status: Public on Aug 15 2014

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_unpaired liver biopsy with relapse rep 8

hyb_protocol: Samples starting with 16P and 24U were hybridized onto Affymetrix HGU219 and samples 5142-5166 were hybridized to GeneChip human gene 2.0 ST arrays according to manufacturer's recommendations

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

data_processing: The data were analyzed with EC 1.1 using Affymetrix default analysis with an RMA-sketch normalization method.

label_protocol: RNA was used to prepare biotinylated aRNA and hybridized to the HGu219 plate;  DNA microarray probes were synthesized using the Ovation Pico WTA system (Nugen Inc., San Carlos, CA) and used for hybridization on the Affymetrix GeneChip Human Gene 2.0 ST array

growth_protocol: Sixty treatment-naïve, chronic HCV genotype-1 patients were treated with SOF (400 mg daily) and low (600 mg daily) or weight-based (400mg AQM with 600mg QPM if < 75kg or 600mg BID if >75kg) RBV for 24 weeks and from this group certain members were selected for the three different microarray experiments.

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

treatment_protocol: Paired liver biopsies: Core liver biopsies obtained transcutaneously with an 18-guage needle were immediately placed in RNAlater (Ambion) and stored at -80°C PBMC: Blood samples were collected at or prior to initiation of treatment, within 6-11 days of treatment initiation, and at EOT.  Blood cells were Ficoll separated from whole blood on the day of collection and re-suspended in RPMI containing 10% FCS and 7.5% DMSO for storage in liquid nitrogen. EOT liver biopsies: Liver biopsies collected in RNAlater then thawed and homogenized in TRizol (Thermofisher Scientific, Waltham, MA) using the FastPrep Green lysing matrix (MP Biomedicals, Solon, OH), combined with 200 µL of 1-bromo-3-chloropropane (Sigma-Aldrich), and centrifuged at 4 °C at 16,000 x g for 15 minutes.

value: unpaired liver biopsy with relapse

tag: gender

value: M

tag: agent/dose


type: RNA

country: USA

description: Gene expression data from_unpaired liver biopsy with relapse rep 7

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: age


description: Gene expression data from_unpaired liver biopsy with relapse rep 5

value: F


title: Snail2R overexpression (FSRR)

status: Public on Aug 16 2014

city: Taipei

first: Dennis

middle: Shin-Shian

last: Hsu

state: Taiwan

address: No.155, Sec.2, Linong Street

department: Clinical medicine

country: Taiwan

institute: National Yang Ming University

description:
FaDu-Snail2R
18636_FSRR.txt:gProcessedSignal(raw)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing:
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature. The complete data matrix including control probesets (2,028 data rows) is linked to Series records.

Please note that sample data table contains Cy3 signal intensity after dye normalization, and the normalized data (generated from gProcessedSignal after quantile normalization) are linked to Series records (18632-18636_samples_analysis*.xls)

source_name: Head and neck cell line

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Cells were cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: Cells were infected with lentivirus harboring ctrl vector,  wild Snail  and mutant Snail .

tag: cell line

value: FaDu

tag: cell type

value: hypopharyngeal carcinoma cell line

tag: transfected with


description: Gene expression data from_unpaired liver biopsy with relapse rep 4


description: Gene expression data from_unpaired liver biopsy with relapse rep 1


title: vector control (FP)

description:
FaDu-Ctrl
18634_FP.txt:gProcessedSignal(raw)

value: pCDH vector (control)


description: Gene expression data from_unpaired liver biopsy with relapse rep 2


description: Gene expression data from_unpaired liver biopsy with relapse rep 6


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 15


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 17


title: intermediate/deep zone rep2

city: Stockholm

first: Michael

last: Chau

address: Astrid Lindgren Children's Hospital, Q2:08

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

description: IDZ #2

hyb_protocol: Following fragmentation and biotinylation (Affymetrix Gene Chip WT Labeling Kit), 5 ug of ss cDNA were hybridized for 16 hr at 45C on GeneChipRat 1.0 STArray. They were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using robust multi-array average (RMA) analysis, which adjusts for background noise on each array using only the PM probe intensitites and subsequently normalizes data across all arrays using quantile normalization followed by median polish summarization to generate a single measure of expression.  These expression measures were then log transformed (base 2) and lists of spatially regulated genes were generated.

organism: Rattus norvegicus

source_name: articular cartilage intermediate/deep zone of 10-day-old rat proximal tibia

label_protocol: ss cDNA was prepared with the Ambion WT Expression kit from 100ng of total RNA

growth_protocol: Animals were maintained under standardized conditions and handled in accordance with the Animal Ethics Committee of Northern Stockholm.

extract_protocol: Total RNA was extracted using phenol:chloroform:isozmyl alcohol (25:24:1), precipitated in 3M NaOAc and then 8M LiCl, and washed with 75% ethanol.  For the complete protocol please refer to Nilsson et al. J Endocrinol April 1, 2007 193 75-84 (doi: 10.1677/joe.1.07099).

treatment_protocol: Proximal tibial epiphyses of 10-day-old Sprague-Dawley rats (n=8) were rapidly excised, trimmed of any soft connective tissues, embedded in Tissue-Tek O.C.T. Compound, sectioned (60 μm thick), mounted on Superfrost Plus slides, and stored at -80°C for subsequent processing.  Slides were thawed for 15 s and then placed in 70% ethanol, fixed in 100% methanol, washed in 95% ethanol, stained in eosin (0.2% eosin, 0.5% acetic acid, 75% ethanol), washed in 70% ethanol, dehydrated in 100% ethanol, and placed in xylene (each step for 1 min, at room temperature).  Microdissection was performed using an inverted microscope, razor blades, and hypodermic needles.  Tissues were microdissected in a xylene droplet and collected in 10 μl of 4M guanidine thiocyanate, 25mM sodium citrate pH7, and 0.1M β-mercaptoethanol on ice.  Enzymatic digestion of microdissected tissues was performed using buffered proteinase K solution (1,500 μl DEPC-treated water, 30 μl 1M Tris-HCl pH7, and 57.5 μl proteinase K (20 mg/ml in glycerol)).

tag: strain

value: Sprague-Dawley

value: proximal tibial epiphysis

tag: number of tissues

value: 4 from animals 3 and 4

value: 10 days postnatal

tag: zone

value: intermediate/deep zone


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 16


description: Gene expression data from_unpaired liver biopsy with relapse rep 3


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 12


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 14


title: Serous ovarian borderline tumor_biological_replicate_Id_16 borderline 16_BD2.a1.lbe1

city: Lund

first: Jenny-Maria

last: Jönsson

address: Scheelevägen 2

department: Division of Oncology, Department of Clinical Sciences

institute: Lund University

description: Biological replicate13

scan_protocol: Standard Illumina iScan N240 scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE

source_name: Serous ovarian tumor

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v 2.2)

extract_protocol: RNA was extracted using the Allprep kit (Qiagen) according to the manufacturer's instructions. RNA concentration was determined using a NanoDrop spectrophotometer (NanoDrop Technologies). Samples with <200 ng RNA and 260/280 ratios <1.8 were excluded. RNA quality control was performed with Agilent Bioanalyzer. RNA integrity numbers >6 were regarded sufficient.

tag: grade

tag: Stage

tag: age (years)

tag: source

value: Ovary

value: Serous ovarian borderline tumor


title: Serous ovarian borderline tumor borderline 86_2.a1.lbe1


title: Serous ovarian borderline tumor borderline 385.a1.lbe1


title: Serous ovarian borderline tumor borderline 48.a1.lbe1


title: Serous ovarian borderline tumor borderline 377_va_ov.a1.lbe1


title: Serous ovarian borderline tumor borderline 16.a1.lbe1

description: Biological replicate13


title: NMBA wk6 1

city: columbus

first: Ni

last: Shi

address: 400w 12th ave

department: comprehensive cancer center

institute: ohio state university

hyb_protocol: Affymetrix protocol

scan_protocol: Affy GeneChip Scanner 3000

data_processing:
The data were analyzed with Expression Console.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Rat230_2
program-version = 1.2.0.20

source_name: rat esophageal epithelia tissue 6 weeks after NMBA treatment

label_protocol: Affymetrix protocol

growth_protocol: rats were housed 3 per cage under standard conditions: 20 ± 2ºC, 50±10% relative humidity, and 12 hours light/dark cycles

extract_protocol: Half of esophagus was stripped of submucosal and muscularis layers and frozen in liquid nitrogen. The total RNA was extracted from frozen rat esophageal tissues using RNeasy Mini Kit.

treatment_protocol: After two weeks of acclimation to the animal facility, the rats were administered s.c. injections of 0.2 ml of either NMBA (0.3 mg/kg body weight) or a 1:4 mixture of dimethyl sulfoxide (DMSO):H2O (the solvent for NMBA) 3 times per week for 5 weeks.

tag: tumor development stage

value: Early stage of tumor development


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 13


title: Serous ovarian adenocarcinoma_biological_replicate_Id_90 90.a1.lbe1

description: Biological replicate12

value: Serous ovarian adenocarcinoma


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 11


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 8


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 9


title: Serous ovarian adenocarcinoma 70_2.a1.lbe1

value: Omentum


title: Serous ovarian adenocarcinoma 90_ov_ovarieoment.a1.lbe1

description: Biological replicate12


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 10


title: Serous ovarian adenocarcinoma 438.a1.lbe1


title: Serous ovarian adenocarcinoma 397_2_ovarieoment.a1.lbe1


title: Serous ovarian adenoma 408.a1.lbe1

value: Serous ovarian adenoma


title: Serous ovarian adenocarcinoma 84.a1.lbe1


title: Serous ovarian adenocarcinoma 402.a1.lbe1


title: Serous ovarian adenocarcinoma 420.a1.lbe1


title: Serous ovarian adenoma_biological_replicate_Id_461 461_2_vanshog.a1.lbe1

description: Biological replicate11


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 3


title: Serous ovarian adenoma 395_1.a1.lbe1

description: Biological replicate10


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 5


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 7


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 4


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 2


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 6


title: Serous ovarian adenoma_biological_replicate_Id_395 395_2_vanshog.a1.lbe1

description: Biological replicate10


description: Gene expression data from_unpaired liver biopsy with sustained virologic response rep 1


title: Serous ovarian adenocarcinoma 393.a1.lbe1


title: Active FVMs_2

city: Fukuoka

first: Keijiro

last: Ishikawa

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

department: Ophthalmology

country: Japan

institute: Kyushu University

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw gene expression data were summarized using the Illumina Bead Studio software. Thresholding of the signal values to 1is done and then normalized the data to 75th percentile and performs baseline transformation to median of all samples.These are performed by Genespring v 11.

source_name: FVMs with active NV

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

extract_protocol: To extract the RNAs, FVMs isolated from patients with PDR were homogenized with a Polytron homogenizer in extraction reagent, extracted with chloroform, and the aqueous phase was precipitated in isopropanol.

tag: disease state

value: Proliferative diabetic retinopathy (PDR)

value: fibrovascular membranes (FVMs)

tag: specimen

value: active NV


title: Serous ovarian adenoma 391.a1.lbe1


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 3

city: Madison

first: Ly

middle: L

last: Pham

state: WI

address: 2015 Linden Drive

department: Pathobiological Sciences

institute: UW-Madison

description: Biological Replicate 3 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US10130359.  Images were quantified using Agilent Feature Extraction Software.

data_processing: Limma was used for LOWESS normalization.

organism: Mus musculus

source_name: Mouse Liver-Two Weeks Transgene Expression-HT

label_protocol: 1.2 ug of RNA which was primed with T7 promoter primer from Agilent's two-color Low RNA Input Linear Amplification kit. Then, 1 ul of 10mM dNTPs, 2ul 0.1M DTT and MMLV RT. That goes 2.5 hours at 40C, then 15 min at 65C. Then transcribed with 3ul DTT, 4 ul NTP mix, 3.2 ul 50% PEG, T7 polymerase, and 1.2 ul cy 3 or 5-CTP per sample for 2.5 hours at 40C

extract_protocol: Total RNA extracted using Qiagen protocol following manufacturer's instructions

tag: gender

value: Female

tag: recipient gender

tag: transgene

value: H-ras and TGFα

source_name: Pooled mixed-gender reference mice

value: Liver


title: Serous ovarian adenocarcinoma 38.a1.lbe1

description: Biological replicate8

tag: tissue


title: Serous ovarian adenoma 461_1.a1.lbe1

description: Biological replicate11


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks


title: Serous ovarian adenoma_biological_replicate_Id_383 383_ovarialbitar_Ho_vanshog.a1.lbe1

description: Biological replicate9


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks

value: Male


title: Serous ovarian adenocarcinoma_biological_replicate_Id_38 38_BD2.a1.lbe1

description: Biological replicate8


title: Liver expressing H-ras and β-catenin transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 4. Liver expressing H-ras and β-catenin transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-HB

value: H-ras and β-catenin


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks


title: Liver expressing H-ras and β-catenin transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 4. Liver expressing H-ras and β-catenin transgene for Two Weeks


title: Liver expressing H-ras and TGFα transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing H-ras and TGFα transgene for Two Weeks


title: Liver expressing H-ras and β-catenin transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 4. Liver expressing H-ras and β-catenin transgene for Two Weeks


title: Liver expressing H-ras and β-catenin transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 4. Liver expressing H-ras and β-catenin transgene for Two Weeks


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-BM

value: β-catenin and c-Myc


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks


title: Serous ovarian adenoma 373.a1.lbe1


title: Serous ovarian adenocarcinoma_biological_replicate_Id_344 344_ov_tum_ho_vanshog.a1.lbe1

description: Biological replicate7


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks


title: Serous ovarian adenoma 336_ror2.a1.lbe1


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks


title: Serous ovarian adenoma 383.a1.lbe1

description: Biological replicate9


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-BT

value: β-catenin and TGFα


title: Serous ovarian adenocarcinoma 344.a1.lbe1

description: Biological replicate7


title: Serous ovarian adenoma 334.a1.lbe1


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks


title: Serous ovarian adenoma 335.a1.lbe1


title: Liver expressing β-catenin and c-Myc transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing β-catenin and c-Myc transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-MH

value: c-Myc and H-ras


title: Serous ovarian adenocarcinoma 330.a1.lbe1

value: Ovary


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-TM

value: TGFα and c-Myc


title: Serous ovarian adenoma 32.a1.lbe1


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks


title: Liver expressing β-catenin and TGFα transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing β-catenin and TGFα transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks


title: Liver expressing c-Myc and H-ras transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing c-Myc and H-ras transgene for Two Weeks


title: Serous ovarian adenoma 320.a1.lbe1


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks


title: Serous ovarian adenocarcinoma 311.a1.lbe1


title: Serous ovarian adenocarcinoma 314.a1.lbe1


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks


title: Liver expressing H-ras transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing H-ras transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-H

value: H-ras


title: Serous ovarian adenocarcinoma_biological_replicate_305 305_oment_ovarieoment.a1.lbe1

description: Biological replicate6

value: Serous ovarian adenocarcinoma


title: Liver expressing H-ras transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing H-ras transgene for Two Weeks


title: Liver expressing H-ras transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing H-ras transgene for Two Weeks


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks


title: Serous ovarian adenocarcinoma 307.a1.lbe1


title: Liver expressing H-ras transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing H-ras transgene for Two Weeks


title: Liver expressing H-ras transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing H-ras transgene for Two Weeks


title: Liver expressing TGFα and c-Myc transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing TGFα and c-Myc transgene for Two Weeks


title: Serous ovarian adenocarcinoma 306.a1.lbe1


title: Serous ovarian adenocarcinoma 297_oment_ovarieoment.a1.lbe1

description: Biological replicate 5


title: Liver expressing c-Myc transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing c-Myc transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-M

value: c-Myc


title: Liver expressing c-Myc transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing c-Myc transgene for Two Weeks


title: Serous ovarian adenocarcinoma 305.a1.lbe1

description: Biological replicate6


title: Liver expressing c-Myc transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing c-Myc transgene for Two Weeks


title: Serous ovarian adenoma 295_pool.a1.lbe1

value: Serous ovarian adenoma


title: Liver expressing c-Myc transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing c-Myc transgene for Two Weeks


title: Liver expressing TGFα transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing TGFα transgene for Two Weeks

source_name: Mouse Liver-Two Weeks Transgene Expression-T

value: TGFα


title: Liver expressing c-Myc transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing c-Myc transgene for Two Weeks


title: Serous ovarian adenocarcinoma_biological_replicate_Id_297 297.a1.lbe1

description: Biological replicate5


title: Liver expressing TGFα transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing TGFα transgene for Two Weeks


title: Liver expressing c-Myc transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing c-Myc transgene for Two Weeks


title: Liver expressing TGFα transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing TGFα transgene for Two Weeks


title: Serous ovarian adenocarcinoma 293.a1.lbe1


title: Serous ovarian adenocarcinoma 284_2.a1.lbe1

value: Omentum


title: Liver expressing TGFα transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing TGFα transgene for Two Weeks


title: Liver expressing TGFα transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing TGFα transgene for Two Weeks


title: PBMC day 24 rep 12

description: Gene expression data from_PBMC day 24 rep 12

source_name: PBMC day 24 rep 12

value: PBMC

tag: time point

value: day 24

tag: agent/dose


title: Liver expressing TGFα transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing TGFα transgene for Two Weeks

value: Female


title: Liver expressing β-catenin transgene for Two Weeks Replicate 4

description: Biological Replicate 4 of 6. Liver expressing β-catenin transgene for Two Week

source_name: Mouse Liver-Two Weeks Transgene Expression-B

value: β-catenin

value: Liver


title: Liver expressing H-ras transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing H-ras transgene for Two Weeks

value: Male


title: Liver expressing β-catenin transgene for Two Weeks Replicate 5

description: Biological Replicate 5 of 6. Liver expressing β-catenin transgene for Two Week


title: PBMC day 24 rep 11

description: Gene expression data from_PBMC day 24 rep 11

source_name: PBMC day 24 rep 11


title: Serous ovarian adenocarcinoma_biological_replicate_id_279 279_om_ovarieoment.a1.lbe1

description: Biological replicate4


title: Serous ovarian adenocarcinoma 275.a1.lbe1


title: Liver expressing β-catenin transgene for Two Weeks Replicate 1

description: Biological Replicate 1 of 6. Liver expressing β-catenin transgene for Two Week


title: Serous ovarian adenocarcinoma 273.a1.lbe1


title: Serous ovarian adenoma 262_2.a1.lbe1


title: Serous ovarian adenocarcinoma 279.a1.lbe1

description: Biological replicate4


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression TGFα and c-Myc transgene

source_name: Individual Liver Tumor-TM


title: Serous ovarian adenocarcinoma 251.a1.lbe1

source_name: Serous ovarian tumor


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression TGFα and c-Myc transgene


title: PBMC day 24 rep 9

description: Gene expression data from_PBMC day 24 rep 9

source_name: PBMC day 24 rep 9


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression TGFα and c-Myc transgene


title: Liver expressing β-catenin transgene for Two Weeks Replicate 3

description: Biological Replicate 3 of 6. Liver expressing β-catenin transgene for Two Week


title: Liver expressing β-catenin transgene for Two Weeks Replicate 6

description: Biological Replicate 6 of 6. Liver expressing β-catenin transgene for Two Week


title: PBMC day 24 rep 10

description: Gene expression data from_PBMC day 24 rep 10

source_name: PBMC day 24 rep 10


title: Serous ovarian adenocarcinoma_biological_replicate_Id_226 226_BD2.a1.lbe1

description: Biological replicate3


title: Liver expressing β-catenin transgene for Two Weeks Replicate 2

description: Biological Replicate 2 of 6. Liver expressing β-catenin transgene for Two Week


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression TGFα and c-Myc transgene


title: PBMC day 24 rep 6

description: Gene expression data from_PBMC day 24 rep 6

source_name: PBMC day 24 rep 6


title: Serous ovarian adenocarcinoma 232_2.a1.lbe1


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression TGFα and c-Myc transgene

source_name: Pooled mixed-gender reference mice


title: PBMC day 24 rep 8

description: Gene expression data from_PBMC day 24 rep 8

source_name: PBMC day 24 rep 8


title: PBMC day 24 rep 7

description: Gene expression data from_PBMC day 24 rep 7

source_name: PBMC day 24 rep 7


title: Liver tumor expressing TGFα transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression TGFα transgene

source_name: Individual Liver Tumor-T


title: Liver tumor expressing TGFα transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression TGFα transgene


title: Liver tumor expressing TGFα and c-Myc transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression TGFα and c-Myc transgene


title: Serous ovarian adenocarcinoma 225.a1.lbe1


title: Liver tumor expressing TGFα transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression TGFα transgene


title: PBMC day 24 rep 5

description: Gene expression data from_PBMC day 24 rep 5

source_name: PBMC day 24 rep 5


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression c-Myc and H-ras transgene

source_name: Individual Liver Tumor-MH


title: PBMC day 24 rep 4

description: Gene expression data from_PBMC day 24 rep 4

source_name: PBMC day 24 rep 4


title: Serous ovarian adenocarcinoma 226.a1.lbe1

description: Biological replicate3


title: PBMC day 24 rep 3

description: Gene expression data from_PBMC day 24 rep 3

source_name: PBMC day 24 rep 3


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression c-Myc and H-ras transgene


title: Serous ovarian adenocarcinoma 219.a1.lbe1

description: Biological replicate2

value: Fallopian tube


title: Liver tumor expressing TGFα transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression TGFα transgene


title: Serous ovarian adenoma 216.a1.lbe1


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression c-Myc and H-ras transgene


title: Liver tumor expressing TGFα transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression TGFα transgene


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression c-Myc and H-ras transgene


title: Liver tumor expressing TGFα transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression TGFα transgene


title: PBMC day 24 rep 2

description: Gene expression data from_PBMC day 24 rep 2

source_name: PBMC day 24 rep 2


title: Serous ovarian adenocarcinoma_biological_replicate_Id_219 219_BD2.a1.lbe1

description: Biological replicate2


title: Liver tumor expressing c-Myc transgene Replicate 10

description: Biological Replicate 10 of 10. Liver tumor expression c-Myc transgene

source_name: Individual Liver Tumor-M


title: Serous ovarian adenocarcinoma 207.a1.lbe1


title: Liver tumor expressing c-Myc transgene Replicate 9

description: Biological Replicate 9 of 10. Liver tumor expression c-Myc transgene


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression c-Myc and H-ras transgene


title: Liver tumor expressing c-Myc transgene Replicate 7

description: Biological Replicate 7 of 10. Liver tumor expression c-Myc transgene


title: PBMC day 10 rep 8

description: Gene expression data from_PBMC day 10 rep 8

source_name: PBMC day 10 rep 8

value: day 10


title: Liver tumor expressing c-Myc transgene Replicate 6

description: Biological Replicate 6 of 10. Liver tumor expression c-Myc transgene


title: Serous ovarian adenocarcinoma 192_2 _ovarieoment.a1.lbe1


title: Serous ovarian adenocarcinoma 190.a1.lbe1


title: Liver tumor expressing c-Myc transgene Replicate 8

description: Biological Replicate 8 of 10. Liver tumor expression c-Myc transgene


title: Serous ovarian adenocarcinoma_biological_replicate_Id_186 186_BD2.a1.lbe1

description: Biological replicate1

value: Cystic fluid


title: PBMC day 10 rep 7

description: Gene expression data from_PBMC day 10 rep 7

source_name: PBMC day 10 rep 7


title: Liver tumor expressing c-Myc transgene Replicate 3

description: Biological Replicate 3 of 10. Liver tumor expression c-Myc transgene


title: Liver tumor expressing c-Myc transgene Replicate 1

description: Biological Replicate 1 of 10. Liver tumor expression c-Myc transgene


title: Liver tumor expressing c-Myc transgene Replicate 4

description: Biological Replicate 4 of 10. Liver tumor expression c-Myc transgene


title: PBMC day 10 rep 6

description: Gene expression data from_PBMC day 10 rep 6

source_name: PBMC day 10 rep 6


title: PBMC day 24 rep 1

description: Gene expression data from_PBMC day 24 rep 1

source_name: PBMC day 24 rep 1


title: Liver tumor expressing H-ras and TGFα transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression H-ras and TGFα transgene

source_name: Individual Liver Tumor-HT

value: H-ras and TGFα


title: Liver tumor expressing c-Myc transgene Replicate 5

description: Biological Replicate 5 of 10. Liver tumor expression c-Myc transgene


title: PBMC day 10 rep 5

description: Gene expression data from_PBMC day 10 rep 5

source_name: PBMC day 10 rep 5


title: PBMC day 10 rep 3

description: Gene expression data from_PBMC day 10 rep 3

source_name: PBMC day 10 rep 3


title: PBMC day 10 rep 4

description: Gene expression data from_PBMC day 10 rep 4

source_name: PBMC day 10 rep 4


title: Serous ovarian adenocarcinoma 153_2 ovarie.a1.lbe1

source_name: Serous ovarian tumor

value: Ovary


title: Liver tumor expressing H-ras and TGFα transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression H-ras and TGFα transgene

source_name: Pooled mixed-gender reference mice


title: Liver tumor expressing H-ras and TGFα transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression H-ras and TGFα transgene


title: Serous ovarian adenocarcinoma 159.a1.lbe1


title: Liver tumor expressing c-Myc transgene Replicate 2

description: Biological Replicate 2 of 10. Liver tumor expression c-Myc transgene


title: Serous ovarian adenocarcinoma 186.a1.lbe1

description: Biological replicate1


title: Serous ovarian adenoma 168.a1.lbe1


title: Liver tumor expressing H-ras and TGFα transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression H-ras and TGFα transgene


title: Liver tumor expressing H-ras and TGFα transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression H-ras and TGFα transgene


title: Serous ovarian adenocarcinoma 137.a1.lbe1


title: PBMC day 10 rep 2

description: Gene expression data from_PBMC day 10 rep 2

source_name: PBMC day 10 rep 2


title: PBMC day 0 rep 3

description: Gene expression data from_PBMC day 0 rep 3

source_name: PBMC day 0 rep 3

value: day 0


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression H-ras and β-catenin transgene

source_name: Individual Liver Tumor-HB

value: H-ras and β-catenin


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression H-ras and β-catenin transgene


title: Liver tumor expressing c-Myc and H-ras transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression c-Myc and H-ras transgene

source_name: Individual Liver Tumor-MH

value: c-Myc and H-ras


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression H-ras and β-catenin transgene


title: Serous ovarian adenoma 149.a1.lbe1

value: Serous ovarian adenoma


title: Serous ovarian adenocarcinoma 125.a1.lbe1

value: Serous ovarian adenocarcinoma


title: Liver tumor expressing H-ras and TGFα transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression H-ras and TGFα transgene


title: PBMC day 0 rep 2

description: Gene expression data from_PBMC day 0 rep 2

source_name: PBMC day 0 rep 2


title: PBMC day 10 rep 1

description: Gene expression data from_PBMC day 10 rep 1

source_name: PBMC day 10 rep 1


title: PBMC day 0 rep 4

description: Gene expression data from_PBMC day 0 rep 4

source_name: PBMC day 0 rep 4


title: Serous ovarian adenocarcinoma 118.a1.lbe1


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression H-ras and β-catenin transgene


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression H-ras and β-catenin transgene


title: PBMC day 0 rep 1

description: Gene expression data from_PBMC day 0 rep 1

source_name: PBMC day 0 rep 1


title: Liver tumor expressing H-ras and β-catenin transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression H-ras and β-catenin transgene


title: Serous ovarian adenoma 129.a1.lbe1


title: Serous ovarian adenocarcinoma 106_pool.a1.lbe1


title: paired liver biopsy pre treatment rep 6

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

source_name: paired liver biopsy pre treatment rep 6

value: paired liver biopsy

value: pre treatment


title: Liver tumor expressing H-ras transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression H-ras transgene

source_name: Individual Liver Tumor-H

value: H-ras


description: Gene expression data from_paired liver biopsy pre-C treatment rep 8

value: pre-C treatment


description: Gene expression data from_paired liver biopsy pre-C treatment rep 7


title: paired liver biopsy pre treatment rep 5

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

source_name: paired liver biopsy pre treatment rep 5


title: Liver tumor expressing H-ras transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression H-ras transgene

value: Female


description: Gene expression data from_paired liver biopsy end of treatment (post-C) rep 8

value: end of treatment (post-C)


title: paired liver biopsy pre treatment rep 2

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

source_name: paired liver biopsy pre treatment rep 2


title: Liver tumor expressing H-ras transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression H-ras transgene

value: Male

value: Liver


title: Liver tumor expressing H-ras transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression H-ras transgene


title: paired liver biopsy pre treatment rep 1

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

source_name: paired liver biopsy pre treatment rep 1


title: Liver tumor expressing H-ras transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression H-ras transgene


title: paired liver biopsy pre treatment rep 4

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

source_name: paired liver biopsy pre treatment rep 4


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 5

value: end of treatment (post)


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 6


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression β-catenin and TGFα transgene

source_name: Individual Liver Tumor-BT

value: β-catenin and TGFα


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression β-catenin and TGFα transgene


description: Gene expression data from_paired liver biopsy end of treatment (post-C) rep 7


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 4


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression β-catenin and TGFα transgene


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 3


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression β-catenin and TGFα transgene


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression β-catenin and TGFα transgene


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 1


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 3

description: Biological Replicate 3 of 6. Liver tumor expression β-catenin and c-Myc transgene

source_name: Individual Liver Tumor-BM

value: β-catenin and c-Myc


description: Gene expression data from_paired liver biopsy end of treatment (post) rep 2


title: Liver tumor expressing β-catenin and TGFα transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression β-catenin and TGFα transgene

source_name: Pooled mixed-gender reference mice


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 5

description: Biological Replicate 5 of 6. Liver tumor expression β-catenin and c-Myc transgene


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 4

description: Biological Replicate 4 of 6. Liver tumor expression β-catenin and c-Myc transgene


title: Salivary tumor from MMTV-ras/p53R172H/R172H mouse, rep 3

city: Stanford

first: Dadi

last: Jiang

state: CA

address: 269 Campus Drive, CCSR-South 1240

institute: Stanford University

hyb_protocol: 20μg of the fragmented cRNA from each sample was hybridized to the Mouse 430A 2.0 chip for 18 to 20 hours.  The chip was then washed and stained with streptavidin phycoerythrin (SAPE; Molecular Probes, Eugene, OR) added with an antistreptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA).

scan_protocol: Each chip was scanned at a 6-μm resolution by the Agilent G2500A Technologies Gene Array scanner (Agilent Technologies, Palo Alto, CA).

data_processing: After scanning, the raw intensities of each probe were stored in electronic files (in .DAT and .CEL formats) by the Microarray Suite 5.0 software (Affymetrix, Santa Clara, CA). .CEL files were compiled and normalized by RMA using BRB-ArrayTools.

label_protocol: Using 2μg cDNA, biotin-labeled cRNA was synthesized using the Enzo BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostic Inc., Farmingdale, NY) with Bio-11-CTP and Bio-16-UTP.

growth_protocol: Salivary tumors isolated from adult MMTV-ras transgenic mice with different p53 genotypic status

extract_protocol: For RNA extraction, 20-40 10μm frozen sections from each candidate tumor were collected.  RNA was extracted using TRIZOL reagent (InvitrogenTM Life Technologies), according to the manufacture’s protocols. Total RNA isolated from the tumor sections was subjected to a cleanup step using the RNeasy Mini Kit (Qiagen Sciences Inc.).

treatment_protocol: Not applicable

tag: genotype


title: Salivary tumor from MMTV-ras/p53R172H/R172H mouse, rep 4


title: Salivary tumor from MMTV-ras/p53R172H/R172H mouse, rep 1


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 2

description: Biological Replicate 2 of 6. Liver tumor expression β-catenin and c-Myc transgene

tag: strain


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 1

description: Biological Replicate 1 of 6. Liver tumor expression β-catenin and c-Myc transgene


title: Control liver with hPAP marker Replicate 5

description: Biological Replicate 5 of 6. Control liver expression hPAP marker

source_name: Mouse Liver, Control

value: hPAP


title: NTera-2 cells SOX2 siRNA, biological replicate 1

city: Dublin

first: Sebastian

last: Vencken

address: Catherine McAuley Centre, Nelson Street

department: Clinical Research Centre

country: Ireland

institute: University College Dublin

hyb_protocol: Hybridisation was performed for 17 hours at 45°C in a Affymetrix GeneChip Hybridization Oven 640. Chips were washed with the Affymetrix GeneChi Hybridization, Wash and Stain Kit on a Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was analysed with R/CRAN statstical software with the Bioconductor 2.9 package and the Linear Models for Microarray Data (limma) plugin

source_name: NTera-2 cells transfected with Ambion Silencer Select SOX2 siRNA

label_protocol: Labelling was performed with the Affymetrix GeneChip WT Terminal Labeling Kit as per manufacturer's protocol.

growth_protocol: 2102Ep and NTera-2 cell lines were grown in normal growth medium containing Dulbecco's Modified Eagle's Medium supplemented with 10% foetal bovine serium and 2% Penicillin-Streptomycin mixture. Cells were kept at 37°C and 5% CO2.

extract_protocol: Samples were extracted with the Ambion miRVana PARIS kit as per manufacturers protocol.

treatment_protocol: 24 hours prior to transfection, 2102Ep and NTera-2 cells were seeded on 6-well plates in normal growth medium without antibiotics. For transfection, old media were replaced with reduced-serum Opti-MEM I medium. siRNA previously incubated with Lipofectamine 2000 (2102Ep cells) or Lipofectamine RNAiMAX (NTera-2 cells) in Opti-MEM I were added to the cells and these were incubated under transfection conditions for 6 hours. After transfection, media were replaced with normal growth medium and sample incubated for 72 hours with daily medium refreshing.

tag: treatment

tag: cell type

value: embryonal carcinoma

tag: cell line

tag: passage


title: paired liver biopsy pre treatment rep 3

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

source_name: paired liver biopsy pre treatment rep 3


title: NTera-2 cells SOX2 siRNA, biological replicate 3

value: transfected with Ambion Silencer Select SOX2 siRNA


title: Salivary tumor from MMTV-ras/p53-/- mouse, rep 4


title: NTera-2 cells SOX2 siRNA, biological replicate 2


title: Control liver with hPAP marker Replicate 4

description: Biological Replicate 4 of 6. Control liver expression hPAP marker


title: Salivary tumor from MMTV-ras/p53-/- mouse, rep 3


title: Salivary tumor from MMTV-ras/p53-/- mouse, rep 2


title: Liver tumor expressing β-catenin and c-Myc transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression β-catenin and c-Myc transgene


title: Salivary tumor from MMTV-ras/p53-/- mouse, rep 1


title: Control liver with hPAP marker Replicate 3

description: Biological Replicate 3 of 6. Control liver expression hPAP marker


title: Salivary tumor from MMTV-ras/p53+/+ mouse, rep 4


title: NTera-2 cells negative control, biological replicate 1

source_name: NTera-2 cells transfected with Ambion Silencer Select Negative Control #1


title: Salivary tumor from MMTV-ras/p53+/+ mouse, rep 3


title: NTera-2 cells negative control, biological replicate 3

value: transfected with Ambion Silencer Select Negative Control #1


title: NTera-2 cells negative control, biological replicate 2


title: 2102Ep cells SOX2 siRNA, biological replicate 3

source_name: 2102Ep cells transfected with Ambion Silencer Select SOX2 siRNA


title: Salivary tumor from MMTV-ras/p53+/+ mouse, rep 2


title: Salivary tumor from MMTV-ras/p53R172H/R172H mouse, rep 2


title: 2102Ep cells SOX2 siRNA, biological replicate 2


title: 2102Ep cells negative control, biological replicate 1

source_name: 2102Ep cells transfected with Ambion Silencer Select Negative Control #1


title: 2102Ep cells negative control, biological replicate 3


title: J0571 DEX repeat2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocolFS450_0002, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.26.6).

label: Biotin

organism: Arabidopsis thaliana

source_name: 4-day-old seedlings, roots protoplasted and cell sorted for GFP+ cells, followed by RNA extraction

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

growth_protocol: All seeds were surface sterilized, sown on solid MS plates and vernalized for two days before growing at a constant temperature of 22°C in a growth room.

extract_protocol: Total RNA was isolated using Trizol-Chlorophorm extraction followed by clean-up using the RNeasy Plant Mini kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: 4-day-old seedlings were transferred to MS medium supplemented with the indicated compound for the indicated time. Next, roots were harvested and either used for total RNA extraction, or protoplasted and used for cell sorting (as described in Brady et al., 2007 Science [PMID: 17975066] with minor modifications), followed by total RNA extraction.

tag: treatment time

value: DEX

value: protoplasted root

value: GFP+ FACS sorted cells

tag: genetic background (ecotype)

tag: introduced construct


title: J0571 DEX repeat3


title: Control liver with hPAP marker Replicate 1

description: Biological Replicate 1 of 6. Control liver expression hPAP marker


title: Control liver with hPAP marker Replicate 6

description: Biological Replicate 6 of 6. Control liver expression hPAP marker


title: Control liver with hPAP marker Replicate 2

description: Biological Replicate 2 of 6. Control liver expression hPAP marker


title: 2102Ep cells negative control, biological replicate 2


title: J0571 DEX repeat1


title: Liver tumor expressing H-ras transgene Replicate 6

description: Biological Replicate 6 of 6. Liver tumor expression H-ras transgene


title: CN5

city: Chicago

first: Cathryn

last: Nagler

state: IL

address: 924 E 57th St

institute: University of Chicago

description: gnotobiotic animals

hyb_protocol: Standard Illumina Protocol

scan_protocol: Illumina BeadStudio

data_processing:
Background subtraction and quantile normalization was performed with Illumina software
Raw or Background-subtracted, quantile normalized intensities from Illumina BeadStudio

source_name: colonic epithelial cells, Bacteroides-uniformis colonized

label_protocol: Illumina TotalPrep RNA

growth_protocol: mice in gnotobiotic isolators

extract_protocol: Qiagen Rneasy Mini

treatment_protocol: Colons were dissected, epithelial cells were liberated by treatment with 5mM EDTA


title: CN4

description: gnotobiotic animals

source_name: colonic epithelial cells, Germ free


title: CN8

description: gnotobiotic animals

source_name: colonic epithelial cells, Clostridia-colonized


title: Apc-Prox1 deleted, Series2, repl3

city: Helsinki

first: Zoltan

last: Wiener

address: Haartmaninkatu 8

department: Molecular Cancer Biology Programme

country: Finland

institute: University of Helsinki

description: Series2, repl3

data_processing: The data were normalized with the default normalization method for Illumina arrays, followed by normalization to chip avarage and to gene avarage in Chipster. Series1 and series 2 were normalized separately. Replicates are samples taken at different passage numbers and series are from different mice.

source_name: ex vivo intestinal organoid

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

growth_protocol: Intestinal organoids were grown according to Sato et al (Nature, 2009). To select the Apc-mutant organoids, the Wnt-agonist R-Spondin1 was removed2 days after the deletion of the genes for 5 days.

extract_protocol: Total RNA was extracted by the NucleoSpin RNA II isolation kit (Macherey-Nagel) according to the manufacturer, including DNase treatment. RNA quality was checked by Agilent Bioanalyzer

treatment_protocol: Tamoxifen for 2 days to activate the intetsinal epithelium-specific expression of the CreER allele.

tag: genotype/variation

value: Apc-Prox1 deleted

tag: age

value: 2-3 months

value: intestinal organoid


title: J0571 control repeat2

value: MS


title: CN7

description: gnotobiotic animals


title: Apc-Prox1 deleted, Series2, repl2

description: Series2, repl2


title: J0571 control repeat3


title: CN3

description: gnotobiotic animals


title: Apc-Prox1 deleted, Series2, repl1

description: Series2, repl1


title: Apc-deleted, Series2, repl3

description: Series2, repl3

value: Apc-deleted


title: CN6

description: gnotobiotic animals


title: NTera-2 cells SOX2 siRNA, biological replicate 1_miRNA

hyb_protocol: not applicable

scan_protocol: qPCR and scanning was performed with an Applied Biosystems Prism 7900HT Sequence Detection System

data_processing:
Ct values were obtained with Applied Biosystems RQ Manager software and were further analysed using Applied Biosystems DataAssist 3.0 software
2^-ddCt method was used to obtain fold changes

label: FAM

label_protocol: cDNA was prepared from total RNA using the Applied Biosystems TaqMan MicroRNA Reverse Transcription Kit and the Applied Biosystems Megaplex RT Human Pool A and RT Human Pool B primer mix. Further pre-amplification was performed with Applied Biosystems TaqMan PreAmp Master Mix combined with the Applied Biosystems Megaplex PreAmp Primers, Human Pool A and Human Pool B. For PCR, the Applied Biosystems TaqMan Array Human MicroRNA A & B cards were used with Applied Biosystems TaqMan Universal Master Mix, No Amperase® UNG. All protocols were performed as per manufacturer’s instructions.


title: NTera-2 cells negative control, biological replicate 3_miRNA


title: NTera-2 cells SOX2 siRNA, biological replicate 2_miRNA


title: CN2

description: gnotobiotic animals


title: NTera-2 cells SOX2 siRNA, biological replicate 3_miRNA


title: CHX repeat3

source_name: 4-day-old seedlings, transfered to CHX for 1h, harvested root tips

value: CHX

value: root


title: NTera-2 cells negative control, biological replicate 2_miRNA


title: Salivary tumor from MMTV-ras/p53+/+ mouse, rep 1


title: DEX+CHX repeat3

source_name: 4-day-old seedlings, transfered to DEX+CHX for 1h, harvested root tips

value: DEX+CHX


title: Apc-deleted, Series2, repl2

description: Series2, repl2


title: DPmut3

city: Frederick

first: David

last: Salomon

state: MD

address: 1050 Boyles Drive, Bldg. 560 Room 1246

department: NCI

description: Thpok-deficient CD4+CD8+ T cells, Biological Replicate 3

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip® Mouse Exon 1.0 ST Array  in the Affymetrix GeneChip Hybridization Oven 640 for 16 hours overnight according to the manufacturer's recommendations (Affymetrix).

scan_protocol: All arrays were scanned using Affymetrix GeneChip Scanner 3000 7G and processed using GeneChip® Command Console Software (AGCC).

data_processing:
Data were processed using Partek GS version 6.12.0530 using RMA Background Correction and  Quantile Normalization
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

label_protocol: cDNA samples were processed using the GeneChip HT 3' IVT Express Kit (Affymetrix, Santa Clara, California) according to the manufacturer's protocol.

growth_protocol: Sorted CD44lo CD4+CD8- or CD4-CD8+ spleen T cells were mixed with 2 x 106 irradiated antigen-presenting cells (obtained from C57BL/6 splenocytes by Thy1.2 magnetic bead depletion and irradiated at 2500 rad) in complete culture medium (RPMI 1640 supplemented with 10% FCS) and activated with anti-CD3 (2C11, 1 μg/ml) and anti-CD28 (3 μg/ml) in the presence of 50 U/ml IL-2, 10 ng/ml IL-12, 10 μg/ml anti-IL-4.

extract_protocol: Total RNA was extracted with RNAqueous (Ambion) following the manufacturer's instructions.

value: Thpokf/f CD2cre

tag: culture

tag: surface phenotype


title: Apc-Prox1 deleted, Series1, repl4

description: Series1, repl4


title: NTera-2 cells negative control, biological replicate 1_miRNA


title: 2102Ep cells SOX2 siRNA, biological replicate 1


title: DPmut2

description: Thpok-deficient CD4+CD8+ T cells, Biological Replicate 2


title: Apc-deleted, Series2, repl1

description: Series2, repl1


title: 2102Ep cells SOX2 siRNA, biological replicate 3_miRNA


title: CN1

description: gnotobiotic animals


title: DPmut1

description: Thpok-deficient CD4+CD8+ T cells, Biological Replicate 1


title: DEX repeat3

source_name: 4-day-old seedlings, transfered to DEX for 1h, harvested root tips


title: CHX repeat2


title: Apc-deleted, Series1, repl4

description: Series1, repl4


title: Apc-deleted, Series1, repl3

description: Series1, repl3


title: MS repeat3

source_name: 4-day-old seedlings, transfered to MS for 1h, harvested root tips


title: J0571 control repeat1


title: DEX+CHX repeat2


title: CD4mut3

description: Thpok-deficient CD4+CD8- T cells, Biological Replicate 3


title: Apc-Prox1 deleted, Series1, repl3

description: Series1, repl3


title: 2102Ep cells negative control, biological replicate 3_miRNA


title: 2102Ep cells SOX2 siRNA, biological replicate 1_miRNA


title: Apc-Prox1 deleted, Series1, repl2

description: Series1, repl2


title: CD4mut1

description: Thpok-deficient CD4+CD8- T cells, Biological Replicate 1


title: DEX repeat2


title: 2102Ep cells negative control, biological replicate 2_miRNA


title: 2102Ep cells negative control, biological replicate 1_miRNA


title: CD8wt2

description: wild-type CD8 T cells, Biological Replicate 2

value: wild-type


title: Le99

status: Public on Aug 14 2014

city: Hyderabad

first: Lekha

middle: Dinesh

last: Kumar

state: Andhra Pradesh

address: Uppal road, habshiguda

department: Cancer biology

country: India

institute: Centre for cellular and molecular biology

data_processing: The microRNA mean cycle threshold values (Ct) were first normalized to their respective endogenous controls (RNA46 and RNU 48) to obtain their - ΔCt values. The mean Δ Ct values (ΔCt) of cancer samples were deducted from the mean Δ Ct values of respective blood and bone marrow collected from normal individuals to obtain the ΔΔCt values. The fold changes were calculated and analyzed using RealTime StatMiner® Software.

source_name: BONE MARROW

label_protocol: The isolated RNA were used for  reverse transcription (RT) reactions  with the help of TaqMan MicroRNA Reverse Transcription Kit followed by PCR Reaction (ABI 7900 HT) as per illustration provided in kit. Real-time PCR was performed using an Applied Biosystems 7900 HT- TLDA Real-Time PCR System. A pre -amplification step of cDNA with pre-amp megaplex pool primers was done to significantly enhance the ability to detect highly down regulated miRNAs.

growth_protocol: Peripheral Blood and Bone Marrow samples were collected after immunophetyping using flow cytometer

extract_protocol: A portion of the samples stored in RNA later was used for RNA isolation. Total RNAs were isolated using miRvana kit from homogenized samples in automated tissue homogenizer. The quantity of these RNAs was checked using nanodrop whereas quality was checked by loading them onto 1% agarose gel.  RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to provide more robust measurement of RNA. The RIN values are algorithm which ranges between 1-10 where 10 indicates total intactness of RNA quality.Those samples >7 was taken for further analysis.

treatment_protocol: The collected bone marrow and peripheral blood samples were separated (1 ml) and mixed with RBC lysis buffer for 15min at RT and centrifuged for 10 min at 2500rpm. This step was repeated to achieve RBC free clear pellet.  The pellet was further washed in PBS by short centrifugation at 5000 RPM, suspended in RNA later (Invitrogen, USA) and stored at -80º C until RNA isolation.

value: T-ALL

tag: gender

value: Male

tag: tag

value: 12 years


title: CD4mut2

description: Thpok-deficient CD4+CD8- T cells, Biological Replicate 2


title: Le174

value: 10 years


title: Le178


title: CD8wt1

description: wild-type CD8 T cells, Biological Replicate 1


title: CD4wt3

description: wild-type CD4 T cells, Biological Replicate 3


title: DEX+CHX repeat1

tag: tissue


title: Le176


title: Le91

value: Female

value: 11 years


title: Apc-Prox1 deleted, Series1, repl1

description: Series1, repl1


title: MS repeat2


title: Le161


title: CD4wt2

description: wild-type CD4 T cells, Biological Replicate 2


title: Apc-deleted, Series1, repl2

description: Series1, repl2


title: CHX repeat1


title: DEX repeat1

value: DEX


title: Le128

value: 13 years


title: Le111

value: 6 years


title: Le142


title: Le82

source_name: PERIPHERAL BLOOD


title: CD4wt1

description: wild-type CD4 T cells, Biological Replicate 1


title: Le78


title: Le72


title: Le71


title: grafted small intestinal epithelium

city: Bunkyo-ku

first: Tetsuya

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

department: Department of Advanced Therapeutics for GI Diseases

institute: Tokyo Medical and Dental University

description:
Gene expression data from short intestine derived grafts of a recipient mouse at 4 weeks post-transplantation
SI_on_Colon

hyb_protocol: Five micrograms of cDNA were hybridized on the GeneChip Mouse Gene 1.0 ST Array using  the GeneChip Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX Version 12.5 software (Agilent). RMA16 was used as summarization algorithm with the settings of Confidence level = All and Baseline Options = Do not perform baseline transformation. The bottom 20% of genes with the lowest expression levels was excluded.

source_name: Mouse small intestinnal epithelium grafted onto colon

label_protocol: cDNA synthesis and amplification were performed with Ovation Pico WTA System V2 using 4.33 ng of total RNA  (Ovation® Pico WTA System V2 Manual,M01113 v3, NuGEN).The following steps of fragmentation and labeling were performed with Encore Biotin Module (Encore® Biotin Module Manual,M01111 v5, NuGEN)

growth_protocol: Murine small intestinal epithelial cells were obtained from EGFP-transgenic mice of C57BL6 background. Cells were grown as stem cell-containing organoids in vitro.

extract_protocol: Total RNA extraction was performed by using RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: After seven days of culture, small intestinal organoids were collected and instilled into colonic lumens of recipient C57BL6 mice. Recipient mice at 4 weeks post-transplantation were sacrificed and subjected for gene analysis. Normal colonic epithelia were obtained from C57BL6 mice and used as reference. Grafted epithelia in recipients or control colonic epithelia were microdissected using Micro Laser System MBIII (PALM/ZEISS).

value: small intestinal epithelium grafted onto colon


title: MS repeat1

value: MS


title: Le33

value: 2 years


title: Le136


title: Le139


title: Le115

value: 16 years


title: Le127


title: Le86

value: B-ALL


title: Le114


title: Le147


title: Le110


title: Le109

value: 3 years


title: Le107


title: Le103


title: Le102

value: 4 years


title: Le100


title: Apc-deleted, Series1, repl1

description: Series1, repl1

value: Apc-deleted

value: 2-3 months

value: intestinal organoid


title: control colonic epithelium

description:
Gene expression data from a C57BL control mouse
Control_Colon

source_name: Mouse control colon tissue

value: control colon


title: Le79

value: Femlae


title: Le53

value: Male


title: Le74

value: 10 years


title: Le152


title: Le65

value: Female


title: Le117


title: Le49

value: 5 years


title: Le52


title: Le58

value: 8 years


title: Le158N

value: NORMAL


title: Le10

value: T-ALL

value: 6 years


title: Le159N

value: 2 years


title: LeNM1

value: 9 years


title: LeNN2


title: Le108

value: B-ALL

value: 12 years


title: Le146N


title: Le134N


title: LeNC2


title: LeND

value: 11 years


title: Le1N


title: Le70


title: Le19


title: Le163N


title: leukocytes P_44_JMB_M_C SNP5

type: genomic

city: Campinas

first: Benilton

middle: Sa

last: Carvalho

state: Sao Paulo

address: Tessália Vieira de Camargo, 126

department: Medical Genetics

country: Brazil

institute: Universidade Estadual de Campinas

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics stations.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 3.0.2). Signal intensities and Genotypes for individual SNPs were obtained from CEL files using the R/BioConductor 'crlmm' package.
Genotype calls are included in the Sample data table; the summarized signals for alleles A and B, and the confidence scores for the genotype calls, are included in supplementary files that are linked to the Series record (GSE46812).

molecule: genomic DNA

source_name: leukocytes from peripheral blood, BTSCC

label_protocol: DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from leukocytes obtained from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: disease status

value: BTSCC

value: peripheral blood

value: male


title: leukocytes P_45_ACS_M_C SNP5


title: leukocytes P_48_ESB_M_C SNP5


title: leukocytes P_49_JRSF2_M_C SNP5


title: leukocytes P_43_JFS_M_C SNP5


title: leukocytes P_41_BA_M_C SNP5


title: leukocytes P_35_AC_M_N SNP5


title: leukocytes P_46_JGS2_M_C SNP5


title: leukocytes P_21_CDM_M_C SNP5


title: leukocytes P_40_JGSRJ_M_C SNP5


title: leukocytes P_38_FSRJ_M_N SNP5


title: leukocytes P_37_JBSO_M_C SNP5


title: leukocytes P_34_BS_M_N SNP5


title: leukocytes P_47_GBS_M_N SNP5


title: 2102Ep cells SOX2 siRNA, biological replicate 2_miRNA

value: embryonal carcinoma


title: leukocytes P_30_JLT_M_C SNP5


title: leukocytes P_28_JF2_M_N SNP5


title: leukocytes P_32_AV_M_C SNP5


title: leukocytes P_31_OBF_M_C SNP5


title: leukocytes P_36_JBR_M_C SNP5


title: leukocytes P_26_PA_M_C SNP5


title: leukocytes P_22_JRF_M_C SNP5


title: leukocytes P_27_DB_M_C SNP5


title: leukocytes P_25_MR_M_C SNP5


title: leukocytes P_23_MM_M_C SNP5


title: leukocytes P_42_EDA_M_C SNP5


title: leukocytes P_24_MPP_M_N SNP5


title: leukocytes P_29_OD_M_C SNP5


title: leukocytes P_20_LCC_M_C SNP5


title: leukocytes P_33_JJ_F_C SNP5

value: female


title: leukocytes P_39_JLGRJ_M_C SNP5


title: leukocytes P_19_MAMS_F_C SNP5


title: leukocytes P_18_ANS_M_C SNP5


title: leukocytes P_16_NGR_M_C SNP5


title: leukocytes P_14_OG_M_C SNP5


title: leukocytes P_15_VRS_M_C SNP5


title: leukocytes P_17_GAC_M_C SNP5


title: leukocytes P_13_JRF_M_N SNP5


title: leukocytes C_46_MDN_M_C SNP5

source_name: leukocytes from peripheral blood, healthy

value: healthy


title: leukocytes P_3_JF_M_N SNP5


title: leukocytes P_9_WS_M_N SNP5


title: leukocytes P_12_JBF_M_C SNP5


title: leukocytes C_41_SLS_M_C SNP5


title: leukocytes P_11_JAR_M_C SNP5


title: leukocytes P_2_EAC_M_C SNP5


title: leukocytes C_42_DRL_M_C SNP5


title: leukocytes C_47_SF_M_C SNP5


title: leukocytes C_44_WLO_M_C SNP5


title: leukocytes P_10_JAOD_M_C SNP5


title: leukocytes P_8_SRJL_M_C SNP5


title: leukocytes C_49_COM_M_C SNP5


title: leukocytes C_43_PSM_M_C SNP5


title: leukocytes C_45_MAV_M_C SNP5


title: leukocytes C_40_IFS_M_C SNP5


title: leukocytes C_39_JAF_M_C SNP5


title: leukocytes P_1_AAP_M_C SNP5


title: leukocytes P_4_PLB_M_C SNP5


title: leukocytes C_38_AMM_M_C SNP5


title: leukocytes C_36_ERR_M_C SNP5


title: leukocytes P_5_RDG_M_C SNP5


title: leukocytes C_48_JAS2_M_N SNP5


title: leukocytes C_37_AOM_M_C SNP5


title: leukocytes P_7_SAC_M_N SNP5


title: leukocytes P_6_SAL_M_C SNP5


title: leukocytes C_35_JPS_M_N SNP5


title: leukocytes C_34_RT_M_N SNP5


title: leukocytes C_32_JRA_M_N SNP5


title: leukocytes C_33_DV_M_N SNP5


title: leukocytes C_31_JSS_M_N SNP5


title: leukocytes C_24_DRC_M_C SNP5


title: leukocytes C_23_AS_M_C SNP5


title: leukocytes C_18_FCM_M_C SNP5


title: leukocytes C_30_RB_M_C SNP5


title: leukocytes C_26_ELB_F_C SNP5


title: leukocytes C_25_SVC_M_C SNP5


title: leukocytes C_29_JBAC_M_N SNP5


title: leukocytes C_15_ABP_M_C SNP5


title: leukocytes C_19_RLMJ_M_C SNP5


title: leukocytes C_10_LS_M_C SNP5


title: leukocytes C_12_AMA_M_C SNP5


title: leukocytes C_14_APS_M_C SNP5


title: leukocytes C_9_MCGP_M_C SNP5


title: leukocytes C_2_JAS_M_N SNP5


title: leukocytes C_5_PGS_M_C SNP5


title: leukocytes C_21_GIO_M_C SNP5


title: leukocytes C_17_IC_M_C SNP5


title: leukocytes C_3_SAIS_M_C SNP5


title: leukocytes C_11_MP_F_C SNP5


title: leukocytes C_20_IPN_M_C SNP5


title: leukocytes C_8_JPR_M_C SNP5


title: leukocytes C_6_AHS_M_N SNP5


title: leukocytes C_27_IJS_M_C SNP5


title: WD

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: epithelial

hyb_protocol: ATLAS Biolabs GmbH

scan_protocol: ATLAS Biolabs GmbH

data_processing: Expression Console v1.2 (Affymetrix)

organism: Canis lupus familiaris

source_name: 30d after TGFb withdrawal

label_protocol: ATLAS Biolabs GmbH

growth_protocol: DMEM 10% FBS, standard CO2/O2/temperature conditions

extract_protocol: TRIZOL and Isopropanol precipitation was used for RNA extraction

treatment_protocol: treatment with TGFβ (R&D systems, Minneapolis, MN) at 5 ng/ml during 30 days, subculturing the cells every 3-4 days

value: MDCK


title: leukocytes C_28_NL_M_C SNP5


title: leukocytes C_16_JVDF_M_C SNP5


title: leukocytes C_7_MJF_M_N SNP5


title: AZA

description: AZA-treated

source_name: 5-AZA 72h post-TGFb


title: ROB12-13-Blood after challenge

city: Atlanta

first: Siddappa

last: Byrareddy

address: 101 Woodruff circle

department: Pathology & Laboratory Medicine

institute: Emory Univeristy

hyb_protocol: Hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols (Affymetrix inc.)

scan_protocol: The gene chips were scanned on Affymetrix scanner 3000

data_processing:
The data from gene chips was processed with GeneChip Operating Software (GCOS) 1.4
Affymetrix CEL files were processed and normalized using the robust multiarray average (RMA) algorithm. Results were adjusted for multiple testing using the Benjamini and Hochberg (BH) method, and significance was determined using a false-discovery-rate cutoff of <5% and a log fold-change cutoff of >2 as compared to baseline (Foldchange_all_Final.xls). Gene interaction network analysis and visualization were performed on significant probe sets using the Ingenuity pathway analysis (IPA) software package.

organism: Macaca mulatta

source_name: ROB12-Bllod after challenge-blood

label_protocol: Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.

extract_protocol: RNA was extracted with Rneasy mini kit (Qiagen)

treatment_protocol:
OSP immunization consisted of subcutaneous administration of 300 μg of each peptide (210 peptides representing SIV Gag, HIV-1 Tat and SIV Nef). Recombinant protein immunization consisted of i.m. administration of 100 μg of each protein (HIV-1 gp160, SIV Gag-Pol particles, HIV-1 Tat, and HIV-1 gp145). Peptides as well as proteins were administered along with IFA and challnged with repeated (5x, one dose/week), low-dose (5000 TCID50) of SHIV-2873Nip by the mucosal (i.r.) route.
Time after SIV infection: Six weeks post SHIV-2873Nip infection

tag: time point

value: after challenge

value: total blood


title: ROB12-11-Blood before vaccination

source_name: ROB12-Blood before vaccination-total blood

value: before vaccination


title: leukocytes C_22_JM_M_C SNP5


title: ROB12-12-Blood before vaccination


title: leukocytes C_1_JBC_M_C SNP5


title: TGF2

description: mesenchymal

source_name: 30d TGFb treatment


title: ROB12-10-Blood naïve

source_name: ROB12-Blood naïve-total blood

value: naïve


title: leukocytes C_4_LN_M_C SNP5


title: ROB12-8-Lymph Node-after challenge

source_name: ROB12-Lymph Node-after challenge -LN biopsy

value: lymph node


title: ROB12-9-Blood naïve


title: ROB12-14-Blood after challenge

source_name: ROB12-Blood after challenge-blood


title: CTL2

description: epithelial

source_name: untreated


title: ROB12-4-Rectal-after challenge

source_name: ROB12-Rectal-after challenge rectal biopsy

value: rectal biopsy


title: leukocytes C_13_VF_M_C SNP5


title: iHep Cdx2 Knockdown_4

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix MG 430 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: Cdx2 shRNA treated iHeps

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: iHeps were transduced with lentivirus carrying shRNA targeting Cdx2. puromycin-treated for two days and cultured for a week before harvesting.

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: iHeps


title: ROB12-1-Rectal-before vaccination

source_name: ROB12-Rectal-before vaccination rectal biopsy


title: ROB12-2-Rectal-before vaccination


title: iHep Cdx2 Knockdown_2


title: iHep Cdx2 Knockdown_3


title: TGF1

description: mesenchymal


title: iHep Cdx2 Knockdown_1


title: ROB12-7-Lymph Node-after challenge


title: iHep Scramble_3

source_name: Scramble shRNA treated iHeps

growth_protocol: iHeps were transduced with lentivirus carrying scramble shRNA. puromycin-treated for two days and cultured for a week before harvesting.


title: iHep Scramble_2


title: ROB12-5-Lymph Node-before vaccination

source_name: ROB12-Lymph Node-before vaccination- LN biopsy


title: Adult Liver_2

source_name: Freshly harvested adult liver from eight-week old C57BL/6J mouse

growth_protocol: Adult hepatocytes were isolated from 10-week-old adult C57BL/6J (The Jackson laboratory: 000664) mouse livers by two-step collagenase digestion.

value: liver

tag: developmental stage

value: 8-week-old adult


title: Colon_1

source_name: Freshly harvested adult colon from eight-week old Rag2gammac-/- mouse

growth_protocol: Colonic crypts were harvested from the colon by EDTA treatment and 0.25% trypsin was used to dissociate the cells.

value: colon


title: Fetal Liver_2

source_name: Freshly harvested fetal liver from E14.5 C57BL/6J mouse fetus

growth_protocol: Fetal liver was harvested from E14.5 C57BL/6J mouse fetuses (The Jackson laboratory: 000664).


title: iHep Scramble_1


title: Colon engrafted iHeps_1

source_name: 12-day engrafted iHeps harvested from DSS-damged colons of Rag2gammac-/- mice

growth_protocol: iHeps were transplanted into the DSS-damaged colons of Rag2gammac-/- recipient mice. After 12 days of engraftment, crypts were harvested from the colon by EDTA treatment and 0.25% trypsin was used to dissociate the cells. GFP positive iHeps were sorted by flow cytometry.


title: Adult Liver_1


title: Fetal Liver_1


title: Ebf1 Knockdown_1

source_name: Induced macrophages derived from Ebf1 shRNA treated C10 cells

growth_protocol: Prior to conversion to induced macrophages, the cells were transduced with lentivirus carrying shRNA targeting Ebf1 and subject to puromycin selection for two days.

value: Induced macrophages


title: CTL1

description: epithelial


title: iHep_1

source_name: Independent iHep cell line derived from C57BL/6J mouse fibroblasts transduced with Foxa1 and Hnf4a

growth_protocol: Mouse embryonic fibroblasts (MEFs) were converted to iHeps as in (Sekiya and Suzuki, 2011). Briefly, MEFs were prepared from E13.5 C57BL/6J mouse embryos (The Jackson laboratory: 000664) and the cultured primary fibroblasts were serially transduced with Foxa1 and Hnf4 retroviruses over a five-day period, followed by culture on gelatin for two weeks in hepato-medium (below), after which the emerging iHeps were cultured on collagen and expanded. iHep cells were grown in hepato-medium, comprising a 1:1 mixture of DMEM and F-12, supplemented with 10% FBS (Omega Scientific), 1 mg/ml insulin (Sigma), 10-27M dexamethasone (Sigma-Aldrich), 10mM nicotinamide (Sigma-Aldrich), 2mM L-glutamine, 50 mM mercaptoethanol (Life Technologies) and penicillin/streptomycin, containing 20 ng/ml hepatocyte growth factor (Sigma-Aldrich) and 20 ng/ml epidermal growth factor (Sigma-Aldrich).

value: Independent iHep cell line


title: Pou2af1 Knockdown_1

source_name: Induced macrophages derived from Pou2af1 shRNA treated C10 cells

growth_protocol: Prior to conversion to induced macrophages, the cells were transduced with lentivirus carrying shRNA targeting Pou2af1 and subject to puromycin selection for two days.


title: ROB12-3-Rectal-after challenge


title: Pou2af1 Knockdown_2


title: iHep_3


title: Colon engrafted iHeps_2


title: Scramble_2

source_name: Induced macrophages derived from scramble shRNA treated C10 cells

growth_protocol: The C10 pre-B cell line was converted to induced macrophages, as in (Bussmann et al., 2009). Briefly, C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 mM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2. They were induced by the addition 100 nM of -estradiol (Sigma) and grown with 10 nM IL-3 and CSF-1 (Peprotech). Prior to conversion, the cells were transduced with lentivirus carrying scramble shRNA and subject to puromycin selection for two days.


title: Colon_2


title: ROB12-6-Lymph Node-before vaccination

source_name: ROB12-Lymph Node-before vaccination-LN biopsy


title: NF-YA, NF-YB, NF-YC triple KD ES cells 96hr, replicate 3

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Cells transfected with NF-YA, NF-YB, and NF-YC siRNAs

hyb_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org).  Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

source_name: E14Tg2a ES Cells

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

growth_protocol: Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For siRNA transfection experiments, passage 20-35 cells were cultured in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen)

tag: strain

value: embryonic stem cells


title: iHep Scramble_4

tag: cell type


title: NF-YA, NF-YB, NF-YC triple KD ES cells 96hr, replicate 1


title: NF-YA, NF-YB, NF-YC triple KD ES cells 96hr, replicate 2


title: NF-YB KD ES cells 96hr, replicate 2

description: Cells transfected with NF-YB siRNA


title: NF-YC KD ES cells 96hr, replicate 2

description: Cells transfected with NF-YC siRNA


title: Ebf1 Knockdown_2


title: Scramble_1


title: NF-YB KD ES cells 96hr, replicate 3

description: Cells transfected with NF-YB siRNA


title: NF-YA KD ES cells 96hr, replicate 2

description: Cells transfected with NF-YA siRNA


title: NF-YA KD ES cells 96hr, replicate 1

description: Cells transfected with NF-YA siRNA


title: NF-YB KD ES cells 96hr, replicate 1

description: Cells transfected with NF-YB siRNA


title: NF-YA KD ES cells 96hr, replicate 3

description: Cells transfected with NF-YA siRNA


title: iHep_2


title: Large fibroid rep5

city: Jinan

first: Zhaojian

last: Liu

state: Shandong

address: 44# Wenhua xi Road

department: Cell Biology

country: China

institute: Shandong University

description: Expression profiling data from large fibroid

hyb_protocol: The labeled cRNAs were hybridized onto the Human lncRNA Array v2.0 (8 x 60K, Arraystar) using agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Large fibroid

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's protocol,followed by RNA easy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -80C

extract_protocol: For RNA extraction, RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Cryopulverization of tissue using the Biopulverizer and then homogenization using the Mini-Bead-Beater-16 before RNA extraction

value: Large fibroid


title: Control ES cells 96hr, replicate 2

description: Cells transfected with control siRNA


title: Control ES cells 96hr, replicate 3

description: Cells transfected with control siRNA


title: Large fibroid rep3

value: female


title: AE-10

city: ShangHai

first: Wang

last: Xiangdong

address: Fenglin Road No.180

institute: Zhongshan Hospital

description: This sample is of AECOPD on 10 day. It is the collection of peripheral blood of six AECOPD persons.

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

scan_protocol: Scanning was performed by Axon GenePix 4000B microarray scanner, following their standard operating protocol.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Genes which had values greater than or equal to the lower cutoff  100.0 in all samples (All Targets Value)  were chosen for data analysis and the rest were excluded.

source_name: Peripheral Blood Mononuclear Cell

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

extract_protocol: PBMCs were isolated by using CPT tubes (Becton Dickinson, Franklin lakes, NT) according to manufacturer’s instructions. Approximately 4 ml whole blood was collected from each subject. Following centrifugation, cells were lysed for RNA isolation. DNAse-free total RNA preparation was performed by using TRIzol reagent (Invitrogen life technologies, Carlsbad, CA) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s recommedations. RNA concentrations were determined by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA quality was assessed on an Agilent 2100 Bioanalyzer; samples with a RNA Integrity Score of ＞6.0 were used in this study.

value: Peripheral Blood Mononuclear Cell

value: AE on 10 day

tag: disease state

value: AECOPD


title: Large fibroid rep2


title: Small fibroid rep2

description: Expression profiling data from small fibroid

source_name: Small fibroid

value: Small fibroid


title: Large fibroid rep4


title: Small fibroid rep5


title: Normal myometrium rep3

description: Expression profiling data from normal myometrium

source_name: uterine normal myometrium

value: uterine normal myometrium


title: Small fibroid rep3


title: Control

description: This sample is of Normal people. It is the collection of peripheral blood of six normal persons.

value: normal


title: HT-29 (Vegetative vs. Control)

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

hyb_protocol: Cy3 and Cy5 labelled cDNA were mixed and hybridized at 50oC for 18h on the Immune Array chips in an ArrayBooster (Advalytix, Beckman Coulter, Germany).

scan_protocol: Each array was scanned with a ScanArray 5000 instrument (Perkin Elmer, Waltham, MA) and acquired images were quantified with QuantArray software (Perkin Elmer).

data_processing: Statistical analyses were done with R software (v. 2.13.0) and the Limma package from Bioconductor. Normalization within slide was obtained by LOWESS correction and between slides normalization was done with Aquantile method.

source_name: HT-29 cells treated with Bacillus subtilis R0179 vegetative state

label_protocol: Poly A mRNA were reverse transcribed from 15 µg of total RNA with SuperScript III (Invitrogen) and labelled with either Cy3 or Cy5 (GE Healthcare Life Sciences, Buckinghamshire, England) before cDNA purification with PCR Purification Kit (QIAGEN).

extract_protocol: Total RNA was extracted by TRIzol Reagent (Invitrogen, Burlington, ON, Canada) following manufacturer's protocol and with PhaseLock tubes (5 Prime, Gaithersburg, MD) for nucleic acids separation. Purification was achieved with RNeasy (QIAGEN, Germantown, MD). Quality was assessed by Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada). RIN over 9.0 were considered good quality RNA for reverse transcription.

treatment_protocol: HT-29 cells were incubated for 3 h with Bacillus spores or vegetative state at a MOI of 100:1.

tag: cell line

value: Colonic adenocarcinoma cells

source_name: unchallenged HT-29 cells


title: Normal myometrium rep4


title: Small fibroid rep4


title: Control ES cells 96hr, replicate 1

description: Cells transfected with control siRNA


title: AE-3

description: This sample is of AECOPD on 3 day. It is the collection of peripheral blood of six AECOPD persons.

value: AE on 3 day


title: Stable

description: This sample is of stable COPD. It is the collection of peripheral blood of six stable COPD persons.

value: stable

value: stabe COPD


title: NF-YC KD ES cells 96hr, replicate 3

description: Cells transfected with NF-YC siRNA


title: Large fibroid rep1


title: Small fibroid rep1


title: FRC_LN_Cult_rep1

city: Boston

first: Jillian

last: Astarita

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45C. The chips are then washed to remove unhybridized cDNA. Bound cDNA is fluorescently labeled using phycoerythrin-conjugated streptavidin, additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. From http://macf-web.dfci.harvard.edu/

scan_protocol: Each cDNA 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. From http://macf-web.dfci.harvard.edu/

data_processing:
Data were processed using GenePattern (Broad Institute). Data were RMA normalized.
probe group file: MoGene-1_0-st

source_name: Purified fibroblastic reticular cells, isolated from lymph nodes, culture-expanded

label_protocol: Single stranded cDNA is synthesised and purified, then fragmented using uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I. Fragmented cDNA is end-labeled with a biotinylated nucleotide analogue.

growth_protocol: Whole lymph node stromal cells were grown in aMEM with 10% batch-selected fetal calf serum for 7-10 days

extract_protocol: Qiagen RNeasy kit was used to isolate whole RNA, according to the manufacturer's instructions


title: HT-29 (Spores vs. Control)

source_name: HT-29 cells treated with Bacillus subtilis R0179 spores


title: Normal myometrium rep5


title: FRC_LN_Cult_rep2


title: AE-1

description: This sample is of AECOPD on 1 day. It is the collection of peripheral blood of six AECOPD persons.

value: AE on 1 day


title: MCF10A_hsa-miR-1-3p_ctrl_2

status: Public on Aug 13 2014

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data were imported and normalized using the Base server (http://base.thep.lu.se).

source_name: MCF10A, non-targeting control

label_protocol: Standard Illumina labeling protocol

growth_protocol: All cell lines were purchased from ATCC and used at low passage numbers. Cells were cultured as reported previously (Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, et al. (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10: 515-52).

extract_protocol: RNA was extracted with TRIZOL (Life Technologies) according to the manufacturer's instructions. RNA quantity and quality were assessed with NanoDrop ND 1000 spectrophotometer (NanoDrop Tech) and LabChip GX (Perkin Elmer) respectively before loading the samples on a HumanHT-12 v3.0.

treatment_protocol: Transfections were performed with Lipofectamine 2000 (Life Technologies) following the manufacturer’s instructions. All oligonucleotides and miRNA mimics were transfected at 100 nM unless stated otherwise. Antisense oligonucleotides contained 2’ O-methyl modifications and were from IDT DNA Technologies. Non-targeting siRNA control was from Thermo Scientific. All miRNA mimics were purchased from Qiagen; the customized mimics corresponding to the mature sequence of miR-4728-3p (25 nt) and a 25 nt control.

value: human mammary epithelial cells

tag: transfected with

value: non-targeting control


title: MCF10A_hsa-miR-1-3p_2

source_name: MCF10A, hsa-miR-1-3p mimic

value: hsa-miR-1-3p mimic


title: MCF10A_hsa-miR-1-3p_3


title: MCF10A_hsa-miR-1-3p_4


title: MCF10A_hsa-miR-1-3p_ctrl_3


title: 8nM_rep2

city: Barcelona

first: José

last: Portugal

address: Parc Cientific de Barcelona, Baldiri Reixac, 10

department: Molecular Genomics

institute: Instituto de Biologia Molecular  de Barcelona-CSIC

description: Gene expression after treatment with 8 nM DIG-MSK

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).  Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: cells, 8 nM, replicate 2

label_protocol: One-Color Microarray-Based Eukaryote Analysis Fair Play III Labeling v. 1.3 (Agilent)

growth_protocol: A2780 cells were maintained in RPMI 1640 medium (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies), 100 U/ml penicillin, 100 g/ml streptomycin and 2 mM sodium pyruvate at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was isolated using the UltraspecRNA reagent (Biotecx) following the manufacturer's recommendations. RNA was digested with RNAse-free DNAse I (Roche Diagnostics) in the presence of RNasin (Promega), phenol extracted and precipitated, and the pellet was dissolved in RNAse-free water. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells sub-cultured at a density of 2.5 x 104 cells/ml were incubated with either 8 nM or 80 nM DIG-MSK at 37 °C for 24 h.

tag: treatment

value: 8 nM DIG-MSK


title: 80nM_rep2

description: Gene expression after treatment with 80 nM DIG-MSK

source_name: cells, 80 nM, replicate 2

value: 80 nM DIG-MSK