title: GC147-UM-EL2_1271

description:
uninvolved margin of breast carcinoma
GC147-UM-EL2


title: MV4-11 Control_scrambled shRNA_2

status: Public on Oct 01 2015

type: RNA

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

country: USA

institute: Sonic Healthcare USA

description:
GG29
Replicate 2 of 3.

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

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries were performed using the log-scale Robust Multiarray Analysis (RMA) method.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human MV4-11 AML cells transfected with scrambled shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The human AML cell lines, U937 and MV4-11, were maintained in RPMI supplemented with 10% Fetal Bovine Serum, and 2% penicillin/streptomycin.

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

treatment_protocol: Lentiviral constructs (pRRL.H1.shRNA) expressing GFP were used as vectors that either contained non-silencing, scramble, short hairpin RNA (shRNA) or shRNAs against CDH4.

tag: cell line

tag: cell type

value: AML cell line

tag: shRNA

value: scrambled


title: U937 CDH4_shRNA_2

description:
GG24
Replicate 2 of 3.

source_name: Human U937 AML cells transfected with CDH4 shRNA


title: U937 Control_scrambled shRNA_1

description:
GG21
Replicate 1 of 3.

source_name: Human U937 AML cells transfected with scrambled shRNA


title: U937 Control_scrambled shRNA_3

description:
GG25
Replicate 3 of 3.


title: U937 CDH4_shRNA_3

description:
GG26
Replicate 3 of 3.


title: MV4-11 CDH4_shRNA_1

description:
GG28
Replicate 1 of 3.

source_name: Human MV4-11 AML cells transfected with CDH4 shRNA


title: U937 CDH4_shRNA_1

description:
GG22
Replicate 1 of 3.


title: U937 Control_scrambled shRNA_2

description:
GG23
Replicate 2 of 3.


title: 140156A_Ec1141w6

city: beijing

first: zhang

last: suwei

address: changping

country: China

institute: capitalbio

description: Gene expression in present-smoker plasma

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: peripheral blood_present-smoker

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

growth_protocol: All subjects are from the same unit , do the same job, and live in the same community .

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

treatment_protocol: 4 mL peripheral venous fasting blood was collected from each subject in EDTA anticoagulant tube. The blood samples were maintained at room temperature for 30 minutes and then centrifuged at 1500g for 15min at 4℃. Then plasma was transferred to another clean EP tube and stored at – 80 ℃ until RNA extraction. Then, the total RNA was extracted from the plasma using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. The quality and quantity of RNA were measured with a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).plasma miRNA expression profiles were determined using the human microRNA array version 19.0 (Agilent, USA). Plasma miRNA from 28 present smokers and 12 never -smokers were detected with the miRNA array respectively.

tag: gender

value: male

tag: age

tag: smoking status

value: present-smoker

tag: tissue

value: peripheral blood


title: 140156A_Ec1144w6


title: GC147-UM-EL_1269

type: genomic

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
uninvolved margin of breast carcinoma
GC147-UM-EL

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

label: biotin

molecule: genomic DNA

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

label_protocol: starndard protocol

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

value: female

tag: age at cancer diagnosis (yrs)

tag: tumor grade

value: Luminal A

tag: tumor focality

value: unifocal


title: GC146-VB2-M_1266

description:
uninvolved margin in the immediate vicinity of the mammilla
GC146-VB2-M


title: Untreated, Rep4

city: Boston

first: Jennifer

middle: Nan-Wah

last: Wu

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: These data were analyzed using Bioconductor package affy using the rma function for normalization and background correction with default parameters.

label_protocol: standard Affymetrix protocol

extract_protocol: Rneasy

value: acute lymphoblastic leukemia cell line

tag: treated with

value: none (no treatment control)


title: MV4-11 Control_scrambled shRNA_1

description:
GG27
Replicate 1 of 3.


title: Untreated, Rep3


title: Untreated, Rep1


title: Untreated, Rep2


title: Dex-treated 8 hours, Rep5

value: 10 nM dexamethasone 8h


title: Dex-treated 8 hours, Rep4


title: GC146-VB1-M_1265

description:
uninvolved margin in the immediate vicinity of the mammilla
GC146-VB1-M


title: Dex-treated 8 hours, Rep2


title: GC146-UM-IU2_1264

description:
uninvolved margin of breast carcinoma
GC146-UM-IU2


title: GC146-UM-IU1_1263

description:
uninvolved margin of breast carcinoma
GC146-UM-IU1


title: GC146-UM-IU_1262

description:
uninvolved margin of breast carcinoma
GC146-UM-IU


title: 140156A_Ec1151w6


title: 140156A_Ec1142w6


title: 140156A_Ec1145w6


title: Dex-treated 24 hours, Rep5

value: 10 nM dexamethasone 24h


title: Dex-treated 8 hours, Rep1


title: 140156A_Ec1154w6


title: 140156A_Ec1174w6


title: GC146-UM-IL_1261

description:
uninvolved margin of breast carcinoma
GC146-UM-IL


title: Dex-treated 24 hours, Rep4


title: Dex-treated 24 hours, Rep3


title: Dex-treated 24 hours, Rep1


title: 140156A_Ec633w6


title: 140156A_Ec624w6


title: 140156A_Ec623w6


title: Dex-treated 24 hours, Rep2


title: GC146-UM-EU1_1260

description:
uninvolved margin of breast carcinoma
GC146-UM-EU1


title: GC146-UM-EU_1259

description:
uninvolved margin of breast carcinoma
GC146-UM-EU


title: C148-Cold-24H

city: Wuhan

first: Hanyan

last: Ye

state: Hubei

address: No. 5, Shizishan street

institute: HuaZhong Agricultural University

description: Gene expression data from C148 accession after cold stress for 24 hours

hyb_protocol: cRNA were hybridized for 16 hr at 45℃ on Affymetrix® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Gcos1.4 (GeneChip Operating Software) referring to Affymetrix Statistical Algorithms Description Document.

organism: Oryza sativa

source_name: rice seedlings in four-leaf-stage of C148 (MH63) accession

label_protocol: Biotinylated cRNA was prepared according to the technical manual of GeneChip® Expression Analysis.

growth_protocol: Rice seedlings of the 8 accessions grew in potting soil until they went into 4-leave stage.

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

treatment_protocol: the 8 accessions in 4-leaf-stage were moved to artificial chamber at a constant 4°C with 14 hours/10 hours of light/darkness, we took the samples before treatment, after 6 hours' treatment and after 24 hours' treatment.

value: shoot and leave

tag: accession

tag: treatment

value: after cold stress for 24 hours


title: C087-N

description: Gene expression data from C087 accession before cold stress

source_name: rice seedlings in four-leaf-stage of C087 (Lixingeng) accession

value: C087 (Lixingeng)

value: before cold stress


title: GC146-UM-EL2_1258

description:
uninvolved margin of breast carcinoma
GC146-UM-EL2


title: C148-Cold-6H

description: Gene expression data from C148 accession after cold stress for 6 hours

value: after cold stress for 6 hours


title: C087-Cold-6H

description: Gene expression data from C087 accession after cold stress for 6 hours


title: C148-N

description: Gene expression data from C148 accession before cold stress


title: C087-Cold-24H

description: Gene expression data from C087 accession after cold stress for 24 hours


title: C079-Cold-6H

description: Gene expression data from C079 accession after cold stress for 6 hours

source_name: rice seedlings in four-leaf-stage of C079 (Muguanuo) accession

value: C079 (Muguanuo)


title: C079-Cold-24H

description: Gene expression data from C079 accession after cold stress for 24 hours


title: GC146-UM-EU2_1720

description:
uninvolved margin of breast carcinoma
GC146-UM-EU2


title: C079-N

description: Gene expression data from C079 accession before cold stress


title: GC146-UM-EL1_1257

description:
uninvolved margin of breast carcinoma
GC146-UM-EL1


title: C070-Cold-24H

description: Gene expression data from C070 accession after cold stress for 24 hours

source_name: rice seedlings in four-leaf-stage of C070 (Youmangzaogeng) accession

value: C070 (Youmangzaogeng)


title: C070-Cold-6H

description: Gene expression data from C070 accession after cold stress for 6 hours


title: EW155-VB2-M_1253

description:
uninvolved margin in the immediate vicinity of the mammilla
EW155-VB2-M

value: Luminal B, HER2-


title: C070-N

description: Gene expression data from C070 accession before cold stress


title: C063-Cold-24H

description: Gene expression data from C063 accession after cold stress for 24 hours

source_name: rice seedlings in four-leaf-stage of C063 (Geng87-304) accession


title: 140156A_Ec630w6

description: Gene expression in present-smoker plasma

value: male

value: present-smoker


title: GC146-UM-EL_1256

description:
uninvolved margin of breast carcinoma
GC146-UM-EL

value: female


title: EW155-VB1-M_1252

description:
uninvolved margin in the immediate vicinity of the mammilla
EW155-VB1-M


title: 140156A_Ec636w6

value: peripheral blood


title: 140156A_Ec637w6


title: 140156A_Ec632w6


title: 140156A_Ec629w6


title: EW155-UM-IU2_1251

description:
uninvolved margin of breast carcinoma
EW155-UM-IU2

value: unifocal


title: C063-N

description: Gene expression data from C063 accession before cold stress


title: C147-Cold-6H

description: Gene expression data from C147 accession after cold stress for 6 hours

source_name: rice seedlings in four-leaf-stage of C147 (ZS97) accession


title: EW155-UM-IU1_1250

description:
uninvolved margin of breast carcinoma
EW155-UM-IU1


title: 140156A_Ec622w6


title: 140156A_Ec631w6


title: 140156A_EC302W6


title: EW155-UM-IU_1249

description:
uninvolved margin of breast carcinoma
EW155-UM-IU


title: C145-Cold-6H

description: Gene expression data from C145 accession after cold stress for 6 hours

source_name: rice seedlings in four-leaf-stage of C145 (9311) accession


title: C153-N

description: Gene expression data from C153 accession before cold stress

source_name: rice seedlings in four-leaf-stage of C153 (IRAT109) accession


title: C145-N

description: Gene expression data from C145 accession before cold stress


title: 140156A_EC304W6


title: C153-Cold-6H

description: Gene expression data from C153 accession after cold stress for 6 hours


title: C145-Cold-24H

description: Gene expression data from C145 accession after cold stress for 24 hours


title: rESC-RPC2, biological rep3

city: Shanghai

first: Zepeng

last: Qu

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression data from rESC-RPC2

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

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

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

organism: Rattus norvegicus

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

growth_protocol: For RPC differentiation, rESCs discarded feeder underwent differentiation following the SFEBq method with Matrigel and IWR-1e, a Wnt inhibitor. Neuroectoderm like sphere structure appeared at day 8. FBS was added into the culture medium from day 8 to day 16. For rESC-RPC1, the aggregates were digested for adherent culture at day 10. The culture medium was changed to N2 with FBS at day 14 and cells were harvested at day 16. For rESC-RPC2, the aggregates were digested for adherent culture at day 14 and harvested at day 16.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: For rESC-RPC1, the differentiated cells were switched to adherent culture at D10, while for rESC-RPC2, the suspension culture was maintained to D14. Primary RPCs were obtained from dissociated neural retina in postnatal 1 day SD rats.

tag: differentiation method

value: Adherent culture from differentiation day 14 to day 16

tag: parental cell line

value: rESC-RPCs were differentiated from rat ES cell line DA8-16

tag: genetic background

value: DA rat


title: EW155-UM-IL1_1247

description:
uninvolved margin of breast carcinoma
EW155-UM-IL1


title: C063-Cold-6H

description: Gene expression data from C063 accession after cold stress for 6 hours


title: C147-Cold-24H

description: Gene expression data from C147 accession after cold stress for 24 hours


title: C153-Cold-24H

description: Gene expression data from C153 accession after cold stress for 24 hours


title: C147-N

description: Gene expression data from C147 accession before cold stress


title: 140156A_EC318W6

description: Gene expression in present-smoker plasma


title: EW155-UM-IL_1246

description:
uninvolved margin of breast carcinoma
EW155-UM-IL


title: rESC-RPC2, biological rep2

description: Gene expression data from rESC-RPC2


title: EW155-UM-EU2_1245

description:
uninvolved margin of breast carcinoma
EW155-UM-EU2


title: EW155-UM-EU1_1244

description:
uninvolved margin of breast carcinoma
EW155-UM-EU1


title: rESC-RPC1, biological rep2

description: Gene expression data from rESC-RPC1

value: Adherent culture from differentiation day 10 to day 16, medium changed to N2 at D14


title: 140156A_EC310W6


title: 140156A_EC315W6


title: 140156A_EC316W6


title: 140156A_EC317W6


title: placental tissue 2 on gestational day 50 in Yorkshire pig

first: Ruize

last: Liu

address: No.1,Shizishan Street

department: College of Animal Science and Technology

institute: Huazhong Agriculture University

description: miRNA expression data from placental tissue on gestational day 50 in Yorkshire pig

hyb_protocol: Fragmentation of the labeled aRNA prepares the target for hybridization to GeneChip miRNA arrays with GeneChip hybridization oven 640. Wash and stain the arrays with GeneChip fluidics station 450.

scan_protocol: Scan the arrays with the GeneArray scanner 3000 by the Command Console (AGCC)Software.

data_processing: The data were analyzed with RMA by using R/Bioconductor.

organism: Sus scrofa

label_protocol: In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from the double-stranded cDNA templates.

growth_protocol: Meishan and Yorkshire gilts were mated naturally to one boar of their respective breed at the onset of estrus (day=0) and again 24h later.

treatment_protocol: These gilts were euthanized on day 26 or on day 50 of gestation

value: placenta

tag: breed

value: Yorkshire


title: EW155-UM-EU_1243

description:
uninvolved margin of breast carcinoma
EW155-UM-EU


title: placental tissue 1 on gestational day 50 in Yorkshire pig

source_name: placental tissue on gestational day 50 in Yorkshire pig


title: placental tissue 3 on gestational day 50 in Yorkshire pig


title: EW155-UM-EL2_1242

description:
uninvolved margin of breast carcinoma
EW155-UM-EL2


title: placental tissue 3 on gestational day 26 in Yorkshire pig

description: miRNA expression data from placental tissue on gestational day 26 in Yorkshire pig


title: P-RPC, biological rep3

description: Gene expression data from P-RPC

source_name: P-RPC

value: SD rat


title: rESC-RPC2, biological rep1

description: Gene expression data from rESC-RPC2


title: rESC-RPC1, biological rep1

description: Gene expression data from rESC-RPC1


title: P-RPC, biological rep1

description: Gene expression data from P-RPC


title: 140156A_EC303W6


title: P-RPC, biological rep2

description: Gene expression data from P-RPC


title: placental tissue 1 on gestational day 50 in Meishan pig

description: miRNA expression data from placental tissue on gestational day 50 in Meishan pig

value: Meishan


title: placental tissue 2 on gestational day 50 in Meishan pig

source_name: placental tissue on gestational day 50 in Meishan pig


title: placental tissue 3 on gestational day 50 in Meishan pig


title: placental tissue 1 on gestational day 26 in Yorkshire pig

source_name: placental tissue on gestational day 26 in Yorkshire pig


title: 140156A_EC307W6


title: EW155-UM-EL_1240

description:
uninvolved margin of breast carcinoma
EW155-UM-EL


title: placental tissue 2 on gestational day 26 in Yorkshire pig


title: 140156A_EC305W6


title: placental tissue 3 on gestational day 26 in Meishan pig

description: miRNA expression data from placental tissue on gestational day 26 in Meishan pig


title: placental tissue 2 on gestational day 26 in Meishan pig

source_name: placental tissue on gestational day 26 in Meishan pig


title: 140156A_EC308W6


title: ER033-UM2_1235

description:
uninvolved margin of breast carcinoma
ER033-UM2

value: Triple negative


title: ER033-UM99_1237

description:
uninvolved margin of breast carcinoma
ER033-UM99


title: ER033-UM98_1236

description:
uninvolved margin of breast carcinoma
ER033-UM98


title: Dex-treated 8 hours, Rep3

tag: cell line

value: acute lymphoblastic leukemia cell line

value: 10 nM dexamethasone 8h


title: EN039-UM99_1231

description:
uninvolved margin of breast carcinoma
EN039-UM99

value: Luminal B, HER2-

value: multifocal


title: EW155-UM-EL1_1241

description:
uninvolved margin of breast carcinoma
EW155-UM-EL1


title: ER033-UM1_1234

description:
uninvolved margin of breast carcinoma
ER033-UM1


title: 140156A_NM105

description: Gene expression in never-smoker plasma

source_name: peripheral blood_never-smoker

value: male

value: never-smoker


title: 140156A_NM85

description: Gene expression in never-smoker plasma

value: peripheral blood


title: EN039-UM98_1230

description:
uninvolved margin of breast carcinoma
EN039-UM98

value: female


title: EN039-UM4_1229

description:
uninvolved margin of breast carcinoma
EN039-UM4


title: EN039-UM3_1228

description:
uninvolved margin of breast carcinoma
EN039-UM3


title: 140156A_NM86

description: Gene expression in never-smoker plasma


title: 140156A_NM102

description: Gene expression in never-smoker plasma


title: 140156A_NM78

description: Gene expression in never-smoker plasma


title: placental tissue 1 on gestational day 26 in Meishan pig


title: 140156A_NM96

description: Gene expression in never-smoker plasma


title: 140156A_NM76

description: Gene expression in never-smoker plasma


title: EN039-UM2_1227

description:
uninvolved margin of breast carcinoma
EN039-UM2


title: EN039-UM1_1226

description:
uninvolved margin of breast carcinoma
EN039-UM1


title: 140156A_NM95

description: Gene expression in never-smoker plasma


title: 140156A_NM99

description: Gene expression in never-smoker plasma


title: EJ001-UM99_1222

description:
uninvolved margin of breast carcinoma
EJ001-UM99

value: unifocal


title: EJ001-UM98_1221

description:
uninvolved margin of breast carcinoma
EJ001-UM98


title: 140156A_NM82

description: Gene expression in never-smoker plasma


title: EJ001-UM3_1220

description:
uninvolved margin of breast carcinoma
EJ001-UM3


title: OvTuMix(106)(2/5/13) vs. 427 OvTuSerMayo(re)

city: Santa Monica

first: Habib

last: Hamidi

state: CA

address: 2825 Santa Monica Blvd., Suite 200

institute: UCLA

description:
reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional cell=1, unknown=7
ovarian tumor samples

hyb_protocol: 825 ng each of labeled reference mix (cy3 label) and individual sample (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol

scan_protocol: Slides were read on an Agilent G2505B scanner.  All  experiments were scanned with extended dynamic range enabled.

data_processing:
Agilent Feature Extraction Software (v9.5.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

source_name: 106 pooled ovarian samples

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's protocol.

value: ovarian

source_name: Ovarian Tumor 427

tag: ageatdx

tag: Stage

tag: substage

value: C

tag: grade

tag: morphology

value: Serous

tag: subtype

tag: histology

tag: figo


title: EW155-UM-IL2_1248

description:
uninvolved margin of breast carcinoma
EW155-UM-IL2

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

tag: gender

tag: age at cancer diagnosis (yrs)

tag: tumor grade

tag: tumor focality


title: 140156A_NM89

description: Gene expression in never-smoker plasma

tag: age

tag: smoking status

tag: tissue


title: OvTuMix(106) 2.5.13 vs. 1235201387 OvTuMayo

source_name: Ovarian Tumor 1692

value: Clear cell


title: OvTuMix(106)(2/5/13) vs. 765 OvTuSerMayo(re)

source_name: Ovarian Tumor 765


title: OvTuMix(106) 2.5.13 vs. 1235201382 OvTuMayo

source_name: Ovarian Tumor 1633

value: Endometrioid


title: EJ001-UM2_1219

description:
uninvolved margin of breast carcinoma
EJ001-UM2


title: OvTuMix(106)(2/5/13) vs. 605 OvTuSerMayo(re)

source_name: Ovarian Tumor 605


title: 140156A_NM97

description: Gene expression in never-smoker plasma


title: Sgordonii_-ARG_rep4

city: Newcastle

first: Matthew

last: Bashton

address: Newcastle

country: United Kingdom

institute: Newcastle Univerity

description: Gene expression after 30 mins without arginine

hyb_protocol: Samples were prepared as per Agilent One-color v6.5 protocol, hybridisation oven GA2545A was used at 65 degree centigrade, with rotator rack G2530-60029.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 041846_D_F_20120627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Streptococcus gordonii

source_name: S gordonii without arginine replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the One-Color Low RNA Input Quick Amplification kit (Agilent 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in a chemically defined medium to mid exponential phase (Jakubovics et. al. 2008, J. Bacteriol, 190, 3646-3657)  Cells were grown in a chemically defined medium to mid exponential phase (Jakubovics et. al. 2008, J. Bacteriol, 190, 3646-3657)

extract_protocol: RNA was prepaired using the Ambion RiboPureKit bead beating in a Qiagen Tissue lyzer at 50Hz for 5 min.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Culture were split and harvested at 3,800g for 10 mins in a swing-out rotor.  From each original culture one portion was resuspended in CDM amended to 5mM arginine and the other portion was resuspended in CDM without arginine.  After 30 mins of exposure to media either with or without arginine (5 mM).

tag: media

value: without arginine


title: OvTuMix(106) 2.5.13 vs. 1133903140 OvTuMayo(re)

source_name: Ovarian Tumor 1809


title: Sgordonii_-ARG_rep3

source_name: S gordonii without arginine replicate 3


title: OvTuMix(106) 2.5.13 vs. 1235201372 OvTuMayo

source_name: Ovarian Tumor 2368


title: OvTuMix(106) 2.5.13 vs. 1235201357 OvTuMayo(re)

source_name: Ovarian Tumor 2350


title: OvTuMix(106)(2/5/13) vs. 1052 OvTuSerMayo(re)

source_name: Ovarian Tumor 1052


title: OvTuMix(106) 2.5.13 vs. 1133903724 OvTuMayo

source_name: Ovarian Tumor 1865

value: A


title: OvTuMix(106) 2.5.13 vs. 1133903528 OvTuMayo

source_name: Ovarian Tumor 1732


title: OvTuMix(106) 2.5.13 vs. 1235201352 OvTuMayo

source_name: Ovarian Tumor 2320


title: OvTuMix(106) 2.5.13 vs. 1235201327 OvTuMayo

source_name: Ovarian Tumor 1268


title: OvTuMix(106) 2.5.13 vs. 1235201332 OvTuMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 2360


title: OvTuMix(106) 2.5.13 vs. 1235201347 OvTuMayo

source_name: Ovarian Tumor 2233


title: EG163-VB2-M_1215

description:
uninvolved margin in the immediate vicinity of the mammilla
EG163-VB2-M

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: Sgordonii_-ARG_rep2

source_name: S gordonii without arginine replicate 2


title: EG163-VB1-M_1214

description:
uninvolved margin in the immediate vicinity of the mammilla
EG163-VB1-M


title: EJ001-UM1_1218

description:
uninvolved margin of breast carcinoma
EJ001-UM1

value: Triple negative


title: EG163-UM-IU2_1213

description:
uninvolved margin of breast carcinoma
EG163-UM-IU2


title: Sgordonii_-ARG_rep1

source_name: S gordonii without arginine replicate 1


title: EG163-UM-IU1_1212

description:
uninvolved margin of breast carcinoma
EG163-UM-IU1


title: EG163-UM-IL_1718

description:
uninvolved margin of breast carcinoma
EG163-UM-IL


title: EG163-UM-EU2_1211

description:
uninvolved margin of breast carcinoma
EG163-UM-EU2


title: Sgordonii_+ARG_rep4

description: Gene expression after 30 mins with arginine

source_name: S gordonii with arginine replicate 4

value: with arginine


title: Sgordonii_+ARG_rep3

source_name: S gordonii with arginine replicate 3


title: Sgordonii_+ARG_rep2

source_name: S gordonii with arginine replicate 2


title: OvTuMix(106) 2.5.13 vs. 1133903688 OvTuMayo

source_name: Ovarian Tumor 2134


title: OvTuMix(106) 2.5.13 vs. 1235201307 OvTuMayo

source_name: Ovarian Tumor 1898


title: OvTuMix(106) 2.5.13 vs. 1235201292 OvTuMayo

source_name: Ovarian Tumor 2334


title: Sgordonii_+ARG_rep1

source_name: S gordonii with arginine replicate 1


title: OvTuMix(106) 2.5.13 vs. 1133903684 OvTuMayo

source_name: Ovarian Tumor 2121


title: OvTuMix(106) 2.5.13 vs. 1235201317 OvTuMayo

source_name: Ovarian Tumor 1916


title: OvTuMix(106) 2.5.13 vs. 1235201312 OvTuMayo

source_name: Ovarian Tumor 2277


title: EG163-UM-EU1_1210

description:
uninvolved margin of breast carcinoma
EG163-UM-EU1


title: OvTuMix(106) 2.5.13 vs. 1133903548 OvTuMayo

source_name: Ovarian Tumor 1970


title: OvTuMix(106) 2.5.13 vs. 1133903704 OvTuMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 1893


title: OvTuMix(106) 2.5.13 vs. 1235201297 OvTuMayo

source_name: Ovarian Tumor 1410


title: OvTuMix(106) 2.5.13 vs. 1133903588 OvTuMayo

source_name: Ovarian Tumor 1796


title: EG163-UM-EL2_1717

description:
uninvolved margin of breast carcinoma
EG163-UM-EL2

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: EG163-UM-EL1_1209

description:
uninvolved margin of breast carcinoma
EG163-UM-EL1


title: EG163-UM_1208

description:
uninvolved margin of breast carcinoma
EG163-UM


title: OvTuMix(106) 2.5.13 vs. 1133903192 OvTuMayo

source_name: Ovarian Tumor 1817


title: OvTuMix(106) 2.5.13 vs. 1133903512 OvTuMayo

source_name: Ovarian Tumor 1758


title: OvTuMix(106) 2.5.13 vs. 1133903468 OvTuMayo

source_name: Ovarian Tumor 1489


title: OvTuMix(106) 2.5.13 vs. 1133903388 OvTuMayo

source_name: Ovarian Tumor 1272


title: OvTuMix(106) 2.5.13 vs. 1133903156 OvTuMayo

source_name: Ovarian Tumor 1393


title: EF046-UM99_1205

description:
uninvolved margin of breast carcinoma
EF046-UM99

value: Luminal A


title: OvTuMix(106) 2.5.13 vs. 1133903536 OvTuMayo

description:
reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional cell=1, unknown=7
ovarian tumor samples

source_name: Ovarian Tumor 1388


title: CtrlL_rep3

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7

data_processing: The microarray data were quantile normalized using the R limma package. The fold change and two-tailed Student’s t test were applied for statistical analysis of differentially expressed genes. Heatmap and Scatterplot were drawn with the functions in R. GSEA (v2.0.13) analysis were conducted with two classes (OverExpression vs Control) against the c2 and hallmark v5.0 of MSigDB.

source_name: control vector

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: HCT116 cells were cultured in Mccoy’s 5A medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.

treatment_protocol: Two SNHG1 isoforms (Short or Long) sequence or control vector were stably expressed in HCT116 cells with lentivirus.

tag: cell line

tag: treatment

value: control vector


title: SNHG1L_rep3

source_name: overexpression SNHG1L

value: overexpression SNHG1L


title: EF046-UM98_1204

description:
uninvolved margin of breast carcinoma
EF046-UM98


title: OvTuMix(106) 1.18.13 vs. 1133902980 OvTuMayo

source_name: Ovarian Tumor 1763

tag: ageatdx

tag: Stage


title: rESC-RPC1, biological rep3

description: Gene expression data from rESC-RPC1

tag: differentiation method

value: Adherent culture from differentiation day 10 to day 16, medium changed to N2 at D14

tag: parental cell line

value: rESC-RPCs were differentiated from rat ES cell line DA8-16

tag: genetic background

value: DA rat


title: OvTuMix(106) 2.5.13 vs. 1133903124 OvTuMayo

source_name: Ovarian Tumor 1261

tag: substage

tag: grade

tag: morphology

tag: subtype

tag: histology


title: OvTuMix(106) 1.18.13 vs. 1133902976 OvTuMayo

source_name: Ovarian Tumor 1439

tag: figo


title: CtrlL_rep2


title: OvTuMix(106) 1.18.13 vs. 1133902992 OvTuMayo

source_name: Ovarian Tumor 1690


title: EF046-UM1_1202

description:
uninvolved margin of breast carcinoma
EF046-UM1

tag: gender

value: female

tag: age at cancer diagnosis (yrs)

tag: tumor grade

tag: tumor focality


title: SNHG1L_rep2

tag: cell line


title: OvTuMix(106) 1.18.13 vs. 1133902972 OvTuMayo

source_name: 106 pooled ovarian samples

tag: tissue

source_name: Ovarian Tumor 1364

value: B


title: SNHG1S_rep3

source_name: overexpression SNHG1S

tag: treatment

value: overexpression SNHG1S


title: EF046-UM2_1203

description:
uninvolved margin of breast carcinoma
EF046-UM2

value: unifocal


title: OvTuMix(106) 1.18.13 vs. 1133902892 OvTuMayo

value: ovarian

source_name: Ovarian Tumor 1529

tag: ageatdx

tag: Stage

value: C


title: OvTuMix(106) 1.18.13 vs. 1133902824 OvTuMayo

source_name: Ovarian Tumor 1798

value: Endometrioid


title: OvTuMix(106) 1.18.13 vs. 1133902800 OvTuMayo

source_name: Ovarian Tumor 1406

value: Clear cell


title: SNHG1L_rep1


title: CtrlS_rep3


title: ED027-UM99_1198

description:
uninvolved margin of breast carcinoma
ED027-UM99

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: multifocal


title: OvTuMix(106) 1.18.13 vs. 1133903056 OvTuMayo

source_name: Ovarian Tumor 1808


title: CtrlL_rep1


title: OvTuMix(106) 1.18.13 vs. 1133902852 OvTuMayo

source_name: Ovarian Tumor 1395


title: ED027-UM98_1197

description:
uninvolved margin of breast carcinoma
ED027-UM98


title: OvTuMix(106) 1.18.13 vs. 1133902764 OvTuMayo

source_name: Ovarian Tumor 1538

value: A


title: OvTuMix(106) 1.18.13 vs. 1133902840 OvTuMayo

source_name: Ovarian Tumor 1425


title: SNHG1S_rep2


title: OvTuMix(106) 1.18.13 vs. 1133902752 OvTuMayo

source_name: Ovarian Tumor 1323


title: OvTuMix(106) 1.18.13 vs. 1133902720 OvTuMayo

source_name: Ovarian Tumor 1945


title: ED027-UM4_1196

description:
uninvolved margin of breast carcinoma
ED027-UM4


title: ED027-UM3_1195

description:
uninvolved margin of breast carcinoma
ED027-UM3


title: CtrlS_rep2

source_name: control vector


title: OvTuMix(106) 1.18.13 vs. 1133902760 OvTuMayo

source_name: Ovarian Tumor 2068


title: OvTuMix(106) 1.18.13 vs. 1133902704 OvTuMayo

source_name: Ovarian Tumor 1441


title: OvTuMix(106) 6.1.10 vs. 2094 OvTuCCMayo

source_name: Ovarian Tumor 2094


title: SNHG1S_rep1


title: OvTuMix(106) 6.1.10 vs. 2107 OvTuCCMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 2107


title: ED027-UM2_1194

description:
uninvolved margin of breast carcinoma
ED027-UM2


title: CtrlS_rep1


title: DO044-UM99_1188

description:
uninvolved margin of breast carcinoma
DO044-UM99


title: OvTuMix(106) 1.18.13 vs. 1133902688 OvTuMayo

source_name: Ovarian Tumor 1731


title: DO044-UM98_1187

description:
uninvolved margin of breast carcinoma
DO044-UM98


title: OvTuMix(106) 6.1.10 vs. 807 OvTuCCMayo

source_name: Ovarian Tumor 807


title: OvTuMix(106) 6.1.10 vs. 822 OvTuCCMayo

source_name: Ovarian Tumor 822


title: OvTuMix(106) 6.1.10 vs. 1993 OvTuCCMayo

source_name: Ovarian Tumor 1993


title: DO044-UM3_1185

description:
uninvolved margin of breast carcinoma
DO044-UM3

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: DO044-UM2_1184

description:
uninvolved margin of breast carcinoma
DO044-UM2


title: OvTuMix(106) 6.1.10 vs. 734 OvTuCCMayo

source_name: Ovarian Tumor 734


title: OvTuMix(106) 6.1.10 vs. 207 OvTuCCMayo

source_name: Ovarian Tumor 207


title: OvTuMix(106) 6.1.10 vs. 2049 OvTuCCMayo

source_name: Ovarian Tumor 2049


title: PR+/-, Dnmt3a-/- GMP rep3

city: St Louis

first: Timothy

middle: J

last: Ley

state: MO

address: 660 S Euclid Avenue

department: Internal Medicine

institute: Washington University School of Medicine

hyb_protocol: Labeled targets were hybridized to Mouse Exon 1.0 ST arrays (Affymetrix), washed, stained, and scanned using standard protocols from the Siteman Cancer Center, Molecular and Genomic Analysis Core Facility (http://pathology.wustl.edu/research/cores/lcg/index.php).

scan_protocol: Affymetrix Expression Console software was used to process array images, export signal data, and evaluate image and data quality relative to standard Affymetrix quality control metrics.

data_processing:
Affymetrix CEL files were imported into Partek Genomics Suite™ 6.6 (Partek Inc., St. Louis, MO). Probe-level data were pre-processed, including background correction, normalization, and summarization, using robust multi-array average (RMA) analysis. RMA adjusts for background noise on each array using only the PM probe intensities; and subsequently normalizes data across all arrays using quantile normalization (Bolstad et.al,; Irizarry et.al.) followed by median polish summarization to generate a single measure of expression (Irizarry et.al.). Data was filtered to include only core probesets having raw expression signal greater than 100 in all samples in order to limit the analysis within well-annotated exons.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

organism: Mus musculus

source_name: PR+/-, Dnmt3a-/- bone marrow

label_protocol: Amplified cDNA was prepared from 20 ng total RNA using the whole transcript WT-Ovation RNA Amplification System and biotin-labeled using the Encore Biotin Module, both from NuGen Technologies, according to the manufacturer's instructions.

extract_protocol: For expression array profiling, total cellular RNA was purified using TRIzol reagent (Invitrogen), quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Experion Bioanalyzer.

tag: genotype

value: whole bone marrow


title: OvTuMix(106) 6.1.10 vs. 518 OvTuCCMayo

source_name: Ovarian Tumor 518


title: OvTuMix(106) 6.1.10 vs. 584 OvTuCCMayo

source_name: Ovarian Tumor 584


title: PR+/- GMP rep2

source_name: PR+/- bone marrow


title: OvTuMix(106) 6.1.10 vs. 774 OvTuCCMayo

source_name: Ovarian Tumor 774


title: DO044-UM1_1183

description:
uninvolved margin of breast carcinoma
DO044-UM1


title: DO044-UM4_1186

description:
uninvolved margin of breast carcinoma
DO044-UM4


title: OvTuMix(106) 6.1.10 vs. 1455 OvTuCCMayo

source_name: Ovarian Tumor 1455


title: OvTuMix(106) 6.1.10 vs. 1414 OvTuCCMayo

source_name: Ovarian Tumor 1414


title: PR+/-, Dnmt3a-/- GMP rep1


title: PR+/-, Dnmt3a-/- GMP rep4


title: OvTuMix(106) 6.1.10 vs. 1908 OvTuCCMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 1908


title: PR+/-, Dnmt3a-/- GMP rep2


title: DM153-VB2-M_1179

description:
uninvolved margin in the immediate vicinity of the mammilla
DM153-VB2-M

value: Triple negative


title: OvTuMix(106) 6.1.10 vs. 306 OvTuCCMayo

source_name: Ovarian Tumor 306


title: OvTuMix(106) 6.1.10 vs. 823 OvTuCCMayo

source_name: Ovarian Tumor 823


title: OvTuMix(106) 6.1.10 vs. 1207 OvTuEndoMayo

source_name: Ovarian Tumor 1207


title: DM153-VB1-M_1178

description:
uninvolved margin in the immediate vicinity of the mammilla
DM153-VB1-M


title: DM153-UM-IU2_1177

description:
uninvolved margin of breast carcinoma
DM153-UM-IU2


title: OvTuMix(106) 6.1.10 vs. 1311 OvTuCCMayo

description:
reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional cell=1, unknown=7
ovarian tumor samples

source_name: Ovarian Tumor 1311


title: Dnmt3a-/- GMP (22301)

description: Dnmt3a-/- GMP

source_name: Dnmt3a -/- bone marrow

tag: strain

tag: genotype/variation

tag: cell type

value: GMP


title: OvTuMix(106) 6.1.10 vs. 1195 OvTuEndoMayo

source_name: Ovarian Tumor 1195

tag: substage

tag: grade

tag: morphology


title: OvTuMix(106) 6.1.10 vs. 1146 OvTuEndoMayo

source_name: Ovarian Tumor 1146

tag: subtype

tag: histology

tag: figo


title: OvTuMix(106) 6.1.10 vs. 985 OvTuEndoMayo

source_name: Ovarian Tumor 985


title: OvTuMix(106) 6.1.10 vs. 997 OvTuCCMayo

source_name: Ovarian Tumor 997


title: DM153-UM-IU1_1176

description:
uninvolved margin of breast carcinoma
DM153-UM-IU1

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

tag: gender

tag: age at cancer diagnosis (yrs)

tag: tumor grade


title: Dnmt3a-/- GMP (22303)

description: Dnmt3a-/- GMP

tag: tissue


title: PR+/- GMP rep1


title: DM153-UM-IU_1175

description:
uninvolved margin of breast carcinoma
DM153-UM-IU

tag: tumor focality


title: Dnmt3a-/- CMP (22302)

description: Dnmt3a-/- CMP

value: CMP


title: OvTuMix(106) 6.1.10 vs. 966 OvTuEndoMayo

source_name: Ovarian Tumor 966

tag: ageatdx


title: DM153-UM-EU2_1173

description:
uninvolved margin of breast carcinoma
DM153-UM-EU2


title: DM153-UM-IL_1174

description:
uninvolved margin of breast carcinoma
DM153-UM-IL


title: OvTuMix(106) 6.1.10 vs. 1006 OvTuEndoMayo

source_name: Ovarian Tumor 1006

tag: Stage


title: DM153-UM-EU1_1172

description:
uninvolved margin of breast carcinoma
DM153-UM-EU1


title: OvTuMix(106) 4.13.10 vs. 718 OvTuEndoMayo

source_name: Ovarian Tumor 718


title: OvTuMix(106) 4.13.10 vs. 714 OvTuEndoMayo

source_name: Ovarian Tumor 714


title: OvTuMix(106) 4.13.10 vs. 699 OvTuEndoMayo

source_name: Ovarian Tumor 699


title: OvTuMix(106) 6.1.10 vs. 971 OvTuEndoMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 971


title: OvTuMix(106) 4.13.10 vs. 694 OvTuEndoMayo

source_name: Ovarian Tumor 694


title: Dnmt3a-/- CMP (22300)

description: Dnmt3a-/- CMP


title: OvTuMix(106) 4.13.10 vs. 657 OvTuEndoMayo

source_name: Ovarian Tumor 657


title: Dnmt3a-/- CMP (22298)

description: Dnmt3a-/- CMP


title: DM153-UM-EL2_1171

description:
uninvolved margin of breast carcinoma
DM153-UM-EL2


title: OvTuMix(106) 4.13.10 vs. 595 OvTuEndoMayo

source_name: Ovarian Tumor 595


title: DM153-UM-EL1_1170

description:
uninvolved margin of breast carcinoma
DM153-UM-EL1


title: OvTuMix(106) 4.13.10 vs. 569 OvTuEndoMayo

source_name: Ovarian Tumor 569


title: OvTuMix(106) 4.13.10 vs. 700 OvTuEndoMayo

source_name: Ovarian Tumor 700


title: Wild-Type GMP (22012)

description: Wild-Type (WT) GMP

source_name: Wild-Type bone marrow

value: WT


title: Wild-Type GMP (22011)

description: Wild-Type (WT) GMP


title: OvTuMix(106) 4.13.10 vs. 649 OvTuEndoMayo

source_name: Ovarian Tumor 649


title: OvTuMix(106) 4.13.10 vs. 547 OvTuEndoMayo

source_name: Ovarian Tumor 547


title: OvTuMix(106) 4.13.10 vs. 565 OvTuEndoMayo

source_name: Ovarian Tumor 565


title: OvTuMix(106) 4.13.10 vs. 648 OvTuEndoMayo

source_name: Ovarian Tumor 648


title: CT055-UM99_1167

description:
uninvolved margin of breast carcinoma
CT055-UM99

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: Luminal B, HER2-


title: Wild-Type GMP (21988)

description: Wild-Type (WT) GMP


title: Wild-Type GMP (21986)

description: Wild-Type (WT) GMP


title: CT055-UM98_1166

description:
uninvolved margin of breast carcinoma
CT055-UM98


title: CT055-UM3_1165

description:
uninvolved margin of breast carcinoma
CT055-UM3


title: CT055-UM2_1164

description:
uninvolved margin of breast carcinoma
CT055-UM2


title: OvTuMix(106) 4.13.10 vs. 419 OvTuEndoMayo

source_name: Ovarian Tumor 419


title: CT055-UM1_1163

description:
uninvolved margin of breast carcinoma
CT055-UM1


title: OvTuMix(106) 6.1.10 vs. 329 OvTuEndoMayo

source_name: Ovarian Tumor 329


title: Wild-Type CMP (22003)

description: Wild-Type (WT) CMP


title: NK cells_nonsense transfected_24hr_3

city: London

first: Robert

middle: Daniel

last: Petty

address: Charterhouse Square

department: Haemato-oncology

institute: Barts Cancer Institute, Queen Mary, University of London

description:
Non-sense-I
nonsense control replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Genespring V10 (Agilent)

source_name: CD56+ NK cells transfected with nonsense control pre-miRNA

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays

growth_protocol: Transfected NK cells were incubated for 24 hrs at 37oC with 5% CO in RPMI 1640 cell culture media supplemented with 10% Fetal bovine serum (Invitrogen), 100μg/ml Streptomycin, 100U/ml penicillin, 2mM GlutaMAX (Invitrogen) and 200 U/ml IL-2 (Miltenyi).

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: CD56+ Natural killer cells were isolated by negative magnetic selection from buffy coat samples and transfected with either hsa-miR-330-3p, hsa-miR-99b or nonsense control pre-miRNA.

tag: disease state

value: CFS/ME

value: NKC

tag: protocol

value: control


title: OvTuMix(106) 6.1.10 vs. 370 OvTuEndoMayo

source_name: Ovarian Tumor 370


title: Wild-Type CMP (21987)

description: Wild-Type (WT) CMP

tag: strain

tag: genotype/variation


title: OvTuMix(106) 6.1.10 vs. 1516 OvTuEndoMayo

source_name: 106 pooled ovarian samples

source_name: Ovarian Tumor 1516

tag: substage


title: OvTuMix(106) 4.13.10 vs. 436 OvTuEndoMayo

source_name: Ovarian Tumor 436

value: B

tag: grade


title: OvTuMix(106) 4.13.10 vs. 515 OvTuEndoMayo

source_name: Ovarian Tumor 515

tag: morphology


title: OvTuMix(106) 4.13.10 vs. 410 OvTuEndoMayo

source_name: Ovarian Tumor 410

tag: subtype


title: Wild-Type CMP (22004)

description: Wild-Type (WT) CMP

tag: cell type


title: NK cells_nonsense transfected_24hr_1

description:
Non-sense-G
nonsense control replicate 1


title: CH048-UM98_1159

description:
uninvolved margin of breast carcinoma
CH048-UM98

value: female

value: Luminal A

value: unifocal


title: NK cells_nonsense transfected_24hr_2

description:
Non-sense-H
nonsense control replicate 2


title: OvTuMix(106) 6.1.10 vs. 577 OvTuEndoMayo

description:
reference_mix: The reference mix contained equal amounts of 106 ovarian samples including the following histologies: adenocarcinama=1, benign=4, clear cell= 3, endothelial=5, goblet cell=1, MMMT=5, mucinous=3. normal=7, serous=67, squamous=1, transitional cell=1, unknown=7
ovarian tumor samples

value: ovarian

source_name: Ovarian Tumor 577

value: Endometrioid

tag: histology

tag: figo


title: OvTuMix(106) 6.1.10 vs. 576 OvTuEndoMayo

source_name: Ovarian Tumor 576

value: C


title: OvTuMix(106) 6.1.10 vs. 338 OvTuEndoMayo

source_name: Ovarian Tumor 338

value: A


title: OvTuMix(106) 6.1.10 vs. 343 OvTuCCMayo

source_name: Ovarian Tumor 343

value: Clear cell


title: OvTuMix(106) 4.13.10 vs. 1855 OvTuCCMayo

source_name: Ovarian Tumor 1855


title: OvTuMix(106) 4.13.10 vs. 1791 OvTuCCMayo

source_name: Ovarian Tumor 1791


title: OvTuMix(106) 4.13.10 vs. 1773 OvTuCCMayo

source_name: Ovarian Tumor 1773


title: OvTuMix(106) 4.13.10 vs. 319 OvTuEndoMayo

source_name: Ovarian Tumor 319


title: OvTuMix(106) 6.1.10 vs. 777 OvTuEndoMayo

source_name: Ovarian Tumor 777


title: NK cells_miR-330-3p transfected_24hr_3

description:
hsa-miR-330-3p-L
miR-330-3p replicate 3

source_name: CD56+ NK cells transfected with miR-330-3p

value: miR-330-3p overexpression


title: NK cells_miR-330-3p transfected_24hr_1

description:
hsa-miR-330-3p-B
miR-330-3p replicate 1


title: OvTuMix(106) 6.1.10 vs. 795 OvTuEndoMayo

source_name: Ovarian Tumor 795


title: NK cells_miR-330-3p transfected_24hr_2

description:
hsa-miR-330-3p-K
miR-330-3p replicate 2


title: CH048-UM99_1160

description:
uninvolved margin of breast carcinoma
CH048-UM99

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

tag: gender

tag: age at cancer diagnosis (yrs)


title: CH048-UM1_1157

description:
uninvolved margin of breast carcinoma
CH048-UM1

tag: tumor grade


title: BSP017-UM99_1155

description:
uninvolved margin of breast carcinoma
BSP017-UM99

value: Luminal B, HER2+

tag: tumor focality

value: multifocal


title: OvTuMix(106) 4.13.10 vs. 294 OvTuEndoMayo

source_name: 106 pooled ovarian samples

tag: tissue

source_name: Ovarian Tumor 294

tag: ageatdx


title: NK cells_miR-99b transfected_24hr_3

description:
hsa-miR-99b-F
miR-99b replicate 3

source_name: CD56+ NK cells transfected with miR-99b

tag: disease state

value: miR-99b overexpression


title: BSP017-UM98_1154

description:
uninvolved margin of breast carcinoma
BSP017-UM98


title: CH048-UM2_1158

description:
uninvolved margin of breast carcinoma
CH048-UM2


title: BSP017-UM4_copy_1153

description:
uninvolved margin of breast carcinoma
BSP017-UM4_2


title: BSP017-UM3_1151

description:
uninvolved margin of breast carcinoma
BSP017-UM3


title: BSP017-UM2_1150

description:
uninvolved margin of breast carcinoma
BSP017-UM2


title: OvTuMix(106) 4.13.10 vs. 1720 OvTuCCMayo

source_name: Ovarian Tumor 1720

tag: Stage


title: OvTuMix(106) 4.13.10 vs. 1567 OvTuCCMayo

source_name: Ovarian Tumor 1567


title: OvTuMix(106) 4.13.10 vs. 296 OvTuEndoMayo

source_name: Ovarian Tumor 296


title: BM003-UM98_1146

description:
uninvolved margin of breast carcinoma
BM003-UM98


title: Dnmt3a-/- GMP (22299)

description: Dnmt3a-/- GMP

source_name: Dnmt3a -/- bone marrow

tag: strain

value: whole bone marrow

value: GMP


title: OvTuMix(106) 4.13.10 vs. 1132 OvTuEndoMayo

source_name: Ovarian Tumor 1132


title: NK cells_miR-99b transfected_24hr_1

description:
hsa-miR-99b-A
miR-99b replicate 1

value: CFS/ME

value: NKC

tag: protocol


title: NK cells_miR-99b transfected_24hr_2

description:
hsa-miR-99b-D
miR-99b replicate 2


title: TotalRNA_celline_VM54

city: vienna

first: Peter

last: Petzelbauer

address: Währinger Gürtel

department: Dermatology

country: Austria

institute: Medical University Vienna

hyb_protocol: Hybridization was carried out for 17 h at 65°C in a hybridization oven (Agilent). Afterwards, slides were washed according to the protocol

scan_protocol: samples were scanned using a G2505B NicraArray scanner (Agilent) with default settings.

data_processing: Data analysis with the GeneSpring software (Agilent Technologies) was performed default parameters (Guided Workflow)

source_name: Cell line

label_protocol: Labeling was done using the Quick Amp Labeling Kit and the Single Color Microarray-Based Gene Expression Analysis Protocol.

growth_protocol: Cells were grown in RPMI1640 and passaged regularly by trypsin detachment at a ratio of 1:4

extract_protocol: Cells were lysed by treatment with 1mL Trizol per 25cm² flask and  incubated for 5' at room temperature. Total RNA was extracted using Chloroform/Isopropanol/Ethanol extraction

tag: cell line

tag: patient id

tag: tumor type

value: lentigo maligna

tag: location

value: brain

tag: metastasis status

value: metastasis

tag: braf v600e mutation status

value: mut

tag: kras mutation status

value: wt


title: TotalRNA_celline_VM08

value: nodular melanoma

value: lymph node

value: mut/wt


title: BM003-UM2_1145

description:
uninvolved margin of breast carcinoma
BM003-UM2

tag: gender

value: female

value: unifocal


title: LNCaP/AR R1881_enzalutamide rep2

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: replicate 2

data_processing: Data was log2 transformed and quantile normalized using Partek Genomics suite

source_name: LNCaP/AR, 1 nM R1881 + 10 uM enzalutamide x 24 hours

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

growth_protocol: Cell were grown in DMEM with 10% charcoal-stripped FBS

extract_protocol: RNA was extracted using Qiagen RNAEasy Kit

treatment_protocol: Cells were treated with the indicated drugs or vehicle (DMSO)

value: LNCaP/AR


title: TotalRNA_celline_VM41

value: unknown


title: TotalRNA_celline_VM48


title: TotalRNA_celline_VM53


title: LNCaP/AR R1881_bicalutamide rep3

description: replicate 3

source_name: LNCaP/AR, 1 nM R1881 + 10 uM bicalutamide x 24 hours


title: TotalRNA_celline_VM47


title: BM003-UM1_1144

description:
uninvolved margin of breast carcinoma
BM003-UM1

tag: age at cancer diagnosis (yrs)


title: LNCaP/AR R1881_enzalutamide rep1

description: replicate 1


title: LNCaP/AR R1881_enzalutamide rep3

description: replicate 3


title: BL049-UM99_1141

description:
uninvolved margin of breast carcinoma
BL049-UM99

tag: tumor grade

value: Luminal A


title: TotalRNA_celline_VM07

value: skin

value: primary tumor


title: TotalRNA_celline_VM44

value: superficial spreading melanoma


title: TotalRNA_celline_VM30


title: TotalRNA_celline_VM04


title: BL049-UM98_1140

description:
uninvolved margin of breast carcinoma
BL049-UM98

tag: tumor focality


title: BL049-UM2_1139

description:
uninvolved margin of breast carcinoma
BL049-UM2


title: TotalRNA_celline_VM24


title: TotalRNA_celline_VM26

value: subcutaneous


title: TotalRNA_celline_VM34

value: not classified


title: LNCaP/AR R1881_bicalutamide rep1

description: replicate 1


title: BL049-UM1_1138

description:
uninvolved margin of breast carcinoma
BL049-UM1


title: LNCaP/AR R1881_bicalutamide rep2

description: replicate 2


title: TotalRNA_celline_VM28


title: TotalRNA_celline_VM21

value: primary


title: LNCaP/AR R1881 rep3

description: replicate 3

source_name: LNCaP/AR, 1 nM R1881 x 24 hours


title: BK008-UM99_1136

description:
uninvolved margin of breast carcinoma
BK008-UM99

value: Luminal B, HER2+


title: TotalRNA_celline_VM14

value: metastasis


title: TotalRNA_celline_VM23

value: wt


title: TotalRNA_celline_VM19


title: BK008-UM2_1135

description:
uninvolved margin of breast carcinoma
BK008-UM2


title: TotalRNA_celline_VM15


title: TotalRNA_celline_VM10

value: mut


title: LNCaP/AR Vehicle rep3

description: replicate 3

source_name: LNCaP/AR, Vehicle x 24 hours


title: BK008-UM1_1134

description:
uninvolved margin of breast carcinoma
BK008-UM1


title: TotalRNA_celline_VM01

value: lymph node


title: BG021-UM99_1131

description:
uninvolved margin of breast carcinoma
BG021-UM99


title: LNCaP/AR R1881 rep1

description: replicate 1


title: TotalRNA_celline_VM25

value: nodular melanoma

value: mut/wt


title: LNCaP/AR Vehicle rep1

description: replicate 1


title: LNCaP/AR R1881 rep2

description: replicate 2


title: BG021-UM3_1130

description:
uninvolved margin of breast carcinoma
BG021-UM3

value: female

value: unifocal


title: LNCaP/AR Vehicle rep2

description: replicate 2

value: LNCaP/AR


title: HRG16_pool11_d

city: RENNES

first: rogue

last: alexandra

address: 2 av du professeur leon bernard

country: France

institute: inserm

description: Gene expression after 24h-treatment with 0.1% DMSO in human hepatocytes

hyb_protocol: 1650 ng of Cy3-RNAs were hybridized using the Hybridisation Kit Plus (Agilent) onto 4×44K Whole Human Genome Microarrays (G4112F, Agilent). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Five hundred ng of total RNA from each cell culture were reverse-transcribed into double-strand cDNAs and amplified for 2 h at 40°C using the Quick Amp Labeling Kit (Agilent). cDNAs were transcribed into antisense cRNA and labeled with CTP-Cy3 fluorescent dye for 2 h at 40°C following the manufacturer's protocol. Cyanine-labeled cRNAs were purified using RNeasy minikit (Qiagen, Inc., Valencia, CA).

growth_protocol: Human hepatocytes undergoing resection for primary and secondary tumors were obtained by collagenase perfusion of histologically normal liver fragments and used for the preparation of RNA samples and primary cultures. Hepatocyte cultures were obtained by seeding 170,000 cells/cm² in 6-well plates in a Williams’ E medium supplemented with 10% FCS, 100 units/µl penicillin, 100 µg/ml streptomycin, 1 µg/ml insulin, 2 mM glutamine, and 1 µg/ml bovine serum albumin. The medium was discarded 12 h after seeding, and cells were thereafter maintained in serum-free medium supplemented with 5 x 10-5 M hydrocortisone hemisuccinate. HH were used 24 h after seeding.

extract_protocol: Cells were harvested in lysis buffer (RLT buffer and β-mercaptoethanol). Total RNA was isolated using the RNeasy mini kit (Qiagen). RNA quantity and purity were assessed with a Nanodrop ND-1000 spectrophotometer (Nyxor Biotech, Paris, France) and RNA integrity was checked with a Bioanalyzer 2100 (Agilent Technologies, Massy, France).

treatment_protocol: All cells received 0.1% DMSO as the vehicle final concentration.

tag: cell type

value: HepaRG

tag: passage

tag: pool

tag: biological replicate

tag: technical replicate


title: HRG16_pool9_c


title: HRG16_pool9_a


title: BG021-UM2_1129

description:
uninvolved margin of breast carcinoma
BG021-UM2

value: Luminal A


title: HRG16_pool9_b


title: HRG16_pool11_b


title: HRG16_pool11_a


title: HRG16_pool7_b


title: 35S_GLK1-SRDX_Arabidopsis_2wks_seedling-rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description:
GLK1SRDX_rep4
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.

hyb_protocol: Hybridized using the Gene Expression Hybridization kit (Agilent) and washed by the Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, the signal of each probe was divided by the median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: 35S:GLK1-SRDX Arabidopsis thaliana 2wks seedlings

label_protocol: 1 ug of total RNA was used for the labeling procedure using the Quick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) agar medium in a 16hr light / 8hr dark cycle in 23 Celsius degrees.

extract_protocol: The Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

tag: ecotype

tag: genotype

tag: age

tag: tissue

value: whole seedlings


title: 35S_GLK1-SRDX_Arabidopsis_2wks_seedling-rep3

description:
GLK1SRDX_rep3
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: HRG16_pool7_a


title: 35S_GLK1-SRDX_Arabidopsis_2wks_seedling-rep2

description:
GLK1SRDX_rep2
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: 35S_GLK1-SRDX_Arabidopsis_2wks_seedling-rep1

description:
GLK1SRDX_rep1
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: BD038-UM99_1122

description:
uninvolved margin of breast carcinoma
BD038-UM99

value: multifocal


title: HRG14_pool5_d


title: HRG16_pool11_c


title: HRG14_pool5_c


title: BD038-UM3_1121

description:
uninvolved margin of breast carcinoma
BD038-UM3


title: HRG16_pool7_c


title: HRG14_pool3_b


title: BG021-UM1_1128

description:
uninvolved margin of breast carcinoma
BG021-UM1


title: HRG14_pool5_b


title: BD038-UM1_1119

description:
uninvolved margin of breast carcinoma
BD038-UM1


title: HRG14_pool5_a


title: glk1_glk2_Arabidopsis_2wks_seedling-rep3

description:
glk1_glk2_rep3
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.

source_name: glk1 glk2 Arabidopsis thaliana 2wks seedlings

value: glk1 glk2


title: glk1_glk2_Arabidopsis_2wks_seedling-rep4

description:
glk1_glk2_rep4
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: HRG14_pool1_c


title: BD038-UM2_1120

description:
uninvolved margin of breast carcinoma
BD038-UM2


title: HRG14_pool1_a


title: AW020-UM99_reRun_1115

description:
uninvolved margin of breast carcinoma
AW020-UM99_2


title: AW020-UM98_1114

description:
uninvolved margin of breast carcinoma
AW020-UM98


title: glk1_glk2_Arabidopsis_2wks_seedling-rep2

description:
glk1_glk2_rep2
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: HRG14_pool1_d


title: HRG14_pool1_b


title: AW020-UM6_1113

description:
uninvolved margin of breast carcinoma
AW020-UM6


title: HRG14_pool3_a

description: Gene expression after 24h-treatment with 0.1% DMSO in human hepatocytes


title: glk1_glk2_Arabidopsis_2wks_seedling-rep1

description:
glk1_glk2_rep1
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: HH6_control rep2

source_name: HH6_control replicate 2

value: primary human hepatocyte

tag: donor


title: HRG14_pool3_d


title: Wild_type_Arabidopsis_2wks_seedling-rep3

description:
control_rep3
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.

source_name: Wild-type Arabidopsis thaliana 2wks seedlings


title: Wild_type_Arabidopsis_2wks_seedling-rep4

description:
control_rep4
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: AW020-UM5_1112

description:
uninvolved margin of breast carcinoma
AW020-UM5

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: HRG14_pool3_e


title: HH4_control rep2

source_name: HH4_control replicate 2


title: AW020-UM4_1111

description:
uninvolved margin of breast carcinoma
AW020-UM4


title: HH6_control

source_name: HH6_control replicate 1


title: HH5_control

source_name: HH5_control replicate 1


title: AW020-UM3_1110

description:
uninvolved margin of breast carcinoma
AW020-UM3


title: HH5_control rep2

source_name: HH5_control replicate 2


title: HH4_control

source_name: HH4_control replicate 1


title: Wild_type_Arabidopsis_2wks_seedling-rep2

description:
control_rep2
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: Wild_type_Arabidopsis_2wks_seedling-rep1

description:
control_rep1
Many seedlings were grown in MS agar medium and were harvested for RNA extraction.


title: HH3_control

source_name: HH3_control replicate 1


title: HH3_control rep2

source_name: HH3_control replicate 2


title: AW020-UM2_1109

description:
uninvolved margin of breast carcinoma
AW020-UM2


title: Krt7 + cells from fetal esophagus, rep2

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing:
Expression console, Partek Genome Suite 6.6
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Krt7 + cells from fetal esophagus

label_protocol: Encore® Biotin Module (Nugen)

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies)

value: Fetal esophagus krt7 + cells

tag: sample type

value: Cultured stem cells


title: AW020-UM1_1108

description:
uninvolved margin of breast carcinoma
AW020-UM1

value: Luminal B, HER2+


title: air liquid interface culture of Krt7 + cells from fetal esophagus, rep2

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

value: ALI differentiation


title: HH1_control

source_name: HH1_control replicate 1


title: HH2_control

source_name: HH2_control replicate 1


title: AL148-VB2-M_1102

description:
uninvolved margin in the immediate vicinity of the mammilla
AL148-VB2-M

value: Triple negative


title: Krt7 + cells from fetal esophagus, rep1


title: Krt5 + cells from fetal esophagus, rep2

source_name: Krt5 + cells from fetal esophagus

value: Fetal esophagus krt5 + cells


title: air liquid interface culture of Krt7 + cells from fetal esophagus, rep1


title: HH2_control rep2

source_name: HH2_control replicate 2


title: KM4-Zfp423/GFP Negative-3

city: Durham

first: Rana

middle: K

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

description: PDGFRb+ Lin- perivascular cells isolated from 5 week old male Epidydimal Fat Tissue

data_processing: The data were normalised using quantile normalization using Illumina GenomeStudio software. Additional Analyses were done using Bioconductor in R.

source_name: PDGFRb+ Lin- cells from Epidydimal Fat Tissue

extract_protocol: total RNA was extracted with Life Technologies RNAquous kit in accordance with the prescribed protocol provided with the kit. RNA amplified using 2-round Epicenter Target Amp Pico Labeling Kit. Quality control was performed with Agilent Bioanalyser.

value: Epidydimal Adipose Tissue

value: PDGFRb+ Lin- (GFP negative)

tag: Sex

value: Male

value: 5 weeks


title: KM1-Zfp423/GFP Positive-3

value: PDGFRb+ Lin- (GFP positive)


title: AL148-VB1-M_1101

description:
uninvolved margin in the immediate vicinity of the mammilla
AL148-VB1-M

value: female

value: unifocal


title: Krt5 + cells from fetal esophagus, rep1


title: RG5-Zfp423/GFP Positive-2


title: RG6-Zfp423/GFP Negative-1


title: AL148-UM-IU2_1100

description:
uninvolved margin of breast carcinoma
AL148-UM-IU2


title: AL148-UM-IU_1098

description:
uninvolved margin of breast carcinoma
AL148-UM-IU


title: air liquid interface culture of Krt5 + cells from fetal esophagus, rep2


title: AL148-UM-IU1_1099

description:
uninvolved margin of breast carcinoma
AL148-UM-IU1


title: RG3-Zfp423/GFP Positive-1


title: AL148-UM-IL_1097

description:
uninvolved margin of breast carcinoma
AL148-UM-IL


title: KM2-Zfp423/GFP Negative-2


title: baselineB_2

city: Singapore

first: Paul

middle: Michael

last: Yen

address: 8 College Road

department: Cardiovascular & Metabolic disorder Program

country: Singapore

institute: Duke-NUS Graduate Medical School Singapore

description: replicate 2

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

source_name: mouse liver tissue

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

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

treatment_protocol: To induce systemic thyrotoxicosis, mice received daily intraperitoneal injection of 20 μg L-T3 (liothyronine; Sigma)/100 g body weight for 14 days.

value: Liver

tag: strain

value: 8 weeks


title: withdrawalT3_3

description: replicate 3

tag: gender


title: baselineB_3

description: replicate 3


title: baselineB_1

description: replicate 1


title: air liquid interface culture of gastric cardia stem cells (patient 7), rep1

description: GC_ALI (GC7)-1

source_name: air liquid interface culture of gastric cardia stem cells_patient 7

tag: patient id

value: patient 7

value: Gastric cardia stem cells


title: withdrawalT3_1

description: replicate 1


title: air liquid interface culture of Krt5 + cells from fetal esophagus, rep1


title: air liquid interface culture of gastric cardia stem cells (patient 7), rep2

description: GC_ALI (GC7)-2


title: acuteT3_3

description: replicate 3


title: chronicT3_2

description: replicate 2


title: withdrawalT3_2

description: replicate 2


title: baselineA_3

description: replicate 3


title: chronicT3_3

description: replicate 3


title: baselineA_2

description: replicate 2


title: AL148-UM-EU2_1096

first: Chiara

last: Rasi

address: Husargatan 3

institute: Uppsala University

description:
uninvolved margin of breast carcinoma
AL148-UM-EU2

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

tag: age at cancer diagnosis (yrs)

tag: tumor grade


title: Gastric cardia stem cells from patient 11, rep1

source_name: Gastric cardia stem cells_patient 11

value: patient 11

tag: cell type


title: AL148-UM-EU_1094

description:
uninvolved margin of breast carcinoma
AL148-UM-EU

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

tag: tumor focality


title: AL148-UM-EL2_1093

description:
uninvolved margin of breast carcinoma
AL148-UM-EL2


title: AL148-UM-EL_1091

description:
uninvolved margin of breast carcinoma
AL148-UM-EL


title: AL148-UM-EU1_1095

description:
uninvolved margin of breast carcinoma
AL148-UM-EU1


title: acuteT3_2

description: replicate 2


title: Gastric cardia stem cells from patient 12, rep2

source_name: Gastric cardia stem cells_patient 12

value: patient 12

value: Cultured stem cells


title: AKK034-UM99_1088

description:
uninvolved margin of breast carcinoma
AKK034-UM99

value: Luminal A

value: multifocal


title: chronicT3_1

description: replicate 1


title: AL148-UM-EL1_1092

description:
uninvolved margin of breast carcinoma
AL148-UM-EL1

value: Triple negative


title: Gastric cardia stem cells from patient 12, rep1


title: AKK034-UM98_1087

description:
uninvolved margin of breast carcinoma
AKK034-UM98


title: acuteT3_1

description: replicate 1


title: baselineA_1

description: replicate 1


title: hyperthyroid plus FoxO1 knockdown rep 2

first: Brijesh

middle: Kumar

last: Singh

address: CVMD Level-8, 8 College Road

department: Cardiovascular and Metabolic Disorders Program

institute: Duke-NUS Gradiate Medical School

description: Sample 8

growth_protocol: Animals were housed and maintained as described in Singh et al. J Biol Chem. 2013;288(42):30365-72.

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

treatment_protocol: Mouse were treated with triiodothyronine (T3) for 3 days to make them hyperthyroid. FOXO1 was knocked down in liver using hydrodynamic tail vein injection of FOXO1 siRNA as described in Singh et al. J Biol Chem. 2013;288(42):30365-72.

tag: condition

value: hyperthyroid plus FoxO1 knockdown


title: Gastric cardia stem cells from patient 10, rep1

source_name: Gastric cardia stem cells_patient 10

value: patient 10


title: hyperthyroid sample rep 2

description: Sample 5

value: hyperthyroid

value: Male


title: Gastric cardias stem cells from patient 8, rep2

source_name: Gastric cardias stem cells_patient 8

value: patient 8


title: Gastric cardia stem cells from patient 10, rep2


title: hyperthyroid plus FoxO1 knockdown rep 1

description: Sample 7


title: O-lenti-iPSCs-LIF(+) B

city: Minneapolis

first: Nobuaki Kikyo

email: kikyo001@umn.edu, hiraih@umich.edu

state: MN

address: 2001 6th St SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Sample name: M10

data_processing:
The obtained data were analyzed with an Illumina Genome Studio.
The data were normalized using rank invariant method.

source_name: Cell Line

label_protocol: Samples with an RNA Integrity Number of 7.5 or greater measured with a LabChip Caliper GX (Perkin Elmer) were applied to an Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies) to generate biotinylated and amplified RNA.

growth_protocol: ESCs and iPSCs-LIF(+) were cultured on irradiated MEF feeder cells in iPSC medium (DMEM, 20% FBS or KnockOut Serum Replacement [Life Technologies], 100 µM MEM non-essential amino acids, 100 µM 2-mercaptoethanol, and 2 mM L-glutamine with or without 1,000 U/ml LIF)

extract_protocol: Total RNA was prepared from each cell type with a PureLink RNA Mini Kit (Life Technologies).

treatment_protocol: LIF was omitted during establishment and maintenance of M3O-lenti-iPSCs-LIF(–).

value: iPSCs

tag: leukemia inhibitory factor (lif) treatment


title: Gastric cardia stem cells from patient 9, rep2

source_name: Gastric cardia stem cells_patient 9

value: patient 9


title: hyperthyroid sample rep 1

description: Sample 4

value: Liver


title: Gastric cardia stem cells from patient 9, rep1


title: Gastric cardias stem cells from patient 8, rep1


title: hyperthyroid sample rep 3

description: Sample 6

value: 8 weeks


title: hyperthyroid plus FoxO1 knockdown rep 3

description: Sample 9


title: euthyroid control rep 3

description: Sample 3

value: euthyroid control


title: O-retro-iPSCs-LIF(+) B

description: Sample name: M9


title: AKK034-UM4_1086

city: Uppsala

description:
uninvolved margin of breast carcinoma
AKK034-UM4

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

value: female


title: M3O-lenti-iPSCs-LIF(+) B

description: Sample name: M11


title: euthyroid control rep 2

description: Sample 2


title: Gastric cardia stem cells from patient 7, rep1

source_name: Gastric cardia stem cells_patient 7

value: patient 7

value: Gastric cardia stem cells


title: M3O-lenti-iPSCs-LIF(-) B

description: Sample name: M12


title: ESCs (CGR8)

description: Sample name: M8

value: ESCs


title: euthyroid control rep 1

description: Sample 1


title: M3O-lenti-iPSCs-LIF(+) A

description: Sample name: M5


title: AKK034-UM2_1084

description:
uninvolved margin of breast carcinoma
AKK034-UM2

value: Luminal A


title: AKK034-UM1_1083

description:
uninvolved margin of breast carcinoma
AKK034-UM1

value: multifocal


title: AH028-UM99_1079

description:
uninvolved margin of breast carcinoma
AH028-UM99

value: Luminal B, HER2-


title: Gastric cardia stem cells from patient 7, rep2

value: Cultured stem cells


title: AH028-UM98_reRun_1078

description:
uninvolved margin of breast carcinoma
AH028-UM98_2


title: AH028-UM5_1077

description:
uninvolved margin of breast carcinoma
AH028-UM5


title: AH028-UM3_1076

description:
uninvolved margin of breast carcinoma
AH028-UM3


title: M3O-lenti-iPSCs-LIF(-) A

description: Sample name: M6


title: MEFs-2

description: Sample name: M7

value: embryonic fibroblasts


title: AKK034-UM3_1085

description:
uninvolved margin of breast carcinoma
AKK034-UM3


title: AH028-UM2_1075

description:
uninvolved margin of breast carcinoma
AH028-UM2


title: Gastric cardia stem cells from patient 5, rep1

source_name: Gastric cardia stem cells_patient 5

value: patient 5


title: Gastric cardia stem cells from patient 5, rep2


title: Gastric cardia stem cells from patient 6, rep1

source_name: Gastric cardia stem cells_patient 6

value: patient 6


title: O-lenti-iPSCs-LIF(+) A

description: Sample name: M4


title: Gastric cardia stem cells from patient 4, rep1

source_name: Gastric cardia stem cells_patient 4

value: patient 4


title: ESCs (CJ7)

description: Sample name: M2


title: Gastric cardia stem cells from patient 6, rep2


title: Gastric cardia stem cells from patient 4, rep2


title: Gastric cardia stem cells from patient 3, rep2

source_name: Gastric cardia stem cells_patient 3

value: patient 3


title: O-retro-iPSCs-LIF(+) A

description: Sample name: M3

value: iPSCs


title: AE031-UM98_1068

description:
uninvolved margin of breast carcinoma
AE031-UM98


title: WT brain replicate 2

city: Cincinnati

first: Nupur

last: dasgupta

state: OH

address: 3333, Burnet Avenue

department: human Genetics

institute: CCHMC

description: 42-45 days old Gene expression data from WT mouse brain

hyb_protocol: Create a hybridization cocktail for a single probe array that contains biotin-labeled low molecular RNA molecules, 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, 4% Formamide, 50 pM Control Oligo B2, and 1X Hybridization Mix.  Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge. Fill probe array with 100 mL of the hybridization cocktail. Incubate at 48°C for 16 -18 hrs in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G scanner  and Genechip Operating Software 1v4 (Affymetrix) was usedfor scanning

data_processing: Data analyses were performed using Gene Spring Software (Agilent Technologies, Inc., Santa Clara, CA). Normalization was performed using the RMA (robust multiarray average) algorithm [42]. Post normalization unpaired T Test (Asymptotic) was performed. The false discovery rate (FDR) was calculated according to the Benjamini and Hochberg algorithm

source_name: 42-45 days old Gene expression data from WT, Isofagamine treated and 4L;C* mouse brain

label_protocol: The FlashTag™ Biotin HSR RNA Labeling Kit is used to biotin label low molecular weight RNA molecules. The labeled samples are hybridized to Affymetrix Mouse Gene 1.0 ST chip GeneChip®.

growth_protocol: Genotype of 4L;C* mice have combined V394L/V394L Gba1 (4L) and saposin C-/- (C*). The strain background of 4L;C* mice was C57BL/6J/129SvEV. The strain- and age-matched WT mice were used as control. All mice were housed under pathogen-free conditions in the barrier animal facility and according to IACUC approved protocol at Cincinnati Children’s Hospital Research Foundation

extract_protocol: RNA samples of whole brain were set by pooling of mRNAs from three individual mice in a cohort , i.e. 4 RNA samples were representing for each genotype . Collected tissues were immediately immersed in RNA Later and RNAs were extracted using the TOTALLY RNA kit

treatment_protocol: The 4L;C* mice were treated with a pharmacological chaperone, isofagamine tartrate (IFG), at 60 mg/kg/d by drinking water as described . The pregnant dames were given drinking water containing IFG staring 3 to 5 days prior to birth and during the weaning period. After weaning, the pups were continued on 60 mg/kg/d IFG in drinking water for entire course .

value: Brain

value: WT


title: Gastric cardia stem cells from patient 3, rep1


title: WT brain replicate 1

source_name: 42-45 days old WTmouse brain


title: AE031-UM3_1067

description:
uninvolved margin of breast carcinoma
AE031-UM3

label_protocol: starndard protocol


title: AE031-UM99_1069

description:
uninvolved margin of breast carcinoma
AE031-UM99


title: Gastric cardia stem cells from patient 2, rep2

source_name: Gastric cardia stem cells_patient 2

value: patient 2


title: MEFs-1

description: Sample name: M1


title: AH028-UM1_1074

description:
uninvolved margin of breast carcinoma
AH028-UM1

value: female


title: AE031-UM2_1066

description:
uninvolved margin of breast carcinoma
AE031-UM2


title: KO brain  replicate 1

description: 42-45 days old Gene expression data from4L;C* mouse brain

source_name: 42-45 days old  4L;C* mouse brain


title: AD171-VB2_1061

description:
uninvolved margin in the immediate vicinity of the mammilla
AD171-VB2

value: unifocal


title: Gastric cardia stem cells from patient 1, rep2

source_name: Gastric cardia stem cells_patient 1

value: patient 1

value: Gastric cardia stem cells


title: Gastric cardia stem cells from patient 1, rep1


title: KO brain replicate 2


title: AD171-VB1_1060

description:
uninvolved margin in the immediate vicinity of the mammilla
AD171-VB1


title: Gastric cardia stem cells from patient 2, rep1


title: AD171-UM-IU2_1716

description:
uninvolved margin of breast carcinoma
AD171-UM-IU2


title: AE031-UM1_1065

description:
uninvolved margin of breast carcinoma
AE031-UM1

value: Luminal A


title: Gastric cardia stem cells from patient 11, rep2

source_name: Gastric cardia stem cells_patient 11

value: patient 11


title: H Control2

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: Hypoxia Control 2

hyb_protocol: Biotin labelled, amplified cRNA (1500 ng per array) was hybridized to the Illumina HumanWG-6_V3 BeadChip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader using BeadScan 3.5.49.29917 software and direct hybridization assay, according to the Manufacturer's instructions.

data_processing: Array data processing and analysis was performed using Illumina BeadStudio 3.2.6 software using the average chip normalization method.

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep96 Amplification Kit from Ambion # 4393543

growth_protocol: MCF7 cell was cultured in Dulbecco's modified Eagle's medium (DMEM), supplemented with 10% fetal bovine serum, penicillin (50 IU/ml) and streptomycin sulphate (50 μg/ml). For hypoxia incubation, cells were exposed to hypoxic conditions (1% O2, 5% CO2 and 94% N2) in a Heto-Holten CellHouse 170 incubator (RS Biotech, Irvine, Scotland).

extract_protocol: Total RNA was extracted using RNAeasy kit from Qiagen

treatment_protocol: ICI182780 or DMSO was added into culture dish for 24-hour treatment.

tag: cell line

tag: stress

value: Hypoxia

tag: agent

value: control


title: H ICI1

description: Hypoxia ICI 1


title: H ICI2

description: Hypoxia ICI 2


title: Normal esophagus stem cells from patient 9, rep1

source_name: Normal esophagus stem cells_patient 9

value: patient 9

value: Normal esophagus stem cells

value: Cultured stem cells


title: ChREBP5, Biological rep5

city: Pars

first: Renaud

last: Dentin

address: 24 rue du Faubourg Saint Jacques

department: Endocrinology, Metabolism and Diabetes

institute: INSERM U1016

description: Liver gene expression data from fed ChREBP expressing mice

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours.  After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix).

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: Liver specific ChREBP overexpressing mice 5

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 50 ng of total RNA is reverse transcribed following the Ovation PicoSL WTA System (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5ug of single strand DNA is used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen)

growth_protocol: The GFP or ChREBP (5.108 pfu / mice) were overexpressed in the liver of 8 weeks old C57BL/6J mice through adenoviral gene delivery (tail vein injection).

extract_protocol: Total RNA were extracted using the SV RNA extraction systeme from Progema according to the manufacturer's instructions.

treatment_protocol: Mice were studied in fed state 3 weeks after the adenovirus injection.

value: male

tag: age

value: 8 weeks

value: Liver

tag: genotype/variation

value: ChREBP overexpressing


title: ChREBP6, Biological rep6

source_name: Liver specific ChREBP overexpressing mice 6

tag: tissue


title: ChREBP4, Biological rep4

source_name: Liver specific ChREBP overexpressing mice 4


title: H Control1

description: Hypoxia Control 1


title: Normal esophagus stem cells from patient 8, rep2

source_name: Normal esophagus stem cells_patient 8

value: patient 8

tag: sample type


title: N ICI2

description: Normoxia ICI 2

value: Normoxia


title: AD171-UM-IU1_1059

description:
uninvolved margin of breast carcinoma
AD171-UM-IU1

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: female

value: Luminal B, HER2-


title: N ICI1

description: Normoxia ICI 1


title: Normal esophagus stem cells from patient 9, rep2


title: ChREBP3, Biological rep3

source_name: Liver specific ChREBP overexpressing mice 3


title: ChREBP2, Biological rep2

source_name: Liver specific ChREBP overexpressing mice 2


title: Normal esophagus stem cells from patient 8, rep1


title: ChREBP1, Biological rep1

source_name: Liver specific ChREBP overexpressing mice 1


title: air liquid interface culture of normal esophagus stem cells (patient 9), rep2

description: Eso _ALI (Eso9)-2

source_name: air liquid interface culture of normal esophagus stem cells_patient 9

value: ALI differentiation


title: N Control2

description: Normoxia Control 2


title: AD171-UM-IL1_1058

description:
uninvolved margin of breast carcinoma
AD171-UM-IL1

value: unifocal


title: GFP 6, Biological rep6

description: Liver gene expression data from fed GFP expressing mice

source_name: Liver specific GFP overexpressing mice 6

value: GFP overexpressing


title: AD171-UM-EU1_1056

description:
uninvolved margin of breast carcinoma
AD171-UM-EU1


title: AD171-UM-EU2_1057

description:
uninvolved margin of breast carcinoma
AD171-UM-EU2


title: AD171-UM-EL2_1715

description:
uninvolved margin of breast carcinoma
AD171-UM-EL2


title: air liquid interface culture of normal esophagus stem cells (patient 9), rep1

description: Eso _ALI (Eso9)-1


title: AD171-UM-EL1_1055

description:
uninvolved margin of breast carcinoma
AD171-UM-EL1


title: ACV037-UM99_1052

description:
uninvolved margin of breast carcinoma
ACV037-UM99

value: Luminal B, HER2+

value: multifocal


title: 3442

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Samples were hybridized on dual color Agilent's custom MCF-7 Microarray (Agilent, Diegem, Belgium; GEO accession number GPL8637).

scan_protocol: After washing, the slides were scanned with a microarray scanner (Agilent) and images were processed using Feature Extraction Software version 8.5 (Agilent).

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v8.5.1.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3) were computed and averaged over the duplicate spots. Control probes were removed prior to analysis.

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 5-CTP (LRILAK, Agilent). The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer.

extract_protocol: RNA was extracted using the RNeasy mini kit from Qiagen, according to the manufacturer's protocol.

treatment_protocol: MCF-7 cells were seeded in T-25 Nunc culture flasks at a density of 300,000 cells per flask. After 72h steroid-deprivation, cells were exposed for 1h, 4h, or 48h at a high or low concentration. The highest concentration represents the highest non-cytotoxic or highest soluble concentration. Non-cytotoxic concentrations were derived from AlamarBlue viability assays (Nociari et al. 1998).

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)

tag: compound

value: solvent control

tag: exposure

label_protocol: From 1 µg of cellular RNA, poly-A RNA was reversed transcribed using a poly dT-T7 primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP (LRILAK, Agilent) The amplified and labeled RNA probes were purified separately with RNeasy purification columns (Qiagen, Belgium). Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm and Cy3 incorporation at 550 nm using a Nanodrop spectrophotometer.

value: Endosulfan

tag: concentration


title: N Control1

description: Normoxia Control 1

value: control


title: GFP 5, Biological rep5

source_name: Liver specific GFP overexpressing mice 5

tag: strain

tag: gender

value: male


title: GFP 4, Biological rep4

source_name: Liver specific GFP overexpressing mice 4

value: 8 weeks


title: 3126

source_name: Ref MCF7


title: 3127


title: air liquid interface culture of Barrett's esophagus stem cells (patient 7), rep2

description: BE_ALI (BE7)-2

source_name: air liquid interface culture of Barrett's esophagus stem cells_patient 7

tag: patient id

value: patient 7

value: Barett's esophagus stem cells


title: 3123


title: 3125


title: 3121


title: GFP 2, Biological rep2

source_name: Liver specific GFP overexpressing mice 2

value: Liver


title: ACV037-UM2_1050

description:
uninvolved margin of breast carcinoma
ACV037-UM2

tag: age at cancer diagnosis (yrs)

tag: tumor grade


title: Barrett's esophagus stem cells from patient 11, rep2

source_name: Barrett's esophagus stem cells_patient 11

value: patient 11

tag: cell type

value: Cultured stem cells


title: air liquid interface culture of Barrett's esophagus stem cells (patient 7), rep1

description: BE_ALI (BE7)-1


title: 3120


title: Phf2-4, Biological rep4

description: Liver gene expression data from fed Phf2 expressing mice

source_name: Liver specific Phf2 overexpressing mice 4

growth_protocol: The GFP or Phf2 (5.108 pfu / mice) were overexpressed in the liver of 8 weeks old C57BL/6J mice through adenoviral gene delivery (tail vein injection).

value: Phf2 overexpressing


title: GFP 1, Biological rep1

source_name: Liver specific GFP overexpressing mice 1


title: Barrett's esophagus stem cells from patient 11, rep1


title: GFP 3, Biological rep3

source_name: Liver specific GFP overexpressing mice 3


title: Phf2-5, Biological rep5

source_name: Liver specific Phf2 overexpressing mice 5


title: Phf2-3, Biological rep3

source_name: Liver specific Phf2 overexpressing mice 3


title: ACV037-UM98_1051

description:
uninvolved margin of breast carcinoma
ACV037-UM98

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

value: female

tag: tumor focality


title: ACV037-UM1_1049

description:
uninvolved margin of breast carcinoma
ACV037-UM1


title: Barrett's esophagus stem cells from patient 12, rep1

source_name: Barrett's esophagus stem cells_patient 12

value: patient 12


title: Barrett's esophagus stem cells from patient 12, rep2


title: 3119

tag: cell line


title: 3122


title: 145MJ-VB2_1045

description:
uninvolved margin in the immediate vicinity of the mammilla
145MJ-VB2

value: Luminal A

value: unifocal


title: Barrett's esophagus stem cells from patient 10, rep1

source_name: Barrett's esophagus stem cells_patient 10

value: patient 10


title: 145MJ-VB1_1044

description:
uninvolved margin in the immediate vicinity of the mammilla
145MJ-VB1


title: Phf2-2, Biological rep2

source_name: Liver specific Phf2 overexpressing mice 2


title: Phf2-1, Biological rep1

source_name: Liver specific Phf2 overexpressing mice 1


title: 145MJ-UM-IU_1043

description:
uninvolved margin of breast carcinoma
145MJ-UM-IU


title: Barrett's esophagus stem cells from patient 10, rep2


title: 3118

value: MCF-7 human breast carcinoma cell line (ECACC No. 86012803)


title: 3117


title: 3116


title: 3115


title: Barrett's esophagus stem cells from patient 9, rep2

source_name: Barrett's esophagus stem cells_patient 9

value: patient 9


title: 145MJ-UM-IL_1042

description:
uninvolved margin of breast carcinoma
145MJ-UM-IL


title: Barrett's esophagus stem cells from patient 8, rep1

source_name: Barrett's esophagus stem cells_patient 8

value: patient 8


title: Barrett's esophagus stem cells from patient 7, rep2

source_name: Barrett's esophagus stem cells_patient 7


title: GFP5, Biological rep5

source_name: Liver specific GFP overexpressing mice 5

value: GFP overexpressing


title: GFP3, Biological rep3

value: male


title: Barrett's esophagus stem cells from patient 8, rep2


title: 145MJ-UM-EU_1041

description:
uninvolved margin of breast carcinoma
145MJ-UM-EU


title: 144BW-VB2_1039

description:
uninvolved margin in the immediate vicinity of the mammilla
144BW-VB2

value: Luminal B, HER2-

value: multifocal??? (1 mm)


title: 3113

value: Endosulfan

value: solvent control


title: GFP4, Biological rep4

source_name: Liver specific GFP overexpressing mice 4

value: 8 weeks

value: Liver


title: Barrett's esophagus stem cells from patient 7, rep1

value: patient 7

value: Barett's esophagus stem cells

value: Cultured stem cells


title: GFP1, Biological rep1


title: Barrett's esophagus stem cells from patient 9, rep1


title: 3114


title: 3112

value: kepone