title: NO_84_CN-AML


title: NO_75_CN-AML

status: Public on Feb 09 2017

type: RNA

city: Taipei

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: cRNA was hybridized to Illumina HumanHT-12 v4 Expression BeadChip according to the manufacturer’s instructions.

scan_protocol: After 14–20 hours hybridization, the BeadChips were stained by Cy3 and were then washed. Intensities of bead fluorescence were detected by Illumina BeadArray Reader, and the results were transformed to numeric values using GenomeStudio v2010.1 software (Illumina).

data_processing: Expression values were processed with log2 transformation and quantile normalization.  The raw data file (Non-normalized_data_.txt) includes instances of null (~100 or fewer per sample ) where the raw signal is not available.  The 104 samples were analyzed in ~10 batches. The raw dataset for each batch was obtained from the service provider with values for a range of 47,219-47,317 probes. When raw data for a specific probe was missing from one of the batches, it was annotated with null.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: de novo acute myeloid leukemia

label_protocol: cDNA was amplified (in vitro transcription) to generate biotin labeled cRNA (Ambion) according to manufacturer's instructions.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions.

tag: disease

value: CN-AML

tag: tissue

value: bone marrow

tag: overall survival (months)

tag: event (1

value: dead, 0:alive):0


title: NO_70_CN-AML


title: NO_80_CN-AML


title: NO_63_CN-AML

value: dead, 0:alive):1


title: NO_73_CN-AML


title: NO_68_CN-AML


title: NO_50_CN-AML


title: NO_66_CN-AML


title: NO_72_CN-AML


title: NO_62_CN-AML


title: NO_65_CN-AML


title: NO_48_CN-AML


title: NO_45_CN-AML


title: NO_57_CN-AML


title: NO_67_CN-AML


title: NO_61_CN-AML


title: NO_47_CN-AML


title: NO_58_CN-AML


title: NO_46_CN-AML


title: NO_37_CN-AML


title: NO_42_CN-AML


title: NO_44_CN-AML


title: NO_41_CN-AML


title: NO_35_CN-AML


title: NO_30_CN-AML


title: NO_36_CN-AML


title: NO_27_CN-AML


title: NO_29_CN-AML


title: NO_7_CN-AML


title: NO_28_CN-AML


title: NO_26_CN-AML


title: NO_34_CN-AML


title: brain_SN_NBIA_BIA2

city: Callaghan

first: Adrienne

middle: E

last: Milward

state: NSW

address: Medical Science Building MSB

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: University of Newcastle

hyb_protocol: Standard Illumina hybridization protocol was used (Illumina HumanHT-12 v4 Expression BeadChips).

scan_protocol: Beadchips were scanned using the Illumina BeadArray Reader and BeadScan software (V2.2.7).

data_processing: Cubic Spline normalization was applied.  Genes were considered differentially expressed if the fold-change of the mean NBIA signal relative to mean control signal was at least 1.5.

source_name: substantia nigra ,NBIA,BIA2

label_protocol: RNA samples were biotin-labelled and amplified using the TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: Total RNA was isolated from substantia nigra and basal ganglia of NBIA  and normal cases  using TRI reagent (Ambion) then purified and concentrated using the RNeasy MinElute Kit (QIAGEN).

tag: disease status

value: NBIA

tag: gender

value: female

tag: age

value: brain

tag: tissue compartment

value: substantia nigra


title: NO_5_CN-AML


title: brain_BG_NBIA_BIA1

source_name: basal ganglia,NBIA,BIA1

value: male

value: basal ganglia


title: spikelet

city: Shanghai

first: Zhaoqing

last: Chu

address: 3888 Chenhua Road, Songjiang

country: China

institute: Shanghai Chenshan Plant Science Research Center, CAS

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 35

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the housekeeping gene GAPDH. Target gene signals normalized to housekeeping genes.
The expression profiles were calculated with –ΔΔCT values.  Fold changes were also calculated with the formula “fold change = 2–ΔΔCT”.  Fold Change worksheet reports test/control. The control sample used is indicated in the Description field of each sample.

label: SYBR Green

organism: Brachypodium distachyon

source_name: Brachypodium distachyon seedling

label_protocol: The cDNA was synthesized with 3.0 µg of total RNA by using PrimeScript Reverse Transcriptase (TAKARA). The reaction mixtures were diluted 20 times with distilled water and used as templates for quantitative real-time PCR. The primers used in this paper were listed in Supplementary Table S3. The qPCR was conducted and repeated three times. The reaction condition was as follows: 95°C for 3 mins, 40 cycles of 95°C for 10 s, 55°C for 30s.

growth_protocol: The seeds of B. distachyon were surface sterilized with 20% NaOCl and planted on 0.6% agar containing 0.5× Murashige and Skoog and 0.3% Sucrose. Plants were grown at 22°C under 16-h-light/8-h-dark conditions and the light intensity was 120 µm m-2 s-1.

extract_protocol: Total RNA was extracted as described X Liu et al.,(J Exp Bot. 2010 Feb;61(4):1193-203. doi: 10.1093/jxb/erp388. Epub 2010 Jan 6, PMID: 20054032 ).

treatment_protocol: 2-week-old seedlings were treated with 3 major treatment groups including group 1- environmental factors ( cold, heat, H2O2, PEG, and NaCl), group 2-heavy metals (Cu, Zn, Mn, Cd, and Pb) and group 3-phytohormones (SA, 6-BA, ABA, and MeJA) (As for detailed treatments, please refer to Supplementary Table S1).

tag: developmental stage

tag: time

value: 40 days


title: stem

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 33

value: 20 days


title: leaf

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 34


title: root

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 32


title: NO_1_CN-AML


title: ABA-6h

description:
Test
CK2 is the control for SAMPLES 28, 29, 30, 31
SAMPLE 29

value: Seedling


title: MeJA-6h

description:
Test
CK2 is the control for SAMPLES 28, 29, 30, 31
SAMPLE 31


title: brain_BG_normal_C2

source_name: basal ganglia_normal_C2

value: normal


title: brain_BG_normal_C4

source_name: basal ganglia_normal_C4


title: brain_SN_Normal_C1

source_name: substantia nigra ,Normal,C1


title: brain_SN_Normal_C3

source_name: substantia nigra ,Normal,C3


title: brain_SN_Normal_C2

source_name: substantia nigra ,Normal,C2


title: brain_SN_NBIA_BIA1

source_name: substantia nigra ,NBIA,BIA1


title: brain_BG_NBIA_BIA2

source_name: basal ganglia_NBIA_BIA2


title: ABA-1h

description:
Test
CK2 is the control for SAMPLES 28, 29, 30, 31
SAMPLE 28


title: SA-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 25


title: 6-BA-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 26


title: 6-BA-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 27


title: gingival_fibroblast_leptin-IL1_donor3

city: Newcastle Upon Tyne

first: John

last: Taylor

state: Tyne and Wear

address: Framlington Place

department: Molecular Immunology

country: United Kingdom

institute: Newcastle University Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalised using RSN VST Normalisation in R with the Lumi Bioconductor Package

source_name: primary human gingival fibroblasts, leptin-IL1

label_protocol: Ambion TotalPrep 96-RNA amplification kit

growth_protocol: Primary human gingival fibroblasts extracted by outgrowth from gingival tissue acquired from canine tooth exposure surgery. Gingival fibroblasts seeded at 1x10^5 cells/well (6-well plate format), and serum-starved 18 h prior to stimulation

extract_protocol: Qiagen Rneasy mini kit as per protocol (no DNase digestion). Quality control by Agilent Bioanalyser.

treatment_protocol: Gingival fibroblasts were stimulated for 24 h with human recombinant leptin (10 µg/ml, R&D systems), human recombinant IL-1β (0.05 ng/ml), or leptin (10 µg/ml) + IL-1β (0.05 ng/ml) in serum-free DMEM. Unstimulated gingival fibroblasts (in serum-free DMEM) served as a control.

value: gingiva

tag: cell type

value: fibroblasts

tag: donor

value: donor 3

tag: treatment

tag: passage number


title: MeJA-1h

description:
Test
CK2 is the control for SAMPLES 28, 29, 30, 31
SAMPLE 30


title: gingival_fibroblast_leptin-IL1_donor1

value: donor 1


title: gingival_fibroblast_leptin-IL1_donor2

value: donor 2


title: SA-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 24


title: gingival_fibroblast_IL1_donor2

source_name: primary human gingival fibroblasts, IL1


title: gingival_fibroblast_IL1_donor1


title: gingival_fibroblast_IL1_donor3


title: Pb-24h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 23


title: Mn-24h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 19


title: Pb-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 22


title: Cd-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 20


title: Cd-24h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 21


title: gingival_fibroblast_leptin_donor3

source_name: primary human gingival fibroblasts, leptin

value: Leptin


title: Zn-24h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 17


title: Mn-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 18


title: Zn-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 16


title: Cu-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 14


title: Cu-24h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 15


title: gingival_fibroblast_unstimulated_donor3

source_name: primary human gingival fibroblasts, unstimulated

value: Unstimulated


title: gingival_fibroblast_leptin_donor2


title: NaCl-6h

description:
Test
CK3 is the control for SAMPLES 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
SAMPLE 13


title: NaCl-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 12


title: PEG-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 11


title: gingival_fibroblast_unstimulated_donor2


title: gingival_fibroblast_leptin_donor1


title: HCC4017 cells,MLS000408882-01 treated for 24h

city: Dallas

first: Elisabeth

last: Martinez

state: TX

address: 6000 Harry Hines Blvd

department: Department of Pharmacology

country: USA

institute: UT Southwestern Medical Center

description:
Gene expression profiling of HCC4017 cells treated with MLS000408882-01 for 24h
HCC4017_MLS000408882-01_24h

hyb_protocol: Standard Illumina procedure.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Microarrays were background-corrected and summarized with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008) and then quantile-normalized and log2-transformed.

label: Biotin

label_protocol: Standard Illumina procedure.

growth_protocol: HCC4017 cells were maintained in 5% FBS RPMI media and HBEC30KT cells (immortalized with cdk4 and h telomerase) were maintained in KSFM media supplemented with pituitary extract and EGF. Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol: RNA was extracted with RNeasy technology from Qiagen.

treatment_protocol: Exponentially growing cells were treated for 4 or 24 h with DMSO, MLS000408882-01 or MLS000573813-01

tag: cell line


title: HBEC30KT cells, MLS000408882-01 treated for 24h

description:
Gene expression profiling of HBEC30KT cells treated with MLS000408882-01 for 24h
HBEC30KT_MLS000408882-01_24h


title: HCC4017 cells, MLS000573813-01 treated for 24h

description:
Gene expression profiling of HCC4017 cells treated withMLS000573813-01 for 24h
HCC4017_MLS000573813-01_24h


title: HCC4017 cells, DMSO treated

description:
Gene expression profiling of HCC4017 cells treated with DMSO
HCC4017_DMSO

source_name: HCC4017 cells, DMSO treated


title: PEG-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 10


title: HCC4017 cells,MLS000408882-01 treated for 4h

description:
Gene expression profiling of HCC4017 cells treated with MLS000408882-01 for 4h
HCC4017_MLS000408882-01_4h


title: HBEC30KT cells, MLS000573813-01 treated for 24h

description:
Gene expression profiling of HBEC30KT cells treated withMLS000573813-01 for 24h
HBEC30KT_MLS000573813-01_24h


title: HBEC30KT cells, DMSO treated

description:
Gene expression profiling of HBEC30KT cells treated with DMSO
HBEC30KT_DMSO

source_name: HBEC30KT cells, DMSO treated


title: HCC4017 cells, MLS000573813-01 treated for 4h

description:
Gene expression profiling of HCC4017 cells treated withMLS000573813-01 for 4h
HCC4017_MLS000573813-01_4h


title: H2O2-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 8


title: H2O2-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 9


title: heat-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 7


title: HBEC30KT cells, MLS000408882-01 treated for 4h

description:
Gene expression profiling of HBEC30KT cells treated with MLS000408882-01 for 4h
HBEC30KT_MLS000408882-01_4h


title: heat-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 6


title: HBEC30KT cells, MLS000573813-01 treated for 4h

description:
Gene expression profiling of HBEC30KT cells treated withMLS000573813-01 for 4h
HBEC30KT_MLS000573813-01_4h


title: CK2

description:
Control
SAMPLE 2


title: CK3

description:
Control
SAMPLE 3


title: MG-P16-KO-4

city: Jouy-en-Josas

first: Fabienne

last: Le Provost

address: domaine de Vilvert

country: France

institute: INRA

hyb_protocol: hybridized to the Affymetrix ® Mouse Gene 1.1 ST Array, representing 28,000 well-annotated genes with more than 770,000 distinct probe sets

scan_protocol: not provided

data_processing: RMA normalized

organism: Mus musculus

source_name: mammary gland pregnancy day-16 KO

label_protocol: 100 ng of total RNA were labelled in accordance with the manufacturer’s protocols

growth_protocol: tranplanted mammary tissue from pregnancy day-12 or day-16 mice

extract_protocol: Tissues were excised from the animals and processed immediately for total RNA extraction using the RNeasy Lipid Tissue kit (Qiagen)

tag: strain

value: FVBN

value: mammary gland

tag: Stage

value: pregnancy day-16

tag: genotype

value: Rspo1 KO


title: cold-1h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 4


title: cold-6h

description:
Test
CK1 is the control for SAMPLES 4, 5, 6,7 ,8 ,9, 10, 11, 12, 24, 25, 26, 27, 32, 33, 34, 35
SAMPLE 5


title: MG-P16-WT-4

source_name: mammary gland pregnancy day-16 WT

value: female

tag: tissue

value: Rspo1 WT


title: CK1

description:
Control
SAMPLE 1


title: MG-P16-KO-1


title: MG-P16-WT-3


title: MG-P16-KO-2


title: MG-P16-WT-2


title: MG-P16-KO-3


title: NO_40_CN-AML

source_name: de novo acute myeloid leukemia

tag: disease

value: CN-AML

value: bone marrow

tag: overall survival (months)

value: dead, 0:alive):1


title: MG-P12-KO-3

source_name: mammary gland pregnancy day-12 KO

value: pregnancy day-12


title: MG-P12-KO-1


title: MG-P12-WT-4

source_name: mammary gland pregnancy day-12 WT


title: MG-P16-WT-1


title: MG-P12-WT-1


title: gingival_fibroblast_unstimulated_donor1

value: gingiva


title: MG-P12-KO-2


title: MG-P12-WT-2


title: MG-P12-WT-3


title: U937_TWIST-1_rep1

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

description: Gene expression data from TWIST-1-transfected U937 cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization, Wash and Stain kit

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data (CEL files) were analyzed using  Affymetrix Expression Console™ Software (version 1.3).

source_name: TWIST-1,acute myeloid leukemia cell line U937

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

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cDNA synthesis and amplification were performed using the cDNA synthesis and amplification kit (Affymetrix).

value: acute myeloid leukemia


title: MG-P12-KO-4


title: U937_Control_rep1

description: Gene expression data from Vector-transfected U937 cells

source_name: Control,acute myeloid leukemia cell line U937


title: si10_hfd_replicate1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: small intestine segment 10, epithelial cell scraping, high fat diet

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Four-week old male C57BL/6J mice (N=12) were purchased from Harlan (Horst, The Netherlands) and were housed in pairs in the light- and temperature-controlled animal facility of Wageningen University. Mice had free access to feed and water and prior to the start of the diet intervention they received standard laboratory chow (RMH-B). All animal procedures were conducted under protocols approved by the Local Committee for Care and Use of Laboratory Animals of Wageningen University, the Netherlands.

extract_protocol: Total RNA was prepared from scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: After 3 weeks, at the age of seven weeks, a subset of mice (n=8) were fed a low fat diet (LFD) for 2 weeks. The remaining mice (n=4) remained on the standard laboratory chow (RMH-B) diet. Subsequently, after these 2 weeks, at the age of nine weeks, half of the mice fed the LFD were put on a high fat diet (HFD; n=4), whereas the remaining mice were kept on the LFD (n=4). The chow fed mice remained on the RHM-B diet. After 2 additional weeks, at the age of 11 weeks, all mice were killed, after which the small intestine was removed, cut into 10 equal parts [1=duodenum, 10=terminal ileum], epithelial cells scraped off, snap-frozen in liquid nitrogen, and stored at -80° until analysis. The standard laboratory chow, RMH-B (cat. no. 2181), containing 5% of energy derived from fat, was obtained from ABDiets, Woerden, the Netherlands. The LFD and HFD contained 10% respectively 45% of energy derived from fat (diet formulations based on formulation D12450B resp. D12451; OpenResearch Diets, Research Diets, Inc). Exact diet formulations are available in the supplemental data. Throughout the whole experiment mice had free access to feed and water.

tag: Sex

value: male

value: small intestine, epithelial cell scraping

tag: peg plate

tag: labeling batch

tag: individual scraped


title: si10_lfd_replicate1

source_name: small intestine segment 10, epithelial cell scraping, low fat diet


title: si10_chow_replicate2

source_name: small intestine segment 10, epithelial cell scraping, chow diet


title: si10_lfd_replicate3


title: si10_hfd_replicate3


title: si9_hfd_replicate2

source_name: small intestine segment 9, epithelial cell scraping, high fat diet


title: si10_lfd_replicate2


title: si9_lfd_replicate2

source_name: small intestine segment 9, epithelial cell scraping, low fat diet


title: si10_hfd_replicate2


title: si10_lfd_replicate4


title: si10_chow_replicate1


title: si9_hfd_replicate3


title: si9_lfd_replicate3


title: si10_chow_replicate4


title: si9_hfd_replicate4


title: si9_lfd_replicate4


title: si9_chow_replicate4

source_name: small intestine segment 9, epithelial cell scraping, chow diet


title: si10_hfd_replicate4


title: si9_chow_replicate1


title: si9_hfd_replicate1


title: si9_lfd_replicate1


title: si9_chow_replicate2


title: si9_chow_replicate3


title: si10_chow_replicate3


title: si8_hfd_replicate1

source_name: small intestine segment 8, epithelial cell scraping, high fat diet


title: si8_hfd_replicate4


title: si8_lfd_replicate1

source_name: small intestine segment 8, epithelial cell scraping, low fat diet


title: si8_lfd_replicate2


title: si8_lfd_replicate4


title: si8_hfd_replicate3


title: si8_lfd_replicate3


title: si8_hfd_replicate2


title: si7_hfd_replicate2

source_name: small intestine segment 7, epithelial cell scraping, high fat diet


title: si7_hfd_replicate3


title: si7_lfd_replicate3

source_name: small intestine segment 7, epithelial cell scraping, low fat diet


title: si7_lfd_replicate2


title: si8_chow_replicate2

source_name: small intestine segment 8, epithelial cell scraping, chow diet


title: si6_hfd_replicate2

source_name: small intestine segment 6, epithelial cell scraping, high fat diet


title: si8_chow_replicate1


title: si6_lfd_replicate2

source_name: small intestine segment 6, epithelial cell scraping, low fat diet


title: si7_hfd_replicate1


title: si7_chow_replicate1

source_name: small intestine segment 7, epithelial cell scraping, chow diet


title: si7_lfd_replicate1


title: si8_chow_replicate3


title: si7_lfd_replicate4


title: si8_chow_replicate4


title: si7_chow_replicate3


title: si6_hfd_replicate1


title: si7_hfd_replicate4


title: si6_hfd_replicate3


title: si7_chow_replicate2


title: si6_lfd_replicate4


title: si6_lfd_replicate3


title: si7_chow_replicate4


title: si6_lfd_replicate1


title: si6_chow_replicate2

source_name: small intestine segment 6, epithelial cell scraping, chow diet


title: si6_chow_replicate1


title: si6_chow_replicate3


title: Oyster mushroom mycelia_irradiated_24h

city: Kami-ina

first: Masanobu

last: Kojima

state: Nagano

address: 8304 Minami-minowa

department: Bioscience and Biotechnology

country: Japan

institute: Shinshu University

hyb_protocol: For each hybridization, 1.65 mg of Cy3 labeled cRNA was fragmented, and hybridized at 65 oC for 17 h to an Agilent GE8x15K custom microarray.

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing:
Intensity values of each scanned feature were quantified using Agilent feature extraction software ver. 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (present flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated, and population outlines (marginal and absent flags).
Normalization was performed using Agilent GeneSpring GX ver. 11.0.2 (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples). There are total of 12,244 probes on an Agilent GE8x15K custom microarray without control probes. The altered transcripts were quantified using the comparative method. In this study we applied more than or equal to 2-fold change in signal intensity to identify the significant differences of gene expression. The differentially expressed genes were also subjected to K-means analysis using GeneSpring ver. 11.0.2 software.

organism: Pleurotus ostreatus

source_name: Oyster mushroom mycelia, irradiated, 24h

label_protocol: Total RNA was amplified and labelled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacture’s instructions. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-100 spectrophotometer and an Agilent Bioanlyzer 2100.

growth_protocol: Modified MA medium consisted of 10 g of malt extract, 10 g of D(+)-glucose, 4 g of yeast extract, and 25 g of agar in 1 liter of distilled water. GPY medium consisted of 50 g of D(+)-glucose, 2.5 g of polypeptone, 1.0 g of KH2PO4, 0.5 g of MgSO4 7H2O, 0.5 g of CaCl2 2H2O, 10 mg of FeCl2 6H2O, 7.2 mg of MnCl2 4H2O, 4.0 mg of ZnCl2, 1.0 mg of CuSO4 5H2O, 2.5 g of yeast extract, and 25 g of agar in 1 liter of distilled water. The initial pH was adjusted to 5.5. The media were autoclaved at 121oC for 20 min before use. The oyster mushroom KH-3 dikaryotic strain was first incubated at 20oC in the dark on an MA medium in a Pyrex Petri dish (diameter, 9 cm). The fungal thread was grown concentrically to form a mycelial colony about 70 mm in diameter. From the periphery of the mycelial colony, a colony 6 mm in diameter was cut out and inoculated at the center of a GPY medium in a Petri dish.

extract_protocol: Total RNAs were extracted from ca. 50 - 100 mg of the frozen colonies with an RNeasy Plant Mini Kit (Qiagen, Tokyo) following the manufacturer’s instructions. Contaminating genomic DNA was removed using an RNase-Free DNase Set (Qiagen). The quantity and quality of total RNAs was evaluated with a Nanodrop ND-1000 spectrophotometer (Themo Fisher Scientific Inc., Waltham, MA) and an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA), as recommended.

treatment_protocol: In experiments on the effect of light stimulation on mycelial growth and in gene expression analysis, colonies about 65 mm in diameter grown on the GPY agar media at 20oC in the dark were used.  An ELUX-1096 LED lighting unit for plant cultivation research (CCS, Kyoto, Japan) was used for the culture of mycelia, and the temperature was kept constant at 20oC in the dark. Light intensity was set using photon flax density (PFD) measurements taken with an LI-190 quantum sensor (LI-COR Bioscience, Lincoln, NE).   Mycelial colonies about 65 mm in diameter grown on GPY agar media at 20oC in the dark were irradiated at 15 oC for 0.5 – 36 h using blue LED at 150 μmol m-2 s-1 of PFD for the analysis of gene expression in the mycelia. The colonies irradiated were then immediately frozen in liquid nitrogen and stored at -80 ºC until use.

value: mycelia

value: blue light


title: si5_hfd_replicate3

source_name: small intestine segment 5, epithelial cell scraping, high fat diet


title: Oyster mushroom mycelia_irradiated_36h

source_name: Oyster mushroom mycelia, irradiated, 36h


title: Colorectal Adenoma tissue_rep33

city: Beijing

first: Kaitai

last: Zhang

state: Beijing

address: NO. 17, Pan Jiayuan South, Chao Yang District

department: Department of Etiology and Carcinogenesis

institute: Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences

description:
miRNA expression of colorectal cancer tissue
86C

hyb_protocol: The fluorescent labeled samples were hybridized to the Human miRNA microarray Version 3 from the Sanger database v12.0 (Agilent Technologies)

scan_protocol: The microarray slides were analyzed with an Agilent Microarray Scanner.

data_processing: microRNA microarray raw data were normalized with the GeneSpring GX software, version 11.5 (Silicon Genetics, Redwood City, CA, USA). Measured microRNAs were estimated as present if their signals could be detected in at least 50% of the samples within each sample type. Finally, the expression profiles of 96 microRNAs were acquired.

source_name: Colorectal Cancer_tissue

label_protocol: Samples were labeled with Cy3 dye using the miRNA Complete Labeling System & Hyb Kit (Agilent Technologies)

extract_protocol: Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications.

value: cancer tissue

tag: gender

value: Male

tag: age

tag: location

value: rectum


title: Colorectal Adenoma tissue_rep30

description:
miRNA expression of colorectal cancer tissue
54C


title: Colorectal Adenoma tissue_rep31

description:
miRNA expression of colorectal cancer tissue
56C

value: Female

value: colon


title: Colorectal Adenoma tissue_rep32

description:
miRNA expression of colorectal cancer tissue
76C


title: Colorectal Adenoma tissue_rep29

description:
miRNA expression of colorectal cancer tissue
53C


title: si5_lfd_replicate3

source_name: small intestine segment 5, epithelial cell scraping, low fat diet


title: si6_chow_replicate4


title: Oyster mushroom mycelia_irradiated_1h

source_name: Oyster mushroom mycelia, irradiated, 1h

tag: time

value: 1 h


title: si5_hfd_replicate4


title: si5_lfd_replicate4


title: si5_hfd_replicate2


title: Oyster mushroom mycelia_irradiated_12h

source_name: Oyster mushroom mycelia, irradiated, 12h

tag: treatment


title: Oyster mushroom mycelia_irradiated_6h

source_name: Oyster mushroom mycelia, irradiated, 6h

value: 6 h


title: si5_hfd_replicate1


title: Oyster mushroom mycelia_irradiated_0h

source_name: Oyster mushroom mycelia, irradiated, 0h

value: 0 h


title: Colorectal Adenoma tissue_rep27

description:
miRNA expression of colorectal cancer tissue
45C


title: si5_chow_replicate3

source_name: small intestine segment 5, epithelial cell scraping, chow diet


title: si5_chow_replicate1


title: si5_lfd_replicate1


title: Oyster mushroom mycelia_irradiated_0.5h

source_name: Oyster mushroom mycelia, irradiated, 0.5h


title: si4_hfd_replicate4

source_name: small intestine segment 4, epithelial cell scraping, high fat diet


title: Oyster mushroom mycelia_irradiated_3h

source_name: Oyster mushroom mycelia, irradiated, 3h

value: 3 h


title: si5_lfd_replicate2


title: Colorectal Adenoma tissue_rep28

description:
miRNA expression of colorectal cancer tissue
49C


title: Colorectal Adenoma tissue_rep26

description:
miRNA expression of colorectal cancer tissue
44C


title: Colorectal Adenoma tissue_rep25

description:
miRNA expression of colorectal cancer tissue
42C


title: Colorectal Adenoma tissue_rep24

description:
miRNA expression of colorectal cancer tissue
40C


title: si5_chow_replicate2


title: Colorectal Adenoma tissue_rep22

description:
miRNA expression of colorectal cancer tissue
38C


title: Colorectal Adenoma tissue_rep23

description:
miRNA expression of colorectal cancer tissue
39C


title: Colorectal Adenoma tissue_rep21

description:
miRNA expression of colorectal cancer tissue
37C


title: Colorectal Adenoma tissue_rep20

description:
miRNA expression of colorectal cancer tissue
36C


title: Colorectal Adenoma tissue_rep18

description:
miRNA expression of colorectal cancer tissue
33C


title: Colorectal Adenoma tissue_rep16

description:
miRNA expression of colorectal cancer tissue
28C


title: Colorectal Adenoma tissue_rep15

description:
miRNA expression of colorectal cancer tissue
25C


title: Colorectal Adenoma tissue_rep14

description:
miRNA expression of colorectal cancer tissue
23C


title: Colorectal Adenoma tissue_rep13

description:
miRNA expression of colorectal cancer tissue
22C


title: si4_hfd_replicate1


title: si4_chow_replicate3

source_name: small intestine segment 4, epithelial cell scraping, chow diet


title: si4_lfd_replicate1

source_name: small intestine segment 4, epithelial cell scraping, low fat diet


title: si4_hfd_replicate3


title: si4_lfd_replicate3


title: Colorectal Adenoma tissue_rep12

description:
miRNA expression of colorectal cancer tissue
13C


title: Colorectal Adenoma tissue_rep11

description:
miRNA expression of colorectal cancer tissue
127C


title: Colorectal Adenoma tissue_rep10

description:
miRNA expression of colorectal cancer tissue
119C


title: si4_lfd_replicate4


title: si3_hfd_replicate2

source_name: small intestine segment 3, epithelial cell scraping, high fat diet


title: Colorectal Adenoma tissue_rep9

description:
miRNA expression of colorectal adenoma tissue
88A

source_name: Colorectal Adenoma tissue

value: adenoma tissue


title: Colorectal Adenoma tissue_rep17

description:
miRNA expression of colorectal cancer tissue
31C


title: si4_lfd_replicate2


title: si5_chow_replicate4


title: Colorectal Adenoma tissue_rep19

description:
miRNA expression of colorectal cancer tissue
35C


title: si4_hfd_replicate2


title: si3_hfd_replicate3


title: si4_chow_replicate2


title: Colorectal Adenoma tissue_rep8

description:
miRNA expression of colorectal adenoma tissue
87A


title: Colorectal Adenoma tissue_rep7

description:
miRNA expression of colorectal adenoma tissue
79A


title: Colorectal Adenoma tissue_rep6

description:
miRNA expression of colorectal adenoma tissue
69A


title: si3_hfd_replicate4


title: si3_lfd_replicate2

source_name: small intestine segment 3, epithelial cell scraping, low fat diet


title: si3_lfd_replicate1


title: Colorectal Adenoma tissue_rep5

description:
miRNA expression of colorectal adenoma tissue
68A


title: si3_lfd_replicate4


title: si4_chow_replicate1


title: si3_chow_replicate4

source_name: small intestine segment 3, epithelial cell scraping, chow diet


title: si3_chow_replicate2


title: si3_lfd_replicate3


title: Colorectal Adenoma tissue_rep4

description:
miRNA expression of colorectal adenoma tissue
65A


title: si3_chow_replicate3


title: si2_chow_replicate4

source_name: small intestine segment 2, epithelial cell scraping, chow diet


title: si3_hfd_replicate1


title: Colorectal Adenoma tissue_rep2

description:
miRNA expression of colorectal adenoma tissue
16


title: Colorectal Adenoma tissue_rep3

description:
miRNA expression of colorectal adenoma tissue
17


title: Colorectal Adenoma tissue_rep1

description:
miRNA expression of colorectal adenoma tissue
14


title: si2_hfd_replicate4

source_name: small intestine segment 2, epithelial cell scraping, high fat diet


title: si1_lfd_replicate4

source_name: small intestine segment 1, epithelial cell scraping, low fat diet


title: Normal rectum mucosa_rep11

description:
miRNA expression of normal colorectal tissue
N32

source_name: Normal colorectal tissue

value: normal tissue


title: si2_hfd_replicate3


title: Normal rectum mucosa_rep10

description:
miRNA expression of normal colorectal tissue
N29


title: si3_chow_replicate1


title: Normal rectum mucosa_rep9

description:
miRNA expression of normal colorectal tissue
N28


title: Normal rectum mucosa_rep8

description:
miRNA expression of normal colorectal tissue
N27


title: si2_hfd_replicate2


title: si2_chow_replicate1


title: si1_chow_replicate3

source_name: small intestine segment 1, epithelial cell scraping, chow diet


title: si2_chow_replicate2


title: Normal rectum mucosa_rep6

description:
miRNA expression of normal colorectal tissue
N23


title: si2_chow_replicate3


title: si1_lfd_replicate2

source_name: small intestine segment 1, epithelial cell scraping, low fat diet, replivate2


title: Normal rectum mucosa_rep5

description:
miRNA expression of normal colorectal tissue
N22


title: si2_hfd_replicate1


title: si1_lfd_replicate1


title: si2_lfd_replicate2

source_name: small intestine segment 2, epithelial cell scraping, low fat diet


title: si1_hfd_replicate3

source_name: small intestine segment 1, epithelial cell scraping, high fat diet


title: KO_young_202

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

hyb_protocol: 2.53 µg of cDNA was hybridized at 48 degrees C on Mouse Gene ST 2.1 arrays

scan_protocol: Arrays were washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515).

data_processing: RMA normalization was performed at the gene level using the “target=core” option for the rma function (R package: oligo).

source_name: flash-frozen liver tissue

label_protocol: Biotinylated cDNA was prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: Female Mrp14(-/-) (KO) and control (WT) mice with C57Bl/6 background were maintained from birth until 5 or 24 months within the Case Western Reserve University (CWRU) animal vivarium. Mice were maintained under specific-pathogen free conditions and provided standard rodent chow diet (Prolab® Isopro® RMH 3000 5P76; 22% protein, 5% fat).

extract_protocol: Tissues were harvested from mice upon sacrifice, flash-frozen in liquid nitrogen, and placed at -80oC until further processing. Extraction of total RNA was then performed using the RNeasy mini kit (Qiagen, cat no. 74104) with on-column DNase digestion (Qiagen, cat. no. 79254). RNA concentrations were measured using a NanoDrop spectrophotometer and RNA integrity was evaluated using the Agilent Bioanalyzer.

treatment_protocol: Mice were fasted 4 hours prior to euthanasia but provided access to water at all times. Sacrifice was performed by cervical dislocation following injection with euthanasia solution (ketamine, 16.5mg/mL; xylazine, 1.65 mg/mL).

value: liver

tag: genotype/strain

value: young, 5 months


title: si2_lfd_replicate3

value: male


title: si1_chow_replicate1

value: small intestine, epithelial cell scraping


title: KO_young_200


title: si1_hfd_replicate2


title: si1_lfd_replicate3


title: Normal rectum mucosa_rep7

description:
miRNA expression of normal colorectal tissue
N24


title: Normal rectum mucosa_rep4

description:
miRNA expression of normal colorectal tissue
N17


title: si1_hfd_replicate4


title: KO_young_203


title: si2_lfd_replicate1

source_name: small intestine segment 2, epithelial cell scraping, low fat diet, replicate


title: KO_young_201


title: KO_young_199


title: si1_chow_replicate2


title: Normal rectum mucosa_rep3

description:
miRNA expression of normal colorectal tissue
N15


title: si1_hfd_replicate1


title: KO_old_197

value: old, 24 months


title: Normal rectum mucosa_rep2

description:
miRNA expression of normal colorectal tissue
N12


title: Normal rectum mucosa_rep1

description:
miRNA expression of normal colorectal tissue
N11


title: Middle_embryonic_colon_rep8

description:
miRNA expression of middle embryonic colon tissue
MF08

source_name: Middle embryonic colon tissue

value: embryonic tissue


title: KO_old_196


title: Middle_embryonic_colon_rep6

description:
miRNA expression of middle embryonic colon tissue
MF04


title: Middle_embryonic_colon_rep5

description:
miRNA expression of middle embryonic colon tissue
MF03


title: KO_old_194


title: Mutant sdg2-1 15-day-old seedlings Replicate 1

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

institute: IBMP-CNRS

description: Biological replicate 1 of mutant sdg2-1 seedlings

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

data_processing: Agilent Feature Extraction Software was used for background subtraction. Signal intensity were normalized using Quantile method. Signal : raw Cy3 signal intensity ; Log2NormSignal : Log2 transformed Normalized Signal

organism: Arabidopsis thaliana

source_name: sdg2-1 seedlins

label_protocol: 2 µg of total RNA were labeled according Aligent's instructions. Please see manufacture’s web site at http://www.aligent.com/

growth_protocol: Plants were grown in the greenhouse under 16h light and 8h dark at 22°C.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up according to manufacturer's instructions.

tag: ecotype

value: Columbia ecotype

tag: organ

value: seedlings

tag: genotype/variation


title: Mutant sdg2-1 15-day-old seedlings Replicate 2

description: Biological replicate 2 of mutant sdg2-1 seedlings

hyb_protocol: Please see manufacture’s web site at http://www.aligent.com/


title: KO_old_195


title: Wild-type 15-day-old seedlings Replicate 3

description: Biological replicate 3 of Wild-type seedlings

source_name: Wild-type seedlings

value: wild type


title: Middle_embryonic_colon_rep7

description:
miRNA expression of middle embryonic colon tissue
MF05

tag: Stage


title: WA01 (H1)_dif_exp1

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in in vitro-differentiated human embryonic stem cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software GX12.0 (Agilent) using default parameters.

source_name: WA01 (H1), in vitro-differentiated, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Each cell line was cultured in the medium with FGFC, in place of bFGF. or with no FGF additive, in the indicated period. For in vitro differentiation assay, H1 ESCs colonies were detached by treatment with 0.25% trypsin (Life Technologies), 1 mg/ml collagenase type IV (Gibco), 20% KSR (Invitrogen), 1 mM CaCl2 in PBS, and were transferred into a HydroCell dish (CellSeed Inc.) in DMEM-F12 medium (Invitrogen) supplemented with 20% KSR (Invitrogen), 0.1 mM of 2-mercaptoethanol (Sigma-Aldrich), MEM non-essential amino acids (Invitrogen), for embryoid body (EB) formation. The medium was changed every other day. EBs were attached to a gelatin-coated multi-well plate at day 8, and cultured in the same medium for another 11 days.

tag: cell characters

value: human embryonic stem cell

tag: cell line name

tag: passage number

tag: basal medium

tag: treatment period

tag: fgf additive


title: Mutant sdg2-1 15-day-old seedlings Replicate 3

description: Biological replicate 3 of mutant sdg2-1 seedlings


title: Wild-type 15-day-old seedlings Replicate 2

description: Biological replicate 2 of Wild-type seedlings


title: WA01 (H1)_dif_exp1_2


title: WT_young_189

tag: tissue


title: KO_old_191


title: KO_old_190


title: Wild-type 15-day-old seedlings Replicate 1

description: Biological replicate 1 of Wild-type seedlings


title: KO_old_193


title: 253G1_p52_36_bFGF_exp1_2

description: Gene expression in human iPS cell

source_name: 253G1, passage 52, cultured with bFGF, experiment 1

growth_protocol: Human Embryonic stem (ES) and induced pluripotent stem (iPS) cells were maintained in an undifferentiated state at 37 ºC in a humidified incubator with 3 or 5% CO2. Human ES cell line, H1 and human iPS cell line, 253G1 were cultured according to WiCell Feeder-Independent Pluripotent Stem Cell Protocols E8 Medium provided by the WiCell Research Institute (www.wicell.org), or according to the Human Pluripotent Stem Cell Protocols provided by the Human Stem Cell Technology Unit, RIKEN Center for Developmental Biology (www.cdb.riken.jp/hsct/protocol.html). Human ES cell line, KhES-1, was maintained as previously described (Suemori et al., 2006). Human iPS cell line, 201B7, was cultured according to the protocols provided by the Project for Realization of Regenerative Medicine, Projects for the development of human iPS cell research centers at the University of Tokyo.

treatment_protocol: Each cell line was cultured in the medium with FGFC, in place of bFGF. or with no FGF additive, in the indicated period.

value: human HDF-derived iPS cell

value: Essential 6 Medium plus 2 ng/mL of TGF-beta 1

value: 36 days

value: 100ng/ml of bFGF


title: 253G1_p43_p_exp1_2

description: Gene expression in human iPS cell

source_name: 253G1, passage 43, pre-cultured, experiment 1


title: KO_old_192


title: WT_young_188


title: 253G1_p52_36_bFGF_exp1

description: Gene expression in human iPS cell


title: 253G1_p52_36_FGFC_exp1

description: Gene expression in human iPS cell

source_name: 253G1, passage 52, cultured with FGFC, experiment 1

value: 100ng/ml of FGFC


title: Middle_embryonic_colon_rep3

description:
miRNA expression of middle embryonic colon tissue
EF03

tag: gender


title: Middle_embryonic_colon_rep4

description:
miRNA expression of middle embryonic colon tissue
EF04

tag: age


title: 253G1_p43_p_exp1

description: Gene expression in human iPS cell


title: 253G1_p52_36_FGFC_exp1_2

description: Gene expression in human iPS cell


title: Middle_embryonic_colon_rep2

description:
miRNA expression of middle embryonic colon tissue
EF02

tag: location


title: Middle_embryonic_colon_rep1

description:
miRNA expression of middle embryonic colon tissue
EF01


title: Early_embryonic_colon_rep6

description:
miRNA expression of early embryonic colon tissue
EF27

source_name: Early embryonic colon tissue


title: Early_embryonic_colon_rep5

description:
miRNA expression of early embryonic colon tissue
EF25


title: Early_embryonic_colon_rep4

description:
miRNA expression of early embryonic colon tissue
EF24


title: Early_embryonic_colon_rep3

description:
miRNA expression of early embryonic colon tissue
EF23


title: WT_young_187


title: WT_young_186


title: KhES-1_p40_MEF_30_bFGF_exp1_2

description: Gene expression in human embryonic stem cell

source_name: KhES-1, passage 40, cultured on feeder cells (MEF) with bFGF, experiment 1

growth_protocol: Human Embryonic stem (ES) and induced pluripotent stem (iPS) cells were maintained in an undifferentiated state at 37 ºC in a humidified incubator with 3 or 5% CO2. Human ES cell line, H1, was cultured according to WiCell Feeder-Independent Pluripotent Stem Cell Protocols E8 Medium provided by the WiCell Research Institute (www.wicell.org), or according to the Human Pluripotent Stem Cell Protocols provided by the Human Stem Cell Technology Unit, RIKEN Center for Developmental Biology (www.cdb.riken.jp/hsct/protocol.html). Human ES cell line, KhES-1, was maintained as previously described (Suemori et al., 2006). Human iPS cell line, 201B7, was cultured according to the protocols provided by the Project for Realization of Regenerative Medicine, Projects for the development of human iPS cell research centers at the University of Tokyo.

value: KhES-1 medium

value: 30 days

value: 5 ng/ml of bFGF


title: WT_young_185

value: liver

value: young, 5 months


title: KhES-1_p40_MEF_30_bFGF_exp1


title: KhES-1_p30_MEF_p_exp1_2

source_name: KhES-1, passage 30, pre-cultured on feeder cells (MEF), experiment 1


title: 201B7_p40_MEF_50_bFGF_exp1_2

description: Gene expression in human iPS cell

source_name: 201B7, passage 40, cultured with bFGF, experiment 1

value: 201B7 medium

value: 50 days

value: 10 ng/ml of bFGF


title: WT_old_184

value: old, 24 months


title: 201B7_p30_MEF_p_exp1_2

description: Gene expression in human iPS cell

source_name: 201B7, passage 30, pre-cultured on feeder, experiment 1


title: KhES-1_p30_MEF_p_exp1


title: KhES-1_p40_MEF_30_FGFC_exp1

source_name: KhES-1, passage 40, cultured on feeder cells (MEF) with FGFC, experiment 1

value: 5 ng/ml of FGFC


title: WA01 (H1)_p63_MEFCM_41_FGFC_exp1_2

source_name: WA01 (H1), passage 63, cultured in MMC-MEF conditioned medium with FGFC, experiment 1

value: MMC-MEF conditioned medium

value: 41 days


title: WT_old_181


title: WA01 (H1)_p53_MEFCM_p_exp1_2

source_name: WA01 (H1), passage 53, pre-cultured in MMC-MEF conditioned medium, experiment 1

value: human embryonic stem cell


title: 201B7_p30_MEF_p_exp1

description: Gene expression in human iPS cell

source_name: 201B7, passage 30, pre-cultured on feeder cells (MEF), experiment 1

value: human HDF-derived iPS cell


title: 201B7_p40_MEF_50_bFGF_exp1

description: Gene expression in human iPS cell


title: 201B7_p40_MEF_50_FGFC_exp1_2

description: Gene expression in human iPS cell

source_name: 201B7, passage 40, cultured with FGFC, experiment 1

value: 10 ng/ml of FGFC


title: KhES-1_p40_MEF_30_FGFC_exp1_2


title: WA01 (H1)_p63_MEFCM_41_FGFC_exp1


title: Early_embryonic_colon_rep2

description:
miRNA expression of early embryonic colon tissue
EF21

value: embryonic tissue


title: 201B7_p40_MEF_50_FGFC_exp1

description: Gene expression in human iPS cell


title: WA01 (H1)_p63_MEFCM_41_bFGF_exp1_2

source_name: WA01 (H1), passage 63, cultured in MMC-MEF conditioned medium with bFGF, experiment 1


title: WT_old_183

source_name: flash-frozen liver tissue


title: Early_embryonic_colon_rep1

description:
miRNA expression of early embryonic colon tissue
EF18


title: Whole_embryo_rep2

description:
miRNA expression of early whole embryo tissue
SWE11

source_name: Whole embryonic tissue


title: Whole_embryo_rep1

description:
miRNA expression of early whole embryo tissue
SWE04


title: Seedling

description:
Test
SAMPLE 37

data_processing: The expression profiles were calculated with –ΔΔCT values. Fold changes were also calculated with the formula “fold change = 2–ΔΔCT”.  Matrix normalized reports normalized signal (against housekeeping genes, Actin). Fold Change file reports test/control. The control sample used is indicated in the Description field of each sample.

source_name: Brachypodium distachyon seedling

label_protocol: The cDNA was synthesized with 3.0 µg of total RNA by using PrimeScript Reverse Transcriptase (TAKARA). The reaction mixtures were diluted 20 times with distilled water and used as templates for quantitative real-time PCR. The primers used in this paper were listed in Supplementary Table S8. The qPCR was conducted and repeated three times. The reaction condition was as follows: 95°C for 3 mins, 40 cycles of 95°C for 10 s, 60°C for 30s.

growth_protocol: The seeds of B. distachyon were surface sterilized with 20% NaClO and planted on 0.6% agar containing 0.5× Murashige and Skoog and 0.3% Sucrose. Plants were grown at 22°C under 16-h-light/8-h-dark conditions and the light intensity was 120 µm m-2 s-1.

extract_protocol: Total RNA was extracted as described M Jiang et al.,(DNA Res. 2014 Jun;21(3):327-39. doi: 10.1093/dnares/dst060. Epub 2014 Jan 21.PMID: 24453041)

treatment_protocol: 2-week-old seedlings were treated with 4 major treatment groups including group 1- environmental factors ( cold, heat, H2O2, PEG, and NaCl), group 2-heavy metals ( Zn, Cd, and Pb) , group 3-phytohormones (SA, ABA, and MeJA) and group 4-biotic treatments(PH14,Guy11 and F0968) (As for detailed treatments, please refer to Supplementary Table S1).

tag: developmental stage

value: Seedling

tag: time

value: 20 days


title: Leaf

description:
Test
SAMPLE 36

value: leaf


title: WT_old_180

tag: genotype/strain


title: F0968 12h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 33


title: Root

description:
Test
SAMPLE 34

value: root


title: WA01 (H1)_p53_MEFCM_p_exp1

value: 5 ng/ml of bFGF


title: WA01 (H1)_p58_30_FGFC_exp1

source_name: WA01 (H1), passage 58, cultured with FGFC, experiment 1

value: Essential 6 Medium plus 2 ng/mL of TGF-beta 1

value: 30 days

value: 100ng/ml of FGFC


title: WA01 (H1)_p63_MEFCM_41_bFGF_exp1


title: WA01 (H1)_p58_30_FGFC_exp1_2


title: WT_old_182

value: liver


title: Guy11 12h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 31


title: WT_old_179

value: old, 24 months


title: WA01 (H1)_p58_30_bFGF_exp1_2

source_name: WA01 (H1), passage 58, cultured with bFGF, experiment 1

value: 100ng/ml of bFGF


title: WA01 (H1)_p58_30_bFGF_exp1


title: WA01 (H1)_p51_4_FGFC_exp3_2

source_name: WA01 (H1), passage 51, cultured with FGFC, experiment 3

value: 4 days


title: Stem

description:
Test
SAMPLE 35

value: stem


title: WA01 (H1)_p51_4_FGFC_exp3

value: human embryonic stem cell


title: Guy11 4h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 30


title: WA01 (H1)_p51_4_no FGF_exp3

source_name: WA01 (H1), passage 51, cultured with no FGF additive, experiment 3


title: WA01 (H1)_p50_p_exp3

source_name: WA01 (H1), passage 50, pre-cultured, experiment 3


title: WA01 (H1)_p59_4_FGFC_exp2_2

source_name: WA01 (H1), passage 59, cultured with FGFC, experiment 2


title: WA01 (H1)_p59_4_bFGF_exp2_2

source_name: WA01 (H1), passage 59, cultured with bFGF, experiment 2


title: F0968 4h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 32


title: WA01 (H1)_p59_4_no FGF_exp2_2

source_name: WA01 (H1), passage 59, cultured with no FGF additive, experiment 2


title: WA01 (H1)_p51_4_bFGF_exp3_2

source_name: WA01 (H1), passage 51, cultured with bFGF, experiment 3


title: WA01 (H1)_p51_4_bFGF_exp3


title: PH14 12h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 29


title: WA01 (H1)_p59_4_FGFC_exp2


title: WA01 (H1)_p59_4_no FGF_exp2


title: WA01 (H1)_p50_p_exp3_2


title: WA01 (H1)_p51_4_no FGF_exp3_2


title: PH14 4h

description:
Test
Mock is the control for SAMPLES 28,29,30,31,32,33.
SAMPLE 28


title: WA01 (H1)_p49_p_exp2_2

source_name: WA01 (H1), passage 49 , pre-cultured, experiment 2


title: Mock

description:
Control
SAMPLE 27


title: WA01 (H1)_p49_4_no FGF_exp1_2

source_name: WA01 (H1), passage 49, cultured with no FGF additive, experiment 1


title: WA01 (H1)_p59_4_bFGF_exp2


title: Zncl2 12h

description:
Test
mCK 12h is the control for SAMPLES 20,22,24,26.
SAMPLE 26


title: WA01 (H1)_p49_p_exp2


title: Zncl2 6h

description:
Test
mCK 6h is the control for SAMPLES 19,21,23,25.
SAMPLE 25


title: PbSO4 6h

description:
Test
mCK 6h is the control for SAMPLES 19,21,23,25.
SAMPLE 23


title: PbSO4 12h

description:
Test
mCK 12h is the control for SAMPLES 20,22,24,26.
SAMPLE 24


title: CdCl2 12h

description:
Test
mCK 12h is the control for SAMPLES 20,22,24,26.
SAMPLE 22


title: WA01 (H1)_p49_4_bFGF_exp1_2

source_name: WA01 (H1), passage 49, cultured with bFGF, experiment 1


title: thymus_down-syndrome_DS9

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: microRNA expression from thymus explant

hyb_protocol: Dried Cy3-labelled miRNA sample was resuspended with 17uL of nuclease-free water and mixed to Hyb Spike-In and 10x GE Blocking Agent solutions, and 2x Hi-RPM Hybridization buffer. The final volume was incubated at 100°C for 5 minutes and hybridized to Human miRNA Microarray slides (8x15K) - V3 (G4470C) - Agilent Technologies, for 20 hours at 55°C in a rotating Agilent hybridization oven (20rpm).

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 8x15k miRNA microarrray slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected miRNA transcripts were used for analysis using the R software and considering up to 1 NA for each group (DS or CT) and the expression values in Log (base 2).

source_name: thymus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the microRNA Complete Labeling and Hyb Kit (Agilent Technologies), without column purification, according to the manufacturer's instructions.

extract_protocol: Thymus explants (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

value: male

tag: age at surgery (yr/mo/d)


title: thymus_down-syndrome_DS1

description: microRNA expression from thymus explant

value: female


title: thymus_down-syndrome_DS3

description: microRNA expression from thymus explant


title: thymus_down-syndrome_DS4

description: microRNA expression from thymus explant


title: thymus_down-syndrome_DS7

description: microRNA expression from thymus explant


title: CdCl2 6h

description:
Test
mCK 6h is the control for SAMPLES 19,21,23,25.
SAMPLE 21


title: WA01 (H1)_p49_4_bFGF_exp1

description: Gene expression in human embryonic stem cell


title: thymus_down-syndrome_DS2

description: microRNA expression from thymus explant


title: WA01 (H1)_p48_p_exp1

source_name: WA01 (H1), passage 48, pre-cultured, experiment 1


title: thymus_down-syndrome_DS6

description: microRNA expression from thymus explant


title: thymus_control_CT10

description: microRNA expression from thymus explant


title: WA01 (H1)_p49_4_FGFC_exp1

source_name: WA01 (H1), passage 49, cultured with FGFC, experiment 1


title: NaCl 6h

description:
Test
mCK 12h is the control for SAMPLES 20,22,24,26.
SAMPLE 20


title: thymus_control_CT9

description: microRNA expression from thymus explant


title: thymus_control_CT6

description: microRNA expression from thymus explant


title: thymus_control_CT8

description: microRNA expression from thymus explant


title: thymus_down-syndrome_DS8

description: microRNA expression from thymus explant


title: thymus_control_CT4

description: microRNA expression from thymus explant


title: WA01 (H1)_p49_4_FGFC_exp1_2


title: thymus_control_CT3

description: microRNA expression from thymus explant


title: WA01 (H1)_p49_4_no FGF_exp1


title: mCK 12h

description:
Control
SAMPLE 18


title: WA01 (H1)_p48_p_exp1_2


title: thymus_control_CT2

description: microRNA expression from thymus explant


title: thymus_control_CT1

description: microRNA expression from thymus explant


title: NaCl 3h

description:
Test
mCK 6h is the control for SAMPLES 19,21,23,25.
SAMPLE 19


title: mCK 6h

description:
Control
SAMPLE 17


title: SA 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 15


title: SA 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 16


title: ABA 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 12


title: ABA 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 11


title: H2O2 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 9


title: differentiated PS cells (EB), 201B7

city: Matsumoto

first: Daihachiro

last: Tomotsune

address: 3-1-1 Asahi

department: Institute for Biomedical Sciences

description: Gene expression of EB-formed hPS cells

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (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: EB 201B7 cells

label_protocol: Agilent one-color Low Input Quick Amp Labeling Kit labeling protocol

growth_protocol: Undifferentiated pluripotent stem cells were prepared using the standard method with MEF-coated dishes (ML) or MEF-conditioned medium method with matrigel-coated dishes (MC).  EB were formed by transferring small clumps (200 µm diameter) of hPSCs to a non-adhesive 60-mm dish coated with Lipidure. Suspension cultures were maintained for 5 days.  Following EB formation, 1 µL/mL of 10% w/v aqueous ammonia (Wako) was added to fresh Lanford medium. This process was repeated every 2 days for 14 days total.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen).

treatment_protocol: 10 µL/mL of dimethyl sulfoxide (DMSO; Sigma–Aldrich, St. Louis, MO, USA) was added to dishes containg EBs. This process was repeated twice. DMSO-treated cells were separated using a cell scraper, transferred into a non-adhesive dish, and cultured in Lanford medium for 2 days. Following EB formation, 1 µL/mL of 10% w/v aqueous ammonia (Wako) was added to fresh Lanford medium. This process was repeated every 2 days for 14 days total.

tag: cell type

value: hiPS cells


title: differentiated PS cells (EB), H1

description: Gene expression of EB-formed hPS cells

source_name: EB of H1 cells

value: hES cells


title: PEG 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 8

source_name: Brachypodium distachyon seedling

value: Seedling

value: 20 days


title: differentiated PS cells (Ammonia), KhES1

description: Gene expression of ammnonia-treated hPS cells

source_name: Ammonia treated KhES1 cells


title: differentiated PS cells (Ammonia), KhES2

source_name: Ammonia treated KhES2 cells


title: differentiated PS cells (Ammonia), KhES3

source_name: Ammonia treated KhES3 cells


title: H2O2 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 10


title: MeJA 3h

description:
Test
SAMPLE 13


title: differentiated PS cells (Ammonia), 253G1

source_name: Ammonia treated 253G1 cells


title: undifferentiated PS cells (ML), 253G1

description: Gene expression of undifferentiated hPS cells

source_name: 253G1, hiPS cell line supplied from RIKEN Bio Resource Center (Tsukuba, Ibaraki, Japan).


title: differentiated PS cells (EB), 3-KhES3

description: Gene expression of EB-formed hPS cells

source_name: EB of KhES3 cells


title: Fibroblasts, h-Fibroblast

description: Gene expression of human fibroblast cells

source_name: human fibroblast cells

value: human fibroblast cells

value: unknown


title: Undifferentiated PS cells (MC), KhES1

source_name: KhES1, hESC line supplied from the Institute for Frontier Medical Science (Kyoto University, Kyoto, Japan)


title: Undifferentiated PS cells (MC), H1

source_name: H1, hESC line purchased from WiCell Research Institute (Madison, WI, USA)


title: Fibroblasts (EB), Fibro-D

description: Gene expression of EB-formed human fibroblast cells

source_name: EB of human fibroblast cells


title: differentiated PS cells (Ammonia), 201B7

source_name: Ammonia treated 201B7 cells


title: Undifferentiated PS cells (MC), KhES2

source_name: KhES2, hESC line supplied from the Institute for Frontier Medical Science (Kyoto University, Kyoto, Japan)


title: differentiated PS cells (EB), KhES1

description: Gene expression of EB-formed hPS cells

source_name: EB of KhES1 cells


title: differentiated PS cells (EB), 253G1

description: Gene expression of EB-formed hPS cells

source_name: EB of 253G1 cells


title: PEG 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 7


title: undifferentiated PS cells(ML), H1


title: undifferentiated PS cells (ML), 201B7

source_name: 201B7 hiPS cell line supplied from RIKEN Bio Resource Center (Tsukuba, Ibaraki, Japan).


title: differentiated PS cells (Ammonia), H1

source_name: Ammonia treated H1 cells


title: 45℃ 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 6

source_name: Brachypodium distachyon seedling


title: 45℃ 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 5


title: undifferentiated PS cells(ML), KhES-2


title: Undifferentiated PS cells (MC), 253G1


title: 4℃ 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 4


title: CK 6h

description:
Control
SAMPLE 2


title: undifferentiated PS cells (ML), KhES-1


title: undifferentiated PS cells(ML), KhES-3

source_name: KhES3, hESC line supplied from the Institute for Frontier Medical Science (Kyoto University, Kyoto, Japan)


title: serum microRNA profile of Control-1

city: Wuhan

first: Li

last: Liu

state: Hubei

address: 1095 Jiefang Road

department: Department of Endocrinology

institute: Huazhong University of Science and Technology

description: Biological replication 1/6

hyb_protocol: Each slide was hybridized with 100ng Cy3‐labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Scanned on an Agilent Microarray Scanner.Images were quantified using Agilent Feature Extraction Software (version A.10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and Quantile normalization.

source_name: serum, Control

label_protocol: Total RNA was labeled by miRNA Complete Labeling and Hyb Kit followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

value: 15 years

value: Female

tag: bmi

tag: disease state

value: Control

tag: disease duration


title: serum microRNA profile of T1DM-5

description: Biological replication 5/6

source_name: serum, T1DM

value: 25 years

value: 9 months


title: serum microRNA profile of T1DM-6

description: Biological replication 6/6

value: 21 years

value: Male

value: 7 months


title: serum microRNA profile of Control-6

description: Biological replication 6/6


title: serum microRNA profile of Control-5

description: Biological replication 5/6

value: 27 years


title: serum microRNA profile of Control-3

description: Biological replication 3/6

value: 26 years


title: serum microRNA profile of Control-4

description: Biological replication 4/6

value: 8 years


title: 4℃ 3h

description:
Test
CK 3h is the control for SAMPLES 3, 5, 7, 9, 11, 13, 15.
SAMPLE 3


title: serum microRNA profile of Control-2

description: Biological replication 2/6


title: CK 3h

description:
Control
SAMPLE 1


title: control_2

city: Hefei

first: yanqing

last: yang

address: huangshan road 443

institute: USTC

description: Gene expression after sorting peritoneal cavity B1a cells from control mice

hyb_protocol: 6 ug of Cy3-labelled cRNA (specific activity >3.0 pmol Cy3/ul 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 SurePrint G3 Mouse EG Array 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 (G2505C) 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 10.7.1.1 (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: p40-/-CD25+/- mice Peritoneal cavity B1a cell, replicate 2

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.

growth_protocol: All mice were maintained in individually ventilated cages under SPF conditions

extract_protocol: total RNA extracted with an RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Suspended freshly isolated B1a cells in TRIzol reagent.

value: Peritoneal cavity

value: female

tag: genotype

tag: background strain


title: case_1

description: Gene expression after sorting peritoneal cavity B1a cells from p40-/-CD25-/- mice

source_name: p40-/-CD25-/- mice Peritoneal cavity B1a cell, replicate 1


title: case_3

source_name: p40-/-CD25-/- mice Peritoneal cavity B1a cell, replicate 3


title: control_3

source_name: p40-/-CD25+/- mice Peritoneal cavity B1a cell, replicate 3


title: case_2

source_name: p40-/-CD25-/- mice Peritoneal cavity B1a cell, replicate 2


title: serum microRNA profile of T1DM-3

description: Biological replication 3/6

value: 3 months


title: serum microRNA profile of T1DM-2

description: Biological replication 2/6

value: 0 months


title: control_1

source_name: p40-/-CD25+/- mice Peritoneal cavity B1a cell, replicate 1


title: MeJA 6h

description:
Test
CK 6h is the control for SAMPLES 4, 6, 8, 10, 12, 14, 16.
SAMPLE 14

value: Seedling

value: 20 days


title: differentiated PS cells (EB), KhES2

description: Gene expression of EB-formed hPS cells

source_name: EB of KhES2 cells

value: hES cells


title: Control DCs Replicate 5

first: Yilun

last: Wang

address: No.12 Wulumuqi Zhong Road

institute: Fudan University

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

scan_protocol: Microarray images were acquired using an Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (V10.7) was used for background subtraction and Quantile normalization.

source_name: monocyte-derived DCs

label_protocol: Total RNA was amplified using the Low Input Quick Amp WT Labeling kit, according to the manufacturer’s instructions (Agilent Technologies, Santa Clara, USA). 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was translated into cRNA in the presence of Cy3-dCTP and amplified by T7 RNA polymerase.

growth_protocol: PBMC were isolated and monocyte-derived dendritic cells were sorted by positive selection of CD14+ monocytes using magnetic beads. The cells were then cultured for 5-7 days supplemented with GM-CSF and IL-4.  For DC maturation, 1μg/ml LPS  was added to the medium at day 6.

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

tag: diagnosis

value: healthy (control)

value: PBMC

value: dendritic cells


title: Control DCs Replicate 4


title: serum microRNA profile of T1DM-1

description: Biological replication 1/6

value: 16 years

value: Female

value: 6 months


title: ESC_Ts15_rep2

first: Meili

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Gene expression data from Ts15 mES cells

hyb_protocol: The cRNA were hybridized for 16 hr at 45 ℃ on Agilent SurePrint G3 Mouse Gene Expression 8×60 K microarrays. Genechips were washed in 2×SSC (0.2% SDS) at  42 ℃ and in 0.2×SSC at room temperature.

scan_protocol: Arrays were scanned on the Agilent G2565CA Microarray Scanner.

data_processing: The images were processed using Agilent Feature Extraction software, which transformed the image signal to digital signal. The raw expression data were normalized with quantile and 75th percentile shift methods by the GeneSpring GX Software (Agilent).  Probe sets that map to genes on aneuploid chromosomes and chromosome Y were excluded when identifying the values of 75th percentile. The values were log transformed.

source_name: embryonic stem cells, with 3 copies of chromosome 15, P14

label_protocol: RNA was transcribed and labelled with a cRNA amplification kit by Eberwine’s linear RNA amplification method (CapitalBio Corporation) followed the manufacturer’s instructions. cDNA labelled with a fluorescent dye (Cy3-dCTP) was produced following subsequent enzymatic reaction.

growth_protocol: ES cells were cultured on a layer of γ-irradiated SNL76/7 feeder cells in knockout Dulbecco’s modified Eagle’s medium supplemented with 15% fetal bovine serum, 2 mM GlutaMAXTM-1, 1% non-essential amino acids (NEAA), 50 U/ml penicillin, 40 ug/ml streptomycin, and 100 μM β-mercaptoethanol. Cells were cultured at 37°C with 5% CO2 in a humidified environment.

extract_protocol: Total RNA was extracted from diploid and aneuploid mES cells by Trizol (Invitrogen). It was purified by NucleoSpin RNA clean-up kit (MACHEREY-NAGEL) according to the manufacturer’s instructions.

treatment_protocol: ES cells were cultured under normal culture conditions and dissociated with 0.05% Trypsin-EDTA. The harvested cells were then allowed to sit in tissue culture plates for 30-40 min to deplete the feeder cells.

value: embryonic stem cell

tag: karyotype

value: trisomy

tag: strain

value: 129 S7/SvEvBrd


title: ESC_Ts15_rep1

source_name: embryonic stem cells, with 3 copies of chromosome 15, P11


title: Control DCs Replicate 2

tag: tissue


title: serum microRNA profile of T1DM-4

description: Biological replication 4/6

value: 8 years

tag: gender

value: 1 months


title: Control DCs Replicate 3

tag: age


title: SLE DCs Replicate 2

value: systemic lupus erythematosus


title: Control DCs Replicate 1


title: SLE DCs Replicate 3


title: SLE DCs Replicate 1


title: ESC_Ts8_rep2

description: Gene expression data from Ts8 mES cells

source_name: embryonic stem cells, with 3 copies of chromosome 8, P13


title: ESC_Ts8_rep1

description: Gene expression data from Ts8 mES cells

source_name: embryonic stem cells, with 3 copies of chromosome 8, P10


title: ESC_Ts11_rep2

description: Gene expression data from Ts11 mES cells

source_name: embryonic stem cells, with 3 copies of chromosome 11, P11


title: SLE DCs Replicate 5


title: SLE DCs Replicate 4


title: ESC_WT_rep2

description: Gene expression data from AB1 mES cells

source_name: embryonic stem cells, AB1, diploid, P20

value: diploid


title: ESC_Ts6_rep1

description: Gene expression data from Ts6 mES cells

source_name: embryonic stem cells, with 3 copies of chromosome 6, P9


title: PBMC from Healthy Volunteer  7.2 at T0

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

institute: Institut national de la santé et de la recherche médicale-INSERM

description: HV, Biological replicate 7 of 8, Technical replicate 2 of 2

hyb_protocol: 1 mg of Cy5-labeled reference aRNA and 1 mg of Cy3-labeled sample aRNA were hybridized on the array for 16 h at 428C in a sealed chamber (Telechem Int., Sunnyval, CA).

scan_protocol: Hybridized slides were scanned by fluorescence confocal microscopy (ScanArray 3000,GSI-Lumonics) using independent laser excitation of the two fluorescent dyes at 532 and 633 nm at a 10 mm/pixel resolution. Fluorescence values and ratios were extracted with the GenePix Pro 5.1 software.

data_processing: The data were normalized using a lowest fit approach independently applied to each log ratio distributions.

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

label_protocol: All aRNA samples were fragmented using RNA fragmentation Reagents (Ambion) according to the manufacturer’s protocols. Fragmented aRNA  were labeled with Cyanine 3 (Cy3; Amersham Biosciences, Buckinghamshire, UK). As the reference for the hybridization, aRNA were prepared as described from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment. This referential aRNA was pooled and labeled with Cyanine 5 (Cy5). Cyanine incorporation and aRNA quantities were confirmed using a Nanodrop ND1000 spectrometer.

extract_protocol: Ten milliliters of peripheral blood were collected in EDTA tubes. Peripheral Blood Mononuclear Cells (PBMC) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and frozen in Trizol1 reagent (Invitrogen, Life Technologies, CA). One microgram of total RNA (tRNA) of each sample was subjected to amplification using the Amino Allyl MessageAmp TM II aRNA Amplification Kit (Ambion, Austin, TX) according to the manufacturer’s protocols. Quality and quantity of tRNA and amplified RNA (aRNA) was tested by an Agilent 2100 Bioanalyser.

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV007.2

value: PBMC from HV007

tag: individual replicate

value: HV 7 of 8

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: ESC_WT_rep1

description: Gene expression data from AB1 mES cells

source_name: embryonic stem cells, AB1, diploid, P18


title: PBMC from Healthy Volunteer  8.1 at T0

description: HV, Biological replicate 8 of 8, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV008.1

value: PBMC from HV008

value: HV 8 of 8

value: Replicate 1 of 2


title: ESC_Ts6_rep2

description: Gene expression data from Ts6 mES cells

source_name: embryonic stem cells, with 3 copies of chromosome 6, P18


title: PBMC from Healthy Volunteer  8.2 at T0

description: HV, Biological replicate 8 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV008.2


title: ESC_Ts11_rep1

source_name: embryonic stem cells, with 3 copies of chromosome 11, P8


title: PBMC from Healthy Volunteer  7.1 at T0

description: HV, Biological replicate 7 of 8, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV007.1


title: 01_E22021

type: genomic

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

country: Germany

institute: Medizinische Hochschule Hannover

description: hybridized to [OncoScan] Affymetrix OncoScan array

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files were generated after scanning by the Affymetrix GeneChip Command Console (AGCC). These CEL files were further processed using OncoScan Console software version 1.3.0.39 to produce OSCHP files.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal. Data was analyzed using Chromosome Analysis Suite (ChAS) version 3.1.0.15.

molecule: genomic DNA

source_name: primary tumor

label_protocol: as given by the manufacturer (Affymetrix)

growth_protocol: primary formalin fixed parafffin embedded tissue

extract_protocol: genomic DANN was extracted from macrodissected with DNAeasy blood and tissue kit (Qiagen)

tag: tag

value: breast tumor tissue


title: 02_E22021


title: PBMC from Healthy Volunteer  6.2 at T0

description: HV, Biological replicate 6 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV006.2

value: PBMC from HV006

value: HV 6 of 8


title: HEK293_Negative Control (scarmble)_2

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description: Gene expression after 24hr Scramble transfected HEK293T cell

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: HEK293_Negative Control (scarmble)_2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.

growth_protocol: Human embryonic kidney cells HEK293T were maintained in RPMI-1640 media  supplemented with 10% fetal bovine serum (FBS). Cells were grown at 37°C in a humidified 5% CO2 incubator.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: HEK293T were transfected with Scramble or BART6-3p mimics using Lipofectamine 2000 according to the manufacturer’s suggested protocol.

value: embryonic kidney

value: male

tag: cell line


title: G2_NC_48h

first: Yunxia

last: Ge

address: NO.15 Of North Three-ring East Road,Chao Yang District  BEIJING,CHINA

institute: Beijing Universicty of Chemicl Technology

hyb_protocol: 1. Remove preheating in 50 ℃ oven chips, after the heating reaction,the aRNA mixture(215 ul)joined a tube in chip slit   2. After the completion of the set on the second floor heat shrinkable film, completed in the hot water hot shrinkage action, (the second heat shrinkable film must be cut to a third hot shrinkage).  3. After the second hot shrinkage,hybridization oven rotary rack in the 50 ℃ , oven set about speed 2rpm/ min, the reaction time to the next day (about 16 hours).  4. Prepare 42 ℃ hybrid cleaning fluid I, II, and 25 ℃ hybrid cleaning fluid II.  5. Pour a small amount of preheatehd 42 ℃ hybrid cleaning fluid I into the cleaning case and the small box.  6. Unwrapped chips in the small box, remaining in the cleaning case, then clean the chip in the 42 ℃ shocking oven for 5 minutes (speed is 80 rpm).  7. After poured out the hybrid cleaning fluid I, add 42 ℃ hybrid cleaning fluid II, then clean the chip in the 42 ℃ shocking oven for 5 minutes (speed is 80 rpm).  8.After poured out the hybrid cleaning fluid II,then add 25 ℃ hybridization cleaning fluid II, then clean the chip in the 25 ℃ shocking oven for 5 minutes (speed is 80 rpm).Take out the chip after cleaning,   then move up and down in the hybrid cleaning fluid III (about 5 seconds).  9. Chip moisture on dry after chip put in black chip box, avoid light waiting for the scan.

scan_protocol: we use the scanner for Agilent Microarray Scanner (G2505C).By the function of the scanner XDR using PMT 100% and 10% at 10 Um for the resolution of the two scans.Reuse GenePix ™ 4 image data capture, gain Two primary GPR data format file, the last use of hualian chip control probe for two Signal strength of GPR data file conversion, and integrate them into a GPR data file for the follow-up According to the analysis.

data_processing: The data were normalized using Rosetta  Resolver®  System  (Rosetta Biosoftware).

label_protocol: Labeled cRNA were prepared according to the standard Phalanx protocol from 200ng total RNA (OneArray plus RNA amplification kit,Phalanx).

growth_protocol: Volumes used in this protocol are for 25 cm^2 flask; proportionally reduce or increase amount of dissociation medium for culture vessels of other sizes.  Remove and discard culture medium.  Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor.  Add 1.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 1 minutes).  Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal.  Add 3.0 to 4.0 mL of complete growth medium and aspirate cells by gently pipetting.  Add appropriate aliquots of the cell suspension to new culture vessels.  Cultures can be established between 2 x 103 and 1 x 104 viable cells/cm2. Do not exceed 7 x 104 cells/cm2.  Incubate cultures at 37°C.  Interval: Maintain cultures at a cell concentration between 6 X 103 and 6 X 104 cell/cm2.  Subcultivation Ratio: A subcultivation ratio of 1:3 to 1:8 is recommended  Medium Renewal: 2 to 3 times per week

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

treatment_protocol: Twenty nanomolar siRNA or miRNA was used for transfection in serum free medium. Total RNA were prepared after transfection 48h.

tag: cell type

value: epithelial

value: liver

tag: disease status

value: hepatocellular carcinoma

value: 15 years adolescent

tag: race

value: Caucasian


title: 03_E22021


title: G2_siHOTTIP_48h


title: G2_miR-192_48h


title: PBMC from Healthy Volunteer  4.1 at T0

description: HV, Biological replicate 4 of 8, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV004.1

value: PBMC from HV004

value: HV 4 of 8


title: PBMC from Healthy Volunteer  5.2 at T0

description: HV, Biological replicate 5 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV005.2

value: PBMC from HV005

value: HV 5 of 8

value: Replicate 2 of 2


title: HEK293_BART6-3p_1

description: Gene expression after 24hr BART6-3p transfected HEK293T cell


title: HEK293_BART6-3p_2


title: PBMC from Healthy Volunteer  4.2 at T0

description: HV, Biological replicate 4 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV004.2


title: Intermediate day-neutral DNA bulk, replicate 1 & 2

city: Bundoora

first: Mian-Chee

last: Gor

state: Victoria

address: Plenty Road

department: School of Applied Sciences

institute: RMIT University

description: Aromatase gene derived from the ovary tissue of Murray River Rainbowfish (Melanotaenia ﬂuviatilis) was included as a spike-in control to normalise the value for each spot within and between slides.

hyb_protocol: The SDA printed slides were pre-hybridised with a filtered sterilised buffer containing 1 % bovine serum albumin (BSA), 25 % formamide, 5 X SSC and 0.1 % SDS for 45 min at 42 °C. The slides were then rinsed with deionised water and dried with an air gun. The biotin-labelled targets were condensed from 50 µL to approximately 16 µL at 70 °C in the G-Storm GS1 thermal cycler. The concentrated DNA was then mixed with 17.5 µL of 2 X hybridisation buffer (5 X SSC, 0.2 % SDS, 50 % formamide); 0.5 µL of 5 µg/µL Human Cot1 DNA (Invitrogen, Carlsbad, CA), 5 µL of 10 mg/mL PolyA (Sigma-Aldrich, St. Louis, MO) and 0.5 µL of 10 mg/mL salmon sperm DNA (Sigma-Aldrich, St. Louis, MO). The DNA mixture was denatured at 100 °C for 2 minutes and immediately applied under a 22 x 25-mm lifter slip (Grale Scientific, Victoria, Australia) covering the printed areas on the slides. The slides were kept in a humidified hybridisation chamber and incubated overnight at 42 °C in a water bath. After hybridisation, the lifter slips were removed and the slides were washed twice in 1 x SSC and 0.1 % SDS at 45 °C for 5 min; followed by 0.1 x SSC and 0.1 % SDS at room temperature for 5 min; and a final wash of 0.1 x SSC at room temperature for 5 min. The biotinylated DNA was then labelled with FluoroLinkTM streptavidin-labelled CyTM5 dye (Amersham Pharmacia, Buckinghamshire, UK). To detect the biotinylated DNA bound onto the SDA, the slides were washed for 5 min at room temperature in 6 x SSPE-T containing 300 mL of 20 X SSPE (175.3 g of NaCl, 27.6 g of NaH2PO4.2H2O and 7.4 g of EDTA), 50 µL of Triton X-100 and 700 mL of Milli-Q water. They were then immediately overlaid with 200 µL Biotin Detection Solution (200 µL 6 X SSPE-T, 0.8 µL of 25 µg/µL bovine serum albumin and 0.5 µL of 0.8µg/µL streptavidin-labelled CyTM5) under a 25 x 60-mm lifter slip and incubated at 37 °C for 1 hour. Finally, the slides were washed three times in 6 X SSPE-T, rinsed with deionised water and dried with an air gun. All hybridisations were performed with six technical replicates and two biological replicates, resulting in 12 data points per feature.

scan_protocol: Slides were scanned in a ScanArray Gx Microarray Scanner (PerkinElmer, USA) and images were analysed using ScanArray Express® software (PerkinElmer, USA). The slides were scanned at a higher resolution of 10 µm to improve sensitivity and a lower PMT gain at 55 % to reduce the background noise.

data_processing: The signal intensities were then quantified using adaptive circle method and LOWESS normalisation. Data filtering by manual flagging eliminated empty features (negative controls and unbound samples) and bad features (contaminated features or features with high background noise). The minimum signal-to-noise ratio (SNR) of 7 was used for quality measurement. Data analysis included: Calculation of the mean SNR for the spike-in control from six technical replicates and two biological replicates; normalisation of the SNR of each feature against the normalised mean SNR of the spike-in control; and calculation of mean of each feature from six technical replicates and two biological replicates, resulting in a single value per feature.

organism: Fragaria x ananassa

source_name: Intermediate day-neutral strawberry genotypes

label_protocol: The preparation of targets in all cases involved digestion of gDNA with AluI and HaeIII followed by purification with QIAquick PCR Purification Kit (Qiagen, Valencia, CA). Approximately 200 ng of purified digested target DNA was labelled with Biotin-11-dUTP molecules using Biotin DecaLabelTM DNA Labeling Kit (Fermentas, Pittsburgh, PA). The labelling reactions were stopped by adding 1 µL of 0.5 M EDTA after 20 hours incubation at 37 °C and purified again with QIAquick PCR Purification Kit (Qiagen, Valencia, CA).

growth_protocol: Young leaves were harvested for all strawberry genotypes and non-angiosperm species.

extract_protocol: gDNA was extracted from young leaves using Qiagen DNeasy Plant Mini Kit

value: Young leaf

tag: phenotype

value: intermediate day


title: PBMC from Healthy Volunteer  5.1 at T0

description: HV, Biological replicate 5 of 8, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV005.1

value: Replicate 1 of 2


title: Weak day-neutral DNA bulk, replicate 1 & 2

source_name: Weak day-neutral strawberry genotypes

value: weak day


title: Short day DNA bulk, replicate 1 & 2

source_name: Short day strawberry genotypes

value: short day


title: Strong day-neutral DNA bulk, replicate 1 & 2

source_name: Strong day-neutral strawberry genotypes

value: strong day


title: PBMC from Healthy Volunteer  3.2 at T0

description: HV, Biological replicate 3 of 8, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV003.2

value: PBMC from HV003

value: HV 3 of 8


title: G2_miR-204_48h

value: male

value: epithelial

value: liver

value: hepatocellular carcinoma


title: HEK293_Negative Control (scarmble)_1

source_name: HEK293_Negative Control (scarmble)_1

value: embryonic kidney


title: PBMC from Healthy Volunteer  3.1 at T0

description: HV, Biological replicate 3 of 8, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV003.1


title: PBMC from Healthy Volunteer  1.2 at T0

description: HV, Biological replicate 1 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV001.2

value: PBMC from HV001

value: HV 1 of 8


title: Amniotic fluid_E17 mice

city: Hangzhou

first: Ting

middle: ting

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Neuroscience and Anatomy

institute: Zhejiang University School of Medicine

description:
AF17
Experimental animals were commercially-available C57BL/6 mice (SLAC, Shanghai, China).

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA microRNA Array, 6th generation (Exiqon) according to array manual.

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities >=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: Amniotic fluid, E17

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: All mice were raised in pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Cellular fractions of amniotic fluid was collected by centrifugation at 1000 g for 10 min and then the total RNA was harvested using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy mini kit (QIAGEN) according to the manufacturers' instructions.

treatment_protocol: After three days of acclimatization period, two females were kept with one male for 12 h during the night. In the morning of the test day, the simultaneous presence of vaginal plug and spermatozoa in vaginal cytology was considered as day 0 of gestation. The pregnancy was further confirmed by weight increase of female mice.

tag: strain/background

value: amniotic fluid

tag: developmental stage


title: PBMC from Healthy Volunteer  2.2 at T0

description: HV, Biological replicate 2 of 8, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV002.2

value: PBMC from HV002

value: HV 2 of 8

value: Replicate 2 of 2


title: Amniotic fluid_E15 mice

description:
AF15
Experimental animals were commercially-available C57BL/6 mice (SLAC, Shanghai, China).

source_name: Amniotic fluid, E15


title: PBMC from Healthy Volunteer  2.1 at T0

description: HV, Biological replicate 2 of 8, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), HV002.1

value: Replicate 1 of 2