title: Male_liver_control_replicate 1

description:
Gene expression in the livers of control male Fisher 344 rats
0_NCT_S01


title: ee78

status: Public on Jul 18 2015

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A) (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: gender

value: Male

tag: population

value: Estonians

tag: region

value: Europe

tag: tissue

value: blood


title: Male_liver_control_replicate 4

type: RNA

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

country: USA

institute: US-FDA National Center for Toxicological Research

description:
Gene expression in the livers of control male Fisher 344 rats
0_NCT_S04

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE Oligo Microarrays (G4853A-028279) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the 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.

extract_protocol: Total RNA was extracted from liver tissue using RNeasy Mini kits (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000C spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male F344 rats were treated by gavage 5 days/week with 0.92 and 2 mg furan/kg bw for 104 weeks. Experimental and control rats were euthanized by exsanguination following deep isoflurane anesthesia 24 hours after the last treatment. The liver was snap-frozen immediately in liquid nitrogen and stored at −80 °C for subsequent analyses.

tag: strain

value: Fisher 344

value: male

tag: age

value: 110 weeks

tag: treated with

value: vehicle (control)

value: liver


title: WTvsM_10minOxidation_rep3

city: Hamilton

first: Ken

last: Belanger

state: NY

address: 13 Oak Drive

department: Biology

institute: Colgate University

description: Biological Replicate 3 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .

hyb_protocol: RNA probes were hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC

scan_protocol: Scanned my MoGene, LC on Agilent Technologies Scanner G2505B US22502547. Protocols are GE2-v5_95_Feb07  for replicate 1/3 and GE2-v5_10_Apr08 for replicates 2/3 and 3/3

data_processing: Scanner performed background correction and linear lowess normalization. Further normalization took place by using GeneSpring GX 13.0 to perform a log2 transformation and percentile shift to the 75th percentile

organism: Saccharomyces cerevisiae

source_name: WT 10minOxidation

label_protocol: RNA generated from wild-type cell extracts was labeled with Cy3 and from ∆Kap108 cells was labeled with Cy5 by MoGene, LC

growth_protocol: Wild-type and kap108∆ cells were grown to A600 = 0.3 in 1L YPD. Two hundred ml of culture was removed, spun at 3,000rpm for 10 min, and frozen at -80 °C. This sample was used as the pre-oxidation condition.

extract_protocol: RNA from cell pellets was isolated using the RiboPure-Yeast RNA isolation kit (Ambion, Inc.)

treatment_protocol: Fresh H2O2 was added to the remaining culture (from growth protocol) to a 1.0 mM final concentration and each culture incubated for 10 min at 30 °C, after which 200 ml of culture was removed, spun, and frozen as above to generate the 10minOxidation samples. This was repeated with another 200 ml of cells 1 hr after H2O2 addition to generate the 60minOxidation samples. The remaining culture was then pelleted, YPD+H2O2 media removed, cells resuspended in 250 ml YPD, and culture incubated for 1 hr at 30 °C. Cells were then pelleted and frozen as before to generate the 120minOxidation samples, which actually are 60 min oxidative stress followed by 60 min no oxidative stress.

tag: genotype

value: wildtype

source_name: ∆Kap108 10minOxidation


title: pks1 knockout Mound rep1

city: Pune

first: Bharat

middle: Ravi

last: Iyengar

address: Dr Homi Bhabha Road

department: Chemical Engineering and Process Development

country: India

institute: CSIR-National Chemical Laboratory

description: US45103024_252202010006_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: Equal amounts of cRNA were mixed and hybridized against each microarray at 65°C for 17 hours and washed afterwards

scan_protocol: The arrays were scanned using Agilent Technologies Scanner G2505B and gene expression information was extracted from microarray scan data by Agilent Feature Extraction (FE) software

data_processing: The normalization was done using GeneSpring GX using the Per Chip and Per Gene Normalization method. Between-array quantile normalization was implemented using the Limma package in R (http://www.R-project.org/)

organism: Dictyostelium discoideum AX2

source_name: Mound

label_protocol: Samples were labeled with Cy3 (for one set of duplicates) and Cy5 (for the second set of duplicates) using Agilent’s Quick-amp labeling kit and T7 promoter based-linear amplification was used to generate labeled complementary RNA.

growth_protocol: Dictyostelium AX2 cells were used for the entire study and grown at 22ºC in HL-5 axenic medium.

extract_protocol: Total RNA and cRNA were further purified using Qiagen’s RNeasy purification kit and RNA quality was checked using Bioanalyzer.

treatment_protocol: Dictyostelium cells were collected by centrifugation at 3000 rpm for 2 min. and washed with 1X KK2 buffer thrice. The pellet was resuspended in 1X KK2 buffer and the cell suspension was poured on to non-nutrient agar (NNA) plate. After cold synchronization for 9 hrs., the plates were incubated at 22ºC for development.

tag: genotype/variation


title: pks1 knockout Streaming rep1

description: US45103024_252202010008_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Streaming


title: ee72


title: pks1 knockout Loose Aggregate rep1

description: US45103024_252202010005_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Loose Aggregate


title: ee68


title: ee66


title: ee59

value: Female


title: WTvsM_10minOxidation_rep1

description: Biological Replicate 1 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .


title: pks1 knockout Fruiting Body rep1

description: US45103024_252202010004_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Fruiting Body


title: WTvsM_10minOxidation_rep2

description: Biological Replicate 2 of 3. RNA probes were labeled and hybridized to Agilent Yeast 4x44K microarray kit by MoGene, LC .


title: pks1 knockout Early Culminant rep1

description: US45103024_252202010003_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Early Culminant


title: ee86


title: pks1 knockout Amoeboid rep1

description: US45103024_252202010002_S01_GE2-v5_95_Feb07_1_3.txt

source_name: Amoeboid


title: WTvsM_Pre_oxidation_rep3

source_name: WT Pre-oxidation

source_name: ∆Kap108 Pre-oxidation


title: WTvsM_Pre-oxidation_rep2


title: WTvsM_120minOxidation_rep3

source_name: WT 60minPostOxidation

source_name: ∆Kap108 60minPostOxidation


title: pks14 knockout Slug rep1

description: US45103024_252202010007_S01_GE2-v5_95_Feb07_1_2.txt

source_name: Slug


title: NPC-Training Set-65

status: Public on Jul 17 2015

city: Toronto

first: Jeff

last: Bruce

state: Ontario

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: Nanostring nCounter Analysis System

scan_protocol: Nanostring nCounter Analysis System

data_processing: variance stabilization and normalization (vsn) called through the NanoStringNorm package for R

label: Nanostring fluorophore barcode

source_name: FFPE Nasopharyngeal Carcinoma Biopsy

label_protocol: Nanostring nCounter Analysis System

extract_protocol: Recover All Total Nucleic Acid Isolation Kit for FFPE (Ambion, Inc)

treatment_protocol: Xylene de-paraffinization

tag: t

tag: n

tag: chemo


title: NPC-Training Set-66


title: NPC-Training Set-67


title: NPC-Training Set-7


title: NPC-Training Set-70


title: WTvsM_Pre-oxidation_rep1


title: NPC-Training Set-77


title: NPC-Training Set-76


title: NPC-Training Set-75


title: NPC-Training Set-73


title: NPC-Training Set-68


title: NPC-Training Set-71


title: NPC-Training Set-72


title: NPC-Training Set-74


title: NPC-Training Set-69


title: NPC-Training Set-62


title: NPC-Training Set-63


title: AV fistula patient 1

city: Hirosaki

first: Yasuhiro

last: Hashimoto

state: Aomori

address: 90 Yamazaki Kozawa

department: Urology

country: Japan

institute: Oyokyo Kidney Research Institute Hirosaki Hospital

description: Gene expression of venous segment of AV fistula

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

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

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1

source_name: venous segment of AV fistula

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

extract_protocol: We obtained six specimens from overflowing AV fistulae and four from normal control cephalic veins. Surgical specimens were cut into 0.5-cm cubes or smaller and stored in RNA later (Ambion, Austin, TX) overnight at 4 ± 3℃, then stored at –80℃ until RNA extraction.

value: venous segment of AV fistula


title: AV fistula patient 6

value: female


title: NPC-Training Set-64


title: control patient 3

description: Gene expression of normal chephalic vein

source_name: normal cephalic vein

value: normal cephalic vein


title: AV fistula patient 3


title: AV fistula patient 2


title: NPC-Training Set-61


title: AV fistula patient 4


title: NPC-Training Set-60


title: control patient 1


title: NPC-Training Set-6


title: AV fistula patient 5


title: NPC-Training Set-59


title: NPC-Training Set-56


title: NPC-Training Set-57


title: NPC-Training Set-58


title: NPC-Training Set-47


title: NPC-Training Set-48


title: NPC-Training Set-55


title: NPC-Training Set-53


title: NPC-Training Set-50


title: NPC-Training Set-5


title: NPC-Training Set-54


title: control patient 4


title: NPC-Training Set-49


title: NPC-Training Set-45


title: NPC-Training Set-52


title: control patient 2


title: NPC-Training Set-44


title: NPC-Training Set-43

value: Tx


title: NPC-Training Set-41


title: NPC-Training Set-42


title: NPC-Training Set-46


title: NPC-Training Set-34


title: NPC-Training Set-33


title: NPC-Training Set-32


title: NPC-Training Set-31


title: NPC-Training Set-30


title: NPC-Training Set-23


title: NPC-Training Set-24


title: NPC-Training Set-29


title: NPC-Training Set-26


title: NPC-Training Set-3


title: NPC-Training Set-28


title: NPC-Training Set-25


title: NPC-Training Set-22


title: NPC-Training Set-18


title: NPC-Training Set-35


title: NPC-Training Set-37


title: NPC-Training Set-36


title: NPC-Training Set-39


title: NPC-Training Set-16


title: NPC-Training Set-40


title: NPC-Training Set-38


title: NPC-Training Set-21


title: NPC-Training Set-20


title: NPC-Training Set-4


title: NPC-Training Set-19


title: NPC-Training Set-2


title: NPC-Training Set-27


title: NPC-Training Set-15


title: NPC-Training Set-17


title: NPC-Training Set-125


title: NPC-Training Set-14


title: NPC-Training Set-124


title: NPC-Training Set-106


title: NPC-Training Set-104


title: NPC-Training Set-108


title: NPC-Training Set-107


title: NPC-Training Set-111


title: NPC-Training Set-112


title: NPC-Training Set-110


title: NPC-Training Set-117


title: NPC-Training Set-118


title: NPC-Training Set-102


title: NPC-Training Set-114


title: NPC-Training Set-116


title: NPC-Training Set-103


title: NPC-Training Set-13


title: NPC-Training Set-119


title: NPC-Training Set-120


title: NPC-Training Set-12


title: NPC-Training Set-121


title: NPC-Training Set-122


title: NPC-Training Set-11


title: NPC-Training Set-115


title: NPC-Training Set-113


title: NPC-Training Set-101


title: NPC-Training Set-109


title: NPC-Training Set-10


title: NPC-Training Set-100


title: NPC-Training Set-123


title: NPC-Training Set-105


title: NPC-Training Set-1


title: Normal Nasopharynx-Validation Set-N9

source_name: FFPE Nasopharyngeal epithelium from quadroscopy


title: Normal Nasopharynx-Validation Set-N10


title: Normal Nasopharynx-Validation Set-N5


title: Normal Nasopharynx-Validation Set-N6


title: NPC-Validation Set-99


title: Normal Nasopharynx-Validation Set-N8


title: Normal Nasopharynx-Validation Set-N7


title: NPC-Validation Set-96


title: NPC-Validation Set-89


title: Normal Nasopharynx-Validation Set-N4


title: NPC-Validation Set-97


title: NPC-Validation Set-9


title: NPC-Validation Set-98


title: Normal Nasopharynx-Validation Set-N3


title: NPC-Validation Set-92


title: NPC-Validation Set-95


title: Normal Nasopharynx-Validation Set-N2


title: NPC-Validation Set-93


title: NPC-Validation Set-88


title: NPC-Validation Set-90


title: NPC-Validation Set-86


title: NPC-Validation Set-87


title: Normal Nasopharynx-Validation Set-N1


title: NPC-Validation Set-91


title: NPC-Validation Set-84


title: NPC-Training Set-51


title: NPC-Validation Set-94


title: NPC-Validation Set-82


title: NPC-Validation Set-81


title: NPC-Validation Set-80


title: NPC-Validation Set-8


title: NPC-Validation Set-77


title: NPC-Validation Set-83


title: NPC-Validation Set-78


title: NPC-Validation Set-72


title: NPC-Validation Set-76


title: NPC-Validation Set-7


title: NPC-Validation Set-79


title: NPC-Validation Set-68


title: NPC-Validation Set-75


title: NPC-Validation Set-67


title: NPC-Validation Set-74


title: NPC-Validation Set-85


title: NPC-Validation Set-73


title: NPC-Validation Set-65


title: NPC-Validation Set-71


title: NPC-Validation Set-70


title: NPC-Validation Set-63


title: NPC-Validation Set-62


title: NPC-Validation Set-66


title: NPC-Validation Set-64


title: NPC-Validation Set-6


title: NPC-Validation Set-60


title: NPC-Validation Set-61


title: NPC-Validation Set-59


title: NPC-Validation Set-58


title: NPC-Validation Set-56


title: NPC-Validation Set-53


title: NPC-Validation Set-51


title: NPC-Validation Set-50


title: NPC-Validation Set-49


title: NPC-Validation Set-48


title: NPC-Validation Set-47


title: NPC-Validation Set-52


title: NPC-Validation Set-55


title: NPC-Validation Set-54


title: NPC-Validation Set-46


title: NPC-Validation Set-42


title: NPC-Validation Set-5


title: NPC-Validation Set-44


title: NPC-Validation Set-45


title: NPC-Validation Set-40


title: NPC-Validation Set-39


title: NPC-Validation Set-4


title: NPC-Validation Set-43


title: NPC-Validation Set-69


title: NPC-Validation Set-41

value: Nx


title: NPC-Validation Set-38


title: NPC-Validation Set-37


title: NPC-Validation Set-35


title: NPC-Validation Set-57


title: NPC-Validation Set-36


title: NPC-Validation Set-34


title: NPC-Validation Set-31


title: NPC-Validation Set-29


title: NPC-Validation Set-27


title: NPC-Validation Set-32


title: NPC-Validation Set-33


title: NPC-Validation Set-2


title: NPC-Validation Set-26


title: NPC-Validation Set-21


title: NPC-Validation Set-22


title: NPC-Validation Set-25


title: NPC-Validation Set-24


title: NPC-Validation Set-28


title: NPC-Validation Set-17


title: NPC-Validation Set-23


title: NPC-Validation Set-18


title: NPC-Validation Set-30


title: NPC-Validation Set-3


title: NPC-Validation Set-19


title: NPC-Validation Set-20


title: NPC-Validation Set-112


title: NPC-Validation Set-110


title: NPC-Validation Set-109


title: NPC-Validation Set-114


title: NPC-Validation Set-108


title: NPC-Validation Set-111


title: NPC-Validation Set-115


title: NPC-Validation Set-12


title: NPC-Validation Set-121


title: NPC-Validation Set-14


title: NPC-Validation Set-118


title: NPC-Validation Set-119


title: NPC-Validation Set-120


title: NPC-Validation Set-15


title: NPC-Validation Set-16


title: NPC-Validation Set-13


title: NPC-Validation Set-107


title: NPC-Validation Set-117


title: NPC-Validation Set-105


title: NPC-Validation Set-104


title: NPC-Validation Set-106


title: NPC-Validation Set-11


title: NPC-Validation Set-102


title: NPC-Validation Set-101


title: NPC-Validation Set-116


title: NPC-Validation Set-113


title: NPC-Validation Set-100


title: NPC-Validation Set-103


title: NPC-Validation Set-10


title: Normal Nasopharynx-Training Set-N5


title: Normal Nasopharynx-Training Set-N7


title: Normal Nasopharynx-Training Set-N2


title: Normal Nasopharynx-Training Set-N4


title: Normal Nasopharynx-Training Set-N6


title: Normal Nasopharynx-Training Set-N3


title: NPC-Training Set-99


title: NPC-Validation Set-1


title: ET-2-treated RGCs, biological rep3

city: Fort Worth

first: Shaoqing

last: He

state: TX

address: 3500 Camp Bowie BLVD

department: Cell Biology and Immunology

institute: UNTHSC

description: Gene expression in RGCs treated with 100 nM ET-2 for 24 hours

hyb_protocol: cRNA were hybridized for 16 hr at 45oC on Affymetrix Rat Genome 230 2.0 Microarray. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Primary rat RGCs isolated from post-natal day 4-6 rat pups

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: Primary rat RGCs were isolated from post-natal day 4-6 rat pups using Thy-1.1 antibody-panning methods and cultured with serum-free DMEM containing brain-derived neurotrophic factor (50 ng/mL), ciliary neurotrophic factor (10 ng/mL), and forskolin (5 ng/mL) at 37 °C in a humidified atmosphere of 10% CO2 and 90% air.

extract_protocol: Trizol extraction of total RNA was performed followed purification with Qiagen RNeasy Mini kit.

treatment_protocol: After 7 day in culture, RGCs was treated with serum-free DMEM without neurotropic factors overnight followed with 100nM ET-1, ET-2 or ET-3 for 24 hours, and untreated RGCs served as the control group.

value: Sprague-Dawley

value: Retina

tag: cell type

value: retinal ganglion

value: post-natal day 4-6


title: NPC-Training Set-98

value: Male


title: Normal Nasopharynx-Training Set-N1


title: ET-3-treated RGCs, biological rep3

description: Gene expression in RGCs treated with 100 nM ET-3 for 24 hours


title: NPC-Training Set-97


title: ET-1-treated RGCs, biological rep2

description: Gene expression in RGCs treated with 100 nM ET-1 for 24 hours


title: ET-1-treated RGCs, biological rep3


title: untreated RGCs, biological rep2

description: Gene expression in RGCs treated with vehicle for 24 hours


title: untreated RGCs, biological rep3


title: untreated RGCs, biological rep1


title: CV-NC/Nga rep2

city: Fukuoka

first: Miho

last: Shiratori-Hayashi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Life Innovation

institute: Graduate School of Pharmaceutical Science, Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with lumi package in R.

organism: Mus musculus

source_name: Mouse cervical spinal cord

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification kit.

growth_protocol: SPF-NC/Nga mice were maintained under a specific-pathogen-free condition. CV-NC/Nga mice were maintained under a conventional condition.

extract_protocol: Total RNA was extracted with TRIsure according to the manifacturer's protocol. Quality control was performed with Experion RNA Analysis kit.

tag: treatment

value: conventiional

tag: phenotype

value: atopic dermatitis

value: NC/Nga

value: 9 weeks

value: cervical spinal cord


title: ET-3-treated RGCs, biological rep2


title: ET-2-treated RGCs, biological rep1


title: ET-1-treated RGCs, biological rep1


title: ET-2-treated RGCs, biological rep2


title: NPC-Training Set-92


title: dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 3

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA (50mg/ml), Biarray Eukaryotic Hybridization Controls (Enzo Life Sciences); heated for 5 min at 65 deg C, 5 min at 99 deg C, 5 min at 45 deg C, centrifuge top speed for 5 min; Hybridize 16 hrs at 45 degC at 60 RPM

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

data_processing: For gene expression analysis, arrays were normalized using RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix, Santa Clara, CA).

source_name: utrn+/-;mdx

label_protocol: Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling Kit (Enzo)

growth_protocol: Mouse quadriceps muscles dissected from 20 week-old dystrophic mice.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies), according to manufacturer’s instructions. RNA concentration was determined spectrophotometrically using a Nanodrop ND-100 (Nanodrop Technologies).  Samples were DNAse treated using RQ1 DNAse (Promega) for 30 minutes at 37⁰C, reaction was stopped with a 25:24:1 phenol: chloroform: isoamyl alcohol mixture (Malinckrodt, Fischer, Sigma) and centrifuged 5 minutes (14,000 x g; room temperature).  A chloroform phase separation was performed; the aqueous layer was removed and ethanol (Fisher) precipitated.  The pellet was washed (75% ethanol), centrifuged (14,000 x g, 10 minutes, 4⁰C), air dried (5 minutes) and re-suspended in autoclaved millipore filtered water.  DNAse treated RNA concentration was determined spectrophotometrically and samples were stored at -80⁰C.  Samples for microarray analysis were further purified using the RNeasy mini kit (Qiagen) RNA cleanup protocol and final RNA concentrations were determined. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  A 100 ng aliquot of total mRNA was linearly amplified.

treatment_protocol: 10 mg/kg x day lisinopril plus 37.5 mg/kg x day spironolactone delivered via water bottles from 4-20 weeks-of-age, or untreated water bottles

value: spironolactone plus lisinopril-treated

value: 20 weeks

tag: Sex


title: dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 2

value: male


title: NPC-Training Set-93


title: NPC-Training Set-96


title: NPC-Training Set-94


title: NPC-Training Set-95


title: dystrophic mouse quadriceps, untreated, biological replicate 2

value: untreated


title: NPC-Training Set-91

value: Female


title: dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 1


title: CV-NC/Nga rep1


title: dystrophic mouse quadriceps, untreated, biological replicate 3

value: female


title: ET-3-treated RGCs, biological rep1


title: dystrophic mouse quadriceps, untreated, biological replicate 1


title: SPF-NC/Nga rep1

value: specific pathogen free

value: normal


title: NPC-Training Set-9


title: SPF-NC/Nga rep2


title: NPC-Training Set-89


title: Early_D3b_test

city: Hampton

first: Venky

last: Ramakrishna

state: NJ

address: Perryville III Bldg., 53 Frontage Rd.

institute: Celldex Therapeutics

description: Gene expression

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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C US22502695) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and quantile normalized median signal intensities

source_name: T cell_co-stimulated_early

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: Purified T cells were stimulated in flat-bottomed multiwell plates (24 or 96 wells) with precoated mAbs. Cultures were maintained for 3-7 days in RPMI culture medium supplemented with 10% FBS and antibiotics at 37C in a humdified incubator. For microarray experiments, cells were harvested, washed in PBS once and pellets snap frozen. Samples were shipped to Miltenyi-Biotec's OMICS lab in Germany or a corresponding wet lab affiliated with FiosGenomics, UK for RNA extraction, array hybridization and bioinformatics work flows.

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: Purified T cells were stimulated in flat-bottomed multiwell plates (24 or 96 wells) with precoated mAbs. Either cell culture supes (cytokine ELISA), Cells (CFSE dilution and marker analysis) or cell pellets were used for microarray experiments

tag: donor id

value: Donor 3

value: Peripheral blood

value: purified T cells

tag: stimulated with

value: anti-CD27 mAb + anti-CD3 mAb

tag: treatment duration/stage

value: 4 hrs (early)


title: NPC-Training Set-90

tag: gender

value: Male


title: NPC-Training Set-88


title: NPC-Training Set-87


title: NPC-Training Set-86


title: NPC-Training Set-85


title: NPC-Training Set-84


title: NPC-Training Set-83


title: Early_D4b_test

description: Gene expression

value: Donor 4

tag: tissue


title: NPC-Training Set-82


title: Early_D1a_iso

description: Gene expression

source_name: T cell_isotype-matched control_early

value: Donor 1

value: control mAb + anti-CD3 mAb


title: Early_D2b_test

description: Gene expression

value: Donor 2


title: NPC-Training Set-81


title: PC3_p21_I

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

country: China

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

description:
PANEL I PC3 p21
miRNA was isolated by p21 probe

data_processing:
Perform initial data analysis using the software supplied with the real-time PCR instrument to obtain raw Cq values (Cp or Ct, depending on PCR instrument). Normalization and further data analysis with the GenExq PCR analysis software (www.exiqon.com/mirna-pcranalysis).
Raw Cq values > 35 or Undetermined was normalized to 35
For the normalization it uses the average of five housekeeping genes: UniSp6 CP.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)
the fold_change.txt  reports test/control.

label: SYBR Green

label_protocol: RT-PCR protocol: Expression analysis of miRNAs was used the Exiqon multiplex miRNA arrays according to the manufacturer’s instructions.

growth_protocol: HepG2 cells were cultured in EMEM media containing 10% FBS. PC-3 was cultured in Ham's F12K media containing 10% FBS. Cells were maintained at 37℃ and 5% CO2.

extract_protocol: The associated mRNA  was purified using Streptavidin Dynabeads (M-280) and isolated by TRIzol.

treatment_protocol: The probe of mRNA was transfected into HepG2 and PC-3 cells to hybridize  mRNA for 24 hours.

tag: cell line

tag: isolation method

value: miRIP

tag: isolation probe

value: p21 probe


title: PC3_p21_II

description:
PANEL II PC3 p21
miRNA was isolated by p21 probe


title: Early_D4a_iso

description: Gene expression


title: NPC-Training Set-80

tag: age


title: Early_D1b_test

description: Gene expression


title: Early_D3a_iso

description: Gene expression


title: Late_D2_Test

description: Gene expression

source_name: T cell_co-stimulated_late

value: 72 hrs (late)


title: NPC-Training Set-8

value: Female


title: PC3_control_II

description:
PANEL II PC3 control
miRNA was isolated by control probe

value: control probe


title: Early_D2a_iso

description: Gene expression


title: Late_D1_Test

description: Gene expression


title: NPC-Training Set-78


title: PC3_control_I

description:
PANEL I PC3 control
miRNA was isolated by control probe


title: HepG2_STAT3_II

description:
PANEL II HepG2 STAT3
miRNA was isolated by STAT3 probe

value: STAT3 probe


title: Late_D3_Test

description: Gene expression


title: HepG2_STAT3_I

description:
PANEL I HepG2 STAT3
miRNA was isolated by STAT3 probe


title: Late_D3_Iso

description: Gene expression

source_name: T cell_isotype-matched control_late


title: Late_D2_Iso

description: Gene expression


title: Late_D1_Iso

description: Gene expression


title: HepG2_p21_II

description:
PANEL II HepG2 p21
miRNA was isolated by p21 probe


title: HepG2_control_II

description:
PANEL II HepG2 control
miRNA was isolated by control probe


title: HepG2_p21_I

description:
PANEL I HepG2 p21
miRNA was isolated by p21 probe


title: NPC-Training Set-79


title: HepG2_control_I

description:
PANEL I HepG2 control
miRNA was isolated by control probe


title: SKOV3Tx600

status: Public on Jul 16 2015

city: Kwei-San

first: Ching-Kuey

middle: Chuck

last: Chao

state: Tao-Yuan

address: 259, Wen-Hwa 1 Rd

department: Biochemistry and Molecular Biology

country: Taiwan

institute: Chang-Gung University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx OneArray Plus Hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The scanned images were analyzed with Agilent G2505C Microarray Scanner and processing by GenePix software GenePix Pro 4.1.1.44 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing:
After hybridization, washing and drying steps, the slides were scanned using an Agilent G2505C Microarray Scanner. The Cy5 ﬂuorescent intensities of each spot were analyzed using the GenePix Pro 4.1.1.44 software (Molecular Devices).  Global median normalization were applied to spots without flag and generated the normalized signal Intensities.
Using Rosetta Resolver System (Rosetta Biosoftware) Error Model to calculate normalized intensity, CV, log2 ratio and p-value (differential expressed). Briefly, exclude probes which flag are -50 within all arrays, squeeze replicated probes within one chip and averaged, then normalize intensities by median scaling and take average of normalized intensity (mean).

source_name: 600 nM Taxol resistant Human Ovarian Cancer cell line SKOV3

label_protocol: Cyanine-5 (Cy5) 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 RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: SKOV3 cells (American Type Culture Collection, Rockville, MD, USA) were grown as monolayers in a 1:1 mixture of DMEM/nutrient F-12 Ham (Life Technologies, Grand Island, NY, USA) supplemented with 1% (w/v) penicillin/streptomycin and 10% (v/v) fetal bovine serum (FBS) at 37°C in a humidified atmosphere containing 5% CO2. Chemoresistant cell lines were maintained in selective medium containing the taxol concentration  used for selection, 50nM and 600nM.

extract_protocol: RNA extraction  using TRIZOL reagent. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are   established as A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 indicating acceptable RNA purity. RIN values are   ascertained using Agilent RNA 6000 Nano assay to determine RNA integrity. Pass criteria for RIN value is   established at ≥ 6 indicating acceptable RNA integrity. gDNA contamination was evaluated by gel   electrophoresis.

treatment_protocol: Taxol-resistant ovarian cancer cells were successfully developed from the parental, drug-sensitive, ovarian cancer cell line SKOV3 by administrating taxol in a conventional dose-escalation schedule. The concentration of taxol was increased stepwise, starting at 50 nM and finishing at 600 nM. Parental SKOV3 cells were first exposed to 50 nM of taxol for 2 months followed by exposure to stepwise double concentrations of taxol for a further 2 months of treatment. Chemoresistant cell lines were maintained in selective medium containing the taxol concentration used for selection of resistance.

value: taxol-resistant SKOV3/Tx600

tag: taxol concentration (nm)


title: ADMA treatment 96h, biological rep1

first: houkai

last: li

state: Shanghai

address: 1200 Cailun Road, Building 1, Room 1531, Pudong New District

institute: Shanghai University of Traditional Chinese Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_PLUS_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with The Affymetrix® GeneChip® Command Console® software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: LoVo cells in serum free medium and treated with 10uM ADMA for 96h

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

growth_protocol: Human colon cancer LoVo cells (CCL-229) from ATCC were routinely cultured in 10cm dishes at 37 ℃ in a humidified atmosphere of 5% CO2 in 10% FBS DMEM supplemented with 100 U/ml penicillin and 100 mg/ml streptomycin.

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

treatment_protocol: Cells were divived into 3 groups, control, serum free and serum free plus 10uM ADMA for 96h, respectively, before the harvest for RNA extraction.

value: LoVo cells


title: Serum free 96h,  biological rep3

source_name: LoVo cells in serum free medium for 96h


title: Control

city: Nan jing

first: He

last: Cui

address: 87# Dingjiaqiao Road

institute: Southeast University

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing:
Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Raw data were normalized by Expression Console.

source_name: Vector were transfected into gastric cancer cell

label_protocol: GeneChip  WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: All cell lines were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum 100 U/ml of penicillin and 100 mg/ml streptomycin in a humidified incubator with a 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA were amplified, labeled and purified by using Affymetrix  WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US).

treatment_protocol: Expression plasmids were transfected into MKN45 and BGC-823 cells using Lipofectamine 2000 according to the manufacturer’s instructions. Cells were subsequently selected with medium containing 0.4 µg/ml puromycin for 30 days, and polyclonal cell lines were established.

value: cell transfected with vector


title: Serum free 96h,  biological rep2


title: ADMA treatment 96h, biological rep4


title: Control cells, biological rep2

source_name: LoVo cells in normal culture medium


title: SKOV3

source_name: Human Ovarian Cancer cell line SKOV3

value: parental SKOV3


title: ADMA treatment 96h, biological rep3


title: 6_GFPscr

city: Essen

first: Bernhard

last: Horsthemke

address: Hufelandstrasse 55

department: Universitaetsklinikum Essen

country: Germany

institute: Institut fuer Humangenetik

description:
Gene expression data from GFP#3 clone, 96 h after treatment with non-targeting control siRNAs
total RNA (>200 nt)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in a GeneArray Scanner (Agilent).

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

label: Biotin

source_name: Flp-In™ T-REx™ 293

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FCS, 1% Pen/Strep and appropriate concentrations of selective antibiotics.

extract_protocol: RNA was extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen) and treated with the RNase-Free DNase Set (Qiagen)

treatment_protocol: Cells were treated either with siRNA against TET1, TET2 and TET3 or a non-targeting pool. All cells carried an inducible, stable GFP transgene whose expression was not induced.

tag: transgene

value: GFP

value: control


title: 4_GFPscr

description:
Gene expression data from GFP#1 clone, 96 h after treatment with non-targeting control siRNAs
total RNA (>200 nt)


title: Serum free 96h,  biological rep1


title: Control cells, biological rep3


title: 3_GFPsiRNA

description:
Gene expression data from GFP#3 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3
total RNA (>200 nt)

value: simultaneous knockdown of TET1, TET2 and TET3


title: ADMA treatment 96h, biological rep2


title: 2_GFPsiRNA

description:
Gene expression data from GFP#2 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3
total RNA (>200 nt)


title: DNMT3A

source_name: DNMT3A construct were transfected into gastric cancer cell

value: cell transfected with DNMT3A


title: 5_GFPscr

description:
Gene expression data from GFP#2 clone, 96 h after treatment with non-targeting control siRNAs
total RNA (>200 nt)


title: 6_GFPscr

description: Methylation data from GFP#3 clone, 96 h after treatment with non-targeting control siRNAs

hyb_protocol: Illumina specific protocol

scan_protocol: Illumina specific protocol

data_processing: RnBeads software version 0.99.15 with default settings, including removal of SNP-enriched probes, Greedycut removal of unreliable probes, SWAN signal intensity normalization, background subtraction using methylumi.noob, removal of non CpG probes; differential methylation p-values on the site level were obtained from linear models employed in the limma package

label: Cy3 and Cy5

label_protocol: Illumina specific protocol

extract_protocol: DNA was extracted using the AllPrep DNA/RNA/Protein Mini kit (Qiagen)


title: 5_GFPscr

description: Methylation data from GFP#2 clone, 96 h after treatment with non-targeting control siRNAs


title: 4_GFPscr

description: Methylation data from GFP#1 clone, 96 h after treatment with non-targeting control siRNAs


title: 11.TET3-B_-Dox

description: Gene expression data from TET3-B clone, not induced

treatment_protocol: Doxycycline was used to induce the expression of the integrated TET1 or TET3 copy.

value: Flp-In™ T-REx™ 293

value: uninduced


title: 2_GFPsiRNA

description: Methylation data from GFP#2 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3


title: 3_GFPsiRNA

description: Methylation data from GFP#3 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3


title: 1_GFPsiRNA

description: Methylation data from GFP#1 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3


title: 7.TET3-A_+Dox

description: Gene expression data from TET3-A clone, 48 h after induced expression of the integrated TET3 gene

value: induced


title: 12.TET3-C_-Dox

description: Gene expression data from TET3-C clone, not induced


title: 9.TET3-C_+Dox

description: Gene expression data from TET3-C clone, 48 h after induced expression of the integrated TET3 gene


title: TET1-G_-DOX

description: Methylation data from TET1-G clone (TET1#3), not induced

treatment_protocol: Doxycycline was used to induce the expression of the integrated TET1 copy.


title: TET1-F_-DOX

description: Methylation data from TET1-F clone (TET1#2), not induced


title: Control cells, biological rep1


title: TET1-A_-DOX

description: Methylation data from TET1-A clone (TET1#1), not induced


title: TET1-F_+DOX

description: Methylation data from TET1-F clone (TET1#2), 48 h after induced expression of the integrated TET1 gene


title: SKOV3Tx50

source_name: 50 nM Taxol resistant Human Ovarian Cancer cell line SKOV3

value: taxol-resistant SKOV3/Tx50


title: 6.TET1-G_-Dox

description: Gene expression data from TET1-G clone, not induced


title: 5.TET1-F_-Dox

description: Gene expression data from TET1-F clone, not induced


title: TET1-A_+DOX

description: Methylation data from TET1-A clone (TET1#1), 48 h after induced expression of the integrated TET1 gene


title: 8.TET3-B_+Dox

description: Gene expression data from TET3-B clone, 48 h after induced expression of the integrated TET3 gene


title: 2.TET1-F_+Dox

description: Gene expression data from TET1-F clone, 48 h after induced expression of the integrated TET1 gene


title: 4.TET1-A_-Dox

description: Gene expression data from TET1-A clone, not induced


title: 1_GFPsiRNA

description:
Gene expression data from GFP#1 clone, 96 h after simultaneous siRNA-mediated knockdown of TET1, TET2, TET3
total RNA (>200 nt)


title: 3.TET1-G_+Dox

description: Gene expression data from TET1-G clone, 48 h after induced expression of the integrated TET1 gene


title: 10.TET3-A_-Dox

description: Gene expression data from TET3-A clone, not induced


title: 1.TET1-A_+Dox

description: Gene expression data from TET1-A clone, 48 h after induced expression of the integrated TET1 gene


title: TET1-G_+DOX

description: Methylation data from TET1-G clone (TET1#3), 48 h after induced expression of the integrated TET1 gene


title: SLOV3Tx600_1

hyb_protocol: Phalanx HOA v5.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 10 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer. After 16 hrs hybridization at 50°C, non-speciﬁc binding targets were washed away by three different washing steps (wash 1, 42°C for 5 mins; wash 2, 42°C for 5 mins and 25°C for 5 mins; wash 3, rinse 20 times), and the slides were dried by centrifugation.

scan_protocol: The scanned images were analyzed with Agilent Scanner and processing by GenePix software 4.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: After hybridization, washing and drying steps, the slides were scanned using an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). The Cy5 ﬂuorescent intensities of each spot were analyzed using the GenePix Pro 4.1.1.44 software (Molecular Devices).  Global median normalization were applied to spots without flag and generated the normalized signal Intensities.

extract_protocol: RNA extraction  using TRIZOL reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).


title: SLOV3Tx50_2


title: SLOV3Tx50_1


title: SLOV3_1


title: SLOV3Tx600_2


title: adjacent noncancerous thyroid tissue_rep3

city: Shenyang

first: Xiabin

last: Lan

state: Liaoning Province

address: No. 155, Nanjing Bei Street, Heping District

department: Department of Thyroid Surgery

institute: The First Hospital of China Medical University

description: lncRNA and mRNA expression in  noncancerous thyroid tissue

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in Hybridization Oven (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, USA) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA, USA), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, USA) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, USA).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, USA).

label: Low Input Quick Amp Labeling Kit

source_name: adjacent noncancerous thyroid tissue samples

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies, Carlsbad, CA, USA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (QIAGEN, GmBH, Germany).

treatment_protocol: All tissue samples were snap-frozen in liquid nitrogen immediately after surgical resection, and were transferred to the freezer at −80℃ before use.

value: female


title: IL-17A plus FGF2

first: Xinyang

last: Song

address: 320 Yue Yang Road

department: Institute of Health Sciences

institute: Shanghai Institutes for Biological Sciences

description: Mouse primary intestinal epithelial cells stimulated for 6 hr with IL-17A plus FGF2

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Intestinal epithelial cells

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

growth_protocol: For culture of mouse primary intestinal epithelial cells, isolated crypts were seeded into fibronectin (10 μg/ml;Sigma) coated plates with DMEM culture medium supplemented with 2.5% (vol/vol) FBS, insulin (0.25 U/ml; Sigma), penicillin (100 U/ml) and streptomycin (100 mg/ml).

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions.

treatment_protocol: Mouse primary intestinal epithelial cells left untreated (UN) or stimulated for 6 hr with IL-17A (50 ng/ml), FGF2 (5 ng/ml), or both (IL-17A plus FGF2).

value: Intestine

value: epithelial

tag: agent

value: IL-17A plus FGF2


title: adjacent noncancerous thyroid tissue_rep5


title: Tetraploid vs diploid Col-0 dark-grown hypocotyls Replicate 2

city: Sendai

first: Kazuhiko

last: Nishitani

state: Miyagi

address: 6-3 Aramaki a2a Aoba Aoba-ku

department: Life Sciences

institute: Tohoku University

hyb_protocol: Hybridization was perfomed using Gene Expression Hybridization kit (Agilent Technologies). cRNAs (835 ng) were fragmented at 60ºC for 30 min. After the fragmentation was terminated, the mixture was loaded onto the microarray slide and hybridized at 65 ºC for 17 h, followed by washing steps.

scan_protocol: The hybridized slide was scanned on a G2539A scanner with scan control software version A.8.5.1 (Agilent Technologies).

data_processing: Data analysis was performed using Feature Extraction software version 10.10.1.1 (Agilent Technologies) and GeneSpring GX software version 12.6.1 (Agilent Technologies).

organism: Arabidopsis thaliana

source_name: diploid replicate2

label_protocol: cRNAs was synthesized from 100 ng of total RNA without detectable degradation using  a Low Input Quick Amp labeling kit two-color (Agilent Technologies) and Agilent RNA Spike-In kit two-color (Agilent Technologies). Incubation time was 2 h at 37 ºC. cRNA quantity and Cy3/Cy5-labelling efficiency was determined using a Nanodrop ND-1000 (Thermo) and Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Following storage at 4°C for 3 days, seeds on Murashige and Skoog (MS)  medium were germinated in continuous white light (45 µmol m-2s-1) at 22°C. After 1 day, MS plates were subsequently double-wrapped in aluminum foil and placed vertically and allowed to grow for additional 6 days in the dark at 22 °C.

extract_protocol: Total RNA samples were separately extracted from three biological replicates of the apical 4 mm region of 7-day-old dark-grown hypocotyls of diploid and tetraploid Arabidopsis using a Qiagen RNeasy plant mini kit (Qiagen Japan).

treatment_protocol: Seeds were surface-sterilized in 70% ethanol and were sown on MS medium containing 2% (w/v) sucrose and 0.4% gellan gum adjusted to pH 5.8.

value: dark-grown hypocotyls

tag: polyploidy

value: diploid

source_name: tetraploid replicate2

value: generated tetraploid line in the Col-0 background

value: tetraploid


title: SLOV3_2

value: parental SKOV3


title: adjacent noncancerous thyroid tissue_rep4

value: male


title: IL-17A

description: Mouse primary intestinal epithelial cells stimulated for 6 hr with IL-17A (50 ng/ml）

tag: cell type


title: adjacent noncancerous thyroid tissue_rep2


title: PTC specimens_rep5

description: lncRNA and mRNA expression in PTC tissue

source_name: PTC specimens


title: SKOV3_taxol50_rep2

scan_protocol: The scanned images were analyzed with Axon 4000B scanner and processing by GenePix software 4.1.1.44 to obtain background subtracted and spatially detrended Processed Signal intensities.

tag: cell phenotype

value: Human Ovarian Cancer cell line

value: 50 nM Taxol resistant line

tag: taxol conc. (nm)


title: SKOV3_taxol600_rep1

value: 600 nM Taxol resistant line


title: UN

description: Mouse primary intestinal epithelial cells left untreated (UN)

value: untreated


title: SKOV3_taxol600_rep2


title: SKOV3_taxol50_rep1


title: PTC specimens_rep1


title: WBS ES line, biological rep1

city: Barcelona

first: Victoria

last: Campuzano

address: Dr Aiguader, 88

department: CEXS

country: Spain

institute: Universitat Pompeu Fabra

hyb_protocol: Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array

scan_protocol: The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values

source_name: WBS deleted region ES cell

growth_protocol: Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.

value: Embrionic stem cell line

tag: genotype


title: PTC specimens_rep3


title: FGF2

description: Mouse primary intestinal epithelial cells stimulated for 6 hr with FGF2 (5 ng/ml)


title: Tetraploid vs diploid Col-0 dark-grown hypocotyls Replicate 3

source_name: diploid replicate3

source_name: tetraploid replicate3


title: PTC specimens_rep4


title: SKOV3_rep2

value: parental celll line


title: Tetraploid vs diploid Col-0 dark-grown hypocotyls Replicate 1

source_name: diploid replicate1

source_name: tetraploid replicate1


title: adjacent noncancerous thyroid tissue_rep1


title: PTC specimens_rep2


title: WBS ES line, biological rep2


title: KM-H2 miR-155-sp IP Cy5

city: Groningen

first: Anke

last: van den Berg

address: Hanzeplein 1

department: Department of Pathology and Medical Biology

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA were combined and hybridized following the Agilent's protocol

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol.

data_processing: Data were extracted using Agilent Feature Extraction software (v10.5.1.1). Two-color microarrays were analyzed as one-color microarrays using GeneSpring GX, version 12.5 (Agilent). Data from TXT files to each microarray were quantile normalized (threshold raw signal to 1.0) without baseline transformation. Probes detected in at least half of the samples (2 out of 4, Cy3 and Cy5 averaged), with consistent Cy3 and Cy5 signal in all samples were analyzed. Control probes were excluded.

source_name: KM-H2_miR-155 sponge

label_protocol: ~100 ng of RNA was Cy3 or Cy5 labeled using two-color Low Input Quick Amp Labeling Kit  (Agilent) following the manufacturer's protocols. Dye incorporation and cRNA yield were checked with the NanoDrop 1000 .

growth_protocol: Cells were maintained in RPMI with 10%FCS, ultraglutamine (2mM), penicillin (100U/ml), streptomycin (0.1mg/ml) under standard culturing conditions

extract_protocol: Imunoprecipitation was performed using Ago2 ab (Clone 2E12-1C9). RNA from IP fraction was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands), following manufacturer's instructions.

treatment_protocol: Cells were transduced with pMSCV-PIG vector containing miR-155 sponge construct and GFP+ cells were sorted

value: Hodgkin lymphoma cell line

tag: tranduced with

tag: molecule subtype

value: Ago2-IP RNA


title: KM-H2 EV Total Cy3

source_name: KM-H2_empty pMSCV-PIG vector

extract_protocol: Total cellular RNA was extracted using the miRNeasy Mini Kit (Qiagen, Venlo, The Netherlands), following manufacturer's instructions.

treatment_protocol: Cells were transduced with empty pMSCV-PIG vector and GFP+ cells were sorted

value: empty pMSCV-PIG vector

value: Total RNA


title: KM-H2 EV Total Cy5


title: KM-H2 EV IP Cy5


title: KM-H2 miR-155-sp Total Cy5

value: pMSCV-PIG vector containing miR-155 sponge construct


title: L1236 miR-155-sp Total Cy5

description: SAMPLE 7

source_name: L1236_miR-155 sponge

label_protocol: ~100 ng of RNA was Cy3 or Cy5 labeled using two-color Low Input Quick Amp Labeling Kit  (Agilent) following the manufacturer's protocols.  Dye incorporation and cRNA yield were checked with the NanoDrop 1000


title: L1236 EV IP Cy3

description: SAMPLE 2

source_name: L1236_empty pMSCV-PIG vector


title: L1236 EV Total Cy3

description: SAMPLE 1


title: L1236 EV IP Cy5

description: SAMPLE 6


title: SKOV3_rep1

source_name: Human Ovarian Cancer cell line SKOV3


title: L1236 miR-155-sp Total Cy3

description: SAMPLE 3


title: KM-H2 miR-155-sp Total Cy3


title: KM-H2 EV IP Cy3


title: anti-FLAG RIP FLAG Control

status: Public on Jul 15 2015

city: Ottawa

first: William

last: Stanford

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute

description:
mESCs constitutively express pCAGGS::3xN-FLAG construct. mESC line is G418-resistant
WLS_RIP_aFLAG_FLAG:Ctrl

hyb_protocol: Standard Affymetrix Protocols (See GeneChip Expression Analysis Technical Manual)

data_processing: CEL files generated by the Affymetrix GeneChip Command Console (v3.0.1.1229) were quantile normalized in GeneSpring GX v11 using PLIER16. The log2 normalized signal values were then filtered to remove entities that show signal vaues in the bottom 20th percentile across all samples. To be considered as mRNA targets of FLAG:MKRN1, probes from anti-FLAG FLAG:MKRN1 RIPs had to be at least two times greater than the signal from corresponding probes from both control RIPs: anti-FLAG FLAG:Ctrl RIP and anti-IgG FLAG:MKRN1 RIP.

source_name: Anti-FLAG RIP RNA, FLAG:Ctrl ESC lysates expanded in LIF + serum

growth_protocol: FLAG:MKRN1 overexpression and FLAG vector control (FLAG:Ctrl) ESC lines were thawed onto mouse embryonic fibroblasts (MEFs) on 6 cm dishes in standard ESC media containing LIF and serum (FBS). After one passage on MEFs, FLAG:MKRN1 and FLAG:Ctrl ESC lines were expanded on 0.1% gelatin coated dishes in standard ESC media containing LIF and serum for at least two passages to remove contaminating MEFs.

extract_protocol: 10^8 ESCs were lysed with ice-cold polysome lysis buffer (100 mM KCl, 5mM MgCl2, 100nM ZnCl2, 10mM HEPES [pH 7.4], 1% NP40, 100 U/mL RNase OUT, 1 mM DTT, 1 mM PMSF, 0.4 mM vanadyl ribonucleoside complexes and 1x Roche Complete protease inhibitors). RNA immunoprecipitation (RIP) was carried out using 4 mg of total protein from FLAG:MKRN1 or FLAG:Ctrl ESC lysates. RIPs proceeded for 1 h at 4oC in 1 mL of NT2 buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM MgCl2, 100 nM ZnCl2, 0.1% NP-40, 100U/mL RNase OUT, 0.2 mM PMSF and 1x Roche Complete protease inhibitors) using 100 µL of a 50% slurry of Protein G dynabeads pre-armed with 10 µg of anti-FLAG, or anti-IgG antibodies. Just prior to immunoprecipitation, 1/10th of the volume of each lysate was saved for extraction of total (Input) RNA. For purification of FLAG:MKRN1 associated mRNAs, anti-FLAG RIP was performed from FLAG:MKRN1 ESC lysates. To control for spurious interactions, two control RIPs were performed in parallel: 1) an anti-FLAG RIP was performed from FLAG:Ctrl ESC lysates and 2) an IgG antibody control RIP was performed from the FLAG:MKRN1 ESC lysates. Following the immunoprecipitation, beads were washed 6x in 1 mL NT2 buffer. After the fianl wash of the beads, RIP and Input samples were treated with 30 µg of proteinase K for 30min at 55oC to elute RNA from the beads. RIP and Input RNA was extraced with ultra pure phenol-choroform-isoamyl alcohol (25:24:1) followed by LiCl ethanol RNA precipitation. RIP and Input RNA was treated with DNase I and subsequently ethanol precipitated. Purified RIP and Input RNA was quantified using the RNA Pico Chip Kit on the Agilent 2100 BioAnalyzer. 10 ng of RIP or Input RNA was used to generate cDNA used fro RIP-chip analysis.

treatment_protocol: FLAG:MKRN1 overexpression and FLAG vector control (FLAG:Ctrl) ESC clones were expanded in feeder-free culture conditions in standard ESC media containing LIF + serum (15% FBS). No additional treatements were performed on the cells

tag: strain

value: inner cell mass

tag: developmental stage

value: blastocyst

value: R1 mouse embryonic stem cells

tag: genotype/variation

value: constitutively expressing pCAGGS::FLAG:Ctrl construct (FLAG:Ctrl)

value: R1 mouse embryonic stem cells (gender = male; strain = 129X1 x 129S1, tissue = inner cell mass, developmental stage = blastocyst


title: L1236 miR-155-sp IP Cy5

description: SAMPLE 8

tag: cell line


title: KM-H2 miR-155-sp IP Cy3


title: L1236 miR-155-sp IP Cy3

description: SAMPLE 4


title: Itga11 het1

first: Ming

last: Tsao

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

description:
xenograph
5534685006_C

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

source_name: xenograph

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

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.

value: SCID

tag: tissue

value: snap-frozen tissue


title: anti-FLAG RIP FLAG MKRN1

description:
mESCs constitutively express pCAGGS::3xN-FLAG:MKRN1 fusion protein. mESC line is G418-resistant
WLS_RIP_aFLAG_FLAG:MKRN1

scan_protocol: Standard Affymetrix Protocols (See GeneChip Expression Analysis Technical Manual)

source_name: Anti-FLAG RIP RNA, FLAG:MKRN1 ESC lysates expanded in LIF + serum

tag: gender

value: male

value: constitutively expressing pCAGGS::FLAG:MKRN1 fusion protein (FLAG:MKRN1)


title: L1236 EV Total Cy5

description: SAMPLE 5


title: Input FLAG Control

description:
mESCs constitutively express pCAGGS::3xN-FLAG construct. mESC line is G418-resistant
WLS_input_FLAG:Ctrl

source_name: Total RNA, FLAG:Ctrl ESC lysates expanded in LIF + serum

label_protocol: Standard Affymetrix Protocols (See GeneChip Expression Analysis Technical Manual)


title: Itga11 wt2

description:
xenograph
5534685006_B


title: Input FLAG MKRN1

description:
mESCs constitutively express pCAGGS::3xN-FLAG:MKRN1 fusion protein. mESC line is G418-resistant
WLS_input_FLAG:MKRN1

source_name: Total RNA, FLAG:MKRN1 ESC lysates expanded in LIF + serum


title: shGFP Control (shGFP_7)

description:
shGFP sequence: 5'-CACAACAGCCACAACGTCTAT-3'
shGFP_7

data_processing: Using the Bioconductor package (v.2.8) in R language environment, CEL files that contained raw signal intensity values were preprocessed and normalized using RMA to correct for background intensity. The expression data was transformed into log2 values and was fit on multiple linear models each probe across available matrix. The contrast design matrix between the shGFP control and the shMKRN1-transfected samples was applied to assess differential expression. Empirical Bayes statistics was applied to shrink the probe-wise sample variances towards a common value, which employed moderated t-statistics test and the moderated F-statistic tests analogous to conventional ANOVA except moderation of residual mean squares and residual degrees of freedom between probes. The P-value that corresponded to the moderated t-statistics was obtained. Benjamini & Hochberg correction method was used to determine the false discovery rate (FDR) and obtain adjusted P-values. Adjusted P-value of <0.05 was used to identify differentially expressed transcripts between shGFP and shMKRN1-transfected ESCs. Transcripts whose abundance were affected more than 1.3-fold (linear range) in either direction were considered up- or down-regulated. Transcripts with modest changes in expression values of less than 1.3-fold (linear range), in either direction, were considered non-regulated.

source_name: 6d shGFP-transfected R1 mESCs_4d puromycin selection

growth_protocol: 1.7 x 10^5 R1 mESCs were seeded in each well of a 12-well gelatinized plate in standard mESC media containing LIF + serum (15% FBS) for 48 h prior to transient transfection with shGFP or shMKRN1 plasmids.

extract_protocol: Total RNA harvested from transiently transfected shGFP control or MKRN1 knockdown ESC populations was isolated using the Macherey-Nagel RNAII columns with on-column DNaseI treatment according to manufacturer’s instructions. Each sample of eluted total RNA was then run through Macherey-Nagel RNA clean-up XS columns clean-up kit according to manufacturer’s instructions. The concentration and quality of the purified RNA was determined using both the NanoDrop and the RNA Nano Chip Kit (Agilent) on the Agilent 2100 BioAnalyzer.

treatment_protocol: 48 h after seeding, mESCs were transfected with 2 µg of either pLKO.1 shGFP (control) or pLKO.1 shMKRN1 in mESC media with Lipofectamine 2000. ESCs were transfected overnight, and the following day mESC media was replaced with 1 mL of fresh mESC media (no selection). 24 h later, mESC media was replaced with 2 mL puromycin selection media (mESC media supplemented with 2 µg/mL puromycin) in each of the transfected wells. Puromycin selection media was changed daily for four days at which point only puromycin-resistant cells remained. At this time point (six days post-transfection; four days post-puromycin selection), cells were lysed for RNA extraction.

tag: transfected with

value: pLKO.1 shGFP

tag: time point

value: 6 days post transfection and 4 days of puromycin selection


title: Itga11 ko2

description:
xenograph
5534685006_F


title: Itga11 ko1

description:
xenograph
5534685006_E


title: Itga11 het2

description:
xenograph
5534685006_D


title: Itga11 wt1

description:
xenograph
5534685006_A


title: anti-IgG RIP FLAG MKRN1

description:
mESCs constitutively express pCAGGS::3xN-FLAG:MKRN1 fusion protein. mESC line is G418-resistant
WLS_RIP_aIgG_FLAG:MKRN1

source_name: Anti-IgG RIP RNA, FLAG:MKRN1 ESC lysates expanded in LIF + serum


title: shMKRN1 (shMKRN1_6)

description:
shMKRN1 sequence: 5'-GCGAGATGTTGCTTATGCTTT-3'
shMKRN1_6

source_name: 6d shMKRN1-transfected mESCs_4d puromycin selection

value: pLKO.1 shMKRN1


title: shMKRN1 (shMKRN1_8)

description:
shMKRN1 sequence: 5'-GCGAGATGTTGCTTATGCTTT-3'
shMKRN1_8


title: shMKRN1 (shMKRN1_2)

description:
shMKRN1 sequence: 5'-GCGAGATGTTGCTTATGCTTT-3'
shMKRN1_2


title: shGFP Control (shGFP_3)

description:
shGFP sequence: 5'-CACAACAGCCACAACGTCTAT-3'
shGFP_3


title: shGFP Control (shGFP_5)

description:
shGFP sequence: 5'-CACAACAGCCACAACGTCTAT-3'
shGFP_5


title: shMKRN1 (shMKRN1_4)

description:
shMKRN1 sequence: 5'-GCGAGATGTTGCTTATGCTTT-3'
shMKRN1_4


title: WIZ siRNA vs control siRNA replicate 2

city: Chapel Hill

first: Sam

last: Pattenden

state: NC

address: 3015 Marsico Hall  125 Mason Farm Road  CB# 7363

department: Center for Integrative Chemical Biology & Drug Discovery

institute: University of North Carolina at Chapel Hill

description: Biological replicate 2

hyb_protocol: Not provided

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Microarray images were processed using Agilent Feature Extractor according to manufacturer-supplied protocols.
The resulting background subtracted and loess normalized log ratio data were collected and filtered to remove data generated from poor quality or low intensity spots.  Probes with >30% missing data were removed from further evaluation. Dye swap replicates were inverted to match the log ratio direction of non-dye swap replicates.

source_name: HEK293T cells treated with control siRNA, 72 hours

label_protocol: Not provided

growth_protocol: HEK 293T cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), and quantified on the Qubit Fluorometer (Invitrogen).  RNA quality was verified on the Agilent Bioanalyzer before hybridization to Human 8x60K arrays (Agilent #28004).

treatment_protocol: Compound treatment: cells were treated with 1 micromolar UNC0638 or a volume equivalent of DMSO for 48 hours.  siRNA knockdown: All siRNAs were purchased from Dharmacon (GE), and transfections were performed as per manufacturer’s instructions with DharmaFECT 4 transfection reagent.

source_name: HEK293T cells treated with WIZ siRNA, 72 hours


title: G9a siRNA vs control siRNA, replicate 1

description: Biological replicate 1

source_name: HEK293T cells treated with G9a siRNA, 72 hours


title: shGFP Control (shGFP_1)

description:
shGFP sequence: 5'-CACAACAGCCACAACGTCTAT-3'
shGFP_1


title: G9a siRNA vs control siRNA, replicate 2

description: Biological replicate 2


title: UNC0638 vs DMSO replicate 2

description: Biological replicate 2

source_name: HEK293T cells treated with DMSO, 48 hours

source_name: HEK293T cells treated with UNC0638, 48 hours


title: n5Ri14_14_expression

city: Moscow

first: Maria

last: Shutova

state: Russia

address: Gubkina 3

department: Epigenetics

country: Russia

institute: Vavilov Institute of General Genetics, Russian Academy of Sciences

description: rpe-derived iPSC line 14, passage 14

scan_protocol: Standard Illumina scanning protocol

source_name: rpe-derived iPSC line 14, passage 14

value: Female

value: iPSCs


title: n5Ni27_10_expression

description: neuron-derived iPSC line 27 passage 10

source_name: neuron-derived iPSC line 27 passage 10


title: UNC0638 vs DMSO replicate 3

description: Biological replicate 3


title: n5Ni29_19_expression

description: neuron-derived iPSC line 29 passage 19

source_name: neuron-derived iPSC line 29 passage 19


title: UNC0638 vs DMSO replicate 4

description: Biological replicate 4


title: n5R_2_expression

description: n5-derived rpe cells, 4 month differentiation

source_name: n5-derived retinal pigment epithelium cells

value: retinal pigment epithelium


title: n5N_2_expression

description: n5-derived neurons, one month differentiation

source_name: n5-derived neurons

value: neurons


title: UNC0638 vs DMSO replicate 2, dye swap

description: Biological replicate 2, dye swap


title: n5Ri22_12_expression

description: rpe-derived iPSC line 22, passage 12

source_name: rpe-derived iPSC line 22, passage 12


title: WIZ siRNA vs control siRNA replicate 1

description: Biological replicate 1


title: n5R_1_expression


title: UNC0638 vs DMSO replicate 1

description: Biological replicate 1


title: WIZ siRNA vs control siRNA replicate 1, dye swap

description: Biological replicate 1, dye swap


title: UNC0638 vs DMSO replicate 5

description: Biological replicate 5


title: UNC0638 vs DMSO replicate 1, dye swap

description: Biological replicate 1, dye swap


title: n5Ni29_13_expression

description: neuron-derived iPSC line 29 passage 13

source_name: neuron-derived iPSC line 29 passage 13


title: n5Ri22_16_expression

description: rpe-derived iPSC line 22, passage 16

source_name: rpe-derived iPSC line 22, passage 16


title: WIZ siRNA vs control siRNA replicate 2, dye swap

description: Biological replicate 2, dye swap


title: n5_3_expression

description: parental hESC line n5, passage 14, containing DOX-inducible lentiviral insertions

source_name: parental hESC line

value: ESCs


title: n5Ni27_6_expression

description: neuron-derived iPSC line 27 passage 6

source_name: neuron-derived iPSC line 27 passage 6


title: n5Fi7_28_expression

description: fibroblast-derived iPSC line 7, passage 28


title: n5Fi7_24_expression

description: fibroblast-derived iPSC line 7, passage 24


title: n5Fi47_6_expression

description: fibroblast-derived iPSC line 47, passage 6


title: n5Fi7_4_expression

description: fibroblast-derived iPSC line 7, passage 4


title: n5N_1_expression


title: n5Fi47_29_expression

description: fibroblast-derived iPSC line 47, passage 29


title: n5Fi47_25_expression

description: fibroblast-derived iPSC line 47, passage 25


title: n5F_2_expression

description: n5-derived fibroblasts, three month differentiation

source_name: n5-derived fibroblasts

value: fibroblasts


title: n5F_1_expression


title: n5_1_expression


title: ES5_2_expression

description: hESM01 ESC line, passage 67

source_name: hESM01 ESC line, passage 67


title: ES5_1_expression

description: hESM01 ESC line, passage 66

source_name: hESM01 ESC line, passage 66


title: H-INV-3

city: Los Angeles

first: Xufeng

last: Chen

state: CA

address: 10833 Le Conte Ave.

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

description:
replicate 3
8981245033_F

scan_protocol: Standard Illumina scanning protocol on HiScan system

data_processing: The data were normalised using quantile normalisation with background correction in GenomeStudio(Illumina, San Diego, CA), further analysis were perfromed in Partek Genomic Suite 6.6 (Partek,St. Louis, MO)

source_name: H-INV cell subline

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA kit for Illumina arrays

growth_protocol: H460 cells were grown in RPMI-1640 medium with 10% fetal bovin serum.

extract_protocol: Total RNA were prepared from three sets of collected H-INV and L-INV cells with validation of invasiveness. Trizol reagent (Life Technologies) were used for RNA extract.

treatment_protocol: 1 × 106 H460 cells in growth medium containing 10% FBS were seeded in 1× BME (Trevigen, Gaithersburg, MD) coated 8.0-μm pore size cell culture inserts of Boyden-type cell invasion chambers (for 6-well plate, Millipore, Danvers, MA). Complete growth medium was also placed outside the chambers. 48 hours later, cells remained in top inserts were collected as cell population with low invasiveness, and invaded cells migrated into the bottom 6-well vessels were collected as cell population with high invasiveness.  Collected cells were then maintained in Glucose-free RPMI-1640 medium with 10%FBS until reaching 70% confluences, and cells were trypsinized and re-seeded in 1× BME coated 8.0-μm pore size cell culture inserts for next round of selection. In this second selection, cells remained in top inserts with plated cells previously collected from top insert in first round selection were collected as cell population with low invasiveness, and cells grown in bottom culture vessels with plated cells previously collected from bottom vessels in first round selection were collected as cell population with high invasiveness. After six rounds of selection, cells remained top inserts were finally collected as low-invasive cells (L-INV), and cells grown in bottom culture vessels were collected as high-invasive cells (H-INV). L-INV and H-INV cells were then maintained in Glucose-free RPMI-1640 medium, and re-selected with procedure as described above once every six passages.

value: lung cancer


title: H-INV-1

description:
replicate 1
8981245033_D


title: H-INV-2

description:
replicate 2
8981245033_E


title: A549 in Itga11 wt2

city: Toronto

description:
xenograph from SCID mice
5504558058_B

source_name: xenograph

tag: host for tumor

value: integrin11 +/+


title: human atrial appendage tissue-SR-sample 0046AD

city: Madrid

first: Susana

last: Cañón

state: Madrid

address: Darwin, 3

department: Dept. Immunology and Oncology

institute: CNB

description:
female-80 years old- SR- 0046AD
miRNA

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol miRNA_105_Jan09. VSN2 normalization. mirBase version 17 was used for miRNA annotation.

label: Cyanine 3-pCp

source_name: human atrial appendage tissue-SR

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: Total RNA from 4 AF patients, 2 SR patients and 2 control (no AF) patients, was extracted  after disruption and homogeneization of  small pieces of frozen atrial appendage biopses from AF and SR patients. Total  RNA, including miRNAs, was purified by Qiagen miRNeasy Mini Kit - catalog number 217004, following

tag: diagnosis

value: sinus rhythm

value: heart

tag: tissue compartment

value: atrial appendage

value: female

tag: age


title: human atrial appendage tissue-AF-sample 0067AD

description:
male-51 years old-AF-0067AD
miRNA

source_name: human atrial appendage tissue-AF

value: chronic atrial fibrillation

value: male


title: human atrial appendage tissue-AF-sample 0049AD

description:
female-65 years old-AF-0049AD
miRNA


title: human atrial appendage tissue-CONTROL-sample 0051AD

description:
male-77 years old- No AF-control 0051AD
miRNA

source_name: human atrial appendage tissue-CONTROL

value: healthy


title: human atrial appendage tissue-AF-sample 0047AD

description:
female-72 years old- AF-0047AD
miRNA


title: L-INV-2

description:
replicate 2
8981245033_B

source_name: L-INV cell subline

tag: cell type


title: human atrial appendage tissue-SR-sample 0042AD

description:
male-70 years old- SR- 0042AD
miRNA


title: human atrial appendage tissue-CONTROL-sample 0001AD

description:
female-61 years old- No AF-control 0001AD
miRNA


title: A549 in Itga11 het2

description:
xenograph from SCID mice
5504558058_D

value: snap-frozen tissue

value: integrin11 +/-


title: A549 in Itga11 wt1

description:
xenograph from SCID mice
5504558058_A


title: L-INV-1

description:
replicate 1
8981245033_A


title: ∆pkaA_CMvsAvicel_24h_B

city: Ribeirão Preto

first: Leandro

middle: Jose

last: Assis

state: São pAULO

address: Av. do Cafe S/N

department: FCFRP

country: Brazil

institute: USP

description: Biological rep 2 of 3

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: A. nidulans ∆pkaA strain was grown in CM for 24h, washed twice with dH2O and then transferred to MM plus avicel as a sole carbon source for 8 or 24 h.

extract_protocol: Total RNA was extracted with RNeasy® Plant Mini Kit  (Qiagen) following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

value: ∆pkaA


title: A549 in Itga11 ko1

description:
xenograph from SCID mice
5504558058_E

hyb_protocol: Standard Illumina hybridization protocol

value: integrin11 -/-


title: human atrial appendage tissue-AF-sample 0054AD

description:
female-50 years old- AF-0054AD
miRNA


title: ∆pkaA_CMvsAvicel_24h_C

description: Biological rep 3 of 3


title: ∆pkaA_CMvsAvicel_8h_A

description: Biological rep 1 of 3


title: A549 in Itga11 het1

description:
xenograph from SCID mice
5504558058_C


title: ∆pkaA_CMvsAvicel_8h_C

description: Biological rep 3 of 3


title: L-INV-3

description:
replicate 3
8981245033_C


title: ∆pkaA_CMvsAvicel_24h_A

description: Biological rep 1 of 3


title: CTL_KU-0063794_Rep2

city: Dundee

first: Jens

middle: Ludger

last: Hukelmann

state: Angus

address: Dow Street

department: Centre for Gene Regulation and Expression

country: United Kingdom

institute: University of Dundee

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 1 uM KU-0063794, biological replicate 2

hyb_protocol: Performed by Turku Centre of Biotechnology

data_processing: CHP files were generated using Expression console 1.3.1

source_name: P14 PCR transgenic CD8 Cytotoxic T lymphocytes cultured in vitro for 6 days, treated with 1 uM KU-0063794 for the last 2 days

growth_protocol: Spleens were harvested (one spleen per biological replicate), disaggregated and CD8 T cells were activated using the antigenic peptide gp33-41 in the presence of IL-2/12 for 48h. Cells were then washed an cultured for a further 96h.

extract_protocol: QIAgen Rneasy kit according to manufactorer specifications.

treatment_protocol: For the last 48h in culture, cells were terated with either DMSO (control), 20 nM rapamycin or 1 uM KU-0063794.

value: spleen

value: wild type

value: d6 P14 TCR CD8 cytotxic T lymphocyte

tag: treatment


title: ∆pkaA_CMvsAvicel_8h_B

description: Biological rep 2 of 3

tag: genotype


title: CTL_KU-0063794_Rep3

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 1 uM KU-0063794, biological replicate 3

scan_protocol: Performed by Turku Centre of Biotechnology


title: CTL_KU-0063794_Rep1

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 1 uM KU-0063794, biological replicate 1

label_protocol: Performed by Turku Centre of Biotechnology


title: Patient 2

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole human Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

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

source_name: Patient 2

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Punch biopsy materials from the skin samples of the two patients and an age-matched control subject were obtained and immediately used for establishment of primary fibroblast cell cultures. Initially, cells were dissociated with Trypsin EDTA, and cells were plated in T25 cell culture flasks, where they were grown in RPMI medium (Gibco-BRL, Bethesda, MA) supplemented with 10% fetal bovine serum (FBS) and 1% PSA at 37°C in a humidified and 5% CO2 incubator. Cells were trypsinized and passaged when they reached approximately %70-confluency.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

tag: subject status

value: patient with SOFT syndrome and POC1A mutation

value: skin

value: fibroblast

source_name: Stratagene universal reference RNA

tag: sample type

value: reference


title: CTL_RAPAMYCIN_Rep3

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 20 nM Rapamycin, biological replicate 3

source_name: P14 PCR transgenic CD8 Cytotoxic T lymphocytes cultured in vitro for 6 days, treated with 20 nM rapamycin for the last 2 days

tag: strain

value: 20 nM Rapamycin


title: diploid episc-2, biological rep3

city: Beijing

first: Ling

last: Shuai

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Chinese Academy of Sciences

description: Gene expression data from mouse diploid episc

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

source_name: mouse diploid epiblast stem cells

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

growth_protocol: Cultured in N2B27 medium supplemented with bFGF and Activin A at 37C and 5% CO2

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

treatment_protocol: Cells were digested with 0.05% trypsin/EDTA, rinsed with PBS, and placed on ice in the Trizol solution (invitrogen).

value: mouse diploid epiblast stem cells


title: haploid episc-1, biological rep2

description: Gene expression data from mouse haploid episc

source_name: mouse haploid epiblast stem cells

value: mouse haploid epiblast stem cells


title: 10007_2_4_Cy5_NormSignal

city: shanghai

first: wenbang

last: yu

address: meilong road 130, east china university of science and technology, shanghai, china

description: Biological replicate 2 of fusaricidin treated sample (170min) vs untreated sample (0min)

hyb_protocol: Each Slide was hybridized with 300ng Cy3-labeled cRNA and 300ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Red&Green, Scan resolution=5μm, PMT 100%, 10% , 16bit. and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Bacillus subtilis

source_name: untreated sample (0min)

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Cat#5190-2306, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Each strain was grown in liquid LB medium, and total RNA were extracted from the mycelia sample harvested at 0min, 5min, 20min and 170min, respectively.

extract_protocol: RNA was extracted from samples derived from two independent culture samples collected at each time point  using the RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer's instructions.

treatment_protocol: The culture were diveded in to two parts, one was treated with fusaricidin and the other remain untreated.

tag: growth condition

value: untreated

tag: time


title: 10007_2_1_Cy5_NormSignal

institute: east china university of science and technology

description: Biological replicate 1 of fusaricidin treated sample (170min) vs untreated sample (0min)


title: haploid episc-2, biological rep2


title: diploid episc-1, biological rep3


title: 10007_2_2_Cy5_NormSignal

description: Biological replicate 2 of fusaricidin treated sample (5min) vs untreated sample (0min)


title: CTL_RAPAMYCIN_Rep2

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 20 nM Rapamycin, biological replicate 2

tag: genotype/variation


title: Control

source_name: Control

value: control

tag: tissue


title: 10007_1_4_Cy5_NormSignal

description: Biological replicate 1 of fusaricidin treated sample (20min) vs untreated sample (0min)


title: CTL_DMSO_Rep2

description: d6 P14 TCR CD8 cytotxic T lymphocyte, DMSO control, biological replicate 2

source_name: P14 PCR transgenic CD8 Cytotoxic T lymphocytes cultured in vitro for 6 days

value: DMSO control


title: diploid episc-2, biological rep1


title: haploid episc-2, biological rep3


title: haploid episc-2, biological rep1


title: CTL_RAPAMYCIN_Rep1

description: d6 P14 TCR CD8 cytotxic T lymphocyte, 20 nM Rapamycin, biological replicate 1


title: haploid episc-1, biological rep1


title: haploid episc-1, biological rep3


title: Patient 1

source_name: Patient 1


title: diploid episc-1, biological rep1


title: 10007_1_2_Cy5_NormSignal

description: Biological replicate 2 of untreated sample (5min) vs untreated sample (0min)


title: CTL_DMSO_Rep3

description: d6 P14 TCR CD8 cytotxic T lymphocyte, DMSO control, biological replicate 3


title: diploid episc-2, biological rep2


title: A549 in Itga11 ko2

description:
xenograph from SCID mice
5504558058_F

tag: cell line

value: snap-frozen tissue


title: CTL_DMSO_Rep1

description: d6 P14 TCR CD8 cytotxic T lymphocyte, DMSO control, biological replicate 1


title: 10007_2_3_Cy5_NormSignal

description: Biological replicate 2 of fusaricidin treated sample (20min) vs untreated sample (0min)


title: 10007_2_4_Cy3_NormSignal

source_name: fus_treated sample (170min)

value: fus-treated


title: 10007_1_3_Cy5_NormSignal

description: Biological replicate 1 of fusaricidin treated sample (5min) vs untreated sample (0min)


title: 10007_2_2_Cy3_NormSignal

source_name: fus_treated sample (5min)


title: 10007_1_4_Cy3_NormSignal

source_name: fus_treated sample (20min)


title: 10007_2_1_Cy3_NormSignal


title: 10007_1_3_Cy3_NormSignal


title: diploid episc-1, biological rep2


title: 10007_1_1_Cy3_NormSignal

description: Biological replicate 1 of untreated sample (5min) vs untreated sample (0min)

source_name: untreated sample (5min)


title: 10007_1_2_Cy3_NormSignal


title: 10007_1_1_Cy5_NormSignal


title: Jarid2_1

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: Gene Expression array for Jarid2-/- mES cells, Replicate 1

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. The arrays are  Mouse430A_2.

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. These measures provide the basis of subsequent biostatistical analysis.

data_processing: dChip-processed with model-based expression, checking outliers.

source_name: embryonic cells

label_protocol: Not provided.

growth_protocol: Mouse ES cell lines were maintained in ES medium: DMEM (Dulbecco’s modified Eagle’s medium- Life Technologies) supplemented with 15% fetal calf serum (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Life Technologies), 0.1 mM nonessential amino acid (Life Technologies), 1% of nucleoside mix (Sigma), 1000 U/ ml recombinant leukemia inhibitory factor (LIF; Chemicon), and 50 U/ml penicillin/streptomycin (Life Technologies).

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
Library construction was done at Dana Farber Cancer Institute under their Affymetrix protocol. Affymetrix processing requires 1 µg or less of RNA and is a modification of the method used in the Core since the Core’s inception in 2002.  The procedure involves the synthesis of double-stranded cDNA which then serves as a template for the synthesis of biotinylated cRNA by in vitro transcription.  The cRNA is hybridized to the 3’ arrays.

treatment_protocol: None.


title: Ezh2_2

description: Gene Expression array for Ezh2-/- mES cells, Replicate 2


title: Eed_1

description: Gene Expression array for Eed-/- mES cells, Replicate 1

value: Eed-/-


title: Eed_2

description: Gene Expression array for Eed-/- mES cells, Replicate 2


title: CJ7-2

description: Gene Expression array for wild-type mES cells, Replicate 2

value: wild-type


title: n5_2_expression

description: parental hESC line n5, passage 14, containing DOX-inducible lentiviral insertions

source_name: parental hESC line

tag: gender

value: Female

value: ESCs


title: Ezh2_1

description: Gene Expression array for Ezh2-/- mES cells, Replicate 1


title: Jarid2_2

description: Gene Expression array for Jarid2-/- mES cells, Replicate 2


title: 10007_2_3_Cy3_NormSignal


title: CJ7_1

description: Gene Expression array for wild-type mES cells, Replicate 1