title: Control_0ngL_MaleBrain_96h_253657410258_1_2_X.txt


title: EE2_0.1ngL_MaleBrain_96h_253657410257_1_2_X.txt

status: Public on Jan 08 2017

type: RNA

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

country: USA

institute: US EPA

description: chemical abbreviations: EE2, 17a-ethynyl estradiol;  DMSO, Dimethyl sulfoxide

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: Agilent Technologies Scanner G2505B was used to scan microarray images at 3 or 5 µm resolution

data_processing:
Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data pre-processing and analysis related to the identification of differentially expressed genes (DEGs) were based on individual chemical conditions and their conrresponding controls using the R package Limma, in the order of backgroundCorrect("normexp"), normalizeBetweenArrays("quantile"), and modified t-test. A subset of DEGs from each chemical treatment condition was then selected as a gene signature.  Individual chemical-treated microarray samples were also processed into rank-ordered gene lists (ROGLs) relative to their approriate controls.  This collection of ROGLs was subsequently interrogated by gene signatures computationally so their underlying chemical conditions could be connected.
supplementary files: log2 intensity after backgroundCorrect("normexp") and normalizeBetweenArrays("quantile") in Limma; various types of control probes were filtered

molecule: total RNA

organism: Pimephales promelas

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Fry and sexually mature adult fathead minnows (5-7 month old) were obtained from an on-site aquatic culture facility at the US EPA Ecological Exposure Research Division, Cincinnati, Ohio, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol: Exposures were conducted in an either static or flow-through system.  To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of water (4 µM filtered, UV sterilized) or test chemical dissolved in water and/or DMSO carrier. There were multiple tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.

tag: chemical

tag: dose

tag: tissue

value: MaleBrain

tag: exposure duration

tag: age

value: 5-7 month

tag: arrayname

tag: featureextractiontime

tag: featureextractionsoftwareversion

tag: experimentid


title: Patient 12 primary tumor

city: Barcelona

first: Juan

middle: Miguel

last: Cejalvo

state: Barcelona

address: Carrer Villaroel 170

department: Oncology

country: Spain

institute: Hospital Clinic Barcelona

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protcol. Detection probres were provided by the manufacturer and were labeled with a propierty flourescent barcode system

scan_protocol: Scaning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files. The data were normalized using 5 HK genes. Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detecction probe and counted by a confocal system

organism: Homo sapiens

source_name: Breast cancer

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO's Translational Genomics Group

extract_protocol: A section of FFPE breast tissue was firs examined with a hematoxylin and eosin staining to confirm the diagnosis and determine the tumor surface area. For RNA purification, three 10um FFPE slides were cut for each tumor, and macrodissection was performed, when needed, to avoid normal breast contamination. A minimum of 100 ng of total RNA was used to measure the expression of 105 breast cancer-related genes and 5 house-keeping genes (ACTB, MRPL19, PSMC4, RLP0 and SF3A1)

tag: individual

value: Patient 12

value: Primary tumor

tag: age_dx primary tumor

tag: time to recurrence

tag: overall survival metastatic (months)

tag: intrinsic subtype breast cancer

value: LumB


title: Patient 11 primary tumor

value: Patient 11


title: Patient 12 metastatic tumor

value: Metastatic tumor

tag: age_dx metastatic tumor

tag: metastatic site

value: Bone


title: Patient 11 metastatic tumor

value: Lung


title: EE2_0.1ngL_MaleBrain_96h_253657410253_1_4_X.txt


title: Control_0ngL_MaleBrain_96h_253657410282_2_4_X.txt

value: Control


title: Control_0ngL_MaleBrain_96h_253657410258_2_3_X.txt


title: Patient 13 metastatic tumor

value: Patient 13

value: Liver


title: Patient 10 primary tumor

value: Patient 10

value: LumA


title: Patient 8 primary tumor

value: Patient 8


title: Patient 8 metastatic tumor

value: Skin


title: Patient 7 primary tumor

value: Patient 7

value: Normal


title: Control_0ngL_MaleBrain_96h_253657410257_2_4_X.txt

value: MaleBrain

value: 5-7 month


title: Patient 10 metastatic tumor


title: Patient 9 primary tumor

value: Patient 9

value: Primary tumor


title: Control_0ngL_MaleBrain_96h_253657410257_1_1_X.txt


title: Control_0ngL_MaleBrain_96h_253657410253_1_3_X.txt


title: Control_0ngL_MaleBrain_96h_253657410254_2_4_X.txt


title: Control_0ugL_Larvae_48h_253657410282_1_1_.txt

value: Larvae

value: 48h post hatch

value: transition


title: Control_0ugL_Larvae_48h_253657410270_2_2_2.txt


title: Control_0ugL_Larvae_48h_253657410282_2_3_.txt


title: Control_0ngL_MaleBrain_96h_253657410254_1_2_X.txt


title: Control_0ugL_Larvae_48h_253657410270_1_4_3.txt


title: Patient 6 primary tumor

value: Patient 6

value: LumB


title: Patient 7 metastatic tumor

value: Metastatic tumor

value: Lymph nodes


title: Patient 6 metastatic tumor

value: Bone


title: Patient 4 primary tumor

value: Patient 4


title: Patient 5 metastatic tumor

value: Patient 5

value: Pleura


title: Patient 9 metastatic tumor

value: Liver


title: Patient 5 primary tumor

value: LumA


title: Control_0ugL_Larvae_48h_253657410270_1_2_1.txt

value: Control


title: Patient 4 metastatic tumor


title: Patient 3 primary tumor

value: Patient 3


title: Patient 3 metastatic tumor

value: Skin


title: Patient 2 primary tumor

value: Patient 2

value: Primary tumor


title: Control_0ugL_Larvae_48h_253657410269_2_4_2.txt

value: Larvae

value: 48h post hatch


title: Patient 2 metastatic tumor


title: Control_0ugL_Larvae_48h_253657410269_2_3_1.txt

value: transition


title: Control_0ugL_Larvae_48h_253657410269_2_1_2.txt


title: Patient 1 metastatic tumor

value: Patient 1

value: Basal

value: Lung


title: Control_0ugL_Larvae_48h_253657410269_1_3_3.txt


title: Control_0ugL_Larvae_48h_253657410267_2_1_1.txt


title: Patient 1 primary tumor


title: Control_0ugL_Larvae_48h_253657410269_1_1_1.txt


title: Control_0ugL_Larvae_48h_253657410268_1_4_2.txt


title: Control_0ugL_Larvae_48h_253657410268_2_2_1.txt


title: Control_0ugL_Larvae_48h_253657410267_2_3_3.txt


title: Control_0ugL_Larvae_48h_253657410268_2_4_3.txt


title: Control_0ugL_Larvae_48h_253657410266_2_4_2.txt


title: Control_0ugL_Larvae_48h_253657410265_2_3_2.txt


title: Control_0ugL_Larvae_48h_253657410264_2_2_2.txt


title: Control_0ugL_Larvae_48h_253657410264_2_4_1.txt


title: Control_0ugL_Larvae_48h_253657410267_1_3_2.txt


title: Control_0ugL_Larvae_48h_253657410266_2_2_3.txt


title: Control_0ugL_Larvae_48h_253657410265_1_1_2.txt


title: Control_0ugL_Larvae_48h_253657410264_1_4_3.txt


title: Control_0ugL_Larvae_48h_253657410265_1_3_1.txt


title: Control_0ugL_Larvae_48h_253657410264_1_2_1.txt


title: Control_0ugL_Larvae_48h_253657410266_1_2_2.txt


title: Control_0ugL_Larvae_48h_253657410266_1_4_1.txt


title: Control_0ugL_Larvae_48h_253657410263_2_1_2.txt


title: Control_0ugL_Larvae_48h_253657410265_2_1_3.txt


title: Control_0ugL_Larvae_48h_253657410263_1_3_3.txt


title: Control_0ugL_Larvae_48h_253657410263_1_1_1.txt


title: Control_0ugL_Larvae_48h_253657410263_2_3_1.txt


title: Control_0ugL_Larvae_48h_253657410267_1_1_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410282_1_4_.txt

value: Bifenthrin


title: Bifenthrin_1.6ugL_Larvae_48h_253657410270_2_4_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410269_1_2_2.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410269_2_2_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410270_2_3_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410268_1_1_2.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410270_1_3_2.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410268_2_1_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410270_1_1_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410269_1_4_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410267_1_4_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410265_2_4_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410267_2_4_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410266_2_3_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410266_1_3_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410268_1_3_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410266_1_1_1.txt


title: Identification of miR-499a-5p target genes in PC3

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

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

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

tag: cell line

tag: cell type

value: prostate cancer

tag: transfection

value: no transfection

source_name: miR-499a-5p transfected cell line


title: Identification of miR-499a-5p target genes in PC3M


title: Bifenthrin_1.6ugL_Larvae_48h_253657410266_2_1_2.txt

tag: chemical

tag: dose

tag: tissue


title: Bifenthrin_1.6ugL_Larvae_48h_253657410265_1_2_3.txt

tag: exposure duration

tag: age

tag: arrayname


title: Identification of miR-148a-5p target genes in SW1990

value: pancreatic cancer

source_name: miR-148a-5p transfected cell line


title: Bifenthrin_1.6ugL_Larvae_48h_253657410265_1_4_2.txt

tag: featureextractiontime

tag: featureextractionsoftwareversion

tag: experimentid


title: Identification of miR-455-3p target genes in PC3

source_name: miR-455-3p transfected cell line


title: Bifenthrin_1.6ugL_Larvae_48h_253657410267_1_2_1.txt


title: Identification of miR-455-5p target genes in PC3

source_name: miR-455-5p transfected cell line


title: Identification of miR-148a-3p target genes in SW1990

source_name: miR-148a-3p transfected cell line


title: Bifenthrin_1.6ugL_Larvae_48h_253657410267_2_2_2.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410265_2_2_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410263_2_2_3.txt


title: Differentially expressed genes by knocking down of ANLN-2 in PANC-1

source_name: si-ANLN-2 transfected cell line


title: Bifenthrin_1.6ugL_Larvae_48h_253657410264_2_3_3.txt


title: Identification of miR-148a-5p target genes in PANC-1


title: Bifenthrin_1.6ugL_Larvae_48h_253657410264_1_1_3.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410264_1_3_2.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410263_1_4_1.txt


title: Identification of miR-148a-3p target genes in PANC-1


title: Bifenthrin_1.6ugL_Larvae_48h_253657410264_2_1_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410270_2_1_1.txt


title: Bifenthrin_1.6ugL_Larvae_48h_253657410263_1_2_2.txt


title: Identification of miR-150-5p target genes in TE-8

value: esophageal cancer

source_name: miR-150-5p transfected cell line


title: Identification of miR-150-5p target genes in A549

value: lung adenocarcinoma


title: Identification of miR-150-3p target genes in A549

source_name: miR-150-3p transfected cell line


title: Identification of miR-10a-5p target genes in A-498

value: renal cell carcinoma

source_name: miR-10a-5p transfected cell line


title: Identification of miR-10a-5p target genes in 786-O


title: Differentially expressed genes by knocking down of ANLN-1 in PANC-1

source_name: si-ANLN-1 transfected cell line


title: Identification of miR-150-3p target genes in TE-8


title: VillousCyto_early_rep_6

status: Public on Jan 07 2017

type: genomic

city: Paris

first: Akpeli

middle: V.

last: Nordor

address: 26, rue d'Ulm

department: Département de Recherche Translationnelle

country: France

institute: Institut Curie - PSL Research University

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 6
SAMPLE 12

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to the Illumina HumanMethylation450 BeadChip using the standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan on a two-color channel

data_processing: GenomeStudio (Illumina) and R software

label: Cy5 and Cy3

molecule: genomic DNA

source_name: first trimester placenta

label_protocol: Standard Illumina protocol for HumanMethylation450 BeadChip

extract_protocol: DNA was extracted using the manufacturer's recommended protocol conversion

value: chorionic villus

tag: cell population

value: villous cytotrophoblasts

tag: sample type

value: genomic

tag: gestational age (weeks)

tag: dna quantity (ng)

tag: date


title: VillousCyto_late_rep_10

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 10
SAMPLE 19


title: VillousCyto_late_rep_9

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 9
SAMPLE 18


title: Bifenthrin_1.6ugL_Larvae_48h_253657410263_2_4_2.txt


title: VillousCyto_late_rep_7

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 7
SAMPLE 16


title: VillousCyto_late_rep_5

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 5
SAMPLE 9


title: VillousCyto_late_rep_6

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 6
SAMPLE 11


title: VillousCyto_early_rep_4

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 4
SAMPLE 8


title: liver_WT_ZT8_rep2

city: Philadelphia

first: Anna

last: King

state: PA

address: 3400 Civic Center Boulevard Building 421

institute: University of Pennsylvania

hyb_protocol: Protocols were conducted as described in the Affymetrix WT Plus Reagent Kit Manual and the Affymetrix GeneChip Expression Analysis Technical Manual. Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Raw CEL files were analyzed with the RMA algorithm (Irizarry, 2003) implemented in the affy package in Bioconductor in R (R 2.14.2) (Gautier et al., 2004)

label: biotin

organism: Mus musculus

source_name: WT, liver at ZT8, biological replicate 2

label_protocol: Biotinylation by terminal transferase end labeling

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified using Qiagen RNeasy Mini Kit. 250ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence. Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA and fragmented.

tag: genotype

value: Wild type

tag: zeitgeber time


title: VillousCyto_early_rep_7

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 7
SAMPLE 13


title: VillousCyto_early_rep_5

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 5
SAMPLE 10


title: VillousCyto_early_rep_2

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 2
SAMPLE 4


title: VillousCyto_late_rep_3

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 3
SAMPLE 5


title: liver_WT_ZT12_rep2

source_name: WT, liver at ZT12, biological replicate 2


title: VillousCyto_early_rep_9

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 9
SAMPLE 15


title: liver_WT_ZT16_rep2

source_name: WT, liver at ZT16, biological replicate 2


title: liver_WT_ZT4_rep2

source_name: WT, liver at ZT4, biological replicate 2


title: VillousCyto_late_rep_8

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 8
SAMPLE 17


title: liver_WT_ZT0_rep2

source_name: WT, liver at ZT0, biological replicate 2


title: VillousCyto_early_rep_1

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 1
SAMPLE 2


title: VillousCyto_late_rep_2

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 2
SAMPLE 3


title: RMAICC (CY5)_Gene Expression

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
US83000164_253530110001_S01_GE2_107_Sep09_1_1.txt
ICC (chickpea cultivar)

hyb_protocol: 3750ng of the labeled cRNA (1875 each of Cy3 and Cy5) were fragmented to an average size of approximately 50 to 100 nucleotides with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404).The samples were hybridized onto array (AMADID 35301). The hybridization was carried out at 65°C for 16 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 1 minute.

scan_protocol: The microarray slide was scanned using Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images Analysis using Agilent Feature Extraction Software to obtain raw data. Probe intensities generated from feature extraction raw data were split based on channel type and analysis was performed by applying 75th percentile shift normalization.

organism: Cicer arietinum

source_name: chickpea, ICC

label_protocol: The sample labeling was performed using Quick-Amp Labeling Kit, Two Color (Agilent Technologies, Part Number: 5190-0444). The control sample was labeled with Cy3 dye whereas test samples were labeled with Cy5 dye. 500ng of total RNA was denatured along with appropriate diluted Spike In controls; Spike A Mix for cyanine 3-CTP samples and spike B mix for Cyanine 5 CTP samples (Agilent Technologies, RNA Spike In Kit, One Color, Part Number 5188-5279) and Oligo dT primer tagged to T7 promoter primer mix at 65°C for 10 min followed by snap chilling on ice for 5 minutes. The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours. The cDNA sample was incubated at 65°C for 15 min in order to inactivate the enzymes. The in vitro transcription master mix was added to the cDNA sample and incubated at 40°C for 3 hours. The cDNA was in vitro transcribed into cRNA in presence of Cyanine 3-CTPdye for control samples and Cyanine 5-CTP for test samples. The labeled cRNA sample was purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The concentration of cRNA and dye incorporation were determined using Nanodrop-1000 (JH Bio)

extract_protocol: Total RNA extracted using Qiagen’s RNeasy minikit and Trizol method following manufacturer's instructions.

tag: cultivar

value: ICC

value: leaf


title: liver_WT_ZT12_rep1

source_name: WT, liver at ZT12, biological replicate 1


title: RMAICC (CY5)_CGH

description:
US83000164_253530110001_S01_CGH_107_Sep09_1_2.txt
ICC (chickpea cultivar)

hyb_protocol: 3800ng each of the Cy5-dUTP and Cy3-dUTP labeled sample were combined and salmon sperm DNA, Blocking agent and hybridization buffer were added to it. The total hybridization volume is 520ul. The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and incubated at 37oC for 30 minutes. The samples were hybridized onto the Agilent 2x400k array (AMADID 35301) at 65oC for 40 hours. 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 37oC for 1 minute.

label_protocol: DNA quality control test was performed using Nanodrop-1000 (JH Bio, USA) and an agarose gel to determine the quality, purity and quantity. 2 µg of DNA was taken in 20.2µl volume into a microfuge tube and 5.8µl of digestion master mix was added to it. The samples were incubated at 37oC for 2 hours followed by heat inactivation of enzymes at 65oC for 20 minutes. The digested DNA samples were labeled with Genomic DNA labeling kit. (Agilent Part No: 5190-0453). 5ul of Random primer mix was added to each of 26ul of digested sample. The DNA was denatured at 95oC for 3 minutes followed by snap chill at 4°C for 5 minutes. 19ul of labeling master mix containing Cy5-dUTP (for test/treated sample) or Cy3-dUTP(for control sample), dNTP, Buffer and Klenow, was added to the denatured DNA sample and incubated at 37oC for 2 hours followed by enzyme heat inactivation at 65oC for 10 minutes. The labeled samples were cleaned up using Amicon 30kDa (Millipore UFC 503096) filter size exclusion filter and eluted the sample from the column. 3800ng each of the Cy5-dUTP and Cy3-dUTP labeled sample were combined and salmon sperm DNA, Blocking agent and hybridization buffer were added to it. The total hybridization volume is 520ul. The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and incubated at 37oC for 30 minutes.

extract_protocol: DNA extracted was done using Trizol method following manufacturer's instructions.


title: RMAP (CY3)_Gene Expression

description:
US83000164_253530110001_S01_GE2_107_Sep09_1_1.txt
PI (chickpea cultivar)

source_name: chickpea, PI

value: PI


title: VillousCyto_early_rep_8

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 8
SAMPLE 14


title: GMAP (CY3)_CGH

description:
US83000164_253530110001_S01_CGH_107_Sep09_1_2.txt
PI (chickpea cultivar)


title: liver_WT_ZT0_rep1

source_name: WT, liver at ZT0, biological replicate 1


title: liver_WT_ZT20_rep1

source_name: WT, liver at ZT20, biological replicate 1


title: VillousCyto_late_rep_1

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 1
SAMPLE 1


title: VillousCyto_late_rep_4

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, after first contact with maternal blood, replicate 4
SAMPLE 7


title: CSC DLD1 3x2Gy irradiation replicate 1

city: Vilnius

first: Egle

last: Strainiene

state: Lithuania

address: P.Baublio 3b

country: Lithuania

institute: National Cancer Institute

description: DLD1 CSCs were cultivated under 3D cell culture and irradiated with fractionated 3x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 2.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Colorectal cancer DLD1 stem-like cells cultivated under 3D cell culture conditions, without irradiation

label_protocol: 500ng of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: iPSC CRL1831 and CSC DLD1 cells were cultured in DMEM: F-12 cell culture medium (Gibco) supplemented with 20% KnockOut Serum Replacement (Gibco), 1% Glutamax (ThermoSCIENTIFIC), 1% Non-essential amino acid (ThermoSCIENTIFIC), 50 µM β-mercapthoethanol (Sigma-Aldrich), 10 ng/ml b-FGF(ThermoSCIENTIFIC) (only in 2D cell cultures), 10 µM ROCK inhibitor (Y-27632, Sigma-Aldrich) (only in 2D cell cultures) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture conditions, cells were plated on 0.15 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose in a 96-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA MiniPrep kit (ZYMO RESEARCH) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Cell were treated with single (2 Gy) or fractionated (3x2 Gy) doses of ionizing radiation

tag: cell line

value: CSC DLD-1

tag: origin

value: Colorectal cancer

tag: treatment

value: Control

source_name: Colorectal cancer DLD1 stem-like cells cultivated under 3D cell culture conditions, irradiated with 3x2 Gy

value: fractionated dose of 3x2Gy


title: liver_WT_ZT16_rep1

source_name: WT, liver at ZT16, biological replicate 1


title: liver_WT_ZT4_rep1

source_name: WT, liver at ZT4, biological replicate 1


title: liver_WT_ZT8_rep1

source_name: WT, liver at ZT8, biological replicate 1


title: VillousCyto_early_rep_3

description:
villous cytotrophoblasts isolated ex vivo from chorionic villi, before first contact with maternal blood, replicate 3
SAMPLE 6

tag: tissue


title: CSC DLD1 3x2Gy irradiation replicate 2

description: DLD1 CSCs were cultivated under 3D cell culture and irradiated with fractionated 3x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 2.


title: liver_WT_ZT20_rep2

source_name: WT, liver at ZT20, biological replicate 2


title: liver_NPYKO_ZT8_rep2

source_name: NPY KO, liver at ZT8, biological replicate 2

value: NPY KO


title: liver_NPYKO_ZT16_rep2

source_name: NPY KO, liver at ZT16, biological replicate 2


title: liver_NPYKO_ZT12_rep2

source_name: NPY KO, liver at ZT12, biological replicate 2


title: CSC DLD1 replicate 2

description: DLD1 CSCs were cultivated under 3D cell culture, without irradiation. For differential gene expression analysis non-treated cells under 2D culture conditions served as a control. Biological replicate 2 of 2.

value: without irradiation


title: CSC DLD1 replicate 1

description: DLD1 CSCs were cultivated under 3D cell culture, without irradiation. For differential gene expression analysis non-treated cells under 2D culture conditions served as a control. Biological replicate 1 of 2.

source_name: Colorectal cancer DLD1 stem-like cells cultivated under 2D cell culture conditions, without irradiation


title: liver_NPYKO_ZT20_rep1

source_name: NPY KO, liver at ZT20, biological replicate 1


title: liver_NPYKO_ZT20_rep2

source_name: NPY KO, liver at ZT20, biological replicate 2


title: liver_NPYKO_ZT0_rep2

source_name: NPY KO, liver at ZT0, biological replicate 2


title: PIE cells + L.rhamnosus CRL1505 + Poly(I:C) challenge 12h

city: San Miguel de Tucumán

first: Julio

last: Villena

state: Tucumán

address: Chacabuco 145

country: Argentina

institute: CERELA-CONICET

description: Gene expression after 48h L. rhamnosus CRL1505 stimulation and 12h Poly(I:C) challenge

hyb_protocol: Hybridisation with Porcine (V2) Gene Expression Microarray (Agilent Technologies) was performed at Hokkaido System Science Co.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing:
Data normalization and expression analysis were performed with GeneSpring software version 6.1 (Agilent Technologies).
Expression data were considered significant when they differed at least 2 fold between treated and untreated PIE cells, and results are expressed as log2 scale (log2 ratio). Genes whose expressions were increased more than 2-fold (log2 > 1) after treatment with Poly(I:C) were selected

organism: Sus scrofa domesticus

source_name: PIE cells, L. rhamnosus CRL1505, 48h, Poly(I:C), 12h, replicate 1

label_protocol: Labelling was done as recommended by Agilent Technologies using 200 ng of RNA

growth_protocol: PIE cells, which are non-transformed intestinal cultured cells originally derived from intestinal epithelia isolated from an unsuckled neonatal swine, were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen Corporation, Carlsbad, CA) supplemented with 10% fetal calf serum (FCS), 100 mg/ml penicillin, and 100 U/ml streptomycin at 37°C in an atmosphere of 5% CO2. PIE cells were seeded at 3 x 104 cells/12-well plate on type I collagen-coated plates (Sumitomo Bakelite Co., Tokyo, Japan) and cultured for 3 days. Control medium or lactobacilli (5 x 108 cells/ml) were added and 48 h later, cells were stimulated with Poly(I:C) (60 ng/ml). 12 h after Poly(I:C) stimulation total RNA was extracted for microarray studies.

extract_protocol: Total RNA was isolated from PIE cells samples using PureLink RNA Mini Kit (life technologies inc. gaithersburg md) with DNase. RNA integrity of all samples were evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), using the RNA 6000 Nano Kit.

value: Porcine intestinal epitheliocytes-derived cell line

tag: age

value: 3 days


title: liver_NPYKO_ZT12_rep1

source_name: NPY KO, liver at ZT12, biological replicate 1


title: PIE cells + L.plantarum CRL1506 + Poly(I:C) challenge 12h

description: Gene expression after 48h L. plantarum CRL1506 stimulation and 12h Poly(I:C) challenge

source_name: PIE cells, L. plantarum CRL1506, 48h, Poly(I:C), 12h, replicate 1


title: iPSC CRL1831 3x2Gy irradiation replicate 2

description: CRL1831 iPSCs were cultivated under 3D cell culture and irradiated with fractionated 3x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 2.

source_name: Colon epithelial normal CRL1831 iPS cells cultivated under 3D cell culture conditions, without irradiation

value: iPSC CRL-1831

value: Colon normal

source_name: Colon epithelial normal CRL1831 iPS cells cultivated under 3D cell culture conditions, irradiated with 3x2 Gy


title: CSC DLD1 2Gy irradiation replicate 1

description: DLD1 CSCs were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 1.

source_name: Colorectal cancer DLD1 stem-like cells cultivated under 3D cell culture conditions, without irradiation

source_name: Colorectal cancer DLD1 stem-like cells cultivated under 3D cell culture conditions, irradiated with 2 Gy

value: single dose of 2Gy


title: PIE cells with challenge

description: Gene expression after 12h Poly(I:C) challenge

source_name: PIE cells, no challenge, replicate 1


title: liver_NPYKO_ZT4_rep1

source_name: NPY KO, liver at ZT4, biological replicate 1


title: iPSC CRL1831 replicate 2

description: CRL1831 iPSCs were cultivated under 3D cell culture, without irradiation. For differential gene expression analysis non-treated cells under 2D culture conditions served as a control. Biological replicate 2 of 2.

source_name: Colon epithelial normal CRL1831 iPS cells cultivated under 2D cell culture conditions, without irradiation


title: iPSC CRL1831 3x2Gy irradiation replicate 1

description: CRL1831 iPSCs were cultivated under 3D cell culture and irradiated with fractionated 3x2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 2.


title: PIE cells + Poly(I:C) challenge 12h

source_name: PIE cells, Poly(I:C), 12h, replicate 1


title: liver_NPYKO_ZT0_rep1

source_name: NPY KO, liver at ZT0, biological replicate 1


title: iPSC CRL1831 2Gy irradiation replicate 2

description: CRL1831 iPSCs were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 2.

source_name: Colon epithelial normal CRL1831  iPS cells cultivated under 3D cell culture conditions, without irradiation

source_name: Colon epithelial normal CRL1831 iPS cells cultivated under 3D cell culture conditions, irradiated with 2 Gy


title: iPSC CRL1831 2Gy irradiation replicate 1

description: CRL1831 iPSCs were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 2.


title: liver_NPYKO_ZT4_rep2

source_name: NPY KO, liver at ZT4, biological replicate 2


title: 3B-CN3-2

status: Public on Jan 06 2017

city: Shanghai

first: Qingan

last: Jia

address: Shanghai City Medical College Road 138

department: Department of General Surgery, Huashan Hospital

country: China

institute: Fudan University

description: high expression of CCN3

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: HCC cells

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: Hep3B were maintained in Dulbecco’s Modified Eagle’s Medium  supplemented with 10% fetal bovine serum at 37°C in a humidified incubator with 5% CO2. Cells were routinely screened for the presence of mycoplasma

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Hep3B were treated with lentiviral with CCN3 and mock vector, and named Hep3B-CCN3 and Hep3B-vector cells

tag: expression levels of ccn3

value: high


title: iPSC CRL1831 replicate 1

description: CRL1831 iPSCs were cultivated under 3D cell culture, without irradiation. For differential gene expression analysis non-treated cells under 2D culture conditions served as a control. Biological replicate 1 of 2.


title: Ighwt-Spleenic Follicular B-cells rep3

city: Boston

first: Duane

middle: R.

last: Wesemann

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

description: Gene expression data from sleepic follicular B cell population

hyb_protocol: Hybridisation to Affymetrix Mouse GeneChip ST 1.0 chips was done using normal Affymetrix protocols, using an Affymetrix 645 oven and washed using standard Affymetric protocols using the Affymetrix Fluidics station 450

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

data_processing: The data were analyzed with Bioconductor package (R version 3.3.1, Bioconductor version 3.4).

source_name: Mus musculus spleenic follicular B cells

label_protocol: 54 - 360 ng total RNA was amplified using the Nugen Ovation PicoWTA kit followed by the processing of 3 ug cDNA through the Nugen WT-Ovation Exon Module then labelling of 2.5 ug cDNA using the Nugen Ovation Biotin Module.

growth_protocol: Cells were sorted from tissue preparations

extract_protocol: Spleen was removed and sorted for follicular B cells.  RNA was extracted using Trizol.

treatment_protocol: Mice were housed in a regular SPF facility

value: Ighwt VJk5

value: Spleen

tag: cell type population

value: Follicular B-cells

value: Post-natal 6-12 weeks


title: 3B-1

description: low expression of CCN3

value: low


title: 3B-1+3B-2

description: low expression of CCN3


title: 3B-2

description: low expression of CCN3


title: Igh[gamma]1/[gamma]1-Spleenic Follicular B-cells rep1

value: Igh[gamma]1/[gamma]1 VJk5


title: 3B-CN3-1

description: high expression of CCN3


title: Ighwt-Spleenic Follicular B-cells rep1


title: Igh[gamma]1/[gamma]1-Spleenic Follicular B-cells rep2


title: Igh[epsilon]/[epsilon]-Spleenic Follicular B-cells rep1

value: Igh[epsilon]/[epsilon] VJk5


title: Igh[epsilon]/[epsilon]-Spleenic Follicular B-cells rep2


title: Igh[gamma]1/[gamma]1-Spleenic Follicular B-cells rep3


title: Igh[epsilon]/[epsilon]-Spleenic Follicular B-cells rep3


title: Ighwt-Spleenic Follicular B-cells rep2


title: liver_NPYKO_ZT16_rep1

source_name: NPY KO, liver at ZT16, biological replicate 1


title: PBC_3 [miRNA]

first: Ryo

last: Nakagawa

address: 1-8-1, Inohana, Chuo-ku

department: Department of Gastroenterology

hyb_protocol: Labeled cRNA was hybridezed using miRNA complete Labeling and Hyb kit (Agilent) according to the manufacturer’s protocol.

scan_protocol: Array images were scanned on Agilent’s G2505C scanner and Feature Extraction software 10.7 (Agilent Technologies) with default settings.

data_processing: Raw data were normalized by 90the percentile algorithm, Gene Spring Software 12.5 (Agilent Technologies).

source_name: PBC

label_protocol: Total RNA (100 ng) was reverse transcribed and Cyanine3-pCp labeled using miRNA complete Labeling and Hyb kit (Agilent) according to the manufacturer’s protocol.

extract_protocol: TotalRNA was extracted by miRNeasy mini kit ((Qiagen, Germantown, MD))

tag: subject status

value: Primay biliary cholangitis (PBC)

value: CD4+ Tcell


title: PBC_5 [miRNA]


title: PBC_6 [miRNA]


title: PBC_4 [miRNA]


title: AIS-068-3

first: Annamarie

middle: D

last: Horan

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 2.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChip 3000 7G scanner with software version AGCC.

data_processing: Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers.  We then validated performance on RT-qPCR.

label: Biotin

source_name: Acuely injured subject #068 Day 3

label_protocol: NuGen Pico v2

extract_protocol: PaxGene microRNA Isolation kit

treatment_protocol: Not applicable for healthy volunteers.  Standard care surgery for Acutely Injured and Nonunion patients.

value: Whole blood

tag: Sex

value: Female

tag: race

value: White


title: AIS-083-3

source_name: Acuely injured subject #083 Day 3


title: AIS-065-4

source_name: Acuely injured subject #065 Day 4

value: Male


title: AIS-052-3

source_name: Acuely injured subject #052 Day 3


title: PBC_2 [miRNA]


title: AIS-055-3

source_name: Acuely injured subject #055 Day 3

value: Black


title: PBC_1 [miRNA]


title: control_5 [miRNA]

source_name: healthy control

value: healthy control


title: control_6 [miRNA]


title: AIS-032-2

source_name: Acuely injured subject #032 Day 2


title: control_2 [miRNA]


title: control_1 [miRNA]


title: control_4 [miRNA]


title: control_3 [miRNA]


title: liver_NPYKO_ZT8_rep1

source_name: NPY KO, liver at ZT8, biological replicate 1

value: NPY KO


title: human term placenta from IUGR pregnancy U6

city: Los Angeles

first: Alison

last: Chu

state: CA

address: 10833 LeConte Avenue

institute: UCLA

description: miRNA expression data from whole term human placenta

hyb_protocol: Hybridization was performed per the manufacturer's protocol (Affymetrix). Briefly, the hybridization cocktail mix is prepared as per the appropriate starting volume, denature the hybridization cocktail and centrifuge with cocktail and transfer into the appropriate well of the hybridization tray.

scan_protocol: The scanner used is the GeneChip Scanner 3000 7G, scanner type M10, hardware version 1.0, software version 4.0.0.16.

data_processing: Microarray analysis was performed by the Clinical Microarray Core facility at UCLA, using the Affymetrix GeneChip miRNA 3.0 Array, which contains 25,015 probe sets covering 153 organisms. Of these probe sets 5,617 are designated as human has proves, which 1,789 are specific for mature human miRNAs. The data obtained was initially analyzed using the Express Console Software version 1.2 (Affymetrix).

source_name: whole human placenta isolated from the fetal aspect

label_protocol: The RNA was labeled using the FlashTag Biotin HSR RNA labeling Kit (Affymetrix), per the manufacturer's protocol starting with 8ug of RNA. Briefly, starting with total RNA, the process involved a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

growth_protocol: not applicable

extract_protocol: total miRNA from human placentas was purified using the Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) per manufacturer's protocol. Tissue was prepared by adding 700uL QIAzol lysis reagent to 50 mg of placental tissue and homogenized for one minute using the Omni tissue homogenizer. After elution of the miRNA, the Qiagen RNeasy MinElute Cleanup Kit was used to remove contaminating DNA and to concentrate the samples. RNA concentration and quality were measured using NonoDrop 2000c spectrophotometer (ThermoFisher Scientific).

treatment_protocol: not applicable

value: placenta from delivery at 40+2 weeks by C-section, M infant, BW 2580g


title: human term placenta from IUGR pregnancy U4

value: placenta from delivery at 38+4 weeks by C-section, M infant, BW 2551g


title: human term placenta from IUGR pregnancy U2

value: placenta from delivery at 37+6 weeks by NSVD, F infant, BW 2475g


title: human term placenta from AGA pregnancy C1

value: placenta from delivery at 41+5 wk gestation, M infant, NSVD, BW 3795g


title: human term placenta from AGA pregnancy C7

value: placenta from delivery at 39+4 wks by C-section, F infant, BW 3940g


title: human term placenta from AGA pregnancy C14

value: placenta from delivery at 39 wks, F newborn, delivered by C/section, BW 3460g


title: Lean_ischemic_Exendin-4 [JT02mi033]

city: Indianapolis

first: Kieren

middle: James

last: Mather

state: IN

address: 1120 West Michigan St, CL365

department: Medicine

institute: Indiana University

description: Osabaw pig

hyb_protocol: Stained and washed using the standard miRNA protocol from Affymetrix using Affymetrix GeneChip Console

scan_protocol: Standard protocol Affymetrix GeneChip Console

data_processing: CEL files were imported into Partek Genomics Suite.  RMA  (Robust multichip average, Bolstad, 2003) expression levels were generated for all probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish.

organism: Sus scrofa

source_name: Myocardium - Left Ventricle

label_protocol: Genisphere Flashtag using 1ug of total RNA

extract_protocol: PureLink RNA Micro Kit by invitrogen

treatment_protocol: Cardiac contractility was assessed in lean and obese Ossabaw swine at rest, following 30 min occlusion of the left circumflex artery, and 2 hours after the release of the occlusion. Swine received either 24 hours of EX-4 at 30 fmol/kg/min or saline. 10 lean and 10 obese swine were used (5 saline and 5 EX-4 for each group). Affymetrix 3.0 microRNA (miR) microarrays were used to measure differential expression of miRs in normally perfused and IRI territory from 19 of the swine used in this study.

tag: phenotype

value: Lean

tag: treatment 1

value: ischemic

tag: treatment 2


title: Obese_ischemic_Exendin-4 [JT02mi037]

description: Osabaw pig

value: Obese


title: Obese_ischemic_Saline [JT02mi027]

description: Osabaw pig

value: Saline


title: Obese_ischemic_Exendin-4 [JT02mi038]

description: Osabaw pig


title: Lean_ischemic_Exendin-4 [JT02mi032]

description: Osabaw pig


title: Obese_ischemic_Saline [JT02mi028]

description: Osabaw pig


title: Obese_ischemic_Exendin-4 [JT02mi034]

description: Osabaw pig


title: Obese_ischemic_Exendin-4 [JT02mi036]

description: Osabaw pig


title: Obese_ischemic_Saline [JT02mi025]

description: Osabaw pig


title: Lean_ischemic_Exendin-4 [JT02mi029]

description: Osabaw pig


title: Lean_ischemic_Exendin-4 [JT02mi031]

description: Osabaw pig


title: Obese_ischemic_Exendin-4 [JT02mi035]

description: Osabaw pig


title: Obese_ischemic_Saline [JT02mi026]

description: Osabaw pig


title: Lean_ischemic_Exendin-4 [JT02mi030]

description: Osabaw pig


title: Lean_ischemic_Saline [JT02mi021]

description: Osabaw pig


title: Lean_ischemic_Saline [JT02mi022]

description: Osabaw pig


title: Obese_Perfused_Exendin-4 [JT02mi019]

description: Osabaw pig

value: perfused


title: Lean_ischemic_Saline [JT02mi024]

description: Osabaw pig


title: Lean_ischemic_Saline [JT02mi023]

description: Osabaw pig


title: Obese_Perfused_Exendin-4 [JT02mi018]

description: Osabaw pig


title: AH016-3 MYB-/- B5

city: Oxford

first: Julian

last: Buchrieser

address: South Parks Road

department: Dunn School of Pathology

country: United Kingdom

institute: Oxford University

description: iPSC-AH016-3 MYB-/- C5

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file humanomniexpress-24-v1-1-a-cluster-file.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, MYB-/- clone AH016-3, clone B5

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; iPSC lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: gender

value: male

tag: cell type

value: MYB-/-


title: AH016-3 SPI1-/-

description: iPSC-AH016-3 SPI1-/-

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SPI1-/- clone AH016-3

tag: genotype


title: Lean_Perfused_Exendin-4 [JT02mi011]

description: Osabaw pig


title: Lean_Perfused_Exendin-4 [JT02mi014]

description: Osabaw pig


title: Obese_Perfused_Exendin-4 [JT02mi017]

description: Osabaw pig


title: Lean_Perfused_Exendin-4 [JT02mi010]

description: Osabaw pig


title: Obese_Perfused_Saline [JT02mi008]

description: Osabaw pig


title: Lean_ischemic_Saline [JT02mi020]

description: Osabaw pig


title: Obese_Perfused_Exendin-4 [JT02mi015]

description: Osabaw pig


title: Lean_Perfused_Exendin-4 [JT02mi012]

description: Osabaw pig


title: 3B-CN3-3

description: high expression of CCN3

value: high


title: Obese_Perfused_Saline [JT02mi007]

description: Osabaw pig


title: AH016-3 MYB-/- E6

description: iPSC-AH016-3 MYB-/- B5

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, MYB-/- clone AH016-3, clone E6


title: Obese_Perfused_Saline [JT02mi006]

description: Osabaw pig


title: AIS-061-2

source_name: Acuely injured subject #061 Day 2

value: Whole blood

value: Male

value: White


title: Obese_Perfused_Saline [JT02mi009]

description: Osabaw pig


title: Lean_Perfused_Saline [JT02mi004]

description: Osabaw pig


title: AIS-040-3

source_name: Acuely injured subject #040 Day 3

value: Black


title: Lean_Perfused_Saline [JT02mi003]

description: Osabaw pig


title: Lean_Perfused_saline [JT02mi001]

description: Osabaw pig


title: NU-001-postop

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 2.0GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Nonunion subject #1 Postop

label_protocol: Affymetrix FlashTag™ Biotin RNA Labeling Kit

value: Whole venous blood

value: Female


title: AH016-3 MYB-/- C5

description: iPSC-AH016-3 MYB-/- E6

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, MYB-/- clone AH016-3, clone C5


title: AH016-3 WT control G4

description: iPSC-AH016-3 WT clone G4

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, Wild Type control clone AH016-3, clone G4

value: wild type control


title: Lean_Perfused_Saline [JT02mi002]

description: Osabaw pig


title: NU-004-3mo.postop

source_name: Nonunion subject #4 3 months postop

value: Asian


title: AH016-3 RUNX1-/-

description: iPSC-AH016-3 RUNX1-/-

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, RUNX1-/- clone AH016-3


title: NU-004-postop

source_name: Nonunion subject #4 Postop


title: NU-004-preop

source_name: Nonunion subject #4 Preop


title: Day 28 Ethylene Glycol Group 2 Rep 4

city: Gainesville

first: Sunil

last: Joshi

state: Florida

address: 1600 S W Archer Road

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

description: Gene expression on Day 28 of Ethylene Glycol group

hyb_protocol: Standard Agilent Hybridization protocol used

scan_protocol: Standard Agilent Scanning protocol (using one color scan setting for 8 x 60k array)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Rat renal cortex

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean up and Dnase 1 treatment with QIAGEN RN easy mini kit  according to protocol provided with the kit. Quality control was  performed with Agilent Bioanalyzer.

treatment_protocol: Rats were fed normal diet (group 1), normal diet supplemented with 1.25% Ethylene Glycol (group 2), and diet same as group 2 but supplemented with 10mg/kg/day spironolactone. Kidneys were extracted from all the 3 different treatment groups.

tag: strain

value: Sprague- Dawley

value: Kidney

tag: day

value: Ethylene Glycol


title: Day 28 Ethylene Glycol Group 2 Rep 1


title: NU-001-preop

source_name: Nonunion subject #1 Preop


title: Day 28 Ethylene Glycol Group 2 Rep 3


title: Day 28 Ethylene Glycol + Spironolactone Group 3 Rep 3

description: Gene expression on Day 28 of Ethylene Glycol and Spironolactone group

value: Ethylene Glycol and Spironolactone


title: Day 28 Ethylene Glycol + Spironolactone Group 3 Rep 2


title: Lean_Perfused_Saline [JT02mi005]

description: Osabaw pig

value: Lean

value: Saline


title: Day 28 Control Group 1 Rep 3

description: Gene expression on Day 28 of Control group

value: control


title: Day 28 Ethylene Glycol + Spironolactone Group 3 Rep 4


title: Day 28 Control Group 1 Rep 4


title: Day 28 Ethylene Glycol Group 2 Rep 2


title: Day 28 Control Group 1 Rep 1


title: NU-001-3mo. Postop

source_name: Nonunion subject #1 3 months postop


title: Day 28 Ethylene Glycol + Spironolactone Group 3 Rep 1


title: Day 14 Ethylene Glycol + Spironolactone Group 3 Rep 3

description: Gene expression on Day 14 of Ethylene Glycol and Spironolactone Group


title: Day 14 Ethylene Glycol + Spironolactone Group 3 Rep 2


title: AH016-3 MYB+/- C1

description: iPSC-AH016-3 MYB+/- C1

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, MYB+/- clone AH016-3, clone C1

value: male

value: MYB+/-


title: Day 14 Ethylene Glycol + Spironolactone Group 3 Rep 1


title: Day 14 Ethylene Glycol Group 2 Rep 3

description: Gene expression on Day 14 of Ethylene Glycol Group


title: Day 14 Ethylene Glycol Group 2 Rep 4


title: Day 28 Control Group 1 Rep 2


title: Day 14 Control Group 1 Rep 3

description: Gene expression on Day 14 of control group


title: Day 14 Control Group 1 Rep 4


title: Day 14 Ethylene Glycol Group 2 Rep 1


title: Day 14 Control Group 1 Rep 2


title: KO_BMM_LPS_6hr_rep1

city: Omaha

first: Xinghui

last: Li

state: Ne

address: 985965 Nebraska Medical Center

department: Pathology and microbiology

institute: the University of Nebraska Medical Center

description: Gene expression after 6hr in LPS BMM

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: KO BMM, 6hr, LPS, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse bone marrow was flushed and cultured under L929-conditional medium for 6 days.

extract_protocol: RNA was prepared using the RNAeasy column purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BMM was treated with or without LPS for 6 hours and collected for TNA preparation.

value: bone marrow derived macrophages

value: female

value: Cullin 3 knockout


title: KO_BMM_LPS_0hr_rep2

description: Gene expression of non-treated BMM

source_name: KO BMM, 0hr, LPS, replicate 2


title: Day 14 Ethylene Glycol Group 2 Rep 2

value: Male


title: KO_BMM_LPS_0hr_rep1

description: Gene expression of non-treated BMM

source_name: KO BMM, 0hr, LPS, replicate 1


title: WT_BMM_LPS_0hr_rep2

description: Gene expression of non-treated BMM

source_name: WT BMM, 0hr, LPS, replicate 2

value: Cullin 3 wildtype


title: KO_BMM_LPS_6hr_rep2

description: Gene expression after 6hr in LPS BMM

source_name: KO BMM, 6hr, LPS, replicate 2


title: WT_BMM_LPS_6hr_rep1

description: Gene expression after 6hr in LPS BMM

source_name: WT BMM, 6hr, LPS, replicate 1


title: 12. tet-Map3k3_Nat1-null_ESC w Dox_3

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 3

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565BA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to 75 percentile.

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 3

label_protocol: Manufature's protocol

growth_protocol: standard mouse ESC medium on gelatin-coated plates  at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNAeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mouse embryonic stem cells were treated  with or witout doxycycline (Dox)

tag: genotype/variation

value: mouse embryonic stem cells


title: 13. tet-EGFP_Nat1-null_ESC w Dox_1

description: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 1

source_name: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 1

value: tet-inducible EGFP-expressing Nat1-null


title: 15. tet-EGFP_Nat1-null_ESC w Dox_3

description: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 3

source_name: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 3


title: Day 14 Control Group 1 Rep 1

tag: treatment


title: 14. tet-EGFP_Nat1-null_ESC w Dox_2

description: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 2

source_name: tet-inducible EGFP-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 2


title: 10. tet-Map3k3_Nat1-null_ESC w Dox_1

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 1

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 1


title: WT_BMM_LPS_6hr_rep2

description: Gene expression after 6hr in LPS BMM

source_name: WT BMM, 6hr, LPS, replicate 2

tag: tissue


title: WT_BMM_LPS_0hr_rep1

description: Gene expression of non-treated BMM

source_name: WT BMM, 0hr, LPS, replicate 1

tag: age


title: 11. tet-Map3k3_Nat1-null_ESC w Dox_2

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured with Dox, replicate 2

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, with Dox, replicate 2


title: 8. tet-Map3k3_Nat1-null_ESC wo Dox_2

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured without Dox, replicate 2

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, without Dox, replicate 2


title: AIS-061-2

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 4.0GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Acuely injured subject #061 Day 2

value: Whole blood

value: White


title: 5. Nat1-null_ESC_2

description: Nat1-null mouse embryonic stem cells, replicate 2


title: 9. tet-Map3k3_Nat1-null_ESC wo Dox_3

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured without Dox, replicate 3

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, without Dox, replicate 3


title: 7. tet-Map3k3_Nat1-null_ESC wo Dox_1

description: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells cultured without Dox, replicate 1

source_name: tet-inducible Map3k3-expressing Nat1-null mouse embryonic stem cells, without Dox, replicate 1


title: 4. Nat1-null_ESC_1

description: Nat1-null mouse embryonic stem cells, replicate 1


title: AIS-052-3

source_name: Acuely injured subject #052 Day 3

value: Female


title: Obese_Perfused_Exendin-4 [JT02mi016]

description: Osabaw pig

source_name: Myocardium - Left Ventricle

value: Obese

value: perfused


title: AIS-065-4

source_name: Acuely injured subject #065 Day 4


title: AIS-040-3

source_name: Acuely injured subject #040 Day 3

value: Black


title: 6. Nat1-null_ESC_3

description: Nat1-null mouse embryonic stem cells, replicate 3


title: 3. WT_ESC_3

description: wild-type mouse embryonic stem cells, replicate 3

value: wild-type


title: 2. WT_ESC_2

description: wild-type mouse embryonic stem cells, replicate 2


title: 1. WT_ESC_1

description: wild-type mouse embryonic stem cells, replicate 1


title: AIS-055-3

source_name: Acuely injured subject #055 Day 3


title: AIS-032-2

source_name: Acuely injured subject #032 Day 2


title: AIS-068-3

source_name: Acuely injured subject #068 Day 3


title: AIS-083-3

source_name: Acuely injured subject #083 Day 3


title: Nat1-null_ESC2_LIF

description: Nat1-null mouse embryonic stem cells cultured with LIF, replicate 2.

hyb_protocol: Manufacturer's protocol.

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Nat1-null mouse embryonic stem cells, LIF

label_protocol: Manufacturer's protocol.

growth_protocol: Standard mouse ESC medium on gelatin-coated plates at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mouse embryonic stem cells were treated with LIF or 2i+LIF.

value: mouse embryonic stem cell line

value: LIF


title: WT_ESC1_ 2i+LIF

description: Wild-type mouse embryonic stem cells cultured with 2i+LIF, replicate 1.

source_name: wild-type mouse embryonic stem cells, 2i+LIF


title: WT_ESC2_ 2i+LIF

description: Wild-type mouse embryonic stem cells cultured with 2i+LIF, replicate 2.


title: Staphylococcus epidermidis strain SE620 Δpsm-mec mutant rep 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from Staphylococcus epidermidis strain SE620 Δpsm-mec mutant

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with Affymetric Expression Console.

organism: Staphylococcus epidermidis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Strains were grown in tryptic soy broth (TSB).

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: wild type vs. mutant

value: (delta)psm-mec mutant


title: Nat1-null_ESC3_LIF

description: Nat1-null mouse embryonic stem cells cultured with LIF, replicate 3.


title: Staphylococcus epidermidis strain SE620 Δpsm-mec mutant rep 3


title: Staphylococcus epidermidis strain SE620 Δpsm-mec mutant rep 1


title: Nat1-null_ESC1_ 2i+LIF

description: Nat1-null mouse embryonic stem cells cultured with 2i+LIF, replicate 1.

source_name: Nat1-null mouse embryonic stem cells, 2i+LIF


title: Nat1-null_ESC3_ 2i+LIF

description: Nat1-null mouse embryonic stem cells cultured with 2i+LIF, replicate 3.


title: Staphylococcus epidermidis strain SE620 Δmec mutant rep 3

description: Gene expression data from Staphylococcus epidermidis strain SE620 Δmec mutant

value: (delta)mec mutant


title: Staphylococcus epidermidis strain SE620 rep 3

description: Gene expression data from Staphylococcus epidermidis strain SE620

source_name: Staphylococcus epidermidis strain SE620

value: wild type


title: Nat1-null_ESC2_ 2i+LIF

description: Nat1-null mouse embryonic stem cells cultured with 2i+LIF, replicate 2.


title: Staphylococcus epidermidis strain SE620 rep 2


title: WT_ESC1_LIF

description: Wild-type mouse embryonic stem cells cultured with LIF, replicate 1.

source_name: wild-type mouse embryonic stem cells, LIF


title: Lean_Perfused_Exendin-4 [JT02mi013]

description: Osabaw pig

value: Lean


title: Staphylococcus epidermidis strain Rp62A isogenic Δpsm-mec deletion mutant rep 1

description: Gene expression data from Staphylococcus epidermidis strain Rp62A isogenic Δpsm-mec deletion mutants

value: isogenic {delta}psm-mec deletion mutant


title: Staphylococcus epidermidis strain Rp62A rep 3

description: Gene expression data from Staphylococcus epidermidis strain Rp62A

source_name: Staphylococcus epidermidis strain Rp62A


title: Staphylococcus epidermidis strain SE620 Δmec mutant rep 2


title: WT_ESC3_LIF

description: Wild-type mouse embryonic stem cells cultured with LIF, replicate 3.


title: WT_ESC2_LIF

description: Wild-type mouse embryonic stem cells cultured with LIF, replicate 2.


title: Staphylococcus epidermidis strain Rp62A isogenic Δpsm-mec deletion mutant rep 2

source_name: Staphylococcus epidermidis strain Rp62A isogenic Δpsm-mec deletion mutants


title: Staphylococcus epidermidis strain SE620 Δmec mutant rep 1


title: WT_ESC3_ 2i+LIF

description: Wild-type mouse embryonic stem cells cultured with 2i+LIF, replicate 3.


title: HV-025 -0

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Healthy volunteer #25

label_protocol: WT Ambion

extract_protocol: Qiagen MicroRNeasy

treatment_protocol: Not applicable for healthy volunteers.  Standard care surgery for Acutely Injured.

value: Whole venous blood

value: Male

value: Asian


title: HV-024 -0

source_name: Healthy volunteer #24


title: Uncomplicated (PFU) vs. Complicated (PFC)

description: AF2D (Cy5) vs. CYD (Cy3)

hyb_protocol: Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). 5 micrograms of cy3 and cy5 labeled samples were hybridized.  The labeled DNA samples were hybridized on a Genotypic designed Plasmodium falciparum 3D7 Custom 2x400K CGH Microarray (AMADID: 025327).Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 40 hours. The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22)

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 Linear normalization and analyzed Agilent Genomic Workbench Software

label: Control _Cy5

organism: Plasmodium falciparum

source_name: clinical isolate showing uncomplicated disease

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 2 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.

extract_protocol: Total DNA was isolated from samples using manufacture’s protocol (TRI- Reagent, Sigma Aldrich, and USA).

tag: isolate

value: uncomplicated disease causing

tag: tissue source

value: blood

source_name: clinical isolate showing complicated disease

value: CYD

value: Complicated disease causing


title: Staphylococcus epidermidis strain Rp62A rep 1


title: Staphylococcus epidermidis strain Rp62A rep 2


title: HV-015 -0

source_name: Healthy volunteer #15

value: Female


title: HV-022 -0

source_name: Healthy volunteer #22

value: Black


title: HV-026 -0

source_name: Healthy volunteer #26

value: White


title: HV-021 -0

source_name: Healthy volunteer #21


title: HV-019 -0

source_name: Healthy volunteer #19


title: HV-017 -0

source_name: Healthy volunteer #17


title: HV-023 -0

source_name: Healthy volunteer #23


title: HV-011 -0

source_name: Healthy volunteer #11


title: HV-007 -0

source_name: Healthy volunteer #7


title: HV-005 -0

source_name: Healthy volunteer #5


title: HV-013 -0

source_name: Healthy volunteer #13


title: Staphylococcus epidermidis strain Rp62A isogenic Δpsm-mec deletion mutant rep 3


title: HV-006 -0

source_name: Healthy volunteer #6


title: HV-003 -0

source_name: Healthy volunteer #3


title: HV-001 -0

source_name: Healthy volunteer #1


title: AIS-006-6

source_name: Acutely injured subject #6 Day 6


title: HV-020 -0

source_name: Healthy volunteer #20


title: HV-012 -0

source_name: Healthy volunteer #12


title: AIS-007-7

source_name: Acutely injured subject #7 Day 7


title: AIS-006-5

source_name: Acutely injured subject #6 Day 5


title: AIS-005-4

source_name: Acutely injured subject #5Day 4


title: AIS-005-3

source_name: Acutely injured subject #5 Day 3


title: AIS-004-7

source_name: Acutely injured subject #4 Day 7


title: NU-001-3mo. Postop

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645.  The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Nonunion subject #1 3 months postop


title: NU-004-3mo.postop

source_name: Nonunion subject #4 3 months postop


title: NU-001-preop

source_name: Nonunion subject #1 Preop


title: iTSCM 2

city: Tokyo

first: Taisuke

last: Kondo

institute: Keio University

description: Gene expression of iTSCM cells

hyb_protocol: 2.5 ug of Biotin-labeled cDNA were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturer’s instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty microliters of hybridization solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm.

scan_protocol: The chip was scanned by Scanner 3000 7G (Affymetrix)

data_processing: The obtained Affymetrix .CEL files were imported into the Expression Console software (Affymetrix). Background correction was carried out using the robust multichip analysis (RMA) algorithm).

source_name: CD8+CD45RA+CD45RO-CCR7+CD95+ T cells cocultured with OP9-hDL2

label_protocol: Biotin labeled cDNA was prepared from 5 ug cDNA using an Encore Biotin Module (NuGEN) according to the manufacturer's instructions.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor. CD8+ T cells which were isolated by human CD8+ T cell isolation kit (Miltenyi) were labeled by CFSE and then stimulated with autologous irradiated lymphoblastoid cell lines (LCL) (ratio 4:1). Seven days after the stimulation, activated cells were sorted as CD8a+CD45RA-CD45RO+CCR7-CD95+CFSElow cells. To activate Notch signaling, activated T cells were subsequently cocultured with Notch ligand-expressing OP9-DL1 cells. T cells were cultured with OP9-DL1 cells with human IL-7 (10ng/ml), anti-human IFN-γ antibody (2ug/ml) in alpha MEM for eleven days.

extract_protocol: RNA was prepared using ReliaPrep RNA Cell Miniprep System (Promega) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies). In addition, RNA was amplified by Ovation PicoSL WTA Ststem V2 (NuGEN) and amplified cDNA were re-quantified using the NanoDrop-1000 spectrophotometer and Agilent 2100 Bioanalyzer.

treatment_protocol: Human CD8+ T cells were isolated from PBMC using human CD8+ T cell isolation kit and MACS LS column (Miltenyi Biotec). Isolated CD8+ T cells were labeled by CFSE and cultured with autologous LCL.

value: female


title: NU-004-postop

source_name: Nonunion subject #4 Postop


title: AIS-003-6

source_name: Acutely injured subject #3 Day 6


title: iTSCM 1

description: Gene expression of iTSCM cells

source_name: CD8+CD45RA+CD45RO-CCR7+CD95+ T cells cocultured with OP9-hDL1

value: male


title: iTSCM3

description: Gene expression of iTSCM cells

source_name: CD8+CD45RA+CD45RO-CCR7+CD95+ T cells cocultured with OP9-hDL3


title: NU-004-preop

source_name: Nonunion subject #4 Preop


title: Staphylococcus epidermidis strain SE620 rep 1

source_name: Staphylococcus epidermidis strain SE620


title: AIS-002-90

source_name: Acutely injured subject #2 Day 90


title: Ring1A-/-;Ring1BΔ/Δ;Ink4a-/- MOZ-TIF2 AML cells (FL) 48h

city: Cho-ku

first: Emi

last: Takamatsu-Ichihara

state: Tokyo

address: 5-1-1, Tsukiji

institute: National Cancer Center Research Institute

description: SAMPLE XII

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45˚C on Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Fluidics Station 450 (Affymetrix).

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: KO (FL) Ink4a-KO 48h

label_protocol: Biotinylated cRNA were prepared from 100 ng of total RNA with the 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

tag: strain/background

value: MOZ-TIF2 AML cells

value: 4-OHT for 48h


title: AIS-001-90

source_name: Acutely injured subject #1 Day 90

tag: Sex


title: PBC_5

city: Chiba

institute: Chiba University

hyb_protocol: Labeled cRNA was hybridezed using gene expression hybridisation kits (Agilent Technologies) according to the manufacturer’s protocol.

source_name: PBC

label_protocol: Total RNA (50 ng) was reverse transcribed and Cyanine3-pCp labeled using Low-input quick amp labelling kits, one color (Agilent Technologies) according to the manufacturer’s protocol.

tag: subject status

value: Primay biliary cholangitis (PBC)

value: CD4+ Tcell


title: PBC_4


title: Day 14 Ethylene Glycol + Spironolactone Group 3 Rep 4

description: Gene expression on Day 14 of Ethylene Glycol and Spironolactone Group

source_name: Rat renal cortex

value: Sprague- Dawley

value: Kidney

value: Ethylene Glycol and Spironolactone


title: Ring1A-/-;Ring1BΔ/Δ MOZ-TIF2 AML cells (BM) 48h, rep3

description: SAMPLE 8

source_name: KO (BM) 48h


title: NU-001-postop

source_name: Nonunion subject #1 Postop

value: Whole venous blood

tag: race


title: Ring1A-/-;Ring1BΔ/Δ MOZ-TIF2 AML cells (FL) 48h

description: SAMPLE X

source_name: KO (FL) 48h


title: PBC_6


title: PBC_2


title: Ring1A-/-;Ring1Bf/f;Ink4a-/- MOZ-TIF2 AML cells (FL) 48h

description: SAMPLE XI

source_name: Control (FL) Ink4a-KO 48h


title: Ring1A-/-;Ring1Bf/f MOZ-TIF2 AML cells (FL) 48h

description: SAMPLE 9

source_name: Control (FL) 48h


title: Ring1A-/-;Ring1BΔ/Δ MOZ-TIF2 AML cells (BM) day7

description: SAMPLE 6

source_name: KO (BM) day7

value: 4-OHT for 7d


title: control_6

source_name: healthy control

value: healthy control


title: PBC_3


title: PBC_1


title: Ring1A-/-;Ring1BΔ/Δ MOZ-TIF2 AML cells (BM) 48h, rep2

description: SAMPLE 4


title: control_5


title: Ring1A-/-;Ring1Bf/f MOZ-TIF2 AML cells (BM) 48h, rep3

description: SAMPLE 7

source_name: Control (BM) 48h


title: Ring1A-/-;Ring1Bf/f MOZ-TIF2 AML cells (BM) day7

description: SAMPLE 5

source_name: Control (BM) day7


title: control_4


title: control_1


title: LPHN2-KO cells that underwent cardiac differentiation at day 4

type: protein

city: Seoul

first: Choon-Soo

last: Lee

address: 28 Yongon-Dong, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

description: LPHN2-KO (4d)

hyb_protocol: Biotin labeled extract was hybridized with antibody-spotted slide for 2hr at room temperature. After hybridization, slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water. Detection Buffer including Cy3-Streptavidin (fullmoon Bio) was treated for 20min at room temperature. And slide was washed with 1X wash buffer (Fullmoon Bio) and de-ionized water.

scan_protocol: Scanned on an Axon 4000B scanner.

data_processing: GenePix Software (v 6.1) was used for data extraction and Genowiz software (v 4.0.5.6) was used for global normalization.

molecule: protein

source_name: cardiac differentiated cell from LPHN2-KO PSC

label_protocol: 50ug of Tissue extract was labeled with Biotin and label buffer (Fullmoon Bio).

extract_protocol: 10~40mg of tissues were washed with cold 1X PBS. And tissue samples were homogenized with Extracting buffer (Fullmoon Bio). Debris was removed from tissue extract with centrifuge.

value: cardiac differentiated cell

tag: time

value: day 4


title: LPHN2-sh cells that underwent cardiac differentiation at day 3

description: LPHN2-Sh (3d)

source_name: cardiac differentiated cell from LPHN2-sh PSC

value: day 3


title: LPHN2-sh cells that underwent cardiac differentiation at day 4

description: LPHN2-Sh (4d)


title: LPHN2-KO cells that underwent cardiac differentiation at day 3

description: LPHN2-KO (3d)


title: control_2


title: control_3


title: Ring1A-/-;Ring1BΔ/Δ MOZ-TIF2 AML cells (BM) 48h, rep1

description: SAMPLE 2


title: Ring1A-/-;Ring1Bf/f MOZ-TIF2 AML cells (BM) 48h, rep1

description: SAMPLE 1


title: Ring1A-/-;Ring1Bf/f MOZ-TIF2 AML cells (BM) 48h, rep2

description: SAMPLE 3


title: control-sh cells that underwent cardiac differentiation at day 4

description: Con-Sh (4d)

source_name: cardiac differentiated cell from con-sh PSC

value: control-sh


title: control-sh cells that underwent cardiac differentiation at day 3

description: Con-Sh (3d)


title: Fruit Fly Fat Body Treatment Rep 1

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

description: Replicate 1

hyb_protocol: Following fragmentation and labelling, 3.5 μg of ss-cDNA was hybridized for 16 hours at 45°C on Affymetrix Drosophila Gene 1.0 ST Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analysed with the Affymetrix Expression Console 1.4.0.38 using the default gene level RMA-Sketch processing algorithm.

organism: Drosophila melanogaster

source_name: larva fat body, treatment

label_protocol: Biotinylated ss-cDNA was prepared with the GeneChip WT PLUS Reagent Kit for Affymetrix arrays from 100 ng of total RNA.

growth_protocol: Larvae of fruit flies (Drosophila melanogaster) were given a semi-purified diet for five days since the egg stage.

extract_protocol: Total RNA was isolated from the fat bodies of the fruit fly larvae using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer.

treatment_protocol: Control group was given the semi-purified diet only, while treatment group was given PFJ supplemented in the semi-purified diet (4 ml for a final concentration of 19,000 mg gallic acid equivalent (GAE) per kg diet or 0.86 mg GAE per kcal diet).

value: fat body

value: 5 days

tag: developmental stage

value: larva

value: semi-purified diet supplemented with palm fruit juice

tag: experimental group

value: treatment


title: Fruit Fly Fat Body Treatment Rep 2

description: Replicate 2


title: Fruit Fly Fat Body Control Rep 1

description: Replicate 1

source_name: larva fat body, control

value: semi-purified diet

value: control


title: Fruit Fly Larva Treatment Rep 2

description: Replicate 2

source_name: larva, treatment

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit, followed by quantification using the NanoDrop spectrophotometer and qualitation using the Agilent Bioanalyzer.

value: whole body


title: DLD-1-D

city: Suzhou

first: Jianming

address: 199 Renai Road

institute: Soochow University

description: Gene expression of colorectal cell line DLD-1 after Dicer knockout

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: colorectal cell line DLD-1 with Dicer knockout, no other treatment

growth_protocol: All colorectal cancer cell lines were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS. Cells were maintained at 37ºC with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Takara, Dalian, China). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Dicer-knockout cell lines of (HCT116, SW480 and DLD1) were kind gifts of Professor Bert Vogelstein from the Sidney Kimmel Comprehensive Cancer and Howard Hughes Medical Institute.

tag: cell line

value: Dicer knockout


title: HCT116-C

description: Gene expression of normal colorectal cell line HCT116

source_name: colorectal cell line HCT116, no treatment

tag: genotype

value: normal


title: RKO-C

description: Gene expression of normal colorectal cell line RKO

source_name: colorectal cell line RKO, no treatment

value: RKO


title: Fruit Fly Larva Treatment Rep 3

description: Replicate 3


title: Fruit Fly Fat Body Control Rep 2

description: Replicate 2


title: Fruit Fly Larva Control Rep 1

description: Replicate 1

source_name: larva, control


title: Nat1-null_ESC1_LIF

description: Nat1-null mouse embryonic stem cells cultured with LIF, replicate 1.

source_name: Nat1-null mouse embryonic stem cells, LIF

tag: cell type

value: mouse embryonic stem cell line

value: LIF


title: DLD-1-C

description: Gene expression of normal colorectal cell line DLD-1

source_name: colorectal cell line DLD-1, no treatment


title: Fruit Fly Larva Control Rep 3

description: Replicate 3


title: RKO-D

description: Gene expression of colorectal cell line RKO after Dicer knockout

source_name: colorectal cell line RKO with Dicer knockout, no other treatment


title: Fruit Fly Larva Treatment Rep 1

description: Replicate 1


title: HCT116-D

description: Gene expression of colorectal cell line HCT116 after Dicer knockout

source_name: colorectal cell line HCT116 with Dicer knockout, no other treatment


title: FS26

status: Public on Jan 05 2017

city: Beijing

first: Yunfeng

last: Yang

address: No.1 Qinghuayuan, Haidian District

department: School of Environment

institute: Tsinghua University

description: replicate 5

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Data normalization and analyses of raw data were described previously (Yang et al 2014). We removed genes detected in less than two out of five biological replicates and then logarithmically transformed the values, followed by normalization of the signal intensity of each spot by dividing with total abundance.

organism: uncultured bacterium

source_name: Soil microbes in Inner Mongolia grasslands

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: The experiment was set up in Spring of 2010 with a full factorial design of the grazing effect×soil erosion or deposition effect. Thirty 4×4 m plots were arranged into 6 rows and 5 columns with 2.5 m buffer zone in between. In the present study, we focus on the ungrazed plots to exclude the grazing effect, which is comprised of three treatments of control, soil erosion and deposition, with 5 replicates of each treatment. The positions of these plots were randomly assigned. In the early growing season, 1.5-3.0 cm topsoil was blown using a fan at the soil eroded plots in 2010 and 2011. The topsoil collected from the eroded plots was added to the dust deposition plots.

extract_protocol: Genomic DNA of soil microbial community was extracted from 5 g soil sample by a freeze-grinding procedure as described previously (J Zhou et al 1996). Then crude DNA was purified phenol extraction and low melting agarose gel electrophoresis. DNA quality was measured by the absorbance ratios of A260/280nm and A260/230nm using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA), and DNA concentrations were quantified with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany).

treatment_protocol: Soil samples were collected from all the 30 plots in middle August of 2012. In each plot, four soil cores of 0-10 cm depth were randomly taken using auger of 5 cm diameter, and mixed to obtain a composite sample. After passing through a 2 mm sieve and removal of visible roots and stones by hand, subsamples were stored in icebox and transported to laboratory for microbial analysis.

tag: different conditions

value: grazing


title: FS2

description: replicate 1

value: deposition+grazing


title: FS22

description: replicate 4


title: FS15

description: replicate 3


title: FS27

description: replicate 5


title: FS12

description: replicate 2


title: FS6

description: replicate 1

value: erosion+grazing


title: FS16

description: replicate 3


title: FS11

description: replicate 2


title: FS23

description: replicate 4


title: FS30

description: replicate 5


title: FS21

description: replicate 4


title: FS7

description: replicate 2


title: FS17

description: replicate 3


title: S33-ES dox-

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data were processed using Genespring software.

source_name: Pluripotent stem cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: RTC, ESC, iPSC, and #45 RTC: Knockout DMEM with 15% FBS, NEAA, L-Glu, 2-ME, LIF, and Pen/Strep  TSC and Min/Min ESC in TS medium: GMEM with 10% FCS, sodium pyruvate, NEAA, 2-ME, recombinant FGF4, and Pen/Strep  Crypt: within Matrigel, covered by Advanced DMDM/F12 with GlutaMax, HEPES, EGF, Noggin, R-spondin, N2, B27, N-Acethylcysteine, and Pen/Strep  MEF: DMEM with 10% FBS, and Pen/Strep

extract_protocol: RNeasy Plus Mini kit

treatment_protocol: 4-OHT(+) samples were treated with 4-OHT (1 uM for intestinal organoids and 2 ug/ml for MEF) containing medium for two days.

value: Pluripotent stem cells


title: MEF 4-OHT(-) (2)

source_name: #45-derived MEF

value: #45-derived MEF


title: MEF 4-OHT(+)


title: S33-MEF dox-

source_name: mouse embryonic fibroblast

value: mouse embryonic fibroblast


title: MEF 4-OHT(+) (2)


title: S33-ES dox+


title: Apc Min/+ ESC


title: MEF 4-OHT(-)


title: FS5

description: replicate 1


title: Crypt 4-OHT(+)

source_name: #45-derived small intestinal orgnoids

value: #45-derived small intestinal orgnoids


title: S33-MEF dox+


title: Crypt 4-OHT(-)


title: Apc +/+ ESC


title: Apc Min/Min ESC


title: HV-008 -0

city: Philadelphia

institute: University of Pennsylvania

data_processing: Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers.  We then validated performance on RT-qPCR.

source_name: Healthy volunteer #8

value: Whole venous blood

value: Female

value: White


title: RTC#1 derivative, #45

source_name: Reprogrammed colon tumor cells

value: Reprogrammed colon tumor cells


title: HV-002-0

description: Healthy volunteer #2

source_name: Whole venous blood

label_protocol: Affymetrix WT Sense

extract_protocol: PaxGene microRNA Isolation kit

value: Male

tag: stress

value: healthy


title: RTC#3


title: HV-009-0

description: Healthy volunteer #9


title: AIS-002-0

description: Acutely injured subject #2 Day 0

value: acutely injured

tag: day


title: AIS-002-4

description: Acutely injured subject #2 day 4


title: HV-018-0

description: Healthy volunteer #18


title: RTC#3 derivative, #9


title: RTC#2


title: RTC#1


title: HV-004-0

description: Healthy volunteer #4


title: AIS-002-3

description: Acutely injured subject #2 day 3


title: Fruit Fly Larva Control Rep 2

description: Replicate 2

tag: tissue

value: whole body

value: 5 days

value: larva

tag: treatment

value: semi-purified diet

value: control


title: AIS-002-2

description: Acutely injured subject #2 day 2

tag: age


title: AIS-001-2

description: Acutely injured subject #1 Day 2


title: HV-026 -0

description: Healthy volunteer #26

hyb_protocol: Labeled  RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

growth_protocol: Not applicable


title: HV-025 -0

description: Healthy volunteer #25

value: Asian


title: AIS-001-1

description: Acutely injured subject #1 Day 1


title: AIS-002-1

description: Acutely injured subject #2 day 1


title: RAW NFAT5 KD Rep1

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description:
SAMPLE 4
RAW264.7 macrophage Stable knock-down of NFAT5 transcript using shRNA (shNFAT5)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were treated using R (version 2.9.1) with beadarray (version 1.12.1)

source_name: RAW264.7_NFAT5 KD

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: RAW264.7 cells were cultured in alpha-MEM containing 10% fetal bovine serum and antibiotics (50 units/ml penicillin, and 50 ug/ml streptomycin) and maintained in a humidified incubator at 37C and 5% CO2

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: RAW264.7 macrophages were transfected with NFAT5 shRNAs and NFAT5 decoy oligonucleotides.

value: macrophage

tag: il1b treatment


title: RAW NFAT5-decoy Rep1

description:
SAMPLE 7
RAW264.7 macrophage Transfected with oligonucleotides harboring the consensus sequence for NFAT5 target genes (NFAT5-decoy)


title: RAW Control Rep1

description:
SAMPLE 1
RAW264.7 macrophage No treatment

value: No treatment


title: RAW NFAT5-decoy Rep2

description:
SAMPLE 8
RAW264.7 macrophage Transfected with oligonucleotides harboring the consensus sequence for NFAT5 target genes (NFAT5-decoy)


title: RAW NFAT5 KD Rep3

description:
SAMPLE 6
RAW264.7 macrophage Stable knock-down of NFAT5 transcript using shRNA (shNFAT5)


title: HV-024 -0

description: Healthy volunteer #24

label_protocol: Affymetrix FlashTag™ Biotin RNA Labeling Kit


title: AIS-001-0

description: Acutely injured subject #1 Day 0


title: HV-022 -0

description: Healthy volunteer #22

value: Black


title: HV-023 -0

description: Healthy volunteer #23


title: RAW Control Rep2

description:
SAMPLE 2
RAW264.7 macrophage No treatment


title: RAW NFAT5 KD Rep2

description:
SAMPLE 5
RAW264.7 macrophage Stable knock-down of NFAT5 transcript using shRNA (shNFAT5)


title: RAW NFAT5-decoy Rep3

description:
SAMPLE 9
RAW264.7 macrophage Transfected with oligonucleotides harboring the consensus sequence for NFAT5 target genes (NFAT5-decoy)


title: HV-021 -0

description: Healthy volunteer #21