title: Medici_Treated_R

city: Orange

first: Omar

last: Khalid

address: 1201 W La Veta Ave

department: Research

institute: Children's Hospital of Orange County

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns  using two color scan setting for 4x44k array slides.

data_processing: Data processed  and normalized using R2.16.0 statistical software

organism: Canis lupus familiaris

label_protocol: A total of 100 ng RNA was used as initial starting template, which was labeled with Cy-3 or Cy-5 cytidine 5’-triphosphate using the low input fluorescent linear amplification kit (Agilent, Santa Clara, CA).

extract_protocol: RNA isolation from canine aortic specimens was performed using the TRIzol RNA Purification System (Life Technologies, Grand Island, NY). RNA concentration and quality, as well as dye incorporation efficiency, was checked with an ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE, USA) and the Agilent Bioanalyzer 2100.

value: Pooled (ascending aorta, descending aorta, carotid artery)

tag: disease state

value: Enzyme Treated


title: IRS2_C1_4_A

status: Public on Mar 05 2016

type: RNA

city: Rochester

first: Marc

middle: A

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

country: USA

institute: Mayo Clinic

description: total RNA

hyb_protocol: Following fragmentation, hybridization, washing and staining was performed using Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

scan_protocol: GeneChips were scanned the Affymetrix GeneTitan® Multi-Channel (MC) Instrument per the manufacturer instructions.

data_processing: Base-2 logarithm transformed intensity data were normalized within each batch using GC-RMA.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: T47D-YA-IRS-2 #1 4h SFM

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: Cells were plated at a density of 3x10^6 in 150 mm dishes, allowed to equilibrate overnight, and the media replaced by SFM alone for 24 h prior to stimulation.

extract_protocol: Total RNA was collected using RNeasy mini kit (Qiagen) or PerfectPure RNA tissue kit (5Prime). RNA quantity was determined by 260:280 assay and quality using the Agilent Bioanalyzer 2100 (1.8-2.0; Agilent Technologies, Palo Alto, CA) to ensure banding conservation.

treatment_protocol: At time = 0 cells were treated with SFM+FN alone or with IGF-I for 4 h or 24 h.

tag: cell line


title: IRS1_C20_24_IGF_B

description: total RNA

source_name: T47D-YA-IRS-1 #20 24h IGF


title: Phloem_Treated_R

state: CA

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_2.txt

tag: tissue


title: IRS1_C20_24_C

description: total RNA

source_name: T47D-YA-IRS-1 #20 24h SFM


title: Lily_Treated_R_3

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_4.txt


title: IRS1_C20_24_IGF_A

description: total RNA


title: Franklin_Treated_R

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_1.txt


title: IRS1_C20_4_IGF_C

description: total RNA

source_name: T47D-YA-IRS-1 #20 4h IGF


title: Xylem_Treated_R

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_4.txt


title: Ramsey_8hr_Control

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

description: Three grapevine genotypes (Vitis vinifera cv. Cabernet Sauvignon clone 8, Vitis riparia cv. Riparia Gloire, and Vitis champinii cv. Ramsey (a naturally occurring hybrid between Vitis candicans and Vitis rupestris)) were pruned to two shoots and grown in 13.3 liter pots containing 10 L SuperSoil® potting mix supplemented with slow release fertilizer (5-10-10). Vines were grown in a greenhouse with supplemental sodium vapor lamp lighting (day/night cycles of 16 h/8h light (minimum 400 E m-2 s-1) and 28°C/18°C). Fully-developed leaves were subjected to dehydration as previously described (Hopper et al., 2014). Leaves were removed from dehydration boxes at 1, 2, 4, 8, and 24 h and frozen immediately in liquid nitrogen. Control leaves were taken from the second shoot of the intact plant at the corresponding daytime of the dehydration assay to account for circadian effects on transcript abundance.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.

organism: Vitis x champinii

source_name: Vitis champinii cv. Ramsey, own-rooted vines, harvested from fully-developed leaves during a 24-hour dehydration time course

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

extract_protocol: Samples were rapidly frozen in liquid nitrogen before storage at -80°C. Frozen leaves were ground using a Retsch MM 301 ball mill (www.restsch.com) for 1 min at 30 revolutions s-1. Total RNA was extracted from ~100 mg of tissue using a CTAB-based method (Gambino et al., 2008; Tattersall et al., 2005). Three independent experimental (and biological) replicates were harvested to compare between the dehydration-treated and untreated samples at each time point. Each biological replicate was ground in a frozen mortar and pestle. Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) based method and RNeasy plant mini kit (Quiagen) following the manufacture’s protocol. The total RNA was treated with RNAse-free DNAse I (Qiagen) to eliminate any genomic DNA contamination and then quantified by using a Nanodrop spectrophotometer (Thermo Scientific NanoDrop 2000c). An aliquot of each RNA sample was also analyzed using an Agilent 2100 Bioanalyzer using RNA LabChip® assays according to the manufacturer's instructions.

tag: cultivar

value: Ramsey

tag: treatment

value: Control leaves excised with corresponding Stress leaves, harvested at 8 hour

tag: year

tag: location

value: University of Nevada, Reno, USA

value: leaves


title: Lily_Treated_R_2

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_3.txt


title: Cass_Treated_R

description: raw data file: US451R2993_252119310410_S01_GE2-v5_95_Feb07_1_4.txt


title: IRS1_C20_24_B

description: total RNA


title: T_Cass_Treated_R

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_3.txt


title: C_Spot_MPS_R

description: raw data file: US451R2993_252119310409_S01_GE2-v5_95_Feb07_1_3.txt

value: Carotid artery

value: MPS


title: IRS1_C20_24_A

description: total RNA


title: D_Spice_MPS_R

description: raw data file: US451R2993_252119310410_S01_GE2-v5_95_Feb07_1_2.txt

value: Descending aorta


title: D_Oksana_MPS_R

description: raw data file: US451R2993_252119310409_S01_GE2-v5_95_Feb07_1_4.txt


title: IRS1_C20_4_C

description: total RNA

source_name: T47D-YA-IRS-1 #20 4h SFM


title: IRS1_C20_4_IGF_B

description: total RNA


title: D_Sphinx_MPS_R

description: raw data file: US451R2993_252119310410_S01_GE2-v5_95_Feb07_1_1.txt


title: C_Sphinx_MPS_R

description: raw data file: US451R2993_252119310409_S01_GE2-v5_95_Feb07_1_1.txt


title: D_Spot_MPS_R

description: raw data file: US451R2993_252119310410_S01_GE2-v5_95_Feb07_1_3.txt


title: A_Oksana_MPS_R

description: raw data file: US451R2993_252119310408_S01_GE2-v5_95_Feb07_1_1.txt

value: Ascending aorta


title: A_Sphinx_MPS_R

description: raw data file: US451R2993_252119310408_S01_GE2-v5_95_Feb07_1_2.txt


title: C_Spice_MPS_R

description: raw data file: US451R2993_252119310409_S01_GE2-v5_95_Feb07_1_2.txt


title: A_Spice_MPS_R

description: raw data file: US451R2993_252119310408_S01_GE2-v5_95_Feb07_1_3.txt


title: IRS1_C20_4_A

description: total RNA


title: IRS1_C20_4_B

description: total RNA


title: ADC_Sphinx_MPS_G_1

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_2.txt


title: ADC_Spot_MPS_G_1


title: ADC_154_Control_G_2

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_2.txt

value: control


title: IRS1_C10_24_IGF_C

description: total RNA

source_name: T47D-YA-IRS-1 #10 24h IGF


title: IRS1_C20_4_IGF_A

description: total RNA


title: ADC_Spice_MPS_G_1


title: ADC_154_Control_G_3


title: ADC_Oksana_MPS_G_1

description: raw data file: US451R2993_252119310412_S01_GE2-v5_95_Feb07_1_1.txt


title: ADC_154_Control_G_1

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_1.txt


title: ADC_158_Control_G_1

description: raw data file: US451R2993_252119310411_S01_GE2-v5_95_Feb07_1_4.txt


title: IRS1_C10_24_IGF_B

description: total RNA


title: IRS1_C10_24_IGF_A

description: total RNA


title: IRS1_C10_24_C

description: total RNA

source_name: T47D-YA-IRS-1 #10 24h SFM


title: D_158_Control_G_1


title: ADC_153_Control_G_1

description: raw data file: US451R2993_252119310410_S01_GE2-v5_95_Feb07_1_4.txt


title: Lily_Treated_R_1


title: D_154_Control_G_2


title: D_154_Control_G_1


title: C_153_Control_G_1


title: A_Spot_MPS_R

description: raw data file: US451R2993_252119310408_S01_GE2-v5_95_Feb07_1_4.txt


title: IRS2_C1_24_IGF_B

description: total RNA

source_name: T47D-YA-IRS-2 #1 24h IGF


title: A_153_Control_G_1


title: C_158_Control_G_1

description: raw data file: US451R2993_252119310409_S01_GE2-v5_95_Feb07_1_3.txt


title: A_154_Control_G_2


title: C_153_Control_G_2


title: IRS1_C10_4h_B

description: total RNA

source_name: T47D-YA-IRS-1 #10 4h SFM


title: IRS2_C1_4_C

description: total RNA


title: IRS1_C10_24_A

description: total RNA


title: A_154_Control_G_1


title: A_158_Control_G_1


title: IRS1_C10_24_B

description: total RNA


title: IRS1_C10_4_IGF_B

description: total RNA

source_name: T47D-YA-IRS-1 #10 4h IGF


title: D_153_Control_G_1


title: IRS1_C10_4h_C

description: total RNA


title: IRS1_C10_4_IGF_C

description: total RNA


title: Activated NKT normal rep2

status: Public on Mar 04 2016

city: Oullins

first: GENESTIER

last: Laurent

address: Faculté de Medecine Lyon Sud. 165 Chemin du petit Revoyet

country: France

institute: INSERM

description: SAMPLE 23

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing:
CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.2.1.20

organism: Mus musculus

source_name: in vitro activated NKT cells from 5-week-old p53 KO mouse

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: p53 deficient mice injected every 2 weeks with PBS or Heat-killer Streptococcus pneumoniae until disease development

extract_protocol: Total RNA were extract with with the Qiagen RNeasy minikit (Qiagen), then 50 ng of total RNA were amplified using GeneChip 3' IVT Express Kit from Affymetrix.

treatment_protocol: Lymphoma cells or normal cells as control were purified by cell sorting from liver or spleen.

tag: strain background

tag: genotype/variation

value: p53 KO

tag: age

value: 5 weeks

tag: tissue/cell type

value: in vitro activated, normal NKT cells


title: Activated NKT normal rep1

description: SAMPLE 22


title: Resting NKT normal rep2

description: SAMPLE 20

source_name: Resting NKT cells from 5-week-old p53 KO mouse

value: resting, normal NKT cells


title: Activated T normal rep1

description: SAMPLE 16

source_name: in vitro activated T cells from 5-week-old p53 KO mouse

value: in vitro activated, normal T cells


title: Activated T normal rep2

description: SAMPLE 17


title: IRS1_C10_4_IGF_A

description: total RNA


title: Resting NKT normal rep3

description: SAMPLE 21


title: Resting T normal rep3

description: SAMPLE 15

source_name: Resting T cells from 5-week-old p53 KO mouse

value: resting, normal T cells


title: Activated T normal rep3

description: SAMPLE 18


title: Resting T normal rep2

description: SAMPLE 14


title: TL 111206

description: SAMPLE 12

source_name: TL from p53 KO mouse injected with PBS

tag: injected with

value: PBS (control)

value: Thymic lymphoma (TL)


title: IRS1_C10_4h_A

description: total RNA


title: Resting NKT normal rep1

description: SAMPLE 19


title: Resting T normal rep1

description: SAMPLE 13


title: TL 120203

description: SAMPLE 10

source_name: TL from p53 KO mouse injected with Spn

value: Streptococcus pneumoniae (Spn)


title: PTCL Spn 110828

description: SAMPLE 8

source_name: PTCL from p53 KO mouse injected with Spn

value: peripheral T-cell lymphoma (PTCL)


title: PTCL Spn 110829

description: SAMPLE 9


title: Treg treated donor2

city: Rennes

first: Patrick

last: Legembre

address: CRLCC Eugène Marquis, Rue Bataille Flandres Dunkerque, Bat. D

department: Chemistry Oncogenesis Stress Signalling

institute: Inserm U1242

description: 8h culture in RPMI supplemented with 8% FCS; 100ng/ml cleaved CD95L treatment

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® human Gene 2.0 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 scanned images were analyzed with the Expression Console software (Affymetrix) to generate raw data (cel files) and metrics for quality controls. Probes were mapped using custom CDF files from Brainarray V20 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/enst.asp) and RMA normalization was performed using R. Supervised statistical analysis (ANOVA) was performed using the Partek® Genomics Suite® software (Partek Inc., St. Louis, MO, USA).

source_name: lymphocyte

label_protocol: 9 ng of total RNA were used to produce target CDNA using Ovation PicoSl WTA system V2 (Nugen) . After purification according to Nugen protocol, 3,6 ug of single strand DNA is used for fragmentation and biotin labelling using Encore Biotin Module (Nugen).

growth_protocol: Cells were cultured for 8 hours in RPMI medium supplemented with 8%FCS

extract_protocol: Macherey Nagel total RNA isolation kit according to the manufacturer's instructions

treatment_protocol: Cells were treated with either 100ng/ml cleaved CD95L(treatment) or the equivalent volume of control media (control).

tag: cell type

value: Regulatory T cell

value: cleaved CD95L


title: Treg treated donor1


title: Treg control donor1

description: 8h culture in RPMI supplemented with 8% FCS; control media treatment

value: control medium


title: Th17 control donor2

value: Th17 cell


title: PTCL PBS 120216

description: SAMPLE 3

source_name: PTCL from p53 KO mouse injected with PBS


title: PTCL PBS 111215

description: SAMPLE 4


title: Th17 control donor1


title: PTCL PBS 120305

description: SAMPLE 5


title: Treg control donor2


title: PTCL PBS 120322

description: SAMPLE 2


title: Th17 treated donor2


title: Th17 treated donor1


title: J3-ZJZ

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

country: China

institute: Huazhong Agricultural University

description: miRNA expression data of shoot meristems of trifoliate orange

hyb_protocol: Standard Affymetrix procedures

scan_protocol: GeneArray scanner 3000 by the GeneChip® Operating Software (GCOS)

data_processing: RMA normalization and probe summarization was carried out on all of species and control probe sets.

organism: Citrus trifoliata

source_name: precocious trifoliate orange (March)

label_protocol: Standard Affymetrix procedures

extract_protocol: total RNA was extracted and purified by the Qiagen RNeasy Mini Kit

value: shoot meristem


title: a12-ZJZ

department: College of Horticulture and Forestry Science

source_name: precocious trifoliate orange (December)


title: a4-ZJZ

source_name: precocious trifoliate orange (April nexty year)


title: ZJZ-J6

source_name: precocious trifoliate orange (June)


title: ZJZ-A4


title: PTCL PBS 120412

description: SAMPLE 1


title: RW4-Shld1-2

city: St. Louis

first: Zongtai

last: Qi

state: Missouri

address: 4515 Mckinley Ave

department: Genetics

institute: Washington University in St Louis

description: treated with 1μM Shld1 (Clontech); duplicate #2

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The software is bioconductor, limma v3.14. rma-gene-default-Signal

source_name: DD-2-with Dnase 1 treatment

label_protocol: Affymetrix protocol

growth_protocol: RW4 mouse embryonic stem cells (ESCs) were cultured in complete media consisting of DMEM supplemented with 10% new born calf serum, 10% fetal bovine serum (FBS; Gibco), and 0.3 mM of each of the following nucleosides: adenosine, guanosine, cytosine, thymidine, and uridine (Sigma-Aldrich). To maintain their undifferentiated state, the cells were also cultured in the presence of 1000 U/mL leukemia inhibitory factor (LIF; Chemicon) and 20 mM β-mercaptoethanol (BME; Invitrogen) in flasks coated with a 0.1% gelatin solution (Sigma-Aldrich).

extract_protocol: RNA was isolated from the RW4 mouse ES cells using the PureLink RNA Mini kit (Ambion) according to the manufacturer's instructions. The quantity of RNA was measured using a spectrophotometer (NanoDrop 2000c; Thermo Scientific). Samples with a RNA concentration (A260/A280 ≥1.8 ng/μl) and purity (A230/A260 ≥2.0 ng/μl) were selected.

treatment_protocol: RW4 ESCs were treated with 1 μM 4-hydroxytamoxifen (4-OHT, Sigma) for the ERT2 based induction system and 1μM Shld1 (Clontech) for FKBP based induction system, respectively

value: RW4 ESC

tag: induction system

value: FKBP

tag: agent

value: Shld1 (Clontech)


title: ZJZ-A12


title: RW4-no-drug-1

description: no treatment; duplicate #1

source_name: WT-1 with Dnase I treatment

value: WT


title: RW4-no-drug-2

description: no treatment; duplicate #2

source_name: WT-2 with Dnase 1 treatment


title: J6-ZJZ


title: RW4-Shld1-1

description: treated with 1μM Shld1 (Clontech); duplicate #1

source_name: DD-1-with Dnase 1 treatment


title: RW4-4OHT-2

description: treated with 1μM 4OHT (Sigma); duplicate #2

source_name: ERT2-2-with Dnase 1 treatment

value: 4OHT (Sigma)


title: RW4-4OHT-1

description: treated with 1μM 4OHT (Sigma); duplicate #1

source_name: ERT2-1-with Dnase 1 treatment


title: MG1363_Glu_10min_rep3

city: Kgs. Lyngby

first: Mogens

last: Kilstrup

address: Building 301 room 158

department: DTU Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Hybridization according to Agilent protocol. Agilent 8x15k custom microarray G2509F

scan_protocol: Agilent Technologies Scanner G2505C. Agilent's Feature Extraction software.

data_processing: Quantile normalization (R Bioconductor package preprocessCore)

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: MG1363, glucose depleted, sampled 10 min after depletion

label_protocol: Labelling according to Agilent protocol using random hexamer and Cy3

growth_protocol: Exponentially growing strains in SA medium with 1% glucose were diluted 100-fold in preformed SA medium with 3 mM glucose. After six generations of exponential growth the culture was diluted 100-fold into prewarmed SA medium

extract_protocol: Cells were pelleted by centrifulation and washed in ice cold saline water (0.9% NaCl). RNA was extracted by the hot phenol method

treatment_protocol: Growth was stopped immidiately by transfer of 10 ml culture sample into a thick glass flask precooled on ice followed by rapid swirling

tag: strain


title: MEF_p53 null rnaseh2b+/+_biological rep4

city: Edinburgh

first: Karen

last: Mackenzie

address: Crewe Road

department: IGMM

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Data was processed using the biocondouctor package limma. Data was normalized using neqc normalization; background correction using negative control probes and quantile normalization using negative and positive control probes.

source_name: MEF_p53 null and rnaseh2b wildtype

label_protocol: Using the Illumina TotalPrep RNA Amplification kit (AMIL1791) as per manufacturer's instructions.

growth_protocol: MEFs generated from E10.5 whole embryos were grown in hypoxic conditions at 37˚C, 5% CO2 and 3% O2 in DMEM containing 10% fetal calf serum, 50U/ml penicillin, 50µg/ml streptomycin and 0.1mM β-Mercaptoethanol and were passage matched for the experiment.

extract_protocol: RNA was extracted from adherent cells using the RNeasy kit (Qiagen) as per manufacturer's instructions.

treatment_protocol: 2x10^5 MEFs were plated per well in a 12 well plate. Culture medium was replaced the following day (800µl used). RNA was extracted after a further 20 hours of culture.

tag: developemental stage

value: E10.5 embryos

tag: celltype

value: murine embryonic fibroblast (MEF)


title: MG1363_Ref_Exp_rep3

source_name: MG1363, reference, glucose excess, OD450=0.21


title: MG1363_Glu_60min_rep2

source_name: MG1363, glucose depleted, sampled 60 min after depletion


title: MG1363_Ref_Exp_rep2

source_name: MG1363, reference, glucose excess, OD450=0.18


title: MG1363_Glu_60min_rep1


title: PTCL Spn 110721

description: SAMPLE 7

source_name: PTCL from p53 KO mouse injected with Spn

value: p53 KO


title: MEF_p53 null rnaseh2b+/+_biological rep3


title: MEF_p53 null rnaseh2b+/+_biological rep1


title: MEF_p53 null rnaseh2b null_biological rep2

source_name: MEF_p53 null and rnaseh2b null


title: MG1363_Glu_10min_rep1


title: HAdV-D58_CR1b_Library_2_2

type: protein

city: South San Francisco

first: Nadia

last: Martinez

state: California

address: 470 East Grand Avenue

institute: Genentech

hyb_protocol: Array slides were loaded onto an automated a-Hyb hybridization station, blocked with 5% milk in PBS.

scan_protocol: Scanned with a GenePix 4000B scanner. GenePix Pro 6.0 software was used for analysis.

data_processing:
The protein microarray analysis was done with a z-score based on the array distribution and scores were standardized with quantile normalization. Probes that bound to 5% of more of the baits were flagged as non-specific binders, as determined by a proportion test of a representative set of screens. After eliminating non-specific binders, probes with a score of 5.0 or higher were counted as hits. Please see Methods section in the accompanying paper for further details on experimental protocol and data analysis. Given the number of human proteins in the collection, samples were randomly distributed in 2 libraries, called 'Array 1' and 'Array 2'. To control for slide variability, duplicate microarrays from separate spotting runs were analyzed in all cases. The average score from the duplicate runs for each of the viral proteins screened is provided in the Matrix table.
Probes with a score of 5 or higher were counted as hits.

molecule: protein

organism: Human mastadenovirus A

source_name: adenoviral E3 protein

label_protocol: An immunoglobulin, utilized as inner carrier, was labeled with a C5y monoreactive dye and incubated with the viral protein and protein A microbead to form multivalent complexes. These complexes were supplemented with soluble protein A microarray to block non-specific binding to the protein microarray slides.

extract_protocol: the viral proteins were generated as recombinant purified proteins carrying an Fc tag.

tag: species

value: human adenovirus species D


title: MEF_p53 null rnaseh2b null_biological rep1


title: MEF_p53 null rnaseh2b+/+_biological rep2


title: HAdV-D58_CR1b_Library_2_1


title: HAdV-D53_CR1b_Library_2_2


title: HAdV-D58_CR1b_Library_1_2


title: HAdV-D53_CR1b_Library_2_1


title: HAdV-D53_CR1b_Library_1_1


title: HAdV-D53_CR1b_Library_1_2


title: HAdV-D51_CR1b_Library_2_1


title: HAdV-D58_CR1b_Library_1_1


title: MG1363_Ref_Exp_rep1

source_name: MG1363, reference, glucose excess, OD450=0.15


title: HAdV-D51_CR1b_Library_1_2


title: HAdV-D47_CR1b_Library_1_1


title: HAdV-D47_CR1b_Library_1_2


title: HAdV-D43_CR1b_Library_2_2


title: HAdV-D47_CR1b_Library_2_2


title: HAdV-D47_CR1b_Library_2_1


title: HAdV-D51_CR1b_Library_2_2


title: MG1363_Glu_10min_rep2


title: HAdV-D43_CR1b_Library_1_2


title: HAdV-D43_CR1b_Library_2_1


title: HAdV-D39_CR1b_Library_2_2


title: HAdV-D43_CR1b_Library_1_1


title: HAdV-D39_CR1b_Library_1_2


title: HAdV-D39_CR1b_Library_2_1


title: HAdV-D39_CR1b_Library_1_1


title: HAdV-D37_CR1b_Library_2_1


title: HAdV-D51_CR1b_Library_1_1


title: HAdV-D37_CR1b_Library_1_2


title: HAdV-D30_CR1b_Library_2_1


title: HAdV-D37_CR1b_Library_1_1


title: PTCL Spn 110704

description: SAMPLE 6


title: HAdV-D30_CR1b_Library_1_1


title: HAdV-D28_CR1b_Library_2_1


title: HAdV-D28_CR1b_Library_1_2


title: HAdV-D30_CR1b_Library_2_2


title: HAdV-D37_CR1b_Library_2_2


title: HAdV-D30_CR1b_Library_1_2


title: TL 111220

description: SAMPLE 11

source_name: TL from p53 KO mouse injected with PBS

value: PBS (control)

value: Thymic lymphoma (TL)


title: HAdV-D24_cr1b_Library_2_2


title: HAdV-D28_CR1b_Library_2_2


title: HAdV-D24_cr1b_Library_2_1


title: HAdV-D28_CR1b_Library_1_1


title: HAdV-D23_cr1b_Library_2_2


title: HAdV-D23_cr1b_Library_1_2


title: HAdV-D24_cr1b_Library_1_1


title: HAdV-D23_cr1b_Library_2_1


title: HAdV-D23_cr1b_Library_1_1


title: HAdV-D19_cr1b_Library_2_2


title: HAdV-D24_cr1b_Library_1_2


title: HAdV-D19_cr1b_Library_2_1


title: HAdV-D19_cr1b_Library_1_2


title: HAdV-D19_cr1b_Library_1_1


title: HAdV-D9_cr1b_Library_2_2


title: HAdV-D9_cr1b_Library_2_1


title: HAdV-D9_cr1b_Library_1_2


title: HAdV-D9_cr1b_Library_1_1


title: HAdV-D30_CR1g_Library_2_2


title: HAdV-D30_CR1g_Library_2_1


title: HAdV-D30_CR1g_Library_1_2


title: HAdV-E3_CR1d_Library_1_2

value: human adenovirus species E


title: HAdV-G52_CR1b_Library_2_2

value: human adenovirus species G


title: HAdV-D30_CR1g_Library_1_1


title: HAdV-E3_CR1d_Library_2_2


title: HAdV-G52_CR1b_Library_2_1


title: HAdV-G52_CR1b_Library_1_2


title: HAdV-G52_CR1b_Library_1_1


title: HAdV-F41_CR1b_Library_1_1

value: human adenovirus species F


title: HAdV-F41_CR1b_Library_2_1


title: HAdV-F41_CR1b_Library_2_2


title: HAdV-B55_CR1b_Library_2_2

value: human adenovirus species B


title: HAdV-F41_CR1b_Library_1_2


title: HAdV-B55_CR1b_Library_1_2


title: HAdV-B55_CR1b_Library_2_1


title: HAdV-B55_CR1b_Library_1_1


title: HAdV-A18_CR1b_Library_2_2

value: human adenovirus species A


title: HAdV-A18_CR1b_Library_2_1


title: HAdV-E3_CR1d_Library_2_1


title: HAdV-E3_CR1d_Library_1_1


title: HAdV-A18_CR1b_Library_1_2


title: HAdV-A18_CR1b_Library_1_1


title: HAdV-G52_CR1a_Library_2_2


title: HAdV-G52_CR1a_Library_2_1


title: HAdV-G52_CR1a_Library_1_2


title: HAdV-G52_CR1a_Library_1_1


title: HAdV-F41_CR1a_Library_2_1


title: HAdV-F41_CR1a_Library_1_2


title: HAdV-F41_CR1a_Library_2_2


title: HAdV-F41_CR1a_Library_1_1


title: HAdV-E4_CR1a_Library_2_2


title: ZJZ-J3

source_name: precocious trifoliate orange (March)

tag: tissue

value: shoot meristem


title: HAdV-E4_CR1a_Library_2_1


title: iPS-control-2

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

hyb_protocol: 12.5ug cRNA was used to make 250ul hyb cocktail, of which 200ul were injected into GeneChip Mouse M430 2.0 arrays and hybridized for 16 hours at 45°C. Arrays were washed and stained using Affymetrix Fluidics Station 450 with reagents from Affymetrix.

scan_protocol: Microarrays were scanned using the GeneChip Scanner 3000 system from Affymetrix.

data_processing: Data were analyzed using RMA, on Affymetrix Expression Console

source_name: iPS cells, healthy control

label_protocol: Simultaneous cRNA synthesis and biotin labeling via 3' IVT Express protocol

growth_protocol: Fibroblasts were grown in DMEM with high glucose and 10% fetal bovine serum. iPS cells were grown on matrigel-coated plates in mTesR1 medium.

extract_protocol: Cells were lysed in RiboZol. RNA was isolated according to manufacturer's instruction.

treatment_protocol: Cells were lysed at confluence with no added insulin or growth factors.

value: iPS cells

tag: individual id


title: iPS-patient-2

source_name: iPS cells, patient with INSR mutation


title: fibroblasts-patient-4

source_name: fibroblast cells, patient with INSR mutation

value: Fibroblast cells


title: fibroblasts-patient-1

value: Minn1 (IR-Mut1)


title: HAdV-E4_CR1a_Library_1_1


title: HAdV-E4_CR1a_Library_1_2


title: iPS-patient-1


title: HAdV-B55_CR1a_Library_2_2


title: fibroblasts-patient-6

value: Can1 (IR-Mut6)


title: HAdV-B55_CR1a_Library_1_2


title: fibroblasts-control-5

source_name: fibroblast cells, healthy control


title: fibroblasts-control-3


title: HAdV-B55_CR1a_Library_1_1


title: HAdV-A18_CR1a_Library_2_1


title: HAdV-A18_CR1a_Library_1_2


title: HAdV-A18_CR1a_Library_2_2


title: fibroblasts-patient-2


title: fibroblasts-patient-3


title: fibroblasts-control-2


title: iPS-control-3


title: iPS-control-1

value: BJ (Con1)


title: fibroblasts-patient-5

value: ARK1 (IR-Mut5)


title: iPS-patient-3


title: HAdV-A18_CR1a_Library_1_1


title: fibroblasts-control-4


title: fibroblasts-control-1


title: HAdV-B55_CR1a_Library_2_1


title: DZ12-highgal_6 (DZHG6)

status: Public on Mar 03 2016

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

description: DZ12-derived isolates from one cycle growth on high-gal medium

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes. In the labels of the oligonucleotides “SF”, “SR”, “YF” and “YR” refer to the orientation and origin of the sequences used for the oligonucleotides on the microarrays. “S” and “Y” indicate whether the oligonucleotide contains sequences identical to the reference S288c genome (closely related to W303-1A) or the YJM789 genome, respectively. “F” and “R” indicate whether the orientation (5’ to 3’) is identical to the orientation in SGD (“F” standing for forward) or opposite to that shown in SGD (“R” for reverse). Thus, “F” and “R” have the sequences of the complementary Watson and Crick strands at each position. For all oligonucleotides for a particular SNP, the number used to label the coordinate is the coordinate of the first base of the oligonucleotide in the “F” orientation. In addition, the oligonucleotides for the YJM789-derived sequences were labeled with the same coordinate as the S288c-derived sequences. The sequence information for the YJM789 sequences was from SGD based on the paper by (Wei et al., 2007. PNAS 104:12825-12830). The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: DZ12-derived isolates

label_protocol: The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were cultured in low-gal (2% yeast extract, 2% peptone and 3% raffinose, 0.005% galactose) or high-gal medium (2% yeast extract, 2% peptone and 3% raffinose, 0.05% galactose) to extract DNA

extract_protocol: Genomic DNA were prepared DNA by standard procedures (St. Charles et al., 2012).

treatment_protocol: The expression of POL3 were downregulated using either low-gal medium or YPD medium.

tag: ploidy

value: Diploid

tag: background

value: diploid strain DZ12

tag: growth protocol

value: one cycle of growth on high-gal medium

source_name: Control strain JSC24

value: control strain JSC24


title: CR1560 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep3

city: Redwood City

first: Ann

last: Kapoun

address: 800 Chesepeake Drive

department: Translational Medicine

institute: Oncomed Pharmaceuticals

hyb_protocol: Following Affymetrix protocol, after fragmentation, cRNA were hybridized on GeneChip HG-U133_plus_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with affy and GCRMA libraries in R package

source_name: PDX model treated by antiRSPO3 and irinotecan for 6wks

label_protocol: 100 ng total RNA were amplied with Ovation RNA Amplification System V2 (NuGene) and the biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix).

growth_protocol: Human colorectal cancer cells were inplanted to NOD/SCID mice by subcutaneous injection.  The tumor reached 200 cubic millimeter, the mice were randomized to different treatment groups with at least 5 mice each group.

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

treatment_protocol: The tumor-bearing mice were treated with 10mg/kg irinotecan or/and 25mg/kg anti-RSPO3 anbidy once a week

tag: tumor type

value: xenograft model of human colorectal cancer

tag: host strain

value: NOD/SCID

tag: treated with

value: antiRSPO3 and irinotecan for 6wks

value: whole xenograft sample containing human tumor cells and mouse stroma


title: HCC1806_MIND_sample3

city: Lausanne

first: George

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

hyb_protocol: Affymetrix Human Genome U133Plus 2.0 arrays were hybridized with 11 micrograms of biotinylated amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0001)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each experiment separately.

source_name: xenograft HCC1806-MIND

label_protocol: For all samples, 100 ng of total RNA was used to perform target preparation using the MessageAmp™ II-Biotin Enhanced kit (Life technologies).

extract_protocol: Xenografted BT20 or HCC1806 were sorted by FACS based on DsRed expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), and quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included.

value: intraductal xenograft


title: CR1560 PDX model treated by antiRSPO3 antibody, biological rep3

source_name: PDX model treated by antiRSPO3 anbidy for 6wks

value: antiRSPO3 antibody for 6wks


title: DZ12-highgal_5 (DZHG5)


title: DZ12-highgal_2 (DZHG2)


title: CR1560 PDX model treated by control antibody, biological rep2

source_name: PDX model treated by control anbidy for 6wks

value: control antibody for 6wks


title: HCC1806_fatpad_sample1

source_name: xenograft HCC1806-FP

value: fat pad xenograft


title: breast_invasive ductal carcinoma_8065

city: ROTTERDAM

first: Maurice

last: Jansen

address: Wytemaweg 80

department: MEDICAL ONCOLOGY

country: Netherlands

institute: ERASMUS MC - CANCER INSTITUTE

description: mRNA profile_GSM1029805

data_processing:
SDS 2.3 Software
Results of the real-time PCR data are presented as Ct values (raw data), with Ct defined as the threshold cycle number of PCRs at first detection of amplified product. Next, ΔCt normalization was performed using a reference Ct. To establish the reproducibility of the 768 miRNA-assays and to define a reference, a pool of total RNAs from a set of 55 tumor specimens (45-series) was run in triplicate. In total, 314 assays were selected as reference since these assays were negative for no template controls, had results in all three runs with a coefficient of variation less than 2.5% between them, and had for each run correct amplification curves (ΔCt=0.75-1.50 between 0.1/0.2 or 0.05/0.1 threshold). Next, for each individual cancer specimen the median Ct was calculated for these 314 microRNA reference assays. Subsequently, the ΔCt-value was calculated by subtraction of this reference median Ct-value from the Ct-value measured for each target miRNA. Those  ΔCt-values that failed quality controls were flagged. Only data with an undetermined or not amplified well flag were replaced by the minimum ΔCt-value of the dataset (i.e. 0.000507083). All other flagged data were removed. Finally, ΔCt-values were log2 transformed for further analyses (processed data).

label: FAM

source_name: fresh frozen primary breast cancer specimen

label_protocol:
500ng of total RNA was reverse transcribed with MegaPlex RT-Pools (A&B) (40 cycles).  The qPCR reaction on the TaqMan microaRNA array was performed with 6 ul megaplex RT product, 450 ul TaqMan Universal PCR Master MIX, No AmpERase UNG (2x) and 444ul nuclease-free water.
Individual Taqman Probes & Primers, Tiled-Low Density Array
7900 Real Time PCR System

extract_protocol: RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.

tag: gender

value: female

tag: age at diagnosis

tag: treatment type

value: exemestane

tag: age at start therapy

tag: menopausal status at start therapy

value: post

value: breast

value: invasive ductal carcinoma

tag: location

tag: grade

tag: estrogen receptor status

value: positive

tag: progesterone receptor status

tag: her2 status

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: TCRG

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8068

description: mRNA profile_GSM1029807

tag: gender

tag: age at diagnosis

tag: treatment type

value: anastrozole

tag: tissue

tag: tumor type

value: negative

tag: pik3ca genotype

value: wildtype


title: breast_invasive ductal carcinoma_8071

description: mRNA profile_GSM1029809

value: letrozole

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

value: EMC


title: breast_invasive ductal carcinoma_8073

description: mRNA profile_GSM1029810

tag: her2 status

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: breast_invasive ductal carcinoma_8066

description: mRNA profile_GSM1029806

tag: gender

tag: age at diagnosis

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR1560 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep2

tag: tumor type

value: xenograft model of human colorectal cancer

tag: host strain

value: NOD/SCID

tag: treated with

value: antiRSPO3 and irinotecan for 6wks

tag: tissue

value: whole xenograft sample containing human tumor cells and mouse stroma


title: breast_invasive ductal carcinoma_8069

description: mRNA profile_GSM1029808

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

tag: pik3ca genotype


title: HCC1806_fatpad_sample3

value: fat pad xenograft


title: CR1560 PDX model treated by Irinotican, biological rep1

source_name: PDX model treated by irinotecan for 6wks

value: irinotecan for 6wks


title: HCC1806_fatpad_sample2


title: DZ12-highgal_3 (DZHG3)

tag: ploidy

value: Diploid

tag: background

tag: strain

value: diploid strain DZ12

tag: growth protocol

value: one cycle of growth on high-gal medium

value: control strain JSC24


title: breast_invasive ductal carcinoma_8064

description: mRNA profile_GSM1029804

tag: gender

value: female

tag: age at diagnosis

value: exemestane

value: post

value: breast

value: invasive ductal carcinoma

value: positive

tag: her2 status

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: DZ12-highgal_1 (DZHG1)


title: HCC1806_MIND_sample2

tag: tissue

value: intraductal xenograft


title: DZ12-highgal_4 (DZHG4)

tag: ploidy


title: HCC1806_MIND_sample1


title: CR1560 PDX model treated by antiRSPO3 antibody, biological rep1

tag: tumor type

value: xenograft model of human colorectal cancer

tag: host strain

tag: treated with

value: antiRSPO3 antibody for 6wks


title: CR1560 PDX model treated by Irinotican, biological rep3

value: NOD/SCID


title: breast_invasive ductal carcinoma_8061

description: mRNA profile_GSM1029802

tag: gender

tag: treatment type

value: letrozole

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

value: negative

tag: pik3ca genotype

value: wildtype

value: TCRG


title: breast_invasive ductal carcinoma_8062

description: mRNA profile_GSM1029803

tag: age at diagnosis

tag: her2 status

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8060

description: mRNA profile_GSM1029801

tag: gender

tag: treatment type

tag: tissue

tag: tumor type

value: EMC

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8059

description: mRNA profile_GSM1029800

tag: age at start therapy

tag: menopausal status at start therapy

value: pre

tag: location

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status


title: CR1560 PDX model treated by control antibody, biological rep3

tag: host strain

tag: treated with

value: control antibody for 6wks

value: whole xenograft sample containing human tumor cells and mouse stroma


title: breast_invasive ductal carcinoma_8058

description: mRNA profile_GSM1029799

value: female

tag: age at diagnosis

value: anastrozole

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: CR1560 PDX model treated by antiRSPO3 antibody, biological rep2

tag: tumor type

tag: tissue


title: CR2513 PDX model treated by antiRSPO3 antibody, biological rep3

source_name: PDX model treated by antiRSPO3 anbidy for 7wks

value: antiRSPO3 antibody for 7wks


title: CR1560 PDX model treated by Irinotican, biological rep2

value: irinotecan for 6wks


title: CR1560 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep1

value: antiRSPO3 and irinotecan for 6wks


title: breast_invasive ductal carcinoma_8057

description: mRNA profile_GSM1029798

tag: gender

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

value: post

value: breast

value: invasive ductal carcinoma

value: positive

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR2513 PDX model treated by antiRSPO3 antibody, biological rep2

value: xenograft model of human colorectal cancer

tag: host strain

value: NOD/SCID

tag: treated with


title: breast_invasive ductal carcinoma_8054

description: mRNA profile_GSM1029796

tag: age at diagnosis

tag: location

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

value: negative

tag: her2 status

tag: pik3ca genotype

value: wildtype

tag: disease-free interval (in months)


title: breast_invasive ductal carcinoma_8053

description: mRNA profile_GSM1029795

tag: gender

tag: treatment type

tag: tissue

tag: tumor type

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: TCRG


title: CR1560 PDX model treated by control antibody, biological rep1

tag: host strain

tag: treated with


title: CR2513 PDX model treated by antiRSPO3 antibody, biological rep1


title: breast_invasive ductal carcinoma_8052

description: mRNA profile_GSM1029794

tag: age at diagnosis

value: exemestane

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR3150 PDX model treated by antiRSPO3 antibody, biological rep3


title: CR2513 PDX model treated by control antibody, biological rep1

source_name: PDX model treated by control anbidy for 7wks

value: control antibody for 7wks


title: breast_invasive ductal carcinoma_8051

description: mRNA profile_GSM1029793

tag: gender

tag: treatment type

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)


title: breast_invasive ductal carcinoma_8055

description: mRNA profile_GSM1029797

tag: tissue

tag: tumor type

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: EMC


title: breast_invasive ductal carcinoma_8048

description: mRNA profile_GSM1029790

value: female

tag: age at diagnosis

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8049

description: mRNA profile_GSM1029791

tag: gender

tag: treatment type

value: anastrozole

tag: grade

tag: estrogen receptor status

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR3150 PDX model treated by control antibody, biological rep3

source_name: PDX model treated by control anbidy for 3wks

tag: tumor type

tag: host strain

tag: treated with

value: control antibody for 3wks

tag: tissue

value: whole xenograft sample containing human tumor cells and mouse stroma


title: CR2513 PDX model treated by control antibody, biological rep3


title: CR2513 PDX model treated by control antibody, biological rep2


title: breast_invasive ductal carcinoma_8046

description: mRNA profile_GSM1029788

value: letrozole

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: breast_invasive ductal carcinoma_8047

description: mRNA profile_GSM1029789

tag: gender

tag: age at diagnosis

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

value: post

tag: location

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: CR3150 PDX model treated by control antibody, biological rep1

tag: tumor type

tag: host strain

tag: treated with

tag: tissue


title: breast_invasive ductal carcinoma_8045

description: mRNA profile_GSM1029787

value: breast

tag: grade

tag: estrogen receptor status

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8044

description: mRNA profile_GSM1029786

tag: gender

tag: age at diagnosis

tag: treatment type

tag: age at start therapy

value: invasive ductal carcinoma

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: CR2506 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep1

source_name: PDX model treated by antiRSPO3 and irinotecan for 7wks

tag: tumor type

tag: host strain

tag: treated with

value: antiRSPO3 and irinotecan for 7wks

tag: tissue


title: CR2506 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep2

value: xenograft model of human colorectal cancer


title: breast_invasive ductal carcinoma_8043

description: mRNA profile_GSM1029785

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

value: positive

tag: progesterone receptor status

tag: her2 status

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: CR2506 PDX model treated by antiRSPO3 antibody, biological rep3

value: NOD/SCID

value: antiRSPO3 antibody for 7wks


title: CR2506 PDX model treated by antiRSPO3 antibody, biological rep1


title: CR2506 PDX model treated by Irinotican, biological rep3

source_name: PDX model treated by irinotecan for 7wks

value: irinotecan for 7wks


title: CR3150 PDX model treated by control antibody, biological rep2


title: CR3150 PDX model treated by antiRSPO3 antibody, biological rep1


title: breast_invasive ductal carcinoma_8041

description: mRNA profile_GSM1029784

tag: gender

tag: age at diagnosis

tag: treatment type

value: exemestane

tag: age at start therapy

value: negative

tag: pik3ca genotype

value: wildtype

tag: disease-free interval (in months)

value: TCRG

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR2506 PDX model treated by Irinotican, biological rep2

tag: tumor type

tag: host strain

tag: treated with

tag: tissue


title: breast_invasive ductal carcinoma_8040

description: mRNA profile_GSM1029783

value: female

tag: menopausal status at start therapy

value: pre

tag: location

tag: grade

tag: estrogen receptor status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: CR2506 PDX model treated by control antibody, biological rep3

source_name: PDX model treated by control anbidy for 4wks

value: control antibody for 4wks

value: whole xenograft sample containing human tumor cells and mouse stroma


title: breast_invasive ductal carcinoma_8039

description: mRNA profile_GSM1029782

tag: gender

tag: age at diagnosis

tag: treatment type

value: anastrozole

tag: age at start therapy

value: post

tag: progesterone receptor status

tag: her2 status

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: CR2506 PDX model treated by control antibody, biological rep2

tag: tumor type

tag: host strain

tag: treated with

tag: tissue


title: CR2506 PDX model treated by antiRSPO3 antibody and Irinotecan, biological rep3


title: breast_invasive ductal carcinoma_8038

description: mRNA profile_GSM1029781

tag: menopausal status at start therapy

value: breast

value: invasive ductal carcinoma

tag: location

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR3150 PDX model treated by antiRSPO3 antibody, biological rep2

value: xenograft model of human colorectal cancer


title: breast_invasive ductal carcinoma_8033

description: mRNA profile_GSM1029778

tag: gender

tag: age at diagnosis

tag: treatment type

value: letrozole

tag: age at start therapy

value: positive

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: EMC/NKI


title: breast_invasive ductal carcinoma_8032

description: mRNA profile_GSM1029777

tag: tissue

tag: tumor type

tag: progesterone receptor status

tag: her2 status

value: EMC

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8037

description: mRNA profile_GSM1029780

value: tamoxifen

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)


title: breast_invasive ductal carcinoma_8034

description: mRNA profile_GSM1029779

tag: gender

tag: age at diagnosis

tag: treatment type

tag: age at start therapy

value: negative

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: CR2506 PDX model treated by Irinotican, biological rep1

tag: tumor type

tag: host strain

value: NOD/SCID

tag: treated with

value: irinotecan for 7wks

tag: tissue


title: CR2506 PDX model treated by antiRSPO3 antibody, biological rep2

value: antiRSPO3 antibody for 7wks


title: breast_invasive ductal carcinoma_8024

description: mRNA profile_GSM1029773

value: female

tag: progesterone receptor status

tag: her2 status

value: wildtype

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: TCRG

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8030

description: mRNA profile_GSM1029775

tag: gender

tag: age at diagnosis

tag: menopausal status at start therapy

tag: location

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)


title: breast_invasive ductal carcinoma_8031

description: mRNA profile_GSM1029776

tag: treatment type

value: anastrozole

tag: age at start therapy

tag: tissue

tag: tumor type

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8026

description: mRNA profile_GSM1029774

value: post

tag: progesterone receptor status

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial


title: S184

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

institute: Cancer Research Center of Toulouse

description: Reanalysis of GSM525989

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm

label: Biotin

source_name: Other

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

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: RNA extracted from frozen tissue of the untreated primary tumor

tag: metastasis

value: No

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support

value: Frozen tumor


title: S180

description: Reanalysis of GSM525896

source_name: Leiomyosarcoma


title: breast_invasive ductal carcinoma_8023

description: mRNA profile_GSM1029772

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

value: breast

value: invasive ductal carcinoma

tag: location

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S181

description: Reanalysis of GSM525897

source_name: Myxofibrosarcoma


title: S310

description: Reanalysis of GSM526115

source_name: Dedifferentiated liposarcoma


title: breast_invasive ductal carcinoma_8022

description: mRNA profile_GSM1029771

value: exemestane

tag: age at start therapy

tag: tissue

tag: tumor type

tag: progesterone receptor status

value: positive

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8019

description: mRNA profile_GSM1029770

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: grade


title: CR2506 PDX model treated by control antibody, biological rep1

value: xenograft model of human colorectal cancer

tag: host strain

tag: treated with

value: control antibody for 4wks

value: whole xenograft sample containing human tumor cells and mouse stroma


title: breast_invasive ductal carcinoma_8018

description: mRNA profile_GSM1029769

tag: age at start therapy

tag: tissue

tag: tumor type

tag: estrogen receptor status

value: negative

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S1

description: Reanalysis of GSM525806

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_8015

description: mRNA profile_GSM1029768

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8014

description: mRNA profile_GSM1029767

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8013

description: mRNA profile_GSM1029766

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status


title: breast_invasive ductal carcinoma_8007

description: mRNA profile_GSM1029763

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a


title: breast_invasive ductal carcinoma_8005

description: mRNA profile_GSM1029761

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_8004

description: mRNA profile_GSM1029760

tag: gender

tag: age at diagnosis

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8003

description: mRNA profile_GSM1029759

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: disease relapse (event)


title: S175

description: Reanalysis of GSM525890

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_8001

description: mRNA profile_GSM1029758

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4561

description: mRNA profile_GSM1029756

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

value: EMC

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_8012

description: mRNA profile_GSM1029765

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status


title: breast_invasive ductal carcinoma_4562

description: mRNA profile_GSM1029757

tag: age at diagnosis

value: letrozole

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

value: NKI

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S308

description: Reanalysis of GSM526113

source_name: Undifferentiated sarcoma

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S174

description: Reanalysis of GSM525889


title: S305

description: Reanalysis of GSM526110

value: Yes


title: breast_invasive ductal carcinoma_8006

description: mRNA profile_GSM1029762

tag: gender

value: female

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

value: wildtype

tag: disease-free interval (in months)

tag: disease relapse (event)

value: TCRG

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S172

description: Reanalysis of GSM525887

value: No


title: S307

description: Reanalysis of GSM526112

value: Frozen tumor


title: S309

description: Reanalysis of GSM526114


title: breast_invasive ductal carcinoma_4560

description: mRNA profile_GSM1029755

tag: age at diagnosis

tag: age at start therapy

value: post

tag: tissue

value: breast

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S303

description: Reanalysis of GSM526108

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S306

description: Reanalysis of GSM526111


title: S170

description: Reanalysis of GSM525885


title: S300

description: Reanalysis of GSM526105


title: S302

description: Reanalysis of GSM526107


title: S298

description: Reanalysis of GSM526103


title: S299

description: Reanalysis of GSM526104


title: S301

description: Reanalysis of GSM526106


title: breast_invasive ductal carcinoma_4558

description: mRNA profile_GSM1029753

tag: gender

tag: treatment type

value: anastrozole

tag: menopausal status at start therapy

value: invasive ductal carcinoma

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4556

description: mRNA profile_GSM1029751

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

value: positive

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4557

description: mRNA profile_GSM1029752

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: S171

description: Reanalysis of GSM525886

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_4559

description: mRNA profile_GSM1029754

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S169

description: Reanalysis of GSM525883


title: breast_invasive ductal carcinoma_4554

description: mRNA profile_GSM1029749

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S297

description: Reanalysis of GSM526102

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S294

description: Reanalysis of GSM526099


title: breast_invasive ductal carcinoma_4555

description: mRNA profile_GSM1029750

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4553

description: mRNA profile_GSM1029748

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S173

description: Reanalysis of GSM525888

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S295

description: Reanalysis of GSM526100


title: breast_invasive ductal carcinoma_4552

description: mRNA profile_GSM1029747

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4548

description: mRNA profile_GSM1029744

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4547

description: mRNA profile_GSM1029743

tag: age at diagnosis

tag: age at start therapy

value: pre

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status


title: S164

description: Reanalysis of GSM525878

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_4546

description: mRNA profile_GSM1029742

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S163

description: Reanalysis of GSM525877


title: S162

description: Reanalysis of GSM525876


title: S154

description: Reanalysis of GSM525867


title: breast_invasive ductal carcinoma_4550

description: mRNA profile_GSM1029746

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4545

description: mRNA profile_GSM1029741

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: breast_invasive ductal carcinoma_4544

description: mRNA profile_GSM1029740

tag: age at diagnosis

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S293

description: Reanalysis of GSM526098

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_4549

description: mRNA profile_GSM1029745

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S161

description: Reanalysis of GSM525875


title: breast_invasive ductal carcinoma_4543

description: mRNA profile_GSM1029739

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S288

description: Reanalysis of GSM526093

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S165

description: Reanalysis of GSM525879


title: S292

description: Reanalysis of GSM526097

source_name: Liposarcoma


title: breast_invasive ductal carcinoma_4541

description: mRNA profile_GSM1029737

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4542

description: mRNA profile_GSM1029738

tag: age at diagnosis

tag: treatment type

value: exemestane

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S290

description: Reanalysis of GSM526095

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S289

description: Reanalysis of GSM526094


title: S151

description: Reanalysis of GSM525864


title: breast_invasive ductal carcinoma_4540

description: mRNA profile_GSM1029736

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

value: negative

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S291

description: Reanalysis of GSM526096


title: breast_invasive ductal carcinoma_4539

description: mRNA profile_GSM1029735

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4537

description: mRNA profile_GSM1029733

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status


title: S152

description: Reanalysis of GSM525865

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_4538

description: mRNA profile_GSM1029734

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S319


title: breast_invasive ductal carcinoma_4535

description: mRNA profile_GSM1029732

tag: gender

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4532

description: mRNA profile_GSM1029729

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: breast_invasive ductal carcinoma_4533

description: mRNA profile_GSM1029730

tag: gender

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S287

description: Reanalysis of GSM526092

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: breast_invasive ductal carcinoma_4531

description: mRNA profile_GSM1029728

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4529

description: mRNA profile_GSM1029727

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4528

description: mRNA profile_GSM1029726

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status


title: S317

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S318


title: S316


title: S148

description: Reanalysis of GSM525860


title: breast_invasive ductal carcinoma_4526

description: mRNA profile_GSM1029724

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S149

description: Reanalysis of GSM525861


title: breast_invasive ductal carcinoma_4527

description: mRNA profile_GSM1029725

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S150

description: Reanalysis of GSM525863

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S285

description: Reanalysis of GSM526090


title: breast_invasive ductal carcinoma_4524

description: mRNA profile_GSM1029723

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4523

description: mRNA profile_GSM1029722

tag: age at diagnosis

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4534

description: mRNA profile_GSM1029731

tag: gender

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: breast_invasive ductal carcinoma_4522

description: mRNA profile_GSM1029721

tag: age at diagnosis

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4520

description: mRNA profile_GSM1029719

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: time-to-progression (in months)


title: S315

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S282

description: Reanalysis of GSM526087


title: breast_invasive ductal carcinoma_4519

description: mRNA profile_GSM1029718

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: S283

description: Reanalysis of GSM526088


title: S279

description: Reanalysis of GSM526084


title: breast_invasive ductal carcinoma_4513

description: mRNA profile_GSM1029714

tag: age at start therapy

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4512

description: mRNA profile_GSM1029713

tag: gender

tag: age at diagnosis

tag: treatment type

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status


title: breast_invasive ductal carcinoma_4514

description: mRNA profile_GSM1029715

tag: age at start therapy

tag: her2 status

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4521

description: mRNA profile_GSM1029720

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)


title: breast_invasive ductal carcinoma_4518

description: mRNA profile_GSM1029717

tag: gender

tag: age at diagnosis

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4517

description: mRNA profile_GSM1029716

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: S280

description: Reanalysis of GSM526085

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S278

description: Reanalysis of GSM526083


title: S276

description: Reanalysis of GSM526081


title: S274

description: Reanalysis of GSM526079


title: S284

description: Reanalysis of GSM526089


title: S273

description: Reanalysis of GSM526078


title: breast_invasive ductal carcinoma_4510

description: mRNA profile_GSM1029711

tag: gender

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4509

description: mRNA profile_GSM1029710

tag: age at diagnosis

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: S281

description: Reanalysis of GSM526086

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S160

description: Reanalysis of GSM525874


title: S277

description: Reanalysis of GSM526082


title: S275

description: Reanalysis of GSM526080


title: S272

description: Reanalysis of GSM526077


title: breast_invasive ductal carcinoma_4508

description: mRNA profile_GSM1029709

tag: gender

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4511

description: mRNA profile_GSM1029712

tag: age at diagnosis

tag: treatment type

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4504

description: mRNA profile_GSM1029707

tag: gender

tag: tissue

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

value: EMC


title: breast_invasive ductal carcinoma_4506

description: mRNA profile_NA

tag: age at diagnosis

tag: disease-free interval (in months)

tag: disease progression (event)

tag: institute biomaterial

tag: barcode tlda_microrna card a

tag: barcode tlda_microrna card b


title: breast_invasive ductal carcinoma_4505

description: mRNA profile_GSM1029708

tag: treatment type

value: letrozole

tag: age at start therapy

tag: menopausal status at start therapy

tag: location

tag: progesterone receptor status

tag: her2 status


title: breast_invasive ductal carcinoma_4503

description: mRNA profile_GSM1029706

tag: gender

tag: tissue

tag: disease relapse (event)

tag: time-to-progression (in months)

tag: brb code 84 patients selection

tag: affiliated with series gse41994 mrna sample id


title: breast_invasive ductal carcinoma_4501

description: mRNA profile_GSM1029704

tag: age at diagnosis

tag: tumor type

tag: grade

tag: estrogen receptor status

tag: pik3ca genotype

tag: disease-free interval (in months)


title: S268

description: Reanalysis of GSM526073

tag: metastasis

tag: time

tag: paired rna-seq

tag: cinsarc

tag: material support


title: S286

description: Reanalysis of GSM526091


title: S271

description: Reanalysis of GSM526076


title: S269

description: Reanalysis of GSM526074


title: S267

description: Reanalysis of GSM526072


title: S270

description: Reanalysis of GSM526075


title: S265

description: Reanalysis of GSM526070


title: S266

description: Reanalysis of GSM526071


title: S264

description: Reanalysis of GSM526069


title: S263

description: Reanalysis of GSM526068


title: S262

description: Reanalysis of GSM526067


title: Type II Enteropathy-associated T-cell lymphoma Sample 065T

city: Singapore

first: Sanjanaa

last: Nagarajan

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression profiling of Type II Enteropathy-associated T-cell lymphoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF was used to reannotate the probes (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.0.0/entrezg.asp).

label_protocol: Standard Affymetrix protocol, 250ug of RNAeasy-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.

tag: tissue status

value: Tumor

tag: tcr coreceptor


title: S259

description: Reanalysis of GSM526064

value: Yes


title: Type II Enteropathy-associated T-cell lymphoma Sample 066T

tag: tissue


title: S146

description: Reanalysis of GSM525858


title: S260

description: Reanalysis of GSM526065


title: S261

description: Reanalysis of GSM526066


title: Type II Enteropathy-associated T-cell lymphoma Sample 064T


title: S144

description: Reanalysis of GSM525856


title: S141

description: Reanalysis of GSM525853


title: S143

description: Reanalysis of GSM525855


title: S147

description: Reanalysis of GSM525859


title: S258

description: Reanalysis of GSM526063


title: Type II Enteropathy-associated T-cell lymphoma Sample 063T


title: S140

description: Reanalysis of GSM525852


title: S142

description: Reanalysis of GSM525854


title: S139

description: Reanalysis of GSM525850


title: Tet3 induced neurons 1dpi

city: Beijing

first: Juan

last: Zhang

address: Beijing 100101, China

department: Institute of Zoology

institute: Chinese Academy of Sciences

description: Gene expression in induced neurons by Tet3 1 dpi

hyb_protocol: Kit and Instruments:Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):10X Blocking Agent 25X Fragmentation Buffer. 2x GEx Hybridization Buffer HI-RPM. Hybridization Chamber, stainless (Agilent p/n G2534A). Hybridization Chamber gasket slides (Agilent p/n G2534-60003) Hybridization oven (Agilent p/n G2545A). Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)

scan_protocol: Instrument: Agilent Microarray Scanner (Agilent p/n G2565BA). Procedure: 1. Assemble the slides into an slide holder. 2. Place assembled slide holders into scanner carousel.3. Verify scan settings for one-color scans. Parameters  Scan region Scan Area (61 x 21.6 mm)   Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Tet3 induced neuons, 1dpi

label_protocol: Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442).RNeasy Mini Kit (Qiagen p/n 74104) NanoDrop ND-1000

extract_protocol: Total RNAs were obtained from the indicated samples using TRIzol Reagent (Invitrogen, 15596-018) referring to the instruction manual.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The E13.5 ICR mouse embryos were employed to get the primary mouse embryonic fibroblasts (MEFs). MEFs were transduced with adenoviral supernatants in the presence of 4 mg/ml polybrene for 8 hours and then the clusters were refreshed by intermediate medium (low glucose with 5% FBS). And on the day 2, the same performance was repeated as that of day 1. And on the day3 and day5 after second infection, half-amount of the cell culture medium was switched to neuronal medium with 20 μM Forskolin (Sigma, F6886). After day 5, half cell culture medium was refreshed with neuronal medium every other day until the cells were ready for the sequent experiments. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: cell

value: induced neuons

tag: age

tag: treatment

value: induced by Tet3 1 dpi


title: Primary neurons

description: Gene expression in primary neurons

source_name: mouse embryonic primary neurons

value: primary neurons


title: Tet3 induced neurons 7dpi

description: Gene expression in induced neurons by Tet3 7 dpi

source_name: Tet3 induced neuons, 7dpi

value: induced by Tet3 7 dpi


title: mouse embryonic fibroblasts

description: Gene expression in mouse embryonic fibroblasts

source_name: mouse embryonic fibroblasts

value: embryonic fibroblasts


title: S138

description: Reanalysis of GSM525849

value: Frozen tumor


title: S137

description: Reanalysis of GSM525848


title: Tet3 induced neurons 3dpi

description: Gene expression in induced neurons by Tet3 3 dpi

source_name: Tet3 induced neuons, 3dpi

value: induced by Tet3 3 dpi


title: Tet3 induced neurons 5dpi

description: Gene expression in induced neurons by Tet3 5 dpi

source_name: Tet3 induced neuons, 5dpi

value: induced by Tet3 5 dpi


title: Tet2+MBD3L2

city: Shanghai

first: Wei

last: Li

address: DongAn Road 130

institute: FuDan University

description: Gene expression after Tet2 and MBD3L2 over-experssion in HEK293T cells

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 3 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).

label_protocol: Ech sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HEK293T cells were cultured in DMEM + serum at 37°C / 5% CO2

extract_protocol: Total RNA was extracted and RNA quality was evaluated using NanoDrop ND-1000 and Denaturing Agarose Gel Electrophoresis. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre)

treatment_protocol: Empty vector,HA-Tet2 or HA-MBD3L2 were transfected simultaneously or individually in HEK 293T cell line.

tag: cell line

tag: genotype/variation

value: Tet2 and MBD3L2 over-expression


title: S136

description: Reanalysis of GSM525847

value: No


title: Control

description: Gene expression after empty vector over-experssion in HEK293T cells

value: empty vector over-expression


title: S135

description: Reanalysis of GSM525846


title: S257

description: Reanalysis of GSM526062


title: MBD3L2

description: Gene expression after MBD3L2 over-experssion in HEK293T cells

value: MBD3L2 over-expression


title: S255

description: Reanalysis of GSM526060


title: S132

description: Reanalysis of GSM525843


title: S134

description: Reanalysis of GSM525845


title: S131

description: Reanalysis of GSM525842


title: S130

description: Reanalysis of GSM525841


title: S254

description: Reanalysis of GSM526059


title: S133

description: Reanalysis of GSM525844


title: S256

description: Reanalysis of GSM526061


title: 10-day iPSC

city: boston

first: Marti

middle: Anne

last: Borkent

state: Massachusetts

address: 185 cambridge street

department: Center for Molecular Biology

institute: MGH Boston

description: iPSC

hyb_protocol: Hybridization was done by the Partners Center for Personalized Genetic Medicine.

scan_protocol: Scanning was done by the Partners Center for Personalized Genetic Medicine.

data_processing: Data was processed using Expression Console software, the processing algorithm was RMA

source_name: 10-day iPSC derived upon Sumo2 KD

label_protocol: Labeling was done by the Partners Center for Personalized Genetic Medicine.

growth_protocol: Cells were grown in ESC media containing 20% FBS

extract_protocol: RNA (Dnase treated) was islolated and extracted using the Rneasy Mini Kit (Qiagen).

treatment_protocol: repMEFs were treated with ascorbic acid and doxycycline

tag: strain

tag: gender

value: pooled male and female

tag: cell type

value: stable iPSC clones derived from Sumo2 knockdown fibroblasts

value: day 10


title: S129

description: Reanalysis of GSM525839


title: S128

description: Reanalysis of GSM525838


title: S127

description: Reanalysis of GSM525837


title: S123

description: Reanalysis of GSM525833


title: S253

description: Reanalysis of GSM526058


title: S124

description: Reanalysis of GSM525834


title: Day 6 repMEFs- Sumo2 knockdown

description: Bulk reprogramming culture, day 6 since doxycycline induction

source_name: Day 6 repMEFs- Sumo2 knockdown

value: reprogrammable MEF

tag: protocol

value: Sumo2 knockdown

value: day 6


title: S120

description: Reanalysis of GSM525830

tag: metastasis


title: 38hr iPSC

description: iPSC

source_name: 38hr iPSC derived upon Sumo2 KD

tag: time

value: hour 38


title: Day 6 repMEFs- Firefly knockdown

source_name: Day 6 repMEFs- Firefly knockdown

value: Firefly knockdown


title: S126

description: Reanalysis of GSM525836

tag: paired rna-seq


title: S125

description: Reanalysis of GSM525835

value: Yes

tag: cinsarc