title: F065

value: fibromyalgia

value: peripheral blood

tag: irritable bowel syndrome

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: 217706_OB_TRP_het

status: Public on Feb 01 2016

type: RNA

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

department: Pathology

country: USA

institute: University of North Carolina

hyb_protocol: Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100)  as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapse by averaging. Sampless from  different batches  were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with brain location and genotype as covariates.  Normalized data provided is the filtered, batch combined,  non-median centered data used to draw conclusions in the study.

molecule: total RNA

organism: Mus musculus

label_protocol: Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent.  1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes.  Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes.  Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.

extract_protocol: Total RNA was extracted from brain regions with Qiagen RNeasy kit according to manufacturer's instructions

treatment_protocol: Brains were harvested from mice.  Brain regions were separated during gross dissection and immediately flash-frozen in liquid nitrogen.

tag: ID

tag: genotype

value: TRPhet

tag: tissue

value: OFB

tag: batch

source_name: Stratagene whole mouse reference RNA

tag: sample type

value: Stratagene whole mouse reference RNA


title: 219921_OB_P_null

value: Pnull


title: N-TC6(Fr)

city: Tokyo

first: Toyoki

last: Yoshimoto

address: Minato-ku, Toranomon 2-2-2

country: Japan

institute: Toranomon Hospital

description:
normal lung tissue, sample1, rep1
microRNA expression

hyb_protocol: Labelled samples were incubated with diluted hybridization Spike-In, 10x Gene Expression Blocking Agent and 2xHi-RPM Hybridization Buffer(Agilent), at 100°C for 5min, and immediately cooled with ice. Next, samples were hybridized to the 8 x 60K format SurePrint G3 Agilent human miRNA array for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Array slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(4000B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and R/G PMT is set to 100%, no XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1. (Agilent) using default parameters (miRNA_1010_Sep10 and Grid: 031181_D_F_20101116).

organism: Homo sapiens

source_name: lung, normal tissue

label_protocol: Samples were labelled with pCp-Cy3 by incubation with T4 ligase at 16°C for two hours according to the manufacturer's instructions. followed by purification by MicroBioSpin6(BioRad) and concentration.

extract_protocol: Total RNA was isolated using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) for fresh frozen samples and a miRNeasy FFPE Kit (Qiagen) for FFPE samples. RNA concentrations were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), while RNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: Fresh tissues obtained during surgery were frozen in liquid nitrogen, typically 15 min after removal, and stored at -80°C until further use. Simultaneously, resected specimens were formalin-fixed and paraffin-embedded (FFPE) for standard histopathological examinations.

value: lung

tag: disease state

value: normal tissue

tag: tissue preparation

value: fresh frozen tissue

tag: gender

value: M

tag: age


title: F061

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing: Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish

label: SAPE

source_name: Peripheral Blood_Fibromyalgia Patient

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

tag: diagnosis

tag: fiqr score

tag: bmi

tag: migraine

value: Yes

value: No


title: RE11(Fr)

description:
rectal carcinoid, sample11, rep1
microRNA expression

source_name: rectum, carcinoid

value: rectum

value: carcinoid

value: F


title: F064

tag: irritable bowel syndrome


title: 220727_OB_T

value: T


title: CD4_RAlowROlow product D3 S005

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
CD4_RAlowROlow product
9231092092_L

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and various software packages from Bioconductor.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Sorted Cells

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: From PBMCs, CD4+ T cells as well as CD4+ T cell subsets were sorted with the FACSAria (Becton Dickinson)

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: For gene array analysis of immune subsets, 10,000 sorted CD4+ T cells were collected directly into RNAse-free 1.5mL eppendorf tubes containing 500µL of RLT buffer with 1% β-mercaptoethanol and stored at -80°C until analysis.

tag: donor

tag: cell subset

tag: time point

value: product

tag: sampleID


title: CD4_Naiive Baseline D1 S019

description:
CD4_Naiive Baseline
9231092100_B

value: Baseline


title: RE10(Fr)

description:
rectal carcinoid, sample10, rep1
microRNA expression


title: 219898_OB_RP_null

tag: ID

tag: genotype

value: RPnull


title: CD4_TM secondTP D4 S066

description:
CD4_TM secondTP
9231092100_F

value: secondTP

tag: batch


title: F057

value: fibromyalgia

tag: tissue

value: peripheral blood

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: CD4_RAlowROlow product D2 S003

description:
CD4_RAlowROlow product
9231092092_K


title: CD4_TM thirdTP D2 S098

description:
CD4_TM thirdTP
9231092100_C

value: thirdTP


title: CD4_TM thirdTP D4 S106

description:
CD4_TM thirdTP
9231092100_D


title: 220062_OB_RP_null

value: OFB

tag: sample type

value: Stratagene whole mouse reference RNA


title: F060

tag: diagnosis


title: 220061_OB_RP_het

value: RPhet


title: CD4_EM product D5 S008

description:
CD4_EM product
9231092092_J


title: TC14(Fr)

description:
typical carcinoid of the lung, sample14, rep1
microRNA expression

source_name: lung, carcinoid

value: lung

tag: disease state

tag: tissue preparation

value: fresh frozen tissue

tag: gender

value: M

tag: age


title: 221184_OB_T


title: F059

tag: fiqr score

tag: bmi

tag: migraine

value: Yes

tag: irritable bowel syndrome

value: No


title: F055


title: TC10(Fr)

description:
typical carcinoid of the lung, sample10, rep1
microRNA expression

value: carcinoid

value: F


title: CD4_EM product D2 S002

description:
CD4_EM product
9231092092_I

tag: donor

tag: cell subset

tag: time point

value: product

tag: sampleID


title: TC19(Fr)

description:
typical carcinoid of the lung, sample19, rep1
microRNA expression

tag: tissue


title: 219594_OB_TP_null

tag: ID

tag: genotype

value: TPnull

tag: batch


title: F054

tag: diagnosis

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: F053


title: 216498_OB_TRP_null

value: TRPnull

tag: sample type


title: TC9(Fr)

description:
typical carcinoid of the lung, sample9, rep1
microRNA expression

tag: disease state

tag: tissue preparation

tag: gender

tag: age


title: TC8(Fr)

description:
typical carcinoid of the lung, sample8, rep1
microRNA expression


title: 219438_OB_TP_het

value: TPhet


title: CD4_EM product D4 S006

description:
CD4_EM product
9231092092_G

tag: donor


title: Innate Baseline D1 S022

description:
Innate Baseline
9231092092_H

tag: cell subset

value: Innate

value: Baseline


title: TC6(Fr)

description:
typical carcinoid of the lung, sample6, rep1
microRNA expression


title: F048

value: fibromyalgia

value: peripheral blood

tag: fiqr score

tag: bmi

tag: migraine

tag: irritable bowel syndrome


title: CD4_CM product D4 S007

description:
CD4_CM product
9231092092_E

tag: time point

tag: sampleID


title: 220057_OB_P_null

tag: ID

tag: genotype

value: Pnull

tag: tissue

value: OFB

tag: batch

value: Stratagene whole mouse reference RNA


title: F052

tag: diagnosis

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: F049


title: F050


title: N-TC19

description:
normal lung tissue, sample6, rep1
microRNA expression

value: lung

tag: disease state

value: normal tissue

tag: tissue preparation

value: formalin fixed paraffin embedded

tag: gender

tag: age


title: CD4_EM product D3 S004

description:
CD4_EM product
9231092092_F

tag: donor

tag: cell subset


title: F047

tag: fiqr score

tag: bmi

tag: migraine

value: No

tag: irritable bowel syndrome


title: 221940_OB_T

tag: ID

tag: genotype

value: T

tag: sample type


title: N-TC14

description:
normal lung tissue, sample5, rep1
microRNA expression

tag: tissue

value: M


title: N-TC10

description:
normal lung tissue, sample4, rep1
microRNA expression

value: F


title: N-TC9

description:
normal lung tissue, sample3, rep1
microRNA expression


title: N-TC8

description:
normal lung tissue, sample2, rep1
microRNA expression


title: CD4_RAlowROlow product D8 S018

description:
CD4_RAlowROlow product
9231092092_C

tag: time point

value: product

tag: batch

tag: sampleID


title: 219439_OB_TRP_het

value: TRPhet


title: 220435_OB_Oil

value: control


title: 225561_OB_R

value: R


title: SJ016800

type: genomic

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: I428-IGH EPOR

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

molecule: genomic DNA

source_name: non-leukemic  bone marrow

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: DNA was extracted from GFP+ leukemic spleen cells derived from C57BL/6 mice transplanted with Arf-/- pre B-cells expressing truncated EPOR ± IK6

extract_protocol: Qiagen AllPrep Mini kit

value: stage-matched bone marrow

source_name: leukemice cells flow sorted from spleen

value: Truncated EPOR primary tumor


title: CD4_RAlowROlow product D10 S012

description:
CD4_RAlowROlow product
9231092092_B


title: CD4_Naiive Baseline D10 S037

description:
CD4_Naiive Baseline
9231092079_K

value: Baseline


title: CD4_RAlowROlow product D7 S014

description:
CD4_RAlowROlow product
9231092092_D


title: F044

tag: diagnosis

value: fibromyalgia

value: peripheral blood

value: Yes

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: N-RE11

description:
normal rectal mucosa, sample3, rep1
microRNA expression

source_name: rectum, normal tissue

value: rectum

tag: disease state

tag: tissue preparation

tag: gender

tag: age


title: F040

tag: fiqr score

tag: bmi

tag: migraine


title: F046

tag: irritable bowel syndrome


title: F041


title: 217857_OB_TP_null

tag: ID

tag: genotype

value: TPnull

value: OFB

tag: sample type

value: Stratagene whole mouse reference RNA


title: 214253_OB_TRP_null

value: TRPnull

tag: tissue

tag: batch


title: CD4_TM Baseline D8 S138

description:
CD4_TM Baseline
9231092079_J

tag: donor

tag: cell subset

tag: time point

tag: sampleID


title: CD8_mem thirdTP D7 S120

description:
CD8_mem thirdTP
9231092079_I

value: thirdTP


title: F042

tag: diagnosis

value: No

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: N-TC6

value: lung

tag: disease state

value: normal tissue

tag: tissue preparation

value: formalin fixed paraffin embedded

tag: gender

value: M

tag: age


title: F039

tag: fiqr score

tag: bmi

tag: migraine

tag: irritable bowel syndrome


title: F043

tag: tissue


title: 221699_OB_Oil

tag: ID

tag: genotype

value: control

tag: batch

tag: sample type


title: CD4_Naiive firstTP D4 S049

description:
CD4_Naiive firstTP
9231092079_H

tag: donor

tag: cell subset

tag: time point

value: firstTP

tag: sampleID


title: 219695_OB_TRP_het

value: TRPhet


title: 219596_OB_TRP_het


title: CD4_Naiive Baseline D8 S047

description:
CD4_Naiive Baseline
9231092079_G

value: Baseline


title: 223979_OB_Oil


title: F038

tag: diagnosis

value: fibromyalgia

value: peripheral blood

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: SJ016801

description: I428-IGH EPOR + Ik6

value: stage-matched bone marrow

value: Truncated EPOR + IK6 primary tumor


title: N-RE5

description:
normal rectal mucosa, sample1, rep1
microRNA expression

value: rectum

tag: disease state

tag: tissue preparation

tag: gender

tag: age


title: CD8_mem Baseline D3 S028

description:
CD8_mem Baseline
9231092079_F


title: F037_2

tag: tissue

tag: fiqr score

tag: bmi

tag: migraine

tag: irritable bowel syndrome


title: CD4_EM product D8 S017

description:
CD4_EM product
9231092079_L

tag: donor

value: product

tag: batch


title: N-RE10

description:
normal rectal mucosa, sample2, rep1
microRNA expression


title: N-DU6

description:
normal duodenal mucosa, sample2, rep1
microRNA expression

source_name: duodenum, normal tissue

value: duodenum


title: N-DU5

description:
normal duodenal mucosa, sample1, rep1
microRNA expression


title: CD8_mem Baseline D1 S021

description:
CD8_mem Baseline
9231092079_E

tag: cell subset

tag: time point


title: N-DU8

description:
normal duodenal mucosa, sample3, rep1
microRNA expression

value: F


title: N-GA6

description:
normal gastric mucosa, sample3, rep1
microRNA expression

source_name: stomach, normal tissue

value: stomach


title: F036

tag: diagnosis

value: No

value: Yes


title: 215697_OB_TRP_nulll

tag: ID

tag: genotype

value: TRPnull

value: OFB

tag: sample type

value: Stratagene whole mouse reference RNA


title: N-GA3

description:
normal gastric mucosa, sample2, rep1
microRNA expression

tag: disease state

value: normal tissue

value: formalin fixed paraffin embedded


title: F037

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: F035

tag: tissue


title: CD8_mem thirdTP D1 S096

description:
CD8_mem thirdTP
9231092079_C

value: thirdTP

tag: sampleID


title: 217494_OB_TRP_het

value: TRPhet


title: 217861_OB_Oil

value: control


title: F034

value: fibromyalgia

value: peripheral blood

tag: fiqr score

tag: bmi


title: CD4_EM Baseline D3 S027

description:
CD4_EM Baseline
9231092064_L

value: Baseline


title: 215217_OB_TP_het

value: TPhet


title: 219699_OB_TP_null

value: TPnull


title: CD4_TM secondTP D7 S080

description:
CD4_TM secondTP
9231092079_D

value: secondTP


title: N-GA2

description:
normal gastric mucosa, sample1, rep1
microRNA expression

value: stomach

tag: tissue preparation

tag: gender

value: M

tag: age


title: CD8_mem Baseline D9 S045

description:
CD8_mem Baseline
9231092079_B

tag: donor

tag: cell subset

tag: batch


title: TC19

description:
typical carcinoid of the lung, sample19, rep1
microRNA expression

value: lung

value: carcinoid


title: TC18

description:
typical carcinoid of the lung, sample18, rep1
microRNA expression

value: F


title: TC17

description:
typical carcinoid of the lung, sample17, rep1
microRNA expression


title: 215534_OB_TRP_null

tag: ID

value: TRPnull

value: OFB

value: Stratagene whole mouse reference RNA


title: TC16

description:
typical carcinoid of the lung, sample16, rep1
microRNA expression

value: formalin fixed paraffin embedded


title: 216188_OB_TP_het

tag: genotype


title: CD4_EM product D10 S011

description:
CD4_EM product
9231092064_K

tag: time point

value: product


title: F030

tag: diagnosis

tag: migraine

value: No

tag: irritable bowel syndrome


title: F031

value: fibromyalgia

value: Yes

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: F033

tag: tissue

value: peripheral blood

tag: fiqr score


title: 219147_OB_T

value: T

tag: sample type


title: 219670_OB_R

value: R


title: CD4_EM product D7 S013

description:
CD4_EM product
9231092064_J

tag: sampleID


title: CD8_mem Baseline D7 S042

description:
CD8_mem Baseline
9231092064_H

value: Baseline


title: CD4_EM product D9 S015

description:
CD4_EM product
9231092064_I


title: F028

tag: bmi


title: TC14

description:
typical carcinoid of the lung, sample14, rep1
microRNA expression

tag: disease state

tag: tissue preparation

tag: gender

tag: age


title: TC15

description:
typical carcinoid of the lung, sample15, rep1
microRNA expression


title: TC13

description:
typical carcinoid of the lung, sample13, rep1
microRNA expression


title: 219892_OB_P_null

tag: ID

tag: genotype

value: Pnull

tag: batch


title: 219147_Forebrain_T

value: Forebrain


title: CD4_CM secondTP D2 S060

description:
CD4_CM secondTP
9231092079_A

tag: donor

tag: cell subset

tag: time point

value: secondTP


title: CD4_RAlowROlow product D9 S016

description:
CD4_RAlowROlow product
9231092064_G


title: F027

tag: diagnosis

tag: migraine

tag: irritable bowel syndrome

tag: major depression

tag: bipolar disorder


title: TC12

description:
typical carcinoid of the lung, sample12, rep1
microRNA expression

tag: tissue

value: lung

value: carcinoid


title: CD4_CM product D5 S010

description:
CD4_CM product
9231092064_F

tag: sampleID


title: TC11

description:
typical carcinoid of the lung, sample11, rep1
microRNA expression

tag: disease state

value: F


title: F029

tag: fiqr score

tag: bmi

tag: chronic fatigue syndrome


title: CD4_RAlowROlow product D5 S009

description:
CD4_RAlowROlow product
9231092064_E


title: F026


title: 221699_Forebrain_Normal

tag: ID

value: control

tag: sample type


title: 216188_Forebrain_TPhet

tag: genotype

value: TPhet

tag: batch

value: Stratagene whole mouse reference RNA


title: TC10

description:
typical carcinoid of the lung, sample10, rep1
microRNA expression

tag: tissue preparation

value: formalin fixed paraffin embedded

tag: gender

tag: age


title: F029_2

tag: diagnosis

tag: migraine


title: TC9

description:
typical carcinoid of the lung, sample9, rep1
microRNA expression


title: F025

tag: irritable bowel syndrome

tag: major depression

value: No


title: F025_2

value: fibromyalgia

tag: tissue

tag: bipolar disorder


title: 217871_Forebrain_T

value: Phet


title: 221182_Forebrain_Normal


title: F024_2

value: peripheral blood


title: F024

value: Yes


title: Innate Baseline D3 S029

description:
Innate Baseline
9231092064_B

tag: donor

tag: cell subset

value: Innate

tag: time point

tag: sampleID


title: 217861_Forebrain_Normal

tag: ID


title: CD8_mem Baseline D4 S032

description:
CD8_mem Baseline
9031292050_K

value: Baseline


title: TC8

description:
typical carcinoid of the lung, sample8, rep1
microRNA expression

tag: disease state

value: M


title: TC7

description:
typical carcinoid of the lung, sample7, rep1
microRNA expression


title: 221940_Forebrain_T

tag: genotype

value: T

value: Forebrain

tag: sample type


title: TC6

description:
typical carcinoid of the lung, sample6, rep1
microRNA expression

value: lung

tag: tissue preparation


title: F021

tag: fiqr score

tag: bmi

tag: chronic fatigue syndrome


title: CD4_EM secondTP D8 S091

description:
CD4_EM secondTP
9031292050_L

value: secondTP

tag: batch


title: CD4_EM product D1 S001

description:
CD4_EM product
9231092064_A

value: product


title: TC5

description:
typical carcinoid of the lung, sample5, rep1
microRNA expression

value: carcinoid

tag: gender

value: F

tag: age


title: 217494_Forebrain_TRPhet

value: TRPhet

tag: tissue

value: Stratagene whole mouse reference RNA


title: 215217_Forebrain_TPhet

value: TPhet


title: CD4_EM Baseline D7 S041

description:
CD4_EM Baseline
9231092064_D


title: F022

tag: diagnosis

value: fibromyalgia

tag: migraine

value: No

tag: irritable bowel syndrome

tag: major depression

tag: bipolar disorder


title: TC4

description:
typical carcinoid of the lung, sample4, rep1
microRNA expression

value: formalin fixed paraffin embedded


title: F020

value: peripheral blood

value: Yes


title: F019


title: TC3

description:
typical carcinoid of the lung, sample3, rep1
microRNA expression


title: F018


title: CD4_Naiive secondTP D2 S059

description:
CD4_Naiive secondTP
9031292050_J

tag: donor

tag: cell subset

tag: time point

tag: sampleID


title: 214253_Forebrain_TRPnull

tag: ID

tag: genotype

value: TRPnull

tag: sample type


title: 219439_Forebrain_TRPhet


title: 219695_Forebrain_TRPhet


title: 216103_Forebrain_TRPnull


title: CD4_EM secondTP D10 S076

description:
CD4_EM secondTP
9031292050_H


title: CD4_TM thirdTP D10 S114

description:
CD4_TM thirdTP
9031292050_G

value: thirdTP


title: CD4_Naiive thirdTP D4 S105

description:
CD4_Naiive thirdTP
9031292050_I


title: TC2

description:
typical carcinoid of the lung, sample2, rep1
microRNA expression

tag: disease state

tag: tissue preparation


title: F017

tag: fiqr score

tag: bmi

tag: chronic fatigue syndrome


title: SM9

description:
small cell lung carcinoma, sample9, rep1
microRNA expression

source_name: lung, small cell carcinoma

tag: tissue

value: small cell carcinoma

tag: gender

value: M

tag: age


title: TC1

description:
typical carcinoid of the lung, sample1, rep1
microRNA expression

value: lung


title: F017_2

tag: diagnosis

tag: migraine

tag: irritable bowel syndrome

tag: major depression


title: SM8

description:
small cell lung carcinoma, sample8, rep1
microRNA expression


title: SM7

description:
small cell lung carcinoma, sample7, rep1
microRNA expression


title: CD4_Naiive firstTP D7 S053

description:
CD4_Naiive firstTP
9031292050_D

tag: donor

tag: cell subset

tag: time point

value: firstTP

tag: batch


title: SM5

description:
small cell lung carcinoma, sample5, rep1
microRNA expression


title: F015

tag: bipolar disorder


title: CD4_EM secondTP D4 S067

description:
CD4_EM secondTP
9031292050_E

value: secondTP

tag: sampleID


title: CD4_EM Baseline D9 S044

description:
CD4_EM Baseline
9031292050_F

value: Baseline


title: F016


title: CD4_TM Baseline D2 S131

description:
CD4_TM Baseline
9031292050_C


title: 215697_Forebrain_TRPnull

tag: ID

tag: genotype

value: Forebrain

tag: sample type


title: CD4_CM secondTP D4 S065

description:
CD4_CM secondTP
9031292050_B


title: F013

tag: fiqr score

tag: bmi

tag: chronic fatigue syndrome


title: CD8_mem secondTP D5 S072

description:
CD8_mem secondTP
9031292044_L


title: 219596_Forebrain_TRPhet

value: TRPhet

tag: tissue


title: F010

tag: diagnosis


title: 215534_Forebrain_TRPnull

value: Stratagene whole mouse reference RNA


title: SM6

description:
small cell lung carcinoma, sample6, rep1
microRNA expression

tag: disease state

tag: tissue preparation

tag: gender

tag: age


title: F011

tag: migraine

tag: irritable bowel syndrome

tag: major depression


title: SM4

description:
small cell lung carcinoma, sample4, rep1
microRNA expression

value: F


title: CD4_EM firstTP D9 S056

description:
CD4_EM firstTP
9031292044_K

tag: donor

tag: cell subset

tag: time point

tag: batch


title: F012

value: fibromyalgia

tag: bipolar disorder


title: F009

tag: fiqr score

value: No


title: SM2

description:
small cell lung carcinoma, sample2, rep1
microRNA expression

value: formalin fixed paraffin embedded


title: CD4_TM secondTP D9 S085

description:
CD4_TM secondTP
9031292044_J

tag: sampleID


title: SM1

description:
small cell lung carcinoma, sample1, rep1
microRNA expression


title: CD8_mem thirdTP D2 S010

description:
CD8_mem thirdTP
9031292044_I


title: CD4_Naiive firstTP D6 S051

description:
CD4_Naiive firstTP
9031292044_G


title: F008

value: peripheral blood

tag: bmi

tag: chronic fatigue syndrome


title: SM3

description:
small cell lung carcinoma, sample3, rep1
microRNA expression

tag: tissue


title: SC2

description:
schwannoma, sample2, rep1
microRNA expression

source_name: extremities, schwannoma

value: extremities

tag: disease state

value: schwannoma


title: SC1

description:
schwannoma, sample1, rep1
microRNA expression

tag: tissue preparation


title: CD8_mem secondTP D10 S077

description:
CD8_mem secondTP
9031292044_F


title: CD4_Naiive Baseline D4 S030

description:
CD4_Naiive Baseline
9031292044_H


title: CD8_mem Baseline D8 S048

description:
CD8_mem Baseline
9031292044_E


title: F007

tag: diagnosis

value: Yes


title: CD4_EM thirdTP D2 S099

description:
CD4_EM thirdTP
9031292044_D

value: thirdTP


title: F005


title: F006


title: RE12

description:
rectal carcinoid, sample12, rep1
microRNA expression

value: rectum

value: carcinoid

tag: gender

value: M

tag: age


title: RE11

description:
rectal carcinoid, sample11, rep1
microRNA expression


title: F003

tag: migraine

tag: irritable bowel syndrome


title: CD8_mem Baseline D10 S039

description:
CD8_mem Baseline
9031292044_C

tag: donor


title: F004

tag: major depression


title: RE10

description:
rectal carcinoid, sample10, rep1
microRNA expression


title: RE9

description:
rectal carcinoid, sample9, rep1
microRNA expression


title: F002


title: RE8

description:
rectal carcinoid, sample8, rep1
microRNA expression


title: C069

source_name: Peripheral Blood_Control

value: healthy control


title: CD4_EM firstTP D6 S052

description:
CD4_EM firstTP
9031292044_B

tag: cell subset

tag: time point

value: firstTP


title: F001_2

tag: bipolar disorder


title: RE7

description:
rectal carcinoid, sample7, rep1
microRNA expression


title: CD4_Naiive thirdTP D3 S101

description:
CD4_Naiive thirdTP
9031292043_L

tag: batch


title: CD4_CM secondTP D8 S089

description:
CD4_CM secondTP
9031292044_A

value: secondTP

tag: sampleID


title: C070

tag: fiqr score

tag: bmi


title: CD4_TM Baseline D5 S134

description:
CD4_TM Baseline
9031292043_K

value: Baseline


title: CD8_mem thirdTP D4 S108

description:
CD8_mem thirdTP
9031292043_J


title: RE5

description:
rectal carcinoid, sample5, rep1
microRNA expression

tag: tissue


title: C068

tag: chronic fatigue syndrome


title: C065_2


title: RE4

description:
rectal carcinoid, sample4, rep1
microRNA expression

tag: disease state

tag: tissue preparation


title: CD4_Naiive thirdTP D2 S097

description:
CD4_Naiive thirdTP
9031292043_I


title: RE6

description:
rectal carcinoid, sample6, rep1
microRNA expression

tag: gender


title: CD4_Naiive secondTP D10 S073

description:
CD4_Naiive secondTP
9031292043_H


title: C066

tag: diagnosis


title: CD4_TM Baseline D4 S133

description:
CD4_TM Baseline
9031292043_G


title: C065

tag: migraine


title: RE3

description:
rectal carcinoid, sample3, rep1
microRNA expression

tag: age


title: RE2

description:
rectal carcinoid, sample2, rep1
microRNA expression


title: blood-Control_6788

city: Valencia

first: Joaquin

last: Dopazo

state: Valencia

address: Eduardo Primo Yúfera, 3

department: Systems Biology

country: Spain

institute: Centro de Investigacion Principe Felipe

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 images were obtained using an Affymetrix GeneChip® Scanner 3000.

data_processing: CEL files were processed using Affymetrix Power Tools (APT v1.15.0) using Birdseed v2 calling algorithm.

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: phenotype

value: Control


title: C067

tag: irritable bowel syndrome

tag: major depression


title: blood-Control_349


title: C064


title: CD4_EM thirdTP D8 S127

description:
CD4_EM thirdTP
9031292043_E

tag: donor

tag: cell subset

tag: time point


title: CD4_TM secondTP D8 S090

description:
CD4_TM secondTP
9031292043_F

tag: batch

tag: sampleID


title: C063

tag: fiqr score

tag: bmi

tag: bipolar disorder


title: blood-Control_6252

tag: tissue


title: RE1

description:
rectal carcinoid, sample1, rep1
microRNA expression

tag: disease state

tag: tissue preparation

value: F


title: blood-Control_1023


title: CD4_TM thirdTP D1 S094

description:
CD4_TM thirdTP
9031292043_D


title: C062

tag: diagnosis

tag: chronic fatigue syndrome


title: CD4_TM secondTP D10 S075

description:
CD4_TM secondTP
9031292043_C


title: blood-Control_397


title: NB6

description:
neuroblastoma, sample6, rep1
microRNA expression

source_name: nasal cavity, neuroblastoma

value: nasal cavity

value: neuroblastoma

tag: gender

tag: age


title: CD4_TM thirdTP D8 S126

description:
CD4_TM thirdTP
9031292043_B


title: C061

tag: migraine

value: No

tag: irritable bowel syndrome


title: NB7

description:
neuroblastoma, sample7, rep1
microRNA expression

value: formalin fixed paraffin embedded


title: NB5

description:
neuroblastoma, sample5, rep1
microRNA expression


title: blood-Control_1124

tag: phenotype

value: peripheral blood


title: CD4_EM thirdTP D1 S095

description:
CD4_EM thirdTP
9031292043_A

tag: donor

tag: cell subset


title: C060

tag: major depression


title: C059


title: NB3

description:
neuroblastoma, sample3, rep1
microRNA expression


title: blood-Control_1350


title: C058


title: CD4_Naiive thirdTP D7 S117

description:
CD4_Naiive thirdTP
9031292040_K

tag: time point

tag: batch

tag: sampleID


title: C057

tag: fiqr score

tag: bmi

tag: bipolar disorder


title: blood-Control_1303

tag: tissue


title: NB4

description:
neuroblastoma, sample4, rep1
microRNA expression

tag: disease state

tag: tissue preparation


title: NB2

description:
neuroblastoma, sample2, rep1
microRNA expression

tag: gender


title: CD4_TM thirdTP D3 S102

description:
CD4_TM thirdTP
9031292040_L


title: blood-Control_1617


title: blood-Control_1344


title: C056

tag: diagnosis

tag: chronic fatigue syndrome


title: CD4_TM Baseline D3 S132

description:
CD4_TM Baseline
9031292040_J


title: blood-Control_1543


title: blood-Control_1626


title: GA7

description:
gastric carcinoid, sample7, rep1
microRNA expression

source_name: stomach, carcinoid

value: stomach

tag: age


title: C054

tag: migraine

tag: irritable bowel syndrome


title: blood-Control_1790

tag: phenotype


title: GA6

description:
gastric carcinoid, sample6, rep1
microRNA expression


title: blood-Control_1536R


title: C055

value: Yes

tag: major depression


title: blood-Control_1987


title: blood-Control_1347


title: CD4_TM Baseline D9 S137

description:
CD4_TM Baseline
9031292040_G

tag: donor

tag: cell subset

tag: time point


title: GA5

description:
gastric carcinoid, sample5, rep1
microRNA expression


title: blood-Control_2004


title: blood-Control_1648


title: GA4

description:
gastric carcinoid, sample4, rep1
microRNA expression


title: C053

tag: fiqr score


title: blood-Control_2000


title: CD4_EM thirdTP D4 S107

description:
CD4_EM thirdTP
9031292040_F

value: thirdTP

tag: batch

tag: sampleID


title: CD8_mem thirdTP D3 S104

description:
CD8_mem thirdTP
9031292040_I


title: C052

tag: tissue

tag: bmi

tag: bipolar disorder


title: C051


title: GA3

description:
gastric carcinoid, sample3, rep1
microRNA expression

tag: disease state

tag: tissue preparation

tag: gender


title: CD8_mem thirdTP D8 S128

description:
CD8_mem thirdTP
9031292040_E


title: blood-Control_2150


title: CD4_Naiive Baseline D2 S023

description:
CD4_Naiive Baseline
9031292040_D


title: CD4_Naiive firstTP D8 S057

description:
CD4_Naiive firstTP
9031292040_H


title: GA2

description:
gastric carcinoid, sample2, rep1
microRNA expression

tag: age


title: C050

tag: diagnosis

tag: migraine

tag: chronic fatigue syndrome


title: GA1

description:
gastric carcinoid, sample1, rep1
microRNA expression


title: blood-Control_2149

tag: phenotype


title: CD4_EM firstTP D4 S050

description:
CD4_EM firstTP
9031292040_C

tag: donor


title: blood-Control_1504


title: DU9

description:
duodenal carcinoid, sample9, rep1
microRNA expression

source_name: duodenum, carcinoid

value: duodenum


title: NB1

description:
neuroblastoma, sample1, rep1
microRNA expression


title: C049

tag: irritable bowel syndrome

tag: major depression


title: CD8_mem secondTP D7 S082

description:
CD8_mem secondTP
9031292040_B

tag: cell subset

tag: time point


title: CD4_Naiive secondTP D4 S064

description:
CD4_Naiive secondTP
9031292031_L

tag: batch

tag: sampleID


title: blood-Control_2209

tag: tissue


title: blood-Control_2170


title: C047

tag: fiqr score

tag: bmi

tag: bipolar disorder


title: DU8

description:
duodenal carcinoid, sample8, rep1
microRNA expression

tag: disease state

value: carcinoid

tag: tissue preparation

tag: gender


title: C045_2

tag: diagnosis

tag: migraine


title: CD4_TM Baseline D10 S135

description:
CD4_TM Baseline
9031292031_J


title: C046

tag: chronic fatigue syndrome


title: DU7

description:
duodenal carcinoid, sample7, rep1
microRNA expression

value: M

tag: age


title: DU6

description:
duodenal carcinoid, sample6, rep1
microRNA expression


title: C045

value: healthy control

tag: irritable bowel syndrome


title: blood-Control_2153

tag: phenotype


title: CD4_EM firstTP D8 S058

description:
CD4_EM firstTP
9031292031_K

tag: donor

tag: cell subset

value: firstTP


title: CD4_Naiive secondTP D8 S088

description:
CD4_Naiive secondTP
9031292031_H

tag: time point

value: secondTP

tag: batch


title: DU5

description:
duodenal carcinoid, sample5, rep1
microRNA expression

tag: tissue


title: blood-Control_2226


title: C048

tag: fiqr score

tag: major depression


title: C044

tag: bmi

tag: bipolar disorder


title: DU3

description:
duodenal carcinoid, sample3, rep1
microRNA expression

tag: disease state

tag: tissue preparation


title: CD4_Naiive thirdTP D9 S121

description:
CD4_Naiive thirdTP
9031292031_G

tag: sampleID


title: DU2

description:
duodenal carcinoid, sample2, rep1
microRNA expression

tag: gender


title: C043

tag: diagnosis

tag: migraine

tag: chronic fatigue syndrome


title: blood-Control_2178

tag: phenotype


title: CD4_CM secondTP D10 S074

description:
CD4_CM secondTP
9031292031_E

tag: donor


title: CD4_TM thirdTP D5 S110

description:
CD4_TM thirdTP
9031292031_F

tag: cell subset


title: CD8_mem thirdTP D10 S116

description:
CD8_mem thirdTP
9031292031_I

tag: time point


title: blood-Control_2216


title: DU1

description:
duodenal carcinoid, sample1, rep1
microRNA expression

tag: age


title: AdR3

description:
rectal adenocarcinoma, sample3, rep1
microRNA expression

source_name: rectum, adenocarcinoma

tag: tissue

value: rectum

value: adenocarcinoma


title: blood-Control_2279

value: Control


title: C044_2

tag: fiqr score

tag: irritable bowel syndrome


title: C040

tag: bmi

tag: major depression


title: blood-Control_2456


title: blood-Control_2417


title: AdR2

description:
rectal adenocarcinoma, sample2, rep1
microRNA expression

tag: disease state


title: CD4_EM thirdTP D7 S119

description:
CD4_EM thirdTP
9031292031_C

tag: batch


title: C039

tag: bipolar disorder


title: DU4

description:
duodenal carcinoid, sample4, rep1
microRNA expression

tag: tissue preparation

tag: gender

value: F


title: blood-Control_2336


title: CD4_Naiive Baseline D3 S026

description:
CD4_Naiive Baseline
9031292031_B

value: Baseline

tag: sampleID


title: blood-Control_2222


title: C038

tag: diagnosis

tag: migraine

value: No

tag: chronic fatigue syndrome


title: AdR1

description:
rectal adenocarcinoma, sample1, rep1
microRNA expression

value: formalin fixed paraffin embedded


title: CD4_EM thirdTP D10 S115

description:
CD4_EM thirdTP
9031292031_A

tag: donor

tag: cell subset


title: C041

value: peripheral blood


title: AdL3

description:
adenocarcinoma of the lung, sample3, rep1
microRNA expression

source_name: lung, adenocarcinoma

value: lung

tag: age


title: blood-Control_2753

tag: phenotype

tag: tissue


title: C037_2

tag: fiqr score

tag: irritable bowel syndrome


title: C037

tag: bmi

tag: major depression


title: CD4_TM thirdTP D7 S118

description:
CD4_TM thirdTP
9023874064_J

tag: time point

tag: batch


title: AdL1

description:
adenocarcinoma of the lung, sample1, rep1
microRNA expression

tag: disease state

tag: tissue preparation


title: CD4_CM secondTP D5 S069

description:
CD4_CM secondTP
9023874064_I

tag: sampleID


title: CD4_CM secondTP D9 S084

description:
CD4_CM secondTP
9023874064_K


title: blood-Control_2635


title: AdL2

description:
adenocarcinoma of the lung, sample2, rep1
microRNA expression

tag: gender


title: AdG3

description:
gastric adenocarcinoma, sample3, rep1
microRNA expression

source_name: stomach, adenocarcinoma

value: stomach


title: CD4_EM thirdTP D9 S123

description:
CD4_EM thirdTP
9031292031_D

source_name: Sorted Cells

value: thirdTP


title: CD4_EM Baseline D1 S020

description:
CD4_EM Baseline
9023874064_H


title: C035

tag: diagnosis

tag: migraine

tag: bipolar disorder


title: blood-Control_3204


title: C034

tag: chronic fatigue syndrome


title: blood-Control_3082


title: AdG1

description:
gastric adenocarcinoma, sample1, rep1
microRNA expression

tag: age


title: blood-Control_2229

tag: phenotype


title: CD4_TM Baseline D1 S130

description:
CD4_TM Baseline
9023874064_F

tag: donor

tag: cell subset


title: CD4_Naiive secondTP D9 S083

description:
CD4_Naiive secondTP
9023874064_G


title: blood-Control_2875

tag: tissue


title: C033_2

tag: fiqr score

tag: bmi

tag: irritable bowel syndrome


title: AC3

description:
atypical carcinoid of the lung, sample3, rep1
microRNA expression

source_name: lung, carcinoid


title: blood-Control_3272


title: AC2

description:
atypical carcinoid of the lung, sample2, rep1
microRNA expression


title: CD8_mem secondTP D8 S092

description:
CD8_mem secondTP
9023874064_E

tag: time point

tag: batch


title: C033

tag: major depression


title: CD8_mem secondTP D9 S087

description:
CD8_mem secondTP
9023874064_D

tag: sampleID


title: C036


title: C031


title: C032


title: AC1

description:
atypical carcinoid of the lung, sample1, rep1
microRNA expression

tag: disease state

tag: tissue preparation

tag: gender


title: CD4_TM thirdTP D9 S122

description:
CD4_TM thirdTP
9023874064_C


title: C030

tag: diagnosis

tag: migraine

tag: bipolar disorder


title: blood-Control_2995

tag: phenotype


title: blood-Control_4271


title: blood-Control_3554


title: SynovialMembraneDerivedStemCells33_control_rep1

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

description: MiRNA expression in undifferentiated SM-MSCs from donor 33

hyb_protocol: All volume of the labeled samples was prepared for hybridization using miRNA Complete Labeling and Hyb Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto SurePrint G3 Human v16 miRNA 8x60K microarrays for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7 (Agilent Technologies) using default parameters (protocol miRNA_1105_Oct12, grid 031181_D_F_20141007 for ADSC6 and ADSC7; protocol miRNA_107_Sep09, grid 031181_D_F_20111226 for GRA9, GRA7, and GOA33; protocol miRNA_1100_Jul11, grid 031181_20101116 for ADSC4-1 and ADSC4-2). Background subtracted and spatially detrended signals were obtained.

source_name: Synovial membrane-derived stem cells, donor 33, passage 3, control

label_protocol: Cyanine-3 labeled RNA was prepared from 100 ng of purified total RNA using miRNA Complete Labeling and Hyb Kit and MicroRNA Spike-In Kit acording to manufacturer's protocol (Agilent Technologies) without purification of the labeled RNA.

growth_protocol: Sections of tissue samples were digested with class I collagenase in Dulbecco’s modified Eagle’s medium (DMEM) at 37°C, filtered through 100 μm filter and cells were seeded in the medium, containing DMEM, supplemented with 10% FCS and antibiotics. MSCs were cultured in a humidified atmosphere with 5% CO2 at 37°C, and passaged at subconfluence of 75-90%.

extract_protocol: Total RNA was extracted from 2 mln. cells on average with mirVana miRNA Isolation Kit according to manufacturer’s protocol (Life Technologies). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Osteogenic differentiation was induced at 3-4 passage by seeding MSCs at density 5·103/cm2 and cultured in DMEM with 4.5 g/L glucose, containing 10% FCS, 1% antibiotics, 10-7 M dexamethasone, and 50 µg/mL ascorbic acid, for 21 days.  Control cells were simultaneously cultured in the complete proliferation medium.

tag: differentiation

value: undifferentiated


title: blood-Control_3824


title: Innate Baseline D9 S041

description:
Innate Baseline
8981245102_J

tag: donor

tag: cell subset

value: Innate


title: C029

tag: tissue

tag: fiqr score

value: Yes

tag: chronic fatigue syndrome


title: blood-Control_4468


title: CD4_Naiive thirdTP D10 S113

description:
CD4_Naiive thirdTP
9023874064_B

tag: time point


title: Innate Baseline D10 S037

description:
Innate Baseline
8981245102_I

tag: batch


title: SynovialMembraneDerivedStemCells7_control_rep1

description: MiRNA expression in undifferentiated SM-MSCs from donor 7

source_name: Synovial membrane-derived stem cells, donor 7, passage 4, control


title: SynovialMembraneDerivedStemCells7_osteo_rep1

description: MiRNA expression in osteogenically differentiated SM-MSCs from donor 7

source_name: Synovial membrane-derived stem cells, donor 7, passage 4, osteogenic differentiation

value: osteogenic differentiation


title: SynovialMembraneDerivedStemCells33_osteo_rep1

description: MiRNA expression in osteogenically differentiated SM-MSCs from donor 33

source_name: Synovial membrane-derived stem cells, donor 33, passage 3, osteogenic differentiation


title: C028

value: healthy control

tag: bmi

tag: irritable bowel syndrome

tag: major depression


title: blood-Control_3921


title: AdG2

description:
gastric adenocarcinoma, sample2, rep1
microRNA expression

tag: disease state

tag: tissue preparation

value: M

tag: age


title: SynovialMembraneDerivedStemCells9_osteo_rep1

description: MiRNA expression in osteogenically differentiated SM-MSCs from donor 9

source_name: Synovial membrane-derived stem cells, donor 9, passage 3, osteogenic differentiation


title: C027

tag: diagnosis

tag: migraine


title: C026

tag: bipolar disorder


title: CD4_CM thirdTP D8 S070

description:
CD4_CM thirdTP
8981245102_H

tag: sampleID


title: CD4_TM_CD25n product D2 S004

description:
CD4_TM_CD25n product
8981245102_G

tag: donor

value: product


title: SynovialMembraneDerivedStemCells9_control_rep1

description: MiRNA expression in undifferentiated SM-MSCs from donor 9

source_name: Synovial membrane-derived stem cells, donor 9, passage 3, control

tag: differentiation


title: C025

tag: tissue


title: AdiposeDerivedStemCells7_osteo_rep1

description: MiRNA expression in osteogenically differentiated ADSCs from donor 7

source_name: Adipose-derived stem cells, donor 7, passage 3, osteogenic differentiation


title: AdiposeDerivedStemCells7_control_rep1

description: MiRNA expression in undifferentiated ADSCs from donor 7

source_name: Adipose-derived stem cells, donor 7, passage 3, control


title: blood-Control_4353R

source_name: peripheral blood

tag: phenotype


title: CD4_TM_CD25n product D5 S013

description:
CD4_TM_CD25n product
8981245102_F

tag: cell subset


title: C024

source_name: Peripheral Blood_Control

tag: fiqr score

tag: chronic fatigue syndrome


title: C023

tag: bmi


title: C022

tag: irritable bowel syndrome


title: CD4_TM_CD25p product D3 S006

description:
CD4_TM_CD25p product
8981245102_D

tag: time point

tag: batch


title: blood-Control_4490


title: AdiposeDerivedStemCells6_osteo_rep1

description: MiRNA expression in osteogenically differentiated ADSCs from donor 6

source_name: Adipose-derived stem cells, donor 6, passage 3, osteogenic differentiation


title: CD4_TM_CD25n product D10 S016

description:
CD4_TM_CD25n product
8981245102_C


title: blood-Control_4486


title: blood-Control_4500


title: AdiposeDerivedStemCells6_control_rep1

description: MiRNA expression in undifferentiated ADSCs from donor 6

source_name: Adipose-derived stem cells, donor 6, passage 3, control


title: blood-Control_4569


title: Innate Baseline D2 S029

description:
Innate Baseline
8981245102_E


title: C021

tag: major depression


title: AdiposeDerivedStemCells4-2_adipo_rep1

description: MiRNA expression in adipogenically differentiated ADSCs from donor 4

source_name: Adipose-derived stem cells, donor 4, passage 3, adipogenic differentiation

value: adipogenic differentiation


title: C020


title: AdiposeDerivedStemCells4-2_osteo_rep1

description: MiRNA expression in osteogenically differentiated ADSCs from donor 4

source_name: Adipose-derived stem cells, donor 4, passage 3, osteogenic differentiation


title: CD4_CM product D9 S020

description:
CD4_CM product
8981245102_B


title: CD4_TM firstTP D8 S053

description:
CD4_TM firstTP
8981245098_K

value: firstTP


title: CD4_CM product D3 S005

description:
CD4_CM product
8981245098_L


title: AdiposeDerivedStemCells4-2_control_rep1

description: MiRNA expression in undifferentiated ADSCs from donor 4

source_name: Adipose-derived stem cells, donor 4, passage 3, control


title: blood-Control_4472

value: Control


title: blood-Control_4578


title: Innate Baseline D8 S043

description:
Innate Baseline
8981245098_J

source_name: Sorted Cells

value: Baseline


title: AdiposeDerivedStemCells4-1_adipo_rep1


title: C017

value: No


title: blood-Control_5296


title: blood-Control_5059


title: AdiposeDerivedStemCells4-1_osteo_rep1


title: C018


title: C016


title: AdiposeDerivedStemCells4-1_control_rep1


title: C015


title: CD4_CM Baseline D4 S032

description:
CD4_CM Baseline
8981245098_H


title: blood-Control_5417


title: blood-Control_4571


title: CD4_CM thirdTP D9 S068

description:
CD4_CM thirdTP
8981245098_G


title: C014_2


title: blood-Control_4603


title: C019


title: macrophages_M2c_3

city: Montreal

first: Luke

middle: Michael

last: Healy

state: Quebec

address: 3801 University Street

department: Neurology and Neurosurgery

country: Canada

institute: Montreal Neurological Institute

description:
Gene expression data from M2c macrophages
3032_JAL086-3_01

hyb_protocol: Sample processing was perfomed by Genome Quebec.

data_processing: CHP data generated using Affymetrix Expression Console, RMA, one-way anova, p < 0.05, fold change > 2 or  < -2

label: biotin

source_name: Human adult peripheral blood-derived macrophages, M2c

growth_protocol: RPMI supplemented with 10% FCS, 0.1% penicillin/streptomycin and 0.1% glutamine

extract_protocol: Cells were harvested in Trizol Reagent, RNA was extracted using the Qiagen Rneasy MiniElute Cleanup Kit

treatment_protocol: Cytokine supplementation over a 7 day period in vitro

tag: developmental stage

value: adult

tag: cell type

value: Macrophages

tag: polarization condition

value: M2c [MSCF (25ng/ml) and IL10 (20ng/ml) for 2 days, MSCF replenished (25ng/ml) with a half media change on day 3. Activated on day 5 with IL4, IL13, IL10 (20ng/ml each), IL14 and IL13 replenished on day 6 and cells harvested on day 7]


title: CD4_CM Baseline D1 S026

description:
CD4_CM Baseline
8981245098_F


title: C014

tag: diagnosis

value: peripheral blood

tag: migraine

tag: bipolar disorder


title: C013


title: blood-Control_4634


title: macrophages_M2c_1

description:
Gene expression data from M2c macrophages
3030_JAL084-3_01

scan_protocol: Sample processing was perfomed by Genome Quebec.

tag: donor


title: blood-Control_5461

tag: tissue


title: C012


title: macrophages_M2c_2

description:
Gene expression data from M2c macrophages
3031_JAL085-3_01

label_protocol: Sample processing was perfomed by Genome Quebec.


title: CD4_TM_CD25p product D4 S009

description:
CD4_TM_CD25p product
8981245098_C

tag: sampleID


title: blood-Control_5459

tag: phenotype


title: blood-Control_5469


title: blood-Control_5486


title: Innate thirdTP D1 S055

description:
Innate thirdTP
8981245098_E

tag: cell subset

value: thirdTP


title: macrophages_M2a_2

description:
Gene expression data from M2a macrophages
3027_JAL082-3_01

source_name: Human adult peripheral blood-derived macrophages, M2a

value: M2a [MSCF (25ng/ml) for 2 days, MSCF replenished (25ng/ml) with a half media change on day 3. Activated on day 5 with IL4 and IL13 (20ng/ml each), IL14 and IL13 replenished on day 6 and cells harvested on day 7]


title: C011

tag: fiqr score

tag: chronic fatigue syndrome


title: macrophages_M2a_3

description:
Gene expression data from M2a macrophages
3028_JAL083-3_01


title: CD4_CM firstTP D4 S044

description:
CD4_CM firstTP
8981245098_B


title: CD4_CM Baseline D8 S042

description:
CD4_CM Baseline
8981245098_I


title: C009_2

tag: bmi

tag: irritable bowel syndrome


title: C009


title: CD4_CM Baseline D3 S030

description:
CD4_CM Baseline
8981245017_L

tag: time point

tag: batch


title: Innate thirdTP D8 S071

description:
Innate thirdTP
8981245098_A

value: Innate


title: CD4_CM Baseline D7 S038

description:
CD4_CM Baseline
8981245017_K


title: CD4_TM_CD25p product D9 S021

description:
CD4_TM_CD25p product
8981245098_D


title: macrophages_M1_2

description:
Gene expression data from M1 macrophages
2760_JAL079-3_01

source_name: Human adult peripheral blood-derived macrophages, M1

tag: developmental stage

value: M1 [GMCSF (5ng/ml) for 2 day, GMSCF replenished on day 3 with half media change. Activated on day 5 with IFNy (20ng/ml) and LPS (100ng/ml) for 2 further days. Cells harvested on day 7]


title: C010

value: Yes

tag: major depression


title: C007

value: healthy control


title: blood-Control_5499


title: macrophages_M1_3

description:
Gene expression data from M1 macrophages
2761_JAL080-3_01

tag: cell type

tag: polarization condition


title: blood-Control_5500


title: C006

tag: diagnosis

tag: migraine


title: CD4_CM Baseline D10 S036

description:
CD4_CM Baseline
8981245017_J

tag: donor


title: blood-Control_5527

tag: tissue


title: blood-Control_5467


title: blood-Control_5583


title: blood-Control_5570


title: blood-Control_5462


title: C005

tag: bipolar disorder


title: macrophages_Mtgf_3

description:
Gene expression data from Mtgf macrophages
2758_JAL077-3_01

source_name: Human adult peripheral blood-derived macrophages, Mtgf

value: Mtgf [MSCF (25ng/ml) + TGFB (50ng/ml) for 2 days, MSCF replenished with half media change on day 3. Activated cells on day 5 with TGFB (50ng/ml) and harvested on day 7]


title: macrophages_M2a_1

description:
Gene expression data from M2a macrophages
2763_JAL081-3_01


title: CD4_CM product D10 S014

description:
CD4_CM product
8981245017_I

value: product

tag: sampleID


title: blood-Control_5487

tag: phenotype


title: blood-Control_5569


title: CD4_TM_CD25n product D4 S010

description:
CD4_TM_CD25n product
8981245017_H

tag: cell subset


title: macrophages_Mtgf_2

description:
Gene expression data from Mtgf macrophages
2676_JAL076-3_01


title: blood-Control_5596


title: blood-Control_5710


title: C004

tag: fiqr score

tag: chronic fatigue syndrome


title: C003

tag: bmi

tag: irritable bowel syndrome


title: blood-Control_5489


title: blood-Control_5716


title: blood-Control_5684


title: macrophages_Mtgf_1

description:
Gene expression data from Mtgf macrophages
2675_JAL075-3_01


title: macrophages_M0_1

description:
Gene expression data from M0 macrophages
2671_JAL072-3_01

source_name: Human adult peripheral blood-derived macrophages, M0

value: M0 [MSCF (25ng/ml) for 2 days, MSCF replenished (25ng/ml) with a half media change on day 3 and cells harvested on day 7]


title: C002


title: Innate Baseline D5 S035

description:
Innate Baseline
8981245017_F

tag: time point

tag: batch


title: CD4_CM firstTP D9 S050

description:
CD4_CM firstTP
8981245017_E

value: firstTP


title: CD4_CM Baseline D9 S040

description:
CD4_CM Baseline
8981245017_B


title: CD4_CM firstTP D8 S052

description:
CD4_CM firstTP
8981245017_G


title: macrophages_M1_1

description:
Gene expression data from M1 macrophages
2759_JAL078-3_01

tag: developmental stage


title: macrophages_M0_2

description:
Gene expression data from M0 macrophages
2672_JAL073-3_01

tag: cell type


title: CD4_CM Baseline D2 S028

description:
CD4_CM Baseline
8981245017_C


title: Innate thirdTP D10 S065

description:
Innate thirdTP
8981245017_D


title: C001

tag: major depression


title: blood-Control_5742

value: Control


title: microglia_M2c_2

description:
Gene expression data from M2c microglia
AJ30_JAL070-3_01

data_processing: CHP data generated using Affymetrix Expression Console, RMA, one-way anova, p < 0.05, fold change > 2 or < -2

source_name: Human adult brain-derived microglia, M2c

growth_protocol: MEM supplemented with 5% FCS, 0.1% penicillin/streptomycin and 0.1% glutamine

value: brain

value: Microglia

tag: polarization condition


title: microglia_M2c_3

description:
Gene expression data from M2c microglia
AJ31_JAL071-3_01

value: adult


title: CD4_TM_CD25p product D2 S003

description:
CD4_TM_CD25p product
8981245017_A


title: blood-Control_5736


title: CD4_CM thirdTP D1 S054

description:
CD4_CM thirdTP
8942422086_L


title: microglia_M2c_1

description:
Gene expression data from M2c microglia
AJ29_JAL069-3_01


title: microglia_M1_3

description:
Gene expression data from M1 microglia
AJ25_JAL065-3_01

source_name: Human adult brain-derived microglia, M1


title: CD4_TM_CD25n product D7 S019

description:
CD4_TM_CD25n product
8942422086_J


title: CD4_CM firstTP D7 S048

description:
CD4_CM firstTP
8942422086_K


title: microglia_M2a_1

description:
Gene expression data from M2a microglia
AJ26_JAL066-3_01

source_name: Human adult brain-derived microglia, M2a


title: microglia_M2a_2

description:
Gene expression data from M2a microglia
AJ27_JAL067-3_01


title: blood-Control_5765


title: CD4_TM_CD25n product D8 S025

description:
CD4_TM_CD25n product
8942422086_H


title: microglia_M2a_3

description:
Gene expression data from M2a microglia
AJ28_JAL068-3_01


title: CD4_CM product D2 S002

description:
CD4_CM product
8942422086_G


title: blood-Control_5823


title: CD4_CM Baseline D5 S034

description:
CD4_CM Baseline
8942422086_F

value: Baseline


title: Gene expression with HIV-2 Day-7 P4-7

city: Silver Spring

first: Indira

last: Hewlett

state: Maryland

address: 10903 New Hampshire Ave

department: DETTD

institute: CBER/FDA

description: Gene expression with HIV-2

hyb_protocol: standard Agilent protocol

scan_protocol: The processed slides were scanned using the Agilent DNA microarray scanner following Agilent Technologies’ guidelines.

data_processing: The resulting .txt files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version11.0) for further analysis. The  microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization).

source_name: Gene expression with HIV-2

label_protocol: RNA sample was Cyanine-3 (Cy3) labeled using the Agilent Quick Amp Labeling Kit

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from these buffy coats by a single step Ficoll-Hypaque density gradient method. Freshly isolated PBMC were stimulated for 72 h by culturing in RPMI-1640 medium supplemented with 10% heat inactivated FBS, penicillin-streptomycin, 10 U/ml IL-2 and 10μg/ml of PHA. The PBMC were cultured for 24 h post stimulation in regular media prior to infection.

extract_protocol: Total RNA was extracted from infected and uninfected cells using  total RNA isolation kit (QIAgen)

treatment_protocol: PBMC cells were infected with known amounts (5ng/ml p24 units per 106 cells) of HIV-1 (MN) and HIV-2 (Rod).

value: PBMC


title: CD4_CM product D7 S017

description:
CD4_CM product
8942422086_E


title: microglia_Mtgf_2

description:
Gene expression data from Mtgf microglia
AJ21_JAL061-3_01

source_name: Human adult brain-derived microglia, Mtgf

value: Mtgf [TGFB (50ng/ml) for 2 days, TGFB replenished with half media change on day 5, cells harvested on day 7]


title: Innate thirdTP D5 S063

description:
Innate thirdTP
8942422086_I

value: thirdTP


title: microglia_Mtgf_3

description:
Gene expression data from Mtgf microglia
AJ22_JAL062-3_01


title: microglia_M1_2

description:
Gene expression data from M1 microglia
AJ24_JAL064-3_01


title: blood-Control_5748

source_name: peripheral blood

value: peripheral blood


title: macrophages_M0_3

description:
Gene expression data from M0 macrophages
2674_JAL074-3_01

value: Macrophages


title: blood-Control_5824


title: Gene expression with HIV-1 Day-7 P3-7

description: Gene expression with HIV-1

source_name: Gene expression with HIV-1


title: CD4_TM_CD25p product D5 S012

description:
CD4_TM_CD25p product
8942422086_D


title: Innate Baseline D7 S039

description:
Innate Baseline
8942422086_C

value: Innate


title: microglia_Mtgf_1

description:
Gene expression data from Mtgf microglia
AJ20_JAL060-3_01


title: microglia_M0_2

description:
Gene expression data from M0 microglia
AJ18_JAL058-3_01

source_name: Human adult brain-derived microglia, M0

value: M0 [Cells grown in basal media for 7 days. One half media change on day 3]


title: blood-Control_5858


title: blood-Control_5825


title: Gene expression with HIV-1 Day-7 43-37

description: Gene expression with HIV-1


title: CD4_TM_CD25p product D10 S015

description:
CD4_TM_CD25p product
8942422086_B


title: blood-Control_5815


title: blood-Control_5826


title: CD4_TM_CD25p product D7 S018

description:
CD4_TM_CD25p product
8942422086_A


title: microglia_M1_1

description:
Gene expression data from M1 microglia
AJ23_JAL063-3_01

value: M1 [GMCSF (5ng/ml) for 2 day, GMSCF replenished on day 3 with half media change. Activated on day 5 with IFNy (20ng/ml) and LPS (100ng/ml) for 2 further days. Cells harvested on day 7]


title: exosomal miR Pt02

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
AML M4
Exosomal microRNA released from CD34+ fraction of leukemic cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Leukemia patient

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Two hundred thausand of primary nomal BM or AML CD34+ cells were cultured on fibronectin-coated dish in the presence of cytokines including SCF, TPO, FL and Delta-like protein 4 for 7 days.

extract_protocol: RNAs were extracted from samples using 3D-Gene RNA extraction reagent from liquid sample (Toray, Kamakura, Japan)

treatment_protocol: 5 mL of supernatant was harvested. Exosomes were isolated by Exosome Precipitation Solution (ExoQuick-TC; System Biosciences, Mountain View, CA).

value: Bone marrow

value: CD34+ fraction of leukemic cells


title: blood-Control_5859


title: Gene expression without virus Day-7 43-17

description: Gene Expression without virus

source_name: Gene Expression without virus


title: Gene expression with HIV-2 Day-7 43-47

description: Gene expression with HIV-2


title: Gene expression without virus Day-7 P1-7

description: Gene Expression without virus


title: microglia_M0_1

description:
Gene expression data from M0 microglia
AJ17_JAL057-3_01


title: blood-Control_5758


title: CD4_CM thirdTP D2 S056

description:
CD4_CM thirdTP
8942422084_L


title: Gene expression with HIV-2 Day-7 22-47

description: Gene expression with HIV-2


title: exosomal miR Pt01

description:
AML M1
Exosomal microRNA released from CD34+ fraction of leukemic cells


title: blood-Control_5974


title: blood-Control_5891


title: blood-Control_5940


title: CD4_CM product D8 S023

description:
CD4_CM product
8942422084_J

value: product


title: blood-Control_5893


title: exosomal miR BM01

description:
Bone marrow CD34+ cell
Exosomal microRNA released from CD34+ fraction of primary BM cells.

source_name: Healthy volunteer

value: Normal BM CD34+ cells


title: blood-Control_5921

value: Control


title: CD4_CM firstTP D10 S046

description:
CD4_CM firstTP
8942422084_K

source_name: Sorted Cells

value: firstTP


title: blood-Control_5935


title: CD4_CM thirdTP D10 S064

description:
CD4_CM thirdTP
8942422084_H


title: Gene expression with HIV-1 Day-7 22-37

description: Gene expression with HIV-1


title: CD4_CM thirdTP D3 S058

description:
CD4_CM thirdTP
8942422084_G


title: Innate thirdTP D3 S059

description:
Innate thirdTP
8942422084_I


title: microglia_M0_3

description:
Gene expression data from M0 microglia
AJ19_JAL059-3_01

value: brain

value: Microglia


title: Gene expression without virus Day-7 22-17

description: Gene Expression without virus


title: 246742_Ctx

hyb_protocol: DNA labeling and hybridization were performed in the UNC LCCC Genomics Core using Agilent CGH ULS Protocol v.3.1 according to manufacturer’s instructions.

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapsed by averaging.

source_name: tumor

extract_protocol: DNA was extracted with Qiagen DNeasy kit according to manufacturer's instructions

treatment_protocol: Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.

value: high-grade astrocytoma (HGA) tumor

tag: ID

tag: genotype

value: TR

tag: brain location

value: Ctx

tag: diagnosis

value: GBM

source_name: Reference DNA pooled from brains of 10 syngeneic littermates

tag: sample type


title: CD4_TM_CD25p product D8 S024

description:
CD4_TM_CD25p product
8942422084_E

tag: donor

tag: sampleID


title: blood-Control_6099

tag: phenotype

tag: tissue

value: peripheral blood


title: CD4_TM_CD25n product D3 S007

description:
CD4_TM_CD25n product
8942422084_F

tag: cell subset


title: blood-Control_6100


title: Innate thirdTP D7 S067

description:
Innate thirdTP
8942422084_D

value: thirdTP


title: blood-Control_6169


title: CD4_TM_CD25n product D9 S022

description:
CD4_TM_CD25n product
8942422084_C


title: blood-Control_6101


title: 245936_BS

label_protocol: DNA labeling and hybridization were performed in the UNC LCCC Genomics Core using Agilent CGH ULS Protocol v.3.1 according to manufacturer’s instructions.

value: TRPhet

value: BS

value: Reference DNA pooled from brains of 10 syngeneic littermates


title: 246270_1_Ctx

value: TRPnull


title: 246300_BS


title: 245660_2_OFB

value: OFB


title: CD4_CM product D1 S001

description:
CD4_CM product
8942422084_B

value: product


title: 245861_Di

value: Di


title: MCF7/Rx2dox cells_Dox+E2 treated_rep3

city: Los Angeles

first: Nyam-Osor

last: Chimge

address: 2250 Alcazar street

department: IGM

institute: USC

description:
8381645100_L
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio

source_name: MCF7/Rx2dox cells

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

growth_protocol: cells were grown in phenol red free DMEM containing 10% charcoal stripped serum

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

treatment_protocol: treated with 500 ng/ml doxycycline and/or 10nM E2

tag: cell line

value: MCF7, with dox inducible RUNX2 expression

tag: treatment


title: MCF7/Rx2dox cells_Dox+E2 treated_rep2

description:
8381645100_K
replicate 2


title: MCF7/Rx2dox cells_Dox+E2 treated_rep1

description:
8381645100_J
replicate 1


title: blood-Control_6253

value: Control


title: 245304_BS


title: MCF7/Rx2dox cells_E2 treated_rep3

description:
8381645100_I
replicate 3


title: 246302_BS


title: 245116_2_Di


title: MCF7/Rx2dox cells_E2 treated_rep2

description:
8381645100_H
replicate 2


title: 244939_2_OFB


title: 245237_Di


title: blood-Control_6210


title: blood-Control_5860


title: 244939_1_Ctx


title: blood-Control_6132


title: blood-Control_6263


title: blood-Control_6283


title: 244190_BS


title: MCF7/Rx2dox cells_Dox treated_rep1

description:
8381645100_D
replicate 1

value: Dox


title: MCF7/Rx2dox cells_E2 treated_rep1

description:
8381645100_G
replicate 1


title: 244706_2_BS


title: MCF7/Rx2dox cells_Dox treated_rep3

description:
8381645100_F
replicate 3


title: blood-Control_6353


title: blood-Control_6293


title: 243852_OFB


title: MCF7/Rx2dox cells_Veh treated_rep3

description:
8381645100_C
replicate 3

value: Veh


title: blood-Control_6300


title: blood-Control_6318


title: blood-Control_6315


title: MCF7/Rx2dox cells_Dox treated_rep2

description:
8381645100_E
replicate 2


title: MCF7/Rx2dox cells_Veh treated_rep2

description:
8381645100_B
replicate 2


title: blood-Control_6388


title: blood-Control_6221


title: MCF7/Rx2dox cells_Veh treated_rep1

description:
8381645100_A
replicate 1


title: 245662_BS

value: high-grade astrocytoma (HGA) tumor


title: MCF7/Rx1dox cells_Dox+E2 treated_rep3

description:
8381645090_L
replicate 3

source_name: MCF7/Rx1dox cells

value: MCF7, with dox inducible RUNX1 expression


title: 245116_1_Ctx

value: Ctx


title: 246270_2_OFB

value: GBM


title: blood-Control_6446

value: peripheral blood


title: blood-Control_6421


title: MCF7/Rx1dox cells_Dox+E2 treated_rep2

description:
8381645090_K
replicate 2


title: 236024_2_OFB


title: 244189_Di


title: 235344_2_Di

value: TR


title: MCF7/Rx1dox cells_E2 treated_rep3

description:
8381645090_I
replicate 3


title: MCF7/Rx1dox cells_Dox+E2 treated_rep1

description:
8381645090_J
replicate 1


title: MCF7/Rx1dox cells_E2 treated_rep2

description:
8381645090_H
replicate 2


title: MCF7/Rx1dox cells_E2 treated_rep1

description:
8381645090_G
replicate 1


title: blood-Control_6316


title: blood-Control_6539


title: 245665_OFB


title: 245586_BS


title: blood-Control_6467


title: 245016_BS

value: TRPhet


title: MCF7/Rx1dox cells_Dox treated_rep3

description:
8381645090_F
replicate 3


title: blood-Control_6463R


title: 244706_1_OFB


title: 244605_Ctx


title: MCF7/Rx1dox cells_Dox treated_rep1

description:
8381645090_D
replicate 1


title: MCF7/Rx1dox cells_Dox treated_rep2

description:
8381645090_E
replicate 2


title: 242486_Di


title: blood-Control_6518


title: MCF7/Rx1dox cells_Veh treated_rep3

description:
8381645090_C
replicate 3


title: blood-Control_6592


title: MCF7/Rx1dox cells_Veh treated_rep2

description:
8381645090_B
replicate 2


title: blood-Control_6647


title: 241898_BS

value: BS

value: GC-GBM


title: 242092_BS

value: Reference DNA pooled from brains of 10 syngeneic littermates


title: blood-Control_6761


title: blood-Control_6778


title: 236070_Ctx

value: TRPnull


title: 241102_Di


title: NCM2

city: Kharagpur

first: Jyotirmoy

last: Chatterjee

state: West Bengal

address: Near Vikramshila complex

department: School of Medical Science and Technology

country: India

institute: Indian Institute of Technology Kharagpur

description:
8106854054_J.idat
Biological Replicate

hyb_protocol: One microgram of the biotinylated sample was then hybridized at 58 °C overnight with an Illumina (San Diego, CA, USA) HumanHT-12 V3.0 expression beadchip.

data_processing: Intensity values from mRNA microarray data were quality checked, log2-transformed and normalized using the Robust Spline Normalization method in GenomeStudio™ Software v2011.1

source_name: Cervical mucosa

label_protocol: RNA was then converted into biotinlated cRNA using the Illumina RNA TotalPrep amplification kit (Ambion/Life Technologies). For preparation of biotinlated cRNA, first 0.5ug of RNA was reverse transcribed to single stranded cDNA using Oligo(dT) primer and later converted into dsDNA. Purified ds cDNA was transcribed into multiple copies of biotinylated cRNA using biotin labelled NTPs.

extract_protocol: Total RNA from tissues was isolated using TRIzol (Invitrogen/Life Technologies) reagent. The extracted RNA was further purified using a Qiagen RNeasy Qiagen, Hilden, Germany) Mini kit in accordance with the manufacturer's protocols. The integrity and purity of RNA was checked by Quib it (invitrogen ) and Bio-analyzer (Agilent, Santa Clara, CA, USA). RNA sample with RIN number above 7

tag: disease state

value: Normal cervical mucosa

value: Cervical mucosa


title: blood-Control_6768


title: CSCC2

description:
6303248059_I.idat
Biological Replicate

value: Cervical squamous cell carcinoma


title: 236024_1_Ctx


title: MCF7/Rx1dox cells_Veh treated_rep1

description:
8381645090_A
replicate 1


title: CIN2

description:
6303248059_H.idat
Biological Replicate

value: Cervical intraepithelial neoplasia


title: 235344_1_BS


title: 235791_BS


title: CSCC


title: MSK0442 nSP

city: Toronto

first: qingxia

last: wei

state: Ontario - ON

address: 4 jardin hill court

institute: The hospital for sick children

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 16

hyb_protocol: Standard Illumina hybridization protocol:1.5ug of labeled cDNA was hybridized at a reduced hybridization temperature of 480C

data_processing: The data was normalized using lumi R package (Du et al. 2008). Background correction was done in Beadstudio, www.illumina.com

source_name: non Side population cells flow sorted from human UPS

label_protocol: Encore BiotinIL Module (NuGen) was used for cDNA fragmentation and biotin labelling of amplified cDNA for subsequent hybridisation to the microarrays (Illumina).

growth_protocol: Human UPS  were manually minced and enzymatically digested at 37°C for 45 min with constant rotation using 10mg/ml of collagenase IV (Worthington), 2.4 U/ml of Dispase (Becton Dickinson), and 0.05% trypsin (Wisent). Digested samples were then centrifuged at 1400 rpm for 5 min and washed three times with PBS. After washing, cells were filtered through 70 μm filters to remove remaining clumps.

extract_protocol: cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer’s instructions. Amplified cDNA was purified using the MinElute system (Qiagen) and total cDNA was quantified by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE).

treatment_protocol: Cells were treated with either alone with 2.5 μg/ml of Hoechst 33342 dye (Sigma), or in combination with 50 μmol/L of verapamil (Sigma), for 90 min at 37°C. To detect for SP, cells were analyzed using a dual wavelength analysis (blue, 424-444nm; red, 675nm) after excitation with 350nm UV light (MoFlow, LSRII, Becton Dickinson). Hematopoietic cells were first excluded using staining with mouse anti-human APC-Cy7 CD45 antibody (BD Pharminogen) at a concentration of 1:200 for 15 minutes at 4°C (Figure 1A). SP and NSP fraction were collected and subjected to further experiments.

value: Grade 3 UPS from Thigh

tag: age

value: 67 years

tag: gender

value: Female


title: blood-Control_6641

value: Control


title: 235316_BS

value: high-grade astrocytoma (HGA) tumor


title: blood-PTC_E14181

value: PTC


title: NCM


title: blood-Control_6972

value: peripheral blood


title: 234458_Di

value: Di

value: GBM


title: CIN


title: 234451_OFB

value: TRPhet

value: OFB


title: blood-PTC_E12594


title: MSK0442 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 15

source_name: Side population cells flow sorted from human UPS


title: 233117_OFB

value: Reference DNA pooled from brains of 10 syngeneic littermates


title: blood-PTC_E11967


title: blood-PTC_E12100


title: MSK0417 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 18

value: Grade 2 UPS from Thigh

value: 62 years


title: 233352_OFB


title: 233106_BS

value: BS


title: 232366_BS

value: TR

source_name: Reference DNA pooled from whole brains of 10 phenotypically wild-type littermates


title: blood-Control_6815


title: MSK0366 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 2

value: Grade 3 UPS dissected from Thigh

value: 57 years


title: blood-PTC_E11521


title: blood-Control_7008


title: MSK0417 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 17


title: blood-Control_6976


title: MSK0286 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 5

value: Grade 3 UPS from low leg

value: 83 years

value: Male


title: blood-PTC_E11373


title: LGA 240942

value: low-grade astrocytoma (LGA) tumor

value: TPhet

value: Forebrain

value: low-grade astrocytoma (LGA)


title: MSK0366 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 1

value: Female


title: MSK0276 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 14

value: Grade 2 UPS dissected from Shoulder

value: 79 years


title: blood-PTC_E11771

value: PTC

value: peripheral blood


title: LGA 236049

value: Reference DNA pooled from brains of 10 syngeneic littermates


title: LGA 240049


title: MSK0276 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 13


title: LGA 238788

value: TPnull


title: blood-PTC_E11214


title: LGA 235784


title: blood-PTC_E11770


title: MSK0286 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 6


title: blood-PTC_E11338


title: blood-PTC_E11587


title: LGA 235837

value: Reference DNA pooled from whole brains of 10 phenotypically wild-type littermates


title: MSK0282 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 8

value: Grade 3 UPS dissected from Thigh

value: 80 years


title: UTSW_ACC112_H3K27ac

type: SRA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description:
antibody: H3K27ac (Abcam, ab4729)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457

library_source: genomic

data_processing:
Reads were aligned to hg19 using BWA.
The resulting alignment files were then filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’ and visualized with IGV.
Peaks were called with HOMER 4.6 (Hypergeometric Optimization of Motif EnRichment). Peaks in Duke excluded regions list (wgEncodeDukeMapabilityRegionsExcludable table from UCSC genome browser) were removed.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generate by igvtools

source_name: ACC cell line

growth_protocol: The HPV-transformed ACC cell line ACC112 was cultured in RPMI supplemented with 10% fetal bovine serum, Epidermal Growth Factor, Hydrocortisone and Insulin (all from R&D).

extract_protocol:
Frozen tissue was chopped up using a scalpel before fixation and then further dissociated after fixation by shearing with an 18G needle. Chromatin from formaldehyde-fixed cells (1–5 × 106 cells per histone mark, 107 cells for MYB binding) was fragmented to a size range of 200–700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with antibody against H3K4me3 (2.5 μl; Millipore, 07-473CA), H3K27ac (2.5 μl; Abcam, ab4729), MYB (10 μl; Bethyl, A304-136A) and TP63 (5 μl; ActiveMotif, #39739). Each of these antibodies was validated by protein blot or dot blot as described45. Antibody-chromatin complexes were pulled down with protein G magnetic beads (Dynabead, 10003D), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was treated with RNase and purified with Agencourt AMPure XP (Beckman Coulter A63880).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

tag: tissue type

value: adenoid cystic carcinoma (ACC)


title: blood-PTC_E11447


title: PT596_H3K27ac

source_name: ACC Primary tumor


title: MSK0282 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 7


title: LGA 233107

value: Tphet


title: MSK0238 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 32

value: 48 years

value: Male


title: MSK0261 NSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 20

value: Grade 2 UPS dissected from Forearm

value: 70 years


title: blood-PTC_E11205

source_name: peripheral blood


title: blood-PTC_E11196


title: X6_H3K27ac

source_name: ACC Primagraft


title: blood-PTC_E11213


title: blood-PTC_E11299


title: MSK0261SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 19


title: LGA 223430

value: low-grade astrocytoma (LGA) tumor

value: T

value: Forebrain

value: low-grade astrocytoma (LGA)


title: X9_H3K27ac


title: MSK0238 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 31


title: MSK0227 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 12

value: 90 years


title: X5M1_H3K27ac


title: blood-PTC_E11154

value: PTC

value: peripheral blood


title: MSK0227 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 11


title: X19_H3K27ac


title: blood-PTC_E11174


title: LGA 235494

value: Reference DNA pooled from brains of 10 syngeneic littermates


title: LGA 225554


title: X16_H3K27ac


title: X11_H3K4me3

description:
antibody: H3K4me3 (Millipore, 07-473CA)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: MSK0210 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 10

value: Grade 2 UPS dissected from Thigh

value: 81 years


title: MSK0189 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 28

value: Grade 3 UPS dissected from Popliteal fossa

value: 57 years


title: X11_H3K27ac

value: adenoid cystic carcinoma (ACC)


title: MSK0189 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 27


title: MSK0210 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 9


title: X19_H3K4me3


title: blood-PTC_E11131


title: MSK0169 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 26

value: Grade 2 UPS dissected from Shoulder

value: 49 years


title: X16_H3K4me3


title: blood-PTC_E11152


title: blood-PTC_E11132A


title: blood-PTC_E11040


title: blood-PTC_E11112


title: X6_H3K4me3


title: X9_H3K4me3


title: X5M1_H3K4me3


title: MSK0169 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 25

value: Male


title: blood-PTC_E11039


title: MSK0130 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 22

value: Grade 3 UPS dissected from Thigh

value: 71 years


title: MSK0130 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 21


title: MSK0151nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 24

value: 84 years


title: X9_Input

description: Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: MSK0151 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 23


title: MSK0114 nSP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 30

value: 18 years


title: UTSW_ACC112_Input


title: X19_Input


title: MSK0114 SP

description:
cDNA was amplified from cell lysates from SP and NSP fractions using WT-Ovation One-Direct RNA amplification system (NuGen) according to the manufacturer's instructions
Sample name: 29


title: blood-PTC_E11029


title: blood-PTC_E11024b


title: X6_Input


title: X5M1_Input


title: blood-MTC_1688R

value: MTC


title: blood-PTC_E10925


title: HEK 293T-miR-195 rep2

city: New Delhi

first: Richa

last: Singh

state: Delhi

address: Mall Road

department: Functional Genomics Unit

institute: Institute of Genomics and Integrative Biology

description: This sample is hybridized to 5504654023_I and 5504654023_J arrays

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Average Normalization using Illumina Beadstudio

source_name: Human embryonic kidney HEK 293T cells treated with 3 ug p195 for 24h

label_protocol: As described in the illumina HumanHT12 V4.0 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol.The RNA was resuspended in diethyl pyrocarbonate-treated water, quantified by UV absorbance at 260/280 nm and immediately used for RNA amplification and labeling by Illumina TotalPrep RNA amplification kit

tag: cell type

value: Human Embryonic Kidney cell line

value: HEK 293T


title: X6_H3K4me1

description:
antibody: H3K4me1 (Abcam, ab8895)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: blood-PTC_E10897

value: PTC

value: peripheral blood


title: X5M1_H3K4me1


title: HEK 293T-Control rep2

description: This sample is hybridized to 5504654023_K and 5504654023_L arrays

source_name: Human embryonic kidney HEK 293T cells


title: LM16R_rep4

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: resistant cell line obtained after repeated exposure to PLX4032

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the AgiMicroRna package. microRNA-level processed signals were obtained using the RMA algorithm with quantile normalization.

source_name: melanoma cell line derived from nodal metastasis

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

growth_protocol: The parental melanoma cell line LM16 and the resistant variant LM16-R were cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics. Cells were grown for 72 hours before recovery for RNA extraction.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.

treatment_protocol: The PLX4032-resistant cell line variant LM16-R was generated by repeated exposures to PLX4032 (3 µM) until the onset of resistance.

tag: plx4032 sensitivity

value: Resistant


title: blood-MTC_2220R


title: HEK 293T-miR-195 rep1


title: HEK 293T-AntimiR rep2

description: This sample is hybridized to 5504654023_G and 5504654023_H arrays

source_name: Human embryonic kidney HEK 293T cells treated with 100nM AntimiR-195 for 24h


title: HEK 293T-Control rep1


title: blood-PTC_E10923


title: blood-PTC_E11089A


title: X9_MYB

description:
antibody: MYB (Bethyl, A304-136A)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: blood-MTC_2114


title: X5M1_MYB


title: LM16R_rep2

value: resistant cell line obtained after repeated exposure to PLX4032


title: HEK 293T-AntimiR rep1


title: MCF7 Control rep2

description: This sample is hybridized to 5504654023_E and 5504654023_F arrays

source_name: Human breast cancer MCF7 cells

value: Human Breast cancer cell line MCF7


title: X9_H3K4me1


title: LM16R_rep1


title: LM16_rep4

description: parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42

value: Sensitive


title: MCF7 Control rep1


title: LM16R_rep3


title: LM16_rep3

value: parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42


title: LM16_rep2


title: blood-MTC_2862R


title: MCF7-miR-195 rep1

description: This sample is hybridized to 5504654023_C and 5504654023_D arrays

source_name: Human breast cancer MCF7 cells treated with 3 ug p195 for 24h


title: MCF7-AntimiR rep2

description: This sample is hybridized to 5504654023_A and 5504654023_B arrays

source_name: Human breast cancer MCF7 cells treated with 100nM AntimiR-195 for 24h


title: blood-MTC_2237R


title: blood-MTC_2742


title: blood-MTC_2873


title: blood-MTC_2766


title: blood-MTC_2769


title: blood-MTC_2744


title: LM16_rep1


title: MCF7-AntimiR rep1


title: PT468_H3K27ac

description:
antibody: H3K27ac (Abcam, ab4729)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457

value: adenoid cystic carcinoma (ACC)


title: MCF7-miR-195 rep2


title: blood-MTC_2743


title: PT485_H3K27ac


title: PT484_H3K27ac


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep6

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

country: China

institute: Nestle research center- Beijing hub

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000 7G system.

data_processing: The data were analyzed with Expression console software using Robust Multichip Average(RMA) as normalization method.

organism: Rattus norvegicus

source_name: high fat diet group combined with pomegrnate skin extract_8 wks feeding

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

growth_protocol: Specific pathogen free Sprague Dawley (SD) male rats were housed in a temperature (22˚C-28˚C) and humidity (60%)-controlled animal room and maintained on a 12-h light/12-h dark cycle (light from 08:00 a.m. to 08:00 p.m.) ad libitum to food and water for 8 weeks.

extract_protocol: The extraction of total RNA was performed using Agencourt RNAdvance tissue kit according to the manufacturer's instructions.

treatment_protocol: Then rats were fasted overnight and sacrificed. Liver samples were collected after sacrifice and immediately stored in liquid nitrogen tank until RNA extraction.

tag: strain

value: Sprague Dawley

value: male

value: adult

tag: diet group

value: high fat diet group combined with pomegrnate skin extract (150mg/Kg/d)

tag: feeding duration

value: 8 weeks

value: liver

tag: tissue condition

value: normal rat liver


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep4


title: X22_H3K27ac


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep5


title: blood-MTC_2118R

value: MTC


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep3


title: X2_H3K27ac


title: X22_H3K4me3

description:
antibody: H3K4me3 (Millipore, 07-473CA)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: blood-MTC_3178


title: X2_H3K4me3


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep1


title: rat liver_high fat diet and 150mg/Kg/d pomegrnate skin extract_biological rep2


title: blood-MTC_3122


title: X22_Input


title: rat liver_high fat diet_biological rep5

source_name: high fat diet group_8 wks feeding

value: high fat diet group

value: fatty rat liver


title: rat liver_high fat diet_biological rep6


title: X11_Input


title: blood-MTC_2134

value: peripheral blood


title: blood-MTC_3183


title: blood-MTC_3310R


title: X16_Input


title: blood-MTC_2241


title: X2_Input


title: rat liver_high fat diet_biological rep4


title: rat liver_high fat diet_biological rep2


title: rat liver_high fat diet_biological rep3


title: PT470_Input


title: blood-MTC_3336R


title: PT596_Input


title: rat liver_high fat diet_biological rep1


title: rat liver_chow diet_biological rep6

source_name: chow diet group_8 wks feeding

value: chow diet group


title: blood-MTC_3356R


title: rat liver_chow diet_biological rep5


title: PT485_Input


title: blood-MTC_3034


title: PT468_Input


title: rat liver_chow diet_biological rep3


title: PT484_Input


title: X9_BRD4

description:
antibody: BRD4 (Bethyl, A301-985A100)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457


title: blood-MTC_3847