title: liver of control mice Replicate 2

description:
Biological replicate 2 of 3.
Control mice liver, untreated.
Raw data for this sample can be found on sample record: GSM1567088


title: Cancer_tissue_Lung_cancer_patient_02

status: Public on Feb 09 2017

type: RNA

city: Beijing

first: Jiao

last: Yuan

address: 15 Datun Road, Chaoyang District

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were subjected to for background subtraction, quality control, log2 transformation and quantile normalization by the GeneSpring software V11.5 (Agilent).

molecule: total RNA

organism: Homo sapiens

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

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

tag: disease

value: lung cancer

tag: tissue

value: Lung

tag: tissue type

value: Cancer tissue


title: liver of miR-155 transgenic mice Replicate 1

city: Guangzhou

first: Lin

last: Xiaolin

address: Tonghe

department: Southern Medical University

institute: Cancer reseach institute

description: Biological replicate 1 of 3.

hyb_protocol: Labeled cDNA was then hybridized to 32K mouse genome arrays.

scan_protocol: Hybridization signals were scanned with a Lux-Scan 3.0 scanner.The resultant images were digitized with Lux-Scan 3.0 image analyzer software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Mus musculus

source_name: liver of miR-155 transgenic mice

label_protocol: cDNA was fluorescently labeled by Cy5-dCTP or Cy3-dCTP (GE Healthcare Cat. No. PA 55021/PA 53021) with Klenow enzyme.

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

value: liver

tag: gender

value: male

tag: age


title: genomic DNA from white adipose tissue nonobese_3988

type: genomic

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

country: Sweden

institute: Karolinska

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: 1 μg of genomic DNA was subjected to bisulphite conversion with the EZ DNA Methylation kit (Zymo research, Orange, CA)

extract_protocol: Genomic DNA was extracted and purified from adipose tissue using standard protocol.

value: Female

value: abdominal subcutaneous adipose tissue

tag: disease state

value: Nonobese


title: liver of control mice Replicate 1

description:
Biological replicate 1 of 3.
Control mice liver, untreated.
Raw data for this sample can be found on sample record: GSM1567086

source_name: liver of control mice


title: liver of miR-155 transgenic mice and control mice Replicate 2

description: Biological replicate 2 of 3.


title: Normal_tissue_Lung_cancer_patient_03

value: Normal tissue


title: Leukocyte  PR541

city: Pittsburgh

first: Shuchang

last: Liu

state: Pennsylvania

address: 130 De Soto Street

country: USA

institute: University of Pittsburgh

description: Affymetrix SNP 6.0

hyb_protocol: Two hundred fifty micrograms of fragmented DNA were hybridized with a pre-equilibrated Affymetrix chip SNP 6.0 at 50oC for 18 hours.  Procedures of washing and scanning of SNP 6.0 chips followed the manuals provided by Affymetrix, Inc.

scan_protocol: The hybridized chips were scanned by 7G Affymetrix scanner.

data_processing:
CEL files were analyzed with Genotyping Console for quality control analysis. Samples with QC call above 80% and QC contrast ratio above 0.4 were admitted into the analysis. To analyze CNV, CEL files were imported into Partek GenomeSuite 6.6 to generate copy number from raw intensity.
Each CEL file represents data from one patient. Deletion or amplification of genomes were analyzed by first limiting to the regions with p-value less than 0.001. The selected regions were subsequently filtered by limiting to the regions with at least 10 markers and 2 kb in size.

label: Biotin

source_name: Leukocyte  PR541

label_protocol: The fragmented DNA was labeled with biotinylated nucleotides through terminal deoxynucleotide transferase for 4 hours at 37oC, following the manual provided by Affymetrix, Inc.

extract_protocol: DNA was extracted using Qiagen blood DNA extraction kit.

tag: cell type

value: Leukocyte

tag: patient

tag: Stage

tag: gleason

tag: nomogram 5 years

tag: recurrence label

value: no

tag: fast relapase label

value: nf


title: Cancer_tissue_Lung_cancer_patient_01


title: genomic DNA from white adipose tissue Obese_4649

value: Obese


title: Leukocyte  PR537

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR537


title: genomic DNA from white adipose tissue Obese_4810


title: Normal_tissue_Lung_cancer_patient_02


title: Leukocyte  PR536

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR536


title: Leukocyte  PR535

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR535


title: genomic DNA from white adipose tissue Obese_3708


title: Leukocyte  PR530

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR530

value: yes


title: Normal_tissue_Liver_cancer_patient_16

value: liver cancer patient

value: Liver


title: Leukocyte  PR529

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR529


title: Corresponding normal breast tissue-2277

city: Shanghai

first: Ji-Gang

last: Wang

address: 138 Yixueyuan Road

institute: Fudan University

hyb_protocol: Agilent Gene Expression Hybridization Kit was using according to the manusfactures

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner.

data_processing:
Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 10 out of 10 samples have flags in Present or Marginal (¡°All Targets Value¡±) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.
Data Analysis for LncRNAs
Raw LncRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs were filtered (LncRNAs that at least 10 out of 10 samples have flags in Present or Marginal were chosen for further analysis).
Data Analysis for mRNAs
Raw mRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity mRNAs were filtered (mRNAs that at least 10 out of 10 samples have flags in Present or Marginal were chosen for further analysis).

source_name: tissue

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling. Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

extract_protocol: Prepare the RNA sample using TRIzol® Reagent. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling.

tag: ID

value: normal tissue


title: genomic DNA from white adipose tissue Obese_4281


title: genomic DNA from white adipose tissue Obese_3698


title: Normal_tissue_Lung_cancer_patient_01

value: lung cancer


title: Corresponding normal breast tissue-2274


title: Cancer_tissue_Liver_cancer_patient_16


title: Cancer_tissue_Liver_cancer_patient_15


title: Leukocyte  PR528

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR528


title: Corresponding normal breast tissue-2273


title: Cancer_tissue_Liver_cancer_patient_14


title: Breast cancer tissue-2273

value: cancer


title: Breast cancer tissue-2277


title: genomic DNA from white adipose tissue Obese_4659


title: genomic DNA from white adipose tissue Obese_4642


title: Leukocyte  PR527

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR527

value: f


title: Corresponding normal breast tissue-2272


title: genomic DNA from white adipose tissue nonobese_199


title: Breast cancer tissue-2274


title: Leukocyte  PR525

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR525


title: Normal_tissue_Liver_cancer_patient_14


title: genomic DNA from white adipose tissue nonobese_404


title: Cancer_tissue_Liver_cancer_patient_13

value: Cancer tissue


title: Corresponding normal breast tissue-2271


title: Normal_tissue_Liver_cancer_patient_15


title: Leukocyte  PR524

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR524


title: genomic DNA from white adipose tissue nonobese_467


title: Breast cancer tissue-2272


title: Normal_tissue_Liver_cancer_patient_13


title: genomic DNA from white adipose tissue Obese_1914


title: Leukocyte  PR490B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR490B


title: Breast cancer tissue-2271


title: Leukocyte  PR485

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR485


title: genomic DNA from white adipose tissue nonobese_4613


title: Leukocyte  PR434B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR434B


title: Cancer_tissue_Liver_cancer_patient_12


title: Leukocyte  PR521B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR521B


title: Leukocyte  PR372

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR372


title: Leukocyte  PR375B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR375B


title: genomic DNA from white adipose tissue Obese_4275


title: genomic DNA from white adipose tissue nonobese_4203


title: Leukocyte  PR363B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR363B


title: Normal_tissue_Liver_cancer_patient_12


title: genomic DNA from white adipose tissue nonobese_101


title: Normal_tissue_Liver_cancer_patient_11


title: Cancer_tissue_Liver_cancer_patient_10


title: genomic DNA from white adipose tissue Obese_4640


title: Leukocyte  PR306B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR306B


title: Normal_tissue_Liver_cancer_patient_09


title: Leukocyte  PR304B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR304B


title: genomic DNA from white adipose tissue Obese_2636


title: Normal_tissue_Liver_cancer_patient_10


title: Cancer_tissue_Liver_cancer_patient_11


title: Cancer_tissue_Liver_cancer_patient_09


title: Cancer_tissue_Liver_cancer_patient_08


title: Leukocyte  PR303B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR303B


title: genomic DNA from white adipose tissue nonobese_3664


title: Leukocyte  PR310B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR310B


title: Leukocyte  PR300B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR300B


title: genomic DNA from white adipose tissue nonobese_83


title: P3.CEL

city: Oviedo

first: Alvaro

middle: J

last: Obaya

state: Asturias

address: Julian Claveria s/n

department: Biología Funcional

country: Spain

institute: Universidad de Oviedo

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit (PN900720)

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

data_processing: The data were normalized with Bioconductor (R 2.15.0, Bioconductor 2.11 and affy package 1.36.0) software using RMA algorithm.

label: biotin

label_protocol: The sense cDNA was prepared from 200 ng of total RNA and then fragmented and biotinylated using Affymetrix GeneChip® WT PLUS Reagent Kit (PN 902281).

growth_protocol: Cells were grown in complete media: MEM-α (supplemented with L-Glutamine, ribonucleosides and desoxirribinucleosides but not with ascorbic acid) with 10% FBS

extract_protocol: 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).

tag: cell line

value: osteoblast


title: genomic DNA from white adipose tissue nonobese_4635

value: Female


title: Normal_tissue_Liver_cancer_patient_08


title: Cancer_tissue_Liver_cancer_patient_07


title: Stat3dm stroma 1

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description:
deltaM s1
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in SensationPlus™ FFPE Amplification.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1.

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.

source_name: Stat3dm stroma (2 tumors of one mouse pooled)

label_protocol: 50ng of total RNA were amplified and labeled using the Sensation Plus FFPE Amplification and WT Labeling Kit (Catalog Number 902042,Affymetrix, Santa Clara, CA). and WT Labeling Kit User Manual (Fluidics Protocol FS450_0002)

growth_protocol: autochtonous colorectal tumors from mice.

extract_protocol: RNA was isolated from laser-capture-microdissected paraffin material using the RNeasy FFPE kit (Qiagen 73504).

treatment_protocol: autochtonous colorectal tumors were induced with the AOM/DSS protocol.

value: autochtonous colorectal tumor induced with the AOM/DSS protocol

tag: genotype/variation

value: stroma


title: C.CEL


title: Stat3dm tumor 3

description:
deltaM t3
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice

source_name: Stat3dm tumor (2 tumors of one mouse pooled)

value: tumor


title: Normal_tissue_Liver_cancer_patient_06

value: Normal tissue


title: Stat3dm stroma 2

description:
deltaM s2
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice


title: Stat3dm stroma 3

description:
deltaM s3
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice


title: Leukocyte  PR236B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR236B

value: Leukocyte


title: Cancer_tissue_Liver_cancer_patient_05


title: Normal_tissue_Liver_cancer_patient_07


title: Leukocyte  PR151B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR151B2

value: nf


title: Normal_tissue_Liver_cancer_patient_05


title: Leukocyte  PR227

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR227

value: no


title: Cancer_tissue_Liver_cancer_patient_06


title: Stat3dm tumor 2

description:
deltaM t2
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice


title: Leukocyte  PR151B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR151B

value: yes


title: Cancer_tissue_Liver_cancer_patient_04

value: liver cancer patient


title: Normal_tissue_Liver_cancer_patient_04

value: Liver


title: Leukocyte  PR073

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR073


title: Leukocyte  PR065

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR065


title: adult peripheral1

city: Berkeley

first: Ravikanth

last: Metlapally

address: 588 Minor Hall

institute: UC Berkeley

hyb_protocol: The labeled RNA was purified using BioSpin6 (Bio-Rad, Hercules CA). Hybridization, washing, staining, imaging, and signal extraction were performed according to Agilent-recommended procedures

data_processing: For each probe, the contribution of signal due to background was estimated and removed by the Agilent Feature Extraction software as part of the data file output. Detection calls also made use of the Agilent Feature Extraction software. All other analyses were performed in R (http://www.r-project.org). Arrays within a specific experiment were normalized together according to the Variance Stabilization and Normalization (VSN) method.

source_name: sclera

label_protocol: miRNA profiling experiments were processed according to standard operating procedures in a GLP-compliant setting. Briefly, total RNA was first dephosphorylated and then the pCp-Cy3 labeling molecule ligated to the 3’ end of the RNA molecules.

extract_protocol: Scleral samples were homogenized and then total RNA extracted using a miRVANA™ isolation kit (Ambion Inc.), which is designed to preserve the small RNAs.

tag: developmental stage

value: adult

value: peripheral sclera


title: fetal peripheral2

scan_protocol: The labeled RNA was purified using BioSpin6 (Bio-Rad, Hercules CA). Hybridization, washing, staining, imaging, and signal extraction were performed according to Agilent-recommended procedures

value: fetal


title: adult peripheral2


title: fetal peripheral1


title: Stat3wt stroma 3

description:
wt s3
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice

source_name: Stat3wt stroma (2 tumors of one mouse pooled)


title: Leukocyte  PR150

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR150


title: Stat3wt stroma 2

description:
wt s2
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice


title: Leukocyte  PR079B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR079B


title: Stat3wt tumor 3

description:
wt t3
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice

source_name: Stat3wt tumor (2 tumors of one mouse pooled)


title: adult peripheral3


title: Stat3wt stroma 1

description:
wt s1
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice


title: Cancer_tissue_Liver_cancer_patient_01

tag: disease


title: Stat3dm tumor 1

description:
deltaM t1
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3dm mice

tag: tissue


title: Cancer_tissue_Liver_cancer_patient_03

tag: tissue type


title: Cancer_tissue_Liver_cancer_patient_02


title: Normal_tissue_Liver_cancer_patient_03


title: Stat3wt tumor 2

description:
wt t2
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice


title: 293T_MBD-TET1-CDwt10_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 293T, MBD-TET1-CDwt10, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Eight stable cell lines derived from human embryonic kidney cell line 293T (HEK293T) was grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum.

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


title: 293T_MBD-TET1-CDmut9_exp1

source_name: 293T, MBD-TET1-CDmut9, experiment 1


title: Leukocyte  PR018B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR018B


title: Normal_tissue_Liver_cancer_patient_02


title: Normal_tissue_Liver_cancer_patient_01


title: Leukocyte  PR048

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR048


title: Ctrl_male_d10

city: Seoul

first: Suyeun

last: Yu

address: 5-Ka, Anam-dong, Sungbuk-Ku

department: preventive medicine

country: South Korea

institute: Korea university medical college

description: Ctr male

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Drosophila Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Drosophila melanogaster

source_name: Control_w1118_10d_whole body_male

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Wild-type Drosophila melanogaster w1118 were raised on fresh medium containing 6% cornmeal, 3% yeast, 3% sugar, 6% glucose, and 0.6% agar.

treatment_protocol: All hyperbaric normoxia (HN; 2ATA in normoxic conditions) exposures were carried out in a custom-made animal incubator designed for pressure control  without change of temperature (25°C), humidity (50 ± 5%) and under a 12:12 h light/dark cycle. Fertilized eggs from 30 3-day-old pairs were collected in batches of 30 into vials, then exposed to HN until eclosion.

tag: strain

value: wild type

tag: gender

value: male

tag: treatment group

value: control

value: whole body


title: 293T_MBD-TET1-CDmut10_exp1

source_name: 293T, MBD-TET1-CDmut10, experiment 1


title: Leukocyte  JB770B

description: Affymetrix SNP 6.0

source_name: Leukocyte  JB770B

tag: cell type

tag: age

value: f


title: Leukocyte  KB170B

description: Affymetrix SNP 6.0

source_name: Leukocyte  KB170B

tag: patient

tag: Stage


title: Stat3wt tumor 1

description:
wt t1
gene expression data from laser-capture microdissected, paraffin embeded colorectal tumors of Stat3wt mice

tag: disease state

value: autochtonous colorectal tumor induced with the AOM/DSS protocol


title: Leukocyte  JB724

description: Affymetrix SNP 6.0

source_name: Leukocyte  JB724


title: Leukocyte  JB426B

description: Affymetrix SNP 6.0

source_name: Leukocyte  JB426B

tag: gleason

tag: nomogram 5 years

tag: recurrence label


title: Leukocyte  IB684B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB684B

tag: fast relapase label


title: Leukocyte  JB378B

description: Affymetrix SNP 6.0

source_name: Leukocyte  JB378B


title: Cancer_tissue_Gastric_cancer_patient_19

value: gastric cancer patient

value: Gastric

value: Cancer tissue


title: Ctrl_female_d10

description: Ctr female

source_name: Control_w1118_10d_whole body_female

tag: genotype/variation

value: female


title: 293T_TET1-CDwt5_exp1

source_name: 293T, TET1-CDwt5, experiment 1

tag: cell line


title: Normal_tissue_Gastric_cancer_patient_20

tag: disease

value: Normal tissue


title: Leukocyte  IB673

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB673

value: Leukocyte

value: yes


title: 293T_MBD-TET1-CDwt3_exp1

source_name: 293T, MBD-TET1-CDwt3, experiment 1


title: 293T_Vec2_exp1

source_name: 293T, Vector2, experiment 1


title: Normal_tissue_Gastric_cancer_patient_19

tag: tissue


title: Cancer_tissue_Gastric_cancer_patient_20

tag: tissue type


title: HN_female_d10

description: Hn female

source_name: HN_w1118_10d_whole body_female

tag: strain

value: prenatal hyperbaric normoxia exposure


title: 293T_Vec1_exp1

source_name: 293T, Vector1, experiment 1


title: Leukocyte  IB627

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB627


title: Cancer_tissue_Gastric_cancer_patient_18


title: Normal_tissue_Gastric_cancer_patient_18


title: Leukocyte  IB608

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB608


title: Cancer_tissue_Gastric_cancer_patient_17


title: Leukocyte  PR311B

description: Affymetrix SNP 6.0

source_name: Leukocyte  PR311B

value: nf


title: Normal_tissue_Gastric_cancer_patient_17


title: HN_male_d10

description: Hn male

source_name: HN_w1118_10d_whole body_male

tag: gender


title: Leukocyte  IB483B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB483B


title: 293T_TET1-CDwt2_exp1

source_name: 293T, TET1-CDwt2, experiment 1


title: Leukocyte  IB304

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB304


title: Leukocyte  IB378

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB378

value: no


title: Cancer_tissue_Gastric_cancer_patient_16


title: Normal_tissue_Gastric_cancer_patient_16


title: Cancer_tissue_Gastric_cancer_patient_15


title: Leukocyte  IB289

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB289


title: duodenal_biopsy_subject10_CIP104448

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

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

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.32.0).

source_name: duodenal biopsy from subject 10, after 7 days of treatment with CIP104448

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

growth_protocol: Healthy subjects were enrolled via public advertising, and were screened, involving a standardized general physical examination. All study participants gave written informed consent prior to inclusion. Exclusion criteria were current gastrointestinal symptoms, a history of severe disease or major abdominal surgery, use of any medication within 14 days or investigational drugs within 180 days prior to inclusion, blood donation within 3 months before the study period, pregnancy, lactation, obesity, smoking, use of drugs or excessive alcohol consumption, and known allergy/hypersensitivity towards intake of NSAIDs, sweeteners or pre- or probiotic supplements of any kind.

extract_protocol: The mucosal biopsies were immediately flash frozen in liquid nitrogen. Total RNA was prepared from the biopsies using TRIzol reagent (1ml) and purified using Qiagen RNeasy Micro Kit columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products.

treatment_protocol: This human study was designed and conducted as a randomized double-blind placebo-controlled cross-over trial. The effects of three potentially beneficial bacterial strains were investigated in each subject during four randomized test periods (Suppl. Table II). During each test period (Figure 1), one of the following supplements has been orally ingested twice a day, during breakfast and dinner, for 7 consecutive days: L. plantarum WCFS1 (2.6x10^10 colony forming units (cfu) per time point; WCFS1), L. plantarum CIP48 (2.4x10^10 cfu/time point; CIP104448), L. plantarum TIFN101 (5.9x10^10 cfu/time point; CIP104450) or placebo. Each test period was followed by a washout period of four weeks. There was no standardised diet for the study participants; however, subjects were instructed to consume on the last day of each test period the same diet as they did on the last day of the first period. Baseline permeability measurements were performed three days and one day prior to the intake of the supplements, in the absence and presence of the intestinal mucosal barrier stressor indomethacin, respectively. Subsequently, subjects consumed one of the three L. plantarum strains or placebo for seven consecutive days. Thereafter, the permeability test with addition of indomethacin (but not the test without indomethacin) was repeated, whereupon the same day standard flexible gastroduodenoscopy was performed to obtain six tissue samples from the duodenum (D2 section), at approximately 15 cm distal to the pylorus.

value: duodenum

tag: treatment

value: Male

tag: subjectid

tag: age (yrs)


title: Leukocyte  IB180

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB180

tag: cell type

tag: patient

tag: age


title: Leukocyte  IB298B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB298B

tag: Stage

tag: gleason


title: duodenal_biopsy_subject10_CIP104450

source_name: duodenal biopsy from subject 10, after 7 days of treatment with CIP104450


title: duodenal_biopsy_subject7_CIP104448

source_name: duodenal biopsy from subject 7, after 7 days of treatment with CIP104448

value: Female


title: duodenal_biopsy_subject7_Placebo

source_name: duodenal biopsy from subject 7, after 7 days of treatment with Placebo

value: Placebo


title: Cancer_tissue_Gastric_cancer_patient_14


title: Cell_30hr_0etoposide

city: Kobe

first: Shinji

last: Kamada

address: 1-1 Rokkodai-cho, Nada-ku

institute: Kobe University

description: Gene expression after treatment with 0 uM of etoposide for 30 hours

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

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026652_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HepG2_30h_0 uM etoposide

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

growth_protocol: HepG2 (a human hepatocellular carcinoma line) cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was isolated using NucleoSpin RNA II (TaKaRa) according to the manufacturer’s instruction.  The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: HepG2 cells were treated with 0, 10, and 100 uM of etoposide for 30 hours

value: hepatocarcinoma HepG2 cells

tag: agent

value: untreated

tag: dose

value: 0 uM


title: Leukocyte  IB135

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB135

tag: nomogram 5 years

tag: recurrence label

tag: fast relapase label

value: f


title: duodenal_biopsy_subject7_CIP104450

source_name: duodenal biopsy from subject 7, after 7 days of treatment with CIP104450

tag: tissue


title: Cell_30hr_10etoposide

description: Gene expression after treatment with 10 uM of etoposide for 30 hours

source_name: HepG2_30h_10 uM etoposide

tag: cell line

value: etoposide

value: 10 uM


title: Leukocyte  IB134B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB134B


title: Normal_tissue_Gastric_cancer_patient_15

tag: disease

value: gastric cancer patient

value: Gastric

tag: tissue type


title: Normal_tissue_Gastric_cancer_patient_13

value: Normal tissue


title: Leukocyte  IB136B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB136B

value: Leukocyte

value: yes


title: duodenal_biopsy_subject7_WCFS1

source_name: duodenal biopsy from subject 7, after 7 days of treatment with WCFS1

tag: treatment

tag: gender


title: Cancer_tissue_Gastric_cancer_patient_13

value: Cancer tissue


title: Cell_30hr_100etoposide

description: Gene expression after treatment with 100 uM of etoposide for 30 hours

source_name: HepG2_30h_100 uM etoposide


title: duodenal_biopsy_subject6_Placebo

source_name: duodenal biopsy from subject 6, after 7 days of treatment with Placebo

tag: subjectid

tag: age (yrs)


title: Leukocyte  IB133

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB133

tag: cell type

tag: patient


title: duodenal_biopsy_subject6_CIP104450

source_name: duodenal biopsy from subject 6, after 7 days of treatment with CIP104450


title: duodenal_biopsy_subject6_CIP104448

source_name: duodenal biopsy from subject 6, after 7 days of treatment with CIP104448


title: Normal_tissue_Gastric_cancer_patient_12


title: Leukocyte  IB113B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB113B

tag: age

tag: Stage

value: nf


title: Cancer_tissue_Gastric_cancer_patient_12


title: duodenal_biopsy_subject6_WCFS1

source_name: duodenal biopsy from subject 6, after 7 days of treatment with WCFS1

value: duodenum


title: Leukocyte  IB112B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB112B

tag: gleason


title: Leukocyte  IB111

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB111

value: no


title: fetal peripheral3

source_name: sclera

tag: developmental stage

value: fetal

value: peripheral sclera


title: duodenal_biopsy_subject3_CIP104450

source_name: duodenal biopsy from subject 3, after 7 days of treatment with CIP104450

value: Female


title: Normal_tissue_Gastric_cancer_patient_14


title: duodenal_biopsy_subject3_Placebo

source_name: duodenal biopsy from subject 3, after 7 days of treatment with Placebo

value: Placebo


title: Leukocyte  HB705

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB705

tag: nomogram 5 years


title: Cancer_tissue_Gastric_cancer_patient_10


title: Leukocyte  HB658

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB658

tag: recurrence label


title: Leukocyte  HB603B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB603B

tag: fast relapase label


title: Leukocyte  HB591B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB591B


title: Normal_tissue_Gastric_cancer_patient_11

tag: tissue


title: Leukocyte  HB568B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB568B


title: Normal_tissue_Gastric_cancer_patient_07


title: duodenal_biopsy_subject9_CIP104448

source_name: duodenal biopsy from subject 9, after 7 days of treatment with CIP104448


title: duodenal_biopsy_subject9_CIP104450

source_name: duodenal biopsy from subject 9, after 7 days of treatment with CIP104450


title: duodenal_biopsy_subject3_WCFS1

source_name: duodenal biopsy from subject 3, after 7 days of treatment with WCFS1


title: Normal_tissue_Gastric_cancer_patient_10


title: Cancer_tissue_Gastric_cancer_patient_11


title: Normal_tissue_Gastric_cancer_patient_09


title: duodenal_biopsy_subject3_CIP104448

source_name: duodenal biopsy from subject 3, after 7 days of treatment with CIP104448


title: Cancer_tissue_Gastric_cancer_patient_09


title: duodenal_biopsy_subject9_WCFS1

source_name: duodenal biopsy from subject 9, after 7 days of treatment with WCFS1


title: duodenal_biopsy_subject9_Placebo

source_name: duodenal biopsy from subject 9, after 7 days of treatment with Placebo


title: Normal_tissue_Gastric_cancer_patient_08


title: duodenal_biopsy_subject8_Placebo

source_name: duodenal biopsy from subject 8, after 7 days of treatment with Placebo

value: Male


title: Leukocyte  HB504B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB504B

value: f


title: duodenal_biopsy_subject8_CIP104448

source_name: duodenal biopsy from subject 8, after 7 days of treatment with CIP104448


title: duodenal_biopsy_subject8_WCFS1

source_name: duodenal biopsy from subject 8, after 7 days of treatment with WCFS1


title: duodenal_biopsy_subject8_CIP104450

source_name: duodenal biopsy from subject 8, after 7 days of treatment with CIP104450


title: Leukocyte  HB492

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB492


title: Cancer_tissue_Gastric_cancer_patient_08


title: Cancer_tissue_Gastric_cancer_patient_07


title: Cancer_tissue_Gastric_cancer_patient_06


title: Normal_tissue_Gastric_cancer_patient_06


title: Leukocyte  HB526B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB526B


title: Cancer_tissue_Gastric_cancer_patient_05


title: Leukocyte  HB46B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB46B


title: Leukocyte  HB340

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB340


title: Leukocyte  HB327

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB327


title: duodenal_biopsy_subject5_Placebo

source_name: duodenal biopsy from subject 5, after 7 days of treatment with Placebo


title: Normal_tissue_Gastric_cancer_patient_05


title: Leukocyte  HB312B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB312B


title: duodenal_biopsy_subject5_WCFS1

source_name: duodenal biopsy from subject 5, after 7 days of treatment with WCFS1


title: duodenal_biopsy_subject5_CIP104448

source_name: duodenal biopsy from subject 5, after 7 days of treatment with CIP104448


title: Leukocyte  HB305B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB305B


title: Leukocyte  HB346

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB346


title: duodenal_biopsy_subject4_WCFS1

source_name: duodenal biopsy from subject 4, after 7 days of treatment with WCFS1


title: Normal_tissue_Gastric_cancer_patient_03


title: duodenal_biopsy_subject5_CIP104450

source_name: duodenal biopsy from subject 5, after 7 days of treatment with CIP104450


title: Leukocyte  HB303

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB303


title: duodenal_biopsy_subject4_CIP104450

source_name: duodenal biopsy from subject 4, after 7 days of treatment with CIP104450


title: Cancer_tissue_Gastric_cancer_patient_03


title: Leukocyte  HB261B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB261B


title: duodenal_biopsy_subject4_Placebo

source_name: duodenal biopsy from subject 4, after 7 days of treatment with Placebo


title: Cancer_tissue_Gastric_cancer_patient_04


title: Cancer_tissue_Gastric_cancer_patient_02


title: Leukocyte  HB235B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB235B


title: Normal_tissue_Gastric_cancer_patient_04


title: Leukocyte  HB207B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB207B


title: duodenal_biopsy_subject4_CIP104448

source_name: duodenal biopsy from subject 4, after 7 days of treatment with CIP104448


title: duodenal_biopsy_subject2_WCFS1

source_name: duodenal biopsy from subject 2, after 7 days of treatment with WCFS1


title: duodenal_biopsy_subject2_CIP104448

source_name: duodenal biopsy from subject 2, after 7 days of treatment with CIP104448


title: Cancer_tissue_Gastric_cancer_patient_01


title: Normal_tissue_Gastric_cancer_patient_01


title: Leukocyte  HB033B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB033B


title: Leukocyte  HB021B

description: Affymetrix SNP 6.0

source_name: Leukocyte  HB021B


title: Cancer_tissue_Colon_cancer_patient_20

value: colon cancer patient

value: Colon


title: Leukocyte  GB400B

description: Affymetrix SNP 6.0

source_name: Leukocyte  GB400B


title: Leukocyte  GB368

description: Affymetrix SNP 6.0

source_name: Leukocyte  GB368


title: Leukocyte  GB222

description: Affymetrix SNP 6.0

source_name: Leukocyte  GB222


title: duodenal_biopsy_subject2_Placebo

source_name: duodenal biopsy from subject 2, after 7 days of treatment with Placebo


title: Normal_tissue_Colon_cancer_patient_20


title: Leukocyte  GB195B

description: Affymetrix SNP 6.0

source_name: Leukocyte  GB195B


title: duodenal_biopsy_subject2_CIP104450

source_name: duodenal biopsy from subject 2, after 7 days of treatment with CIP104450


title: duodenal_biopsy_subject1_WCFS1

source_name: duodenal biopsy from subject 1, after 7 days of treatment with WCFS1


title: duodenal_biopsy_subject1_CIP104450

source_name: duodenal biopsy from subject 1, after 7 days of treatment with CIP104450


title: duodenal_biopsy_subject1_Placebo

source_name: duodenal biopsy from subject 1, after 7 days of treatment with Placebo


title: Cancer_tissue_Colon_cancer_patient_19


title: Normal_tissue_Colon_cancer_patient_19


title: Cancer_tissue_Colon_cancer_patient_17


title: Normal_tissue_Colon_cancer_patient_17


title: Leukocyte  FB635

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB635


title: Cancer_tissue_Colon_cancer_patient_18


title: Cancer_tissue_Colon_cancer_patient_16


title: Normal_tissue_Colon_cancer_patient_16


title: Leukocyte  FB493B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB493B


title: Normal_tissue_Colon_cancer_patient_18


title: Leukocyte  FB95

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB95


title: Leukocyte  FB421B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB421B


title: Leukocyte  FB222B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB222B


title: Leukocyte  FB238B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB238B


title: Leukocyte  FB586B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB586B


title: Leukocyte  FB94B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB94B


title: Leukocyte  FB183B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB183B


title: Leukocyte  FB41B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB41B


title: Leukocyte  FB174B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB174B


title: Leukocyte  FB120B

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB120B


title: Normal_tissue_Gastric_cancer_patient_02

value: gastric cancer patient


title: Cancer_tissue_Colon_cancer_patient_14


title: Cancer_tissue_Colon_cancer_patient_13


title: Normal_tissue_Colon_cancer_patient_13


title: duodenal_biopsy_subject1_CIP104448

source_name: duodenal biopsy from subject 1, after 7 days of treatment with CIP104448


title: Normal_tissue_Colon_cancer_patient_12


title: Ecoli_Ag8.5_rep3

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

description: This sample is the culture with 8.5 µM of AgNO3. It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.

scan_protocol: Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.

data_processing:
Raw probe intensities ( .pair files three replicates for each growth condition with respectively 0, 5.0, 6.5 and 8.5 µM of AgNO3 in the medium) was processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Raw data were submitted to a RMA-base background correction [Irizarry et al, 2003, Biostatistics 4(2): 249-264]. After background correction, intra-replicate quantil normalization was performed for each growth condition. A set of probes in the background for which the ranks were roughly invariant across all the twelve arrays was selected. The median value of the invariant probeset intensities on each array was used as a scaling factor for normalization between growth conditions.
After normalization, the expression of a gene was calculated by a RMA-summarization procedure within each growth condition.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli, 8.5 µM AgNO3

label_protocol: According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit

growth_protocol: The laboratory strain E. coli K12 MG1655 was grown for 24 h at 37 °C under continuous shaking (120 rpm), in 200 mL M9 medium (Merck Prolabo) complemented with 2.5 g/L of anhydrous glucose, and inoculated at 108 CFU/mL (corresponding to an optical density at 595 nm [OD595 nm] of 0.12). The inoculum for this culture was prepared in 40 mL M9 broth inoculated with approximately 1.5x107 CFU/mL (corresponding to an OD595 nm of 0.12) and incubated overnight under the same conditions (37 °C, 120 rpm). This inoculum was obtained by adding 1 mL of stock culture of the bacterial cells in 5 mL of Luria Bertani broth (Biokar Diagnotics, PRS Panreac) in a 15-mL half-opened BD FalconTM tube, followed by 8 h of incubation at 37 °C and 120 rpm.

extract_protocol: At 3 h of culture, 60 mL of culture (at OD595 nm = 0.73 ± 0.07, 0.63 ± 0.02, 0.12 ± 0.01 and 0.11 ± 0.02 for cultures subjected to 0, 5.0, 6.5 and 8.5 µM AgNO3, respectively) were sampled and centrifuged (4000 rpm, 5 min, 4 °C), then the pellet was frozen in liquid nitrogen. The pellet was resuspended with 1 mL of TE buffer (Tris-HCl 10 mM, pH 8, EDTA 1 mM, 1 mg lysozyme) and incubated 5 min at room temperature. Total RNA was extracted with a RNeasy midi kit (Qiagen), including the DNase I treatment described in the manufacturer’s instructions. Total RNA quantity and integrity were checked by Nanodrop® and Agilent BioAnalyzer, respectively.

treatment_protocol: Ionic silver stock solutions were prepared from AgNO3 powder (Fisher Scientific Bioblock) as previously described (Saulou, Jamme et al., 2013) and stored in darkness. The final tested concentrations (5.0, 6.5, and 8.5 µM) were obtained by diluting the corresponding AgNO3 stock solution directly into the M9 growth medium. Control experiment was simultaneously performed by adding deionised water into the M9 broth. In both cases, a stabilization period of 24 h (at 37 °C and 120 rpm) was carried out before cell inoculation.

tag: agno3 concentration in µm


title: Ecoli_Ag8.5_rep2

description: This sample is the culture with 8.5 µM of AgNO3. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Cancer_tissue_Colon_cancer_patient_15

tag: disease


title: Normal_tissue_Colon_cancer_patient_15

tag: tissue type


title: Leukocyte  DB237B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  DB237B2


title: Normal_tissue_Colon_cancer_patient_14


title: Cancer_tissue_Colon_cancer_patient_11


title: Leukocyte  DB237B

description: Affymetrix SNP 6.0

source_name: Leukocyte  DB237B


title: Normal_tissue_Colon_cancer_patient_11


title: Cancer_tissue_Colon_cancer_patient_12


title: Cancer_tissue_Colon_cancer_patient_10


title: Ecoli_Ag6.5_rep2

description: This sample is the culture with 6.5 µM of AgNO3. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli, 6.5 µM AgNO3


title: Leukocyte  IB071B

description: Affymetrix SNP 6.0

source_name: Leukocyte  IB071B


title: Ecoli_Ag6.5_rep3

description: This sample is the culture with 6.5 µM of AgNO3. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Ecoli_Ag8.5_rep1

description: This sample is the culture with 8.5 µM of AgNO3. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Leukocyte  9122B

description: Affymetrix SNP 6.0

source_name: Leukocyte  9122B


title: Normal_tissue_Colon_cancer_patient_10


title: Cancer_tissue_Colon_cancer_patient_09


title: Leukocyte  9122B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  9122B2


title: Ecoli_Ag6.5_rep1

description: This sample is the culture with 6.5 µM of AgNO3. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Leukocyte  7270B

description: Affymetrix SNP 6.0

source_name: Leukocyte  7270B


title: Leukocyte  678B

description: Affymetrix SNP 6.0

source_name: Leukocyte  678B


title: Ecoli_Ag5.0_rep2

description: This sample is the culture with 5.0 µM of AgNO3. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli, 5 µM AgNO3


title: Cancer_tissue_Colon_cancer_patient_08


title: Normal_tissue_Colon_cancer_patient_09


title: Leukocyte  FB104

description: Affymetrix SNP 6.0

source_name: Leukocyte  FB104


title: Leukocyte  6634B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  6634B2


title: Cancer_tissue_Colon_cancer_patient_07


title: Leukocyte  6634B

description: Affymetrix SNP 6.0

source_name: Leukocyte  6634B


title: Normal_tissue_Colon_cancer_patient_08


title: Leukocyte  7504B

description: Affymetrix SNP 6.0

source_name: Leukocyte  7504B


title: Normal_tissue_Colon_cancer_patient_07


title: Cancer_tissue_Colon_cancer_patient_06


title: Leukocyte  5396B

description: Affymetrix SNP 6.0

source_name: Leukocyte  5396B


title: Leukocyte  562B

description: Affymetrix SNP 6.0

source_name: Leukocyte  562B


title: Ecoli_Ag5.0_rep1

description: This sample is the culture with 5.0 µM of AgNO3. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Ecoli_Ag0.0_rep1

description: This sample is the culture with 0 µM of AgNO3. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli, 0 µM AgNO3


title: Leukocyte  4851B

description: Affymetrix SNP 6.0

source_name: Leukocyte  4851B


title: Leukocyte  4336B

description: Affymetrix SNP 6.0

source_name: Leukocyte  4336B


title: Ecoli_Ag0.0_rep3

description: This sample is the culture with 0 µM of AgNO3. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Ecoli_Ag0.0_rep2

description: This sample is the culture with 0 µM of AgNO3. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli,  0 µM AgNO3


title: Leukocyte  4308B

description: Affymetrix SNP 6.0

source_name: Leukocyte  4308B


title: Ecoli_Ag5.0_rep3

description: This sample is the culture with 5.0 µM of AgNO3. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Liver_High-fat diet_rep 3

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

description: non-exercised mice remained sedenrary

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Affemetrix miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing:
Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 75 percent of samples in any 1 condition out of 2 conditions have flags in P were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: Mouse liver, high-fat diet, 16 weeks

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Liver tissues were collected and frozen immediately in liquid nitrogen.

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

value: liver

tag: treatment

value: high-fat diet

tag: strain

value: male

value: 8 to 10 week old


title: Liver_High-fat diet_rep 5

description: non-exercised mice remained sedenrary

tag: gender


title: Normal_tissue_Colon_cancer_patient_04

value: Normal tissue


title: Leukocyte  28685B

description: Affymetrix SNP 6.0

source_name: Leukocyte  28685B

value: Leukocyte

value: yes

value: nf


title: Normal_tissue_Colon_cancer_patient_05


title: Liver_High-fat diet_rep 1

description: non-exercised mice remained sedenrary


title: Cancer_tissue_Colon_cancer_patient_04

value: Cancer tissue


title: Cancer_tissue_Colon_cancer_patient_05


title: Leukocyte  27086B

description: Affymetrix SNP 6.0

source_name: Leukocyte  27086B

value: no


title: Normal_tissue_Colon_cancer_patient_03


title: Cancer_tissue_Colon_cancer_patient_02


title: Normal_tissue_Colon_cancer_patient_06


title: Normal_tissue_Colon_cancer_patient_02


title: Cancer_tissue_Colon_cancer_patient_03


title: Leukocyte  1942B

description: Affymetrix SNP 6.0

source_name: Leukocyte  1942B


title: Liver_High-fat diet_rep 4

description: non-exercised mice remained sedenrary


title: Leukocyte  18176B

description: Affymetrix SNP 6.0

source_name: Leukocyte  18176B


title: L1_AluY_Breast6_MDA_468

city: Baltimore

first: John

middle: G

last: Zampella

state: MD

address: 733 N Broadway

department: Dermatology

institute: Johns Hopkins University School of Medicine

description: TIP-chip L1:Alu ratio files were used to detect L1 peaks for L1 and then Alu:L1 ratio files were used to detect Alu peaks

hyb_protocol: The labeled product was hybridized to the Nimblegen HD 2.1 M custom tiled arrays according to the manufacturer’s instructions.

scan_protocol: Each array was scanned in a microarray core facility using Nimblegen or Agilent instruments. Each scanned array yielded a raw .tff file.

data_processing:
Nimblescan called peaks using a sliding window threshold. A PERL script removed probes overlapping repeats to reduce noise (RepeatMasking). Nimblescan called peaks using a sliding window threshold. Peaks were ranked by the threshold of the log2 transformed ratio of red (Alu) and green (L1) channels or the reciprocal (settings: percent (p) start=90, p step=1, #steps=76, width of sliding window=1500bp, min probes>4, all probes>2)
Peaks were called on a log2 transformed scale of channel1/channel2 for L1 peaks and then channel2/channel1 for Alu peaks. Gff files containing "_532" contain the log2 data for L1 and .gff files containing "_635" contain log2 data for Alu.

source_name: L1 from MDA_468

label_protocol: Five micrograms of genomic DNA of each cell line was digested overnight in parallel reactions using four restriction enzymes (AseI, BspHI, HindIII, and Xbal). Sticky ends were ligated to annealed, partially complementary vectorette oligonucleotide adapters. Each template was aliquoted into 3 separate PCR reactions for L1Hs, AluYa5/8, and AluYb8/9 mobile DNA families. Vectorette PCR using the ExTaq Hotstart DNA polymerase and specific forward primers for each mobile element was performed on each of the samples. The PCR amplicons were digested using MseI, MspI and HpyCH4V restriction enzymes to generate smaller fragments and subsequently concentrated. These were then labeled with Cy3-dUTP for L1 and Cy5-dUTP for Alu reactionsusing exo- Klenow polymerase and random 9-mers.

growth_protocol: DNA obtained directly from NCI. Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0,5 x 10-6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 370C.

extract_protocol: isolated gDNA for each cell line was obtained from the NCI who used the Qiagen Maxi Kit Spin Protocol to extract DNA according to the manufacturers instructions

tag: mapped te_cell line info

tag: cell line

value: MDAN

tag: cell line source

value: Breast

tag: tissue/cell info.

value: Ductal carcinoma- mammary gland; breast; duct; metastatic site:pleural effusion;

source_name: Alu from MDA_468


title: L1_AluY_Breast5_T47D

source_name: L1 from T47D

value: infiltrating ductal carcinoma

source_name: Alu from T47D


title: Cancer_tissue_Colon_cancer_patient_01

value: colon cancer patient


title: Leukocyte  25313B

description: Affymetrix SNP 6.0

source_name: Leukocyte  25313B

tag: cell type

tag: patient

tag: age

tag: Stage


title: Liver_High-fat diet+Exercise_rep 5

description: exercised mice were put on a running machine at the speed 10 m/min per day for 16 weeks

source_name: Mouse liver, high-fat diet, exercised, 16 weeks

value: high-fat diet, exercised


title: Normal_tissue_Colon_cancer_patient_01

value: Colon


title: Liver_High-fat diet_rep 2

description: non-exercised mice remained sedenrary

value: liver


title: Leukocyte  28685B2

description: Affymetrix SNP 6.0

source_name: Leukocyte  28685B2

tag: gleason

tag: nomogram 5 years

tag: recurrence label


title: L1_AluY_Breast4_MDA_MB_231

source_name: L1 from MDA_MB_231

value: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site:pleural effusion;

source_name: Alu from MDA_MB_231


title: Leukocyte  13745B

description: Affymetrix SNP 6.0

source_name: Leukocyte  13745B

tag: fast relapase label


title: Leukocyte  1199B

description: Affymetrix SNP 6.0

source_name: Leukocyte  1199B


title: Liver_High-fat diet+Exercise_rep 4

tag: tissue

value: male


title: Liver_High-fat diet+Exercise_rep 2

value: 8 to 10 week old


title: Liver_High-fat diet+Exercise_rep 3


title: Leukocyte  11563B

description: Affymetrix SNP 6.0

source_name: Leukocyte  11563B


title: L1_AluY_Breast1_BT_549

source_name: L1 from BT_549

value: Papillary infiltrating ductal carcinoma-mammary gland; breast

source_name: Alu from BT_549


title: Liver_High-fat diet+Exercise_rep 1


title: Liver_Normal diet_rep5

description: non-exercised mice remained sedenrary

source_name: Mouse liver, normal diet, 16 weeks

value: normal diet


title: L1_AluY_Prostate1_DU_145

source_name: L1 from DU_145

value: Prostate

value: prostate; metastatic site:brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Alu from DU_145


title: L1_AluY_Prostate2_PC_3

source_name: L1 from PC_3

value: Adenocarcinoma- prostate; metastatic site:bone;

source_name: Alu from PC_3


title: Liver_Normal diet_rep4

description: non-exercised mice remained sedenrary


title: L1_AluY_Renal8_UO_31

source_name: L1 from UO_31

value: Renal

value: Renal cell carcinoma-vpd

source_name: Alu from UO_31


title: Leukocyte  16464B

description: Affymetrix SNP 6.0

source_name: Leukocyte  16464B

value: Leukocyte

value: yes

value: nf


title: Liver_Normal diet_rep1

description: non-exercised mice remained sedenrary


title: Liver_Normal diet_rep3

description: non-exercised mice remained sedenrary


title: Liver_Normal diet_rep2

description: non-exercised mice remained sedenrary


title: L1_AluY_Renal7_TK_10

source_name: L1 from TK_10

value: Renal Spindle cell carcinoma

source_name: Alu from TK_10


title: L1_AluY_Breast3_MCF7

source_name: L1 from MCF7

value: Breast

value: Adenocarcinoma- mammary gland; breast; metastatic site:pleural effusion;

source_name: Alu from MCF7


title: L1_AluY_Renal6_SN12C

source_name: L1 from SN12C

value: Renal cell carcinoma-pd

source_name: Alu from SN12C


title: L1_AluY_Breast2_HS578T

source_name: L1 from HS578T

value: Carcinosarcoma-mammary gland; breast

source_name: Alu from HS578T


title: fetal peripheral6

source_name: sclera

tag: developmental stage

value: fetal

value: peripheral sclera


title: L1_AluY_Renal4_CAKI_1

source_name: L1 from CAKI_1

value: Clear cell carcinoma

source_name: Alu from CAKI_1


title: fetal peripheral4


title: fetal peripheral5


title: L1_AluY_Renal3_ACHN

source_name: L1 from ACHN

value: ACHN

value: Renal cell carcinoma-p/md

source_name: Alu from ACHN


title: L1_AluY_Renal2_A498

source_name: L1 from A498

value: Adenocarcinoma

source_name: Alu from A498


title: adult peripheral4

value: adult


title: L1_AluY_Renal5_RXF_393

source_name: L1 from RXF_393

value: Renal

value: hypernephroma-pd

source_name: Alu from RXF_393


title: L1_AluY_Ovarian7_SK_OV_3

source_name: L1 from SK_OV_3

value: Ovarian

value: Adenocarcinoma-vpd

source_name: Alu from SK_OV_3


title: L1_AluY_Ovarian6_OVCAR_8

source_name: L1 from OVCAR_8

value: Carcinoma-ud

source_name: Alu from OVCAR_8


title: fetal posterior3

value: posterior sclera


title: L1_AluY_Ovarian5_OVCAR_5

source_name: L1 from OVCAR_5

value: Adenocarcinoma-wd

source_name: Alu from OVCAR_5


title: L1_AluY_Ovarian4_OVCAR_4

source_name: L1 from OVCAR_4

value: Adenocarcinoma-md

source_name: Alu from OVCAR_4


title: fetal posterior5

source_name: sclera


title: fetal posterior4


title: fetal posterior6


title: L1_AluY_Renal1_786_0

source_name: Alu from 786_0


title: L1_AluY_Ovarian3_OVCAR_3

source_name: L1 from OVCAR_3

source_name: Alu from OVCAR_3


title: adult posterior3


title: fetal posterior1


title: adult posterior4


title: fetal posterior2


title: L1_AluY_Ovarian2_NCI_ADR_RES

source_name: L1 from NCI_ADR_RES

value: NCIADRRES

value: Adenocarinoma

source_name: Alu from NCI_ADR_RES


title: L1_AluY_Ovarian1_IGROV1

source_name: L1 from IGROV1

value: Cystoadenocarcinoma-pd

source_name: Alu from IGROV1


title: L1_AluY_Melanoma9_UACC_62

source_name: L1 from UACC_62

value: Melanoma

value: Melanotic melanoma

source_name: Alu from UACC_62


title: L1_AluY_Melanoma8_UACC_257

source_name: L1 from UACC_257

source_name: Alu from UACC_257


title: adult posterior2


title: L1_AluY_Melanoma7_SK_MEL_5

source_name: L1 from SK_MEL_5

value: Malignant melanotic melanoma

source_name: Alu from SK_MEL_5


title: L1_AluY_Melanoma6_SK_MEL_28

source_name: L1 from SK_MEL_28

source_name: Alu from SK_MEL_28


title: adult posterior1


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_paired liver biopsy EOT treatment rep 19

hyb_protocol: Samples were hybridized onto Affymetrix  GeneChip human gene 2.0 ST arrays according to manufacturer's recommendations

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

data_processing: The data were analyzed with EC 1.4 using Affymetrix default analysis with an Scale factor normalization method (mas5).

label_protocol: labeling was performed using the Ovation Pico WTA system (Nugen Inc., San Carlos, CA) and used for hybridization on the Affymetrix GeneChip Human Gene 2.0 ST array

growth_protocol: Study subjects were enrolled in a phase 2, single-center, prospective, community-based clinical trial (SYNERGY, NCT01805882) that evaluated all-oral DAA treatment at the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) in Bethesda, MD

extract_protocol: RNA was extracted using the RNeasy 96 kit according to manufacturer’s recommendations

treatment_protocol: Paired liver biopsies: Pre-treatment liver biopsies were obtained within 1.2 years of starting therapy and EOT biopsies were obtained within 5 days of completing treatment.

tag: treatment time

value: EOT

tag: paired mate

value: sample 9


title: L1_AluY_Melanoma5_SK_MEL_2

source_name: L1 from SK_MEL_2

source_name: Alu from SK_MEL_2


description: Gene expression data from_paired liver biopsy EOT treatment rep 18

value: sample 8


description: Gene expression data from_paired liver biopsy EOT treatment rep 20

value: sample 10


description: Gene expression data from_paired liver biopsy EOT treatment rep 16

value: sample 6


title: L1_AluY_Melanoma3_MALME_3M

source_name: L1 from MALME_3M

source_name: Alu from MALME_3M


title: L1_AluY_Melanoma4_MDA_MB_435

source_name: L1 from MDA_MB_435

value: Ductal carcinoma- mammary gland; breast; duct; metastatic site:pleural effusion;

source_name: Alu from MDA_MB_435


description: Gene expression data from_paired liver biopsy EOT treatment rep 14

value: sample 4


description: Gene expression data from_paired liver biopsy EOT treatment rep 13

value: sample 3


description: Gene expression data from_paired liver biopsy EOT treatment rep 15

value: sample 5


description: Gene expression data from_paired liver biopsy EOT treatment rep 12

value: sample 2


title: L1_AluY_Melanoma2_M14

source_name: L1 from M14

source_name: Alu from M14


title: L1_AluY_Melanoma1_LOXIMVI

source_name: L1 from LOXIMVI

value: LOXIMVI

value: Malignant amelanotic melanoma

source_name: Alu from LOXIMVI


description: Gene expression data from_paired liver biopsy EOT treatment rep 11

value: sample 1


title: L1_AluY_CNS6_U251

source_name: L1 from U251

value: CNS

value: Glioblastoma,ud

source_name: Alu from U251


title: paired liver biopsy PRE treatment rep 9

description: Gene expression data from_paired liver biopsy PRE treatment rep 9

source_name: paired liver biopsy PRE treatment rep 9

value: PRE

value: sample 19


title: RNA-26-08_2

type: SRA

first: Abu Musa Md Talimur

last: Reza

address: 604, Animal Science Building

department: Stem Cell and Regenerative Biology

institute: Konkuk University

description: smRNA

library_source: transcriptomic

data_processing:
Illumina RTA (Real Time Analysis. v1.18) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt 1.9.dev3.
To estimate expression levels, the smRNA-Seq reads were mapped to the pre-miRNA and mature miRNA sequence of Homo sapiens using bowtie 1.1.1.
The pre-miRNA and mature miRNA sequence of Homo sapiens (hg19) were downloaded from miRBase (release 21). The read counts of mature miRNA were calculated from mapping results.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each samples.

source_name: Exosomes

growth_protocol: Human adipose mesenchymal stem cells (hAMSCs) were cultured in a complete α-MEM medium

extract_protocol:
Exosomes were isolated using Exoquick-TC kit (SBI, USA) and the exosomal-miRNA was isolated using SeraMir Exosomal miRNA isolation kit (SBI, USA)
Libraries were constructed from smRNA using the TruSeq Small RNA Library Prep Kit following  manufacturer's protocols.

treatment_protocol: At 6,7&8 passage, 2×10^6 cells were seeded and incubated overnight. On the next day, cells were fed with new medium for another 48 h and the result medium was collected as conditioned medium (CM).

tag: primary source

value: Conditioned medium

value: Adipose Mesenchymal Stem Cells

tag: cell passages


title: gastric tumor sample 91228050T SNP6

city: Singapore

first: Ioana

last: Cutcutache

state: Singapore

address: 8 College Rd

department: Centre for Computational Biology

country: Singapore

institute: Duke-NUS

description: Hybridized to SNP6 array

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

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

data_processing: The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched non-malignant CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.

source_name: gastric tumor sample 91228050T

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.

value: gastric primary tumor tissue


title: L1_AluY_CNS5_SNB_75

source_name: L1 from SNB_75

tag: mapped te_cell line info

tag: cell line

value: Astrocytoma

source_name: Alu from SNB_75


title: gastric non-malignant sample 91228050N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 91228050N

value: gastric non-malignant tissue


title: gastric non-malignant sample 20020720N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 20020720N


title: gastric non-malignant sample 2000877N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 2000877N


title: paired liver biopsy PRE treatment rep 8

description: Gene expression data from_paired liver biopsy PRE treatment rep 8

source_name: paired liver biopsy PRE treatment rep 8

value: sample 18


title: gastric tumor sample 20020448T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 20020448T


title: gastric non-malignant sample 20020011N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 20020011N


title: gastric non-malignant sample 2000892N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 2000892N


title: gastric non-malignant sample 20020448N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 20020448N


title: gastric non-malignant sample 990474N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990474N


title: L1_AluY_CNS3_SF_539

source_name: L1 from SF_539

tag: cell line source

tag: tissue/cell info.

value: Glial cell neoplasm

source_name: Alu from SF_539


title: L1_AluY_CNS2_SF_295

source_name: L1 from SF_295

value: Glioblastoma, ud

source_name: Alu from SF_295


description: Gene expression data from_paired liver biopsy PRE treatment rep 10

value: sample 20


title: gastric tumor sample 20020011T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 20020011T


title: gastric tumor sample 990195T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990195T


title: L1_AluY_CNS4_SNB_19

source_name: L1 from SNB_19

source_name: Alu from SNB_19


description:
agr mutant savirin
Gene expression data from_Staphylococcus aureus agr mutant savirin rep 3

hyb_protocol: Samples were hybridized onto custom Affymetrix GeneChip containing Sa according to manufacturer's recommendations

data_processing: The data were analyzed with EC 1.1 using Affymetrix default analysis

organism: Staphylococcus aureus

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: frozen stocks were cultured in trypticase soy broth (TSB) (Becton Dickinson)

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: presence or absence of savirin (5 μg ml-1)

tag: genotype

value: agr mutant

tag: treatment

value: savirin


description:
agr mutant savirin
Gene expression data from_Staphylococcus aureus agr mutant savirin rep 2


description:
agr mutant savirin
Gene expression data from_Staphylococcus aureus agr mutant savirin rep 1


title: paired liver biopsy PRE treatment rep 5

description: Gene expression data from_paired liver biopsy PRE treatment rep 5

source_name: paired liver biopsy PRE treatment rep 5

value: sample 15


title: paired liver biopsy PRE treatment rep 4

description: Gene expression data from_paired liver biopsy PRE treatment rep 4

source_name: paired liver biopsy PRE treatment rep 4

value: sample 14


title: paired liver biopsy PRE treatment rep 6

description: Gene expression data from_paired liver biopsy PRE treatment rep 6

source_name: paired liver biopsy PRE treatment rep 6

value: sample 16


title: gastric non-malignant sample 990228N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990228N


title: L1_AluY_CNS1_SF_268

description: TIP-chip L1:Alu ratio files were used to detect L1 peaks for L1 and then Alu:L1 ratio files were used to detect Alu peaks

source_name: L1 from SF_268

value: CNS

source_name: Alu from SF_268


title: paired liver biopsy PRE treatment rep 3

description: Gene expression data from_paired liver biopsy PRE treatment rep 3

source_name: paired liver biopsy PRE treatment rep 3

value: PRE

value: sample 13


title: gastric tumor sample 990228T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990228T


title: gastric non-malignant sample 990195N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990195N


title: gastric non-malignant sample 990108N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990108N


title: L1_AluY_Colon6_KM12

source_name: L1 from KM12

value: Colon

value: Adenocarcinome-pd

source_name: Alu from KM12


title: L1_AluY_Colon7_SW_620

source_name: L1 from SW_620

value: Carcinoma-ud

source_name: Alu from SW_620


title: paired liver biopsy PRE treatment rep 2

description: Gene expression data from_paired liver biopsy PRE treatment rep 2

source_name: paired liver biopsy PRE treatment rep 2

value: sample 12


title: L1_AluY_Colon5_HT29

source_name: L1 from HT29

value: Adenocarcinoma-md

source_name: Alu from HT29


description:
agr mutant vehicle
Gene expression data from_Staphylococcus aureus agr mutant vehicle rep 3

value: vehicle


title: L1_AluY_Colon4_HCT_15

source_name: L1 from HCT_15

value: Adenocarcinoma p/md

source_name: Alu from HCT_15


title: gastric tumor sample 2000877T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 2000877T

value: gastric primary tumor tissue


title: paired liver biopsy PRE treatment rep 1

description: Gene expression data from_paired liver biopsy PRE treatment rep 1

source_name: paired liver biopsy PRE treatment rep 1

value: sample 11


title: Staphylococcus aureus LAC-savirin rep 3

description:
LAC savirin
Gene expression data from_Staphylococcus aureus LAC-savirin rep 3

source_name: Staphylococcus aureus LAC-savirin rep 3

value: LAC


title: Staphylococcus aureus LAC-savirin rep 2

description:
LAC savirin
Gene expression data from_Staphylococcus aureus LAC-savirin rep 2

source_name: Staphylococcus aureus LAC-savirin rep 2

value: savirin


title: PlasmaEV_grazing_2

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

description:
microRNA
Gene expression in plasma EVs of grazing cattle

hyb_protocol: Each labeled Samples were prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Custom miRNA, Bovine 8X60K Microarrays (Agilent®), and then rotated at 20 rpm for 20 h at 55°C. Agilent Gene Expression Wash Buffers 1(RT) and 2(37°C) were used after hybridization as recommended by Agilent miRNA Microarray System.

scan_protocol: The signals of hybridized probes were scanned on a Agilent Technologies G4900DA SureScan scanner at 3 µm resolution, setting for custom microarray SurePrint G3 8x60K slide (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction 11.0.1.1 (Agilent) using default parameters. The data were imported to GeneSpring GX (Agilent, ver. 13.1) and were normalized to 90 percentile.

organism: Bos taurus

source_name: plasma EVs, grazing

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to the manufacturer's recommended protocol. The Agilent microRNA Spike-In Kit was used for in-process control to measure labeling and hybridization efficiency. Briefly, 100ng total RNA was dephosphorylated at 37°C for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100°C for 7min. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16°C for 2 hour. The labeled RNA samples were purified in a Vacuum Concentrator for one hour. Once samples are completely dried.

growth_protocol: In the first 4 months from early June to late October, the grazing cattle were fed on the pasture, whereas the housed cattle were fed in a free-stall barn. In the last 3 months, from late October to the following mid-January, both groups were fed with grass silage in the free-stall barn.

extract_protocol: Total RNA including miRNA was extracted from plasma exosome samples using the mirVana microRNA isolation kit (Ambion, Austin, TX) for microarray analysis of plasma samples according to the manufacturer’s protocols. The quantity and quality of the RNA were determined by Agilent Bioanalyzer 2100 with an RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Blood samples were drawn from the jugular vein of each animal and the plasma was prepared as 0.1% EDTA, followed by storage at -80ºC until use. The blood samples were collected after 5-month experimental period. The plasma sample was mixed with PBS at 2:1, and centrifuged at 1,200 g, 4ºC for 20 min. The supernatant was centrifuged at 12k g, 4ºC for 45 min, and further centrifuged at 110k g, 4ºC for 120 min. The precipitation was suspended in PBS and centrifuged at 110k g, 4ºC for 70 min to obtain EV sample pellet.

tag: breed

value: Japanese Black

value: Plasma EVs

tag: feeding status

value: Grazing


title: PlasmaEV_grazing_1


title: gastric non-malignant sample 990098N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990098N

value: gastric non-malignant tissue


title: L1_AluY_Colon3_HCT_116

source_name: L1 from HCT_116

value: carcinoma-vpd

source_name: Alu from HCT_116


title: gastric tumor sample 2000892T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 2000892T


title: PlasmaEV_grazing_3


title: gastric tumor sample 990098T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990098T


title: L1_AluY_Colon1_COLO205

source_name: L1 from COLO205

value: Adenocarcinoma

source_name: Alu from COLO205


title: PlasmaEV_grain-fed_3

description:
microRNA
Gene expression in plasma EVs of grain-fed cattle

source_name: plasma EVs, grain-fed

value: Grain-fed


title: L1_AluY_Lung9_NCI_H522

source_name: L1 from NCI_H522

value: Lung

value: Adenocarcinoma-vpd

source_name: Alu from NCI_H522


title: gastric tumor sample 20020720T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 20020720T


title: PlasmaEV_grain-fed_1


title: Staphylococcus aureus LAC-savirin rep 1

description:
LAC savirin
Gene expression data from_Staphylococcus aureus LAC-savirin rep 1

source_name: Staphylococcus aureus LAC-savirin rep 1


title: L1_AluY_Lung8_NCI_H460

source_name: L1 from NCI_H460

value: Large Cell Carcinoma-ud

source_name: Alu from NCI_H460


title: Staphylococcus aureus LAC vehicle rep 3

description:
LAC vehicle
Gene expression data from_Staphylococcus aureus LAC vehicle rep 3

source_name: Staphylococcus aureus LAC vehicle rep 3


description:
agr mutant vehicle
Gene expression data from_Staphylococcus aureus agr mutant vehicle rep 2

value: agr mutant


title: gastric tumor sample 990097T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990097T


title: Staphylococcus aureus LAC vehicle rep 1

description:
LAC vehicle
Gene expression data from_Staphylococcus aureus LAC vehicle rep 1

source_name: Staphylococcus aureus LAC vehicle rep 1

value: vehicle


title: L1_AluY_Lung5_NCI_H226

source_name: L1 from NCI_H226

value: Squamous cell carcinoma-vpd

source_name: Alu from NCI_H226


title: L1_AluY_Lung6_NCI_H23

source_name: L1 from NCI_H23

value: Adenocarcinoma-ud

source_name: Alu from NCI_H23


title: Sclera myopia 3

city: New York

first: Andrei

middle: V

last: Tkatchenko

state: NY

address: 160 Ft Washington Ave

department: Ophthalmology

institute: Columbia University

description:
M3_Sclera
miRNA expression, myopic sclera.

hyb_protocol: Microarray hybridization was carried out using miRNA Complete Labeling and Hybridization Kit (Agilent) followed by washing using Gene Expression Wash Buffer Kit following manufacturer's instructions.

scan_protocol: Microarrays were scanned on a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings.

data_processing: Gene expression data were analyzed using Partek Genomics Suite 6.6. Data were adjusted to bring the minimal signal to 0.5, normalized using quantile normalization procedure, and log2-transformed. This was followed by the removal of absent features and outliers. The normalized data were then analyzed using ANOVA to identify the differences in miRNA expression levels between myopic and control eyes. Differentially expressed miRNAs were identified using an FDR-adjusted P-value threshold of 0.05 and a cutoff of 2-fold change in expression. Differential expression was calculated as fold change (FC, myopic samples vs control).

source_name: Mouse 3, right eye, myopic sclera, 10 days visual form deprivation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Both myopic and control eyes were enucleated, cleaned by removing surrounding tissues and the crystalline lens, retina and sclera were dissected, snap-frozen in liquid nitrogen and stored in RNAlater®-ICE (Life Technologies, Grand Island, NY). In order to obtain sufficient amount of tissue for RNA isolation, the retinas or scleras from three myopic or control eyes were pooled for RNA extraction. Three replicates (3 eyes per replicate) were processed in parallel. Total RNA was isolated from the retina and sclera samples using mirVanaTM miRNA isolation kit (Life Technologies, Grand Island, NY) according to the manufacturer’s instructions. RNA concentration was measured using NanoDrop 8000 spectrophotometer (Thermo Scientific, Wilmington, DE). The quality of the total RNA was assessed using Agilent RNA 6000 Nano kit and 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) following the manufacturer’s instructions.

treatment_protocol: Visual form deprivation (VFD) was induced in 12 mice by applying a unilateral frosted hemispherical plastic diffusers over the right eyes. Briefly, frosted hemispherical plastic diffusers were hand-made using caps from 0.2 ml PCR tubes (Molecular BioProducts, San Diego, CA) and rings made from medical tape (inner diameter 6 mm; outer diameter 8 mm). A cap was frosted with fine sandpaper and attached to a ring with Loctite™ Super Glue (Henkel Consumer Adhesives, Avon, OH). On the first day of the experiment (P24), animals were anesthetized via intraperitoneal injection of ketamine (90 mg/kg) and xylazine (10 mg/kg), and diffusers were attached to the skin surrounding the right eye with several stitches using size 5-0 ETHILON™ microsurgical sutures (Ethicon, Somerville, NJ) and reinforced with Vetbond™ glue (3M Animal Care Products, St. Paul, MN). The contralateral untreated left eyes were used as control. Toenails were covered with adhesive tape to prevent mice from removing the diffusers. Animals recovered on a warming pad and were then housed in transparent plastic cages for the duration of the experiment (10 days). A control group comprised of 8 age-matched C57BL/6J mice was maintained under the same experimental conditions as experimental group, but without VFD.

tag: strain/background

value: whole sclera

value: visual form deprivation

tag: age

tag: mouse identifier


title: L1_AluY_Lung7_NCI_H322M

source_name: L1 from NCI_H322M

value: Small cell Bronchioalveolar Carcinoma

source_name: Alu from NCI_H322M


title: L1_AluY_Lung3_HOP_62

source_name: L1 from HOP_62

value: adenocarcinoma-ud

source_name: Alu from HOP_62


title: R. sphaeroides WT 2.4.1_pPos19 versus pBBR after 7 min of singlet oxygen stress_replicate A

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

description:
pPos19 vs. pBBR (A)
Biological samples 1-3.

hyb_protocol: Total RNA of three independent experiments of Rhodobacter sphaeroides 2.4.1 pPos19 and pBBR were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: LOESS normalization with Limma package for Bioconductor in R was applied for dye-bias correction.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides crude extracts_pPos19 7 min

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.

growth_protocol: R. sphaeroides strains were grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light for 7 min.

extract_protocol: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy® MinElute™ spin columns (Qiagen).

tag: genotype/variation

value: WT

tag: vector

value: singlet oxygen stress for 7min

source_name: R. sphaeroides crude extracts_pBBR 7 min

value: pBBR


title: Sclera myopia 1

description:
M1_Sclera
miRNA expression, myopic sclera.

source_name: Mouse 1, right eye, myopic sclera, 10 days visual form deprivation

tag: tissue


title: R. sphaeroides WT 2.4.1_pPos19 versus pBBR after 7 min of singlet oxygen stress_replicate B

description:
pPos19 vs. pBBR (B)
Biological samples 4-6.


title: Retina myopia 3

description:
M3_Retina
miRNA expression, myopic retina.

source_name: Mouse 3, right eye, myopic retina, 10 days visual form deprivation

value: whole retina


title: L1_AluY_Lung4_HOP_92

description: TIP-chip L1:Alu ratio files were used to detect L1 peaks for L1 and then Alu:L1 ratio files were used to detect Alu peaks

source_name: L1 from HOP_92

value: Large cell-ud

source_name: Alu from HOP_92


title: L1_AluY_Lung2_EKVX

source_name: L1 from EKVX

value: EKVX

value: Adenocarcinoma-md

source_name: Alu from EKVX


title: L1_AluY_Lung1_A549ATCC

source_name: L1 from A549ATCC

value: Lung

value: Adenocarcinoma-p/md

source_name: Alu from A549ATCC


title: gastric non-malignant sample 980390N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 980390N

value: gastric non-malignant tissue


title: gastric non-malignant sample 990060N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990060N


title: L1_AluY_Leukemia6_SR

source_name: L1 from SR

value: SR

value: Leukemia

value: Lymphoma

source_name: Alu from SR


title: L1_AluY_Leukemia5_RPMI_8226

source_name: L1 from RPMI_8226

value: Myeloma

source_name: Alu from RPMI_8226


title: gastric non-malignant sample 990097N SNP6

description: Hybridized to SNP6 array

source_name: gastric non-malignant sample 990097N


title: Sclera myopia 2

description:
M2_Sclera
miRNA expression, myopic sclera.

source_name: Mouse 2, right eye, myopic sclera, 10 days visual form deprivation

value: whole sclera

value: visual form deprivation


title: Retina myopia 2

description:
M2_Retina
miRNA expression, myopic retina.

source_name: Mouse 2, right eye, myopic retina, 10 days visual form deprivation


title: Sclera control 3

description:
C3_Sclera
miRNA expression, control sclera.

source_name: Mouse 3, left eye, control sclera, no visual form deprivation

value: control


title: Retina myopia 1

description:
M1_Retina
miRNA expression, myopic retina.

source_name: Mouse 1, right eye, myopic retina, 10 days visual form deprivation


title: L1_AluY_Leukemia4_MOLT_4

source_name: L1 from MOLT_4

value: ALL (cells were taken when patient was in relapse)

source_name: Alu from MOLT_4


title: gastric tumor sample 990108T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990108T

value: gastric primary tumor tissue


title: gastric tumor sample 990060T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990060T


title: L1_AluY_Leukemia2_HL_60

source_name: L1 from HL_60

value: Pro myelocytic leukemia

source_name: Alu from HL_60


title: L1_AluY_Leukemia3_K_562

source_name: L1 from K_562

value: CML

source_name: Alu from K_562


title: gastric tumor sample 990474T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 990474T


title: Sclera control 1

description:
C1_Sclera
miRNA expression, control sclera.

source_name: Mouse 1, left eye, control sclera, no visual form deprivation


title: Sclera control 2

description:
C2_Sclera
miRNA expression, control sclera.

source_name: Mouse 2, left eye, control sclera, no visual form deprivation


title: L1_AluY_Leukemia1_CCRF_CEM

source_name: L1 from CCRF_CEM

value: CCRFCEM

value: ALL

source_name: Alu from CCRF_CEM


title: Retina control 3

description:
C3_Retina
miRNA expression, control retina.

source_name: Mouse 3, left eye, control retina, no visual form deprivation

value: whole retina


title: Retina control 2

description:
C2_Retina
miRNA expression, control retina.

source_name: Mouse 2, left eye, control retina, no visual form deprivation


title: Retina control 1

description:
C1_Retina
miRNA expression, control retina.

source_name: Mouse 1, left eye, control retina, no visual form deprivation


title: gastric tumor sample 980390T SNP6

description: Hybridized to SNP6 array

source_name: gastric tumor sample 980390T


title: L1_AluY_Colon2_HCC_2998

source_name: L1 from HCC_2998

value: Colon

value: carcinoma

source_name: Alu from HCC_2998


description:
agr mutant vehicle
Gene expression data from_Staphylococcus aureus agr mutant vehicle rep 1

value: agr mutant

value: vehicle


title: Decidua parietalis from preeclampsia pregnancy 3

status: Public on Feb 08 2017

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene level expression data quality was confirmed, normalized (RMA) and summarized (Affymetrix Expression Console Software). Significant differential expression was determined by statistical analysis of false discovery rate (ANOVA p < 0.05) and absolute linear fold change >2 (Affymetrix Transcriptome Analysis Console Software).

source_name: decidua parietalis

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: We used laser microdissection to isolate the decidua basalis and parietalis from sPE and nPTB samples (n=4/ group). Biopsies of the placenta/decidua basalis and smooth chorion/decidua parietalis were washed repeatedly in cold PBS to remove blood contaminants then placed in cryomolds containing OCT, frozen over a dry ice/ethanol slurry, and stored at -80C. The blocks were sectioned at 20 microns by using a Leica CM3050 cryostat. The sections were mounted on UV treated PEN-membrane slides, and stored under dry ice prior to laser capture microdissection later that day. Immediately prior to the procedure, sections were immersed in cold PBS until the OCT dissolved (~1 min), dipped in 0.1% toluidine blue for 30 s, washed in cold PBS, dehydrated (30 s/treatment) in a graded ethanol series (75%, 75%, 95%, 100%), then rapidly dried with compressed nitrogen. All solutions were made with nuclease-free water. Decidua basalis and parietalis were laser microdissected (Leica LMD 7000) and collected directly into RLT Plus (Qiagen RNeasy Plus Micro kit). Total RNA was isolated according to the manufacturer’s protocol and concentrations were measured photometrically (NanoDrop 2000c). RNA integrity was determined via microfluidic phoresis (Agilent Bioanalyzer 2100). The samples were stored at -80C.

value: preeclampsia


title: Decidua parietalis from control pregnancy 4

value: preterm birth control


title: Liver_maternal chromium restriction diet_32week_rep1

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: gene expression data from liver from maternal chromium restriction

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

source_name: maternal chromium restriction diet, 32week

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

value: Liver

value: 32 week


title: Decidua basalis from control pregnancy 3

source_name: decidua basalis


title: Decidua parietalis from preeclampsia pregnancy 1


title: Decidua parietalis from control pregnancy 2


title: Decidua basalis from control pregnancy 4


title: Decidua basalis from preeclampsia pregnancy 3


title: PlasmaEV_grain-fed_2

description:
microRNA
Gene expression in plasma EVs of grain-fed cattle

source_name: plasma EVs, grain-fed

value: Japanese Black

value: Plasma EVs

value: Grain-fed


title: Decidua basalis from preeclampsia pregnancy 4


title: Liver_control diet_32week_rep2

source_name: control diet, 32 week


title: Decidua parietalis from control pregnancy 1


title: Decidua basalis from control pregnancy 2


title: Decidua basalis from preeclampsia pregnancy 2


title: Liver_control diet_32week_rep1


title: Liver_maternal chromium restriction diet_32week_rep2


title: Liver_maternal chromium restriction diet_32week_rep3