title: rat liver_chow diet_biological rep2


title: X5M1_TP63

status: Public on Feb 01 2016

type: SRA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

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

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description:
antibody: TP63 (ActiveMotif, #39739)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: ACC Primagraft

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

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

tag: tissue type

value: adenoid cystic carcinoma (ACC)


title: blood-MTC_3969

type: genomic

city: Valencia

first: Joaquin

last: Dopazo

state: Valencia

address: Eduardo Primo Yúfera, 3

department: Systems Biology

country: Spain

institute: Centro de Investigacion Principe Felipe

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and images were obtained using an Affymetrix GeneChip® Scanner 3000.

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

label: Biotin

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

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

tag: phenotype

value: MTC

tag: tissue

value: peripheral blood


title: blood-MTC_4093


title: X5M1_BRD4

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


title: blood-MTC_3867R


title: X2_MYB

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


title: human fetal incisor secretory ameloblasts, rep3

type: RNA

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 513 Parnassus Avenue

department: Orofacial Sciences

country: USA

institute: UCSF

description: gene expression data from human secretory ameloblasts

hyb_protocol: The recovered biotinylated cDNA probes were hybridized onto a GeneChip® human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 16 hours at 45°C.

scan_protocol: The array chips were imaged using an Affymetrix Gene Chip Scanner 3000

data_processing: The Robust Multichip Average (RMA) method was used for background adjustment, quantile normalization, and median polish summarization using Affymetrix Expression Console software.

label: biotin

molecule: total RNA

source_name: secretory ameloblasts laser microdissected from incisors of second trimester human fetus

label_protocol: Fragmented ST-cDNA product was biotinylated using an Encore Biotin Module according to the manufacturer’s instructions (NuGEN Technologies).

growth_protocol: NIH registered WA09 cell line was purchased from WiCell Institute. HESCs were induced into epithelial cells. The human fetal tissues including oral mucosa and mandibles were freshed dissected based on a tissue sharing program, embedd immediately, crosectioned first. Then OE, PAB and SAB was laser microdissected from cyosections.

extract_protocol: Total RNA was purified from microdissected cells using QIAGEN RNeasy Micro Kit following the manufacturer’s instruction.

treatment_protocol: HESCs were induced to adopt epithelial phenotype by incubating the HESCs in medium supplemented with 12.5 ng/ml BMP4 and 1um retinoid acid for seven days.

value: mandibular incisor

tag: genotype

value: wild type

tag: age

value: 18-19 weeks


title: rat liver_chow diet_biological rep1

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

country: China

institute: Nestle research center- Beijing hub

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

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

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

organism: Rattus norvegicus

source_name: chow diet group_8 wks feeding

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

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

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

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

tag: strain

value: Sprague Dawley

tag: gender

value: male

value: adult

tag: diet group

value: chow diet group

tag: feeding duration

value: 8 weeks

value: liver

tag: tissue condition

value: normal rat liver


title: X16_MYB


title: human fetal incisor secretory ameloblasts, rep2


title: rat liver_chow diet_biological rep4


title: blood-MTC_3550R


title: blood-MTC_4354


title: human fetal incisor secretory ameloblasts, rep1


title: human fetal incisor presecretory ameloblasts, rep3

description: gene expression data from human presecretory ameloblasts

source_name: presecretory ameloblasts laser microdissected from incisors of second trimester human fetus


title: blood-MTC_3569


title: human fetal incisor presecretory ameloblasts, rep1


title: blood-MTC_4267R


title: blood-MTC_4711


title: blood-MTC_4147R


title: human fetal oral epithelial cells,  rep2

description: gene expression data from human OE

source_name: oral epithelial cells laser microdissected from second trimester human fetus

value: oral mucosal epithelium


title: blood-MTC_4209R


title: human fetal incisor presecretory ameloblasts, rep2


title: blood-MTC_4487


title: blood-MTC_4948


title: blood-MTC_4594


title: human fetal oral epithelial cells,  rep1

description: gene expression data from human OE


title: epithelial cells differentiated from HESC, rep3

description: gene expression data from ES-EC

source_name: epithelial cells induced from human embrryonic stem cells (line H9)

value: cell line


title: human fetal oral epithelial cells,  rep3

description: gene expression data from human OE


title: blood-MTC_5227


title: U87 GBM xenographt treated with scrambled siRNA 1

city: Beer-Sheva

first: Varda

last: Shoshan-Barmatz

address: Ben Gurion

department: Life Sciences

institute: Ben Gurion University

description: Gene expression data from U87 GBM xenographt treated with scrambled siRNA

hyb_protocol: Following fragmentation, 2.3 ug of biotin-labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix G7  GeneChips Scanner.

data_processing: CEL files were imported to Partek® Genomics Suite® and all probes except control probes were preprocessed by RMA background correction, log2 transformation and probeset summarization using median polish. Probesets having signal < 5 in all samples were filtered out. Subsequently, global scaling was carried out by shifting the mean of each sample to the grand mean

label_protocol: Fragmented and biotin-labeled  single strand cDNA were prepared from 100 ng total RNA starting material by using the  Affymetrix WT plus kit.

growth_protocol: U-87MG glioblastoma cells (2 x106) were inoculated s.c. into the hind leg flanks of athymic eight-week old male nude mice.  The developing tumors were measured in two dimensions with a digital caliper and tumor volume was calculated as follows: volume = X2 x Y/2, where X and Y are the short and long tumor dimensions, respectively. The mice with tumor reaching a volume of 50-80 mm3 were randomized for different treatments (8 or 9 animals in each group).

extract_protocol: Total RNA was extracted by using the Rneasy mini kit of QIAGEN according to the manufacturer's instructions. Samples with RIN>8 (Agilent 2100 BioAnalyzer) were used at downstream work.

treatment_protocol: Animals were treated with scrambled siRNA or siRNA against VDAC1. Each treatment substance was injected into the established s.c. tumors using the jetPEI (according to manufacture protocol) delivery reagent (50 nM). The xenograft were injected (20 µl per tumor) every three days, for 8 times.

value: GBM xenograft


title: epithelial cells differentiated from HESC, rep2

description: gene expression data from ES-EC


title: epithelial cells differentiated from HESC, rep1

description: gene expression data from ES-EC


title: U87 GBM xenographt treated with scrambled siRNA 2


title: blood-MTC_5288


title: U87 GBM xenographt treated with VDAC1 siRNA 2

description: Gene expression data from U87 GBM xenographt treated with VDAC1 siRNA


title: blood-MTC_4970


title: blood-MTC_4534


title: blood-MTC_4223R


title: U87 GBM xenographt treated with VDAC1 siRNA 1


title: blood-MTC_5419


title: CD11B NOD CPG 3

city: Bethesda

first: Kristin

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 Rm 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

description: flow cytometry sorted

hyb_protocol: cDNA samples were mixed with hybridization cocktail and hybridized to Affymetrix Mouse Gene 1.0 ST array for 16 hrs using Affymetrix hybridization oven at 45˚C rotating at 60 rpm. Gene chips were washed and stained with Affymetrix HWS regents using Affymetrix Fluidic Station 450 and FS450_0007 scripts followed by manufactures guidelines.

scan_protocol: Arrays were scanned using Affymetrix GCS 3000 7G operating with GCOS 1.4 software to generate .CEL files.

data_processing: Data were background corrected with RMA normalized with Partek Genome Suite 6.6.

organism: Mus musculus

source_name: NOD sorted CD11b+ cDC from NOD mice, CpG tx, 12h

label_protocol: cDNA targets were prepared from 5 ng of total RNA using NuGen Ovation pico WTA system V2. The amplified 2.5 µg of cDNA was fragmented and labeled using the Encore Biotin Module.

extract_protocol: PicoPure® RNA Isolation Kit (Life Technologies) was used according to manufacturer's guide.

treatment_protocol: CD8+ cDC and CD11b+ cDC from NOD and B6 mice were sorted and RNA was purified and converted to cDNA for use with GeneChip® Mouse Genome 430 array analysis.

value: NOD/ShiLt

value: female

value: 8-10 weeks

value: spleen

tag: cell type

value: CD11b+ cDC


title: blood-MTC_5332

value: MTC

value: peripheral blood


title: blood-MTC_5522


title: CD11B NOD CPG 1

description: flow cytometry sorted


title: blood-MTC_5345R


title: blood-MTC_5877


title: CD11B NOD PBS 3

description: flow cytometry sorted

source_name: NOD sorted CD11b+ cDC from NOD mice, PBS control, 12h


title: blood-MTC_5566R


title: DAPT 3 (Biological Replicate 3)

city: Baltimore

first: Angelika

last: Doetzlhofer

address: 855 North Wolfe St.

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

description: After 24 hours of culture, DAPT treated cochlear explants were pooled and cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment.

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: cultured cochlear epithelium treated with DAPT

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue was isolated from wild type embryos. Cochlear explants including cochlear duct and innervating neurons were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin.

extract_protocol: Total RNA was purified from enzymatically purified cochlear epithelia using the RNeasy Micro kit (QIAGEN).

treatment_protocol: E15.5 cochlear explants were cultured in the presence of 3.3µM DAPT for 24 hours.

tag: developmental stage

value: cochlear epithelium

tag: culture time

value: 24 hours

tag: treatment

value: 3.33 µM DAPT

value: wild-type


title: CD11B NOD PBS 1

description: flow cytometry sorted


title: DAPT 2 (Biological Replicate 2)

description: After 19 hours of culture, cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment.

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue was isolated from wild type embryos. Cochlear explants including cochlear duct and innervating neurons were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin

extract_protocol: Total RNA was purified from lysed tissue using the Qiagen RNEasy Micro kit

treatment_protocol: E15.5 cochlear explants were cultured in the presence of 3.3µM DAPT for 19 hours

value: 19 hours


title: CD11B B6 CPG 2

description: flow cytometry sorted

source_name: B6 sorted CD11b+ cDC from B6 mice, CpG tx, 12h


title: blood-MTC_5879


title: CD11B B6 CPG 3

description: flow cytometry sorted


title: blood-MTC_6276


title: CD11B B6 CPG 1

description: flow cytometry sorted


title: blood-MTC_6278b


title: blood-MTC_6170


title: DAPT 1 (Biological Replicate 1)

description: Cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment.

source_name: Cultured Cochlear Epithelium treated with DAPT

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue, were isolated from wild type embryos. Cochlear explants including cochlear duct and innervating neurons were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin

extract_protocol: Total RNA was purified from enzymatically purified cochlear epithelia using the RNeasy Micro kit (QIAGEN)

treatment_protocol: E15.5 cochlear explants were cultured in the presence of 3.3µM DAPT for 23 hours.

value: 23 hours


title: CD11B B6 PBS 2

description: flow cytometry sorted

source_name: B6 sorted CD11b+ cDC from B6 mice, PBS control, 12h


title: CD11B NOD PBS 2

description: flow cytometry sorted


title: CD11B B6 PBS 3

description: flow cytometry sorted


title: Control 1 (Biological Replicate 1)

description: After 23 hours of culture, cochlear epithelial tissue was isolated from cochlear explants using collagenase/ dispase treatment.

source_name: Cultured Control Cochlear Epithelium

growth_protocol: Embryonic Day 15.5 (E15.5) mouse cochlear tissue, including cochlear duct and innervating neurons were dissected from wild type embryos. Cochlear explants were cultured in DMEM-F12 with 1X N2 supplement, 2.5 ng/ml EGF, 2.2ng/ml FGF, 100 U/ml Penicillin

extract_protocol: Total RNA was isolated from enzymatically purified cochlear epithelia using the  RNeasy Micro kit (QIAGEN)

treatment_protocol: Tissue for control sample was cultured in the presence of 0.013% DMSO for 23 hours.

value: 0.013% DMSO (vehicle control)


title: REST -/- d9_1

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

description:
SAMPLE 15
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: REST -/- d9, Differentiated

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

growth_protocol: REST+/+ and  REST-/-  ESCs were cultured feeder-free on 0.1% gelatin coated dishes with mouse ES growth media composed of Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% ES Cell Qualified Fetal Bovine Serum (ES-FBS), 1 mM non-essential amino acids (NEAA), 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, and 1 mM penicillin/streptomycin (P/S) (all from Invitrogen, USA) in the presence of Leukemia Inhibitory Factor (LIF).

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: To generate embryoid bodies (EBs), REST+/+ and REST-/- ESCs were dissociated with 0.05% trypsin, counted and 1,000 cells were aggregated in 20 μL hanging drops. Cells were grown in mouse ESC growth media without LIF to induce differentiation. After 2 days, resulting EBs were transferred to ultra-low attachment 6-well plates for expansion in suspension. After 7 days in suspension, EBs were plated onto 0.1% gelatin-coated 6-well plates with 160 EBs per well for analyzing mRNA expression.

value: ESC

tag: genotype/variation

value: REST -/-

value: Embryoid bodies induced differentiation

tag: time (days of treatment)

tag: differentiated cell type

value: EB


title: REST -/- d9_2

description:
SAMPLE 16
replicate 2


title: CD8 NOD CPG 3

description: flow cytometry sorted

source_name: NOD sorted CD8+ cDC from NOD mice, CpG tx, 12h

value: NOD/ShiLt

value: female

value: CD8+ cDC


title: blood-MTC_6399


title: CD8 NOD CPG 2

description: flow cytometry sorted

value: 8-10 weeks

value: spleen


title: CD11B NOD CPG 2

description: flow cytometry sorted

value: CD11b+ cDC


title: REST -/- d6_2

description:
SAMPLE 14
replicate 2

source_name: REST -/- d6, Differentiated


title: CD8 NOD CPG 1

description: flow cytometry sorted


title: blood-MTC_6978

value: MTC

value: peripheral blood


title: CD8 NOD PBS 2

description: flow cytometry sorted

source_name: NOD sorted CD8+ cDC from NOD mice, PBS control, 12h


title: REST -/- d3_2

description:
SAMPLE 12
replicate 2

source_name: REST -/- d3, Differentiated


title: blood-MTC_7654

source_name: peripheral blood


title: REST -/- d6_1

description:
SAMPLE 13
replicate 1


title: CD8 NOD PBS 3

description: flow cytometry sorted


title: REST -/- d0_1

description:
SAMPLE 9
replicate 1

source_name: REST -/- d0, Undifferentiated

value: undifferentiated control


title: REST -/- d3_1

description:
SAMPLE 11
replicate 1


title: CD8 B6 CPG 3

description: flow cytometry sorted

source_name: B6 sorted CD8+ cDC from B6 mice, CpG tx, 12h


title: CD8 NOD PBS 1

description: flow cytometry sorted


title: CD11B B6 PBS 1

description: flow cytometry sorted


title: REST -/- d0_2

description:
SAMPLE 10
replicate 2


title: blood-MTC_7311


title: REST +/+ d9_2

description:
SAMPLE 8
replicate 2

source_name: REST +/+ d9, Differentiated

value: REST +/+


title: CD8 B6 CPG 1

description: flow cytometry sorted


title: CD8 B6 PBS 3

description: flow cytometry sorted

source_name: B6 sorted CD8+ cDC from B6 mice, PBS control, 12h


title: Neonatal CPC clone 2 (7 Day Microgravity)

city: Loma Linda

first: Mary

last: Kearns-Jonker

address: 25094 Daisy Ave

department: Anatomy

institute: Loma Linda University

description: Test

data_processing:
The delta delta Ct method was used for calculation of fold changes.  The average of 2 housekeeping genes (SNORD72 & SNORD96a) was used for normalization, each individual clone was compared with its own control, and then a student's paired ttest was used to calculate significant differences.
Fold change matrix reports test/control  (i.e. Neonatal CPC clone 7 Day Microgravity/Neonatal CPC clone) ratios.

label: SYBER Green

source_name: Atrial Tissue, collagenase digested

label_protocol: PCR arrays were performed using the cell development & differentiation miRNA PCR array (SA Biosciences, Frederick, MD) following the Manufacturer's instructions.  Reverse transcription was performed using 200ng of total RNA with the miScript II RT Kit (SA Biosciences).  Quantitative real-time PCR were performed (IQ5, Bio-rad) with 40 cycles at 94oC for 15 seconds, 55oC for 60 seconds, 70oC for 30 seconds.

growth_protocol: Cells were grown in M199 media (Invitrogen, Grand Island, NY) supplemented with EGM-2 media (Invitrogen) at 5% CO2.

extract_protocol: Total RNA was extracted using Trizol Reagent Protocol.

treatment_protocol: Test samples were grown for 7 Days in a 2D Clinostat (Bioserve, Beltsville, MD) to simulate microgravity prior to isolation of RNA.

value: Neonatal cardiovascular progenitor cell clones


title: blood-MTC_9238


title: REST +/+ d6_2

description:
SAMPLE 6
replicate 2

source_name: REST +/+ d6, Differentiated


title: CD8 B6 PBS 2

description: flow cytometry sorted


title: CD8 B6 CPG 2

description: flow cytometry sorted


title: blood-MTC_7383


title: Neonatal CPC clone 1 (7 Day Microgravity)

description: Test


title: Neonatal CPC clone 3 (7 Day Microgravity)

description: Test


title: blood-MTC_8257


title: Neonatal CPC clone 2

description: Control


title: blood-MTC_8077


title: REST +/+ d3_2

description:
SAMPLE 4
replicate 2

source_name: REST +/+ d3, Differentiated


title: CD8 B6 PBS 1

description: flow cytometry sorted


title: Neonatal CPC clone 3

description: Control


title: REST +/+ d9_1

description:
SAMPLE 7
replicate 1


title: REST +/+ d3_1

description:
SAMPLE 3
replicate 1


title: REST +/+ d6_1

description:
SAMPLE 5
replicate 1


title: blood-MTC_9480


title: blood-MTC_9620


title: 130479A_N6

city: Shanghai

first: Xin

last: Huang

state: Shanghai

address: No.2699 Gaoke east road

department: Reproductive Medicine Centre

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description:
Gene expression of cumulus cells isolated from non-PCOS patients
Normal-5

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V11.5 (Agilent). The data were normalized by percentile 75 normalization. To select the differentially expressed genes, we used threshold values of ≥2.0 and ≤-2.0 -fold change and a Benjamini-Hochberg corrected p value of 0.05.

source_name: cumulus cells of non-PCOS

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

extract_protocol: The cumulus cells isolated from one patients were pooled together to extract Total RNA. Total RNA isolation was performed using the Qiagen RNeasy Mini Kit (Qiagen, Hilder, Germany) according to the manufacturer’s instructions.

treatment_protocol: Both patients’ groups underwent COS (combination of GnRH agonist protocols with recombinant or purified FSH). That is, all the patients were administered GnRH agonist triptorelin acetate (Diphereline, Ipsen Pharma Biotech, Paris, France) from the mid-luteal phase at a daily dose of 0.05 mg subcutaneously. Once adequate pituitary downregulation was confirmed (serum LH levels < 3.0 ng/ml and serum estradiol (E2) levels < 30 pg/ml), the patients were subcutaneously administered 150–187.5 IU recombinant FSH (Gonal-f, Follitropin Alfa, Serono) for COS. When two or more follicles were at least 18 mm in diameter and the serum E2 levels were at least 300 pg/ml per dominant follicle, all the patients were administered 250 μg hCG (Profasi, Serono). Cumulus-oocyte complex (COC) retrieval was performed by vaginal puncture under ultrasound echo-guidance 36 h after hCG administration. After COC retrieval, a proportion of the CCs surrounding a single oocyte were removed using a sharp needle, lysed in 80 ml of RLT buffer (RNeasy Mini Kit, Qiagen) supplemented with 1% (v/v) 2-β- mercaptoethanol (M-3148; Sigma, Lyon, France), and stored at −80°C (CCs from one oocyte per vial) until RNA extraction. Oocytes were further inseminated and embryos were cultured in sequential media of SAGE (CooperSurgical, Leisegang Medical, Berlin) individually in 20 μl droplets covered by mineral oil. Embryos were transferred or vitrified on Day 3 and the other embryos were cultured to blastula stage on Day 5–6. The cumulus cells isolated from ten patients (5 PCOS and 5 non-PCOS patients) were used for microarray analysis of lncRNAs and that isolated from the other sixty patients (30 PCOS and 30 non-PCOS patients) were used for an extra evaluation.

tag: subject group

value: women without PCOS

value: cumulus cells


title: Neonatal CPC clone 1

description: Control


title: SNCA CN 2.1 (5% increase)

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

description: 5% Case_931_P8

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
normalized log10 ratio (Cy5/Cy3) representing test/reference

source_name: PBL from SNCA duplication carrier diluted with PBL from control (1:9 parts, to simulate 10% mosaicism)

label_protocol: 500ng of DNA was used, with hybridisation performed according to manufacturer protocol. DNA was digested with AluI and RsaI for 2 h at 37 °C. Genomic DNA was fluorescently labelled with the SureTag DNA Labelling Kit (Agilent).

extract_protocol: blood lymphocyte DNA provided by Institute of Neurology Neurogenetics department, extracted with Qiagen spin columns

value: peripheral blood lymphocyte

source_name: Agilent reference female DNA cat. no. 5190-3797

tag: reference


title: SNCA CN 2 (wild type)

description: wt Case_925_P2

source_name: PBL from control sample

tag: tissue

value: Agilent reference female DNA cat. no. 5190-3797


title: SNCA CN 2.15 (7.5% increase)

description: 7.5% Case_930_P7

source_name: PBL from SNCA duplication carrier diluted with PBL from control (1.5:8.5 parts, to simulate 15% mosaicism)


title: blood-MTC_7660

tag: phenotype


title: blood-MTC_9805


title: blood-MTC_9030


title: SNCA CN 2.25 (12.5% increase)

description: 12.5% Case_928_P5

source_name: PBL from SNCA duplication carrier diluted with PBL from control (2.5:7.5 parts, to simulate 25% mosaicism)


title: blood-MTC_10538


title: SNCA CN 2.2 (10% increase)

description: 10% Case_929_P6

source_name: PBL from SNCA duplication carrier diluted with PBL from control (2:8 parts, to simulate 20% mosaicism)


title: REST +/+ d0_1

description:
SAMPLE 1
replicate 1

source_name: REST +/+ d0, Undifferentiated

value: ESC


title: E2 treated rep1

city: Los Angeles

first: Nyam-Osor

last: Chimge

address: 2250 Alcazar street

department: IGM

institute: USC

description: SAMPLE 17; 5406940023_A

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio V2011.1.

source_name: NeMCO_E2 treated

growth_protocol: cells were grown in phenol red free MEM containing 20% charcoal stripped serum

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

value: primary Newborn mouse calvarial osteoblast (NeMCO) cells

tag: transduced with

value: lentivirus conditionally (doxycycline) expressing RUNX2

value: dox inducible RUNX2 expression

tag: treated with

value: 10nM E2


title: REST +/+ d0_2

description:
SAMPLE 2
replicate 2


title: Dox+E2 treated rep3

description: SAMPLE 23; 5406940023_G

source_name: NeMCO_Dox+E2 treated

value: 500 ng/ml doxycycline and 10nM E2


title: Dox treated rep2

description: SAMPLE 6; 5388876042_F

source_name: NeMCO_Dox treated

value: 500 ng/ml doxycycline


title: SNCA CN 2.4 (20% increase)

description: 20% Case_926_P3

source_name: PBL from SNCA duplication carrier diluted with PBL from control (4:6 parts, to simulate 40% mosaicism)


title: 130479A_P5

description:
Gene expression of cumulus cells isolated from PCOS patients
PCOS-4

source_name: cumulus cells of PCOS

value: women with PCOS


title: 130479A_N3

description:
Gene expression of cumulus cells isolated from non-PCOS patients
Normal-3


title: 130479A_P6

description:
Gene expression of cumulus cells isolated from PCOS patients
PCOS-5


title: Dox+E2 treated rep2

description: SAMPLE 22; 5406940023_F


title: E2 treated rep2

description: SAMPLE 18; 5406940023_B


title: 130479A_N4

description:
Gene expression of cumulus cells isolated from non-PCOS patients
Normal-4


title: E2 treated rep3

description: SAMPLE 19; 5406940023_C


title: SNCA CN 3 (heterozygous)

description: 50% Case_924_P1

source_name: PBL from SNCA duplication carrier


title: 130479A_N2

description:
Gene expression of cumulus cells isolated from non-PCOS patients
Normal-2


title: blood-MTC_9512

source_name: peripheral blood

value: MTC


title: Dox treated rep1

description: SAMPLE 5; 5388876042_E


title: Veh treated rep2

description: SAMPLE 2; 5388876042_B

source_name: NeMCO_Veh treated

value: vehicle (control)


title: SNCA CN 2.3 (15% increase)

description: 15% Case_927_P4

source_name: PBL from SNCA duplication carrier diluted with PBL from control (3:7 parts, to simulate 30% mosaicism)


title: 130479A_N1

description:
Gene expression of cumulus cells isolated from non-PCOS patients
Normal-1

source_name: cumulus cells of non-PCOS


title: blood-MTC_10884

value: peripheral blood


title: 130479A_P3

description:
Gene expression of cumulus cells isolated from PCOS patients
PCOS-3


title: p53-/-MEF (old)_rep1

status: Public on Aug 13 2015

city: Seoul

first: Dong-Hoon

last: Jin

address: 88 Olympicro-43gil, Songpa-gu

country: South Korea

institute: Asan Medical Center

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader following the standard Illumina scanning protocol.

data_processing: The data were background subtracted and normalized using Illumina GenomeStudio

source_name: p53-/-MEF (passage 7)

label_protocol: Cy3- cRNA were prepared with the Illumina TotalPrep™ RNA amplification kit for Illumina arrays.

growth_protocol: mouse embryonic fibroblast & p53-/-mouse embryonic fibroblast (normal culture condition), HCT116 &HCT116 p53null with or without Ectoposide

extract_protocol: Total RNA was isolated using TRIZOL reagent according to manufacturer's instruction.

value: p53-/- MEF (passage 7)

tag: strain


title: 130479A_P1

description:
Gene expression of cumulus cells isolated from PCOS patients
PCOS-1


title: HCT116 p53 null control

source_name: HCT116 p53 null control

treatment_protocol: HCT116 &HCT116 p53null with or without Ectoposide

value: colon cancer

tag: cell line

value: HCT116 p53 null


title: 130479A_P2

description:
Gene expression of cumulus cells isolated from PCOS patients
PCOS-2

value: cumulus cells


title: MEF (young)_ rep1

source_name: MEF (passage 3)

value: MEF (passage 3)


title: MEF (old)_rep1

source_name: MEF (passage 7)

value: MEF (passage 7)


title: HCT116 control

source_name: HCT116 control


title: p53-/-MEF (young)_rep1

source_name: p53-/-MEF (passage 3)

value: p53-/- MEF (passage 3)


title: HCT116 p53 null Eto

source_name: Etoposide treated HCT116 p53 null


title: Veh treated rep1

description: SAMPLE 1; 5388876042_A

value: primary Newborn mouse calvarial osteoblast (NeMCO) cells


title: HCT116 Eto

source_name: Etoposide treated HCT116


title: DNA from PB S45, SGA, no rhGH treatment

status: Public on Jan 23 2015

city: Kiel

first: Susanne

last: Bens

address: Arnold-Heller-Str.3 (Haus 10)

department: Institute of Human Genetics

country: Germany

institute: Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein

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

scan_protocol: Arrays were scanned using the Illumina iScan

data_processing: GenomeStudio software (version 2011.1, Methylation module version 1.9.0)

label: Cy5 and Cy3

source_name: peripheral blood (PB) cells from child born small for gestational age (SGA), no treatment

label_protocol: Standard Illumina Protocol

extract_protocol: various DNA extraction methods

value: Peripheral Blood (PB)

tag: diagnosis

value: born small for gestational age (SGA)

tag: rhgh treatment

value: no treatment


title: DNA from PB S35, SGA, long-term rhGH treatment

source_name: peripheral blood (PB) cells from child born small for gestational age (SGA), treated long-term (median: 33 months) with rhGH

value: rhGH treatment


title: DNA from PB S54, SGA, no rhGH treatment


title: DNA from PB S33, SGA, long-term rhGH treatment


title: DNA from PB S42, SGA, no rhGH treatment


title: DNA from PB S48, SGA, no rhGH treatment


title: DNA from PB S36, SGA, long-term rhGH treatment


title: DNA from PB S44, SGA, no rhGH treatment


title: DNA from PB S28, SGA, long-term rhGH treatment


title: DNA from PB S46, SGA, no rhGH treatment


title: DNA from PB S32, SGA, long-term rhGH treatment


title: DNA from PB S34, SGA, long-term rhGH treatment


title: DNA from PB S26, SGA, long-term rhGH treatment


title: DNA from PB S43, SGA, no rhGH treatment


title: DNA from PB S18, SGA, long-term rhGH treatment


title: DNA from PB S29, SGA, long-term rhGH treatment


title: DNA from PB S19, SGA, long-term rhGH treatment


title: DNA from PB S23, SGA, long-term rhGH treatment


title: DNA from PB S21, SGA, long-term rhGH treatment


title: DNA from PB S16, SGA, long-term rhGH treatment


title: DNA from PB S27, SGA, long-term rhGH treatment


title: DNA from PB S31, SGA, long-term rhGH treatment


title: DNA from PB S24, SGA, long-term rhGH treatment


title: DNA from PB S25, SGA, long-term rhGH treatment


title: DNA from PB S15, SGA, long-term rhGH treatment


title: DNA from PB S30, SGA, long-term rhGH treatment


title: DNA from PB S17, SGA, long-term rhGH treatment


title: DNA from PB S20, SGA, long-term rhGH treatment


title: DNA from PB S14, SGA, long-term rhGH treatment


title: Min6 DC Scrambled 4

status: Public on Dec 23 2014

city: Dresden

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

hyb_protocol: 5.5 ug of biotinylated and fragmented cDNA were hybridized for 17 hr at 45C on Affymetrix Mouse Gene ST 1.0  Arrays according to the GeneChip WT Terminal Labeling and Hybridization User Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with the Agilent GeneSpring software version 12.5 using Affymetrix default analysis settings and quantile normalization. No baseline transformation was done.

source_name: Min6 cells

label_protocol: Biotinylated cDNA samples were prepared according to the Ambion WT Expression Kit (4411973) protocol in conjunction with the GeneChip WT Terminal Labeling and Hybridization User Manual from 250 ng total RNA.

growth_protocol: Min6 cells were first maintained in serum containing medium (DMEM 15% Fetal Calf Serum, 70 µM 2-Mercaptoethanol, 100 µg/mL Pen-Strep).

extract_protocol: RNA was extracted from MIN6 cells using the High Pure RNA isolation kit as described by the manufacturer. RNA Integrity Number (RIN) for each sample was checked using Agilent Bioanalyzer. Duplicate or quadruplicate samples from a single experiment were run in DNA microarray equipment.

treatment_protocol: MIN6 cells were plated at 50,000 cells per well in a 24-well plate. 24 hours later, cells were transfected with Hes3 siRNA (2 µM final concentration in the culture medium)  or scrambled control siRNA (Santa Cruz, sc-37942, sc-37007) using DharmaFECT4 (Thermo Scientific, T-2004-001) as described by the manufacturer. Cells were assayed 12-24 hours after transfection for changes in proliferation and in gene expression as determined by gene array analysis, immunocytochemistry, and western blot.

tag: cell type

tag: transfection

value: scrambled control siRNA in serum free medium at 5% oxygen (Defined Conditions (DC))


title: Min6 DC Scrambled 2


title: Min6 DC Scrambled 3


title: Min6 DC Hes3 5

value: Hes3 siRNA in serum free medium at 5% oxygen (Defined Conditions (DC))


title: Min6 CC Scrambled 2

value: scrambled control siRNA in serum containing medium at 20% oxygen (Classic Conditions (CC))


title: DNA from PB S22, SGA, long-term rhGH treatment


title: Min6 DC Hes3 1


title: Min6 CC Scrambled 1


title: Min6 RC 4

label_protocol: Biotinylated cDNA samples were prepared according to the Ambion WT Expression Kit (4411973) protocol  inconjunction with the GeneChip WT Terminal Labeling and Hybridization User Manualfrom 500 ng total RNA.

growth_protocol: Min6 cells were maintained in serum containing medium (DMEM 15% Fetal Calf Serum, 70 µM 2-Mercaptoethanol, 100 µg/mL Pen-Strep).

extract_protocol: RNA was extracted from MIN6 cells grown in T75 flasks using the High Pure RNA isolation kit as described by the manufacturer. RNA Integrity Number (RIN) for each sample was checked using Agilent Bioanalyzer. Quadruplicate samples from a single experiment were run in DNA microarray equipment.

treatment_protocol: Min6 cells were first maintained in serum containing medium (DMEM 15% Fetal Calf Serum, 70 µM 2-Mercaptoethanol, 100 µg/mL Pen-Strep) at 20% oxygen (Classic Conditions (CC)) for 5 days. The cells were then passaged and grown under serum free conditions  (DMEM-F12, 100 µg/mL Apo-Transferrin, 20 nM Progesterone, 100 µM Putrescine, 30 nM Selenite, 100 µg/mL Pen-Strep) at 5% oxygen (Defined Conditions (DC)) for another 5 days. The cells were then passaged again, back into serum containing medium at 20% oxygen for an additional 5 days prior to analysis (Return Condition (RC).  Serum (CC) and serum free (DC) controls were run in parallel in which the cells were maintained in either serum containing or serum free conditions for the final 10 days of the experiment.

value: medium for 5 days, serum free medium for additional 5 days, serum containing medium for a final 5 days

tag: conditions

value: return condition


title: Min6 DC Scrambled 1


title: DNA from PB S10, SGA, long-term rhGH treatment


title: Min6 DC Hes3 7


title: Min6 CC Hes3 2

value: Hes3 siRNA in serum containing medium serum at 20% oxygen (Classic Conditions (CC))


title: Min6 DC Hes3 2


title: DNA from PB S6, SGA, long-term rhGH treatment


title: Min6 RC 1

tag: treatment


title: DNA from PB S11, SGA, long-term rhGH treatment


title: DNA from PB S13, SGA, long-term rhGH treatment


title: Min6 RC 2


title: Min6 DC 2

value: medium for 5 days, serum free medium for additional 5 days, serum free medium for a final 5 days

value: defined condition


title: DNA from PB S1, SGA, long-term rhGH treatment


title: Min6 DC 4


title: DNA from PB S3, SGA, long-term rhGH treatment


title: DNA from PB S7, SGA, long-term rhGH treatment


title: Min6 DC 1


title: DNA from PB S9, SGA, long-term rhGH treatment


title: DNA from PB S4, SGA, long-term rhGH treatment


title: DNA from PB S5, SGA, long-term rhGH treatment


title: DNA from PB S8, SGA, long-term rhGH treatment


title: Min6 RC 3


title: Min6 CC 1

value: medium for 5 days, serum containing medium for an additional 5 days, serum containing medium for a final 5 days

value: classic condition


title: Min6 CC 3


title: ubp1c-1/35S:FLAG-UBP1C_Total-RNA_2hHypoxia_Rep2

status: Public on Jan 13 2014

city: Riverside

first: Reed

middle: S

last: Sorenson

address: 4126 Genomics Bldg

department: Botany and Plant Science

institute: University of California, Riverside

description:
7 day old whole seedlings grown on MS + 1% Suc in long day (16h L: 8h D ) at 22C, in 125 uE m-2 s-1
Total RNA

hyb_protocol: Standard affy Workstation protocols

scan_protocol: Standard affy Workstation protocols

data_processing:
Microarray features of the above data sets were background corrected, normalized, and probe set intensities were summarized using the affy (22) and limma (linear models for microarray data) (23) packages. Present, marginal, absent (PMA) calls were made using the Wilcoxon signed rank-based gene expression presence/absence detection algorithm as implemented by MAS5. The “expresso” function calculated expression values using rma background adjustment, constant normalization for microarray scaling, and median polish method for probe set summarization of perfect match only features, specified as PMonly.
Bioconductor affy and limma package expresso funcion, rma background adjustment, constant normalization, median polish method for probe set summarization of  perfect macth only features specified as PMonly

organism: Arabidopsis thaliana

source_name: ubp1c-1 35S:FLAG-UBP1C, Total RNA, 2 h hypoxia, Rep2

label_protocol: For microarray analysis, 150 ng total and 15 ng UBP1C IP RNA were used to synthesize biotinylated, amplified RNA (aRNA) via 15 rounds of in vitro transcription using the 3' IVT Express Kit (Affymetrix, Santa Clara, CA). aRNA was fragmented and probed using the Arabidopsis ATH1 Genome Array (Lot 4160460; Affymetrix). Hybridizations were performed with 15 µg fragmented aRNA at 45oC for 16 h on a rotating platform.

extract_protocol: two aliquots of approximately 100 mg frozen ground powder tissue were thawed in 1.5 mL ice cold RNP extraction buffer modified from Oeffinger et al. (17) for plant extracts (200 mM Tris [pH 9.0], 110 mM potassium acetate, 0.5% (v/v) Triton-X100, 0.1% (v/v) Tween-20, 1.5% (v/v) protease inhibitor cocktail for plant cell and tissues extracts (Sigma P9599, St. Louis, MO), 5 mM dithiothrietol, 0.1% (v/v) RNaseOUT (Invitrogen, Carlsbad, CA)). The sample tube was briefly vortexed and the extract filtered through two layers of sterilized Miracloth (EMD Millipore, Billerica, MA) into a clean 1.5 mL microfuge tube. The filtrate was centrifuged in a swinging bucket clinical centrifuge at approximately 1500g for 2 min at 4oC.The supernatant (S-1.5K) was removed and a sample aliquoted for RNA extraction (100 µL per replicate sample). The remaining S-1.5K was transferred to a 1.5 mL microfuge tube containing antibody-conjugated beads for the IP. Protein G-conjugated paramagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA) were prepared according to the manufacturer’s directions. Briefly, for each 100 mg of tissue processed, 100 µL of resuspended Dynabeads were magnetically separated from the storage solution and resuspended in 400 µL α-FLAG M2 monoclonal antibody (Sigma F1804) in phosphate buffered saline Tween (PBST; 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate dibasic, 2 mM sodium phosphate monobasic [pH 7.4], 0.02% (v/v) Tween-20). The final FLAG M2 monoclonal antibody concentration was 25 ng µL-1 α-FLAG M2, The bead antibody mixture was incubated for 1 h on a rocker at 20-23oC. Following antibody conjugation to the beads, excess antibody was removed by magnetic separation and washing. IP of FLAG-UBP1C-containing complexes was accomplished by rocking the S-1.5K-Dynabead slurry at 4 oC for 1.5 h. Following incubation, the Dynabeads were magnetically separated, 30 µL supernatant was saved as the unbound fraction, and the beads were washed with 0.75 mL RNP extraction buffer for 5 min with rocking at 4oC and magnetically collected. Bead washing steps were repeated five more times. FLAG-UBP1C was eluted in 100 µL RNP extraction buffer plus 400 ng µL-1 3X Flag® Peptide (Sigma F4799) at 4oC for 30 min with rocking. Eluates of replicate IPs were combined for a total of 200 µL. 180 µL was used for RNA extraction.

treatment_protocol: Control light plants were maintained in light. Control dark plants were transferred to near darkness (<0.05 µE m-1 s-1) for 2 h in a humidified 13.5 L Plexiglas chamber open to ambient air (dark control, D). For hypoxia treatment (H), plants were placed under the same low light and deprived of oxygen for 2 h by sealing the chamber and continuously flushing it with humidified 99.99% Ar(g) at a rate of 50 mL s-1 for 2 h at 20oC. For 2 h hypoxia followed by 20 min reoxygenation (R), reoxygenation was facilitated by removing the top of the chamber and fanning with a rigid plastic fan (~25 x 40 cm) immediately and again after 10 min for 1 minute. All seedlings were harvested rapidly into N2(l), ground to a powder and stored at -80oC.

tag: sample type

value: Total RNA

value: seedling

value: 2 h mock dark

tag: genotype

value: ubp1c-1 35S:FLAG-UBP1C

tag: antibody


title: Primary Hepatocytes

status: Public on Dec 03 2013

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description: Primary hepatocytes were isolated from liver tissue of 8- to 10-week-old male C57/B6 mice by collagenase perfusion method, and then cultured in Hep medium.

hyb_protocol: The fragmented cRNA was hybridized to Affymetrix GeneChip arrays for 16 h. The Chips were washed and stained using an Affymetrix Fluidics Station.

scan_protocol: Fluorescence was detected using the Affymetrix Imaging Station.

data_processing: Raw data were background-corrected and subsequently normalized using Partek Express Affymetrix Edition under the Robust Microarray Analysis (RMA) algorithm.

source_name: Primary isolated hepatocytes

label_protocol: 100 ng of total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: All iHep lines were cultured in standard Hep medium: DMEM/F-12 supplemented with 10% FBS (Biowest), 0.1 μM dexamethasone (Sigma), 10 mMnicotinamide (Sigma), 1% ITS (insulin-transferrin-selenium) premix (Gibco), and penicillin/streptomycin/glutamine (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech) and both hepatocyte growth factor (Peprotech) and epidermal growth factor (Peprotech) at a final concentration of 20 ng/ml on Type I collagen-coated dish (Sigma)

extract_protocol: Total RNA was prepared from MEFs, iHeps and primary hepatocytes using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Fibroblasts were transduced with replication-defective retroviral particles coding for the defined sets of hepatic transcription factors in the presence or absence of c-Myc, and Klf4. After 48 h, the transduced fibroblasts were cultured in standard Hep medium.

tag: age

value: 8-10 weeks

tag: Sex

value: male

value: control hepatocytes


title: iHeps_4a1CK transduced

description: Epithelial colonies appeared within 5 days post-transduction and established as expandable iHep lines with several passaging.

source_name: iHeps, 4a1CK-transduced

value: induced hepatocyte-like cells

tag: transcription factors

value: Hnf4a, Foxa1, c-Myc and Klf4


title: Min6 CC 4


title: iHeps_4a3CK transduced

source_name: iHeps, 4a3CK-transduced

value: Hnf4a, Foxa3, c-Myc and Klf4


title: ubp1c-1/35S:FLAG-UBP1C_IP-RNA_2hHypoxia_Rep2

description:
7 day old whole seedlings grown on MS + 1% Suc in long day (16h L: 8h D ) at 22C, in 125 uE m-2 s-1
UBP1C IP RNA

source_name: ubp1c-1 35S:FLAG-UBP1C, FLAG-IP RNA, 2 h hypoxia, Rep2

value: UBP1C IP RNA

tag: tissue

value: 2 h hypoxia

value: FLAG


title: iHeps_4a3 transduced

description: Epithelial colonies appeared within 2 weeks post-transduction and established as expandable iHep lines with several passaging.

source_name: iHeps, 4a3-transduced

value: Hnf4a and Foxa3


title: Min6 CC 2


title: MEFs, 2

description: MEFs are mesenchymal cells showing flat and elongated morphology.

source_name: Primary isolated mouse embryonic fibroblasts

value: embryos at embryonic day (E)13.5

value: mouse embryonic fibroblasts


title: Min6 DC 3

value: medium for 5 days, serum free medium for additional 5 days, serum free medium for a final 5 days

value: defined condition


title: IDH1mut replicate 2

status: Public on Nov 05 2013

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

description: Gene expression data from sorted mouse bone marrow cells transduced with IDH1mut vector

hyb_protocol: Samples were hybridized to an identical lot of Affymetrix GeneChip for 16 hours at 45°C on MOE430 2.0. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the mini_euk2v3_FS450 protocol (Affymetrix; Santa Clara, CA)

scan_protocol: Image Analysis was performed on  GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA)

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: sorted mouse bone marrow cells

label_protocol: For biotin-labeled target synthesis starting from 3 µg of total RNA, reactions were performed using standard protocols supplied by the manufacturer (Affymetrix; Santa Clara, CA). Briefly, 3 µg total RNA were converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec; Seraing, Belgium) containing a T7 promotor. The cDNA was then used directly in an in-vitro transcription reaction in the presence of biotinylated nucleotides

growth_protocol: in vivo from C57BJ6 mice

extract_protocol: Qiagen Rneasy plus Mini Kit according to manufacturers instructions

treatment_protocol: Transduction with Retrovirus, transplantation in syngenic mice, isolation of bone marrow  four weeks post transplantation, sorting of GFP positive cells than RNA Preparation

value: sorted mouse bone marrow cells

tag: genotype/variation


title: IDH1mut replicate 3


title: IDH1wt replicate 2

description: Gene expression data from sorted mouse bone marrow cells transduced with IDH1wt vector


title: DNA from PB S12, SGA, long-term rhGH treatment

value: Peripheral Blood (PB)

value: born small for gestational age (SGA)

value: rhGH treatment


title: IDH1wt replicate 1


title: IDH1mut replicate 1


title: IDH1wt replicate 3


title: CTL replicate 2

description: Gene expression data from sorted mouse bone marrow cells transduced with EGFP control vector

value: CTL


title: CTL replicate 1


title: CTL replicate 3


title: Min6 CC Hes3 1

value: Hes3 siRNA in serum containing medium serum at 20% oxygen (Classic Conditions (CC))


title: NAFLD liver biopsy tissue 15228

status: Public on Aug 30 2013

city: Durham

first: Cynthia

last: Moylan

state: NC

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

description: Methylation data from NAFLD patient

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: quantile normalization

label: Cy3, Cy5

source_name: Liver, percutaneous biopsy

growth_protocol: Human liver tissues from percutaneous biopsies were stored at -80 degrees celsius prior to DNA extraction.

extract_protocol: DNA was extracted from frozen liver biopsies using the AllPrep Micro Kit (Qiagen) and 800 ng bisulfite modified using the Zymo EZ DNA Methylation Kit

value: Non-Alcoholic Fatty Liver Disease (NAFLD)

value: Liver

tag: Stage

value: mild


title: NAFLD liver biopsy tissue 15433

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15298

description: Methylation data from NAFLD patient

value: advanced


title: NAFLD liver biopsy tissue 15812

description: Methylation data from NAFLD patient


title: DNA from PB S2, SGA, long-term rhGH treatment


title: NAFLD liver biopsy tissue 15525

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15012

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15771

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15751

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15342 (replicate 2)

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15794

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15304

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15864

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15883

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15445 (replicate 2)

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15777 (replicate 2)

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15928

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15022

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15681

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15341

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15311

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15919

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15742

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15033

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15277

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15903

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15342 (replicate 1)

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15684

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15400

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15262

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15177

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15367

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15020

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15776

description: Methylation data from NAFLD patient


title: 517OM-I

status: Public on Dec 17 2010

city: Boston

first: Mi-Jeong

last: Lee

state: MA

address: 650 Albany St 810

department: Medicine

institute: Boston University

description: OM AT_treated with insulin (7nM)_7d_rep4

hyb_protocol: Following fragmentation, 10ug of CRNA were hybridized for overnight at 45C on homo sapiense genome array. GeneChips were washed and stained with streptavidin phycoerythrin.

data_processing: Expression data was processed as probeset summaries using Affymetrix MAS 5.0 algorithm, and imported to BRB-ArrayTools. Dex affected genes were indentified using class comparision tools in the BRB-Array tools.

source_name: omental AT, cultured with insulin for 7days

label_protocol: Biotinylated cRNA were prepared accoding to standard Affymetrix protocol.

growth_protocol: omental and subcutaneous adipose tissue obtained during elective surgeries were placed in organ culture

extract_protocol: total RNA was extracted using RNAagents total RNA isolation systmem (Promega) followed by a purification using RNAseay kit (Qiagen)

treatment_protocol: adipose tissue fragments were cultured with insulin (7nM) for 7 days

tag: gender

value: female


title: NAFLD liver biopsy tissue 15495

description: Methylation data from NAFLD patient


title: 506OM-ID

description: OM AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep3

source_name: omental AT, cultured with insulin and dexamethasone for 7days

treatment_protocol: adipose tissue fragments were cultured with insulin (7nM) plus dexamethasone (25nM) for 7 days

value: male


title: NAFLD liver biopsy tissue 15956

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15102

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15902

description: Methylation data from NAFLD patient


title: 506SC-ID

description: SC AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep3

source_name: subcutaneous AT, cultured with insulin and dexamethasone for 7days


title: 506SC-I

description: SC AT_treated with insulin (7nM)_7d_rep3

source_name: subcutaneous AT, cultured with insulin for 7days


title: 503OM-ID

description: OM AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep2

data_processing: Expression data was processed as probeset summaries using Affymetrix MAS 5.0 algorithm, and imported to BRB-ArrayTools. Dex affected genes were indentified using class comparisiojavascript:ValidateSubmitForm()n tools in the BRB-Array tools.


title: 506OM-I

description: OM AT_treated with insulin (7nM)_7d_rep3


title: NAFLD liver biopsy tissue 15757

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15004

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15878

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15386

description: Methylation data from NAFLD patient


title: 503SC-I

description: SC AT_treated with insulin (7nM)_7d_rep2


title: NAFLD liver biopsy tissue 15350

description: Methylation data from NAFLD patient


title: 503OM-I

description: OM AT_treated with insulin (7nM)_7d_rep2

treatment_protocol: adipose tissue fragments were cultured insulin (7nM) for 7 days


title: NAFLD liver biopsy tissue 15639

description: Methylation data from NAFLD patient


title: 503SC-ID

description: SC AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep2

treatment_protocol: adipose tissue fragments were cultured insulin (7nM) plus dexamethasone (25nM) for 7 days


title: NAFLD liver biopsy tissue 15214

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15893

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15554

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15972

description: Methylation data from NAFLD patient


title: 518OM-I

description: OM AT_treated with insulin (7nM)_7d_rep1


title: 517OM-ID

description: OM AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep4


title: NAFLD liver biopsy tissue 15066

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15442

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15873

description: Methylation data from NAFLD patient


title: 518SC-ID

description: SC AT_treatment with insulin (7nM)+dexamethasone (25nM)_7d_rep1


title: NAFLD liver biopsy tissue 15568

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15029

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15151

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15800

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15914

description: Methylation data from NAFLD patient


title: NAFLD liver biopsy tissue 15445 (replicate 1)

description: Methylation data from NAFLD patient


title: 518SC-I

description: SC adipose tissue (AT)_treated with insulin (7nM)_7d_rep1


title: AtT-20_PBS_Dexstudy_control_rep1

status: Public on Nov 16 2009

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: AtT-20 corticotroph cells treated with PBS

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Raw data were extracted with GCOS software and preprocessed with GC-RMA algorithm.

label_protocol: Standard Affymetrix protocol

growth_protocol: AtT-20 cells were plated on adherent culture dishes to obtain about 70% confluence after 3 days. They are cultured in DMEM + 10% FBS.

extract_protocol: Total RNA was extracted with Qiagen RNeasy mini prep columns using the manufacturer's protocol, without adding B-mercaptoethanol in the lysis buffer (RLT).

treatment_protocol: On the second day after plating, the treatment agent was added directly into the culture medium (DMEM + 10% FBS) and left for 3h.

tag: agent

value: control

value: pituitary corticotroph cell line


title: AtT-20_LIF_3h_rep1

description: AtT-20 corticotroph cells treated with LIF for 18h

source_name: AtT-20 corticotroph cells treated with LIF for 3h

value: LIF

tag: time


title: AtT-20_Dex+LIF_18h_rep1

description: AtT-20 corticotroph cells treated with Dex+LIF for 18h

treatment_protocol: On the second day after plating, the treatment agent was added directly into the culture medium (DMEM + 10% FBS) and left for 18h (or 3h before harvesting for the Dex+LIF 3h samples).

value: Dex+LIF


title: AtT-20_PBS_Dexstudy_control_rep2

source_name: AtT-20 corticotroph cells treated with PBS


title: AtT-20_Dex_18h_A_rep2

description: AtT-20 corticotroph cells treated with Dex for 18h

treatment_protocol: On the second day after plating, the treatment agent was added directly into the culture medium (DMEM + 10% FBS) and left for 18h.

value: Dex


title: AtT-20_PBS_A_rep2


title: AtT-20_Dex+LIF_3h_rep2

description: AtT-20 corticotroph cells treated with Dex+LIF for 3h


title: AtT-20_Dex_3h_rep2

description: AtT-20 corticotroph cells treated with Dex for 3h


title: AtT-20_LIF_3h_rep2


title: AtT-20_PBS_A_rep1


title: NAFLD liver biopsy tissue 15966

description: Methylation data from NAFLD patient

tag: diagnosis


title: AtT-20_LIF_18h_rep2

source_name: AtT-20 corticotroph cells treated with LIF for 18h


title: NAFLD liver biopsy tissue 15777 (replicate 1)

description: Methylation data from NAFLD patient


title: AtT-20_PBS_rep1


title: AtT-20_LIF_18h_rep1


title: AtT-20_Dex+LIF_3h_rep1

source_name: AtT-20 corticotroph cells treated with Dex+LIF for 3h


title: NAFLD liver biopsy tissue 15238

description: Methylation data from NAFLD patient


title: AtT-20_PBS_rep2


title: AtT-20_PBS_LIFstudy_control_rep1


title: AtT-20_Dex_18h_B_rep2

source_name: AtT-20 corticotroph cells treated with Dex for 18h


title: AtT-20_Dex_18h_B_rep1


title: AtT-20_Dex+LIF_18h_rep2

source_name: AtT-20 corticotroph cells treated with Dex+LIF for 18h


title: AtT-20_PBS_B_rep2


title: AtT-20_PBS_LIFstudy_control_rep2


title: AtT-20_PBS_B_rep1


title: Bovine liver at 48h, bio rep 1

status: Public on Nov 03 2008

city: Tjele

first: Peter

last: Sørensen

address: Blichers Alle 1

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

hyb_protocol: 15 microgram of cRNA was loaded onto the probe array cartridge of Bovine Genome Array

scan_protocol: Probe arrays were scanned at 560 nm using a confocal laser-scanning microscope (Hewlett Packard GeneArray Scanner G2500A).

data_processing: The data were analyzed using GeneChip Robust Multi-array Analysis (GCRMA) algorithm. In this algorithm, raw intensity values are background corrected based on a model using sequence information followed by quantile normalization. The expression measure is given as log base 2 scale.

organism: Bos taurus

source_name: Bovine liver sample of 48 hours after LPS intra-mammary infusion

label_protocol: 5 microgram RNA was labeled using the SuperScript Choice System (Life Technologies) according to the manufacturer’s instructions, except for using an oligo-dT primer containing a T7 RNA polymerase promoter site. Biotin labeled cRNA was prepared using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale NY, USA).

growth_protocol: 8 healthy, high yielding Holstein-Friesian dairy cows in their first lactation (9 to 12 weeks after calving) were chosen for this study. The udder health of the cows was evaluated based on somatic cell count (SCC) and bacteriological examinations. All cows had SCC < 100000 on both front quarters and SCC < 138000 on both behind quarters, and were free from mastitis pathogens.

extract_protocol: RNA from liver biopsies was isolated using Trizol Reagent (Invitrogen, Taastrup, Denmark)

treatment_protocol: Sterile polyvinyl catheters (Micro-Renathane) were inserted into the jugular vein of the cows. The catheters were flushed with a sterile 0.9% NaCl solution containing 50 IU Na-heparin (Loevens Kemiske Fabrik, Ballerup, Denmark). At time 0 the right front quarter was infused with 200 microgram E. coli LPS (0111:B4) (Sigma-Aldrich, Brøndby, Denmark) dissolved in 10 mililiter 0.9% NaCl solution, the left front quarter serving as control was infused with 10 mililiter 0.9% NaCl solution.

tag: cow id


title: AtT-20_Dex_3h_rep1

source_name: AtT-20 corticotroph cells treated with Dex for 3h


title: Bovine liver at 9h, bio rep 8

source_name: Bovine liver sample of 9 hours after LPS intra-mammary infusion


title: Bovine liver at 48h, bio rep 3


title: Bovine liver at 9h, bio rep 6


title: Bovine liver at 6h, bio rep 2

source_name: Bovine liver sample of 6 hours after LPS intra-mammary infusion


title: Bovine liver at 6h, bio rep 4


title: Bovine liver at 9h, bio rep 2


title: Bovine liver at 12h, bio rep 3

source_name: Bovine liver sample of 12 hours after LPS intra-mammary infusion


title: Bovine liver at 12h, bio rep 1


title: Bovine liver at 6h, bio rep 3


title: Bovine liver at 3h, bio rep 4

source_name: Bovine liver sample of 3 hours after LPS intra-mammary infusion


title: Bovine liver at 9h, bio rep 7


title: Bovine liver at 48h, bio rep 7


title: Bovine liver at 12h, bio rep 2


title: Bovine liver at 48h, bio rep 4


title: Bovine liver at 6h, bio rep 1


title: Bovine liver at 48h, bio rep 5


title: Bovine liver at 9h, bio rep 1


title: Bovine liver at 9h, bio rep 4


title: Bovine liver at 12h, bio rep 4


title: Bovine liver at 9h, bio rep 3


title: Bovine liver at 48h, bio rep 2


title: Bovine liver at 9h, bio rep 5


title: Bovine liver at 48h, bio rep 6


title: Bovine liver at 48h, bio rep 8


title: Bovine liver at 3h, bio rep 3


title: Bovine liver at 3h, bio rep 2


title: 518OM-ID

description: OM AT_treated with insulin (7nM)+dexamethasone (25nM)_7d_rep1


title: Bovine liver at -22h, bio rep 3

source_name: Bovine liver sample of 22 hours prior to LPS intra-mammary infusion


title: Bovine liver at -22h, bio rep 8


title: Bovine liver at -22h, bio rep 2


title: LCM tumor epithelium sample from patient #26

status: Public on Sep 30 2007

city: Bethesda

first: Stefan

last: Ambs

address: 37 Convent Dr Bldg 37 Room 3050

institute: NCI

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: I, Cyclin E: POS

hyb_protocol: Standard Affy protocol

scan_protocol: Standard Affy protocol

data_processing: RMA

source_name: human breast cancer tumor epithelium

label_protocol: Small Sample Labeling Protocol vII from Affymetrix

extract_protocol: PicoPure kit (Arcturus)

value: non-IBC

tag: status

value: Deceased

tag: race

value: African American

value: I

value: NEG

value: Tumor


title: Bovine liver at -22h, bio rep 1


title: Bovine liver at 3h, bio rep 1


title: Bovine liver at -22h, bio rep 5


title: Bovine liver at -22h, bio rep 4


title: Bovine liver at -22h, bio rep 6


title: LCM tumor epithelium sample from patient #35

description: Chemo: Yes, ER: NEG, Her2Neu: POS, Stage: IIB, Cyclin E: POS

value: European American

value: IIB


title: LCM tumor epithelium sample from patient #30

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIB, Cyclin E: POS


title: LCM tumor epithelium sample from patient #31

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIA, Cyclin E: POS

value: IIA


title: Bovine liver at -22h, bio rep 7


title: LCM tumor epithelium sample from patient #32

description: Chemo: Yes, ER: NEG, Her2Neu: POS, Stage: IIB, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #20

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIB, Cyclin E: NEG

value: POS


title: LCM tumor epithelium sample from patient #29

description: Chemo: No, ER: NEG, Her2Neu: POS, Stage: IIA, Cyclin E: POS


title: LCM tumor epithelium sample from patient #21

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIB; Cyclin E: POS


title: LCM tumor epithelium sample from patient #28


title: LCM tumor epithelium sample from patient #24

description: Chemo: No, ER: POS, Her2Neu: U, Stage: IIA, Cyclin E: unknown


title: LCM tumor epithelium sample from patient #25

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIB, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #23


title: LCM tumor epithelium sample from patient #33

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIA, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #34

description: Chemo: Yes, ER: NEG, Her2Neu: U, Stage: IIIA, Cyclin E: unknown

value: IIIA


title: LCM tumor epithelium sample from patient #19

description: Chemo: No, ER: NEG, Her2Neu: POS, Stage: IIB, Cyclin E: POS


title: LCM tumor epithelium sample from patient #18


title: LCM tumor epithelium sample from patient #22


title: LCM tumor epithelium sample from patient #16

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIA, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #17

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: I, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #27


title: LCM tumor epithelium sample from patient #15

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIB, Cyclin E: POS

value: Alive


title: LCM tumor epithelium sample from patient #11


title: LCM tumor epithelium sample from patient #14

description: Chemo: Yes, ER: U, Her2Neu: U, Stage: IIIA, Cyclin E: unkown


title: AtT-20_Dex_18h_A_rep1

description: AtT-20 corticotroph cells treated with Dex for 18h


title: LCM tumor epithelium sample from patient #7


title: LCM tumor epithelium sample from patient #12

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIA, Cyclin E: POS


title: LCM tumor epithelium sample from patient #6


title: LCM tumor epithelium sample from patient #1


title: LCM tumor epithelium sample from patient #5

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIA, Cyclin E: NEG


title: LCM tumor epithelium sample from patient #48

description: Chemo: U, ER: NEG, Her2Neu: U, Stage: IIIA, Clinical IBC: Yes

value: IBC


title: LCM tumor epithelium sample from patient #47

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IV, Clinical IBC: Yes


title: LCM tumor epithelium sample from patient #10

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIA, Cyclin E: POS


title: LCM tumor epithelium sample from patient #43

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIA, Clinical IBC: Yes


title: LCM tumor epithelium sample from patient #3


title: LCM tumor epithelium sample from patient #40

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIA, Clinical IBC: No


title: LCM tumor epithelium sample from patient #9


title: LCM tumor epithelium sample from patient #2

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIA, Cyclin E: POS


title: LCM tumor epithelium sample from patient #38

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIB, Clinical IBC:Yes


title: LCM tumor epithelium sample from patient #8


title: LCM tumor epithelium sample from patient #13

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIB, Cyclin E: POS


title: LCM tumor epithelium sample from patient #50

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIB, Clinical IBC: Yes


title: LCM tumor epithelium sample from patient #4

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: I, Cyclin E: POS


title: LCM tumor epithelium sample from patient #44

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIB, Clinical IBC: No


title: LCM tumor epithelium sample from patient #42

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIB, Clinical IBC: Yes


title: LCM tumor epithelium sample from patient #41

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIB, Clinical IBC: No


title: LCM tumor epithelium sample from patient #37

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIA, Clinical IBC: No


title: LCM stroma sample from patient #31

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIA

source_name: human breast cancer stroma

value: Stroma


title: LCM tumor epithelium sample from patient #36

description: Chemo: Yes, ER: NEG, Her2Neu: U, Stage: IIIB, Clinical IBC: Yes


title: LCM tumor epithelium sample from patient #45

description: Chemo: No, ER: POS, Her2Neu: POS, Stage: IIIA, Clinical IBC: No


title: LCM stroma sample from patient #35

description: Chemo: Yes, ER: NEG, Her2Neu: POS, Stage: IIB


title: LCM tumor epithelium sample from patient #46


title: LCM stroma sample from patient #28

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: IIB


title: LCM stroma sample from patient #29

description: Chemo: No, ER: NEG, Her2Neu: POS, Stage: IIA


title: LCM stroma sample from patient #34

description: Chemo: Yes, ER: NEG, Her2Neu: U, Stage: IIIA


title: LCM stroma sample from patient #26

description: Chemo: No, ER: NEG, Her2Neu: NEG, Stage: I


title: LCM stroma sample from patient #27

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIB


title: LCM stroma sample from patient #33

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIA


title: LCM stroma sample from patient #11


title: LCM stroma sample from patient #18


title: LCM stroma sample from patient #25


title: LCM stroma sample from patient #10

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIA


title: LCM stroma sample from patient #22


title: LCM stroma sample from patient #17

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: I


title: LCM stroma sample from patient #8


title: LCM stroma sample from patient #7


title: LCM stroma sample from patient #24

description: Chemo: No, ER: POS, Her2Neu: U, Stage: IIA


title: LCM stroma sample from patient #23


title: LCM stroma sample from patient #13

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIB


title: LCM stroma sample from patient #30


title: LCM stroma sample from patient #16


title: LCM stroma sample from patient #21


title: LCM stroma sample from patient #6


title: LCM stroma sample from patient #19

description: Chemo: No, ER: NEG, Her2Neu: POS, Stage: IIB


title: LCM stroma sample from patient #15

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIB


title: LCM stroma sample from patient #1


title: LCM stroma sample from patient #2


title: LCM stroma sample from patient #50

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIB, Clinical IBC: Yes


title: LCM stroma sample from patient #14

description: Chemo: Yes, ER: U, Her2Neu: U, Stage: IIIA


title: LCM stroma sample from patient #49

description: Chemo: Yes, ER: NEG, Her2Neu: U, Stage: IIIB, Clinical IBC: Yes


title: LCM stroma sample from patient #20


title: LCM stroma sample from patient #12

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIA


title: LCM stroma sample from patient #48

description: Chemo: U, ER: NEG, Her2Neu: U, Stage: IIIA, Clinical IBC: Yes


title: LCM stroma sample from patient #38

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIB, Clinical IBC:Yes


title: LCM stroma sample from patient #44

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIB,  Clinical IBC: No


title: LCM stroma sample from patient #42

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIB, Clinical IBC: Yes


title: LCM stroma sample from patient #4


title: LCM stroma sample from patient #9


title: LCM stroma sample from patient #46

description: Chemo: Yes, ER: POS, Her2Neu: NEG, Stage: IIIA, Clinical IBC: No


title: LCM stroma sample from patient #40


title: LCM stroma sample from patient #41

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIB, Clinical IBC: No


title: LCM stroma sample from patient #32

description: Chemo: Yes, ER: NEG, Her2Neu: POS, Stage: IIB


title: LCM stroma sample from patient #45

description: Chemo: No, ER: POS, Her2Neu: POS, Stage: IIIA, Clinical IBC: No


title: LCM stroma sample from patient #43

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIA, Clinical IBC: Yes


title: LCM stroma sample from patient #47

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IV, Clinical IBC: Yes


title: LCM stroma sample from patient #37

description: Chemo: Yes, ER: NEG, Her2Neu: NEG, Stage: IIIA, Clinical IBC: No


title: LCM stroma sample from patient #5

description: Chemo: No, ER: POS, Her2Neu: NEG, Stage: IIA