title: IL-33 activated mLN ILC2s at week 2, biological rep 2

description: W2 mLN ILC2s_2


title: SVH04

status: Public on Jun 30 2016

type: genomic

city: Fitzroy

first: Ruth

middle: N

last: MacKinnon

state: Vic

address: PO Box 2900

department: Victorian Cancer Cytogenetics Service

country: Australia

institute: St Vincent's Hospital (Melbourne)

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Illumina Karyostudio version 1.2

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow from 75-year-old male with MDS (RAEB-1)

label_protocol: Illumina CytoSNP 12 arrays were processed using manufacturer's protocol

growth_protocol: SVH07 was cultured overnight in RPMI with 5% foetal bovine serum and cytogenetic preparations prepared by KCl treatment and fixation with methanol:acetic acid 3:1

extract_protocol: DNA was extracted with the Qiagen DNeasy Cell and Tissue kit

treatment_protocol: SVH06 was stored uncultured at 4 degrees Celcius for four days. SVH06 and fixed SVH07 specimens were then stored at -80 degrees Celcius before DNA extraction.

tag: age

tag: Sex

value: male

tag: tissue

value: bone marrow

tag: diagnosis

value: MDS (RAEB-1)


title: WT 3

type: RNA

city: San Diego

first: Gavin

last: Lewis

state: Ca

address: 3210 Merryfield Row

department: Immunology

country: USA

institute: Janssen R&D

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCSD Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Iterplier algorithm for gene-level estimates. Bonferoni P value <0.001 and an Intensity value >100 using VAMPIRE software

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Healthy female

label_protocol: GeneChip labeling kit per manufacturer (Ambion)

growth_protocol: CD4+ PD1+ CD49d+ CD8a- splenic T cells were FACS sorted based on congenic marker.

extract_protocol: RNA was isolated from cell pellet using RNeasy Micro Kit (Qiagen) and  amplified (Ambion) according to the manufacturer’s instructions.

value: Male

tag: infection

value: LCMV

tag: genotype/variation

value: WT

value: Spleen

tag: cell type

value: CD4+ T cell


title: IL-33 activated lung ILC2s at 4 months, biological rep 2

city: Vancouver

first: Laura

last: Mathae

state: British Columbia

address: 675 W.10th Ave

country: Canada

institute: British Columbia Cancer Research Centre

description: 4M lung ILC2s_2

hyb_protocol: cDNA was prepared from total RNA using Nugen Pico WTA kit according to the manufacturer's protocol. Fragmented cDNA was labeled and hybridized to Affymetrix GeneChip Mouse Gene 2.0ST Array. Washing and staining were performed by Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed by Expression Console software by Affymetrix. Normalization was performed using RMA algorithm (by FlexArray 1.6.3).

source_name: Mus musculus lung ILC2s 4 months after intranasal IL-33 treatment

label_protocol: Labeling was performed using Nugen Encore biotin kit according to the manufacturer's instructions.

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

tag: time point

value: 4 months

value: lung

value: Group 2 innate lymphoid cells

tag: strain


title: TGFbRII KO 3

value: TGFbRII KO


title: IL-33 activated lung ILC2s at 4 months, biological rep 1

description: 4M lung ILC2s_1


title: TGFbRII KO 2


title: IL-33 activated lung ILC2s at week 2, biological rep 1

description: W2 lung ILC2s_1

source_name: Mus musculus lung ILC2s 2 weeks after intranasal IL-33 treatment

value: week 2


title: TGFbRII KO 1


title: SVH06

source_name: bone marrow from 61-year-old female with AML

value: female

value: AML


title: SVH07

source_name: bone marrow from 82-year-old female with MDS (RAEB-2)

value: MDS (RAEB-2)


title: IL-33 activated lung ILC2s at week 2, biological rep 3

description: W2 lung ILC2s_3


title: IL-33 activated lung ILC2s at week 2, biological rep 2

description: W2 lung ILC2s_2


title: IL-33 activated mLN ILC2s at day 4, biological rep 1

description: D4 mLN ILC2s_1

source_name: Mus musculus mLN ILC2s 4 days after intranasal IL-33 treatment

value: day 4

value: mediastinal lymph node (mLN)


title: IL-33 activated lung ILC2s at day 4, biological rep 2

description: D4 lung ILC2s_2

source_name: Mus musculus lung ILC2s 4 days after intranasal IL-33 treatment


title: IL-33 activated lung ILC2s at day 4, biological rep 3

description: D4 lung ILC2s_3


title: IL-33 activated lung ILC2s at day 4, biological rep 1

description: D4 lung ILC2s_1


title: naive lung ILC2s, biological rep 2

description: Naive lung ILC2s_2

source_name: Mus musculus naive lung ILC2s

value: naive


title: lung_RIP4ko_rep3

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: shRNA against RIP4

hyb_protocol: Affymetrix mouse gene 2.0ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 3.7μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0002)

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).  Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA), using the Affymetrix Expression Console Software (version 1.3.0.187)

data_processing: R/Bioconductor package xps (v 1.30.0), robust multi-array average (RMA) algorithm

label_protocol: cDNA was generated from RNA using Ambion WT Expression kit (4411973, Life Tech). cDNA was fragmented and labeled with GenChip WT Terminal Labeling Kit (901525, Affymetrix)

extract_protocol: RNA was extracted from freshly harvested tumors using trizol. Extracted RNA was further purified using Sodium acetate, glycogen and ethanol to remove traces of trizol.

treatment_protocol: Mice were infected with lentivirus expressing shp53 (control) or shRIP4 at 13 weeks of age. 18.5 weeks later the tumors were extracted

value: lung tumors

value: RIP4 KO

value: 32 weeks


title: Maternal Blood_8503

city: Newtown Square

first: Don

middle: A.

last: Baldwin

state: PA

address: 4240 Fairview Ave

institute: Signal Biology Inc

hyb_protocol: Manufacturer's protocols for hybridization and washes using Human Gene 1.1ST Array Plates (Affymetrix, Santa Clara CA, USA).

scan_protocol: Manufacturer's protocols for GeneTitan instrument (Affymetrix, Santa Clara CA, USA).

data_processing: Affymetrix Expression Console, Partek Genomics Suite with RMA normalization.

source_name: Maternal Blood

label_protocol: The Ovation Pico WTA System v2 (NuGEN Technologies, San Carlos CA, USA) was used with 50 ng of input total RNA, providing linear expansion of all transcripts without interference from ribosomal or globin RNAs. The resulting cDNA was labeled with biotin (Encore Biotin Module, NuGEN).

extract_protocol: Maternal and fetal cord blood samples collected in PAXgene Blood RNA tubes were processed according to the vendor’s protocol (PreAnalytiX/Qiagen, Valencia CA, USA) for purification of total RNA. Tissue samples, collected in TRIzol, were homogenized before phase separation with chloroform, and RNA in the aqueous phase was purified using RNeasy spin columns (Qiagen, Valencia CA, USA). RNA quality and quantity were assessed by spectrophotometry and on a Bioanalyzer 2100 with RNA 6000 Nano LabChips (Agilent Technologies, Santa Clara CA, USA).

tag: subject id

tag: gender

value: Female

tag: tissue type

value: Maternal Blood

tag: outcome

value: TL term with labor


title: WT 2

value: Male

value: LCMV

value: WT

value: Spleen

value: CD4+ T cell


title: WT 1


title: Decidua_8503

source_name: Decidua

value: Decidua


title: Lower Segment_8502

source_name: Lower Segment

value: Lower Segment

value: TNL term no labor


title: lung_RIP4ko_rep1

description: shRNA against RIP4


title: lung_control_rep2

description: shRNA against p53 (control)

value: control


title: lung_control_rep3

description: shRNA against p53 (control)


title: Chorion_8503

source_name: Chorion

value: Chorion


title: HSC,Old,floxedAhr,rep6

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: Arrays were hybridized overnight with 2.8 ug cDNA using using an Affymetrix hyb station, with hybridization solutions and conditions recommended by the kit manufacturer (Nugen).

scan_protocol: After arrays were washed they were stained with phycoerythrin-streptavidin as recommended by Affymetrix (including anti-SAPE antibody enhancement), and phycoerythrin fluorescence was determined with an Affymetrix scanner. Affymetrix Cammand Console software was used to control the scanner and generate raw image files (DAT) and to consolidate data from individual pixels into array features (CEL files).

data_processing: CEL files were quantile normalized and background subtracted with the Iterplier algorithm of Affymetrix Expression Console. Data from probes for which there was no association with a known gene in the Affymetrix annotations were removed from the analysis.

source_name: hematopoietic stem cells, Ahr-KO mouse

label_protocol: Biotinylated cDNA was prepared from total RNA with the Nugen WT-Ovation PicoSL Kit.

growth_protocol: Mice were weaned at 3 weeks and fed ad libitum thereafter.

extract_protocol: Mice were killed by carbon dioxide inhalation at either 2 (young) or 18 months of age (old). Bone marrow was depleted of Lin+ cells as described by Singh et al. 2009 (Carcinogenesis 30;11-19). SLAM+ HSC were extracted from Lin- cells as described by Kiel et al. 2005 (Cell 121;1109-1121). Selected cells were collected in RNAlater reagent (Ambion) and frozen at -80C until total RNA was extracted with a Micro RNeasy kit (Qiagen).

value: hematopoietic stem cells, Ahr-KO mouse

tag: genotype

value: floxed Ahr


title: HSC,Old,floxedAhr,rep5


title: HSC,Old,floxedAhr,rep4


title: lung_control_rep1

description: shRNA against p53 (control)

value: lung tumors


title: Decidua_8502


title: HSC,Old,floxedAhr,rep3


title: Placenta_8502

source_name: Placenta

value: Placenta


title: lung_RIP4ko_rep2

description: shRNA against RIP4

value: RIP4 KO

value: 32 weeks


title: Maternal Blood_8502

value: Female

value: Maternal Blood


title: Fundus_8502

source_name: Fundus

value: Fundus


title: HSC,Old,floxedAhr,rep1


title: HSC,Old,floxedAhr,rep2


title: naive lung ILC2s, biological rep 1

description: Naive lung ILC2s_1

value: naive

value: lung

value: Group 2 innate lymphoid cells


title: HSC,Young,floxedAhr,rep3


title: Cord Blood_8502

source_name: Cord Blood

value: Cord Blood


title: HSC,Young,floxedAhr,rep4


title: Chorion_8502


title: HSC,Young,floxedAhr,rep1


title: HSC,Young,floxedAhr,rep5


title: HSC,Old,AhrKO,rep5

value: Ahr knockout


title: HSC,Old,AhrKO,rep4


title: HSC,Old,AhrKO,rep6


title: HSC,Old,AhrKO,rep2


title: Lower Segment_5650

value: Lower Segment

value: PNL preterm no labor


title: HSC,Young,floxedAhr,rep2


title: HSC,Old,AhrKO,rep1


title: Amnion_8502

source_name: Amnion

value: Amnion

value: TNL term no labor


title: HSC,Old,AhrKO,rep3

value: hematopoietic stem cells, Ahr-KO mouse


title: HSC,Young,AhrKO,rep5


title: Maternal Blood_5650


title: Chorion_5650

value: Chorion


title: HSC,Young,AhrKO,rep1


title: Decidua_5650

value: Decidua


title: Cord Blood_5650


title: HSC,Young,AhrKO,rep3


title: HSC,Young,AhrKO,rep4


title: Fundus_5650


title: Lower Segment_5648

value: TL term with labor


title: Placenta_5648

value: Placenta


title: Amnion_5650

value: Female


title: Maternal Blood_5648

value: Maternal Blood


title: Fundus_5648

value: Fundus


title: HSC,Young,AhrKO,rep2


title: Amnion_5648


title: Fundus_5647

value: PL preterm with labor


title: Chorion_5648


title: Maternal Blood_5647


title: Placenta_5647


title: Cord Blood_5646


title: Fundus_5637

value: pPROM no labor


title: Cord Blood_5648


title: Chorion_5637


title: Placenta_5627


title: Cord Blood_5647


title: Placenta_5637


title: Amnion_5637


title: Maternal Blood_5627


title: Fundus_5549


title: Decidua_5627


title: Lower Segment_5647


title: Placenta_5549


title: Lower Segment_5549


title: Amnion_5627


title: Fundus_5627


title: Cord Blood_5549


title: Decidua_5549


title: Chorion_5549


title: Placenta_5548


title: Maternal Blood_5544

value: pPROM with labor


title: Lower Segment_5544


title: Lower Segment_5548


title: Lower Segment_5627


title: Amnion_5548


title: Cord Blood_5627

value: Cord Blood


title: Amnion_5544


title: Chorion_5544


title: Fundus_5544


title: Amnion_5539


title: Lower Segment_5539


title: Lower Segment_5537


title: Cord Blood_5548


title: Fundus_5537


title: Maternal Blood_5549


title: Chorion_5537


title: Maternal Blood_5539


title: Chorion_5539


title: Cord Blood_5537


title: Decidua_5539


title: Decidua_5544


title: Lower Segment_5535


title: Placenta_5535


title: Maternal Blood_5535


title: Decidua_5537


title: Maternal Blood_5537


title: Chorion_5535


title: Cord Blood_5535


title: Fundus_5535


title: Amnion_5535


title: Decidua_5535


title: Placenta_5534


title: Decidua_5534


title: Fundus_5531


title: Cord Blood_5534


title: Chorion_5534


title: Maternal Blood_5531


title: Lower Segment_5531


title: Placenta_5531


title: Chorion_5531


title: Decidua_5531


title: Cord Blood_5531


title: Amnion_5534


title: Lower Segment_5524


title: Fundus_5524


title: Decidua_5524


title: Amnion_5531


title: Cord Blood_5524


title: Amnion_5524


title: Amnion_5537


title: Lower Segment_5523


title: Fundus_5523


title: Cord Blood_5523


title: Decidua_5523


title: Chorion_5524


title: Lower Segment_5520


title: Placenta_5520


title: Maternal Blood_5524


title: Maternal Blood_5523


title: Fundus_5520


title: Maternal Blood_5520


title: Amnion_5523


title: Chorion_5523


title: Amnion_5520


title: Fundus_5517


title: Placenta_5517


title: Lower Segment_5517


title: Cord Blood_5520


title: Maternal Blood_5517


title: Decidua_5517


title: Decidua_5520


title: rdm4 mutant at 3h after chilling rep2

city: Wuhan, Hubei Province

first: Zhulong

last: Chan

address: Moshan, Wuchang District

department: Wuhan Botanic Garden

country: China

institute: Chinese Academy of Sciences

description: Gene expression without chilling treatment

hyb_protocol: Fragmented cRNAs (15 μg) were hybridized to the 24K GeneChip Arabidopsis ATH1 Genome Array (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned with a GeneChip® Scanner 3000 (Affymetrix), and raw image files were converted to probe set data (*.CEL files), using the Affymetrix GeneChip® Operating Software according to the manufacturer’s instructions.

data_processing:
All of the raw data (*.CEL files) were then analyzed using the affylmGUI package in the statistical computing environment R
All genes with a P value < 0.05 and a fold-change > 2 were chosen for further analysis

organism: Arabidopsis thaliana

source_name: rdm4 mutant, chilling treatment for 3h, replicate 2

label_protocol: Total RNA from rdm4 and C24 WT seedlings with or without cold treatment (0, 3 or 48 h) was and used to make biotin-labeled cRNA targets. Two biological replicates from different growth chambers were prepared for each combination of ecotype and cold treatment.

growth_protocol: Arabidopsis seeds of rdm4 mutant and Col WT were sown in MS plates and grown at 23/18°C in a growth room with a 16-h light/8-h dark cycle at 150 μmol m-2s-1 and 70% relative humidity

extract_protocol: Total RNA was extracted and purified from leaves of at least 30 seedlings per plate using QIAGEN-RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to guidelines specified by the manufacturer. Two biological replicates were prepared for each combination. RNA was quantified using a Nanodrop-ND 8000 spectrophotometer (Thermo Fisher Scientific) and RNA quality was assessed by agarose gel analysis and using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol. Samples with the RNA integrity number of 7.5 and above were chosen for further analysis.

treatment_protocol: Two-week-old seedlings were transferred to 4 degree for 0, 3, and 48 h. Plant materials were then collected for RNA extraction.

value: leaf

tag: ecotype

value: Col


title: rdm4 mutant at 48h after chilling rep2

description: Gene expression after 3h of chilling treatment

source_name: rdm4 mutant, chilling treatment for 48h, replicate 2


title: Fundus_5512


title: rdm4 mutant without chilling rep2

description: Gene expression after 48h of chilling treatment

source_name: rdm4 mutant, control, replicate 2


title: Chorion_5517


title: Amnion_5517


title: Cord Blood_5517


title: Placenta_5512


title: C24 WT at 48h after chilling rep2

source_name: Col WT, chilling treatment for 48h, replicate 2

value: wildtype


title: Chorion_5512


title: rdm4 mutant at 3h after chilling rep1

source_name: rdm4 mutant, chilling treatment for 3h, replicate 1


title: C24 WT without chilling rep2

description: Gene expression after drought stress treatment

source_name: Col WT, control, replicate 2


title: Amnion_5512

value: Amnion


title: rdm4 mutant at 48h after chilling rep1

source_name: rdm4 mutant, chilling treatment for 48h, replicate 1


title: Maternal Blood_5512

value: TNL term no labor


title: C24 WT at 3h after chilling rep1

source_name: Col WT, chilling treatment for 3h, replicate 1


title: rdm4 mutant without chilling rep1

source_name: rdm4 mutant, control, replicate 1


title: Lower Segment_5503

value: Lower Segment


title: Decidua_5512

source_name: Decidua


title: C24 WT at 48h after chilling rep1

source_name: Col WT, chilling treatment for 48h, replicate 1


title: Cord Blood_5512


title: Lower Segment_5512

source_name: Lower Segment


title: C24 WT at 3h after chilling rep2

source_name: Col WT, chilling treatment for 3h, replicate 2


title: C24 WT without chilling rep1

source_name: Col WT, control, replicate 1


title: H157_MNU_72h_rep2

city: Athens

first: Olga

last: Papadodima

address: 48, Vasileos Konstantinou av.

country: Greece

institute: National Hellenic Research Foundation

description: SAMPLE 33

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Background-corrected values were log2 transformed and normalized using Quantile method.

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

growth_protocol: H157 cells were grown in RPMI 1640 and A549 in DMEM (containing glucose 4.5 g/l, L-glutamine and pyruvate), both media supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin.

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

treatment_protocol: Cells were treated with N-methyl-N-nitrosourea (MNU) or DMSO as control for 24, 48 and 72h.

tag: cell line

value: non-small-cell lung cancer (NSCLC) cell line

tag: treatment

value: N-methyl-N-nitrosourea (MNU)


title: Lower Segment_2517


title: Decidua_2517

value: Decidua


title: H157_MNU_48h_rep2

description: SAMPLE 28


title: Chorion_2517

source_name: Chorion

value: Chorion


title: H157_MNU_72h_rep1

description: SAMPLE 32


title: H157_DMSO_72h_rep2

description: SAMPLE 31

value: DMSO


title: H157_DMSO_72h_rep1

description: SAMPLE 30


title: H157_DMSO_48h_rep3

description: SAMPLE 26


title: Placenta_2517

source_name: Placenta

value: Female

value: Placenta


title: Fundus_2517

source_name: Fundus

value: Fundus


title: Maternal Blood_2517

source_name: Maternal Blood

value: Maternal Blood

value: pPROM no labor


title: Decidua_2512

value: PL preterm with labor


title: H157_MNU_48h_rep3

description: SAMPLE 29


title: Chorion_2512


title: H157_MNU_48h_rep1

description: SAMPLE 27


title: Amnion_2517

source_name: Amnion


title: Cord Blood_2515

source_name: Cord Blood

value: Cord Blood

value: PNL preterm no labor


title: Cord Blood_2512


title: H157_DMSO_48h_rep2

description: SAMPLE 25


title: Placenta_2513


title: H157_MNU_72h_rep3

description: SAMPLE 34


title: H157_DMSO_24h_rep3

description: SAMPLE 20


title: H157_DMSO_48h_rep1

description: SAMPLE 24


title: H157_MNU_24h_rep1

description: SAMPLE 21


title: H157_MNU_24h_rep3

description: SAMPLE 23


title: H157_MNU_24h_rep2

description: SAMPLE 22


title: H157_DMSO_24h_rep2

description: SAMPLE 19


title: H157_DMSO_24h_rep1

description: SAMPLE 18


title: A549_MNU_72h_rep1

description: SAMPLE 16


title: Lower Segment_2510

value: TL term with labor


title: Decidua_2510


title: Chorion_2510


title: Maternal Blood_2510


title: Placenta_2510


title: A549_MNU_72h_rep2

description: SAMPLE 17


title: Lower Segment_2508

value: pPROM with labor


title: Amnion_2510

value: Amnion


title: Cord Blood_2510


title: A549_DMSO_72h_rep1

description: SAMPLE 13


title: A549_DMSO_72h_rep2

description: SAMPLE 14


title: A549_DMSO_72h_rep3

description: SAMPLE 15


title: A549_MNU_48h_rep3

description: SAMPLE 12


title: Fundus_2508


title: A549_DMSO_48h_rep3

description: SAMPLE 9


title: Maternal Blood_2508


title: A549_MNU_24h_rep2

description: SAMPLE 5


title: A549_MNU_48h_rep1

description: SAMPLE 10


title: A549_MNU_24h_rep3

description: SAMPLE 6


title: A549_DMSO_48h_rep2

description: SAMPLE 8


title: Cord Blood_2508


title: Chorion_2508


title: A549_DMSO_24h_rep3

description: SAMPLE 3


title: Amnion_2508


title: A549_DMSO_48h_rep1

description: SAMPLE 7


title: A549_MNU_24h_rep1

description: SAMPLE 4


title: Placenta_2507

value: TNL term no labor


title: A549_MNU_48h_rep2

description: SAMPLE 11

value: non-small-cell lung cancer (NSCLC) cell line


title: Lower Segment_2506

value: Lower Segment


title: Maternal Blood_2506


title: Glucose, biological rep.2

city: Higashihiroshima

first: Ken

last: Oda

state: Hiroshima

address: 3-7-1 Kagamiyama

department: Fundamental research division

country: Japan

institute: National research institute of brewing

description: Gene expression data from 1hr glucose induction

hyb_protocol: The fragmented cRNA was hybridized to an AoDNAChip.  The A. oryzae GeneChip microarray (AoDNAChip; NCBI Gene Expression Omnibus [GEO] platform GPL16184) which was designed by Affymetrix was used for transcriptome analysis using probes of 13,765 ORFs set on this microarray.

scan_protocol: This GeneChip was washed, stained, and scanned  using a GeneChip FS-450 ﬂuidics station (ﬂuidics protocol FS450_001) and a GeneChip 3000 scanner.

data_processing: Scanned probe array images were converted into CEL ﬁles and normalized using the GCOS v.1.4 program (Affymetrix). Calculations of signal intensity and detection P values were also performed using GCOS v.1.4. The trimmed mean signal of the array was scaled to the target signal of 500 with the all probe sets scaling option. The detection call was used for detection of a particular transcript, with a detection P value of < 0.04 considered present (P), 0.04 ≦P < 0.06 considered marginal (M), and a  P value of ≧ 0.06 considered absent (A). These calculation data were exported as CHP ﬁles. For microarray data analysis, CHP ﬁles were imported into GeneSpring v.7.3 (Agilent Technologies). Expression data were normalized per chip to the 50th percentile. Genes with statistically signiﬁcant changes in transcript abundance were identiﬁed using a cutoff value of 2-fold and a Welch’s t test value of less than 5%.

organism: Aspergillus oryzae RIB40

source_name: A.oryzae 1hr induction in glucose medium

label_protocol: Fragmented biotin-labeled cRNA was prepared using a GeneChip one-cycle target labeling and control reagent kit (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: Aspergillus oryzae RIB40 were pre-cultured in MM medium (1g glucose, 3g  glutamate, 2 g NH4Cl, 1 g (NH4 )2SO4 , 0.5 g KCl, 1 g KH2 PO4 , 0.5 g MgSO47H2O, 0.02 g FeSO4 , 1.5 g L -methionine, in 1liter, pH6.5) at 100rpm for 24hr at 30°C. Mycelia was recovered by filtration using Miracloth (Calbiochem) and transferred to 100ml of each induction medium. MM and GM (MM+1% galactose without glucose), and SM (MM+1% sorbitol without glucose) medium were used. Induction culture was performed at 100rpm for 1hr at 30°C with each three medium.

extract_protocol: Mycelium was frozen by liquid N2 and ground. Total RNA was extracted with Isogen (Wako) according manufacturer’s instruction. Total RNA was puriﬁed for microarray analysis using an RNeasy minikit (Qiagen). RNA quality was determined using a BioAnalyzer 2100 system (Agilent Technology), and the quantity was determined using an Ultrospec 3300 pro spectrophotometer (Amersham Pharmacia Biotech).

treatment_protocol: Induction culture was performed at 100rpm for 1hr at 30°C with each three medium. Mycelium was harvested with Miracloth, washed with ice-chilled water twice and was dried with paper towel.

tag: condition

value: glucose 1hr induction


title: Placenta_2506


title: Sorbitol, biological rep.2

description: Gene expression data from 1hr sorbitol induction

source_name: A.oryzae 1hr induction in sorbitol medium

value: sorbitol 1hr induction


title: Galactose, biological rep.2

description: Gene expression data from 1hr galacotse induction

source_name: A.oryzae 1hr induction in galactose medium

value: galactose 1hr induction


title: Glucose, biological rep.1


title: Decidua_2508

value: Female

value: Decidua


title: Fundus_2506

value: Fundus


title: CD3+T_twin_27_2

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

description: Healthy human donors

hyb_protocol: 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B (GE CodeLink) are brougth to a final volume of 260 μl with water and then incubated at 90 oC for 5 minutes and immediately chill on ice for 5–30 minutes. 250 μl of hybridization reaction mixture are injected into array slides, slides are shaked at 300 rpm and incubated for 18–24 h at 37 oC.

scan_protocol: Detection of the hybridizations occurs via Cy-5-conjugated streptavidin. Analysis is performed with CodeLink Expression Analysis software.

data_processing: raw data have been log2 processed, then a quantile normalization was applied

source_name: CD3+ T lymphocytes

label_protocol: Biotin-labelled cRNA target is prepared by a linear amplification method starting from total extracted RNA plus control bacterial mRNA.

extract_protocol: Peripheral blood mononuclear cells were obtained from 20 ml whole blood by Ficoll gradient separation. CD3+ T lymphocytes were separated by negative magnetic cell sorting (MACS, Miltenyi Biotec) using Pan T-cell Kit II (Miltenyi Biotec) microbeads. Purity and viability of samples were determined by flow cytometry, labelling T-cells respectively with mAb CD3-FITC and propidium iodide. Purity and viability were >95% in all cases. The resulting purified cell population was resuspended in TRIzol Reagent (Invitrogen, Paisley, UK) and stored at -80°C before RNA extraction.

tag: age (years)

tag: Sex

value: F


title: A549_DMSO_24h_rep2

description: SAMPLE 2

value: DMSO


title: A549_DMSO_24h_rep1

description: SAMPLE 1


title: Chorion_2506

value: Chorion


title: CD3+T_twin_27_1

description: Healthy human donors


title: Amnion_2506


title: Cord Blood_2506

value: Cord Blood


title: Galactose, biological rep.1


title: CD3+T_twin_26_1

description: Healthy human donors


title: NONc 22w biological rep2 (microRNA)

city: Edogawa-ku

first: Tsuyoshi

last: Hirata

state: Tokyo

address: 1-16-13, Kitakasai

department: Discovery Science and Technology Department

institute: DAIICHI SANKYO RD NOVARE CO., LTD

description: GeneChip miRNA 3.0 Array

hyb_protocol: Labeled RNA was hybridyzed for 16 hr at 48°C on GeneChip miRNA 3.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed using the Robust Multiarray Average and differentially expressed genes between two groups were identified by R/Bioconductor using limma package.

source_name: pancreas from 22-week old NONcNZO10/LtJ mouse

label_protocol: Total RNA was labeled with FlashTag Biotin HSR.

extract_protocol: Preserved pancreases in RNA later were homogenized using TRIzol, and total RNA, including small RNA, was isolated using PureLink RNA Mini (Life Technologies) according to the manufacturer’s protocol. After DNase treatment with RNase-Free DNase Set (QIAGEN), 10 volume of QIAzol to one volume of total RNA solution was added and the total RNA, including small RNA, was cleaned-up using an miRNeasy Mini Kit (QIAGEN).

tag: tissue

value: pancreas

tag: age


title: NONc 22w biological rep3 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Lower Segment_2504

value: PNL preterm no labor


title: CD3+T_twin_25_2

description: Healthy human donors


title: Placenta_2504

value: Placenta


title: CD3+T_twin_26_2

description: Healthy human donors


title: NONc 13w biological rep3 (microRNA)

description: GeneChip miRNA 3.0 Array

source_name: pancreas from 13-week old NONcNZO10/LtJ mouse


title: NONc 13w biological rep2 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Placenta_2505


title: CD3+T_twin_24_2

description: Healthy human donors

value: M


title: NONc 13w biological rep1 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Maternal Blood_2504

value: Maternal Blood


title: CD3+T_twin_23_2

description: Healthy human donors


title: NONc 22w biological rep1 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Decidua_2504

source_name: Decidua


title: CD3+T_twin_25_1

description: Healthy human donors


title: NONc 7w biological rep3 (microRNA)

description: GeneChip miRNA 3.0 Array

source_name: pancreas from 7-week old NONcNZO10/LtJ mouse


title: CD3+T_twin_23_1

description: Healthy human donors


title: NONc 7w biological rep2 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Chorion_2504


title: NONc 7w biological rep1 (microRNA)

description: GeneChip miRNA 3.0 Array


title: Chorion_2503

value: PL preterm with labor


title: Amnion_2504

value: Amnion


title: Maternal Blood_2503


title: CD3+T_twin_22_2

description: Healthy human donors


title: CD3+T_twin_21_1

description: Healthy human donors


title: Amnion_2503


title: CD3+T_twin_22_1

description: Healthy human donors


title: CD3+T_twin_21_2

description: Healthy human donors


title: Lower Segment_2502

source_name: Lower Segment

value: Lower Segment

value: TNL term no labor


title: CD3+T_twin_20_2

description: Healthy human donors


title: MP17_(miRNA-3_0)

city: Shanghai

first: Feng

last: Xu

state: Shanghai

address: 600 Yishan Road

department: Hematology

institute: Shanghai Jiaotong University Affiliated Sixth People's Hospital

hyb_protocol: RNA was labeled and hybridized to the array according to the manufacturer's instructions.

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

data_processing:
Statistical analysis was performed using Partek Genomics Suite software (Partek Inc., St. Louis, MO, USA). A robust multi-array average (RMA) algorithm was used to normalize the data. The false discovery rate (FDR) was less than 0.2 to minimize the false identification of genes. Changes greater than 2-fold were analyzed for up- or down-regulated genes.
Normalized probe intensity and allele ratio data were visualized in Nexus v7.5.

source_name: CD34+ cells

label_protocol: Labelling were performed according to protocols from Affymetrix

growth_protocol: primary MDS CD34+ cells, no growth protocol

extract_protocol: Total RNA was extracted from CD34+ cells of primary MDS at diagnosis using the Qiagen RNA Blood Mini Kit. RNA quality and quantity was assessed using a Spectrophotometer and agarose gel electrophoresis.

value: bone marrow

value: CD34+ cells

tag: diagnosis

value: myelodysplastic syndromes


title: CD3+T_twin_19_2

description: Healthy human donors


title: Placenta_2509

value: Female


title: MP19_(miRNA-3_0)

tag: cell type


title: MP16_(miRNA-3_0)


title: Maternal Blood_2502


title: MP15_(miRNA-3_0)


title: MDSL_(miRNA-3_0)


title: Fundus_2502

value: Fundus


title: CD3+T_twin_24_1

description: Healthy human donors


title: MP21_(miRNA-3_0)


title: CD3+T_twin_20_1

description: Healthy human donors


title: CD3+T_twin_19_1

description: Healthy human donors

value: F


title: Decidua_2502

value: Decidua


title: Chorion_2502

value: Chorion


title: MP14_(miRNA-3_0)


title: CD3+T_twin_17_2

description: Healthy human donors


title: Cord Blood_2502

value: Cord Blood


title: MP12_(miRNA-3_0)


title: Amnion_2502


title: CD3+T_twin_18_2

description: Healthy human donors


title: MP2_(miRNA-3_0)


title: p53 shRNA, rep2

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

hyb_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing:
The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: MDA-MB-468_p53si-1 lentiviral shRNA

growth_protocol: MDA-MB-468 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37°C, 5% CO2.

extract_protocol: Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm.

treatment_protocol: Cells were transduced with either a non-targeting lentiviral shRNA (NS) or a p53-targeting lentiviral shRNA (p53si-1)

value: Breast cancer cell line

tag: transduced with

value: lentiviral shRNA targeting endogenous p53-R273H mutant (p53si-1)


title: MP8_(miRNA-3_0)


title: Decidua_2506

value: TL term with labor


title: CD3+T_twin_18_1

description: Healthy human donors


title: HC14_(miRNA-3_0)

value: normal volunteers


title: MP1_(miRNA-3_0)


title: CD3+T_twin_16_1

description: Healthy human donors

value: M


title: Non-targeting shRNA, rep 2

label_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA). The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.

value: non-targeting shRNA (NS)


title: CD3+T_twin_15_2

description: Healthy human donors


title: CD3+T_twin_15_1

description: Healthy human donors


title: p53 shRNA, rep1


title: HC12_(miRNA-3_0)


title: RDM4 overexpression after 48h chilling treatment rep2

description: Gene expression at 4 degree for 48 h

hyb_protocol: Microarray analysis was performed using Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version). In total 150ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe with the help of low RNA input linear amplification/labeling kit  (Agilent technologies) and 1.65µg of Labeled cRNA probes were fragmented using fragmentation buffer (Agilent Technologies) and hybridized to the Arabidopsis arrays according to manufacturer’s instructions.

scan_protocol: The arrays were scanned using the high resolution array scanner (Agilent technologies) with the appropriate settings for the one color gene expression arrays after hybridization.

data_processing:
Array images were acquired with Agilent's dual-laser microarray scanner and signal intensities were extracted from the scanned images with dedicated Agilent Feature Extraction software (Agilent technologies). The outliers and the abnormal features were flagged and the data was normalized using the intra-array percentile shift normalization (threshold of 75 and above) and median based inter-array normalization. The GeneSpring software (Agilent technologies) was used to calculate the intensity ratios and fold changes.
All the genes with a P value below 0.05 and a fold change above 2 were chosen for further analysis.

source_name: RDM4 OX, 4 degree for 48 h, replicate 2

growth_protocol: Arabidopsis seeds of RDM4 overexpression lines and Col WT were sown in MS plates and grown at 23/18°C in a growth room with a 16-h light/8-h dark cycle at 150 μmol m-2s-1 and 70% relative humidity

value: leaf

tag: genotype/variation

value: Col


title: CD3+T_twin_17_1

description: Healthy human donors


title: Non-targeting shRNA, rep 1


title: HC9_(miRNA-3_0)

value: bone marrow


title: CD3+T_twin_16_2

description: Healthy human donors


title: RDM4 overexpression after 48h chilling treatment rep1

description: Gene expression at 4 degree for 48 h

source_name: RDM4 OX, 4 degree for 48 h, replicate 1

label_protocol: Microarray analysis was performed using Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) (Probe Name version). In total 150ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled probe with the help of low RNA input linear amplification/labeling kit  (Agilent technologies) and 1.65µg of Labeled cRNA probes were fragmented using fragmentation buffer (Agilent Technologies) and hybridized to the Arabidopsis arrays according to manufacturer’s instructions.


title: RDM4 overexpression after 3h chilling treatment rep2

description: Gene expression at 4 degree for 3 h

source_name: RDM4 OX, 4 degree for 3 h, replicate 2


title: CD3+T_twin_13_2

description: Healthy human donors


title: CD3+T_twin_14_1

description: Healthy human donors


title: HC8_(miRNA-3_0)

value: CD34+ cells


title: Sorbitol, biological rep.1

value: sorbitol 1hr induction


title: CD3+T_twin_11_2

description: Healthy human donors


title: RDM4 overexpression after 3h chilling treatment rep1

description: Gene expression at 4 degree for 3 h

source_name: RDM4 OX, 4 degree for 3 h, replicate 1


title: CD3+T_twin_12_1

description: Healthy human donors


title: CD3+T_twin_13_1

description: Healthy human donors


title: Col after 48h chilling treatment rep2

description: Gene expression at 4 degree for 48 h

source_name: Col WT, 4 degree for 48 h, replicate 2

value: wildtype


title: HC4_(miRNA-3_0)


title: CD3+T_twin_11_1

description: Healthy human donors


title: CD3+T_twin_14_2

description: Healthy human donors


title: CD3+T_twin_10_1

description: Healthy human donors


title: Col after 3h chilling treatment rep2

description: Gene expression at 4 degree for 3 h

source_name: Col WT, 4 degree for 3 h, replicate 2


title: Col room temperature rep2

description: Gene expression at room temperature

source_name: Col WT, room temperature, replicate 2


title: CD3+T_twin_12_2

description: Healthy human donors


title: Col after 3h chilling treatment rep1

description: Gene expression at 4 degree for 3 h

source_name: Col WT, 4 degree for 3 h, replicate 1


title: CD3+T_twin_10_2

description: Healthy human donors


title: Col room temperature rep1

description: Gene expression at room temperature

source_name: Col WT, room temperature, replicate 1


title: Male gonad_11m

city: Guangzhou City

first: Zhang

last: Xiujuan

state: Guangdong Province

address: 105 Xingang West Road, Haizhu District

institute: Guangdong Entomological Institute

description: earlier sex differentiation

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Acipenser schrenckii

source_name: Male gonad

label_protocol: The assay started from 2 to 5 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using miRNeasy Kit(Qiagen, 217004), following the manufacturer's recommended protocol.

value: Male

value: gonad

value: normal

value: 11 months


title: CD3+T_twin_9_2

description: Healthy human donors

source_name: CD3+ T lymphocytes


title: NF_9

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

hyb_protocol: Standard Illumina Hybridization Protocol

scan_protocol: Standard Illumina Scanning Protocol

data_processing: The image was processed using Illumina's GenomeStudio Software, and the probe level data was quantile normalized across samples with no background subtraction

source_name: Nodular fasciitis

label_protocol: 200ng of RNA from each sample was subjected to Human WG-DASL Assay with Human HT12 v4.0 BeadChips (Illumina)

extract_protocol: Total RNA was extracted from FFPE materials using miRNeasy FFPE Kit (Qiagen)

value: Nodular fasciitis

value: with USP6 fusion


title: HC6_(miRNA-3_0)


title: Caco-2_Control_5

city: Pamplona

first: Fermin

middle: I

last: Milagro

state: Navarra

address: c/ Irunlarrea 1

department: Centre for Nutrition Research

country: Spain

institute: University of Navarra

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: Human enterocytes,non-treated, sample5

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: Caco-2 cells were maintained in an incubator set at 37°C and 5% carbon dioxide and 90% of relative humidity. The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, gibco), 1% of non-essential amino acids (NEAA, Lonza, Basel, Switzerland), 1% penicillin (10000 U/mL)-streptomicyn (10000 μg/mL) (Gibco) and 1% amphoterizin B (250 μg/mL, Gibco). The culture medium was changed every 2 days. Once cells reached 80% confluence, confirmed by microscopic observance, they were dissociated with 0.05% trypsin-EDTA solution and subcultured on a 75 cm2 flasks at a density of 250000 cells per cm2. The cells were seeded in 6-well cell culture plate at 30 000 cells per cm2. Culture medium was replaced every 2 days until the day of the experiment. Experiments were conducted 15-19 days post-seeding.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: For the experiments, cells were treated with standard LPS from E. coli K12 strain- TLR4 ligand (InvivoGen, San Diego, CA, USA). Concentrations of LPS (1 μg/mL) and time of exposure (48h) were established based on previous studies. Before LPS stimulation, some samples were pre-treated with 50 μM of trans-resveratrol, dissolved in ethanol, kindly provided by Prof. María Puy Portillo (Nutrition and Obesity group, University of the Basque Country, Vitoria, Spain). This dose was reported to be a realistic polyphenol concentration commonly found in the gut following the intake of 500 mg of polyphenols. Upon 1h of incubation at 37°C, cell cultures were stimulated with endotoxin as previously mentioned. Untreated cells were used as controls.

value: Non-treated


title: RDM4 overexpression room temperature rep2

description: Gene expression at room temperature

source_name: RDM4 OX, room temperature, replicate 2


title: CD3+T_twin_9_1

description: Healthy human donors


title: MP9_(miRNA-3_0)

value: myelodysplastic syndromes


title: Female gonad_11m

description: earlier sex differentiation

source_name: Female gonad

value: Female


title: Col after 48h chilling treatment rep1

description: Gene expression at 4 degree for 48 h

source_name: Col WT, 4 degree for 48 h, replicate 1


title: Caco-2_Control_4

source_name: Human enterocytes,non-treated, sample4


title: CD3+T_twin_8_2

description: Healthy human donors

value: F


title: CD3+T_twin_7_2

description: Healthy human donors


title: AhDOF OE normal condition

city: Irapuato

first: John P

last: Délano-Frier

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Biotechnology and Biochemistry

country: Mexico

institute: CINVESTAV Irapuato

description:
Plants growth under normal conditions
AhDOF.OE

hyb_protocol: For pre-hybridization, the slide was re-hydrated with water vapor at 60ºC and fixed with two cycles of UV ligth. Then, the slide was submerged in boiling water for two minutes (92ºC) and washed with 95% ethanol for one minute. After that, the oligo array was prepared for hybridization in a buffer solution 5X SSC, 0.1% SDS and 1% BSA for one hour at 41ºC. Finally, the array was washed and dried for hybridization. Equal quantities of labeled cDNA were hybridized to the Arabidopsis array using hybridization solution UniHyb (TeleChem International INC) for 14 hr at 42ºC.

scan_protocol: Scanned on an ScanArray 4000 scanner with ScanArray 4000 software from Packard BioChips.

data_processing: The analysis of the microarray data: background correction, Lowess normalization, intensity filter and selection of differentially expressed genes, was performed with the software genArise (http://www.ifc.unam.mx/genarise/). The identification of differentially expressed genes was done by the calculation of a Z score using a sliding-window approach, where the algorithm calculates the mean and standard deviation (SD) within a window surrounding each data point to define a Z score, where Z is the number of SD a data point is from the window mean. To obtain the Z score, the next formula was applied, zi = (Ri - mean(R))/sd(R), where zi is the Z score for a given data point, Ri is the log ratio of signal intensity for each element, mean(R) and sd(R) are the mean and SD of the log ration of signal intensity of the surrounding window. Only the elements with an absolute Z score greater than 2 were considered differentially expressed (|Zscore| > 2) (Cheteleadle et al., 2003).

source_name: Rossete leaves, 5-week old Wt plants

label_protocol: Total RNA were used for cDNA synthesis incorporating Alexa555 or Alexa647 making use of First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was tested by measuring the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: Arabidospis plants were grown in controlled conditions of light (photosynthetic photon flux density (PPFD) of ≈ 200 µmol m-2 s-1), photoperiod (16 h light/ 8 h dark) and temperature (22 ± 1°C).

extract_protocol: Total RNA was extracted from 100–200 mg of frozen rosette tissue with the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, with modifications. These consisted of the addition of a salt solution (sodium citrate 0.8 M + 1.2 M NaCl) during precipitation in a 1:1 v/v ratio with isopropanol and further purification with LiCl (8 M) for one hour at 4°C. All RNA samples were analyzed by formaldehyde agarose gel electrophoresis and visual inspection of the ribosomal RNA bands upon ethidium bromide staining.

treatment_protocol: In specified cases, plants were subjected to 5 days of water stress. Tissue was collected at day 5 and 24 hrs later after the reestablishment of normal watering. Also, in specified cases, plants were watered with 40mL of a 400mM NaCl solution for three straight days.

tag: ecotype background

value: wild type

value: Rossete leaves

tag: growth condition

value: normal condition

source_name: Rossete leaves, 5-week old transgenic plants

tag: ecotype/background

value: overexpressing AhDOF


title: Caco-2_Control_1

source_name: Human enterocytes,non-treated, sample1


title: Caco2_LPS+RSV_5

source_name: Human enterocytes, stimulated with lipopolysaccharide-treated with resveratrol, sample5

value: Resveratrol pretreatment, 1h, 50 Μm


title: NF_5


title: CD3+T_twin_8_1

description: Healthy human donors


title: CD3+T_twin_7_1

description: Healthy human donors


title: AhDOF OE salt stress

description:
Tissue leaves from plants watered with 40 mL of a 400mM NaCl solution three days in a row
AhDOF.OE.SaltStress

value: salt stress


title: NF_8


title: Caco-2_Control_2

source_name: Human enterocytes,non-treated, sample2


title: NF_6


title: Caco-2_Control_3

source_name: Human enterocytes,non-treated, sample3


title: NF_4


title: Caco2_LPS+RSV_4

source_name: Human enterocytes, stimulated with lipopolysaccharide-treated with resveratrol, sample4


title: NF_2


title: NF_3


title: CD3+T_twin_6_2

description: Healthy human donors

value: M


title: AhERF OE water stress

description:
Tissue was collected from plants subjected to a non-irrigation treatment for 5 days
AhERF.OE.WaterStress

value: water stress

value: overexpressing AhERF


title: CD3+T_twin_6_1

description: Healthy human donors


title: AhERF OE recovery

description:
Tissue leaves were collected 24 hrs after normal watering was reestablished in water-stressed plants
AhERF.OE.Recovery

value: recovery


title: CD3+T_twin_5_2

description: Healthy human donors


title: AhERF OE normal conditions

description:
Plants were growth under normal conditions
AhERF.OE


title: Caco2_LPS+RSV_2

source_name: Human enterocytes, stimulated with lipopolysaccharide-treated with resveratrol, sample2


title: NF_1


title: Caco2_LPS+RSV_1

source_name: Human enterocytes, stimulated with lipopolysaccharide-treated with resveratrol, sample1


title: Caco2_LPS+RSV_3

source_name: Human enterocytes, stimulated with lipopolysaccharide-treated with resveratrol, sample3


title: CD3+T_twin_5_1

description: Healthy human donors

source_name: CD3+ T lymphocytes


title: Caco2_LPS_5

source_name: Human enterocytes, stimulated with lipopolysaccharide,sample5

value: LPS exposure, 48h, 1μg/Ml


title: Caco2_LPS_2

source_name: Human enterocytes, stimulated with lipopolysaccharide,sample2


title: Caco2_LPS-4

source_name: Human enterocytes, stimulated with lipopolysaccharide,sample4


title: Caco2_LPS_3

source_name: Human enterocytes, stimulated with lipopolysaccharide,sample3


title: CD3+T_twin_4_1

description: Healthy human donors


title: CD3+T_twin_4_2

description: Healthy human donors


title: rabbit basilar artery SMC_hemodynamic insult_rep3

first: Zhaolong

last: Zhang

address: Changhai Road 168

department: Neurosurgery

institute: Changhai Hospital

description: hemodynamic insult

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit in Hybridization Oven, according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit, followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

organism: Oryctolagus cuniculus

source_name: rabbit basilar artery smooth muscle cells, exposed to hemodynamic insult in vivo, 5 days,rep3.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color  following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit

growth_protocol: Rabbits were euthanized by intravenous administration of 100 mg/kg sodium pentobarbital. Then the whole basilar arteries were removed. The arteries were cleaned in PBS buffer,cannulated and perfused at a constant flow with a cocktail which contains PBS and 0.4 mg/ml elastase (Sigma) and 1 mg/ml collagenase (type 1A, Sigma). After an incubation time of 45 min, the tissue left was removed and stored in PBS. Smooth muscle cells were released from the artery by trituration. Then total RNA was extracted from the rabbit basilar artery smooth muscle cells.

extract_protocol: Total RNA was extracted using TRIZOL Reagent 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). Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set .

treatment_protocol: In the case groups, bilateral common carotid arteries of female New Zealand White rabbits were ligated to increase vascular flow.The control group was performed the same procedure to expose the common carotid arteries without ligation. Rabbits were euthanized by intravenous administration of 100 mg/kg sodium pentobarbital at day 5 after ligation or exposure of bilateral CCAs in both groups (n=3 for each group). The rabbits used and all procedures in this study were approved by the local Institutional Animal Care and Use Committee.

value: rabbit basilar artery smooth muscel cells

value: hemodynamic insult


title: CD3+T_twin_3_2

description: Healthy human donors


title: Caco2_LPS_1

source_name: Human enterocytes, stimulated with lipopolysaccharide,sample1


title: CD3+T_twin_2_1

description: Healthy human donors


title: CD3+T_twin_2_2

description: Healthy human donors


title: CD3+T_twin_3_1

description: Healthy human donors


title: rabbit basilar artery SMC_hemodynamic insult_rep2

description: hemodynamic insult

source_name: rabbit basilar artery smooth muscle cells, exposed to hemodynamic insult in vivo, 5 days,rep2.


title: rabbit basilar artery SMC_sham control_rep3

description: sham control

source_name: rabbit basilar artery smooth muscle cells, sham control, rep3.

value: sham control


title: CD3+T_twin_1_1

description: Healthy human donors


title: CD3+T_twin_1_2

description: Healthy human donors


title: rabbit basilar artery SMC_sham control_rep2

description: sham control

source_name: rabbit basilar artery smooth muscle cells, sham control, rep2.


title: rabbit basilar artery SMC_hemodynamic insult_rep1

description: hemodynamic insult

source_name: rabbit basilar artery smooth muscle cells, exposed to hemodynamic insult in vivo, 5 days,rep1.


title: RDM4 overexpression room temperature rep1

description: Gene expression at room temperature

source_name: RDM4 OX, room temperature, replicate 1

value: leaf

value: Col


title: CKO.4

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to theIllumina MouseRef-8 v2.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Group gene profile option of this software was used.

label: Biotin

source_name: Pals1 CKO with hGFAP-Cre

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

value: cerebellum tissue

value: Pals1 fl/fl;Cre+

tag: developmental stage


title: CKO.3


title: rabbit basilar artery SMC_sham control_rep1

description: sham control

source_name: rabbit basilar artery smooth muscle cells, sham control, rep1.


title: WT.3

source_name: WT

value: Pals1 fl/fl;Cre-


title: CKO.1


title: WT.4


title: WT.2


title: CKO.2


title: mbf1 embryo

city: Taian

first: Dan

last: Wang

state: Shandong

address: No. 61 Daizong Street

institute: Shandong Agricultural University

description: Gene expression data from mbf1 embryos

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Following Affymetrix GeneChip Expression Analysis 2000 manual.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Drosophila melanogaster

source_name: Drosophila mbf1 embryos

label_protocol: Biotinylated cRNA probes were prepared from total RNA of each sample following the Affymetrix IVT labeling protocol.

growth_protocol: Incubate embryos for 16 hours after egg laying on an apple juice plate at 25°C.

extract_protocol: Total RNA was extracted separately for each of the yw and homozygous mbf1 mutant embryos using the QIAGEN RNeasy isolation kit.

treatment_protocol: mbf1 mutant embryos could be achieved directly.

value: embryo

tag: genotype


title: WT.1


title: yw embryo

description: Gene expression data from yw embryos

source_name: Drosophila yw embryos

value: yw


title: yw embryo

first: Chong

middle: lei

last: Fu

description: Gene expression data from yw embryos

extract_protocol: Total RNA was extracted separately for each of the yw and homozygous mid mutant embryos using the QIAGEN RNeasy isolation kit.

treatment_protocol: mid mutant embryos were identified using CyOact-GFP balancer chromosome.


title: mid embryo

description: Gene expression data from mid embryos

source_name: Drosophila mid embryos

value: mid


title: NF_7

source_name: Nodular fasciitis

value: Nodular fasciitis

value: with USP6 fusion


title: InVivoThyroid_24h_injectionof0kBq_animal4

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

country: Sweden

institute: Gothenburg university

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: Quantile normalized using Partek

organism: Rattus norvegicus

source_name: Thyroid, 0 kBq, 24 h

label_protocol: Standard Agilent labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Animals were intra venously injected with 131I accordoing to activities described above.

tag: strain

value: Sprague Dawley


title: patient 17 / cyst 18

city: The Hague

first: Edgar

last: Wills

address: Andrej Sacharowstraat 37

department: Gastroenterology & Hepatology

country: Netherlands

institute: RadboudUMC

hyb_protocol: Affymetrix Cytoscan HD array manufacturer's protocol

data_processing:
ChAS analysis suite
affymetrix-algorithm-name: CYTO2
affymetrix-algorithm-version: 1.2.0
affymetrix-array-type: CytoScanHD_Array
affymetrix-algorithm-param-ArraySet: CytoScanHD_Array
program-name: apt-copynumber-cyto
program-version: 1.14.3-rc5

source_name: cyst epithelium

extract_protocol: DNA isolation by QIAamp DNA Micro kit (Qiagen, Hilden, Germany) according to manufacturer's protocol

tag: subject status

value: patients with polycystic or sporadic hepatic cysts

tag: patient id

value: patient 17

tag: gender

value: Female

tag: tissue/cell type

value: cyst epithelium


title: patient 1 / peripheral blood

scan_protocol: Affymetrix Cytoscan HD array manufacturer's protocol

source_name: peripheral blood

value: patient 1

value: Male

value: peripheral blood


title: patient 14 / cyst 15

label_protocol: Affymetrix Cytoscan HD array manufacturer's protocol

value: patient 14


title: patient 21 / cyst 22

source_name: cyst fluid cells

value: patient 21

value: cyst fluid cells


title: patient 18 / cyst 19

value: patient 18


title: InVivoThyroid_24h_injectionof0kBq_animal3


title: patient 20 / cyst 21

value: patient 20


title: patient 15 / cyst 16

value: patient 15


title: patient 12 / cyst 13

value: patient 12


title: Adrenal Gland

city: Ghent

first: Sarah

last: Vergult

state: Not Applicable

address: De Pintelaan 185, MRB, second floor

country: Belgium

institute: Ghent University

hyb_protocol: 600 ng 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 25 µl containing 10x Gene Expression Blocking Agent and 25x Fragmentation Buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) 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 10.5 (Agilent) using protocol GE1_105_Dec08 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Adrenal Gland

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

extract_protocol: RNA samples were bought from Agilent and Stratagene

value: adrenal gland


title: InVivoThyroid_24h_injectionof0kBq_animal2


title: patient 6 / cyst 6

value: patient 6


title: patient 11 / cyst 12

value: patient 11


title: patient 16 / cyst 17

value: patients with polycystic or sporadic hepatic cysts

value: patient 16


title: patient 9 / cyst 10

value: patient 9

value: Female


title: patient 8 / peripheral blood

value: patient 8


title: patient 10 / cyst 11

value: patient 10


title: patient 23 / cyst 24

value: patient 23


title: patient 13 / cyst 14

value: patient 13


title: patient 22 / cyst 23

value: patient 22


title: patient 3 / cyst 3

value: patient 3

value: cyst fluid cells


title: InVivoThyroid_24h_injectionof1300kBq_animal2

source_name: Thyroid, 1300 kBq, 24 h

value: Sprague Dawley


title: InVivoThyroid_24h_injectionof4700kBq_animal4

source_name: Thyroid, 4700 kBq, 24 h


title: InVivoThyroid_24h_injectionof4700kBq_animal2


title: patient 7 / cyst 7

value: patient 7


title: Kidney

source_name: Kidney

value: kidney


title: InVivoThyroid_24h_injectionof4700kBq_animal1


title: patient 18 / peripheral blood

value: patient 18

value: peripheral blood


title: InVivoThyroid_24h_injectionof1300kBq_animal3


title: patient 5 / cyst 5

value: patient 5


title: patient 8 / cyst 9

value: patients with polycystic or sporadic hepatic cysts

value: cyst epithelium


title: patient 19 / cyst 20

value: patient 19


title: patient 8 / cyst 8

value: Female


title: InVivoThyroid_24h_injectionof1300kBq_animal1


title: Fetal Brain

source_name: Fetal Brain

value: fetal brain


title: patient 2 / cyst 2

value: patient 2


title: InVivoThyroid_24h_injectionof0kBq_animal1


title: Colon

source_name: Colon

value: colon


title: InVivoThyroid_24h_injectionof760kBq_animal4

source_name: Thyroid, 760 kBq, 24 h


title: InVivoThyroid_24h_injectionof760kBq_animal3


title: patient 4 / cyst 4

value: patient 4


title: InVivoThyroid_24h_injectionof4700kBq_animal3


title: InVivoThyroid_24h_injectionof760kBq_animal2


title: Occipital Cortex

source_name: Occipital Cortex

value: occipital cortex


title: Striatum

source_name: Striatum

value: striatum


title: Whole Adult brain

source_name: Whole Adult brain

value: whole brain


title: InVivoThyroid_24h_injectionof340kBq_animal4

source_name: Thyroid, 340 kBq, 24 h

value: Sprague Dawley


title: Brain Parietal Cortex

source_name: Brain Parietal Cortex

value: brain parietal cortex


title: Liver

source_name: Liver

value: liver


title: InVivoThyroid_24h_injectionof760kBq_animal1


title: Frontal Cortex

source_name: Frontal Cortex

value: frontal cortex


title: Brain Stem

source_name: Brain Stem

value: brain stem


title: InVivoThyroid_24h_injectionof1300kBq_animal4


title: Lung

source_name: Lung

value: lung


title: InVivoThyroid_24h_injectionof340kBq_animal3


title: InVivoThyroid_24h_injectionof340kBq_animal2


title: Breast

source_name: Breast

value: breast


title: Cerebellum

source_name: Cerebellum

value: cerebellum


title: InVivoThyroid_24h_injectionof340kBq_animal1


title: Patient 12

city: Caen cedex 05

first: Christophe

last: DENOYELLE

address: 3 Avenue général Harris BP 5026

department: Centre de Lutte Contre le Cancer François Baclesse

country: France

institute: Université de Caen Normandie

hyb_protocol: Then samples were hybridized during 16 hours at 48°C on GeneChip microRNA V4 arrays of Affymetrix.

scan_protocol: Scan performed with scanner GC30007G (Affymetrix).

data_processing: Raw data were normalized using Expression Console (Affymetrix) based on RMA method.

source_name: Patient 12

label_protocol: Small RNAs were labelled with Flash Tag Biotin HSR kit according to manufacter's (Genisphere) recommendations.

extract_protocol: Small RNAs were isolated using the Macherey-Nagel NucleoSpin® miRNA Plasma kit

value: blood serum

tag: Stage

value: patients with FIGO stages III/IV

tag: condition

value: Ovarian cancer patient


title: InVivoThyroid_24h_injectionof260kBq_animal3

source_name: Thyroid, 260 kBq, 24 h


title: InVivoThyroid_24h_injectionof260kBq_animal2


title: InVivoThyroid_24h_injectionof170kBq_animal3

source_name: Thyroid, 170 kBq, 24 h


title: InVivoThyroid_24h_injectionof260kBq_animal1


title: InVivoThyroid_24h_injectionof170kBq_animal1


title: Patient 11

source_name: Patient 11

tag: tissue


title: InVivoThyroid_24h_injectionof170kBq_animal4


title: InVivoThyroid_24h_injectionof170kBq_animal2


title: Patient 8

source_name: Patient 8


title: InVivoThyroid_24h_injectionof260kBq_animal4


title: Patient 9

source_name: Patient 9


title: Patient 10

source_name: Patient 10


title: Patient 5

source_name: Patient 5


title: Patient 6

source_name: Patient 6


title: InVivoThyroid_24h_injectionof88kBq_animal4

source_name: Thyroid, 88 kBq, 24 h


title: Patient 4

source_name: Patient 4


title: InVivoThyroid_24h_injectionof9kBq_animal3

source_name: Thyroid, 9 kBq, 24 h


title: Patient 7

source_name: Patient 7


title: InVivoThyroid_24h_injectionof88kBq_animal1


title: Patient 3

source_name: Patient 3


title: Patient 2

source_name: Patient 2


title: InVivoThyroid_24h_injectionof88kBq_animal2


title: InVivoThyroid_24h_injectionof88kBq_animal3


title: InVivoThyroid_24h_injectionof9kBq_animal1


title: patient 1 / cyst 1

source_name: cyst fluid cells

value: patients with polycystic or sporadic hepatic cysts

value: patient 1

value: Male

value: cyst fluid cells


title: InVivoThyroid_24h_injectionof9kBq_animal2


title: InVivoThyroid_24h_injectionof9kBq_animal4


title: Patient 1

source_name: Patient 1


title: Heart

source_name: Heart

value: heart


title: MP14_(PrimeView)

description: GeneChip® PrimeView™ Human Gene Expression Array

data_processing: Statistical analysis was performed using Partek Genomics Suite software (Partek Inc., St. Louis, MO, USA). A robust multi-array average (RMA) algorithm was used to normalize the data. The false discovery rate (FDR) was less than 0.2 to minimize the false identification of genes. Changes greater than 2-fold were analyzed for up- or down-regulated genes.

source_name: CD34+ cells

value: bone marrow

value: myelodysplastic syndromes


title: HC9_(PrimeView)

value: normal volunteers


title: HC12_(PrimeView)


title: HC14_(PrimeView)


title: MP15_(PrimeView)


title: MP1_(PrimeView)


title: MP17_(PrimeView)


title: MP16_(PrimeView)


title: MP12_(PrimeView)


title: MP19_(PrimeView)


title: MDSL_(PrimeView)


title: MP21_(PrimeView)


title: HC8_(PrimeView)


title: HC6_(PrimeView)


title: MP8_(PrimeView)


title: UPN6-post

city: bei jing

first: Jing

last: Nie

state: bei jing

address: 28 fuxing road

institute: PLA General Hospital

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

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

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

source_name: UPN6 2 cycles following decitabhine therapy

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

growth_protocol: PBLs were isolated from heparinized blood by Ficoll-Hypaque density gradient centrifugation.

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

treatment_protocol: Solid tumor patients were given decitabine therapy as 10 mg per day for 5 days/28 day cycle, and the blood samples were collected before and after 2 cycles of decitabine therapy.

tag: disease state

value: solid tumor patient

value: PBMC


title: UPN7-post

source_name: UPN7 2 cycles following decitabhine therapy


title: HC4_(PrimeView)


title: MP9_(PrimeView)


title: MP2_(PrimeView)


title: Control biological replicate 1 [C1]

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

country: India

institute: CSIR-National Environmental Engineering Research Institute

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and RMA as normalization method used. The probes of intensities less than the 20.0 percentile in the raw data were excluded.

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

growth_protocol: HOS cells grown in MEM media containing 10% fetal bovine serum.

extract_protocol: Total RNA prepared using RNeasy mini kit.

treatment_protocol: Treated with 8 ppm (8 mg/L) of fluoride for 30 days.

tag: cell line

value: HOS

tag: cell type

value: osteosarcoma cell line

tag: exposed to

value: none (untreated control)


title: Treated biological replicate 3 [T3]

value: fluoride (8 ppm) for 30 days


title: Treated biological replicate 1 [T1]


title: Patient 13

source_name: Patient 13

value: blood serum


title: Treated biological replicate 2 [T2]


title: Control biological replicate 3 [C3]


title: UPN7-pre

source_name: UPN7 baseline


title: UPN6-pre

source_name: UPN6 baseline


title: Sh#9

city: Amiens

first: Antoine

last: Galmiche

address: avenue Laennec

institute: Centre Hospitalier Universitaire Amiens

description: Gene expression data from shRb cells. This is the third of the three biological replicates used in this study.

hyb_protocol: Hybridization was performed on Gene Atlas array strips (Human Gene 2.1 ST Array Strip) at 48°C for 19 hours on the Affymetrix GeneAtlas Hybridization Station.

scan_protocol: Strips were scanned using the Gene Atlas imaging station.

data_processing: Data were normalized using the Expression Console software (Affymetrix) using default RMA-sketch normalization. Normalized .chp files were then analyzed using TAC software (Affymetrix) using default settings.

source_name: shRb cells

label_protocol: Labeling was performed according to the GeneChip WTPLUS Reagent kit protocol

growth_protocol: cells were cultivated in DMEM with 10 % fetal calf serum and exposed to sorafenib (10 µM) for 9h

extract_protocol: Total RNA was extracted using the Trizol protocol.  DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (thermo scientific) and RNA quality was assessed using the agilent 2100 Bioanalyzer with an RNA pico chip kit. All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire 5Université de picardie Jules Verne, Amiens).

treatment_protocol: Cells were treated with 10µM Sorafenib for 9 hours. After nine hours treatment, culture medium was removed and replaced by Trizol. Cells were then collected and immediately frozen in liquid nitrogen.

value: hepatocarcinoma cells

value: shRb

tag: treatment


title: Sh+S#10

description: Gene expression data from Sorafenib treated shRb cells. This is the first of the three biological replicates used in this study.

source_name: Sorafenib treated (10 µM) shRb cells 9 hours of treatment

value: Sorafenib


title: WBC_Formaldehyde_Rep5

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from circulating white blood cells of cynomologus macaques exposed to filtered air for 2-day, 6-hour whole body inhalation exposure

hyb_protocol: Following fragmentation, cRNA was hybridized on the Cynomolgus Gene 1.0 ST Array.

scan_protocol: Microarrays were scanned using Affymetrix Microarray Scanner.

data_processing: Dana were normalized by robust multi-chip averging using Partek® Genomics Suite TM software (version 6.5)

label: terminal deoxynucleotidyl transferase (TdT) in the presence of a proprietary biotinylated compound, GeneChip® DNA Labeling Reagent

organism: Macaca fascicularis

source_name: white blood cells from male cynomolgous macaque collected immediately following the second 6-hour exposure to 6 ppm formaldehyde

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

extract_protocol: Nasal epithelial tissue samples were disrupted and homogenized using a TissueRuptor (Qiagen) and RNA isolated using the AllPrep DNA/RNA/Protein kit (Qiagen). WBC samples were homogenized using QIAshredders (Qiagen) and RNA isolated using the AllPrep DNA/RNA/Protein kit. Extracted RNA was quantified with a Nanodrop 1000 spectrophotometer (Thermo Scientific, Waltham, MA) and its integrity verified with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol:
Animals were exposed, sedated, and euthanized using protocols approved by the Lovelace Respiratory Research Institute’s animal care and use committee.
A total of 14 primates received two consecutive days of 6-hour whole body inhalation exposures consisting of either filtered air (n = 6) or a target of 6 ppm formaldehyde (n = 8). To generate the exposure conditions, deuterated/13C labeled paraformaldehyde (Cambridge Isotope Laboratories, Inc) was vaporized and directed through a delivery line and into a Tedlar® bag. During each of the exposures, Tedlar® bags were diluted with pre-filtered air and delivered to the chambers. Chamber concentrations were monitored approximately twice per hour by collecting Waters XpoSure Aldehyde Sampler cartridges for five minutes. Cartridges were extracted with acetonitrile and analyzed by high-performance liquid chromatography. The average chamber formaldehyde concentrations during the exposure days ranged between 6.0 and 6.5 ppm.

value: circulating white blood cells

value: male


title: Sh+S#12

description: Gene expression data from Sorafenib treated shRb cells. This is the third of the three biological replicates used in this study.


title: WBC_Formaldehyde_Rep2


title: WBC_Formaldehyde_Rep3


title: Sh+S#11

description: Gene expression data from Sorafenib treated shRb cells. This is the second of the three biological replicates used in this study.


title: Huh+S#6

description: Gene expression data from Huh7 Sorafenib treated cells. This is the second of the two biological replicates used in this study.

source_name: Sorafenib treated (10µM) Huh7 cells  9 hours of treatment


title: Sh#7

description: Gene expression data from shRb cells. This is the first of the three biological replicates used in this study.


title: Sh#8

description: Gene expression data from shRb cells. This is the second of the three biological replicates used in this study.


title: WBC_Formaldehyde_Rep4


title: WBC_Air_Rep4

source_name: white blood cells from male cynomolgous macaque collected immediately following the second 6-hour exposure to filtered air


title: WBC_Air_Rep5


title: Huh#3

description: Gene expression data from Huh7 cells. This is the second of the two biological replicates used in this study.

source_name: Huh7 cells


title: Huh#1

description: Gene expression data from Huh7 cells. This is the first of the two biological replicates used in this study.


title: WBC_Air_Rep3


title: WBC_Air_Rep2


title: WBC_Formaldehyde_Rep1


title: YAPS94A -5

city: Basel

first: Yann

last: Abraham

address: Postfach

department: NIBR/DMP

institute: Novartis Pharma AG

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed using a custom Bioconductor script based on the affycoretools package

source_name: HuCCT1 cholangiocarcinoma cell line

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 - Affymetrix Hybridization control kit (including B2)

growth_protocol: HuCCT1 cells were maintained in RPMI-1640 supplemented with 10% (v/v) fetal bovine serum, 2mM L-Glutamine, 1mM sodium pyruvate and 0.1mM MEM non-essential amino acids

extract_protocol: Total RNA was isolated from cells using the RNeasy Plus mini kit according to the manufacturer’s instructions (Qiagen). RNA quality was assessed with the RNA 6000 Nano Kit (Agilent). 500 µg RNA of each sample were reverse-transcribed using the high capacity cDNA reverse transcription kit (Applied Biosystems)

tag: vector


title: Huh+S#5


title: DEP treated HBE_No3

city: Nanjing

first: Xiaobo

last: Li

address: Dingjiaqiao 87

institute: Southeast University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant miRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated miRNAs.

source_name: HBE cells

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: human bronchial epithelial (HBE) cell line

value: diesel exhaust particles (DEP)


title: DEP treated HBE_No2


title: WBC_Air_Rep1


title: Nose_Formaldehyde_Rep4

description: Gene expression data from nasal epithleium of cynomologus macaques exposed to 6ppm formaldehyde for 2-day, 6-hour whole body inhalation exposure

source_name: nasal epithleium of male cynomolgus macaque collected immediately following the second 6-hour exposureto 6 ppm formaldehyde

value: nasal epithleium


title: DEP treated HBE_No1


title: YAPS94A -3


title: Nose_Formaldehyde_Rep3


title: wild type HBE _No3

value: control


title: Nose_Air_Rep4

description: Gene expression data from nasal epithleium of cynomologus macaques exposed to filtered air for 2-day, 6-hour whole body inhalation exposure

source_name: nasal epithleium of male cynomolgus macaque collected immediately following the second 6-hour exposure to filtered air


title: Nose_Formaldehyde_Rep1


title: Nose_Formaldehyde_Rep2


title: Nose_Air_Rep3


title: YAPS94A -1


title: YAPS94A -2


title: empty vector -5

value: empty vector


title: empty vector -4


title: wild type HBE_No1


title: Nose_Air_Rep2


title: empty vector -3


title: YAPS94A -4


title: Nose_Air_Rep1


title: LNCaP siNTC replicate 2

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan

hyb_protocol: Approx 10 ug of labeled target was hybridized with Affymetrix GeneChip Human Genome U133 Plus 2.0 Array at 45 degrees overnight.  Arrays were washed and stained on Affymetrix Fluidics Station 450 using fluidics script FS450-0001.

scan_protocol: 349JA: Arrays were scanned using an Affymetrix GS 3000 scanner with the 7G upgrade; Image processing was performed using Affymetrix GeneChip Operating System (GCOS) v 1.4.036, 484JA,526JA: Arrays were scanned using an Affymetrix GS 3000 scanner with the 7G upgrade; Image processing was performed using Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 .,

data_processing: RMA  normalization from the R Bioconductor package affy was used to background correct and quantile normalize C42B and LNCaP replicates separately.

source_name: LNCaP

label_protocol:
349JA: Affymetrix One Cycle cDNA synthesis protocol with Affymetrix IVT with 2ug total RNA input
484JA,526JA: Ambion Message Amp Premier RNA amplification protocol with 200ng total RNA input

growth_protocol: LNCaP cells were plates in 6-well plates with 230K cells per well in RPMI+10% FBS.

extract_protocol: RNA was extracted with Trizol followed by Qiagen RNEasy cleanup column according to the manufacturers’ instructions. RNA from two wells was pooled for each of 3 biological replicates.

treatment_protocol: Plated LNCaP cells were transfected with siRNA at 50nM using Dharmafect 3 and grown for 96 hours in RPMI+10% FBS.

value: LNCaP


title: LNCaP siNTC replicate 3


title: empty vector -1


title: LNCaP siNTC replicate 1


title: LNCaP siLSD1 replicate 1


title: empty vector -2


title: LNCaP siLSD1 replicate 3


title: LNCaP siLSD1 replicate 2


title: C42B Veh+ replicate 4

growth_protocol: C42B cells were plated in 6-well plates with 150K cells per well in RPMI+10%FBS.

extract_protocol: RNA was extracted from four separate wells to yield 4 replicates with Trizol and Rneasy mini column.

treatment_protocol: plated C42B cells were incubated in RPMI+10% CSS for 72hrs. The cells were then treated with 100nM DHT or same volume of ethanol in RPMI+10% CSS for 16hrs.


title: 12hGX_2000pM_rep1

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: Gene expression after 12 h in 2000 pM emamectin benzoate exposed Daphnia magna replicate 1

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 50 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies).

growth_protocol: OECD Test Guideline 202

extract_protocol: Total RNA was extracted from pooled Daphnia using Zymo Tissue&Insect RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/280>1.8, yield >50 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Daphnia magna were exposed 5 concentrations of emamectin benzoate for 12h. After exposure, the organisms were pooled and sampled in RNALater (Qiagen, Hilden, Germany) and stored in -80°C until further use.

value: Whole organism

value: <24h juvenile


title: 12hGX_2000pM_rep4

source_name: Gene expression after 12 h in 2000 pM emamectin benzoate exposed Daphnia magna replicate 4


title: 12hGX_2000pM_rep3

source_name: Gene expression after 12 h in 2000 pM emamectin benzoate exposed Daphnia magna replicate 3


title: C42B Veh+ replicate 3


title: C42B Veh+ replicate 2


title: 12hGX_2000pM_rep2

source_name: Gene expression after 12 h in 2000 pM emamectin benzoate exposed Daphnia magna replicate 2


title: C42B Veh+ replicate 1


title: C42B DHT replicate 4


title: 12hGX_500pM_rep3

source_name: Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna replicate 3


title: C42B DHT replicate 3


title: C42B DHT replicate 2


title: C42B DHT replicate 1


title: 12hGX_500pM_rep1

source_name: Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna replicate 1


title: 12hGX_125pM_rep4

source_name: Gene expression after 12 h in 125 pM emamectin benzoate exposed Daphnia magna replicate 4


title: 12hGX_500pM_rep2

source_name: Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna replicate 2


title: 12hGX_125pM_rep3

source_name: Gene expression after 12 h in 125 pM emamectin benzoate exposed Daphnia magna replicate 3


title: 12hGX_500pM_rep4

source_name: Gene expression after 12 h in 500 pM emamectin benzoate exposed Daphnia magna replicate 4


title: C42B siNTC replicate 3

growth_protocol: C42B cells were plated in 6-well plates with 200K cells per well in RPMI+10%FBS.

extract_protocol: RNA was extracted from 6 separate wells to yield 3 replicates with Trizol and Rneasy mini column.

treatment_protocol: Plated C42B cells were trasfected with siRNA for 6 hrs then changed to RPMI+10%CSS and grown for 96hrs.


title: Unaffected Relative 4

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

description: Unaffected 4

hyb_protocol: As per manufacturer's instructions. Protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling for Blood Cells or Tissues - Version 6,3, October 2010.

scan_protocol: Agilent Feature Extraction V 11.5.1.

data_processing: Agilent CytoGenomics 3.0.1.1 software. Genome build hg19. Default Analysis Method - CGH+SNP v2. Normalization: GC correction and Diploid Peak Centralization.

source_name: blood leukocytes, unaffected

extract_protocol: Genomic DNA was isolated using the FlexiGene DNA kit as per manufacturer's recommendations.

tag: disease status

value: unaffected

value: blood leukocytes

value: female

source_name: Human reference DNA (Agilent 5190-4371)

tag: sample type

value: reference


title: PPCD Affected Individual 4

description: Affected 4

source_name: blood leukocytes, affected

label_protocol: As per manufacturer's instructions. Protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling for Blood Cells or Tissues - Version 6,3, October 2010.

value: posterior polymorphous corneal dystrophy 1 (PPCD1)


title: PPCD Affected Individual 3

description: Affected 3


title: Control biological replicate 2 [C2]

value: HOS

value: osteosarcoma cell line

value: none (untreated control)


title: 12hGX_125pM_rep2

source_name: Gene expression after 12 h in 125 pM emamectin benzoate exposed Daphnia magna replicate 2

tag: developmental stage


title: PPCD Affected Individual 2

description: Affected 2


title: 12hGX_125pM_rep1

source_name: Gene expression after 12 h in 125 pM emamectin benzoate exposed Daphnia magna replicate 1


title: Unaffected Relative 3

description: Unaffected 3

value: male


title: C42B siNTC replicate 2


title: C42B siNTC replicate 1


title: 12hGX_31.2pM_rep4

source_name: Gene expression after 12 h in 31.2 pM emamectin benzoate exposed Daphnia magna replicate 4


title: Unaffected Relative 2

description: Unaffected 2


title: C42B siLSD1 replicate 3


title: 12hGX_31.2pM_rep2

source_name: Gene expression after 12 h in 31.2 pM emamectin benzoate exposed Daphnia magna replicate 2


title: C42B siLSD1 replicate 1


title: Unaffected Relative 1

description: Unaffected 1


title: Nucleus pulposus_degenerated_4_miRNA

city: Xi'an

first: Hai-Qiang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

description:
Sample name: R4
Same sample as in GSM1354772.

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA microRNA Array, 7th generation (v.18.0) (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.The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged. We use Median Normalization Method to obtain Normalized Data, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

source_name: Nucleus pulposus tissue, degenerated

label_protocol: The miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) was used according to the manufacturer’s guideline for miRNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity were measured by using NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: All the specimens were collected from intervertebral discs of cadaveric donors or patients within 3 hours after anatomy or surgery, respectively. Following rinse with phosphate-buffered saline, the nucleus pulposus tissue was carefully collected under stereoscopic microscope.

value: nucleus pulposus

value: degenerated

tag: idd related disease

value: intervertebral disc herniation

tag: degeneration grading

value: V

tag: disc level

tag: age

value: 45 years


title: Nucleus pulposus_degenerated_5_miRNA

description:
Sample name: R5
Same sample as in GSM1354773.

tag: gender

value: 27 years


title: 12hGX_31.2pM_rep3

source_name: Gene expression after 12 h in 31.2 pM emamectin benzoate exposed Daphnia magna replicate 3

value: Whole organism


title: 12hGX_31.2pM_rep1

source_name: Gene expression after 12 h in 31.2 pM emamectin benzoate exposed Daphnia magna replicate 1

value: <24h juvenile


title: Nucleus pulposus_degenerated_1_miRNA

description:
Sample name: R1
Same sample as in GSM1354769.

value: 32 years


title: 12hGX_7.8pM_rep4

source_name: Gene expression after 12 h in 7.8 pM emamectin benzoate exposed Daphnia magna replicate 4


title: Nucleus pulposus_degenerated_3_miRNA

description:
Sample name: R3
Same sample as in GSM1354771.

value: IV

value: 42 years


title: 12hGX_7.8pM_rep3

source_name: Gene expression after 12 h in 7.8 pM emamectin benzoate exposed Daphnia magna replicate 3


title: C42B siLSD1 replicate 2