title: 1/2_Kidney_7dpi_Replicate4

city: Columbus

first: Ashley

middle: R

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

description: Gene expression in 7-days post infection C3H/HeOuJ mouse kidney

hyb_protocol: 1.5mg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250mL containing 1X Agilent fragmentation buffer and 2X Agilent blocking according to the manufacturers recommendations. On completion of the fragmentation reaction, 250mL of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays (G4852A) 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: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. Samples were hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray and slides were scanned using Agilent G2505C Microarray Scanner.

data_processing: The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files was imported into the mathematical software package “R”, which was used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. The dataset was filtered to remove positive control elements and any elements that were flagged as outliers. Present (P), Marginal (M) or Absent (A) calls were made for each element on the array using in-house methodologies that took into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. The algorithm for normalization of this Agilent One-Color Analysis consisted of the following: The median green (Cy3) intensities were normalized between the arrays using the Quantile Normalization package in “R” (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array. This is a significantly more robust approach than simply normalizing to the median valueof each array.

source_name: 1/2 Kidney, 7dpi Replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared usingAglient’s One-Color Microarray-based Gene Expression Analysis Low Input Quick Amp Labeling according to the manufacturer's instructions, followed by purification using Qiagen's RNAeasy column-based kit.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from snap frozen kidneys using the mirVanaTM kit (Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA integrity was analyzed using Agilent 2100 Bioanalyzer Lab-On-A-Chip 6000 Series II chip (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Six week old C3H/HeOuJ (Jackson Laboratories, Bay Harbor, ME) female mice were acclimated on standard low-fat chow (Harlan) with 12 hour light/dark cycles for one week, housed in ventilated cages, transferred to a BL2 room and inoculated transurethrally using 10^8 cfu CFT073. At 0 days (control) and 7 days following infection, steriley dissected longitudinally halved kidneys were snap frozen in liquid nitrogen and stored at -80°C.

value: 1/2 Kidney

value: Female

tag: age

value: 6 weeks


title: BJ6

status: Public on Dec 29 2016

type: genomic

city: Beijing

first: Tengxu

last: Wang

address: Tsinghua Yuan Street, No.1

department: School of Environment

country: China

institute: Tsinghua University

description: GeoChip data for sludge sample collected in Beijing WWTP, June

hyb_protocol: Subsequently, the mixed solution was kept at 90 °C for 3 min for denaturation, and incubated at 37°C for 30 min before GeoChip hybridization was carried out at 67 °C for 24 hrs with a rotation at 20rpm in Agilent hybridization oven.

scan_protocol: After hybridization, Agilent Wash Buffers were applied to wash away unbounded DNA at ordinary temperature, and the arrays were scanned with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA) at 633 nm. Eventually the images data were extracted by Agilent Feature Extraction program.

data_processing: The raw microarray data was analyzed by GeoChip Microarray Data Manager pipeline (http://ieg.ou.edu/microarray/) as previously described (Xu et al., 2010). We processed raw GeoChip data using the following steps: (i) remove the spots with a signal-to-noise ratio (SNR) less than 2.0; (ii) log-transformed the data and then, on each microarray, divide them by the mean intensity of all the genes; and (iii) remove genes detected only once in each digester. Finally we acquired GeoChip data for further analysis.

molecule: genomic DNA

organism: uncultured bacterium

source_name: sludge microbes in anaerobic digestion systems

label_protocol: Purified DNA was first labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random priming as described previously (Cong et al., 2015), then purified by a QIAquick Purification kit (Qiagen, Valencia, CA, USA), and dried in a SpeedVac (Thermo Savant, NY, USA) at 45 °C for 45 min. The dried DNA was then resuspended into ??? μl of DNase/RNase-free distilled water and evenly mixed with ??? μl of hybridization solution, which contains 1 × Acgh blocking, 1 × HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05 μg/μl Cot-1 DNA, and 10% formamide (final concentrations).

extract_protocol:
Sludge samples were collected on the monthly basis from during October, 2012 to September, 2013. Briefly, 2 liters of each sludge sample were obtained near the outlets of anaerobic tanks, stored in a portable dry ice container and immediately transported to laboratory. A small part of each sample was kept at 4°C for physicochemical properties analysis, while others were precipitated by centrifugation at 14,000 g for 10 minutes. After centrifugation, the pellet was air dried for 30 min and stored at -80°C for DNA extraction, while the supernatant was decanted. It was noted that the solid content of all 48 samples was less than 10%.
DNA was extracted by MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) and then purified by agarose gel electrophoresis followed by extractions with phenol and chloroform, and precipitation with butanol. After purifying, NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) were applied to access DNA quality, confirming that the A260/A280 ratio was between 1.8 to 2.0 and A260/A230 over 1.5.

tag: collected

value: Beijing, Jun


title: 1/2_Kidney_7dpi_Replicate3

type: RNA

country: USA

molecule: total RNA

organism: Mus musculus

source_name: 1/2 Kidney, 7dpi Replicate 3

tag: tissue

tag: gender

tag: strain


title: BJ7

description: GeoChip data for sludge sample collected in Beijing WWTP, July

value: Beijing, Jul


title: breast tumor_relapse lesion_patient 4

city: Chengdu

first: Xiaorong

last: Zhong

state: Sichuan

address: 5 Gongxing Lane, Wuhou District

institute: West China Hospital, Sichuan University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Shapiro-Wilk test using open source software R (function “shapiro.test()”), Paired t-test and Wilcoxon-test in Matlab computation environment were performed to determine statistical significance of expressed miRNAs.

organism: Homo sapiens

source_name: breast tumor, relapse lesion

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was extracted from deparaffinized FFPE tissue sections using TRIzol (Invitrogen, Carlsbad, CA, USA) and miRNeasy mini kit (QIAGEN, Hilden, Germany) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) .

treatment_protocol: 6 hormone receptor positive BC women (stage I~III) relapsed after standard adjuvant tamoxifen treatment in West China Hospital. MiRNA expression profiles in the primary tumors and their matched recurrent/metastatic lesions from those patients were compared.

tag: age at diagnosis

tag: Sex

tag: clincal stage

tag: tumor histology

value: Invasive ductal carcinoma

tag: er

value: positive

tag: pr

value: negative

tag: menopause when receiving tamoxifen

value: Premenopause

tag: adjuvant chemotherapy

value: Yes

tag: disease-free survival following tamoxifen treatment_months

tag: death

value: Dead


title: NRVCM_6 h stretch_2

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

country: Germany

institute: University Medical Center Kiel

description:
Neonatal rat cardiomyocyte, stretched for 6 hours, replicate 2
Gene expression in stretched cardiomyocytes for 6 hours
356_8

hyb_protocol: Hybridization was performed using laboratory standarized protocol by Comprehensive Biomarker Center (Heidelberg)

scan_protocol: Scanning was performed on Latest high-resolution microarray scanner GS2505_C commercially by Comprehensive Biomarker Center (Heidelberg)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences.

organism: Rattus norvegicus

label_protocol: Labeling was performed by using Agilent’s Low Input Quick Amp Labeling Kit commercially by Comprehensive Biomarker Center (Heidelberg)

growth_protocol: Isolated cardiomyocytes were cultured in DMEM supplemented with 10% (v/v) FCS, 100 U/ml penicillin and 100 µg/ml streptomycin (Life Technologies), and 2 mmol/L L-glutamine (Life Technologies) for 24 h prior to stretch treatment.

extract_protocol: Total RNA was isolated from NRVCMs using QIAzol (Qiagen) according to manufacturer’s instructions

treatment_protocol: Phasic biomechanical stretch was used as the primary stimulus in NRVCMs for microarray and other experiments used in this manuscript. NRVCMs were seeded in 0.02 inch thick, collagen type I coated silicone Bioflex 6-well plates (Dunn Labortechnik), in DMEM containing 10% FCS supplemented with penicillin/streptomycin, and L-glutamine. Cells were washed and incubated in a special incubation chamber to apply biaxial pulsatile stretch to a total of 120% (+20%) for 24 h (or a specified time period) composed of a CO2 series incubator (SHEL LAB) and FlexLink FX5000T (Dunn Labortechnik). Non-stimulated and un-stretched NRVCMs plated in similar silicone-membrane 6-well plates were served as controls in the respective experiments.

tag: developmental stage

value: neonate

tag: cell type

value: Cardiomyocytes

tag: treatment

value: stretched

tag: time

value: 6 hours


title: breast tumor_primary lesion_patient 4

source_name: breast tumor, primary lesion

value: IIIA


title: NRVCM_6 h stretch_1

description:
Neonatal rat cardiomyocyte, stretched for 6 hours, replicate 1
Gene expression in stretched cardiomyocytes for 6 hours
356_7


title: breast tumor_relapse lesion_patient 3

value: uncertain

value: Postmenopause


title: 1/2_Kidney_7dpi_Replicate2

source_name: 1/2 Kidney, 7dpi Replicate 2

tag: tissue

value: 1/2 Kidney

value: Female

tag: age


title: BJ4

description: GeoChip data for sludge sample collected in Beijing WWTP, April

tag: collected

value: Beijing, Apr


title: NRVCM_6 h stretch_3

description:
Neonatal rat cardiomyocyte, stretched for 6 hours, replicate 3
Gene expression in stretched cardiomyocytes for 6 hours
356_9


title: breast tumor_primary lesion_patient 3

tag: age at diagnosis


title: NRVCM_2 h stretch_1

description:
Neonatal rat cardiomyocyte, stretched for 2 hours, replicate 1
Gene expression in stretched cardiomyocytes for 2 hours
356_4

value: 2 hours


title: NRVCM_2 h stretch_2

description:
Neonatal rat cardiomyocyte, stretched for 2 hours, replicate 2
Gene expression in stretched cardiomyocytes for 2 hours
356_5


title: 1/2_Kidney_Control_Replicate4

description: Gene expression in baseline C3H/HeOuJ mouse kidney

source_name: 1/2 Kidney, Control Replicate 4

tag: gender

tag: strain

value: 6 weeks


title: 1/2_Kidney_7dpi_Replicate1

source_name: 1/2 Kidney, 7dpi Replicate 1


title: NRVCM_Control_2

description:
Neonatal rat cardiomyocyte, control, replicate 2
Gene expression in unstretched cardiomyocytes to serve as control
356_2

source_name: Neonatal rat cardiomyocyte, control

value: unstretched

value: control


title: NRVCM_Control_1

description:
Neonatal rat cardiomyocyte, control, replicate 1
Gene expression in unstretched cardiomyocytes to serve as control
356_1


title: NRVCM_Control_3

description:
Neonatal rat cardiomyocyte, control, replicate 3
Gene expression in unstretched cardiomyocytes to serve as control
356_3


title: 1/2_Kidney_Control_Replicate3

source_name: 1/2 Kidney, Control Replicate 3


title: BJ1

description: GeoChip data for sludge sample collected in Beijing WWTP, January

value: Beijing, Jan


title: BJ11

description: GeoChip data for sludge sample collected in Beijing WWTP, November

value: Beijing, Nov


title: breast tumor_relapse lesion_patient 2

tag: Sex

tag: clincal stage

tag: tumor histology

value: Invasive ductal carcinoma

value: positive

value: negative

value: Premenopause

value: Yes

value: Alive


title: BJ12

description: GeoChip data for sludge sample collected in Beijing WWTP, December

value: Beijing, Dec


title: BJ2

description: GeoChip data for sludge sample collected in Beijing WWTP, February

value: Beijing, Feb


title: BJ3

description: GeoChip data for sludge sample collected in Beijing WWTP, March

value: Beijing, Mar


title: 1/2_Kidney_Control_Replicate1

source_name: 1/2 Kidney, Control Replicate 1

value: 1/2 Kidney

value: Female


title: breast tumor_primary lesion_patient 2

value: IIIA

tag: er

tag: pr

value: postive

tag: menopause when receiving tamoxifen


title: 35d Flu 5_repeat

status: Public on Dec 28 2016

city: Pittsburgh

first: John

middle: F

last: Alcorn

state: PA

address: 4401 Penn Ave

department: Pediatrics

institute: Children's Hospital of Pittsburgh

description:
5398599020_D_Grn.idat
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Cubic Spline normalization was applied to the data using R

label: Biotin

source_name: mouse lung_35d Flu

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

extract_protocol: Whole lung RNA was isolated using the Agilent Absolutely RNA Miniprep Kit

treatment_protocol: Mice were infected with 150 PFU of influenza A/PR/8/34 (FLU) in 50 ul of sterile PBS by oropharyngeal aspiration. Vehicle controls are labeled PBS.

value: lung


title: 1/2_Kidney_Control_Replicate2

source_name: 1/2 Kidney, Control Replicate 2

value: 6 weeks


title: BJ10

description: GeoChip data for sludge sample collected in Beijing WWTP, October

value: Beijing, Oct


title: 35d Flu 6_repeat

description:
5398599053_C_Grn.idat
replicate 2


title: NHM8

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, August

value: Ninghai, mesophilic, Aug


title: 35d Flu 2_repeat

description:
5398599053_D_Grn.idat
replicate 2


title: 35d PBS 4_repeat

description:
5398599058_D_Grn.idat
replicate 2

source_name: mouse lung_35d PBS


title: 35d PBS 2_repeat

description:
5398599006_A_Grn.idat
replicate 2


title: 21d FLU 6_repeat

description:
5398599058_C_Grn.idat
replicate 2

source_name: mouse lung_21d FLU


title: 35d PBS 1_repeat

description:
5398599053_E_Grn.idat
replicate 2


title: 21d FLU 4_repeat

description:
5398599006_E_Grn.idat
replicate 2


title: 21d PBS3_repeat

description:
5398599058_E_Grn.idat
replicate 2

source_name: mouse lung_21d PBS


title: 21d FLU 2_repeat

description:
5398599020_A_Grn.idat
replicate 2


title: 35d Flu 4_repeat

description:
5398599006_F_Grn.idat
replicate 2


title: 21d FLU 3_repeat

description:
5398599053_A_Grn.idat
replicate 2


title: 21d PBS2_repeat

description:
5398599053_F_Grn.idat
replicate 2


title: 35d PBS 3_repeat

description:
5398599020_B_Grn.idat
replicate 2


title: 21d PBS1_repeat

description:
5398599006_B_Grn.idat
replicate 2


title: 35d Flu 4

description:
5398599041_C_Grn.idat
replicate 1


title: 35d Flu 5

description:
5388497014_B_Grn.idat
replicate 1


title: 21d PBS5_repeat

description:
5398599020_C_Grn.idat
replicate 2


title: 35d Flu 6

description:
5388497015_F_Grn.idat
replicate 1


title: 35d Flu 2

description:
5398599052_B_Grn.idat
replicate 1


title: 35d PBS 1

description:
5398599041_F_Grn.idat
replicate 1


title: 21d FLU 6

description:
5398599052_A_Grn.idat
replicate 1


title: 35d PBS 4

description:
5398599052_D_Grn.idat
replicate 1


title: 35d PBS 2

description:
5388497014_A_Grn.idat
replicate 1


title: 21d FLU 3

description:
5388497015_C_Grn.idat
replicate 1


title: 35d PBS 3

description:
5388497015_A_Grn.idat
replicate 1


title: 21d PBS3

description:
5398599041_B_Grn.idat
replicate 1


title: 21d FLU 4

description:
5388497014_F_Grn.idat
replicate 1


title: 21d PBS5

description:
5398599052_F_Grn.idat
replicate 1


title: 21d PBS1

description:
5388497014_C_Grn.idat
replicate 1


title: 21d PBS2

description:
5388497015_E_Grn.idat
replicate 1


title: Patient IT242

city: Houston

first: Simone

last: Anfossi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit

scan_protocol: Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)

data_processing: Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library.  The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same ncRNA were averaged.

source_name: primary colorectal adenocarcinoma

label_protocol: Labbeling was done according to Nimblegen one color DNA Labeling kit.

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

value: primary colorectal adenocarcinoma

tag: overall survival months from surgery date, last updated 02/01/2016

tag: vital status at the time of last follow up,2/1/2016

tag: adjuvant chemoradiation or radiation therapy

value: unknown whether adjuvant chemoradiation or radiation theraphy received

tag: tumor grade

value: moderately differentiated

tag: msi status summary based on combined ihc and molecular assay

tag: tumor location

value: right side, left side or both:right

tag: lympho-vascular invasion

tag: age at diagnosis (years)

value: Male

tag: simplified crc stage at diagnosis

value: Stage IV


title: 21d FLU 2

description:
5398599041_E_Grn.idat
replicate 1

tag: tissue


title: Patient IT201

value: Alive

value: no adjuvant chemoradiation or radiation reported

value: poorly differentiated

value: MSS (including MSI-L)

value: Yes

value: Stage III


title: Patient IT248

value: right side, left side or both:left


title: Patient IT251

value: Deceased


title: Patient IT249

value: No

value: Stage II


title: Patient IT081

value: MSI-H

value: Female


title: Patient IT255

value: primary colorectal adenocarcinoma


title: Patient IT239

value: unknown whether adjuvant chemoradiation or radiation theraphy received


title: Patient IT256

value: moderately differentiated


title: Patient IT253

value: right side, left side or both:right

value: Male


title: Patient IT250

value: Alive


title: Patient IT087

value: any adjuvant chemoradiation or radiation therapy reported

value: right side, left side or both:both


title: NRVCM_2 h stretch_3

description:
Neonatal rat cardiomyocyte, stretched for 2 hours, replicate 3
Gene expression in stretched cardiomyocytes for 2 hours
356_6

tag: developmental stage

value: neonate

tag: cell type

value: Cardiomyocytes

tag: treatment

value: stretched

tag: time

value: 2 hours


title: Patient IT113

value: Deceased

value: no adjuvant chemoradiation or radiation reported

value: MSS (including MSI-L)

value: right side, left side or both:left

value: Yes

tag: Sex

value: Stage III


title: Patient IT187

value: primary colorectal adenocarcinoma

value: Stage II


title: Patient IT154

value: moderately differentiated

value: No


title: Patient IT106

value: Alive

value: poorly differentiated

value: MSI-H

value: right side, left side or both:right

value: Male


title: Patient IT179


title: Patient IT159

value: Female


title: Patient IT037


title: Patient IT145

value: unknown whether adjuvant chemoradiation or radiation theraphy received


title: Patient IT096


title: Patient IT259


title: Patient IT072

value: Deceased


title: Patient IT210

value: no adjuvant chemoradiation or radiation reported


title: breast tumor_primary lesion_patient 5

tag: age at diagnosis

tag: clincal stage

value: Unknown

tag: tumor histology

value: Invasive ductal carcinoma

tag: er

value: positive

tag: pr

value: negative

value: Postmenopause

tag: adjuvant chemotherapy

tag: disease-free survival following tamoxifen treatment_months

tag: death


title: Patient IT019

value: primary colorectal adenocarcinoma

tag: overall survival months from surgery date, last updated 02/01/2016

tag: vital status at the time of last follow up,2/1/2016

tag: adjuvant chemoradiation or radiation therapy

tag: tumor grade

tag: msi status summary based on combined ihc and molecular assay

value: MSS (including MSI-L)

tag: tumor location

value: right side, left side or both:left

tag: lympho-vascular invasion

value: Stage II


title: Patient IT167

tag: tissue

value: Alive

value: moderately differentiated

value: Yes

tag: age at diagnosis (years)

tag: simplified crc stage at diagnosis


title: Patient IT012

tag: Sex

value: Male

value: Stage III


title: Patient IT020

value: right side, left side or both:right

value: No


title: Patient IT169

value: no adjuvant chemoradiation or radiation reported


title: Patient IT035

value: Deceased

value: Female


title: Patient IT166

value: poorly differentiated

value: MSI-H


title: Patient IT230

value: unknown whether adjuvant chemoradiation or radiation theraphy received


title: Patient IT057

value: primary colorectal adenocarcinoma


title: Patient IT004


title: Patient IT160


title: Patient IT164

value: MSS (including MSI-L)


title: Patient IT234

value: right side, left side or both:left


title: Patient IT022

value: Stage II


title: Patient IT043

value: Alive


title: Patient IT165

value: moderately differentiated


title: Patient IT002

value: Yes


title: Patient IT170

value: Male


title: Patient IT008


title: Patient IT042


title: Patient IT044

value: Stage III


title: Patient IT235

value: right side, left side or both:right


title: Patient IT032

value: any adjuvant chemoradiation or radiation therapy reported


title: Patient IT152

value: no adjuvant chemoradiation or radiation reported


title: Patient IT026

value: Deceased


title: Patient IT029

value: Female


title: Patient IT163

value: poorly differentiated

value: right side, left side or both:both


title: Patient IT148


title: Patient IT007

value: No


title: Patient IT151

value: primary colorectal adenocarcinoma


title: Patient IT224

value: unknown whether adjuvant chemoradiation or radiation theraphy received

value: MSS (including MSI-L)

value: Stage IV


title: Patient IT135

value: Alive

value: right side, left side or both:left

value: Stage II


title: Patient IT149

value: moderately differentiated

value: Yes


title: Patient IT129

value: right side, left side or both:right

value: Stage III


title: Patient IT150

value: no adjuvant chemoradiation or radiation reported

value: Male


title: Patient IT130


title: Patient IT124

value: MSI-H

value: Female


title: Patient IT100


title: Patient IT120


title: Patient IT121

value: Deceased

value: poorly differentiated


title: Patient IT093

value: primary colorectal adenocarcinoma

value: No


title: Patient IT086


title: Patient IT222

value: unknown whether adjuvant chemoradiation or radiation theraphy received

value: MSS (including MSI-L)


title: Patient IT094

value: Alive


title: Patient IT233

value: right side, left side or both:left

value: Stage IV


title: Patient IT221

value: moderately differentiated


title: Patient IT105

value: Yes


title: Patient IT099

value: right side, left side or both:right

value: Stage II


title: Patient IT092

value: no adjuvant chemoradiation or radiation reported

value: Stage III


title: Patient IT123


title: Patient IT126


title: Patient IT078

value: MSI-H


title: Patient IT082

value: Female


title: Patient IT075


title: Patient IT101


title: Patient IT125

value: Male


title: Patient IT080

value: Deceased


title: Patient IT070

value: primary colorectal adenocarcinoma


title: Patient IT074


title: Patient IT076


title: Patient IT219


title: Patient IT065

value: poorly differentiated


title: Patient IT066

value: No


title: Patient IT213

value: unknown whether adjuvant chemoradiation or radiation theraphy received


title: Patient IT064

value: Alive

value: MSS (including MSI-L)


title: Patient IT062


title: Patient IT157

value: right side, left side or both:left


title: Patient IT054

value: moderately differentiated


title: Patient IT217

value: Yes

value: Stage IV


title: Patient IT147


title: Patient IT146


title: Patient IT218

value: right side, left side or both:right


title: Patient IT143

value: no adjuvant chemoradiation or radiation reported

value: Stage II


title: Patient IT136

value: Stage III


title: Patient IT139

value: Female


title: Patient IT140

value: Male


title: Patient IT137


title: Patient IT156


title: Patient IT142


title: Patient IT132


title: Patient IT220

value: Deceased


title: Patient IT127

value: primary colorectal adenocarcinoma

value: MSI-H


title: Patient IT052

value: No


title: Patient IT131


title: Patient IT117


title: Patient IT115


title: Patient IT133


title: Patient IT058


title: Patient IT134

value: right side, left side or both:both


title: Patient IT114

value: Alive


title: Patient IT112

value: MSS (including MSI-L)


title: Patient IT111


title: Patient IT098

value: right side, left side or both:left


title: Patient IT107

value: poorly differentiated


title: Patient IT091

value: moderately differentiated

value: Yes


title: Patient IT102

value: right side, left side or both:right


title: Patient IT014

value: no adjuvant chemoradiation or radiation reported


title: Patient IT103

value: Stage II


title: Patient IT110


title: Patient IT085


title: Unstimulated MDA468

city: Oxford

first: Zhichao

last: Ai

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

data_processing: For each gene, ΔCt was calculated using the same threshold (0.2) for all genes and Ct>35 considered as no expression, followed by normalization to 5 housekeeping genes (Hsp90ab1, Gusb, Hprt1, Gapdh, and Actb) included in each array, followed by calculation of ΔΔCt for each gene from two arrays: ΔΔCt = ΔCt1 – ΔCt2, where ΔCt1 is the DSS-treated mice group and ΔCT2 is the untreated mice group, using the program provided by Qiagen/SA Biosciences

label: SYBR Green

source_name: MDA-MB-468(ATCC® HTB-132™)

label_protocol: Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the colon using inflammatory gene RT2 Profiler PCR Arrays manufactured by Qiagen/SA Biosciences. The arrays included 84 assay genes, 5 housekeeping genes, and reverse transcription efficiency and DNA contamination controls. cDNA synthesis was performed from 1 µg of total RNAs using RT2 PCR Array First Strand Kit(Qiagen/SA Biosciences).

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.
Total RNA was extracted and reverse-transcribed using, and loaded onto RT² Profiler™ PCR Arrays. Quantitative real-time PCR was performed for the expression of genes that encodeseveral classes of protein factors including cell adhesion, ECM components, cell cycle, cell growth and proliferation, apoptosis, transcription factors and regulators and other genes related to tumor metastasis.

tag: cell line

tag: treatment

value: unstimulated

tag: sample type

value: Control


title: Patient IT109

value: Female

value: Stage III


title: Patient IT006

value: primary colorectal adenocarcinoma

value: Male


title: Patient IT009


title: Patient IT090


title: Lens Msx2 WT

city: Shenyang

first: ziyan

last: yu

state: Liaoning

address: 11 Xinhua Road

institute: China  Medical University

description: Gene expression in Msx2WT mice at P1.

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

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

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).
Subsequent analyses conducted using SAS statistical software online (http://sas.ebioservice.com/)

source_name: Lens,P1,replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: We generated Msx2 conditional knockout mice using a Le-Cre line, which allow us to selective delete Msx2 in the lens.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Lens isolated from Msx2WT and Msx2CKO mice of P1

value: Lens

tag: age

tag: genotype/variation

value: wild type


title: Patient IT005

value: Alive

value: MSI-H

value: No


title: Patient IT095


title: mouse_511_nu4

city: Fribourg

first: Viktoria

last: Szabolcsi

address: Rte Albert-Gockel 1

country: Switzerland

institute: University of Fribourg, Anatomy

hyb_protocol: Samples were hybridized to Affymetrix Mouse Gene ST 2.0 arrays.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Data were pre-processed and normalized using the robust multi-array average (RMA) approach and  the software Expression Console provided by Affymetrix (version 1.2.1.20). The data were evaluated using the programming language R (version 2.14.2) and Partek® Genomics Suite™ software (Partek Inc., St. Louis, Missouri, USA). Gene lists were prepared using the Bioconductor package limma in R.

label: biotin

source_name: parvafox nucleus

label_protocol: biotin

extract_protocol: Using vessels as landmarks, the corresponding parvafox region on the MMI-membranes was excised using the CellCut-Plus laser microdissection apparatus (MMI, Glattbrugg, Switzerland). The previously-drawn trajectory was automatically excised using the precisely-focused UV-laser beam. The dissected tissue samples were collected in special tubes bearing an adhesive surface on the interior of the cap (MMI, Glattbrugg, Switzerland). Finally, 350 μl of lysis buffer [Buffer RLT (Qiagen), supplemented with 1:100 β-mercaptoethanol] were added to each tube and the samples were immediately frozen at -80°C. The same protocol was used to extract the tissue from the cerebral cortex and the hippocampus. The entire RNA-pool of the microdissected cryosections was purified using the RNAeasy Plus Micro Kit (Qiagen, Hilden, Germany). The quantity and the quality of the RNA-extracts were respectively monitored in a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, California, USA). The RNA-samples were stored at -80°C until the time of amplification using the NuGEN Ovation® Pico WTA System V2 (NuGEN Technologies, San Carlos, California, USA).

treatment_protocol: C57BL/6 mice were killed by cervical dislocation. The brains were rapidly removed, mounted on cork platforms in OCT (Sakura Tissue-Tek), and frozen on pulverized dry ice. Prior to sectioning in a cryostat, the samples were stored at -80°C. Starting from the ventral surface, the brains were cut into 16-μm-thick horizontal sections at -18°C until the fornix was reached. At this point, the sections were respectively mounted in an alternating manner on MMI-membranes (Molecular Machines & Industries, Glattbrugg, Switzerland) and Superfrost-Plus glass slides (Menzel-Gläser, Braunschweig, Germany). The MMI-mounted sections were chemically fixed for 5 min in 100% ethanol at -18°C, air dried for one hour in the cryostat chamber, likewise at -18°C and stored at -80°C for various periods of time until the time of laser-capture microdissection. The Superfrost-Plus-mounted sections were chemically fixed for 10 min at ambient temperature in 4% paraformaldehyde diluted in phosphate-buffered saline (0.1M, pH 7.3). These sections were incubated overnight at 4°C with the horseradish-peroxidase-conjugated lectin Vicia villosa (EY Laboratories, San Mateo, California, USA) at a concentration of 20µg/ml in 0.1M Tris-buffered saline containing 0.1mM MnCl2, 0.1mM CaCl2, 0.1mM MgCl2 and 0.1% Triton-X. The presence of the lectin-staining was revealed after treatment with diaminobenzidine / hydrogen peroxide. Lectins such as Vicia villosa are markers of the perineuronal nets (Celio and Blumcke, 1994), which are abundant around the Parv-immunopositive neurons of the rodent parvafox nucleus (Meszar et al., 2012). The pattern of lectin-staining on the Superfrost-Plus-mounted sections aided the localization of the parvafox nucleus on the adjacent, MMI-membrane-mounted ones.

value: brain

tag: brain region

value: parvafox nucleus

value: adult


title: Patient IT079

tag: overall survival months from surgery date, last updated 02/01/2016

value: moderately differentiated

value: MSS (including MSI-L)

value: right side, left side or both:right


title: Patient IT068

tag: vital status at the time of last follow up,2/1/2016

value: no adjuvant chemoradiation or radiation reported

value: right side, left side or both:left

value: Yes

value: Stage II


title: Patient IT141

value: primary colorectal adenocarcinoma

tag: adjuvant chemoradiation or radiation therapy


title: Patient IT073

tag: tumor grade

value: Female

value: Stage III


title: Patient IT104

tag: msi status summary based on combined ihc and molecular assay

value: Male


title: Patient IT122

value: Deceased

tag: tumor location


title: Patient IT077

value: Alive

tag: lympho-vascular invasion


title: Patient IT118

tag: tissue


title: Patient IT069

tag: age at diagnosis (years)


title: MDA468 under MDMs conditioned medium

value: conditioned medium

value: Test


title: MDA231 under MDMs conditioned medium

source_name: MDA-MB-231(ATCC® HTB-26™)


title: Unstimulated MDA231

value: unstimulated

value: control


title: mouse_511_cx5

source_name: cerebral cortex

tag: strain

value: brain

value: cerebral cortex

value: adult


title: mouse_355_hp3

source_name: hippocampus

value: hippocampus


title: Patient IT061

value: no adjuvant chemoradiation or radiation reported

value: moderately differentiated

value: MSS (including MSI-L)

value: right side, left side or both:right

value: No

tag: Sex

tag: simplified crc stage at diagnosis


title: mouse_355_nu1

value: parvafox nucleus


title: Patient IT059

value: primary colorectal adenocarcinoma

value: right side, left side or both:left

value: Male

value: Stage II


title: Patient IT053

value: Alive

value: Yes

value: Female

value: Stage III


title: Patient IT055

value: Deceased


title: mouse_355_cx2

value: brain

value: cerebral cortex

value: adult


title: Patient IT060

value: no adjuvant chemoradiation or radiation reported

value: poorly differentiated


title: mouse_511_hp6

value: hippocampus


title: Patient IT063

value: moderately differentiated


title: Patient IT049

value: MSS (including MSI-L)

value: right side, left side or both:right


title: Patient IT045

value: primary colorectal adenocarcinoma

value: right side, left side or both:left


title: Patient IT047

value: any adjuvant chemoradiation or radiation therapy reported

value: No

value: Male


title: pH7.8 replicate 4

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

description: cells of a 24-well-plate

hyb_protocol: The hybridization was carried out at 45°C in the GeneChipR Hybridisation Oven 645 (Affymetrix) over night.

scan_protocol: The prepared microarrays were scanned using the GeneChip Scanner 3000 (Affymetrix) at 0.7 micron resolution.

data_processing: Primary data analysis was carried out with the Affymetrix Expression Console 1.4.1.46 software including the Robust Multiarray Average module for normalization.

source_name: pH7.8 replicate 4

label_protocol: 200 ng of each total RNA sample was amplified. Non-labeled aRNA was produced by in vitro transcription according to Eberwine. Endpoint fragmentation was performed with uracyl-DNA-glycosylase in combination with apurinic apyrimidinic endonuclease 1. Desoxy

growth_protocol: cells were obtained from the German collection of microorganisms and cell culture (DSMZ, Braunschweig, Germany) and cultured in carbonate-free alpha medium (Pan Biotech, Aidenbach, Germany) buffered with 20 mM HEPES in an incubator with 95% humidity under

extract_protocol: cells were lyzed and the RNeasy Plus Kit (Qiagen, Hilden, Germany) used to extract the RNA according to the manufacturers protocol. The expression profiling was performed according to the manufacturers instructions with Affymetrix GeneChip Mouse 2.0 ST

treatment_protocol: In total, 20,000 cells were seeded per well of a 24-well plate and cultured at pH 7.4, 7.8 or 8.4 for 14 days. After seven days, 10 mg/ml beta-glycerol phosphate and 10 ng/ml calcitriol were added to restrict the proliferation and support the differentiat

tag: cell type

value: MC3T3 sc14 cells

tag: gender

value: mixed

value: passage 11


title: pH8.4 replicate 2

description: cells of a 24-well-plate

source_name: pH8.4 replicate 2

tag: age


title: pH8.4 replicate 1

description: cells of a 24-well-plate

source_name: pH8.4 replicate 1


title: pH8.4 replicate 4

description: cells of a 24-well-plate

source_name: pH8.4 replicate 4


title: Patient IT144

value: Alive

value: Stage II


title: Patient IT039

value: Yes

value: Female

value: Stage III


title: Patient IT040


title: pH8.4 replicate 3

description: cells of a 24-well-plate

source_name: pH8.4 replicate 3


title: Lens Le-Cre Msx2 CKO

description: Gene expression in Msx2CKO mice at P1.

value: Lens

tag: genotype/variation

value: CKO


title: pH7.8 replicate 1

description: cells of a 24-well-plate

source_name: pH7.8 replicate 1


title: Patient IT036

value: Deceased

value: no adjuvant chemoradiation or radiation reported

value: moderately differentiated


title: pH7.8 replicate 2

description: cells of a 24-well-plate

source_name: pH7.8 replicate 2


title: pH7.4 replicate 4

description: cells of a 24-well-plate

source_name: pH7.4 replicate 4


title: pH7.8 replicate 3

description: cells of a 24-well-plate

source_name: pH7.8 replicate 3


title: Patient IT038

value: primary colorectal adenocarcinoma

value: right side, left side or both:right


title: pH7.4 replicate 1

description: cells of a 24-well-plate

source_name: pH7.4 replicate 1


title: VCAP NTC, rep2

city: Boston

first: Fen

last: Ma

state: MA

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC

description: Gene Expression in VCaP with non target control SiRNA knockdown

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneCHIP Human Genome U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: VCaP prostate cancer cell line

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

growth_protocol: VCaP cells were cultured in DMEM medium with 10% FBS

extract_protocol: Total RNA were extracted using RNeasy Plus Mini Kit(Cat. No. 74134).

treatment_protocol: VCaP cells were transfected with two independent SOX9 siRNAs or non target control(NTC) siRNAs and total RNA was collected at 72hrs post transfection.

tag: genotype

tag: cell line

value: VCaP


title: pH7.4 replicate 2

description: cells of a 24-well-plate

source_name: pH7.4 replicate 2


title: 20mGyU6/ reference male mouse6

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse6


title: pH7.4 replicate 3

description: cells of a 24-well-plate

source_name: pH7.4 replicate 3

value: MC3T3 sc14 cells


title: VCAP SOX9i-B, rep 2

description: Gene Expression in VCaP with SOX9i-B knockdown


title: Patient IT025

source_name: primary colorectal adenocarcinoma

tag: overall survival months from surgery date, last updated 02/01/2016

tag: vital status at the time of last follow up,2/1/2016

value: any adjuvant chemoradiation or radiation therapy reported

value: MSI-H

value: right side, left side or both:left

value: Male


title: Patient IT030

value: Alive

tag: adjuvant chemoradiation or radiation therapy

tag: tumor grade

value: MSS (including MSI-L)

value: Yes

value: Stage II


title: Patient IT028

tag: msi status summary based on combined ihc and molecular assay

tag: tumor location

value: No


title: Patient IT027

tag: tissue

value: poorly differentiated

tag: lympho-vascular invasion

value: Female

value: Stage III


title: VCAP NTC, rep1


title: VCAP SOX9i-B, rep 1


title: reference male mouse6/ 20mGyU7

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

tag: strain


title: Patient IT034

value: primary colorectal adenocarcinoma

value: no adjuvant chemoradiation or radiation reported

value: moderately differentiated

tag: age at diagnosis (years)

tag: Sex


title: Patient IT033

value: Deceased

value: right side, left side or both:right

tag: simplified crc stage at diagnosis


title: reference male mouse6/ 20mGyU6

value: tail


title: MDMs Control

source_name: Monocyte-derived macrophages

extract_protocol: Total RNA was extracted and reverse-transcribed using, and loaded onto RT² Profiler™ PCR Arrays. Quantitative real-time PCR was performed for the expression of 84 key genes mediating the inflammatory response.

tag: cell type

value: Monocyte-derived macrophages

value: control


title: reference male mouse6/ 20mGyU4


title: Patient IT021

value: right side, left side or both:left

value: Male


title: VCAP SOX9i-A, rep 2

description: Gene Expression in VCaP with SOX9i-A knockdown

value: VCaP


title: 20mGyU8/ reference male mouse6


title: MDMs MDA231


title: Patient IT015

value: Alive

value: MSS (including MSI-L)


title: VCAP SOX9i-A, rep 1


title: 20mGyU4/ reference male mouse6


title: 20mGyU7/ reference male mouse6


title: MDMs MDA468


title: reference male mouse6/ 20mGyU8


title: Patient IT011

value: Yes

value: Stage II


title: LASS2-/- HFD

status: Public on Dec 27 2016

city: Xuzhou

first: Shaohua

last: Fan

state: Jiangsu

address: No. 101, Shanghai Road

department: School of Life Science

institute: Jiangsu Normal University

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

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

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

source_name: liver of LASS2-/- mice fed by high-fat diet

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

growth_protocol: All mice were maintained in a temperature-controlled barrier facility with a 12-h light/dark cycle and were given free access to food and water.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Dietary intervention with a high fat diet (60% calories from fat, Cat. #D12492, Research Diets Inc.) or a chow diet (10% calories from fat, Cat. #D12450B, Research Diets Inc.) started from 3 weeks of age in LASS2-/- and WT mice.

tag: gender

value: male

value: liver


title: WT HFD

source_name: liver of wild-type mice fed by high-fat diet

value: wild-type


title: 20mGyU2/ reference male mouse6


title: LASS2-/- chow

source_name: liver of LASS2-/- mice fed by standard chow diet


title: 20mGyU5/ reference male mouse6


title: Patient IT024

value: primary colorectal adenocarcinoma

value: no adjuvant chemoradiation or radiation reported

value: Stage III


title: Patient IT017

value: moderately differentiated


title: IH28D_1

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

label_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cDNA.

value: hippocampus

tag: treatment

value: intermittent hypoxia 28 days


title: WT chow

source_name: liver of wild-type mice fed by standard chow diet

tag: genotype


title: IH5D_2

value: intermittent hypoxia 5 days


title: control_3

source_name: control

value: control


title: IH5DR2_3

value: intermittent hypoxia 5 days recovery 2 days


title: IH5DR2_1


title: IH5D_3


title: IH28D_2


title: reference male mouse6/ 20mGyU3

value: tail


title: IH5D_1


title: reference male mouse6/ 20mGyU2


title: reference male mouse6/ 20mGyU5


title: reference male mouse6/ 20mGyU1


title: IH5DR2_2


title: control_1


title: 20mGyU1/ reference male mouse6


title: control_2


title: 20mGyUF/ reference male mouse6


title: Patient IT001

value: Deceased

value: well differentiated

value: right side, left side or both:left

value: No

value: Male


title: reference male mouse6/ 20mGyUM


title: N-BLR shRNA #3-1, biological rep1 vs empty vector control

description: N-BLR shRNA #3-1 vector, replicate 1

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HCT116 cell line

label_protocol: Labbeling was done according to Agilent Gene Expression Hybridization Kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

growth_protocol: The human colon cancer cell line HCT116 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown according to ATCC recommendations. Cells were cultured at 37°C in 5% CO2.

extract_protocol: Cell were transduce with lentivirus containing the specific vectors. Total RNA was extracted using Trizol following manufacturer's instructions

tag: cell line

tag: vector

value: N-BLR shRNA #3-1

source_name: Empty vector control

value: Empty


title: 14-Control

city: Tokyo

first: Fumika

last: Shigiyama

address: 6-11-1, Omori Nishi, Otaku

department: Internal Medicine

institute: Toho University

hyb_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit (Part# 902280) User Manuall.

scan_protocol: GeneChip were scaned by GeneChip Scaner 3000(Affymetrix 690036) using GeneChip Command Console Software ver3.2(Affymetrix 702569). The procedure of scan is followed by  Affymetrix GeneChip WT PLUS Reagent Kit (Part# 902280) User Manuall.

data_processing: Data is processed by RMA-Skech algorythm using Expression ConsoleTM Softwere ver.1.3（Affymetrix 702387）

source_name: Mouse Liver sample

label_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit (Part#902280) User Manuall. 100ng Total RNA was used for this assay.

extract_protocol: Total RNA was extracted from flash frozen 15~20 mg liver sample using the RNeasy mini kit (Qiagen, Tokyo, Japan). RNA was reverse-transcribed into cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany).

value: liver

tag: insuline response

value: Control


title: 11-Control


title: N-BLR shRNA #4-7, biological rep2 vs empty vector control

description: N-BLR shRNA #4-7 vector, replicate 2

value: N-BLR shRNA #4-7


title: 7-Control


title: N-BLR shRNA #3-1, biological rep2 vs empty vector control

description: N-BLR shRNA #3-1 vector, replicate 2


title: 5-Sleep deprivation group

value: Sleep deprivation group


title: control_12m_1

value: hippocampus

value: Control 12 months


title: N-BLR shRNA #4-7, biological rep1 vs empty vector control

description: N-BLR shRNA #4-7 vector, replicate 1


title: reference male mouse6/ 20mGyUF


title: 13-Sleep deprivation group


title: 3-Sleep deprivation group


title: 10-Sleep deprivation group


title: 12-Control


title: 1-Sleep deprivation group


title: control_12m_3


title: 9-Control


title: control_12m_2


title: 2-Sleep deprivation group


title: 8-Control


title: 4-control


title: 20mGyU3/ reference male mouse6


title: 6-Sleep deprivation group


title: 20mGyUM/ reference male mouse6


title: Trp53-/-  Neural Stem/Progenitor Cells Replicate 1

city: Tondabayashi

first: Akiko

last: Okuda

state: Osaka

address: 3-11-1 Nishikiori-kita

department: Faculty of Pharmacy

institute: Osaka Ohtani University

hyb_protocol: 24 µl of oligoarray control targets, 1 µl of fragmentation buffer and 25 µl of hybridization buffer were added, and samples were applied to microarrays at 65°C for 17h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

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

source_name: NSPC-PJ34 treated

label_protocol: Labeled using Low Input Quick Amp Labeling Kit (Agilent)

growth_protocol: NSPCs were were dissociated and suspended at density of 2x10^6 cells in 1xDMEM/F-12 neurosphere medium supplemented with B-27 (GIBCO), 20 ng/ml human recombinant EGF, and 20 ng/ml human recombinant FGF-basic.

extract_protocol: Total RNA extracted using Rneasy Mini Kit (QIAGEN) following manufacturer's instructions

treatment_protocol: Total RNA was extracted from NSPCs with or without treatment with 20 microM PJ34 .

tag: age

value: Neural stem progenitor cells

source_name: NSPC-control


title: wild-type Neural Stem/Progenitor Cells Replicate 2

value: wildtype


title: Trp53-/-  Neural Stem/Progenitor Cells Replicate 2


title: wild-type Neural Stem/Progenitor Cells Replicate 1


title: HCT116 Tumor cell, M1 virus, 24h

city: Guang Zhou

first: Jing

last: Cai

address: Zhongshan School of Medicine, Sun Yat-sen University   74 Zhongshan 2nd Road

institute: Sun yat-sen university

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

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

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software

source_name: HCT116 Tumor cell, M1 virus, 24h

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

growth_protocol: HCT116 tumor cells are grown in DMEM supplied with 10%FBS and 1%Penicillin-Streptomycin

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

treatment_protocol: HCT116 tumor cells were treated with 1 pfu per cell M1 virus for 0h, 24h

value: colorectum

value: HCT116 colorectal cancer cell line

tag: infection

value: oncolytic virus M1


title: Sample14_TBT_D10_n3

city: Wageningen

first: Myrthe

last: van den Dungen

address: Tuinlaan 5

country: Netherlands

institute: Wageningen University

description:
Independent experiment 3
TBT exposed differentiated adipocytes Day 10

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R-based open software (R 3.1.2)

label: Cy5 and Cy3

source_name: Bone-marrow derived hMSCs from 43-years-old black male

label_protocol: Standard Illumina Protocol

growth_protocol: hMSCs were obtained and cultured according to the standard protocols (Lonza, Walkersville, USA).

extract_protocol: DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: Cells were either exposed to the vehicle control (DMSO) or continuously to either TCDD, PFOS or TBT (started 1 day before differentiation was induced).

value: human mesenchymal stem cells (hMSCs)


title: Sample9_PFOS_D10_n2

description:
Independent experiment 2
PFOS exposed differentiated adipocytes Day 10


title: Sample15_TBT_D10_n4

description:
Independent experiment 4
TBT exposed differentiated adipocytes Day 10


title: HCT116 Tumor cell, M1 virus, 0h

source_name: HCT116 Tumor cell, M1 virus, 0h

value: control


title: Sample11_PFOS_D10_n4

description:
Independent experiment 4
PFOS exposed differentiated adipocytes Day 10


title: GIST_imatinib60w_rep1

city: Tsukiji, Chuuoo-ku

first: Momoko

last: NAGAI

state: Tokyo

department: Department of Bioinformatics

institute: National Cancer Center Research Institute

description: Gene expression of GIST cell line exposed to imatinib for 60 weeks.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes. The resultant cRNA was hybridized to the Agilent-039494 SurePrint G3 Human GE 8x60K v2 Microarray under the condition of 17 hours, 65°C, 10 r.p.m. The hybridization underwent a quality control evaluation.

scan_protocol: The arrays were washed, stained, and scanned using the Gene Expression Hybridization Kit, Gene Expression Wash Buffers Pack and Agilent DNA Microarray Scanner (G2565CA).

data_processing:
Expression values were generated using Feature Extraction (Agilent).
(1) Filtering step: control samples were excluded with setting "ControlType" to 0.
(2) The trimmed-mean was calculated by excluding probes with the 2% highest and the 2% lowest signal intensity values in "gProcessedSignal".
(3) The scaling factor was calculated by dividing the target signal constant (2500) by the trimmed-mean.
(4) Normalized signal intensities (gScale Signal) were obtained by multiplying the signal values by the scaling factor.

source_name: GIST cell line, derived from T1, exposed to imatinib for 60 weeks, cultured for 96 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNeasy kit (Qiagen, Valencia, CA). The resultant underwent a quality control evaluation.

growth_protocol: T1 cells were cultured in DMEM 1640 medium supplemented with 10% fetal bovine serum (FBS) (HyClone Laboratories, Logan, UT) and 1% penicillin-streptomycin (Nacalai Tesque, Kyoto, Japan) at 37°C in a humidified atmosphere of 5% CO2. Resistant cells were maintained as polyclonal populations under constant 1 μM imatinib selection.

extract_protocol: Total RNA was extracted from each cell line and tumor sample by using an RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: To create imatinib-resistant lines, parental cells were cultured with increasing concentrations of imatinib starting with the 10 nM imatinib (IC70). Fresh drug was added every 72-96 h. Resistant cells that grew in 10 μM imatinib were established after 20-60 weeks of culture with the drug.

value: gastrointestinal stromal tumor (GIST) cell line

value: imatinib

tag: time

value: 60 weeks

tag: imatinib-resistance

value: fully resistant


title: Sample10_PFOS_D10_n3

description:
Independent experiment 3
PFOS exposed differentiated adipocytes Day 10


title: Sample7_TCDD_D10_n4

description:
Independent experiment 4
TCDD exposed differentiated adipocytes Day 10


title: Sample2_DMSO_D10_n2

description:
Independent experiment 2
Unexposed differentiated adipocytes Day 10


title: Sample3_DMSO_D10_n4

description:
Independent experiment 4
Unexposed differentiated adipocytes Day 10


city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#3341
7T_Cy5 vs. 7N_Cy3

hyb_protocol: Equal amount of labeled Test & Control DNA sample was added into a fresh tube containing 25 µl of Human Cot-1 DNA (1mg/ml),  26ul of Agilent 10X blocking agent and 130ul Agilent 2X hybridization buffer. The total hybridization volume was 45ul. The above hybridization mix was denatured at 95°C for 3 minutes and incubated the microfuge tubes at 37°C for 30 minutes.  The samples were hybridized at 65°C for 40 hours in the hybridization chamber. After hybridization, the slides were washed using aCGH Wash Buffer1 (Agilent Technologies, Part Number 5188-5221) at room temperature for 5 minutes and aCGH Wash Buffer 2 (Agilent Technologies, Part Number 5188-5222) at 37°C for 1 minutes. The slides were then washed with Acetonitrile for 10 seconds.

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images were quantified using Agilent Feature Extraction Software . Feature extracted raw data was normalized using Lowes normalization and analyzed Agilent CytoGenomics 2.7 SoftwarE.

source_name: Primary tumor_#3341

label_protocol: Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that,  the  control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.

growth_protocol: Primary uterine cervical lesions and corresponding peripheral blood lymphocytes (PBL) were collected from the hospital section of Chittaranjan National Cancer Institute, Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients were taken.

extract_protocol: Genomic DNA from cryosections (5µm) of tumor tissue specimen and PBL were isolated by standard phenol/chloroform method.

tag: subject status

value: Indian CACX (cancer of the uterine cervix) patient

tag: subject id

tag: Stage

value: Stage IVA

value: F

tag: tissue/cell type

value: Primary uterine cervical lesions

tag: hpv type

source_name: matched normal blood_#3341

tag: age (yrs)


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#6109
4N_Cy5 vs. 4T_Cy3 (Dye swap)

source_name: matched normal blood_#6109

value: Stage IVB

value: corresponding peripheral blood lymphocytes (PBL)

source_name: Primary tumor_#6109


title: Sample8_PFOS_D10_n1

description:
Independent experiment 1
PFOS exposed differentiated adipocytes Day 10

tag: cell type


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#6341
6N_Cy5 vs. 6T_Cy3 (Dye swap)

source_name: matched normal blood_#6341

value: Stage IIIB

tag: gender

source_name: Primary tumor_#6341


title: Sample1_DMSO_D10_n1

description:
Independent experiment 1
Unexposed differentiated adipocytes Day 10


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#4253
1T_Cy5 vs. 1N_Cy3

source_name: Primary tumor_#4253

source_name: matched normal blood_#4253


title: GIST_imatinib52w_rep1

description: Gene expression of GIST cell line exposed to imatinib for 52 weeks.

source_name: GIST cell line, derived from T1, exposed to imatinib for 52 weeks

tag: treatment

value: 52 weeks


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#3389
10N_Cy5 vs. 10T_Cy3 (Dye swap)

source_name: matched normal blood_#3389

source_name: Primary tumor_#3389


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#1856
2N_Cy5 vs. 2T_Cy3 (Dye swap)

source_name: matched normal blood_#1856

source_name: Primary tumor_#1856


title: genomic DNA from  female control 6

city: Seoul

first: Yeong-Wook

last: Song

address: Yungon-dong, Chongro-gu

country: South Korea

institute: Seoul National University College of Medicine

description: Female Normal Sample

data_processing: BeadStudio software v3.2

source_name: whole blood

extract_protocol: Genomic DNA purification was done by DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). The EZ DNA methylation kit (Zymo Research, Irvine, CA) was utilized for bisulfite conversion of blood DNA samples, using 500 ng as the input amount. DNA amplification, hybridization, and allele-specific extension for Beadchip array procedure were performed according to the manufacturers protocol.

value: Female

tag: tissue

value: whole blood

tag: disease state


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#2702
9T_Cy5 vs. 9N_Cy3

source_name: Primary tumor_#2702

source_name: matched normal blood_#2702


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#1711
3T_Cy5 vs. 3N_Cy3

source_name: Primary tumor_#1711

source_name: matched normal blood_#1711


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#1960
11T_Cy5 vs. 11N_Cy3

source_name: Primary tumor_#1960

source_name: matched normal blood_#1960


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#1763
8N_Cy5 vs. 8T_Cy3 (Dye swap)

source_name: matched normal blood_#1763

source_name: Primary tumor_#1763


title: Sample5_TCDD_D10_n2

description:
Independent experiment 2
TCDD exposed differentiated adipocytes Day 10

source_name: Bone-marrow derived hMSCs from 43-years-old black male


title: Sample12_TBT_D10_n1

description:
Independent experiment 1
TBT exposed differentiated adipocytes Day 10


title: genomic DNA from  female control 5

description: Female Normal Sample


description:
Primary Tumor vs matched normal blood_Cervical cancer patient_#854
5T_Cy5 vs. 5N_Cy3

source_name: Primary tumor_#854

source_name: matched normal blood_#854


title: Sample13_TBT_D10_n2

description:
Independent experiment 2
TBT exposed differentiated adipocytes Day 10


title: Sample6_TCDD_D10_n3

description:
Independent experiment 3
TCDD exposed differentiated adipocytes Day 10


title: Sample4_TCDD_D10_n1

description:
Independent experiment 1
TCDD exposed differentiated adipocytes Day 10


title: GIST_imatinib45w_rep1

description: Gene expression of GIST cell line exposed to imatinib for 45 weeks.

source_name: GIST cell line, derived from T1, exposed to imatinib for 45 weeks

tag: cell line

value: 45 weeks


title: genomic DNA from  female control 4

description: Female Normal Sample


title: GIST_imatinib20w_rep1

description: Gene expression of GIST cell line exposed to imatinib for 20 weeks.

source_name: GIST cell line, derived from T1, exposed to imatinib for 20 weeks

value: 20 weeks


title: genomic DNA from  female control 2

description: Female Normal Sample

value: control


title: genomic DNA from  female control 3

description: Female Normal Sample


title: GIST_imatinib7w_rep1

description: Gene expression of GIST cell line exposed to imatinib for 7 weeks.

source_name: GIST cell line, derived from T1, exposed to imatinib for 7 weeks

value: gastrointestinal stromal tumor (GIST) cell line

value: 7 weeks


title: genomic DNA from  female SLE patient 4

description: Female SLE patient Sample

value: systemic lupus erythematosus


title: genomic DNA from  female control 1

description: Female Normal Sample


title: genomic DNA from  female SLE patient 6

description: Female SLE patient Sample


title: reference male mouse6/ 20mGyV6

source_name: reference male mouse6

tag: strain

value: tail


title: 04-1618

status: Public on Dec 26 2016

city: Pescara

first: Anna

middle: Concetta

last: Berardi

address: Via Fonte Romana 8

country: Italy

institute: Hospital Santo Spirito

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos. Within-array normalization occured by quantile normalization.

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: According to the available RNA amount 0.5 µg otal RNA from the samples 04-1618, 08-1148 and 02-1490C, 0.8 µg total RNA from the samples 95-719, 11-930 and 04-217C, 1.5 µg total RNA from the sample 11-2088C, 1.8 µg total RNA from the sample 98-230 and 2 µg total RNA from the remaining samples were used for labeling. The respective total RNA as well as 2 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

extract_protocol: Total RNA was isolated from human FFPE tissue samples (slices) with the use of the miRNeasy® FFPE Kit (Qiagen). RNA quality and integrity were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified with the Qubit® flurometer (Life Technologies).

treatment_protocol: The eligibility criteria of the patients enrolled in this study were as follows: diagnosis of ES according to the WHO classification; age younger than 40 years; no starting therapy; no evidence of metastasis.

tag: reference type

value: synthetic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus


title: 20mGyV6/ reference male mouse6


title: genomic DNA from  female SLE patient 5

description: Female SLE patient Sample

source_name: whole blood


title: genomic DNA from  female SLE patient 2

description: Female SLE patient Sample


title: GIST_parent_rep1

description:
Gene expression of GIST sample. T1 is a marketed cell line:
http://www.cosmobio.co.jp/export_e/products/detail/gist-t1_culture_kit.asp?entry_id=12717

source_name: GIST cell line from patient


title: 11-930


title: 95-719


title: genomic DNA from  female SLE patient 1

description: Female SLE patient Sample


title: 20mGyV5/ reference male mouse6


title: genomic DNA from  female SLE patient 3

description: Female SLE patient Sample


title: 02-1490 C

source_name: control

value: normal mesenchymal stromal cells


title: 08-1148


title: 98-230


title: 05-53


title: 96-409


title: 96-484


title: 95-328


title: 07-2145


title: 03-81


title: 08-1709 C


title: 98-385


title: 09-332 C


title: 01-273


title: 04-1995


title: 10-1179


title: 05-1324


title: 95-627


title: reference male mouse6/ 20mGyV5


title: 07-627


title: 02-1493


title: reference male mouse6/ 20mGyV3


title: PBMC-300-1h-repeat1 - mAdbID:82147

city: Doha

first: Francesco

middle: Maria

last: Marincola

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

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 82147

hyb_protocol: Sample Hybridization Protocol Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt's blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.12 Temperature: 28.71

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Briefly, the raw data set was filtered according to standard procedure to exclude spots with minimum intensity that arbitrarily was set to an intensity parameter of 200 for in both fluorescence channels. If the fluorescence intensity of one channel was great than 200 and that of the other but was below 200, the fluorescence of the low intensity channel was arbitrarily set to 200. Spots with diameters < 20um and flagged spots were also excluded from the analyses. Then, the filtered data were normalized using Lowess Smoother for gene expression microarray.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 labelling protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted using RNeasy Mini kit (Qiagen, Valencia, CA).

value: Peripheral Blood Mononuclear Cell (PBMC)

tag: sample pooling protocol

value: Total RNA from PBMCs pooled from six normal donors was extracted and amplified into aRNA to serve as the reference.

label_protocol:
Cy5 labelling protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

treatment_protocol:
Treatment type: compound
Agent: glucose
Treatment dose: 16.7 mM
Treatment time: 1 hour
Treatment temperature: 37 C
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 2h, and then stimulated with 16.7 mM glucose for 1h under 5% CO2 and 95% humidity.

value: blood

value: peripheral blood mononuclear cells (PBMC)

tag: agent

value: glucose

tag: treatment time

value: 1 hour


title: PBMC-300-1h-repeat2 - mAdbID:82138

description: mAdb experiment ID: 82138

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 5.19 Temperature: 27.09


title: PBMC-30-24h-repeat2 - mAdbID:82134

description: mAdb experiment ID: 82134

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 3.99 Temperature: 29.04

treatment_protocol:
Treatment type: compound
Agent: glucose
Treatment dose: 1.67 mM
Treatment time: 24 hours
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 2h, and then cultured with 1.67 mM glucose for 24h under 5% CO2 and 95% humidity.

value: 24 hours


title: PBMC-30-1h-repeat1 - mAdbID:82146

description: mAdb experiment ID: 82146

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.97 Temperature: 29.87

treatment_protocol:
Treatment type: compound
Agent: glucose
Treatment dose: 1.67 mM
Treatment time: 1 hour
Treatment temperature: 37 C
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 2h, and then cultured with 1.67 mM glucose for 1h under 5% CO2 and 95% humidity.


title: PBMC-300-24h-repeat2 - mAdbID:82143

description: mAdb experiment ID: 82143

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.98 Temperature: 29.68

treatment_protocol:
Treatment type: compound
Agent: glucose
Treatment dose: 16.7 mM
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 24h, and then stimulated with 16.7 mM glucose for 24h under 5% CO2 and 95% humidity.


title: PBMC-30-1h-repeat2 - mAdbID:82133

description: mAdb experiment ID: 82133

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.08 Temperature: 28.86


title: PBMC-30-2h-repeat1 - mAdbID:82131

description: mAdb experiment ID: 82131

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 5.09 Temperature: 27.91

treatment_protocol:
Agent: glucose
Treatment dose: 1.67 mM
Treatment time: 2 hours
Treatment temperature: 37 C
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 2h, and then cultured with 1.67 mM glucose for 2h under 5% CO2 and 95% humidity.

value: 2 hours


title: 20mGyV4/ reference male mouse6

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).


title: PBMC-300-2h-repeat1 - mAdbID:82132

description: mAdb experiment ID: 82132

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.17;; 5.19 Temperature: 26.66

treatment_protocol:
Treatment type: compound
Agent: glucose
Treatment dose: 16.7 mM
Treatment time: 2 hours
Treatment temperature: 37 C
In-vitro treatment: Human cells were first incubated with 3.34 mM glucose in serum-free RPMI medium for 2h, and then stimulated with 16.7 mM glucose for 2h under 5% CO2 and 95% humidity.

value: pancreas

value: islets


title: 20mGyV2/ reference male mouse6


title: PBMC-30-24h-repeat1 - mAdbID:82125

description: mAdb experiment ID: 82125

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.97 Temperature: 30.23


title: PBMC-300-24h-repeat1 - mAdbID:82126

description: mAdb experiment ID: 82126

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.97 Temperature: 30.05


title: Islet-30-24h-repeat4 - mAdbID:80407

description: mAdb experiment ID: 80407

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.57 Temperature: 30.36


title: 20mGyV3/ reference male mouse6


title: 04-1332


title: Islet-300-1h-repeat5 - mAdbID:80408

description: mAdb experiment ID: 80408

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.24;; 4.16 Temperature: 29.07


title: Islet-300-24h-repeat5 - mAdbID:80406

description: mAdb experiment ID: 80406

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 5.02 Temperature: 31.7


title: PBMC-30-2h-repeat2 - mAdbID:82130

description: mAdb experiment ID: 82130

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.19;; 5.16 Temperature: 27.46


title: PBMC-300-2h-repeat2 - mAdbID:82142

description: mAdb experiment ID: 82142

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.03 Temperature: 29.2


title: reference male mouse6/ 20mGyV2


title: Islet-30-1h-repeat4 - mAdbID:80381

description: mAdb experiment ID: 80381

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.01 Temperature: 29.38


title: reference male mouse6/ 20mGyVM


title: Islet-30-2h-repeat5 - mAdbID:80382

description: mAdb experiment ID: 80382

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.92 Temperature: 31.85


title: 20mGyVF/ reference male mouse6


title: reference male mouse6/ 20mGyV4


title: Hepatocyte-300-24h-repeat2 - mAdbID:78184

description: mAdb experiment ID: 78184

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 3.96 Temperature: 28.65

value: liver

value: hepatocyte (Lonza, Walkersville, MD)


title: 20mGyVM/ reference male mouse6


title: Hepatocyte-300-1h - mAdbID:78166

description: mAdb experiment ID: 78166

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 3.98 Temperature: 27.67


title: Hepatocyte-30-1h - mAdbID:78165

description: mAdb experiment ID: 78165

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.96 Temperature: 28.86


title: Islet-300-2h-repeat3 - mAdbID:78132

description: mAdb experiment ID: 78132

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 3.96 Temperature: 27.91


title: Hepatocyte-300-2h - mAdbID:78168

description: mAdb experiment ID: 78168

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.16;; 5 Temperature: 24.07


title: 04-217 C

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).


title: reference male mouse6/ 20mGyV1

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).


title: 20mGyV1/ reference male mouse6


title: Hepatocyte-30-24h-repeat2 - mAdbID:78094

description: mAdb experiment ID: 78094

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 4.98 Temperature: 25.41


title: Islet-300-1h-repeat4 - mAdbID:78098

description: mAdb experiment ID: 78098

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.19;; 4.67 Temperature: 26.2


title: Islet-30-24h-repeat3 - mAdbID:78097

description: mAdb experiment ID: 78097

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 4.86 Temperature: 25.78


title: Islet-300-24h-repeat4 - mAdbID:78136

description: mAdb experiment ID: 78136

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.17;; 5.1 Temperature: 24.95


title: Islet-30-2h-repeat4 - mAdbID:78096

description: mAdb experiment ID: 78096

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.47 Temperature: 26.75


title: reference male mouse6/ 20mGyVF


title: Adult 18 (9965280062_L)

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

institute: University of Oxford

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalised using robust-spline normalisation

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

extract_protocol: RNA was extracted from PAXgene tubes using PAXgene RNA extraction kit, and globin depleted using GLOBINclear™

treatment_protocol: PAXgene tubes. Baseline is pre-vaccination. Post-vaccinatio is 7 days post first vaccination. Post-booster is 7 days post second (booster) vaccination. Vaccine group 1 is first vaccination with Menveo (intramuscular), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 3 is first vaccination with ACWYVax (subcutaneous), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 4 is first vaccination with ACWYVax (1/5th dose intramuscular), followed by Menveo (intramuscular) booster 28 days later.Vaccine group 2 is first vaccination with ACWYVax (intramuscular), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 3 is first vaccination with ACWYVax (subcutaneous), followed by Menveo (intramuscular) booster 28 days later. Vaccine group 4 is first vaccination with ACWYVax (1/5th dose intramuscular), followed by Menveo (intramuscular) booster 28 days later.

tag: sample time

value: Post booster

tag: vaccine group

tag: adult


title: Adult 17 (9965280062_K)

value: Baseline


title: Adult 1 (9965280062_G)

value: Post vaccination


title: Adult 19 (9965280062_I)


title: Adult 19 (9965280062_J)


title: Adult 3 (9965280062_F)


title: Islet-300-24h-repeat3 - mAdbID:77647

description: mAdb experiment ID: 77647

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.35 Temperature: 26.39


title: Adult 7 (9965280062_E)


title: Hepatocyte-30-2h-repeat2 - mAdbID:78093

description: mAdb experiment ID: 78093

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.35 Temperature: 27.21


title: Adult 4 (9965280062_H)


title: Islet-30-24h-repeat2 - mAdbID:77641

description: mAdb experiment ID: 77641

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 5.16 Temperature: 25.99


title: Islet-300-1h-repeat3 - mAdbID:77580

description: mAdb experiment ID: 77580

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4 Temperature: 27.33


title: Islet-30-2h-repeat3 - mAdbID:77565

description: mAdb experiment ID: 77565

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.03 Temperature: 28.77


title: Islet-300-2h-repeat2 - mAdbID:77587

description: mAdb experiment ID: 77587

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.36 Temperature: 27.64


title: Adult 4 (9879671105_L)


title: Islet-30-1h-repeat2 - mAdbID:77564

description: mAdb experiment ID: 77564

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.26;; 3.93 Temperature: 29.44


title: Adult 9 (9965280062_C)


title: Fibroblast-300-24h - mAdbID:77500

description: mAdb experiment ID: 77500

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.7 Temperature: 26.69

value: lung

value: fibroblasts (ATCC, Manassas, VA)


title: ILC3_WT

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: This is wild-type ILC3s

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing:
 Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.
high quality expression values (for example, where at least 1 out of 2 samples have values within cut-off, cut-off =100) will be selected for analysis. Then differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups. Hierarchical clustering was performed using R scripts. GO analysis and Pathway analysis were performed using the standard enrichment computation methods.

source_name: Wild-type ILC3s

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: TRIZOL reagent (TRIzol Plus RNA Purification Kit, Invitrogen life technologies)

tag: genotype

value: Wild-type


title: ILC3_KO

description: This is lncKdm2b-deficient ILC3s

source_name: lncKdm2b knockout ILC3s

value: lncKdm2b deletion


title: Adult 2 (9879671105_J)


title: Adult 15 (9965280062_A)


title: Adult 6 (9879671105_G)


title: Islet-30-1h-repeat3 - mAdbID:78095

description: mAdb experiment ID: 78095

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 3.95 Temperature: 28.37

value: Peripheral Blood Mononuclear Cell (PBMC)

value: Total RNA from PBMCs pooled from six normal donors was extracted and amplified into aRNA to serve as the reference.


title: Adult 2 (9879671105_K)


title: Adult 14 (9879671105_F)


title: Adult 11 (9879671105_B)


title: Adult 19 (9879671105_H)


title: Adult 1 (9879671105_D)


title: Adult 12 (9965280062_D)


title: Fibroblast-30-1h - mAdbID:77469

description: mAdb experiment ID: 77469

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.34 Temperature: 27.61

value: glucose


title: Adult 14 (9879671105_I)


title: Fibroblast-30-2h - mAdbID:77470

description: mAdb experiment ID: 77470

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.84 Temperature: 25.62


title: Adult 8 (9879671105_A)


title: Adult 8 (9879671105_C)


title: Adult 20 (9879671133_L)


title: Adult 15 (9879671105_E)


title: Adult 5 (9879671133_K)


title: Adult 4 (9879671133_I)


title: Adult 16 (9879671133_J)


title: Adult 12 (9879671133_F)


title: Adult 1 (9879671133_G)


title: Fibroblast-300-2h - mAdbID:77383

description: mAdb experiment ID: 77383

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 5.02 Temperature: 26.3


title: Islet-30-2h-repeat2 - mAdbID:76818

description: mAdb experiment ID: 76818

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.33;; 4.12 Temperature: 30.69


title: Adult 20 (9879671133_B)


title: Islet-300-24h-repeat1 - mAdbID:76817

description: mAdb experiment ID: 76817

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.75 Temperature: 26.24


title: Hepatocyte-30-2h-repeat1 - mAdbID:76750

description: mAdb experiment ID: 76750

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.3;; 4.92 Temperature: 28.46


title: Adult 7 (9879671133_D)

scan_protocol: Standard Illumina scanning protocol


title: Islet-300-2h-repeat1 - mAdbID:76827

description: mAdb experiment ID: 76827

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.34;; 4.05 Temperature: 30.97


title: Hepatocyte-300-24h-repeat1 - mAdbID:76774

description: mAdb experiment ID: 76774

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 33 LaserPower: 3.37;; 3.45 Temperature: 27.39


title: Adult 18 (9879671133_E)


title: Fibroblast-30-24h - mAdbID:77366

description: mAdb experiment ID: 77366

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.39 Temperature: 27.43


title: Hepatocyte-30-24h-repeat1 - mAdbID:76751

description: mAdb experiment ID: 76751

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.34;; 3.94 Temperature: 31.3


title: Adult 9 (9879671133_C)


title: Adult 5 (9879671133_A)


title: Islet-30-2h-repeat1 - mAdbID:76772

description: mAdb experiment ID: 76772

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.98 Temperature: 27.09


title: Adult 2 (9965280031_L)


title: Adult 10 (9965280031_C)


title: Adult 13 (9879671133_H)


title: Islet-300-1h-repeat1 - mAdbID:76738

description: mAdb experiment ID: 76738

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 100;; 33 LaserPower: 3.37;; 3.43 Temperature: 27.03

value: 1 hour


title: Adult 8 (9965280031_B)


title: Adult 11 (9965280031_D)


title: Adult 3 (9965280031_G)


title: Adult 15 (9965280031_H)


title: Islet-30-1h-repeat1 - mAdbID:76773

description: mAdb experiment ID: 76773

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.33;; 4.17 Temperature: 30.14


title: Adult 11 (9965280031_K)


title: Adult 10 (9965280031_F)


title: Adult 20 (9965280031_E)


title: Adult 6 (9965280031_A)


title: Adult 6 (9879671086_L)


title: Adult 5 (9965280031_J)


title: Islet-300-1h-repeat2 - mAdbID:76708

description: mAdb experiment ID: 76708

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.34;; 4.13 Temperature: 30.9


title: Islet-300-24h-repeat2 - mAdbID:76721

description: mAdb experiment ID: 76721

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.33;; 4.35 Temperature: 30.57

value: 24 hours


title: Adult 10 (9879671086_D)


title: Adult 16 (9965280062_B)


title: Islet-30-24h-repeat1 - mAdbID:76687

description: mAdb experiment ID: 76687

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.34;; 3.96 Temperature: 31.06


title: Adult 17 (9879671086_J)


title: Adult 14 (9879671086_G)


title: Adult 3 (9879671086_K)


title: Adult 13 (9879671086_B)


title: Adult 9 (9879671086_C)


title: Adult 13 (9879671086_E)


title: PGC_dev9_rep4

status: Public on Dec 25 2016

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

description: PGCs (AEL:13h20m - 16h20m), biological replicate 4

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/5-screw Hyb Chamber). See manufacturer's manual (#G4140-90010).

scan_protocol: Scanned using Agilent microarray scanner (G2565BA)

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization

organism: Drosophila melanogaster

source_name: PGC, stage: 13h20m - 16h20m AEL

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Protocol. 100ng of total RNA was used.

growth_protocol: incubated at 25C

extract_protocol: Total RNA extracted using RNeasy (QIAGEN) manufacturer's instructions

treatment_protocol: Embryo cells were dissociated by Tripsin treatment and then subjected to FACS sorting

value: primordial germ cells

tag: developmental stage

value: EGFP-vasa

source_name: poole whole embryos

value: whole embryos

value: 0 - 24h AEL


title: Adult 16 (9879671086_I)


title: Adult 7 (9879671086_F)


title: PGC_dev8_rep4

description: PGCs (AEL:11h20m - 13h20m), biological replicate 4

source_name: PGC, stage: 11h20m - 13h20m AEL


title: PGC_dev2_rep4

description: PGCs (AEL:2h20m - 3h20m), biological replicate 4

source_name: PGC, stage: 2h20m - 3h20m AEL

value: 2h20m - 3h20m AEL


title: PGC_dev7_rep4

description: PGCs (AEL:9h20m - 11h20m), biological replicate 4

source_name: PGC, stage: 9h20m - 11h20m AEL


title: Adult 17 (9879671086_A)

value: Post booster


title: PGC_dev5_rep4

description: PGCs (AEL:5h20m - 7h20m), biological replicate 4

source_name: PGC, stage: 5h20m - 7h20m AEL

value: 5h20m - 7h20m AEL


title: PGC_dev1_rep4

description: PGCs (AEL:1h20m - 2h20m), biological replicate 4

source_name: PGC, stage: 1h20m - 2h20m AEL

value: 1h20m - 2h20m AEL


title: PGC_dev10_rep3

description: PGCs (AEL:16h20m - 19h20m), biological replicate 3

source_name: PGC, stage: 16h20m - 19h20m AEL