days

tag: strain

value: 21 days

source_name: spleen 21 days (reference pool)


title: rdr6 control, rep1


title: spleen 28 days [S28_30]


title: spleen 14 days [S14_48]

source_name: spleen 14 days

value: 14 days

source_name: spleen 14 days (reference pool)


title: spleen 21 days [S21_50]


title: WT dry, rep3

source_name: WT plant, drought condition

value: WT


title: MDT-MB-1330

value: M


title: spleen 14 days [S14_47]


title: MDT-MB-1326


title: MDT-MB-1202


title: WT dry, rep2

value: Columbia

value: flower buds


title: MDT-MB-707

value: LCA


title: WT control, rep3

source_name: WT plant, control condition

value: 1 week


title: spleen 10 days [S10_39]

source_name: spleen 10 days

value: 10 days

source_name: spleen 10 days (reference pool)


title: spleen 10 days [S10_38]

value: BALB/c


title: MDT-MB-1204


title: WT dry, rep1

value: drought stress


title: spleen 14 days [S14_46]

value: female

value: 8 weeks


title: spleen 21 days [S21_49]

value: 2x10^5 cfu Bordetella pertussis B1917

value: spleen


title: WT control, rep2

value: unstressed


title: MDT-MB-107

value: classic


title: spleen 10 days [S10_37]


title: PD-His-4

city: Gainesville

first: Michael

last: Kilberg

state: Florida

address: 1600 SW Archer Road

department: Biochemistry & Molecular Biology

institute: University of Florida

description: 2.5M PD98059-depleted for Histidine

hyb_protocol: Labeled targets were hybridized to Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA 2.0) for 16 h at 45°C and washed according to Affymetrix standard protocols.

scan_protocol: The Genechips were scanned with an Affymetrix G7 scanner.

data_processing:
For gene expression analysis, arrays were normalized using RMA as implemented in Partek Genomics Suite 6.6 (Partek Incorporated, St Louis MO).
probe group file:HTA-2_0.r1.pgf
meta-probeset_file: HTA-2_0.na33.1.hg19.transcript.csv

source_name: Human Heptoma (HepG2)

label_protocol: A 100 ng aliquot of total RNA from four independent incubations for each of four conditions (DMEM vs DMEM lacking histidine, each with or without 2.5 uM PD98059) was   amplified using the GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions and then 5.5 ug of cDNA was fragmented and terminally labeled.

growth_protocol: All of the cell lines used in these studies were cultured in Dulbecco’s modified Eagle’s medium (DMEM, pH 7.4, Mediatech, Herndon, VA), supplemented with 1X non-essential AA, 2 mM glutamine, 100 μg/ml streptomycin sulfate, 100 U/ml penicillin G, 0.25 μg/ml amphotericin B, and 10% v/v fetal bovine serum.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination, following the manufacturer’s directions.

treatment_protocol: The MEK inhibitor PD98059 (Sigma-Aldrich, St. Louis, MO) was diluted in dimethyl sulfoxide (DMSO). Cells were pre-treated with an equal volume of DMSO (control) or PD98059 for 1 h prior to activation of the AAR for the indicated times in the continued presence of inhibitor

tag: cell line

tag: treatment

value: 2.5M PD98059-depleted for Histidine


title: spleen 7 days [S7_36]

source_name: spleen 7 days

value: 7 days

source_name: spleen 7 days (reference pool)


title: MDT-MB-201


title: MDT-MB-1250

value: F


title: MDT-MB-1325


title: PD-His-3

description: 2.5M PD98059-depleted for Histidine


title: WT control, rep1

value: WT


title: spleen 7 days [S7_35]


title: PD-His-2

description: 2.5M PD98059-depleted for Histidine


title: Bos taurus_thymus_P32

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Sample of bovine thymus

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using cyclic lowess by R 2.11.1 statistical software

label: Cyanine 3

source_name: Bovine thymus samples collected at the slaughterhouse

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

extract_protocol: Extracted using the Invitrogen TRIzol reagent and purified according to the QiAgen RNeasy MinElute Cleanup Kit protocol for tissue samples

treatment_protocol: prednisolone 30 mg/head daily per os for 35 days

value: thymus

tag: breed

value: holstein


title: MDT-MB-1264

source_name: Primary medulloblastoma tumor tissue


title: PD-DMEM-3

description: 2.5M PD98059-complete medium

value: 2.5M PD98059-complete medium


title: PD-His-1

description: 2.5M PD98059-depleted for Histidine


title: PD-DMEM-4

description: 2.5M PD98059-complete medium


title: spleen 4 days [S4_32]

source_name: spleen 4 days

value: 4 days

source_name: spleen 4 days (reference pool)


title: spleen 4 days [S4_33]


title: MDT-MB-110

value: desmoplastic


title: Bos taurus_thymus_P29

description: Sample of bovine thymus

value: prednisolone 30 mg/head daily per os for 35 days


title: MDT-MB-1328

value: medulloblastoma, NOS


title: spleen 4 days [S4_31]

value: BALB/c

value: female


title: PD-DMEM-1

description: 2.5M PD98059-complete medium


title: DMSO-His-4

description: control-depleted for Histidine

value: control-depleted for Histidine


title: PD-DMEM-2

description: 2.5M PD98059-complete medium


title: Bos taurus_thymus_P31

description: Sample of bovine thymus


title: Bos taurus_thymus_P28

description: Sample of bovine thymus


title: MDT-MB-138

value: M


title: spleen 2 days [S2_30]

source_name: spleen 2 days

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: spleen

value: 2 days

source_name: spleen 2 days (reference pool)


title: MDT-MB-1218

value: F

value: LCA


title: Bos taurus_thymus_P27

description: Sample of bovine thymus

value: thymus


title: spleen 2 days [S2_29]


title: MDT-MB-1187


title: DMSO-His-2

description: control-depleted for Histidine


title: MDT-MB-53


title: Bos taurus_thymus_P30

description: Sample of bovine thymus

value: holstein


title: spleen 1 days [S1_26]

source_name: spleen 1 days

value: 1 days

source_name: spleen 1 days (reference pool)


title: Bos taurus_thymus_P25

description: Sample of bovine thymus


title: Bos taurus_thymus_P26

description: Sample of bovine thymus


title: spleen 1 days [S1_27]


title: spleen 2 days [S2_28]


title: MDT-MB-704


title: MDT-MB-446


title: Bos taurus_thymus_C24

description: Sample of bovine thymus


title: DMSO-DMEM-4

description: control-complete medium

value: control-complete medium


title: MDT-MB-1196

value: desmoplastic


title: DMSO-His-1

description: control-depleted for Histidine


title: spleen 1 days [S1_25]


title: MDT-MB-1243


title: MDT-MB-1215


title: spleen 7 days [S7_34]

value: 7 days


title: Bos taurus_thymus_C20

description: Sample of bovine thymus


title: Bos taurus_thymus_C22

description: Sample of bovine thymus


title: spleen 4 hours [S0-4_19]

source_name: spleen 4 hours

value: 4 hours

source_name: spleen 4 hours (reference pool)


title: DMSO-DMEM-2

description: control-complete medium


title: spleen 4 hours [S0-4_20]

value: BALB/c


title: DMSO-DMEM-1

description: control-complete medium


title: Glucocorticoid stimulated monocytes 3

city: Muenster

first: Georg

last: Varga

address: Albert-Schweitzer-Campus 1, Gebaeude W30

department: Pediatric Rheumatology and Immunology

institute: University of Muenster

description: Total RNA of murine bone marrow derived monocytes after stimulation with M-CSF and dexamethasone for 16 hours.

hyb_protocol: Ten micrograms of fragmented cRNA hybridized for 16 hours under constant rotation at 45°C to Murine Genome 430-2.0 arrays (Affymetrix). Arrays were washed and stained using the Gene Chip Fluidics Station 400 (Affymetrix).

scan_protocol: Fluorescent signals were detected by the HP G2500A Gene Array Scanner (Affymetrix)

data_processing:
For analysis of data from individual donors, raw data of GC-treated samples were analyzed by GCOS Software (Affymetrix) using data from corresponding control samples as baseline and further studied applying the Expressionist Suite software package (GeneData), which allows identification of genes that are significantly regulated in multiple independent experiments.
Signals were scaled to a target intensity of 500 and log-transformed.

source_name: Bone marrow derived monocytes after 16h culture and stimulation with dexamethasone

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA ( Expression Analysis Technical Manual, 2001, Affymetrix ).

growth_protocol: For monocyte enrichment, fresh bone marrow cells were applied to a density gradient (ficoll) and subsequently deprived of CD11c+, CD19+, and CD90+ cells using MACS (magnetic cell sorting) technology. Monocytes were then cultured for 16 hours with 10-7M (40 ng/ml) dexamethasone in medium supplemented with M-CSF (50 ng/ml) using Teflon bags; they are further referred to as GCsM. Control monocytes (Ctr-Mo) were cultured identically, i.e. with M-CSF (50 ng/ml), but with only the solvent (PBS; Ctr-Mo) instead of GC.

extract_protocol: Total RNA isolation was performed according to the manufacturer’s instructions (Macherey-Nagel, Dueren, Germany).

value: bone marrow

tag: cell type

value: monocyte

tag: culture time

value: M-CSF + dexamethasone


title: Bos taurus_thymus_C18

description: Sample of bovine thymus


title: spleen 4 hours [S0-4_21]

value: female

value: 8 weeks


title: Control monocytes 3

description: Total RNA of murine bone marrow derived monocytes after stimulation with M-CSF for 16 hours.

source_name: Bone marrow derived monocytes after 16h culture

value: M-CSF


title: MDT-MB-1246

value: MBEN


title: Glucocorticoid stimulated monocytes 2


title: spleen 0 hours [S0-0_3]

source_name: spleen 0 hours

value: 2x10^5 cfu Bordetella pertussis B1917

value: spleen

value: 0 hours

source_name: spleen 0 hours (reference pool)


title: spleen 0 hours [S0-0_2]


title: MDT-MB-1263

value: M

value: classic


title: Bos taurus_thymus_C17

description: Sample of bovine thymus

value: thymus

value: holstein


title: MDT-MB-601


title: Glucocorticoid stimulated monocytes 1


title: lung 28 days [L28_30]

source_name: lung 28 days

value: lung

value: 28 days

source_name: lung 28 days (reference pool)


title: MDT-MB-1174

value: F

value: desmoplastic


title: Bos taurus_thymus_C23

description: Sample of bovine thymus


title: DMSO-His-3

description: control-depleted for Histidine

source_name: Human Heptoma (HepG2)

value: control-depleted for Histidine


title: MDT-MB-595


title: 6M_47A

city: Trondheim

first: Duan

last: Chen

address: Erling Skjalgssons Gate 1

department: Department of Cancer Research and Molecular Medicine

institute: Norwegian University of Science and Technology

description: Gene expression of vagtomized anterior stomach at 12 months old mice

hyb_protocol: 1.5ug of the labeled probes were mixed with hybridization reagents and hybridized overnight at 58°C to the MouseWG-6 v2.0 BeadChips.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Reader.

data_processing: Data was log2 transformed and quantile normalized using the Lumi package implemented in Bioconductor/R. The data was filtered using a detection p-value <= 0.01 in more than one sample for each probe.

source_name: Anterior abdomen, 6 months post surgery

label_protocol: Biotin labeling was performed using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.)

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA were purified with Trizol reagent

treatment_protocol: Mice were anterior vagotomized at 6 months, and sacrificed at 8, 10, or 12 months.

value: FVB/N

value: Female

tag: genotype

value: INS-GAS

value: 12 months

value: vagotomized anterior stomach


title: 6M_46A

tag: gender


title: Control monocytes 2

value: BALB/c

value: bone marrow

value: monocyte

value: M-CSF


title: spleen 0 hours [S0-0_1]

value: female

tag: age

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: spleen

value: 0 hours


title: Control monocytes 1

source_name: Bone marrow derived monocytes after 16h stimulation with m-csf and dexamethasone


title: Bos taurus_thymus_C21

description: Sample of bovine thymus

source_name: Bovine thymus samples collected at the slaughterhouse

value: thymus

value: holstein


title: MDT-MB-225

source_name: Primary medulloblastoma tumor tissue

value: M

tag: histology

value: desmoplastic


title: 6M_47P

description: Gene expression of unvagtomized posterior stomach at 12 months old mice

source_name: Posterior abdomen, 6 months post surgery

value: FVB/N

value: Female

value: unvagotomized posterior stomach


title: 6M_46P

value: INS-GAS

value: 12 months


title: MDT-MB-1211

value: classic


title: lung 28 days [L28_29]

value: BALB/c

value: lung

value: 28 days


title: 4M_43A

description: Gene expression of vagtomized anterior stomach at 10 months old mice

source_name: Anterior abdomen, 4 months post surgery

value: 10 months

value: vagotomized anterior stomach


title: MDT-MB-429

value: Classic


title: DMSO-DMEM-3

description: control-complete medium

value: control-complete medium


title: Wild type GM-BMMs, biological rep2

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: Gene expression data of tumor treated BMM

hyb_protocol: The IVT products were column-purified, fragmented and hybridized at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

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

data_processing: The data were analyzed using R package Affy (version 1.36.1), affycoretools (version 1.34.0), limma (version 3.14.4) and gcrma (version 2.30.0).  The QC of the data was assessed using AffyQCReport (version 1.36.0). RMA function with default setting was used to globally normalize the data. Probes with absent call values in any of the samples using mas5calls function were treated as non-expressed probes and excluded from the downstream analysis. The probe annotation is done using mouse4302.db package (version 2.9.0) from BioConductor.

source_name: Bone marrow from naive C57BL/6 mice

label_protocol: Microarray analysis was conducted according to the manufacture's instructions for Affymetrix 3' IVT Express Kit.  RNA quality was assessed by Agilent Bioanalyzer. Reverse transcription to second strand cDNA was generated from 100 ng of high quality total RNA. Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: Bone marrow cells were collected from naive C57BL/6 and E-FABP knockout mice of 6~8 week old. GM-BMMs were derived using GM-CSF(20ng/ml) in RPMI1640 with 5%FBS for 7 days in 100mm plates before tumor treatment. Fresh media with GM-CSF were added every 2 days to replace about half the old media.

extract_protocol: Total RNA was extracted from tumor-stimulated GM-BMMs of WT and E-FABP-/- mice using RNeasy Mini Kit (Qiagen), following the manufacturer's protocol.

treatment_protocol: BM-GMMs were lifted off the plate and replated in a 12-well tissue culture plate. After cells were re-attached, E0771 tumor cells were added to the well using cell culture insert. After 18hr of GM-BMM, E0771 co-culture, tumor cell inserts were tossed away. Treated GM-BMMs were lysed for total RNA isolation.

value: mouse bone marrow

value: wild type

value: 1x10^6 cells in a 12-well plate co-cultured overnight with 1x10^6 E0771 tumor cells in an sterile insert


title: lung 21 days [L21_51]

source_name: lung 21 days

value: female

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: 21 days

source_name: lung 21 days (reference pool)


title: MDT-MB-158

value: F

value: MBEN


title: MDT-MB-709

value: medulloblastoma, NOS


title: lung 28 days [L28_28]

value: BALB/c


title: 2M_60P

description: Gene expression of unvagtomized posterior stomach at 8 months old mice

source_name: Posterior abdomen, 2 months post surgery

value: FVB/N

value: Female

value: INS-GAS

value: 8 months

value: unvagotomized posterior stomach


title: E-FABP knockout GM-BMMs, biological rep3

value: E-FABP knockout


title: E-FABP knockout GM-BMMs, biological rep2

value: mouse bone marrow


title: Wild type GM-BMMs, biological rep1

value: wild type


title: MDT-MB-1247

value: M

value: desmoplastic


title: 2M_60A

description: Gene expression of vagtomized anterior stomach at 8 months old mice

source_name: Anterior abdomen, 2 months post surgery

value: vagotomized anterior stomach


title: Plasma 10_exercised_30min_rep3

city: Harbin

first: Yue

last: Li

state: Heilongjiang

address: 23 Youzheng Street

department: Cardiovascular Department

institute: the First Affiliated Hospital of Harbin Medical University

description: replicate 3

hyb_protocol: labeled miRNA was hybridized according to the manufacturer's instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile Normalization

source_name: plasma of forearm veins,exercised,30min

label_protocol: Labeling was performed according to the protocol in the Illumina MicroRNA Expression Profiling kit

extract_protocol: Total RNA was extracted using miRVana isolation kit

value: male

value: plasma

tag: patient

value: ISR 6


title: 6M_45A

value: 12 months


title: lung 21 days [L21_49]

value: female

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: lung

value: 21 days


title: MDT-MB-226


title: lung 14 days [L14_47]

source_name: lung 14 days

value: BALB/c

value: 14 days

source_name: lung 14 days (reference pool)


title: lung 14 days [L14_48]


title: Plasma 9_exercised_30min_rep3

description: replicate 3

value: ISR 5


title: Plasma 8_exercised_30min_rep3

description: replicate 3

value: ISR 4


title: Plasma 7_exercised_30min_rep3

description: replicate 3

value: ISR 3


title: 4M_42P

description: Gene expression of unvagtomized posterior stomach at 10 months old mice

source_name: Posterior abdomen, 4 months post surgery

value: FVB/N

value: Female

value: INS-GAS

value: 10 months

value: unvagotomized posterior stomach


title: Plasma 6_exercised_30min_rep3

description: replicate 3

value: plasma

value: ISR 2


title: MDT-MB-1333

value: M

value: desmoplastic


title: 4M_42A

value: vagotomized anterior stomach


title: Plasma 5_exercised_30min_rep3

description: replicate 3

value: female

value: ISR 1


title: 4M_43P


title: lung 14 days [L14_46]

value: BALB/c

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: lung


title: MDT-MB-13


title: Plasma 3_exercised_30min_rep3

description: replicate 3

value: male

value: Non-ISR 3


title: 2M_59A

value: FVB/N

value: Female

value: 8 months


title: lung 10 days [L10_39]

source_name: lung 10 days

value: 10 days

source_name: lung 10 days (reference pool)


title: lung 10 days [L10_38]


title: Plasma 4_exercised_30min_rep3

description: replicate 3

value: plasma

value: Non-ISR 4


title: MDT-MB-842

value: F

value: medulloblastoma, NOS


title: Plasma 2_exercised_30min_rep3

description: replicate 3

value: Non-ISR 2


title: lung 7 days [L7_36]

source_name: lung 7 days

value: female

value: 7 days

source_name: lung 7 days (reference pool)


title: Wild type GM-BMMs, biological rep3

value: mouse bone marrow

value: wild type

value: 1x10^6 cells in a 12-well plate co-cultured overnight with 1x10^6 E0771 tumor cells in an sterile insert


title: 2M_59P

value: INS-GAS

value: unvagotomized posterior stomach


title: 4M_41A

value: 10 months

value: vagotomized anterior stomach


title: 6M_44P

value: FVB/N

value: Female

value: 12 months


title: lung 7 days [L7_35]

value: BALB/c

value: 8 weeks

value: 2x10^5 cfu Bordetella pertussis B1917

value: lung


title: 6M_44A

source_name: Anterior abdomen, 6 months post surgery


title: lung 4 days [L4_33]

source_name: lung 4 days

value: 4 days

source_name: lung 4 days (reference pool)


title: lung 7 days [L7_34]

value: female


title: 2M_58P

value: 8 months


title: Plasma 1_exercised_30min_rep3

description: replicate 3

value: plasma

value: Non-ISR 1


title: lung 4 days [L4_31]