title: XVE 6 hr

first: Jychian

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

description: gene expression after treatment

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 021169_D_F_20110524) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Alexa 555

organism: Arabidopsis thaliana

source_name: XVE SAM, 17b-estradiol, 6 hr

label_protocol: cDNA prepared from 10μg of total RNA were labeled with Alexa Fluor 555-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).

growth_protocol: Plants were grown in potting soil at 23°C under a 16-hr light/8-hr dark photoperiod with illumination at 120 μmol quanta m-2sec-2.

extract_protocol: Total RNA was extracted using TRIZOL reagent. Leaf tissue (150 mg) was homogenized with 1 mL TRIZOL reagent. Supernatants were mixed with 500 mL 95% (v/v) ethanol and 500 mL 0.8 M Na-citrate/1.2 M NaCl. Samples were then centrifuged at 4°C, and supernatants were poured off. RNA pellets were washed with 70% (v/v) ethanol. After briefly dried, the pellets were dissolved in nuclease-free water

treatment_protocol: Twenty μM 17-β-estradiol or DMSO was applied on meristems using a paintbrush

value: shoot apical meristem and juvenile leaves

tag: age

value: 21 day


title: XVE AMY3C-EY DMSO 6 hr

status: Public on Mar 01 2017

type: RNA

city: Taipei

last: Chen

country: Taiwan

institute: Academia Sinica

description: gene expression after treatment

molecule: total RNA

source_name: XVE AMY3C-EY SAM, DMSO, 6 hr

tag: tissue


title: A-149_ARR_D34

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

hyb_protocol: Samples were hybridized on  HG-133 plus 2.0  chips

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish using JMP Genomics v. 6.0 (SAS Institute, Cary NC USA)

label: Biotin

organism: Homo sapiens

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject id

tag: subject status

value: healthy malaria-naïve volunteer

tag: vaccine

value: ARR

tag: time

tag: positive blood smear (1=yes, 0=no)

value: PBMC


title: A-103_ARR_D57


title: A-103_ARR_D62


title: XVE AMY3C-EY 3 hr

description: gene expression after treatment

source_name: XVE AMY3C-EY SAM, 17b-estradiol, 3 hr


title: Fertilized flowers_atnaod mutant_rep3

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

country: Italy

institute: University of Verona

description:
Gene expression of A. thaliana fertilized flowers collected from atnaod mutant plants at flowering stage 15.
atnaod_3(T-DNA)

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis thaliana Microarrays (V4) (Design ID 021169) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Fertilized flowers_atnaod mutant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds were directly sown on soil and grown to maturity in a growth chamber set at a constant temperature of 25°C with a 16 h light/8 h dark photoperiod, with an average light intensity of 120 µmol m-2 s-1.

extract_protocol: Total RNA was extracted from the whole floral organs collected at stage 15 from atnaod mutant and wild-type plants following the protocol of Suzuki et al. (2004). RNA was isolated using 20 v/w of high-sodium extraction buffer [100 mM Tris-HCl (pH 9.5), 10 mM EDTA (pH 8.0), 2% (w/v) lithium dodecyl sulfate, 0.6 M NaCl, and 0.4 M trisodium citrate and 5% 2-mercaptoethanol].

treatment_protocol: The fertilised flowers once sampled were immediately frozen in liquid nitrogen prior to extracts preparation.

tag: developmental stage

value: Flowering stage 15

tag: genotype/variation

value: atnaod mutant

value: Fertilized flowers


title: Fertilized flowers_wild type_rep3

description:
Gene expression of A. thaliana fertilized flowers collected from wild type plants at flowering stage 15.
Wt_3

source_name: Fertilized flowers_wild type

value: wild type


title: A-149_ARR_D57


title: XVE AMY3C-EY 1 hr

description: gene expression after treatment

source_name: XVE AMY3C-EY SAM, 17b-estradiol, 1 hr


title: XVE AMY3C-EY 6 hr

description: gene expression after treatment

source_name: XVE AMY3C-EY SAM, 17b-estradiol, 6 hr


title: A-149_ARR_D82


title: XVE AMY3C-EY 0 hr

description: gene expression after treatment

source_name: XVE AMY3C-EY SAM, 17b-estradiol, 0 hr


title: R-159_RRR_D57

value: RRR


title: Fertilized flowers_wild type_rep2

description:
Gene expression of A. thaliana fertilized flowers collected from wild type plants at flowering stage 15.
Wt_2


title: Fertilized flowers_atnaod mutant_rep2

description:
Gene expression of A. thaliana fertilized flowers collected from atnaod mutant plants at flowering stage 15.
atnaod_2(T-DNA)


title: Fertilized flowers_atnaod mutant_rep1

description:
Gene expression of A. thaliana fertilized flowers collected from atnaod mutant plants at flowering stage 15.
atnaod_1(T-DNA)


title: A-149_ARR_D6


title: Fertilized flowers_wild type_rep1

description:
Gene expression of A. thaliana fertilized flowers collected from wild type plants at flowering stage 15.
Wt_1


title: R-72_RRR_D78


title: R-72_RRR_D77


title: R-159_RRR_D28


title: R-159_RRR_D82


title: R-72_RRR_D82


title: R-159_RRR_D29


title: A-149_ARR_D28


title: R-159_RRR_D56


title: A-149_ARR_D62


title: R-159_RRR_Pre

value: Pre


title: R-72_RRR_D62


title: R-72_RRR_D57


title: A-149_ARR_D14


title: A-172_ARR_Pre


title: R-72_RRR_D56


title: R-159_RRR_D6


title: A-172_ARR_D6


title: A-149_ARR_D56


title: A-103_ARR_D29


title: A-172_ARR_D28


title: R-159_RRR_D14


title: A-149_ARR_D78


title: A-172_ARR_D29


title: A-103_ARR_D28


title: R-159_RRR_D1


title: R-81_RRR_Pre


title: A-172_ARR_D82


title: R-159_RRR_D34


title: A-172_ARR_D78


title: R-159_RRR_D62


title: A-172_ARR_D56


title: A-103_ARR_D2


title: R-81_RRR_D1


title: BreastTumor_COCA-424-U-T1

city: Oslo

first: Miriam

middle: Ragle

last: Aure

address: Ullernchauséen 70

department: Dept. of Cancer Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010

scan_protocol: Scanning on Agilent scanner G2565A and Feature Extraction (FE) v10.7.3.1 was used to extract signals

data_processing: Signals were extracted using FE v.10.7.3.1 and protocol GE1_107_Sep09 (Agilent Technologies). Arrays were log2-transformed, quantile normalized and hospital-adjusted by subtracting from each probe value the mean probe value among samples from the same hospital.

source_name: Breast primary tumor

growth_protocol: Human primary tumors

extract_protocol: TRIzol, following manufactors protocol

treatment_protocol: Fresh frozen in liquid nitrogen

value: Breast tumor tissue

tag: hospital id

tag: estrogen receptor (er) status

tag: human epidermal growth factor receptor 2 (her2) status

tag: histological grade

tag: pam50 subtype

value: Normal


title: BreastTumor_COCA-241-U-T4

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, v.6.5, May 2010

value: pos

value: neg

value: LumA


title: BreastTumor_COCA-420-U-T1


title: BreastTumor_COCA-409-U-T1

value: Basal


title: BreastTumor_COCA-394-U-T1


title: BreastTumor_COCA-205-U-T6


title: BreastTumor_COCA-296-U-T1


title: BreastTumor_COCA-415-U-T1


title: BreastTumor_COCA-398-U-T1


title: A-172_ARR_D2


title: BreastTumor_COCA-279-U-T1


title: R-81_RRR_D77


title: BreastTumor_COCA-189-U-T1


title: R-159_RRR_D77


title: A-103_ARR_D14


title: BreastTumor_COCA-206-U-T5


title: R-81_RRR_D6


title: BreastTumor_COCA-153-U-T1


title: BreastTumor_COCA-417-U-T1


title: BreastTumor_COCA-148-U-T1


title: BreastTumor_COCA-122-U-T1

value: LumB


title: BreastTumor_COCA-78-R-T3


title: A-172_ARR_D77


title: R-81_RRR_D2


title: BreastTumor_COCA-81-R-T2


title: BreastTumor_COCA-113-U-T1


title: BreastTumor_COCA-73-R-T1


title: A-103_ARR_D6


title: BreastTumor_COCA-121-U-T1


title: BreastTumor_COCA-91-R-T4


title: R-75_RRR_D14


title: BreastTumor_COCA-126-U-T1


title: A-172_ARR_D34


title: A-172_ARR_D14


title: BreastTumor_COCA-90-R-T3


title: A-172_ARR_D1


title: BreastTumor_COCA-95-U-T1


title: A-103_ARR_Pre


title: R-159_RRR_D78


title: BreastTumor_COCA-68-A-T


title: BreastTumor_COCA-145-U-T1


title: R-112_RRR_D1


title: BreastTumor_COCA-66-A-T


title: R-112_RRR_D77


title: BreastTumor_COCA-65-A-T


title: BreastTumor_COCA-62-A-T


title: BreastTumor_COCA-69-A-T


title: R-112_RRR_D6


title: BreastTumor_COCA-405-U-T1


title: BreastTumor_COCA-64-A-T


title: BreastTumor_COCA-63-A-T


title: R-112_RRR_D2


title: R-112_RRR_D82


title: BreastTumor_COCA-58-A-T


title: BreastTumor_COCA-57-A-T


title: BreastTumor_COCA-60-A-T


title: BreastTumor_COCA-52-A-T


title: BreastTumor_COCA-55-A-T


title: R-112_RRR_D57


title: R-112_RRR_D34


title: BreastTumor_COCA-61-A-T


title: BreastTumor_COCA-56-A-T


title: BreastTumor_COCA-53-A-T


title: BreastTumor_COCA-50-A-T


title: R-112_RRR_D29


title: R-112_RRR_D56


title: R-112_RRR_D62


title: R-112_RRR_D78


title: R-112_RRR_D14


title: R-112_RRR_D28


title: R-36_RRR_D82


title: BreastTumor_COCA-51-A-T


title: BreastTumor_COCA-59-A-T


title: BreastTumor_COCA-48-A-T


title: BreastTumor_COCA-38-A-T


title: BreastTumor_COCA-43-A-T


title: BreastTumor_COCA-42-A-T


title: BreastTumor_COCA-40-A-T


title: BreastTumor_COCA-54-A-T


title: BreastTumor_COCA-37-A-T


title: BreastTumor_COCA-36-A-T


title: BreastTumor_COCA-427-A-T


title: BreastTumor_COCA-45-A-T


title: BreastTumor_COCA-39-A-T


title: BreastTumor_COCA-49-A-T


title: BreastTumor_COCA-33-A-T


title: BreastTumor_COCA-44-A-T


title: BreastTumor_COCA-32-A-T


title: BreastTumor_COCA-46-A-T


title: BreastTumor_COCA-47-A-T


title: BreastTumor_COCA-41-A-T


title: A-33_ARR_D77


title: R-36_RRR_D14


title: BreastTumor_COCA-29-A-T


title: BreastTumor_COCA-30-A-T


title: A-33_ARR_D1


title: R-155_RRR_D57


title: A-33_ARR_D62


title: R-155_RRR_D62


title: R-36_RRR_D6


title: A-33_ARR_D14


title: A-33_ARR_D57


title: R-75_RRR_D6


title: R-75_RRR_D28


title: BreastTumor_COCA-9-A-T


title: R-36_RRR_D28


title: BreastTumor_COCA-31-A-T


title: BreastTumor_COCA-5-A-T


title: BreastTumor_COCA-14-A-T


title: BreastTumor_COCA-34-A-T


title: R-36_RRR_D56


title: BreastTumor_COCA-15-A-T


title: BreastTumor_COCA-16-A-T


title: BreastTumor_COCA-3-A-T


title: BreastTumor_COCA-20-A-T


title: BreastTumor_COCA-19-A-T


title: BreastTumor_COCA-18-A-T


title: BreastTumor_COCA-28-A-T


title: BreastTumor_COCA-22-A-T


title: BreastTumor_COCA-23-A-T


title: BreastTumor_COCA-426-A-T


title: R-155_RRR_D78


title: A-33_ARR_D78


title: BreastTumor_COCA-17-A-T


title: BreastTumor_COCA-27-A-T


title: BreastTumor_COCA-24-A-T


title: BreastTumor_COCA-67-A-T


title: BreastTumor_COCA-21-A-T


title: R-36_RRR_Pre


title: BreastTumor_COCA-2-A-T


title: BreastTumor_COCA-8-A-T


title: BreastTumor_COCA-7-A-T


title: BreastTumor_COCA-6-A-T


title: R-155_RRR_D56


title: BreastTumor_COCA-70-A-T


title: BreastTumor_COCA-25-A-T


title: BreastTumor_COCA-1-A-T


title: BreastTumor_COCA-10-A-T


title: R-155_RRR_D77


title: R-36_RRR_D57


title: A-33_ARR_D2


title: BreastTumor_COCA-35-A-T


title: R-36_RRR_D2


title: BreastTumor_COCA-4-A-T


title: R-75_RRR_D2


title: A-41_ARR_D34


title: BreastTumor_COCA-26-A-T


title: HCT116 DGKG-CA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: Gene expression in HCT116 cells overexpressing DGKG-CA

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

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

source_name: HCT116 cells overexpressing DGKG-CA

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Thermo Fisher Scientific).

treatment_protocol: HCT116 cells were infected with an adenoviral vector for expressing LacZ, or DGKG-KD or DGKG-CA. Twenty-four hours after infection, total RNA was extracted.

tag: vector

value: DGKG-CA

tag: cell line


title: HCT116 LacZ

description: Gene expression in HCT116 cells overexpressing LacZ

source_name: HCT116 cells overexpressing LacZ

value: LacZ


title: HCT116 DGKG-KD

description: Gene expression in HCT116 cells overexpressing DGKG-KD

source_name: HCT116 cells overexpressing DGKG-KD

value: DGKG-KD


title: R-155_RRR_D34

value: healthy malaria-naïve volunteer

value: PBMC


title: R-75_RRR_D78


title: BreastTumor_COCA-11-A-T


title: BreastTumor_COCA-12-A-T


title: BT549 Suspended 4

city: Aurora

first: Jennifer

middle: K

last: Richer

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: One ug of biotinylated RNA from each sample was hybridized onto AffymetrixÂ® Human Gene 1.0 ST array according to the manufacturer's recommendations.

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

data_processing: Affymetrix CEL files from all samples hybridized to the mRNA arrays were loaded on to Partek Genoimcs Suite. Signal intensities for all probe sets were obtained using Robust Multichip Averaging summarization algorithm which involves three steps - background correction, quantile normalization and probe summarization (median polish). Quality control was performed by principal component analysis to identify outliers (no outliers detected).

label: biotin

source_name: Human TNBC cell line, 24 hours suspended

label_protocol: One ug of total RNA from each sample was labelled with FlashTag Biotin RNA Labeling kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Cells grown in attached culture conditions or on poly-HEMA coated plates (suspended culture conditions) for 24 hours in RPMI + 10% FBS + insulin

extract_protocol: RNA was harvested after 24 hours using the TRIZOL method, following the manufacturer's instructions.

treatment_protocol: Cells were grown in RPMI + 10% FBS + insulin for 48 hours on normal tissue culture plates (attached) or on poly-HEMA coated plates (suspended) for 24 hours.

tag: cell type

value: Human triple negative breast cancer (TNBC)

tag: growth condition

value: Suspended


title: BT549 Suspended 3


title: BT549 Suspended 2


title: BT549 Attached 4

source_name: Human TNBC cell line, 24 hours attached

value: Attached


title: BT549 Suspended 1


title: BT549 Attached 2


title: R-75_RRR_Pre

value: RRR

tag: tissue


title: BT549 Attached 1


title: BT549 Attached 3


title: R-75_RRR_D29

tag: subject id


title: A-33_ARR_Pre

tag: subject status

value: ARR

value: Pre


title: metastatic cell line #4

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Expression Console was used for primary analysis, RMA algorithm with default settings.

source_name: melanoma cell line

label_protocol: Labeling, hybridization and image scan were performed according to the recent laboratory protocol of UD-GenoMed Medical Genomic Technologies Ltd.

growth_protocol: Human melanoma cell lines were maintained in RPMI 1640 medium supplemented with 10% foetal bovine serum, 300 mg/l L-glutamine and antibiotics. All cell lines were obtained from Coriell Cell Repositories of the Coriell Institute for Medical Research, and all chemicals were obtained from Sigma-Aldrich.

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus Mini kit.

value: melanoma cell line

tag: sample type

value: lung xenografted


title: primray cell line #2


title: primray cell line #3


title: primray cell line #4


title: metastatic cell line #2

value: cutan


title: reference tissue

source_name: fresh/frozen skin tissue

value: fresh/frozen skin tissue

value: pool of 5 independent samples


title: metastatic tissue #1

source_name: fresh/frozen melanoma tissue

value: fresh/frozen melanoma tissue

value: lymph node


title: R-36_RRR_D1

tag: vaccine

tag: time


title: metastatic cell line #3


title: reference cell line

source_name: melanocyte cell line

value: melanocyte cell line


title: primray cell line #1


title: metastatic tissue #2


title: metastatic cell line #1


title: R-112_RRR_Pre

tag: positive blood smear (1=yes, 0=no)


title: A-41_ARR_D78


title: R-155_RRR_D6


title: primary tissue #2

value: NM, male, grade III


title: R-36_RRR_D78

value: healthy malaria-naïve volunteer


title: R-155_RRR_D1

value: PBMC


title: A-33_ARR_D28


title: R-75_RRR_D56


title: primary tissue #1

value: SSM, male, grade III


title: reference tissue naevus

source_name: fresh/frozen naevus tissue

value: fresh/frozen naevus tissue

value: pool of 8 independent samples


title: miR-322 line H7

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: six days of induction

hyb_protocol: As per affymetric instructions

scan_protocol: As per affymetric instructions

data_processing: Expression data were normalized and analyzed using R Bioconductor libraries, affy, oligo and limma

organism: Mus musculus

source_name: induced embryonic stem cells

label_protocol: As per affymetric instructions

growth_protocol: Mouse R1 embryonic stem cells (ESCs) obtained from the laboratory of Janet Rossant were cultured on MEF15.5 seeded dishes with DMEM (Gibco-Life Technologies) supplemented with 15% FBS, 0.1mM 2-mercaptoethanol, 2mM GlutaMAX, 1mM sodium pyruvate, 0.1mM NEAA, PenStrep (50ug/ml), and LIF (1000U/ml). Mouse trophoblast stem cells were seeded onto E12.5 mosue embryonic fibroblasts and cultured with RPMI 1640 (Sigma Aldrich) supplemented with 20% FBS, PenStrep (50ug/ml), 1mM sodium pyruvate, 100uM 2-mercaptoethanol, 2mM GlutaMAX, FGF4 (1000x), Heparin (1000x) or on plastic feeder free in 3 day feeder conditioned medium (70%) RPMI 1640 (Sigma Aldrich) supplemented with 20% FBS, PenStrep (50ug/ml), 1mM sodium pyruvate, 100uM 2-mercaptoethanol, 2mM GlutaMAX supplemented with 30% unconditioned media and  FGF4 (1000x), Heparin (1000x)

extract_protocol: Total RNA was harvested from monolayers using the Norgen Biotek RNA Isolation Kit or were harvested directly into Trizol (Ambion Life Technologies).

treatment_protocol: Transgenic R1-ESC lines were seeded at a density of 2x10^4 per well of a MEF15.5- containing 6 well plate, and cultured in ESC media for the first 24 hours until initiation of induction.  Following 24 hours, media was changed to RPMI 1640 (Sigma Aldrich) supplemented with 20% FBS, PenStrep (50ug/ml), 1mM sodium pyruvate, 100uM 2-mercaptoethanol, 2mM GlutaMAX, FGF4 (1000x), Heparin (1000x), doxycycline (1ug/ul). Twenty-four hours following doxycycline induction, valproic acid (2mM) was added to the media.  Lines were cultured for a length of 10 days and harvested accordingly.

tag: cell fate state

value: miR-322 expression


title: R-36_RRR_D34

value: RRR


title: miR-467g line D3

description: six days of induction

value: miR-467g expression


title: miR-467g line G2

description: six days of induction


title: miR-322 line D10

description: six days of induction


title: Mock skeletal muscle

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

institute: China Medical University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Rattus norvegicus

source_name: Rat skeletal muscle

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

growth_protocol: Animals were housed in plexiglass cages at a constant room temperature of 22 ± 2◦C with a relative humidity of 65 ± 5%.

extract_protocol: Total RNA was extracted from skeletal muscle using an RNeasy Mini kit.

treatment_protocol: STZ-induced diabetic rats were punctured at ST36 acupoint with 1.27 cm, 32 gauge acupuncture needles. After a 5-min needling period, EA was performed for 60 minutes at a frequency of 15 Hz with amplitude of 10 mA. Total RNA was then extracted from skeletal muscle for microarray analysis.

tag: strain

value: Wistar

tag: age

value: 8-10 week-old

tag: gender

value: Male


title: miR-15b line F7

description: six days of induction

value: miR-15b expression


title: A-41_ARR_Pre

value: ARR

value: Pre


title: A-41_ARR_D1


title: cKI ileum 3

city: Milwaukee

first: Michele

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

hyb_protocol: Affymetrix Whole Transcript Sense Protocol

data_processing: Partek Genomic Suite

source_name: adult Gata4 cKI

label_protocol: Affymetrix Whole Transcript Sense Labeling

growth_protocol: Mice were raised under normal conditions

extract_protocol: Qiagen Rneasy Mini

treatment_protocol: Small intestinal tissue was harvested, epithelial cells were isolated, and RNA was prepared.

value: ileal epithelium


title: A-41_ARR_D6


title: R1 ESC

description: control

source_name: embryonic stem cells

value: embryo derived ESC


title: Cdx2 inducible ESC

description: six days of induction

value: Cdx2 expression


title: cKO Jejunum 2

scan_protocol: Affymetrix Whole Transcript Sense Protocol

source_name: adult Gata4 cKO

value: Jejunal epithelium


title: miR-15b line F3

description: six days of induction


title: cKO Jejunum 1


title: control ileum 3

source_name: adult control


title: R-155_RRR_Pre

value: healthy malaria-naïve volunteer

value: PBMC


title: F4 TSC

description: control

source_name: trophoblast stem cells

value: embryo derived TSC


title: R-75_RRR_D1


title: cKI ileum 1


title: cKO Jejunum 3


title: cKI ileum 2


title: control ileum 1


title: R-75_RRR_D82


title: control ileum 2


title: A-33_ARR_D6


title: jejunum 1

source_name: adult wildtype cd1


title: ileum 3


title: EA (electroacupuncture) skeletal muscle

description: replicate 1


title: jejunum 3


title: jejunum 2


title: ileum 1


title: A-41_ARR_D82


title: ileum 2


title: A-41_ARR_D77


title: R-155_RRR_D82


title: A-41_ARR_D14


title: R-36_RRR_D77


title: R-36_RRR_D29


title: A-41_ARR_D56


title: cmo IL1R-/- rep1

city: Iowa City

first: Polly

last: Ferguson

state: IA

address: 25 South Grand Ave

department: Pediatrics

institute: University of Iowa

description: cmo IL1R-/- rep1

hyb_protocol: 750ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina-Mouse WG-6 v2.0 BeadChips (Part No. BD-201-0202), and incubated at 58ºC for 17h, with rocking, in an Illumina Hybridization Oven. Following hybridization, the arrays were washed, blocked, and then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ)

scan_protocol: Beadchips were scanned with the Illumina iScan System (ID #N0534) and data were collected using the GenomeStudio software v2011.1

data_processing: Normalized expression values were analyzed for differential expression using Partek Genomics Suite software (version 6.12, Partek Inc., St. Louis, MO, USA.)

source_name: femur bone marrow derived macrophages

label_protocol: 100 nanograms total RNA was converted to amplified Biotin-aRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924)

growth_protocol: BMDMs were isolated and cultured in 20 ml media (α-MEM + 10% FBC + 5% CMG).  Cells were incubated at 37°C in 5% CO2 for 2 days

extract_protocol: RNA extraction was performed using Qiagen’s RNA purification kit (Cat#74104) according to the manufacturer’s instruction.

value: cmo IL1R-/-


title: cmo IL1R-/- rep2

description: cmo IL1R-/- rep2


title: cmo IL1R-/- rep3

description: cmo IL1R-/- rep3


title: cmo IL1R+/- rep1

description: cmo IL1R+/- rep1

value: cmo IL1R+/-


title: R-75_RRR_D57

value: RRR


title: cmo IL1R+/- rep3

description: cmo IL1R+/- rep3


title: cmo IL1R+/- rep2

description: cmo IL1R+/- rep2


title: cmo rep3

description: cmo rep3

value: cmo


title: cmo rep2

description: cmo rep2


title: xct_T3_3

city: Singapore

first: Brijesh

middle: Kumar

last: Singh

address: CVMD Level-8, 8 College Road

department: Cardiovascular and Metabolic Disorders Program

country: Singapore

institute: Duke-NUS Gradiate Medical School

description: Sample 12

data_processing: Data was quantile normalized in Partek Genomics Suite software (version 6.6)

growth_protocol: Animals were maintained on a 12 hour light/dark cycle and had access to food and water ad libitum.

extract_protocol: Total RNA was prepared from mouse liver (15–20 mg) with TRIzol reagent (Invitrogen) followed by InviTrap Spin Cell RNA Mini Kit (Stratec) according to the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice received daily intraperitoneal injection of XCT790 (ESRRA inverse agonist; Sigma) for 4 days and L-T3 (liothyronine; Sigma) for last 3 days, and were sacrificed.

value: male

value: 8 weeks

tag: daily intraperitoneal injection of

value: XCT790 for 4 days and L-T3 for last 3 days

value: liver


title: xct_T3_2

description: Sample 11


title: R-75_RRR_D34


title: xct_cnt_3

description: Sample 9

value: XCT790 for 4 days


title: cmo rep1

description: cmo rep1


title: xct_cnt_1

description: Sample 7


title: A-41_ARR_D2

value: ARR


title: xct_T3_1

description: Sample 10


title: A-33_ARR_D56


title: R-155_RRR_D28


title: xct_cnt_2

description: Sample 8


title: T3_3

description: Sample 6

value: L-T3 for 3 days


title: T3_2

description: Sample 5


title: R-155_RRR_D14


title: NCI-H929_siRRM2, replicate1

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured according to the manufacturer's instructions.

data_processing: R/Bioconductor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg of total RNA.

growth_protocol: NCI-H929 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol: After 24 hours of treatment, total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: NCI-H929 cells were transduced with siRNA by electroporation.

value: Myeloma

tag: transduced with

value: siRNA targeting RRM2


title: Cont_2

description: Sample 2

value: none (control)


title: Cont_3

description: Sample 3


title: Arabidopsis_Col0_27degrees.vs.Control_rep4

city: Colchester

first: Ruben

last: Alvarez-Fernandez

address: Wivenhoe Park

department: Biological Sciences

country: United Kingdom

institute: University of Essex

scan_protocol: Genepix 4000B scanner

data_processing: limma for R (see attached Rscript and spottypes file)

label_protocol: Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (manual part number G4140-90050), 500 ng of starting RNA

growth_protocol: Plants were grown in a growth chamber for 5 weeks in short day (8/16 light/dark cycle) at 22 degrees, 150 umol*m2*s-1 (fluorescent lights) and 55% RH in 100-ml pots with Levington's L2+S

extract_protocol: The outer leaves from four biological replicates were ground and RNA purified with Trizol (Life Technologies). RNA was resuspended in water and DNAse-treated (TurboDNAse, Life Technologies), then column-purified (Qiagen RNAeasy cleanup protocol) and eluted in water. Integrity tested on a Bioanalyzer (QuickRNA600nano kit), concentration re-assessed on a nanodrop and DNA contamination assessed by PCR with RNA template against a DNA template control.

treatment_protocol: On the day of the experiment, two hours after the lights turned on we collected the Control plants and snap-froze them in liquid nitrogen. Then we set the growth chamber at 27.5C, waited until it reached that temperature (around 10min) and started the experiment timing 25 min (since in 30 min mild-light-stress experiments the plants need about 5 min to reach 27.5 degrees under the isolight). The aerial parts of the plants were inmmediately snap-frozen in liquid nitrogen after the experiment. The temperature was 27 ± 1 degrees Celsius.

tag: ecotype

value: fully developed leaves

value: 5 weeks post germination

tag: treatment

value: Temperature 27C

value: Control


title: A-41_ARR_D28

value: healthy malaria-naïve volunteer

value: PBMC


title: NCI-H929_siRRM1, replicate2

tag: cell line

tag: cell type

value: siRNA targeting RRM1


title: Arabidopsis_Col0_27degrees.vs.Control_rep3

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (manual part number G4140-90050)

tag: tissue


title: NCI-H929_siRRM2, replicate2


title: R-75_RRR_D62

tag: subject id

value: RRR


title: Arabidopsis_Col0_27degrees.vs.Control_rep2


title: R-75_RRR_D77

tag: subject status


title: NCI-H929_siRRM1, replicate1


title: OCIAML3-DMSO-3

city: Belfast

first: Ken

last: Mills

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

description: Gene expression data from OCI-AML3 cells treated with DMSO alone

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as a scaling

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: OCI-AML3 (DSMZ, Berlin, Germany) were maintained in RPMI 1640 media with L-Glutamine, supplemented with 10% Fetal Calf Serum (FCS) and 5% Penicillin/Streptomycin (Penicillin 100 µg/µl: Streptomycin 100 µg/µl) (Thermo Fisher Scientific, Paisley, UK).

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Manchester, UK) was performed according to the manufacturer's instructions.

treatment_protocol: 1 uM SAHA (Vorinostat) for 24 hrs in

value: Acute,myeloid,leukemia


title: OCIAML3-1uM-SAHA-3

description: Gene expression data from OCI-AML3 cells treated with 1uM SAHA (Vorinostat)


title: NCI-H929_scramble, replicate1

value: non-targeting siRNA (control)


title: Arabidopsis_Col0_Lightstress.vs.Control_rep1

treatment_protocol: On the day of the experiment, two hours after the lights turned on they were subjected to high light stress (approx. 1000 umol*m-2*s-1) for 30 min under an Isolight machine (white LED array), and immediately snap-frozen in liquid nitrogen. Control plants (from the same batch and growing alongside the treated ones) were collected at the same time as the high-light treated ones.

value: Light stress 30 min


title: OCIAML3-1uM-SAHA-2


title: NCI-H929_scramble, replicate2


title: Arabidopsis_Col0_Lightstress.vs.Control_rep2


title: OCIAML3-1uM-SAHA-1


title: Arabidopsis_Col0_27degrees.vs.Control_rep1


title: Arabidopsis_Col0_Lightstress.vs.Control_rep4


title: T3_1

description: Sample 4

value: male

value: 8 weeks

value: liver


title: Cont_1

description: Sample 1


title: Arabidopsis_Col0_Lightstress.vs.Control_rep3


title: OCIAML3-DMSO-1


title: OCIAML3-DMSO-2


title: TIL CD8 T #3 IL-2 + IL-10

city: Durham

first: You-Wen

last: He

state: NC

address: 207 Resarch Drive

department: Immunology

institute: Duke University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw intensities from the CEL files were analyzed using Partek Genomics Suite 6.6 (Partek Incorporated, St. Louis, MO) with standard background correction to generate an RMA (robust multi-array average intensity) on a log2 scale for each probe set.

source_name: In vitro cultured human TIL CD8 T_IL-2 + IL-10

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

growth_protocol: TILs were cultured in completed PRMI medium with or without IL-10 for 20 days

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

treatment_protocol: T cells were activated for 6 hrs

value: CD8+ tumor infiltrating lymphocytes (TILs)

tag: tissue source

value: human lung cancer

tag: expanded with

value: 6000µ/ml rIL-2 and 100µ/ml rIL-10

tag: activated with

value: 3µg/ml anti-CD3 and anti-CD28 for 6hrs


title: TIL CD8 T #3 IL-2

source_name: In vitro cultured human TIL CD8 T_IL-2


title: TIL CD8 T #2 IL-2 + IL-10


title: TIL CD8 T #2 IL-2


title: Leukemia sample 29

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description: Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA and removal batch effect were applied using ComBat in the sva package

source_name: White blood human cells

label_protocol: Batch1: Biotinylated cRNA were prepared according to work-up protocol descriped in J.Clin.Oncol (2010) 28(15): 2529-37;  Batch2: Biotinylated cRNA were prepared according to the standard 3' IVT Affymetrix protocol.

extract_protocol: For Batch1: RNA was extracted from mononuclear cells using selective binding columns; for Batch2:  RNA was extracted from mononuclear cells using Trizol

treatment_protocol: White blood cells were isolated by density gradient centrifugation (Ficoll separating solution, Biochrome AG, Berlin, Germany).

tag: disease

value: Leukemia

tag: batch

tag: groups


title: Leukemia sample 30


title: TIL CD8 T #1 IL-2 + IL-10


title: Leukemia sample 27


title: Leukemia sample 25


title: Leukemia sample 28


title: TIL CD8 T #1 IL-2


title: Ss-rehydrted for 24h_rep1

city: Columbia

first: Abou

last: Yobi

state: Missouri

address: 214 Curtis Hall

department: Plant Genetics Unit

institute: USDA-ARS

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Sporobolus stapfianus

source_name: Sporobolus stapfianus leaf tissues

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Sporobolus stapfianus plants were grown on 1 gallon pots filled with ProMix potting soil and alowed to grow for three months under green house conditions. Watering and fertilization were provided as needed and water content measurements were conducted at the time of havest. Leaves were harvested at fully hydrated state, four dehydrating states, a desiccated state, a 12 h rehydrating state, and a 24 h rehydrating state. Leaves were then grinded and used for RNA extraction.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). After gel elecrophoresis analysis on formaldehyde-containing 1.2% agarose gel, RNA was quantified using an NanoDrop (NanoDrop Technologies, Inc., Rockland, DE).

tag: genotype

value: Grass

tag: phenotype

value: Recovering from desiccation

tag: accession

value: leaf


title: Ss-rehydrted for 12h_rep3


title: Ss-dehydrted to 0.5gwater/gtissue_rep3


title: Ss-rehydrted for 24h_rep3


title: Ss-rehydrted for 12h_rep2


title: Leukemia sample 26


title: Ss-dehydrted to 0.5gwater/gtissue_rep1

value: Water stressed


title: Ss-dehydrted to 0.75gwater/gtissue_rep1


title: Ss-rehydrted for 24h_rep2


title: Ss-rehydrted for 12h_rep1


title: Ss-dehydrted to 0.5gwater/gtissue_rep2


title: Ss-dehydrted to 1gwater/gtissue_rep3


title: Leukemia sample 23


title: Ss-dehydrted to 0.75gwater/gtissue_rep3


title: Leukemia sample 22


title: Leukemia sample 21


title: Ss-dehydrted to 0.75gwater/gtissue_rep2


title: Ss-dehydrted to 1gwater/gtissue_rep2


title: Ss-dehydrted to 1gwater/gtissue_rep1


title: Leukemia sample 24


title: Ss-dehydrted to 1.5gwater/gtissue_rep3


title: Ss-dehydrted to 1.5gwater/gtissue_rep2


title: Ss_hydrated_rep3

value: normal


title: Ss-dehydrted to 1.5gwater/gtissue_rep1


title: Leukemia sample 19


title: Leukemia sample 14


title: Ss-dehydrted to 2gwater/gtissue_rep2


title: Ss-dehydrted to 2gwater/gtissue_rep1


title: Ss_hydrated_rep1


title: Leukemia sample 16


title: Leukemia sample 17


title: Leukemia sample 18


title: Leukemia sample 20


title: Leukemia sample 13


title: Ss-dehydrted to 2gwater/gtissue_rep3


title: Leukemia sample 15


title: Ss_hydrated_rep2


title: Leukemia sample 11


title: No activation_3

city: Paris

first: Richard

last: Lo-Man

address: 25-28 Rue du Docteur Roux

country: France

institute: Institut Pasteur

description:
Gene expression after activation
SAMPLE 15

hyb_protocol: according to MiltenyiBiotec procedures

scan_protocol: according to MiltenyiBiotec procedures

data_processing: Microarrays agilent files were processed, background corrected, and normalized using the quantile method with R and package Limma (Richie et al, Nucleic Acids Research 43(7), e47). Genes were averaged using ProbeID and GeneName.

source_name: CD19+CD5+CD10NegCD3Neg cells

label_protocol: according to MiltenyiBiotec procedures

growth_protocol: Culture for 24h

extract_protocol: according to MiltenyiBiotec procedures

treatment_protocol: activated with anti-IgM, R848, Respiratory Syncitial Virus (RSV), Influenza virus (Flu-PR8)

value: Cord Blood

value: B cells

tag: cell markers

tag: gender

value: female


title: Leukemia sample 12


title: Leukemia sample 9


title: Leukemia sample 10


title: No activation_2

description:
Gene expression after activation
SAMPLE 14


title: Leukemia sample 6


title: FLU-PR8 activation_3

description:
Gene expression after activation
SAMPLE 12


title: No activation_1

description:
Gene expression after activation
SAMPLE 13


title: RSV-A2 activation_3

description:
Gene expression after activation
SAMPLE 11


title: Leukemia sample 8


title: Leukemia sample 7


title: Leukemia sample 4


title: R848 activation_3

description:
Gene expression after activation
SAMPLE 10


title: Leukemia sample 5


title: aIgM activation_3

description:
Gene expression after activation
SAMPLE 9


title: Leukemia sample 3


title: FLU-PR8 activation_2

description:
Gene expression after activation
SAMPLE 8


title: R848 activation_2

description:
Gene expression after activation
SAMPLE 6


title: Leukemia sample 2


title: RSV-A2 activation_2

description:
Gene expression after activation
SAMPLE 7


title: Leukemia sample 1


title: FLU-PR8 activation_1

description:
Gene expression after activation
SAMPLE 4


title: aIgM activation_2

description:
Gene expression after activation
SAMPLE 5


title: SMC4EPC4

first: Lisa

middle: L

last: Satterwhite

state: North Carolina

address: 101 Science Drive

department: Department of Civil and Environmental Engineering

description: gene expression data from endothelial cells in layers

hyb_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: Scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: In preparation for statistical analysis, data were normalized onto a single array using the Robust Multichip Average (RMA) algorithm.

source_name: Cord blood endothelial cells

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE)

extract_protocol: Total RNA was isolated from lamellar co-cultures or from EC monocultures using an Qiagen RNeasy Kit (#74104) and RNase-free DNase treatment (#79254)

value: endothelial cells from confluent layers

tag: cord blood source

value: Cord blood donor 4


title: EPCMONO1

description: gene expression data from endothelial cells in monoculture

value: endothelial cells in monoculture

value: Cord blood donor 1


title: EPCMONO2

value: Cord blood donor 2


title: SMC4EPC3

value: Cord blood donor 3


title: RSV-A2 activation_1

description:
Gene expression after activation
SAMPLE 3


title: R848 activation_1

description:
Gene expression after activation
SAMPLE 2


title: SMC4EPC1


title: aIgM activation_1

description:
Gene expression after activation
SAMPLE 1


title: EPCMONO4


title: SMC4EPC2


title: SMC1EPC4

description: gene expression data from endothelial cells in networks

value: endothelial cells from networks


title: EPCMONO3


title: SMC1EPC2


title: Blood Sample Case 2 [SNP]

type: genomic

first: Jack

last: Brzezinski

state: ON

address: 555 University Avenue

description: Genomic DNA extracted from blood was genotyped using the HumnaOmni2.5M SNP array (Illumina)

hyb_protocol: Standard Illumina Protocol

scan_protocol: Using an Illumina HiScan

data_processing: Genomic DNA extracted from blood was genotyped using the Illumina HumanOmni2.5M-8v1-1_B. The processed data file omni2.5M_matrix_processed.txt (available on the series record) contains the GC score, theta, R, B allele frequency, and log R ratios.

label: cy3 and cy5

molecule: genomic DNA

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications. Prior to extraction, red cells were lysed by exposure of the sample to 2x Lysis Buffer for 5 minutes in ice. The remaining cells were pelletted by centrifugation at 2300 RPM at 4 degrees celsius.

value: Male

value: Blood

tag: disease state

value: Beckwith-Wiedemann Syndrome


title: metastatic cell line #2

data_processing: Affymetrix Genotyping Console was used for primary analysis. Copy number values were extracted and converted from CEL files into signal intensities using apt-copynumber-cyto 1.14.4 software, and CYCHP files were generated by Chromosome Analysis Suite (ChAS) 2.0 software according to the current protocol of UD-GenoMed Medical Genomic Technologies Ltd. ChAS 2.0 and Nexus 6.1 Copy Number Discovery softwares were used for further analysis.

source_name: melanoma cell line

extract_protocol: Genomic DNA was purified using Intron G-Spin Genomic DNA Extraction kit.

tag: cell type

value: melanoma cell line

tag: cell line

tag: sample type

value: cutan


title: metastatic cell line #3

value: lymph node


title: primray cell line #2


title: SMC1EPC3


title: SMC1EPC1


title: Blood Sample Case 1 [SNP]

value: Female

tag: tissue


title: Pz 184 CTR

city: Naples

first: Angela

last: Nebbioso

state: Italy

address: Vico Luigi De Crecchio 7

department: Biophysics, Biochemestry and General Patology

institute: Seconda Università degli Studi di Napoli

description: replicate 4

data_processing: Data were pre-processed using the Bioconductor package lumi, normalized using quantile method and signals were log2-transformed

source_name: blasts of AML patient

growth_protocol: CD34+ normal progenitors were cultured in ex vivo medium as recommended by the supplier. AML blasts were cultured in RPMI with 20% FBS (Sigma), 2 mM L-glutamine (Euroclone) and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin and 250 ng/mL amphotericin-B).

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: SAHA (Merck) was dissolved in DMSO (Sigma) and used at 5x10-6 M for 6 hours.

value: blasts of AML patient

tag: treatment


title: primray cell line #4


title: reference male mouse9/ 20mGyUM

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

description: 20mGyUM Cy3

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

source_name: reference male mouse9

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

value: tail


title: Pz 189 SAHA

description: replicate 5

value: SAHA (Merck)


title: metastatic cell line #4

first: Laura

last: Vizkeleti

address: Üllői str. 93.

value: lung xenografted


title: Pz 184 SAHA

description: replicate 4


title: Pz 189 CTR

description: replicate 5


title: 20mGyUF/ reference male mouse9

description: 20mGyUF Cy5

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: 20mGyU1/ reference male mouse9

description: 20mGyU1 Cy5


title: anaplastic glioma patient 2

city: Heidelberg

first: Maximilian

middle: Georg

last: Schliesser

address: INF 280

country: Germany

institute: DKFZ

hyb_protocol: Agilent ChIP-on-chip protocol v9

scan_protocol: DNA Microarray scanner (Agilent, no G2565CA); Feature Extraction Software 10.5 (Agilent) and the standard ChIP protocol (Agilent)

data_processing: Feature extracted data was processed using the R statistical environment, version 2.13. (http://www.R-project.org) and bioconductor. Background correction and log-ratio (M-value, test/reference) transformation were performed according to the NormExp method with offset=50 correction methods for two-color microarrays. To reduce variations between co-hybridized samples, intensity-based LOESS normalization on rank-invariant probes and negative controls was applied.

label: Alexa flour 5

source_name: anaplastic glioma patient 2

label_protocol: BioPrime Total Genomic DNA Labeling System (Invitrogen)

growth_protocol: tumor material

extract_protocol: QIAamp DNA Mini Kit

treatment_protocol: tumor material

value: brain

tag: tissue type

value: anaplastic glioma tumor sample

label: Alexa flour 3

source_name: healthy

value: normal control


title: reference male mouse9/ 20mGyUF

description: 20mGyUF Cy3


title: reference male mouse9/ 20mGyU1

description: 20mGyU1 Cy3


title: 20mGyUM/ reference male mouse9

description: 20mGyUM Cy5


title: Pz 183 CTR

description: replicate 3


title: anaplastic glioma patient 1

source_name: anaplastic glioma patient 1


title: anaplastic glioma patient 4

source_name: anaplastic glioma patient 4


title: Pz 178 SAHA

description: replicate 1


title: primray cell line #3


title: primary tissue #3

source_name: fresh/frozen melanoma tissue

value: fresh/frozen melanoma tissue

value: SSM, male, grade III-IV


title: anaplastic glioma patient 3

source_name: anaplastic glioma patient 3


title: Pz 182 SAHA

description: replicate 2


title: Pz 182 CTR

description: replicate 2


title: Pz 178 CTR

description: replicate 1


title: 3C7-DR148

city: Shanghai

first: Chao

last: Zhang

address: 320 Yueyang Road

country: China

institute: Partner Institute for Computational Biology (PICB)

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

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

data_processing:
Data was genotyped by Birdsuite; CHP data in tables was processed by Affymetrix Power Tools (CHP files not provided)
Genotypes (typical .inp format) for each individual in matrix_processed_data.txt. Each line in the processed data includes genotypes of one lolus for all individuals.Take the first locus for example, A represents the corresponding individual habors homozygotes of the first allele in column 6, that is C allele for rs6650104. B, homozygotes of the second allele in column 6; H, heterozygotes containing both alleles in column 6; U and N represent missing data.

source_name: blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: population

value: Tibetan

value: blood


title: 3C6-DR42


title: 3C9-DR53


title: 3C8-DR139


title: 3C5-DR161


title: 3C4-DR50


title: primary tissue #2

city: Budapest

institute: Semmelweis University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

label_protocol: Labeling, hybridization and image scan were performed according to the recent laboratory protocol of UD-GenoMed Medical Genomic Technologies Ltd.

value: NM, male, grade III


title: Saha CD34 rep1

description: replicate 1

source_name: cd34+ normal progenitors

value: cd34+ normal progenitors


title: primray cell line #1

value: melanoma cell line


title: metastatic cell line #1


title: Control CD34 rep2

description: replicate 2


title: 3C4-DR50_4


title: metastatic tissue #1


title: 3C2-DR169


title: 3C1-DR196


title: 231-PAR

city: Houston

first: chunru

last: lin

state: TX

address: 1515 Holcombe Blvd

department: Molecular & Cellular Oncology

institute: MD Anderson Cancer Center

description: LncRNA expression in breast cancer tissue of patient 1

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: breast cancer parental cell line

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: 231-BM and 231-PAR cells cultured in DMEM medium. The media were supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37°C in a humidified chamber with 5% CO2.

extract_protocol: RNA was extracted from human breast cancers and their matched adjacent normal tissues using the TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: female

value: parental cell line


title: 3B8-DR20


title: Saha CD34 rep2

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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


title: metastatic tissue #3

value: lymph node


title: 3B9-DR5


title: 3B7-DR126


title: 3C3-DR215


title: 3B12-DR116


title: 3C11-DR138


title: 231-BRN

description: LncRNA expression in normal adjacent breast tissue of patient 1

source_name: breast cancer brain metastasis cell line

value: breast cancer metastasis cell line


title: 3B11-DR124


title: metastatic tissue #2


title: 3B5-X153

value: Sherpa


title: 3B4-X146


title: 3B3-X148


title: Control CD34 rep1

description: replicate 1


title: 3B1-X155


title: I08-63


title: 3B6-DR212


title: I07-63


title: MCAo model treated with IV-hUMSC #10

city: Seongnam-si

first: Jinkwon

last: Kim

address: Yatap-ro

department: Neurology

country: South Korea

institute: CHA medical University

description: Gene expression after 72hr rat MCAo model

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

scan_protocol: Array was scanned using the Agilent Technologies G2600D SG12494263 (Agilent Inc., CA, USA).

data_processing: Array data-exporting processing and analysis were performed using Agilent Feature Extraction software (v100.0.1.1). The data were filtered by flag A, log transformation, and quantile normalization.

source_name: Brain tissue after 72 hours post-MCAo

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

growth_protocol: Rat at 8 weeks

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: control VS saline VS IV-hUMSC (1x10^6) infusion

value: brain tissue

value: Treatment with IV-hUMSC


title: I05-63


title: I05-62_Rep2


title: MCAo model treated with IV-hUMSC #7


title: I03-62


title: I07-62_Rep2


title: primary tissue #1

value: SSM, male, grade III


title: MCAo model treated with IV-hUMSC #8


title: G08-63_Rep2


title: H02-62_Rep2


title: G05-63_Rep2


title: G05-62_Rep2


title: G04-62_Rep2


title: MCAo model treated with IV-hUMSC #9


title: MCAo model treated with saline #5

value: Saline


title: G03-62_Rep2


title: Pz 183 SAHA

description: replicate 3

value: blasts of AML patient

value: SAHA (Merck)


title: MCAo model treated with IV-hUMSC #5


title: MCAo model treated with saline #3


title: MCAo model treated with saline #4


title: MCAo model treated with saline #1


title: MCAo model treated with saline #2


title: G02-63_Rep2


title: G02-62_Rep2


title: Normal control without MCAo #4

value: normal control


title: G07-62_Rep2


title: Normal control without MCAo #3


title: Normal control without MCAo #5


title: G01-62_Rep2


title: Normal control without MCAo #2


title: F08-62_Rep2


title: Normal control without MCAo #1


title: F06-62_Rep2


title: F05-62_Rep2


title: F03-63


title: F01-62_Rep2


title: F02-62


title: HC_16

city: Bonn

first: Joerg

last: Wenzel

address: Sigmund Freud Str 25

department: Dermatology

institute: University of Bonn

description:
Healthy control Group
SAMPLE 16

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: HC_skin biopsy

label_protocol: 100 ng total RNA  was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: Human total RNA was isolated from the tissue samples with the use of Trizol (Sigma-Aldrich).

treatment_protocol: Lesional skin biopsies were taken from patients with active, untreated lupus skin disease. In every case, two 4mm punch biopsies were taken. One was flash-frozen in liquid nitrogen and afterwards processed for mRNA isolation and gene expression analyses. The second biopsy was fixed in 5% formalin solution overnight, and was proceeded for histological investigation.

tag: subject status

value: healthy control

value: 4mm skin biopsy


title: 73_MS010_L1_73

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

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

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

data_processing: Probe-level measurements were normalized, summarized and log2-transformed by dCHIP software using perfect-match-only and invariant-set methods.

organism: Caenorhabditis elegans

source_name: complex I mutant gas-1(fc21)_MS010

label_protocol: Biotinylated cRNA were prepared according to the MessageAmp Premier Amplification Kit protocol using 200 ng of total RNA as input (MessageAmp Premier Ampification Kit Manual, Revision G, Ambion).

growth_protocol: C. elegans were grown on NGM agar 10 cm plates spread with OP50 E. coli.  Synchrony was obtained by bleaching gravid adults, plating the recovered eggs on unspread NGM plates overnight, after which L1-stage arrested animals were transferred to NGM plates spread with OP50 E. coli.

extract_protocol: Trizol reagent was used according to the manufacturer's instructions to extract total RNA with a modified methods of using Qiagen Kit to finish total RNA extraction from  adult worms.

treatment_protocol: Synchronized animals of each strain were grown in 4 biological replicates until they reached young adult hood (start to lay eggss). Wild type N2 Bristol and gas-1(fc21) were treated wit water as a control for 24 hors, and gas-1(fc21) worms separately were treated with the different anioxidant drugs for 24 hours.

tag: strain background

value: N2 Bristol

tag: genotype/variation

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

tag: age

value: from L1 to young adults

value: whole worms

tag: buffer

value: water

tag: bacteria strain

value: E coli OP50

tag: drug concentration

value: MS010 (MitoQ) - 10 uM


title: 75_dTPP_L1_75

source_name: complex I mutant gas-1(fc21)_Decyl TPP

value: Decyl TPP - 10 uM


title: E08-63

value: Sherpa

value: blood


title: 74_CoQ10_L1_74

source_name: complex I mutant gas-1(fc21)_Coenzyme Q10

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: MCAo model treated with IV-hUMSC #6

value: brain tissue

value: Treatment with IV-hUMSC


title: HC_14

description:
Healthy control Group
SAMPLE 14


title: HC_13

description:
Healthy control Group
SAMPLE 13


title: 68_Gas1_L1_68

source_name: complex I mutant gas-1(fc21)_untreated


title: 70_Orot_L1_70

source_name: complex I mutant gas-1(fc21)_Orotic Acid

value: Orotic Acid - 50 uM


title: 71_Lipo_L1_71

source_name: complex I mutant gas-1(fc21)_Lipoic Acid

value: Lipoic Acid - 10 uM


title: E07-63


title: SCLE_11

description:
Disease Group 2
SAMPLE 11

source_name: SCLE_skin biopsy

value: active, untreated lupus skin disease

tag: disease group

value: subacute cutaneous lupus erythematosus; SCLE


title: 69_NaAsc_L1_69

source_name: complex I mutant gas-1(fc21)_Vitamin C

value: N2 Bristol

value: Vitamin C (Sodium Ascorbate) - 100 mM


title: 72_NaAc_L1_72

source_name: complex I mutant gas-1(fc21)_N-Acetylcysteine

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

value: from L1 to young adults

value: N-Acetylcysteine - 2.5 mM


title: HC_15

description:
Healthy control Group
SAMPLE 15

value: healthy control

value: 4mm skin biopsy


title: 67_dTPP_L1_67

value: whole worms

value: water

value: E coli OP50

value: Decyl TPP - 10 uM


title: SCLE_10

description:
Disease Group 2
SAMPLE 10


title: SCLE_9

description:
Disease Group 2
SAMPLE 9


title: HC_12

description:
Healthy control Group
SAMPLE 12


title: 66_CoQ10_L1_66

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: SCLE_7

description:
Disease Group 2
SAMPLE 7


title: SCLE_8

description:
Disease Group 2
SAMPLE 8


title: 65_MS010_L1_65

value: MS010 (MitoQ) - 10 uM


title: 64_NaAc_L1_64


title: E05-63

value: Sherpa

value: blood


title: CDLE_6

description:
Disease Group 1
SAMPLE 6

source_name: CDLE_skin biopsy

value: active, untreated lupus skin disease

value: chronic discoid lupus erythematosus; CDLE


title: E03-63


title: D08-63


title: CDLE_4

description:
Disease Group 1
SAMPLE 4


title: D02-63


title: D05-63


title: CDLE_3

description:
Disease Group 1
SAMPLE 3


title: E07-62_Rep2


title: 61_NaAsc_L1_61

value: N2 Bristol


title: CDLE_2

description:
Disease Group 1
SAMPLE 2


title: D02-62_Rep2


title: E04-63


title: C09-63


title: CDLE_5

description:
Disease Group 1
SAMPLE 5


title: 60_Gas1_L1_60


title: 59_dTPP_L1_59


title: 63_Lipo_L1_63

value: Lipoic Acid - 10 uM


title: 57_MS010_L1_57

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)


title: 56_NaAc_L1_56

value: from L1 to young adults


title: 62_Orot_L1_62

value: Orotic Acid - 50 uM


title: 58_CoQ10_L1_58


title: D07-63_Rep2


title: C03-62_Rep2


title: 54_Orot_L1_54


title: C04-60


title: CDLE_1

description:
Disease Group 1
SAMPLE 1


title: B07-63_Rep2


title: C01-63_Rep2


title: C07-62_Rep2


title: 55_Lipo_L1_55


title: 3C10-DR214

value: Tibetan


title: 53_NaAsc_L1_53

value: Vitamin C (Sodium Ascorbate) - 100 mM


title: 51_dTPP_L1_51

value: whole worms


title: B06-63_Rep2


title: LS292 Transport control con

city: Dalian

first: Ying

last: Gao

state: Liaoning

address: Linghai Road 1

institute: Dalian Maritime university

description: This sample is of dys-1 mutant Caenorhabditis elegans. The sample was kept in a incubator at Dalian Maritime University as a transport-control group.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.  Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: Caenorhabditis elegans LS292, Ground 1g,No transport

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

growth_protocol: Worms were cultured on Nematode Growth Medium (NGM) at 23°C and synchronized to dauer larvae by 1% sodium dodecyl sulfonate (SDS) (Sangon Biotec, Shanghai, China) according to the protocols in Wormbook (Stiernagle 2006).

extract_protocol: Total RNA was isolated using InvitrogenTM TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher, Wilmington, DE, USA) and RNA quality monitored by GelDoc-ItTM 310 Imaging System (UVP, Cambridge, CA, EUA).

treatment_protocol: Shenzhou-8 was launched in the Jiuquan Satellite Launch Center on 1 November 2011. About 10 h before the launch, fresh solid NGM and approximately 100,000 dauer worms were successively loaded in the containers.Containers were settled into the centrifugal and static slots of BIOBOX. The Shenzhou-8 mission was ﬂown from 1 – 17 November 2011, with a total mission time of 16.5 days. Throughout the duration of the experiment, the containers maintained a temperature of 23 0.5℃. G-force peaks did not exceed levels of 0.01 g, while most of the time values oscillated between 0.005 g. Space radiations dose was measured in the static slot (1.92 mGy) and centrifuge slot (2.27 mGy), respectively. Seven hours after landing, worms were collected and kept in liquid nitrogen. The corresponding ground controls of the experiment were performed in parallel at the Payload Integration Test Center in Beijing 2 days later. Here, the samples were kept in a static slot in BIOBOX and temperature was maintained at 23 0.5°C. The ground group was stopped after 16.5 days and  the samples were collected after 7 h later.

tag: genotype

value: dys-1(cx18) I

tag: condition

value: Ground condition without transport to the launch lad at Jiuquan,China

tag: major environmental factor


title: B05-63_Rep2

source_name: blood


title: 52_Gas1_L1_52

value: water

value: E coli OP50


title: 50_CoQ10_L1_50

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: A03-62_Rep2

value: Sherpa


title: N2 Ground control con

description: This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with ground control condition.

source_name: Caenorhabditis elegans N2, Ground 1g

value: Wild-type

value: Ground control condition


title: 49_MS010_L1_49

value: MS010 (MitoQ) - 10 uM


title: N2 Transport control con

description: This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was kept in a incubator at Dalian Maritime University as a transport-control group.

source_name: Caenorhabditis elegans N2, Ground 1g,No transport


title: A02-62_Rep2

value: blood


title: MT4930 Ground control con

description: This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with ground control condition.

source_name: Caenorhabditis elegans MT4930, Ground 1g


title: A01-63_Rep2


title: B06-62_Rep2


title: MT4930 Spaceflgiht 1g-centrifugal con

description: This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.

source_name: Caenorhabditis elegans MT4930, Space radiation+1g

value: Spaceflight 1g-centrifugal condition

value: Space radiation+1g


title: LS292 Ground control con

description: This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with ground control condition.

source_name: Caenorhabditis elegans LS292, Ground 1g


title: MT4930 Spaceflgiht Static con

description: This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight static condition.

source_name: Caenorhabditis elegans MT4930, Space radiation+μg

value: Spaceflight static condition

value: Space radiation+μg


title: N2 Spaceflgiht 1g -centrifugal con

description: This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.

source_name: Caenorhabditis elegans N2, Space radiation+1g


title: H06-62


title: 47_Lipo_L1_47

value: N2 Bristol

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

value: from L1 to young adults

value: Lipoic Acid - 10 uM


title: I06-62


title: 46_Orot_L1_46

value: whole worms

value: Orotic Acid - 50 uM


title: 48_NaAc_L1_48

value: water

value: E coli OP50

value: N-Acetylcysteine - 2.5 mM


title: 45_NaAsc_L1_45

value: Vitamin C (Sodium Ascorbate) - 100 mM


title: 44_Gas1_L1_44


title: E09-62

value: Sherpa


title: H04-62


title: E06-63


title: 43_N2_L1_43

value: wild-type


title: LS292 Spaceflgiht 1g-centrifugal con

description: This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.

source_name: Caenorhabditis elegans LS292, Space radiation+1g

value: dys-1(cx18) I


title: 42_N2_L1_42


title: LS292 Spaceflgiht Static con

description: This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight static condition.No replicate used in this experiment.

source_name: Caenorhabditis elegans LS292, Space radiation+μg


title: 41_N2_L1_41


title: E01-62

value: blood


title: I09-63


title: 38_dTPP_A_38

source_name: complex I mutant gas-1(fc21)_Decyl TPP

value: young adults

value: Decyl TPP - 10 uM


title: D09-63


title: N2 Spaceflgiht Static con

description: This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with spaceflight static condition .

source_name: Caenorhabditis elegans N2, Space radiation+μg

value: Wild-type

value: Spaceflight static condition

value: Space radiation+μg


title: D09-62


title: 37_CoQ10_A_37

source_name: complex I mutant gas-1(fc21)_Coenzyme Q10

value: N2 Bristol

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: 39_N2_L1_39

value: from L1 to young adults

value: whole worms


title: 40_N2_L1_40

value: water

value: E coli OP50


title: D01-63


title: 36_MS010_A_36

source_name: complex I mutant gas-1(fc21)_MS010

value: MS010 (MitoQ) - 10 uM


title: C08-63

value: Sherpa


title: 35_NaAc_A_35

source_name: complex I mutant gas-1(fc21)_N-Acetylcysteine

value: N-Acetylcysteine - 2.5 mM


title: C04-63


title: 20mGyW6/ reference male mouse9

description: 20mGyW6 Cy5

value: tail

source_name: reference male mouse9


title: 34_Lipo_A_34

source_name: complex I mutant gas-1(fc21)_Lipoic Acid

value: Lipoic Acid - 10 uM


title: 33_Orot_A_33

source_name: complex I mutant gas-1(fc21)_Orotic Acid

value: young adults

value: Orotic Acid - 50 uM


title: C02-63_2

source_name: blood

value: blood


title: 20mGyW5/ reference male mouse9

description: 20mGyW5 Cy5


title: reference male mouse9/ 20mGyW5

description: 20mGyW5 Cy3


title: 32_NaAsc_A_32

source_name: complex I mutant gas-1(fc21)_Vitamin C

value: Vitamin C (Sodium Ascorbate) - 100 mM


title: 31_Gas1_A_31

source_name: complex I mutant gas-1(fc21)_untreated


title: D08-62


title: A04-63


title: 20mGyW4/ reference male mouse9

description: 20mGyW4 Cy5


title: reference male mouse9/ 20mGyW3

description: 20mGyW3 Cy3


title: A01-64


title: 20mGyW3/ reference male mouse9

description: 20mGyW3 Cy5


title: 20mGyU7/ reference male mouse9

description: 20mGyU7 Cy5


title: 20mGyU8/ reference male mouse9

description: 20mGyU8 Cy5


title: reference male mouse9/ 20mGyU8

description: 20mGyU8 Cy3


title: 29_oQ10_A_29


title: MT4930 Transport control con

description: This sample is of ced-1 mutant Caenorhabditis elegans. The sample was kept in a incubator at Dalian Maritime University as a transport-control group.

source_name: Caenorhabditis elegans MT4930, Ground 1g,No transport

value: Ground condition without transport to the launch lad at Jiuquan,China


title: 20mGyU6/ reference male mouse9

description: 20mGyU6 Cy5


title: 27_NaAc_A_27

value: N2 Bristol


title: 24_NaAsc_A_24

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)


title: 20mGyWM/ reference male mouse9

description: 20mGyWM Cy5


title: reference male mouse9/ 20mGyU7

description: 20mGyU7 Cy3


title: 25_Orot_A_25


title: reference male mouse9/ 20mGyW1

description: 20mGyW1 Cy3


title: 20mGyW2/ reference male mouse9

description: 20mGyW2 Cy5


title: 20mGyU5/ reference male mouse9

description: 20mGyU5 Cy5


title: 30_dTPP_A_30

value: Decyl TPP - 10 uM


title: 26_Lipo_A_26


title: reference male mouse9/ 20mGyU6

description: 20mGyU6 Cy3


title: 20mGyWF/ reference male mouse9

description: 20mGyWF Cy5


title: 28_MS010_A_28


title: 23_Gas1_A_23


title: reference male mouse9/ 20mGyW2

description: 20mGyW2 Cy3


title: reference male mouse9/ 20mGyWF

description: 20mGyWF Cy3


title: reference male mouse9/ 20mGyWM

description: 20mGyWM Cy3


title: reference male mouse9/ 20mGyU5

description: 20mGyU5 Cy3


title: 20mGyW1/ reference male mouse9

description: 20mGyW1 Cy5


title: GM

city: guangzhou

first: jiafan

last: liu

address: No. 601 West Whampoa Road, Tianhe District, guangzhou

institute: Jinan University

description: lncRNAs expression data from MuSCs in GM (growth media/GM)

hyb_protocol: The CustomArray™ microarray was pre-hybridized in nuclease-free water at 65°C for 10 min, and then loaded the microarray onto the rotisserie in the hybridization oven and incubated at 37°C for 60 min with gentle rotation.The hybridization solution was prepared with labeled RNA target and denatured the hybridization solution at 95°C for 3 min, and then cooled for 20 s on ice. Then the microarray was loaded with the hybridization solution and incubated at 37°C for 16 h with gentle rotation.

scan_protocol: Removed the microarray from the hybridization solution and washed the microarray by using the wash solution to remove nonspecific hybridization. Then covered the semiconductor microarray surface with the imaging solution and loaded the microarray into the scanner to scan. Imaging was performed using a laser scanner GenePix4000B (Molecular Device).

data_processing: The data was analyzed by Guangzhou Ribo Bio Co., Ltd. normalization method is quantile.

source_name: MuSCs-RNA

label_protocol: 1.5 ug total RNA was labelled on Cy5 using ULS.

extract_protocol: Total RNAs was extracted from undifferentiated  MuSCs (GM, growth media/GM) ) and differentiated MuSCs (DM, differentiation media/DM) by TRIzol Reagent (Life Technologies). Then the RNA quality was assessed by formaldehyde agarose gel electrophoresis, quantified spectrophotometrically and Agilent 2200 Bioanalyzer (Agilent, USA).

tag: cell type

value: adult skeletal muscle stem cells (MuSCs)

value: muscle


title: 21_CoQ10_A_21

tag: tissue

value: whole worms

value: water

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: 20mGyU4/ reference male mouse9

description: 20mGyU4 Cy5


title: 22_dTPP_A_22

value: E coli OP50


title: 19_NaAc_A_19

value: N-Acetylcysteine - 2.5 mM


title: 20_MS010_A_20

value: MS010 (MitoQ) - 10 uM


title: DM

description: lncRNAs expression data from MuSCs in DM (differentiation media/DM)


title: reference male mouse9/ 20mGyU4

description: 20mGyU4 Cy3

value: tail


title: reference male mouse9/ 20mGyU2

description: 20mGyU2 Cy3


title: 17_Orot_A_17

value: young adults


title: reference male mouse9/ 20mGyW4

description: 20mGyW4 Cy3


title: 18_Lipo_A_18

value: Lipoic Acid - 10 uM


title: reference male mouse9/ 20mGyW6

description: 20mGyW6 Cy3


title: reference male mouse9/ 20mGyU3

description: 20mGyU3 Cy3


title: 20mGyU2/ reference male mouse9

description: 20mGyU2 Cy5


title: 20mGyU3/ reference male mouse9

description: 20mGyU3 Cy5


title: Blood Sample Case 3

city: Toronto

institute: University of Toronto

description: Genomic DNA extracted from blood had DNA methylation measured using the HumanMethylation 450K  array (Illumina)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: Using an Illumina HiScan

label: Cy3 and Cy5

source_name: Blood

tag: gender

value: Male

value: Blood

tag: disease state

value: Beckwith-Wiedemann Syndrome


title: 16_NaAsc_A_16

value: N2 Bristol

value: Vitamin C (Sodium Ascorbate) - 100 mM


title: Blood Sample Case 2


title: 15_Gas1_A_15

value: homozygous p.R290K in K09A9.5 (NDUFS2 homologue)


title: Control Blood Sample EP17

value: Female

value: Control


title: Blood Sample Case 1


title: Control Blood Sample EP16


title: 14_dTPP_A_14

value: whole worms

value: Decyl TPP - 10 uM


title: 09_Orot_A_9

value: water

value: Orotic Acid - 50 uM


title: 11_NaAc_A_11

value: E coli OP50

value: N-Acetylcysteine - 2.5 mM


title: 13_CoQ10_A_13

value: Coenzyme Q10 (Novasol) - 1:40 dilution


title: 07_Gas1_A_7

value: young adults


title: 10_Lipo_A_10

value: Lipoic Acid - 10 uM


title: 08_NaAsc_A_8


title: 12_MS010_A_12

value: MS010 (MitoQ) - 10 uM


title: Control Blood Sample EP22

value: Male

value: Blood


title: Control Blood Sample EP15


title: 05_N2_A_5

value: N2 Bristol

value: wild-type


title: 04_N2_A_4


title: Control Blood Sample EP21


title: Control Blood Sample EP18


title: 03_N2_A_3


title: 06_N2_A_6


title: 01_N2_A_1


title: lnc-mg

description: miRNAs expression data from myoblast

hyb_protocol: The CustomArray™ microarray was pre-hybridized in nuclease-free water at 65°C for 10 min, and then loaded the microarray onto the rotisserie in the hybridization oven and incubated at 37°C for 60 min with gentle rotation.The hybridization solution was prepared with labeled microRNA target and denatured the hybridization solution at 95°C for 3 min, and then cooled for 20 s on ice. Then the microarray was loaded with the hybridization solution and incubated at 37°C for 16 h with gentle rotation.

source_name: myoblast-RNA_lnc-mg overexpression

extract_protocol: Total RNAs was extracted from cells of lnc-mg overexpression or lnc-mg knockdown by TRIzol Reagent (Life Technologies). Then the RNA quality was assessed by formaldehyde agarose gel electrophoresis, quantified spectrophotometrically and Agilent 2200 Bioanalyzer (Agilent, USA).

tag: cell line

value: muscle


title: 02_N2_A_2


title: CAF3-Replication

first: Ming

last: Tsao

address: 610 University Avenue

department: Ontario Cancer Institute

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: CAF, Replication

growth_protocol: Fibroblasts were cultured from collagenase digested primary adult human pancreatic cancer tissue; samples were minced and plated in DMEM/HamF12 media with 10% bovine serum. Control cell lines were passage 5.

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 Bioanalyzer.

treatment_protocol: Peroxide treated cell lines were exposed to 550 µM hydrogen peroxide for 2 hours to induce cellular senescence; Replication senescence cell lines were continuously passaged until their morphology changed and growth ceased.  Senescent cells stained positively on β-galactosidase assay

value: pancreatic cancer associated fibroblasts

tag: protocol

value: Replication

tag: growth state

value: senescent

value: Female


title: SW620

city: Madrid

first: Ignacio

last: Casal

state: Madrid

address: Ramiro de Maeztu 9

department: Department of Cellular and Molecular Medicine.

country: Spain

institute: Centro de Investigaciones Biológicas

description: Test

data_processing: Data were collected and processed using the Plate Utility and Automation Controller software (Applied Biosystems). U6 snRNA was used as a control. Data analysis was performed using “Expression suite software V1.01” (Applied Biosystems) for comparative CT analysis normalized to U6 snRNA

label: FAM

source_name: colorectal cancer cell

label_protocol: Total RNA was reverse-transcribed with the Multiplex real-time pool set (Applied Biosystems), and real-time products were subsequently amplified with sequence-specific primers on a 7900 HT Real-Time PCR system (Applied Biosystems).

growth_protocol: Cell lines were cultured in DMEM (Gibco-Life Technologies) containing 10% fetal calf serum (FCS) and antibiotics at 37ºC in a 5% CO2-humidified atmosphere.

extract_protocol: Total RNA was purified using mirVana miRNA Isolation Kit (Applied Biosystems).

treatment_protocol: No treatment

value: highly metastatic


title: CAF3-Peroxide

source_name: CAF, Peroxide

value: Peroxide


title: CAF3-Control

source_name: CAF, Control

value: Control

value: non-senescent


title: SW480

description: Control

value: poorly metastatic


title: KM12SM

description: Test


title: control

description: miRNAs expression data from myoblast


title: shRNA-NC

description: miRNAs expression data from myoblast


title: CAF2-Replication


title: CAF2-Peroxide


title: Control Blood Sample EP13


title: Control Blood Sample EP8


title: Control Blood Sample EP9


title: Control Blood Sample EP11


title: CAF2-Control


title: Control Blood Sample EP12


title: Control Blood Sample EP5


title: Control Blood Sample EP10


title: Control Blood Sample EP4


title: strain T73, time point 96h, replicate 2

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

institute: Centro Superior de Investigaciones Científicas

description: Biological replicate two of three

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing:
Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After lowess normalization, data were filtered to remove spots flagged as not found.
Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.

organism: Saccharomyces cerevisiae

source_name: strain T73, time point 96h, replicate 2

label_protocol:
2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA).
The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.

growth_protocol: Fermentations in synthetic agave must at 28 ºC

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: strain

tag: time point

source_name: sample mix

value: mixed


title: Control Blood Sample EP3


title: Control Blood Sample EP52


title: strain T73, time point 96h, replicate 1

description: Biological replicate one of three

source_name: strain T73, time point 96h, replicate 1


title: strain T73, time point 48h, replicate 1

description: Biological replicate one of three

source_name: strain T73, time point 48h, replicate 1


title: strain ITD00185, time point 96h, replicate 3

description: Biological replicate three of three


title: strain ITD00185, time point 96h, replicate 2

description: Biological replicate two of three


title: Control Blood Sample EP1


title: strain T73, time point 48h, replicate 3

description: Biological replicate three of three

source_name: strain T73, time point 48h, replicate 3


title: Control Blood Sample EP2


title: KM12C

description: Control


title: strain T73, time point 48h, replicate 2

description: Biological replicate two of three

source_name: strain T73, time point 48h, replicate 2


title: strain ITD00185, time point 48h, replicate 3

description: Biological replicate three of three


title: THP1 71239505

status: Public on Feb 28 2017

city: Istanbul

first: Nihan

middle: Erginel

last: Unaltuna

address: Capa Millet Cad. Fatih

department: Genetics

country: Turkey

institute: University of Istanbul

description: Chip-chip of CGP52608-treated THP1 cells for ROR-alpha

hyb_protocol: Hybridization was performed by NimbeGen

scan_protocol: Arrays were scanned on the scanner in NimbleGen (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction.

source_name: ROR-alpha ChIP DNA from CGP52608 treated THP1 cells

label_protocol: Amplified ChIP DNA was labelled by NimbeGen as a service.

growth_protocol: THP1 cells were grown to confluence in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 1% penicilin/strerptomycin at 37 oC with 5% CO2.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature. Before chromatin fixation, medium of HUVEC was carefully removed avoiding the disturbance of the cells. Then formaldehyde was added directly to newly supplied medium. For chromatin fixation of THP1, formaldehyde was added directly to newly supplied medium. The crosslinking reaction was quenched with 0,125 M glycine for 5 min. The cells were washed twice with ice-cold PBS supplemented with proteinase inhibitor cocktail. Then, the cells were tranferred to pre-chilled tube for centrifugation. Nuclear extraction from cell pellets was performed with Millipore EZ-ChIP Chromatin Immunoprecipitation Kit. Nuclear pellets were resuspended in 0,5 ml nuclear lysis buffer supplemented by Kit. Crosslinked chromatin was sheared to 200-1,000 bp with sonicator (Thermo Fisher Scientific). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. 50 μl sonicated supernatant was diluted 10-fold in ChIP dilution buffer. Diluted chromatin supernatant was then incubated overnight with 1 µg of polyclonal anti-RORα antibody (Santa Cruz Biotechnology, sc-133973)  or 1 μg anti-IgG antibody (Millipore) in the presence of Protein A and G, at 4C. After the incubation, immune complexes were collected by magnetic seperator and washed with wash buffers (Low Salt Immune Complex Wash Buffer, High Salt Immune Complex Wash Buffer, LiCl Immune Complex Wash Buffer and TE Buffer) at room temperature. Protein A and G magnetic beads were re-suspended with 100 μl ChIP elution Buffer plus 1 μ proteinase K and incubated at 62 C for 2 hours with rotation, then 95 C for 10 min. DNA was recovered with spin fitler and collected in 50 μl Elution Reagent. Eluted DNA was then quantified and amplified by using GenomePlex Whole Genome Amplification (WGA) kit (Sigma) to yield required amount for NimbleGen ChIP-chip array.

treatment_protocol: THP1 cells were cultured for 24 hours in the presence of 5 nM CGP52608.

tag: treatment

value: Monocytic cell line

tag: chip antibody

value: ROR-alpha

source_name: IgG ChIP DNA from CGP52608 treated THP1 cells

value: anti IgG


title: Control Blood Sample EP7

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications. Prior to extraction, red cells were lysed by exposure of the sample to 2x Lysis Buffer for 5 minutes in ice. The remaining cells were pelletted by centrifugation at 2300 RPM at 4 degrees celsius.

value: Male

value: Blood


title: HUVEC 71158605

description: Chip-chip of CGP52608-treated HUVEC cells for ROR-alpha

source_name: ROR-alpha ChIP DNA from CGP52608 treated HUVEC cells

growth_protocol: HUVEC cells were grown to confluence in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 1% penicilin/strerptomycin at 37 oC with 5% CO2.

treatment_protocol: HUVEC cells were cultured for 24 hours in the presence of 5 nM CGP52608.

value: Endothelial cell line

source_name: IgG ChIP DNA from CGP52608 treated HUVEC cells


title: THP1 71157105


title: strain ITD00185, time point 48h, replicate 2

description: Biological replicate two of three


title: HUVEC 71158305


title: THP1 71158005


title: THP1 71157705


title: strain ITD00185, time point 48h, replicate 1

description: Biological replicate one of three


title: HUVEC 71198305


title: THP1 71553505


title: strain T73, time point 96h, replicate 3

description: Biological replicate three of three

source_name: strain T73, time point 96h, replicate 3


title: THP1 71189005


title: HUVEC 71167105


title: THP1 71193205


title: shRNA

description: miRNAs expression data from myoblast

value: muscle


title: CAF1-Control

value: pancreatic cancer associated fibroblasts


title: THP1 71190505


title: Control Blood Sample EP14

source_name: Blood


title: Control Blood Sample EP6


title: CAF1-Replication

value: Replication


title: HUVEC 71286105


title: HUVEC 71166805


title: THP1 71198905


title: HUVEC 71231105


title: HUVEC 71228405


title: HUVEC 71226605


title: HUVEC 71228105


title: THP1 71198605