title: 9days w/o acetic acid-treated plants, biological rep2

description:
2w_W9_2
Gene expression data from 9d water treated Col-0 plants.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-021169 Arabidopsis 4 Oligo Microarray (V4) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

source_name: Water-treated Arabidopsis Col-0 plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in soil for 2 weeks under 16-h-light/8-h-dark.

extract_protocol: The total RNA was extracted from the aerial parts of plants before or after drought treatment using Plant RNA Purification Reagent (Invitrogen) according to manufacturer's instruction.

treatment_protocol: The plants were treated with or without acetic acid for 9days, followed by 6, 9, or 12 days of drought treatment.

value: 9d water


title: 9days acetic acid and subsequent 12days drought-treated plants, biological rep1

status: Public on Apr 29 2017

type: RNA

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description:
2w_A9_D12_1
Gene expression data from 9d acetic acid and subsequent 12d drought treated Col-0 plants.

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

data_processing: The scanned images were analyzed with GeneSpring (Agilent). Percentile normalization (75 percentile) was performed for each chip.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Acetic acid and subsequent 12d drought-treated Arabidopsis Col-0 plants

tag: ecotype

tag: tissue

value: aerial parts

tag: treatment


title: 9days w/o acetic acid and subsequent 6days drought-treated plants, biological rep1

description:
2w_W9_D6_1
Gene expression data from 9d water and subsequent 6d drought treated Col-0 plants.

source_name: Water and subsequent 6d drought-treated Arabidopsis Col-0 plants

value: 9d water and subsequent 6d drought


title: 9days w/o acetic acid and subsequent 12days drought-treated plants, biological rep2

description:
2w_W9_D12_2
Gene expression data from 9d water and subsequent 12d drought treated Col-0 plants.

source_name: Water and subsequent 12d drought-treated Arabidopsis Col-0 plants

value: 9d water and subsequent 12d drought


title: 9days w/o acetic acid and subsequent 12days drought-treated plants, biological rep1

description:
2w_W9_D12_1
Gene expression data from 9d water and subsequent 12d drought treated Col-0 plants.


title: axe1-5, 6days_drought-treated plants, biological rep2

description:
axe1-5_drought_6d_2
Gene expression data from 6d drought-treated axe1-5 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer' s instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-015059 Arabidopsis Ver.3 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

source_name: Drought-treated Arabidopsis axe1-5 plants, 6 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in soil for 3 weeks under 16-h-light/8-h-dark.

extract_protocol: The total RNA was extracted from the above-ground plants before or after drought treatment using Plant RNA Purification Reagent (Invitrogen) according to manufacturer's instruction.

treatment_protocol: The plants were treated with or without 6, 9, 12, 15 days of drought treatment by withholding water supply.

value: Columbia

tag: line

tag: genotype

value: drought

tag: treatment duration

value: 6 days


title: 9days acetic acid and subsequent 12days drought-treated plants, biological rep2

description:
2w_A9_D12_2
Gene expression data from 9d acetic acid and subsequent 12d drought treated Col-0 plants.


title: axe1-5, 15days_drought-treated plants, biological rep2

description:
axe1-5_drought_15d-2
Gene expression data from 15d drought-treated axe1-5 plants

source_name: Drought-treated Arabidopsis axe1-5 plants, 15 days

value: 15 days


title: axe1-5, 6days_drought-treated plants, biological rep3

description:
axe1-5_drought_6d_3
Gene expression data from 6d drought-treated axe1-5 plants


title: axe1-5, Untreated plants, biological rep3

description:
axe1-5_control_3
Gene expression data from untreated axe1-5 plants

source_name: Untreated Arabidopsis axe1-5 plants


title: 9days w/o acetic acid and subsequent 9days drought-treated plants, biological rep2

description:
2w_W9_D9_2
Gene expression data from 9d water and subsequent 9d drought treated Col-0 plants.

source_name: Water and subsequent 9d drought-treated Arabidopsis Col-0 plants

value: 9d water and subsequent 9d drought


title: axe1-5, 6days_drought-treated plants, biological rep1

description:
axe1-5_drought_6d_1
Gene expression data from 6d drought-treated axe1-5 plants


title: axe1-5, 15days_drought-treated plants, biological rep1

description:
axe1-5_drought_15d-1
Gene expression data from 15d drought-treated axe1-5 plants


title: 9days w/o acetic acid and subsequent 12days drought-treated plants, biological rep3

description:
2w_W9_D12_3
Gene expression data from 9d water and subsequent 12d drought treated Col-0 plants.


title: 9days w/o acetic acid and subsequent 6days drought-treated plants, biological rep3

description:
2w_W9_D6_3
Gene expression data from 9d water and subsequent 6d drought treated Col-0 plants.


title: axe1-5, 9days_drought-treated plants, biological rep3

description:
axe1-5_drought_9d-3
Gene expression data from 9d drought-treated axe1-5 plants

source_name: Drought-treated Arabidopsis axe1-5 plants, 9 days

value: 9 days


title: axe1-5, 9days_drought-treated plants, biological rep1

description:
axe1-5_drought_9d-1
Gene expression data from 9d drought-treated axe1-5 plants


title: 9days w/o acetic acid-treated plants, biological rep3

description:
2w_W9_3
Gene expression data from 9d water treated Col-0 plants.


title: 9days w/o acetic acid and subsequent 9days drought-treated plants, biological rep3

description:
2w_W9_D9_3
Gene expression data from 9d water and subsequent 9d drought treated Col-0 plants.


title: 9days acetic acid and subsequent 12days drought-treated plants, biological rep3

description:
2w_A9_D12_3
Gene expression data from 9d acetic acid and subsequent 12d drought treated Col-0 plants.


title: axe1-5, Untreated plants, biological rep2

description:
axe1-5_control_2
Gene expression data from untreated axe1-5 plants


title: 9days w/o acetic acid-treated plants, biological rep1

description:
2w_W9_1
Gene expression data from 9d water treated Col-0 plants.


title: axe1-5, 12days_drought-treated plants, biological rep2

description:
axe1-5_drought_12d-2
Gene expression data from 12d drought-treated axe1-5 plants

source_name: Drought-treated Arabidopsis axe1-5 plants, 12 days

value: 12 days


title: NT_V, biological rep 1

status: Public on Apr 30 2017

city: Pittsburgh

first: Rebecca

middle: Jean

last: Watters

state: PA

address: 204 Craft Avenue

country: USA

institute: University of Pittsburgh

description: Gene expression data from U2OS-ER-alpha cell lines, EtOH treatment control, non targeting siRNA

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human 1.0 ST Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Affymetrix CEL files of the microarray experiments were processed using the “affy” package and differential expression was assessed using the “limma” package of the Bioconductor Suite (http://www.bioconductor.org/).
The threshold for detecting differential expression was set at p-value < 0.01 and q-value < 0.05.

label: biotin

organism: Homo sapiens

source_name: U2OS-ER-alpha cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: U2OS-ER-alpha cell lines were grown and maintained in phenol red free IMEM with 5% charcoal stripped serum.

extract_protocol: RNA was isolated using Qiagen RNeasy kit

treatment_protocol: Cells were treated with siRNA that was either targeting SRC-1 or a non-targeting control.  Both of these groups were then treated with either ethanol vehicle control or 17-B-estradiol for 3 hours.

value: bone

tag: cell line

tag: sirna

value: non-targeting control siRNA

value: Ethanol


title: 9days w/o acetic acid and subsequent 6days drought-treated plants, biological rep2

description:
2w_W9_D6_2
Gene expression data from 9d water and subsequent 6d drought treated Col-0 plants.


title: 9days w/o acetic acid and subsequent 9days drought-treated plants, biological rep1

description:
2w_W9_D9_1
Gene expression data from 9d water and subsequent 9d drought treated Col-0 plants.


title: 9days acetic acid and subsequent 9days drought-treated plants, biological rep3

description:
2w_A9_D9_3
Gene expression data from 9d acetic acid and subsequent 9d drought treated Col-0 plants.

source_name: Acetic acid and subsequent 9d drought-treated Arabidopsis Col-0 plants


title: 9days acetic acid and subsequent 9days drought-treated plants, biological rep2

description:
2w_A9_D9_2
Gene expression data from 9d acetic acid and subsequent 9d drought treated Col-0 plants.


title: 9days acetic acid-treated plants, biological rep3

description:
2w_A9_3
Gene expression data from 9d acetic acid-treated Col-0 plants.

source_name: Acetic acid-treated Arabidopsis Col-0 plants

value: 9d acetic acid


title: 9days acetic acid and subsequent 6days drought-treated plants, biological rep3

description:
2w_A9_D6_3
Gene expression data from 9d acetic acid and subsequent 6d drought treated Col-0 plants.

source_name: Acetic acid and subsequent 6d drought-treated Arabidopsis Col-0 plants


title: axe1-5, Untreated plants, biological rep1

description:
axe1-5_control_1
Gene expression data from untreated axe1-5 plants


title: 9days acetic acid and subsequent 6days drought-treated plants, biological rep2

description:
2w_A9_D6_2
Gene expression data from 9d acetic acid and subsequent 6d drought treated Col-0 plants.


title: 9days acetic acid-treated plants, biological rep1

description:
2w_A9_1
Gene expression data from 9d acetic acid-treated Col-0 plants.


title: Untreated plants, biological rep1

description:
2w_1
Gene expression data from untreated Col-0 plants.

source_name: Untreated Arabidopsis Col-0 plants


title: 9days acetic acid and subsequent 6days drought-treated plants, biological rep1

description:
2w_A9_D6_1
Gene expression data from 9d acetic acid and subsequent 6d drought treated Col-0 plants.


title: Untreated plants, biological rep2

description:
2w_2
Gene expression data from untreated Col-0 plants.


title: DR5, 12days_drought-treated plants, biological rep2

description:
DR5_drought_12d-2
Gene expression data from 12d drought-treated DR5 plants

source_name: Drought-treated Arabidopsis DR5 plants, 12 days

value: wild-type


title: DR5, 15days_drought-treated plants, biological rep2

description:
DR5_drought_15d-2
Gene expression data from 15d drought-treated DR5 plants

source_name: Drought-treated Arabidopsis DR5 plants, 15 days


title: 9days acetic acid-treated plants, biological rep2

description:
2w_A9_2
Gene expression data from 9d acetic acid-treated Col-0 plants.


title: 9days acetic acid and subsequent 9days drought-treated plants, biological rep1

description:
2w_A9_D9_1
Gene expression data from 9d acetic acid and subsequent 9d drought treated Col-0 plants.


title: Untreated plants, biological rep3

description:
2w_3
Gene expression data from untreated Col-0 plants.


title: DR5, 12days_drought-treated plants, biological rep1

description:
DR5_drought_12d-1
Gene expression data from 12d drought-treated DR5 plants


title: DR5, 9days_drought-treated plants, biological rep3

description:
DR5_drought_9d-3
Gene expression data from 9d drought-treated DR5 plants

source_name: Drought-treated Arabidopsis DR5 plants, 9 days


title: DR5, 15days_drought-treated plants, biological rep1

description:
DR5_drought_15d-1
Gene expression data from 15d drought-treated DR5 plants


title: DR5, 15days_drought-treated plants, biological rep3

description:
DR5_drought_15d-3
Gene expression data from 15d drought-treated DR5 plants


title: DR5, 12days_drought-treated plants, biological rep3

description:
DR5_drought_12d-3
Gene expression data from 12d drought-treated DR5 plants


title: DR5, 9days_drought-treated plants, biological rep2

description:
DR5_drought_9d-2
Gene expression data from 9d drought-treated DR5 plants


title: MCF7_MT3NT_3

city: Grand Forks

first: Donald

last: Sens

state: ND

address: 1301 North Columbia Road

department: Pathology

institute: University of North Dakota

description: MCF7 cell transfected with MT3 with an N-terminal mutation where the two essential prolines were converted to threonines

hyb_protocol: standard as recommended by Illumina

scan_protocol: standard as recommended by Illumina

data_processing: Raw signal intensities were obtained and normalized by the rank invariant algorithm using Illumina Beadstudio data analysis software.

source_name: MCF7 breast cancer cells

label_protocol: standard as recommended by Illumina

growth_protocol: The MCF7 cell line was obtained from the American Type Culture Collection (Rockville, MD), grown in Dulbecco's Modified Eagles' medium supplemented with 5% (v/v) fetal calf serum, and routinely passaged at a 1:4 ratio upon attaining confluence.

extract_protocol: The Qiagen Rneasy Mini Kit was used to prepare RNA samples.

treatment_protocol: The MCF7 cells were stably transfected with the gene construct.

tag: gene construct


title: DR5, 6days_drought-treated plants, biological rep2

description:
DR5_drought_6d_2
Gene expression data from 6d drought-treated DR5 plants

source_name: Drought-treated Arabidopsis DR5 plants, 6 days


title: MCF7_MT3CT_2

description: MCF7 cell transfected with MT3 with a C-terminal deletion where the unique EAAEAE C-terminal sequence was deleted.


title: MCF7_MT1ENT_3

description: MCF7 cell transfected with MT1E where the MT3 N-terminal sequence was inserted into the corresponding position of MT1E.


title: MCF7_MT3CT_1

value: MT3 with a C-terminal deletion where the unique EAAEAE C-terminal sequence was deleted


title: MCF7_MT1ECT_1

description: MCF7 cell transfected with MT1E where the C-terminal sequence EAAEAE of MT3 was inserted into the corresponding position of MT1E


title: MCF7_blank_3

description: MCF7 cell transfected with blank vector.

value: blank


title: MCF7_MT3NT_2

description: MCF7 cell transfected with MT3 with an N-terminal mutation where the two essential prolines were converted to threonines.


title: MCF7_MT3NT_1

value: MT3 with an N-terminal mutation where the two essential prolines were converted to threonines


title: DR5, 6days_drought-treated plants, biological rep3

description:
DR5_drought_6d_3
Gene expression data from 6d drought-treated DR5 plants

value: aerial parts


title: MCF7_MT1ECT_2

description: MCF7 cell transfected with MT1E where the C-terminal sequence EAAEAE of MT3 was inserted into the corresponding position of MT1E.


title: MCF7_blank_2


title: MCF7_MT3_2

description: MCF7 cell transfected with MT3.


title: MCF7_MT3CT_3


title: MCF7_blank_1


title: DR5, 6days_drought-treated plants, biological rep1

description:
DR5_drought_6d_1
Gene expression data from 6d drought-treated DR5 plants


title: MCF7_MT1ENT_2

value: MT1E where the MT3 N-terminal sequence was inserted into the corresponding position of MT1E


title: DR5, Untreated plants, biological rep2

description:
DR5_control_2
Gene expression data from untreated DR5 plants

source_name: Untreated Arabidopsis DR5 plants

value: Columbia


title: DR5, Untreated plants, biological rep3

description:
DR5_control_3
Gene expression data from untreated DR5 plants


title: DR5, Untreated plants, biological rep1

description:
DR5_control_1
Gene expression data from untreated DR5 plants


title: MCF7_MT1E_2

description: MCF7 cell transfected with MT1E.


title: MCF7_MT1ECT_3

value: MT1E where the C-terminal sequence EAAEAE of MT3 was inserted into the corresponding position of MT1E


title: MCF7_MT1E_1

description: MCF7 cell transfected with MT1E.


title: MCF7_MT3_3

description: MCF7 cell transfected with MT3.


title: MCF7_MT1ENT_1


title: MCF7_MT3_1

description: MCF7 cell transfected with MT3.


title: HSC FBXL5KO biological rep2

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

description: Gene expression data from c-Kit+Sca-1+Lin–CD150+CD48– HSCs from a mouse with conditional FBXL5 knockout

hyb_protocol: All samples were hybridized to Affymetrix Mouse Transcriptome Assay 1.0 microarrays according to the manufacturer's instruction (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were analyzed with Gene Expression console (Affymetrix) using the RMA algorithm and resulting signal intensities for transcript-level data were transferred to flat files in Excel.

organism: Mus musculus

source_name: 3000 HSCs, FBXL5KO mouse

label_protocol: Single-stranded cDNA was generated from the amplified cRNA and then fragmented and labeled with WT Pico Reagent Kit (Affymetrix).

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

tag: cell type

value: c-Kit+Sca-1+Lin–CD150+CD48– bone marrow cells

value: Hematopoietic stem cells (HSCs)

tag: gender

value: Female

tag: age

value: 14 weeks of age

tag: strain

value: C57Bl/6 background


title: HSC control biological rep1

description: Gene expression data from c-Kit+Sca-1+Lin–CD150+CD48– HSCs from a control mouse

source_name: 3000 HSCs, control mouse

value: control


title: HSC FBXL5KO biological rep1


title: HSC control biological rep2


title: HSC control biological rep3


title: HSC FBXL5KO biological rep3


title: marsanne, 48 hpf, biological rep1

status: Public on Apr 28 2017

city: Flora Hill

first: M Cristina

last: Keightley

state: VIC

address: Edwards Rd

department: Rural Clinical Sciences

country: Australia

institute: La Trobe University

description: whole embryo, pooled

hyb_protocol: Samples were hybridized using WT PLUS Reagent Kit materials as per Affymetrix standard protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were analysed using Bioconductor and R packages (http://www.bioconductor.org).
ZebGene-1_0-st.pgf
ZebGene-1_0-st.mps

organism: Danio rerio

source_name: marsanne, 48 hpf embryo

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT PLUS Reagent Kit (Affymetrix)

growth_protocol: Whole embryos raised at 28 C.

extract_protocol: Mne-/- mutants were derived from a mne+/- in-cross, manually identified by phenotype and sorted from siblings at 48 hpf. Wild-type embryos were derived from a wild-type in-cross set up separately and harvested at 48 hpf. Total RNA was isolated from three biologically independent pools of WT and mne  embryos using Trizol / chloroform extraction and isopropanol precipitation and treated with RNase-free DNase (Ambion). Any remaining phenol was removed using an RNeasy micro kit (QIAGEN). Samples were provided to the Ramaciotti Centre for Genomics (University of New South Wales, Australia) for QC and processing.

treatment_protocol: not applicable

value: 48 hpf

value: whole embryo

value: marsanne (mne-/- mutant)


title: EB at day 7, treated with bexarotene

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

description:
EB_D7-BEX
Mouse embryonic stem cells after 7 days of differentiation with bexarotene treatment.

hyb_protocol: Biotin-labeled cDNA probes were hybridized for 17 hr at 45C on the Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with the Affymetrix Expression Console™ (version 1.1.2637.26569) using default analysis settings and GC-RMA normalization.

source_name: Mouse embryonic stem cells after 7 days of differentiation, bexarotene

label_protocol: cDNA were prepared from 300ng of total RNA using the Ambion WT Expression Kit, and fragmentation and labeling were performed using the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer's instructions.

growth_protocol: Mouse ES cells were grown for 2 days as hanging drops and maintained for an additional 5 days to form embryoid bodies.

extract_protocol: Total RNA was isolated using the RNeasy Minikit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Embryoid bodies were treated with 5 µM retinoic acid or 50 nM bexarotene. Untreated embryoid bodies were used as control.

value: embryoid bodies

tag: time

value: 7 days of differentiation

value: bexarotene


title: wild-type, 48 hpf, biological rep2

description: whole embryo, pooled

source_name: wild-type, 48 hpf embryo

value: wild-type


title: ActD_4OHT_1

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: The biotinylated DNA was added to a hybridization cocktail for hybridization to the Human/Mouse/Rat Gene 1.0ST Array, also containing 50pM control oligonucleotide B2, eukaryotic hybridization controls (bioB, bioC, bioD, 1,5, 5; 25 pM respectively), accordingly to the manufacturer’s protocol (Hybridization Wash and Stain Kit, Affymetrix). The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16hrs, the staining and washing, processed in the Fluidics Station 450, were carried out as recommended by Affymetrix (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: GeneChipScanner 3000 G7

data_processing: All samples (except ActD-treated samples) were background normalised, quantile normalised and summarised in R with RMA (BioConductor package 'oligo'). ActD-treated samples were background normalised and summarised in R with RMA, but not quantile normalised. Instead, distributions were normalised to median value of long-lived genes identified in Friedel et al. 2009 and Yang et al. 2003.

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent actinomycin D 1h

label_protocol: For the first cycle cDNA synthesis 100 - 300ng of total RNA was used. During the following in vitro transcription reaction cRNA was obtained and used as starting material for the second cycle cDNA synthesis. The second cycle random-primed single strand DNA synthesis resulted in a product containing incorporated deoxyuridine at predefined ratios relative to thymidine WT Expression Plus Kit (Affymetrix Inc., Santa Clara, CA, USA). Subsequently, 5.5 μg of this generated single-strand DNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled using the WT terminal labeling kit (Affymetrix catalogue #900671).

growth_protocol: HEK293∆RAF1:ER cells were cultured in DMEM complete w/o phenol red. Cells were serum starved over night before treatment.

extract_protocol: Total RNA was extraced with Trizol. RNA integrity was checked by analyzing on the 2100 Bioanalyzer. (Agilent technologies, PA, USA)

treatment_protocol: Treatment durations lasted between 30 minutes and 10 hours.


title: marsanne, 48 hpf, biological rep3

description: whole embryo, pooled


title: EB at day 7, no treatment

description:
EB_D7-CTL
Mouse embryonic stem cells after 7 days of differentiation with no treatment.

source_name: Mouse embryonic stem cells after 7 days of differentiation, untreated


title: wild-type, 48 hpf, biological rep3

description: whole embryo, pooled


title: wild-type, 48 hpf, biological rep1

description: whole embryo, pooled


title: ActD_1

source_name: HEK293∆Raf-1:ER Actinomycin D 1h


title: P9 TNF - TNFα treated (Senescence induced by TNF)_2

city: Barcelona

first: Renuka

last: Kadhaya Pillai

state: Barcelona

address: Passeig Vall d’Hebron

department: Aging Basic Research Group, Molecular Biology and Biochemistry Research Center for Nanomedicine

country: Spain

institute: CIBBIM-Nanomedicine

description:
TNF
TNFα Passage 9
middle passage
Gene expression data from senescent cells or cells treated with TNFα

hyb_protocol: The labeled samples were hybridized to Human Gene ST 1.0 Arrays (Affymetrix)

scan_protocol: The arrays were scanned in a GeneChip Scanner 3000 (Affymetrix). CEL files were generated from DAT files using GCOS software (Affymetrix).

data_processing: To generate the log2 expression estimates, overall array intensity was  normalized between arrays and the probe intensity of all probes in a probeset summarized to a single value using RMA (Robust Multichip Average) algorithm .

source_name: HUVEC (Lonza)

label_protocol: Briefly, cDNA library preparation and amplification were performed from 50ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 10 µg cDNA was subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from Clonetics/Lonza (Bazel, Switzerland) were grown in EGM-2 medium supplemented with growth factors (EGM-2 bullet kit; Clonetics/Lonza).

extract_protocol: RNA was collected using TRIzol.

treatment_protocol: Human umbilical vein endothelial cells (HUVECs) were untreated or treated with TNF (5ng/ml) for 26 days (or Passged until senecence with TNF α).

value: umbilical vein endothelial cells (HUVEC)

tag: phenotype

value: Senescent Cells (upon TNFα treatment)


title: ActD_2

source_name: HEK293∆Raf-1:ER Actinomycin D 2h


title: ActD_4

source_name: HEK293∆Raf-1:ER Actinomycin D 4h


title: P9CTRL - Middle Passage (Control)_2

description:
CTRL
Control Passage 9
middle passage
Gene expression data from control or untreated cells

value: Non-senescent Cells


title: ActD_4OHT_8

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent actinomycin D 8h


title: IGF_4h

source_name: HEK293∆Raf-1:ER IGF 4h


title: marsanne, 48 hpf, biological rep2

description: whole embryo, pooled


title: IGF_1h

source_name: HEK293∆Raf-1:ER IGF 1h


title: ActD_8

source_name: HEK293∆Raf-1:ER Actinomycin D 8h


title: EB at day 7, treated with retinoic acid

description:
EB_D7-RA
Mouse embryonic stem cells after 7 days of differentiation with RA treatment.

source_name: Mouse embryonic stem cells after 7 days of differentiation, retinoic acid

value: retinoic acid


title: EGF_2h

source_name: HEK293∆Raf-1:ER EGF 2h


title: ActD_4OHT_4

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent actinomycin D 4h


title: P8 TNF - TNFα treated (Senescence induced by TNF)

description:
TNF
TNFα Passage 8
middle passage
Gene expression data from senescent cells or cells treated with TNFα


title: EGF_4h

source_name: HEK293∆Raf-1:ER EGF 4h


title: FGF_1h

source_name: HEK293∆Raf-1:ER FGF 1h


title: ActD_4OHT_2

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent actinomycin D 2h


title: mESC at D0

description:
mESC_D0
Undifferentiated mouse embryonic stem cells.

source_name: Undifferentiated mouse embryonic stem cells, untreated

value: embryonic stem (ES) cells


title: IGF_2h

source_name: HEK293∆Raf-1:ER IGF 2h


title: FGF_4h

source_name: HEK293∆Raf-1:ER FGF 4h


title: FGF_2h

source_name: HEK293∆Raf-1:ER FGF 2h


title: EGF_1h

source_name: HEK293∆Raf-1:ER EGF 1h


title: DR5, 9days_drought-treated plants, biological rep1

description:
DR5_drought_9d-1
Gene expression data from 9d drought-treated DR5 plants

source_name: Drought-treated Arabidopsis DR5 plants, 9 days

value: Columbia

value: aerial parts

value: drought

value: 9 days


title: UT_3_n

source_name: HEK293∆Raf-1:ER New untreated replicate 3


title: UT_1_n

source_name: HEK293∆Raf-1:ER New untreated replicate 1


title: T4h_CYHX_4h

source_name: HEK293∆Raf-1:ER Tamoxifen and CYHX 4h


title: UT_2_n

source_name: HEK293∆Raf-1:ER New untreated replicate 2


title: T1h_CYHX_1h

source_name: HEK293∆Raf-1:ER Tamoxifen and CYHX 1h


title: T2h_U0126+2h

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent U0126 2h


title: T10h

source_name: HEK293∆Raf-1:ER Tamoxifen 10h


title: T3h

source_name: HEK293∆Raf-1:ER Tamoxifen 3h


title: T4h

source_name: HEK293∆Raf-1:ER Tamoxifen 4h


title: T2h_2

source_name: HEK293∆Raf-1:ER Tamoxifen 2h replicate 2


title: T2h_U0126+4h

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent U0126 4h


title: T2h_U0126+1h

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent U0126 1h


title: T6h

source_name: HEK293∆Raf-1:ER Tamoxifen 6h


title: T2h_DMSO+4h

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent DMSO 4h


title: T2h_DMSO+2h

source_name: HEK293∆Raf-1:ER Tamoxifen 2h and subsequent DMSO 2h


title: T2h_1

source_name: HEK293∆Raf-1:ER Tamoxifen 2h replicate 1


title: T0.5h

source_name: HEK293∆Raf-1:ER Tamoxifen 0.5h


title: T8h

source_name: HEK293∆Raf-1:ER Tamoxifen 8h


title: UT_3

source_name: HEK293∆Raf-1:ER Untreated replicate 3


title: UT_2

source_name: HEK293∆Raf-1:ER Untreated replicate 2


title: T2h_3

source_name: HEK293∆Raf-1:ER Tamoxifen 2h replicate 3


title: T2h_CYHX_2h

source_name: HEK293∆Raf-1:ER Tamoxifen and CYHX 2h


title: UT_1

source_name: HEK293∆Raf-1:ER Untreated replicate 1


title: Ptch tumor_rep1

city: Sioux Falls

first: Haotian

last: Zhao

state: SD

address: 2301 E. 60th St. North

department: Children's Health Research Center

institute: Sanford Research

description: Primary tumor in Ptch1+/- mice replicate 1

hyb_protocol: Standard Illumina hybridization protocol: the labeled cRNA (1500 ng) was hybridized overnight at 58°C to the Sentrix ® MouseWG-6 Expression BeadChip (>46,000 gene transcripts; Illumina, San Diego, CA, USA) according to the manufacturer's instructions. BeadChips were subsequently washed and developed with fluorolink streptavidin- Cy3 (GE Healthcare).

scan_protocol: Standard Illumina scanning protocol: BeadChips were scanned with an Illumina BeadArray Reader.

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

source_name: SHH medulloblastoma

label_protocol: Biotinylated cRNA were prepared from 500 ng RNA using the Illumina® RNA Amplification Kit from Ambion for Illumina arrays (Life Technology, USA).

extract_protocol: Primary and metastatic tumors from Math1-cre;A1G;Ptch1+/- and Ptch1+/-  mice were removed, homogenized in Trizol reagent, and flash frozen on dry ice. RNA was harvested  and treated with DNase I using Life Technologies PureLink RNA Mini Kit (Cat#12183018A) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: Ptch tumor_rep4

description: Primary tumor in Ptch1+/- mice replicate 4


title: T1h

source_name: HEK293∆Raf-1:ER Tamoxifen 1h


title: Ptch tumor_rep3

description: Primary tumor in Ptch1+/- mice replicate 3


title: Metastatic tumor_rep2

description: Metastatic tumor replicate 2

value: Metastatic tumor in Math1-cre;A1G;Ptch1+/- mice


title: Metastatic tumor_rep3

description: Metastatic tumor replicate 3


title: Primary tumor_rep3

description: Primary tumor replicate 3


title: Primary tumor_rep4

description: Primary tumor replicate 4


title: Metastatic tumor_rep4

description: Metastatic tumor replicate 4


title: Metastatic tumor_rep1

description: Metastatic tumor replicate 1


title: Ptch tumor_rep2

description: Primary tumor in Ptch1+/- mice replicate 2


title: Primary tumor_rep2

description: Primary tumor replicate 2


title: e46c14_5 xenos2 GnTn

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label: Biotin

source_name: e46c14_5 xenos2 GnTn

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: human PDO were grown in vitro in specific stem cell media and modified using the CRISPR/Cas9 technique and injected subcutaneously in BEIGE mice

extract_protocol: RNA was isolated using magnetic beads from 1000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 22 cycles.

tag: protocol

value: injected subcutaneously in BEIGE mice

tag: gfp

value: neg

tag: tomato


title: e46c3_8 xenos2 GpTn

source_name: e46c3_8 xenos2 GpTn

value: pos


title: CD34/G_Rep

city: Palermo

first: Flavia

last: Contino

address: Viale delle Scienze, Edificio 16

department: Dpt. of Biological, Chemical and Pharmaceutical Sciences and Technologies

country: Italy

institute: University of Palermo

description: Sample 2 is the technical replicate of Sample 1

hyb_protocol: For each hybridization, 825 ng of cyanine-labeled cRNA obtained from CD34/G or CD34/G+pl samples was mixed with equal amount of reverse-color cyanine labeled cRNA from Universal Human Reference RNA (Stratagene, La Jolla, CA), that was used as common reference. Hybridization and washing was performed using the in situ Hybridization Kit following the manufacturer's instructions (Agilent Technologies).

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Sure Scan, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version . 9.5.3)

data_processing: The GeneSpring software (GX software ver. 11, Agilent Technologies) was used to generate lists of selected genes and for different statistical and visualization methods.   The data from CD34/G+pl and CD34/G RNA samples were than normalized to the Universal Human Reference RNA (Stratagene, La Jolla, CA), and an initial gene list was created by filtering on confidence at p <0.01 (using as measure of confidence the t-test p-value, and as multiple testing correction the Benjamini and Hochberg false discovery rate)

source_name: RNA is composed of total RNA from 10 human cell lines

label_protocol: Fluorescently labeled cRNA targets were generated from 150 ng of total RNA in each reaction using the Low RNA Input Linear Amplification Kit and Cyanine 3- or Cyanine5-labeled CTP, according to the manufacturer’s protocol (Agilent Technologies)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: tissue

value: Cell Lines

source_name: purified CD34+ PBPC of patient 1 mobilized with G-CSF

value: Peripheral blood progenitor cell


title: e46c3_8 xenos1 GnTp

source_name: e46c3_8 xenos1 GnTp


title: e46c3_8 xenos1 GnTn

source_name: e46c3_8 xenos1 GnTn


title: Primary tumor_rep1

description: Primary tumor replicate 1


title: e46c3_8 xenos1 GpTp

source_name: e46c3_8 xenos1 GpTp


title: e46c3_8 xenos2 GnTn

source_name: e46c3_8 xenos2 GnTn


title: e46c14_5 xenos1 GnTn

source_name: e46c14_5 xenos1 GnTn


title: e46c3_8 xenos2 GnTp

source_name: e46c3_8 xenos2 GnTp


title: e46c3_8 xenos1 GpTn

source_name: e46c3_8 xenos1 GpTn


title: e46c14_5 xenos2 GnTp

source_name: e46c14_5 xenos2 GnTp


title: e46c14_5 xenos1 GpTn

source_name: e46c14_5 xenos1 GpTn


title: e46c14_5 xenos2 GpTp

source_name: e46c14_5 xenos2 GpTp


title: e46c14_5 xenos1 GnTp

source_name: e46c14_5 xenos1 GnTp


title: CD34/G

description: Sample 1 is the technical replicate of Sample 2


title: CD34/G+pl

description: Sample 3 is the technical replicate of Sample 4

source_name: purified CD34+ PBPC of patient 1 mobilized with G-CSF + Plerixafor


title: e46c3_8 xenos2 GpTp

source_name: e46c3_8 xenos2 GpTp


title: e46c14_5 xenos2 GpTn

source_name: e46c14_5 xenos2 GpTn


title: CD34/G+pl_Rep

description: Sample 4 is the technical replicate of Sample 3


title: e46c14_5 xenos1 GpTp

source_name: e46c14_5 xenos1 GpTp


title: e26.LLFGg4_3.xenoI2.N

description: 1246 2015

extract_protocol: RNA was isolated using magnetic beads from 1000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 23 cycles.


title: e26.LLFGg4_3.xenoD2.N

description: 948 2015


title: e26.LLFGg4_3.xenoD2.H

description: 945 2015


title: e26.LLFGg4_3.xenoI2.H

description: 1243 2015


title: High-GC-1

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: high methylation gastric cancer case

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

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

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

value: Male

tag: sample type

value: clinical sample

tag: disease state

value: gastric cancer


title: Bptf KD_D6

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on MO430A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

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

source_name: Bptf KD-66cl4-derived mammary gland tumors from BALB/c mice.

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

growth_protocol: 67NR and 66cl4 mouse mammary tumor cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% NEAA, 1% glutamine and 1% penicillin/streptomycin. For tumor inoculation, 4T1 cells were harvested with 0.05% trypsin-EDTA, washed twice with DMEM and resuspended in DMEM.

extract_protocol: Tumor tissues were subjected to gross histological analysis using hematoxylin and eosin staining to determine percentages of tumor, necrotic and stromal cells before total RNA extraction. If present, necrotic tissue was selected out by macrodissection. Total RNA was then extracted from frozen tumor tissues with TRI reagent and the MagMAX-96 Total RNA Isolation Kit in a MagMAX Express Magnetic Particle Processor, according to the manufacturer's instructions.

treatment_protocol: Bptf was KD in 67NR and 66cl4 cells by two different short-hairpin RNA (shRNA) sequences that were introduced in the cells using retrovirus MMLV. 1x105 67NR cells or 1x104 66cl4 cells were injected into the fourth mammary fat pad of NOD/SCID/Ifrg2r -/- (NSG) and/or in BALB/c mice and sacrificed 21 days (67NR) or 28 days (66cl4) later. Primary tumors (from Control and shRNA cells) were snap-frozen and weighed and total RNA was extracted from biological triptlicates.

value: BALB/c

value: Bptf KD-66cl4

value: mammary gland tumor


title: Low-GC-2

description: low methylation gastric cancer case


title: Bptf KD_D3


title: Low-GC-1

description: low methylation gastric cancer case

value: Female


title: Bptf KD_D2


title: Infloresence_Cyclohexamide+treatment_3h_3

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment, and cyclohexamide
Biological Replicate 3: Cyclohexamide present several plants (approx 20-25) pooled per replicate and genotype

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization

source_name: inflorescence; 3h; mock

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

value: inflorescence

tag: time after treatment (hours)

tag: treatment

value: mock

source_name: inflorescence; 3h; DEX

tag: tag

value: DEX


title: Bptf KD_D5

tag: cell line


title: Bptf KD_D4


title: Infloresence_Cyclohexamide+treatment_3h_1

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment, and cyclohexamide
Biological Replicate 1: Cyclohexamide present. several plants (approx 20-25) pooled per replicate and genotype


title: Infloresence_Cyclohexamide+treatment_3h_4

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment, and cyclohexamide
Biological Replicate 4: Cyclohexamide present. several plants (approx 20-25) pooled per replicate and genotype


title: Rep_5_0h

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment
Biological Replicate 5: several plants (approx 20-25) pooled per replicate and genotype

source_name: inflorescence; 0 h; DEX

value: 0 h

source_name: inflorescence; 0 h; mock


title: Infloresence_Cyclohexamide+treatment_3h_2

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment, and cyclohexamide
Biological Replicate 2: Cyclohexamide present. several plants (approx 20-25) pooled per replicate and genotype


title: High-GC-2

description: high methylation gastric cancer case


title: NFGM-1

description: normal fundic gland mucosa

value: normal


title: Bptf KD_D1


title: GES1_rEBV+_day-19

description: immortalised normal gastric epithelial cell

source_name: GES1 day19

value: cell line


title: NFGM-2

description: normal fundic gland mucosa


title: MKN7_rEBV+_day-17

description: low methylation gastric cancer cell

source_name: MKN7 EB+ day17


title: GES1_rEBV+_day-14

source_name: GES1 day14


title: Control_D3

source_name: 66cl4-derived mammary gland tumors from BALB/c mice.


title: GES1_rEBV+_day-17

source_name: GES1 day17


title: Control_D2


title: MKN7_rEBV+_day-1

description: low methylation gastric cancer cell

source_name: MKN7 EB+ 0hr


title: Rep_5_4h

source_name: inflorescence; 4 h; DEX

value: 4 h

source_name: inflorescence; 4 h; mock


title: Control_D1


title: Bptf KD_C6

source_name: Bptf KD-67NR-derived mammary gland tumors from BALB/c mice.

value: Bptf KD-67NR


title: GES1_rEBV+_day-8

source_name: GES1 day8


title: Rep_5_12h

source_name: inflorescence; 12 h; DEX

source_name: inflorescence; 12 h; mock


title: Rep_5_8h

source_name: inflorescence; 8 h; DEX

value: 8 h

source_name: inflorescence; 8 h; mock


title: GES1_rEBV+_day-11

source_name: GES1 day11


title: GES1_rEBV+_day-23

source_name: GES1 day23


title: MKN7_rEBV+_day-8

description: low methylation gastric cancer cell

source_name: MKN7 EB+ day8


title: MKN7_WT

description: low methylation gastric cancer cell

source_name: MKN7 P2


title: Bptf KD_C4


title: GES1_rEBV+_day-28

source_name: GES1 day28


title: GES1_rEBV+_day-21

source_name: GES1 day21


title: Rep_4_0h

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment
Biological Replicate 4: several plants (approx 20-25) pooled per replicate and genotype


title: Rep_5_2h

source_name: inflorescence; 2 h; DEX

value: 2 h

source_name: inflorescence; 2 h; mock


title: GES1_WT

source_name: GES1 WT

value: Male


title: Rep_2_12h

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment
Biological Replicate 2: several plants (approx 20-25) pooled per replicate and genotype

source_name: inflorescence; 4 h; DEX


title: Rep_1_0h

description:
Arabidopsis infloresence after treatment with solution containing dexamethasone or a mock treatment
Biological Replicate 1: several plants (approx 20-25) pooled per replicate and genotype

source_name: inflorescence; 0 h; DEX

source_name: inflorescence; 0 h; mock


title: MKN7_rEBV+_day-28

description: low methylation gastric cancer cell

source_name: MKN7 EB+ day28


title: Bptf KD_C3

source_name: Bptf KD-67NR-derived mammary gland tumors from BALB/c mice.


title: Rep_2_8h


title: Bptf KD_C1


title: Control_C2

source_name: 67NR-derived mammary gland tumors from BALB/c mice.


title: Rep_2_2h

source_name: inflorescence; 12 h; mock

source_name: inflorescence; 12 h; DEX


title: Rep_2_0h

source_name: inflorescence; 8 h; mock

source_name: inflorescence; 8 h; DEX


title: Control_C3


title: Bptf KD_C5


title: Rep_4_8h

source_name: inflorescence; 4 h; mock


title: Rep_4_12h


title: Bptf KD_B6

source_name: Bptf KD-66cl4-derived mammary gland tumors from NSG mice.

value: NSG


title: Rep_2_4h


title: Control_C1


title: Bptf KD_B5


title: Rep_4_4h


title: Bptf KD_B2


title: Bptf KD_B3


title: Bptf KD_B4


title: Bptf KD_C2


title: Rep_1_4h


title: Rep_1_12h


title: Rep_4_2h


title: Bptf KD_B1


title: Control_B3

source_name: 66cl4-derived mammary gland tumors from NSG mice.


title: Rep_1_2h


title: Control_B1


title: Bptf KD_A5

source_name: Bptf KD-67NR-derived mammary gland tumors from NSG mice.


title: Bptf KD_A6


title: Bptf KD_A1


title: Bptf KD_A4


title: Bptf KD_A2


title: Control_A3

source_name: 67NR-derived mammary gland tumors from NSG mice.


title: untreated_Chelerythrine_Replicate3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using GeneSpring GX 12.5 software (Agilent Technologies Inc, Santa Clara, USA).

source_name: HeLa cell line

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

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

value: HeLa

tag: agent


title: Control_A1


title: treated_Chelerythrine_Replicate2

value: Chelerythrine


title: Control_B2


title: Control_A2


title: treated_Chelerythrine_Replicate3


title: Bptf KD_A3


title: untreated_Chelerythrine_Replicate1


title: treated_Chelerythrine_Replicate1


title: kidney biopsy TR10

status: Public on Apr 27 2017

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: kidney

tag: type

value: Technical replicate:Technical replicate


title: kidney biopsy TR12


title: untreated_Chelerythrine_Replicate2


title: 3_HA9+Meis1_KOmiR155_III

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

description: Mouse cell culture

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing:
Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.mps

source_name: bone marrow cells, HA9+Meis1_KOmiR155

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Qiagens RNeasy Plus mini kit

tag: Sex

value: Female

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow

tag: developmental stage

value: Progenitor cells

tag: cell type

value: Primary bone marrow culture

tag: genetic modification

value: Transduced with MSCV construct

tag: genotype/variation

value: Overexpression of HOXA9 and Meis1 in miR-155 KO

tag: growth condition

value: DMEM 15% FCS, IL3, SCF, IL6


title: 5_HA9+Meis1_WT_I

description: Mouse cell culture

source_name: bone marrow cells, HA9+Meis1_WT

tag: strain

tag: age

value: Overexpression of HOXA9 and Meis1


title: 1_HA9+Meis1_KOmiR155_I

description: Mouse cell culture

tag: tissue


title: kidney biopsy TR9


title: 4_HA9+Meis1_WT_I

description: Mouse cell culture


title: 6_HA9+Meis1_WT_I

description: Mouse cell culture


title: kidney biopsy TR8


title: kidney biopsy TR11


title: 2_HA9+Meis1_KOmiR155_II

description: Mouse cell culture


title: kidney biopsy TR7


title: kidney biopsy TR3


title: kidney biopsy TR5


title: kidney biopsy TMn12

value: Technical replicate:Main


title: kidney biopsy TR6


title: kidney biopsy TR2


title: kidney biopsy TMn10


title: kidney biopsy TMn9


title: kidney biopsy TMn3


title: kidney biopsy TMn5


title: kidney biopsy TR4


title: kidney biopsy TMn11


title: kidney biopsy TR1


title: kidney biopsy TMn7


title: kidney biopsy TMn6


title: kidney biopsy TMn8


title: kidney biopsy TMn1


title: kidney biopsy TMn4


title: kidney biopsy BR31


title: kidney biopsy BR33


title: kidney biopsy BR29


title: kidney biopsy TMn2


title: kidney biopsy BR32


title: kidney biopsy BR23


title: kidney biopsy BR24


title: kidney biopsy BR36


title: kidney biopsy BR34


title: kidney biopsy BR28


title: kidney biopsy BR27


title: kidney biopsy BR22


title: kidney biopsy BR35


title: kidney biopsy BR17


title: kidney biopsy BR20


title: kidney biopsy BR21


title: kidney biopsy BR25


title: kidney biopsy BR16


title: kidney biopsy BR13


title: kidney biopsy BR14


title: kidney biopsy BR18


title: Rep_1_8h

value: inflorescence

value: 8 h

value: DEX

value: mock


title: kidney biopsy BR11


title: kidney biopsy BR37


title: kidney biopsy BR12


title: kidney biopsy BR9


title: kidney biopsy BR6


title: kidney biopsy BR15


title: kidney biopsy BR4


title: kidney biopsy BR8


title: kidney biopsy BR3


title: kidney biopsy BR7


title: kidney biopsy BR26


title: kidney biopsy BR5


title: kidney biopsy BR10


title: kidney biopsy BMn36

value: Biological replicate:Main


title: kidney biopsy BR2

value: kidney


title: kidney biopsy BR1


title: kidney biopsy BMn37


title: kidney biopsy BMn30


title: kidney biopsy BMn35


title: kidney biopsy BMn32


title: kidney biopsy BMn29


title: kidney biopsy BMn31


title: kidney biopsy BMn22


title: kidney biopsy BMn19


title: kidney biopsy BMn27


title: kidney biopsy BMn21


title: kidney biopsy BMn25


title: kidney biopsy BMn33


title: kidney biopsy BMn26


title: kidney biopsy BMn20


title: kidney biopsy BMn13


title: kidney biopsy BMn28


title: kidney biopsy BMn34


title: kidney biopsy BMn16


title: kidney biopsy BMn23


title: kidney biopsy BMn17


title: kidney biopsy BMn12


title: kidney biopsy BMn24


title: kidney biopsy BMn15


title: kidney biopsy BMn18


title: kidney biopsy BMn14


title: kidney biopsy BMn8


title: kidney biopsy BMn10


title: kidney biopsy BR30


title: kidney biopsy C26

value: Cortex


title: kidney biopsy BMn1


title: kidney biopsy BMn2


title: kidney biopsy C29


title: kidney biopsy C22


title: kidney biopsy C25


title: kidney biopsy BMn3


title: kidney biopsy C27


title: kidney biopsy C19


title: kidney biopsy C21


title: kidney biopsy C28


title: kidney biopsy C24


title: kidney biopsy BMn5


title: HOXA9+MEIS1DHD w4 #1 mi

description: 11.  HOXA9+MEIS1DHD w4 #1 mi

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials  Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes.  Transfer 130l of hyb solution to each array, then tape holes.  Hybridize 16-18 hours at 48° at 60rpm Fluidics washing is FS450_0002

data_processing: Data were processed using Expression Console software. Probe intensities, gene level expression were RMA summarized and then quantile normalized.

source_name: Mouse cell culture

label_protocol: The RNA molecule is poly (A) tailed and then labelled with biotin 3 DNA using the Flash Tag Ligation mix from Affymetrix.

growth_protocol: DMEM 15% FCS, IL3, SCF, IL6

extract_protocol: Qiagens MicroRNeasy according to the manufacturer's protocol

value: Female

value: Overexpression of HOXA9 and MEIS1dHD


title: kidney biopsy C16


title: HOXA9+MEIS1DHD w4 #2 mi

description: 12.  HOXA9+MEIS1DHD w4 #2 mi

value: Cells from 12 week old 5-FU treated mice

value: Bone marrow


title: kidney biopsy C18


title: kidney biopsy BMn7


title: kidney biopsy C20


title: kidney biopsy C23


title: kidney biopsy BMn9


title: HOXA9+MEIS1DHD w3 #2 mi

description: 10.  HOXA9+MEIS1DHD w3 #2 mi

value: Progenitor cells

value: Primary bone marrow culture


title: kidney biopsy C17


title: kidney biopsy C15


title: kidney biopsy BMn4


title: kidney biopsy BMn6


title: kidney biopsy C14


title: HOXA9+MEIS1 w3 #2 mi

description: 6.    HOXA9+MEIS1 w3 #2 mi

value: Transduced with MSCV construct

value: Overexpression of HOXA9 and MEIS1


title: HOXA9+MEIS1DHD w3 #1 mi

description: 9.    HOXA9+MEIS1DHD w3 #1 mi


title: kidney biopsy C13


title: HOXA9+MEIS1 w4 #1 mi

description: 7.    HOXA9+MEIS1 w4 #1 mi


title: HOXA9+MEIS1 w4 #2 mi

description: 8.    HOXA9+MEIS1 w4 #2 mi


title: HOXA9+MEIS1 w3 #1 mi

description: 5.    HOXA9+MEIS1 w3 #1 mi


title: HOXA9+MIY w4 #2 mi

description: 4.    HOXA9+MIY w4 #2 mi

value: Overexpression of HOXA9


title: kidney biopsy C10


title: kidney biopsy C11


title: kidney biopsy C9


title: HOXA9+MIY w4 #1 mi

description: 3.    HOXA9+MIY w4 #1 mi


title: HOXA9+MIY w3 #1 mi

description: 1.    HOXA9+MIY w3 #1 mi


title: HOXA9+MIY w3 #2 mi

description: 2.    HOXA9+MIY w3 #2 mi


title: kidney biopsy C5


title: kidney biopsy C3


title: kidney biopsy C4


title: kidney biopsy C6


title: kidney biopsy C12


title: kidney biopsy C2


title: kidney biopsy C7


title: kidney biopsy C1


title: kidney biopsy C8


title: kidney biopsy BMn11


title: kidney biopsy M25

value: Medulla


title: kidney biopsy M21


title: kidney biopsy M20


title: kidney biopsy M17


title: kidney biopsy M14


title: kidney biopsy M26


title: kidney biopsy M23


title: kidney biopsy M27


title: kidney biopsy M12


title: kidney biopsy M22


title: kidney biopsy M16


title: kidney biopsy M8


title: kidney biopsy M11


title: kidney biopsy M13


title: kidney biopsy M15


title: kidney biopsy M19


title: kidney biopsy M24


title: kidney biopsy M18


title: kidney biopsy M9


city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: Hybridization for patient S5 - TUMOR

hyb_protocol: Hybridization were performed according to the Agilent miRNA Microarray Protocol (Agilent Technologies, Santa Clara, CA). Briefly, the labeled RNA samples were concentrated in a Vacuum Concentrator and prepared for hybridization by adding nuclease-free water, Hyb Spike-In solution, 10X GE Blocking Agent and 2X Hi-RPM Hybridization Buffer. 45 microliter of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human miRNA 8X60K, V19.0 Microarrays and then rotated at 20 rpm for 20 hours at 55 degrees Celsius.

scan_protocol: After hybridization, all slides were washed using Agilent Gene Expression Wash Buffers 1(at room temperature) and 2 ( at 37 degrees Celsius). The slides were immediately scanned on a Agilent Technologies G4900DA SureScan scanner at 3 micrometer resolution.

data_processing: Data were acquired with Agilent Feature Extraction 10.7.3.1 software for miRNA microarray, generating both probe-level signal intensities from all probes and summarized expression levels for each miRNA. The AgiMicroRna Bioconductor package was used to pre-process the raw data. First control, undetected probes, and outliers were filtered, then gene level expression summaries were obtained after normalization at the probe level using the RMA algorithm and quantile-normalization across samples.

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S5

label_protocol: The miRNA Microarray System with miRNA Complete Labeling and hybridization Kit (Agilent Technologies) was used according to manufacturer′s protocols. The Agilent microRNA Spike-In Kit was used to measure labeling and hybridization efficiency. Briefly, 150ng total RNA was dephosphorylated at 37 degrees Celsius for 30 min with calf intestinal phosphatase and denatured by using 100% DMSO at 100 degrees Celsius for 7 minutes. Samples were labeled with pCp-Cy3 using T4 ligase by incubation at 16 degrees Celsius for 2 hour.

extract_protocol: Representative formalin fixed paraffin embedded (FFPE) tissue samples were selected for RNA preparation. The FFPE blocks were cored with a sterile 16-gauge needle, and tumor areas showing at least 50% neoplastic cellularity were selected microscopically to enrich for neoplastic cells. Total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion Inc., Austin, TX, USA) per manufacturer’s protocol. RNA quality was evaluated using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). All analyzed samples showed 28S to 18S ratio > 1.2, an RNA Integrity Number (RIN) > 8, and detectable microRNAs.

tag: disease status

value: Tumor

tag: patient


title: kidney biopsy M7


description: Hybridization for patient S3 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S3


description: Hybridization for patient S2 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S2

value: Normal


description: Hybridization for patient S3 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S3


title: kidney biopsy M3


title: kidney biopsy M1


description: Hybridization for patient S4 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S4


title: kidney biopsy M4


description: Hybridization for patient S4 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S4


title: kidney biopsy M6


title: kidney biopsy M5


description: Hybridization for patient S8 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S8


description: Hybridization for patient S7 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S7


description: Hybridization for patient S2 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S2


title: kidney biopsy M2


description: Hybridization for patient S8 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S8


description: Hybridization for patient S5 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S5


description: Hybridization for patient S6 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S6


description: Hybridization for patient S1 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S1


description: Hybridization for patient S6 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S6


description: Hybridization for patient S1 - NORMAL

source_name: Hybridization for  Xp11 renal cell carcinoma sample: NORMAL.S1


title: 500 mGy: PN1-4: MB-24

status: Public on Apr 26 2017

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 40 hours at 65°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 (Protocol v.7.1) in an ozone-depleted hood.

scan_protocol: The slides were scanned in an Agilent DNA Microarray scanner (G2565CA)

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for computing ratios

source_name: Medulloblastoma

label_protocol: 300 ng of RNase-treated DNA (test or reference) was labelled using the Agilent SureTag DNA labeling kit (Protocol v.7.1), following all instructions for a 8x60K array.

extract_protocol: DNA was extracted from frozen medulloblastoma tissue and ear skin tissue using a Maxwell 16 Tissue DNA Purification Kit on a Maxwell 16 Instrument (Promega)

treatment_protocol: A portion of each medulloblastoma tumour mass taken at autopsy, and normal ear tissue were snap-frozen in liquid nitrogen before long-term storage at -80°C.

value: Medulloblastoma

value: C3H/HeNcrlCrlj x B6.129-Ptch1tm1Zim/Cnrm (F1)

source_name: Ear

value: Ear


title: kidney biopsy BR19

source_name: kidney biopsy

value: kidney


title: 500 mGy: PN1-4: MB-21


title: kidney biopsy M10


title: 500 mGy: PN1-4: MB-25

value: Male


title: 500 mGy: PN1-4: MB-27

value: Female


title: 500 mGy: PN1-4: MB-23


title: 500 mGy: PN1-4: MB-20


title: 500 mGy: PN1-4: MB-22


title: 500 mGy: PN1: MB-31


title: 500 mGy: PN1: MB-21


title: 500 mGy: PN1: MB-23


title: 500 mGy: PN1: MB-33


title: 500 mGy: PN1: MB-25


description: Hybridization for patient S7 - TUMOR

source_name: Hybridization for  Xp11 renal cell carcinoma sample: TUMOR.S7


title: 500 mGy: PN1: MB-35


title: 500 mGy: PN1: MB-30


title: 500 mGy: PN1: MB-34


title: 500 mGy: PN1: MB-32


title: 500 mGy: PN1-4: MB-26


title: 500 mGy: PN1: MB-18


title: 500 mGy: PN1: MB-20


title: 500 mGy: PN1: MB-29


title: 500 mGy: PN1: MB-26


title: 500 mGy: PN1: MB-28


title: 500 mGy: PN1: MB-27


title: 500 mGy: PN1: MB-24


title: SAM618815 Nerve control

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description: SAM618815 Nerve cre.neg control jun.wt

hyb_protocol: 750 ng of labeled cRNA was fragmented and hybridized to Agilent’s Whole Mouse Genome 4x44Kv2 arrays as described in manufacturer’s hybridization kit, against an equal amount of Cy3-labeled universal mouse reference (Stratagene).

scan_protocol: Following hybridization, microarrays were washed, dried, and scanned on Agilent’s G2505C scanner. Agilent’s Feature Extraction 11.5 software was used to analyze acquired array images.

data_processing: Data were analyzed using the limma package from Bioconductor. ControlType weights were set to 0, spots with background signal more than 50 above the foreground signal were set to the median background intensity, background correction was performed with limma::backgroundCorrect() using the "normexp" method and an offset of 50, limma::normalizeWithinArrays() with the "loess" method,  and finally limma::normalizeBetweenArrays() with the "Aquantile" method. This gives the "test" and "reference" normalized probe intensities. Finally, for each probe an "expression ratio" was calculated, the ratio of the normalized signals in the test and reference channels.

source_name: Total RNA from L3/L4 DRGs 3 days after sciatic nerve transection in adult mice

label_protocol: The method for preparation of Cy-dye labeled cRNA and array hybridization was provided by Agilent. Briefly, 1 μg total RNA was converted to double-stranded cDNA and then to Cy5-labeled cRNA using Quick Amp Labeling Kit (Agilent). The labeled cRNA was purified using RNeasy mini kit (Qiagen). cRNA yield and Cy5 incorporation was determined using ND-1000 spectrophotometer.

extract_protocol: DRGs were dissected and immediately transferred to RNAlater (Qiagen) and RNA isolated using RNeasy Plus Mini Kit (Qiagen). RNA sample quantity and quality were determined using an ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies), respectively.

value: Nerve (L3/L4 dorsal root ganglion)

tag: cre

value: control

tag: genotype

source_name: universal mouse reference (Stratagene)

label_protocol: Method for Cy-dye labeled cRNA preparation was provided by Agilent.

extract_protocol: By vendor


title: SAM628396 Nerve lesion

description: SAM628396 Nerve cre.neg lesion jun.wt

tag: treatment

value: lesion


title: SAM619451 Nerve control

description: SAM619451 Nerve cre.neg control jun.wt


title: SAM626964 Nerve lesion

description: SAM626964 Nerve cre.neg lesion jun.wt


title: SAM628395 Nerve control

description: SAM628395 Nerve cre.neg control jun.wt


title: SAM628397 Nerve lesion

description: SAM628397 Nerve cre.neg lesion jun.wt


title: SAM627975 Nerve control

description: SAM627975 Nerve cre.neg control jun.wt


title: SAM621084 Nerve lesion

description: SAM621084 Nerve cre.neg lesion jun.wt


title: Genomic DNA from patient 663 [663T]

city: Dunedin

first: Parry

last: Guilford

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: Colon biopsy

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol

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

data_processing: Beadstudio software v1.8

source_name: Colon biopsy sample 663

extract_protocol: Genomic DNA was extracted and purified from fresh frozen tissue using Quick-gDNA miniPrep kit (Zymo Research) according to standard instructions

tag: gender

tag: disease state

value: Tumour

tag: colon subdivision


title: SAM627490 Nerve lesion

description: SAM627490 Nerve cre.neg lesion jun.wt


title: Genomic DNA from patient 647 [647N]

description: Colon biopsy

source_name: Colon biopsy sample 647

value: M

value: Recto-sigmoid


title: Genomic DNA from patient 656 [656N]

description: Colon biopsy

source_name: Colon biopsy sample 656


title: Genomic DNA from patient 663 [663N]

description: Colon biopsy


title: Genomic DNA from patient 618 [618T]

description: Colon biopsy

source_name: Colon biopsy sample 618

value: F

value: Ascending


title: Genomic DNA from patient 815 [815N]

description: Colon biopsy

source_name: Colon biopsy sample 815


title: Genomic DNA from patient 815 [815T]

description: Colon biopsy


title: Genomic DNA from patient 651 [651T]

description: Colon biopsy

source_name: Colon biopsy sample 651

value: Caecum


title: Genomic DNA from patient 639 [639N]

description: Colon biopsy

source_name: Colon biopsy sample 639


title: Genomic DNA from patient 647 [647T]

description: Colon biopsy


title: Genomic DNA from patient 588 [588T]

description: Colon biopsy

source_name: Colon biopsy sample 588


title: Genomic DNA from patient 556 [556N]

description: Colon biopsy

source_name: Colon biopsy sample 556


title: Genomic DNA from patient 521 [521T]

description: Colon biopsy

source_name: Colon biopsy sample 521


title: Genomic DNA from patient 656 [656T]

description: Colon biopsy


title: Genomic DNA from patient 743 [743T]

description: Colon biopsy

source_name: Colon biopsy sample 743


title: Genomic DNA from patient 521 [521N]

description: Colon biopsy


title: Genomic DNA from patient 743 [743N]

description: Colon biopsy


title: Genomic DNA from patient 498 [498T]

description: Colon biopsy

source_name: Colon biopsy sample 498


title: Genomic DNA from patient 498 [498N]

description: Colon biopsy


title: Genomic DNA from patient 651 [651N]

description: Colon biopsy


title: Genomic DNA from patient 576 [576T]

description: Colon biopsy

source_name: Colon biopsy sample 576

value: Sigmoid


title: Genomic DNA from patient 559 [559T]

description: Colon biopsy

source_name: Colon biopsy sample 559


title: Genomic DNA from patient 556 [556T]

description: Colon biopsy


title: Genomic DNA from patient 492 [492N]

description: Colon biopsy

source_name: Colon biopsy sample 492

value: Normal

value: Descending


title: Genomic DNA from patient 588 [588N]

description: Colon biopsy


title: Genomic DNA from patient 492 [492T]

description: Colon biopsy


title: Genomic DNA from patient 618 [618N]

description: Colon biopsy


title: Genomic DNA from patient 486 [486N]

description: Colon biopsy

source_name: Colon biopsy sample 486


title: Genomic DNA from patient 639 [639T]

description: Colon biopsy


title: Genomic DNA from patient 559 [559N]

description: Colon biopsy


title: Genomic DNA from patient 467 [467T]

description: Colon biopsy

source_name: Colon biopsy sample 467

value: Splenic Flexure


title: Genomic DNA from patient 455 [455T]

description: Colon biopsy

source_name: Colon biopsy sample 455


title: Genomic DNA from patient 467 [467N]

description: Colon biopsy


title: Genomic DNA from patient 465 [465N]

description: Colon biopsy

source_name: Colon biopsy sample 465


title: Genomic DNA from patient 576 [576N]

description: Colon biopsy


title: Genomic DNA from patient 465 [465T]

description: Colon biopsy


title: Genomic DNA from patient 486 [486T]

description: Colon biopsy


title: Genomic DNA from patient 455 [455N]

description: Colon biopsy


title: Genomic DNA from patient 450 [450N]

description: Colon biopsy

source_name: Colon biopsy sample 450


title: Genomic DNA from patient 341 [341N]

description: Colon biopsy

source_name: Colon biopsy sample 341


title: Genomic DNA from patient 381 [381N]

description: Colon biopsy

source_name: Colon biopsy sample 381


title: Genomic DNA from patient 288 [288T]

description: Colon biopsy

source_name: Colon biopsy sample 288


title: Genomic DNA from patient 449 [449T]

description: Colon biopsy

source_name: Colon biopsy sample 449


title: Genomic DNA from patient 450 [450T]

description: Colon biopsy


title: Genomic DNA from patient 341 [341T]

description: Colon biopsy


title: Genomic DNA from patient 170 [170T]

description: Colon biopsy

source_name: Colon biopsy sample 170

value: Transverse


title: Genomic DNA from patient 288 [288N]

description: Colon biopsy


title: Genomic DNA from patient 249 [249T]

description: Colon biopsy

source_name: Colon biopsy sample 249


title: Genomic DNA from patient 249 [249N]

description: Colon biopsy


title: Genomic DNA from patient 381 [381T]

description: Colon biopsy


title: Genomic DNA from patient 388 [388T]

description: Colon biopsy

source_name: Colon biopsy sample 388


title: Genomic DNA from patient 449 [449N]

description: Colon biopsy


title: Genomic DNA from patient 244 [244N]

description: Colon biopsy

source_name: Colon biopsy sample 244


title: Genomic DNA from patient 244 [244T]

description: Colon biopsy


title: Genomic DNA from patient 89 [89N]

description: Colon biopsy

source_name: Colon biopsy sample 89


title: Genomic DNA from patient 170 [170N]

description: Colon biopsy


title: Genomic DNA from patient 192 [192N]

description: Colon biopsy

source_name: Colon biopsy sample 192


title: Genomic DNA from patient 652 [652T]

description: Colon biopsy

source_name: Colon biopsy sample 652


title: Genomic DNA from patient 338 [338N]

description: Colon biopsy

source_name: Colon biopsy sample 338


title: Genomic DNA from patient 657 [657T]

description: Colon biopsy

source_name: Colon biopsy sample 657

value: Hepatic flexure


title: Genomic DNA from patient 693 [693T]

description: Colon biopsy

source_name: Colon biopsy sample 693


title: Genomic DNA from patient 192 [192T]

description: Colon biopsy


title: Genomic DNA from patient 624 [624T]

description: Colon biopsy

source_name: Colon biopsy sample 624


title: Genomic DNA from patient 646 [646T]

description: Colon biopsy

source_name: Colon biopsy sample 646


title: Genomic DNA from patient 669 [669T]

description: Colon biopsy

source_name: Colon biopsy sample 669


title: Genomic DNA from patient 636 [636T]

description: Colon biopsy

source_name: Colon biopsy sample 636


title: Genomic DNA from patient 666 [666T]

description: Colon biopsy

source_name: Colon biopsy sample 666


title: Genomic DNA from patient 89 [89T]

description: Colon biopsy


title: Genomic DNA from patient 678 [678T]

description: Colon biopsy

source_name: Colon biopsy sample 678


title: Genomic DNA from patient 599 [599T]

description: Colon biopsy

source_name: Colon biopsy sample 599


title: Genomic DNA from patient 557 [557T]

description: Colon biopsy

source_name: Colon biopsy sample 557


title: Genomic DNA from patient 654 [654T]

description: Colon biopsy

source_name: Colon biopsy sample 654


title: Genomic DNA from patient 674 [674T]

description: Colon biopsy

source_name: Colon biopsy sample 674


title: Genomic DNA from patient 328 [328T]

description: Colon biopsy

source_name: Colon biopsy sample 328


title: Genomic DNA from patient 357 [357T]

description: Colon biopsy

source_name: Colon biopsy sample 357


title: Genomic DNA from patient 454 [454T]

description: Colon biopsy

source_name: Colon biopsy sample 454


title: Genomic DNA from patient 469 [469T]

description: Colon biopsy

source_name: Colon biopsy sample 469


title: Genomic DNA from patient 612 [612T]

description: Colon biopsy

source_name: Colon biopsy sample 612


title: Genomic DNA from patient 547 [547T]

description: Colon biopsy

source_name: Colon biopsy sample 547


title: Genomic DNA from patient 348 [348T]

description: Colon biopsy

source_name: Colon biopsy sample 348


title: Genomic DNA from patient 514 [514T]

description: Colon biopsy

source_name: Colon biopsy sample 514


title: Genomic DNA from patient 350 [350T]

description: Colon biopsy

source_name: Colon biopsy sample 350


title: Genomic DNA from patient 500 [500T]

description: Colon biopsy

source_name: Colon biopsy sample 500


title: Genomic DNA from patient 638 [638T]

description: Colon biopsy

source_name: Colon biopsy sample 638


title: Genomic DNA from patient 703 [703T]

description: Colon biopsy

source_name: Colon biopsy sample 703


title: Genomic DNA from patient 515 [515T]

description: Colon biopsy

source_name: Colon biopsy sample 515


title: Genomic DNA from patient 627 [627T]

description: Colon biopsy

source_name: Colon biopsy sample 627


title: Genomic DNA from patient 474 [474T]

description: Colon biopsy

source_name: Colon biopsy sample 474


title: Genomic DNA from patient 447 [447T]

description: Colon biopsy

source_name: Colon biopsy sample 447


title: Genomic DNA from patient 614 [614T]

description: Colon biopsy

source_name: Colon biopsy sample 614


title: Genomic DNA from patient 604 [604T]

description: Colon biopsy

source_name: Colon biopsy sample 604


title: Genomic DNA from patient 610 [610T]

description: Colon biopsy

source_name: Colon biopsy sample 610


title: Genomic DNA from patient 592 [592T]

description: Colon biopsy

source_name: Colon biopsy sample 592


title: Genomic DNA from patient 597 [597T]

description: Colon biopsy

source_name: Colon biopsy sample 597


title: Genomic DNA from patient 564 [564T]

description: Colon biopsy

source_name: Colon biopsy sample 564


title: Genomic DNA from patient 335 [335T]

description: Colon biopsy

source_name: Colon biopsy sample 335


title: Genomic DNA from patient 580 [580T]

description: Colon biopsy

source_name: Colon biopsy sample 580


title: Genomic DNA from patient 529 [529T]

description: Colon biopsy

source_name: Colon biopsy sample 529


title: Genomic DNA from patient 471 [471T]

description: Colon biopsy

source_name: Colon biopsy sample 471


title: Genomic DNA from patient 520 [520T]

description: Colon biopsy

source_name: Colon biopsy sample 520


title: Genomic DNA from patient 470 [470T]

description: Colon biopsy

source_name: Colon biopsy sample 470


title: Tip110-/- outgrowth, biological rep1

city: Fort Worth

first: Johnny

middle: J

last: He

state: TX

address: 3500 Camp Bowie Blvd

department: Cell Biology, Immunology & Microbiology

institute: University of North Texas Health Science Center at Fort Worth

description: Gene expression data from Tip110-/- blastocyst-derived outgrowths (pooled sample; 3 outgrowths) - 165 pg total RNA collected. 144 pg used.

hyb_protocol: Hybridization was performed at the UTSW Genomics and Microarray Core (Dallas, TX) according to the Affymetrix GeneChip WT Pico protocol (Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays, 2015, Affymetrix).

scan_protocol: GeneChips were scanned using at the UTSW Genomics and Microarray Core (Dallas, TX) - Contact Indu.Raman@UTSouthwestern.edu FMI.

data_processing: The data were analyzed with the Affymetrix Expression Console and Transcriptome Analysis Console. Affymetrix default analysis settings were used.

source_name: 3.5 dpc mouse blastocyst grown to outgrowth in vitro

label_protocol: Labeling was performed at the UTSW Genomics and Microarray Core (Dallas, TX) according to the Affymetrix GeneChip WT Pico protocol from 144 pg total RNA (Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays, 2015, Affymetrix).

growth_protocol: 3.5 dpc blastocysts cultured individually in vitro in KOSR-ESCM at 37°C and 5% CO2 for 4-6 days to form blastocyst-derived outgrowths. Culture was in U-bottom 96-well plates.

extract_protocol: RNeasy Micro Kit (Qiagen; Cat No./ID: 74004) was used. Extraction of total RNA was performed according to the manufacturer's instructions. No carrier RNA was used and RNA was eluted 2x in 11-14 ul of RNase free H2O.

treatment_protocol: No treatment. After culture, media was aspirated and RNA isolation was immediately performed on outgrowths.

value: blastocyst-derived outgrowth

value: 3.5 dpc blastocyst cultured 4-6 days in vitro in KOSR-ESCM to form blastocyst-derived outgrowth


title: wild-type outgrowth, biological rep1

description: Gene expression data from wild-type blastocyst-derived outgrowths (pooled sample; 3 outgrowths) - 746 pg total RNA collected. 144 pg used.

value: wild-type


title: Genomic DNA from patient 508 [508T]

description: Colon biopsy

source_name: Colon biopsy sample 508


title: Genomic DNA from patient 446 [446T]

description: Colon biopsy

source_name: Colon biopsy sample 446


title: Genomic DNA from patient 466 [466T]

description: Colon biopsy

source_name: Colon biopsy sample 466


title: Genomic DNA from patient 464 [464T]

description: Colon biopsy

source_name: Colon biopsy sample 464


title: Genomic DNA from patient 402 [402T]

description: Colon biopsy

source_name: Colon biopsy sample 402


title: wild-type outgrowth, biological rep2

description: Gene expression data from wild-type blastocyst-derived outgrowths (single sample; 1 outgrowths) - 178 pg total RNA collected. 144 pg used.


title: Genomic DNA from patient 331 [331T]

description: Colon biopsy

source_name: Colon biopsy sample 331


title: Genomic DNA from patient 669 [669N]

description: Colon biopsy

source_name: Colon biopsy sample 669


title: Genomic DNA from patient 334 [334T]

description: Colon biopsy

source_name: Colon biopsy sample 334


title: Tip110-/- outgrowth, biological rep2

description: Gene expression data from Tip110-/- blastocyst-derived outgrowths (single sample; 1 outgrowths) - 144 pg total RNA collected. 144 pg used.


title: Genomic DNA from patient 693 [693N]

description: Colon biopsy

source_name: Colon biopsy sample 693


title: Genomic DNA from patient 678 [678N]

description: Colon biopsy

source_name: Colon biopsy sample 678


title: Genomic DNA from patient 666 [666N]

description: Colon biopsy

source_name: Colon biopsy sample 666


title: Genomic DNA from patient 636 [636N]

description: Colon biopsy

source_name: Colon biopsy sample 636


title: Genomic DNA from patient 515 [515N]

description: Colon biopsy

source_name: Colon biopsy sample 515


title: Genomic DNA from patient 500 [500N]

description: Colon biopsy

source_name: Colon biopsy sample 500


title: Genomic DNA from patient 646 [646N]

description: Colon biopsy

source_name: Colon biopsy sample 646


title: Genomic DNA from patient 514 [514N]

description: Colon biopsy

source_name: Colon biopsy sample 514


title: Genomic DNA from patient 624 [624N]

description: Colon biopsy

source_name: Colon biopsy sample 624


title: human pluripotent stem cells, naïve, control, 2

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

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

data_processing: Partek Genomics Suite 6.6 methylation workflow

source_name: human pluripotent stem cells

growth_protocol: Human induced pluripotent stem cells were cultured on Matrigel [BD Biosciences] in MEF conditioned medium (MEF-CM) supplemented with 8 ng/ml bFGF [Invitrogen] or maintained on irradiated feeder MEFs (iMEFs) with hPSC medium (DMEM/F12 [Gibco] with 20% Knockout Serum Replacement [Gibco], 100 mM b-mercaptoethanol, 100 mM nonessential amino acid [Gibco], 1 mM L-glutamine [Gibco], and 10 ng/ml bFGF, as previously described (Werbowetski-Ogilvie et al., 2009). Cells were routinely passaged every 5-7 days by mechanical transfer using 1 mg/ml Collagenase IV [Invitrogen]. For the derivation of naïve hPSCs, cells in primed pluripotent states were switched into hPSC medium supplemented with 1 mM MEK inhibitor PD0325901, 3 mM GSK3 inhibitor CHIR99021, and 10 ng/ml LIF (abbreviated LIF/2i) as previously reported (Buecker et al., 2010; Hanna et al., 2010; Li et al., 2009) or de novo reprogramming of somatic cells in naïve conditions. We also established naïve hPSCs using 10 ng/ml LIF and a combination of inhibitors for MEK/ERK (1 mM PD0325901), GSK3 (0.3 mM CHIR99021), LCF/SRC (1 mM WH-4-023), BRAF (0.5 mM SB590885) and ROCK (10 mM Y-27632) (5i)(Theunissen et al., 2014). Emerging colonies with a mESC-like morphology (appeared after 10-20 days of culture) were individually picked and subcultured by trypsinization or mechanical passaging onto feeder-free Matrigel or iMEFs with LIF/2i

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen Dneasy Blood and Tissue Kit according to standard instructions

value: human pluripotent stem cells, naïve

tag: shRNA

value: control


title: Genomic DNA from patient 657 [657N]

description: Colon biopsy

source_name: Colon biopsy sample 657


title: human pluripotent stem cells, naïve, shPOU5F1, 1


title: human pluripotent stem cells, primed, control, 2

value: human pluripotent stem cells, primed


title: Genomic DNA from patient 652 [652N]

description: Colon biopsy

source_name: Colon biopsy sample 652


title: Genomic DNA from patient 447 [447N]

description: Colon biopsy

source_name: Colon biopsy sample 447


title: Genomic DNA from patient 454 [454N]

description: Colon biopsy

source_name: Colon biopsy sample 454


title: human pluripotent stem cells, naïve, shNANOG, 1

value: shNANOG


title: Genomic DNA from patient 350 [350N]

description: Colon biopsy

source_name: Colon biopsy sample 350


title: Genomic DNA from patient 348 [348N]

description: Colon biopsy

source_name: Colon biopsy sample 348

value: M


title: Genomic DNA from patient 474 [474N]

description: Colon biopsy

source_name: Colon biopsy sample 474


title: Genomic DNA from patient 547 [547N]

description: Colon biopsy

source_name: Colon biopsy sample 547

value: F


title: Genomic DNA from patient 557 [557N]

description: Colon biopsy

source_name: Colon biopsy sample 557

value: Ascending


title: Genomic DNA from patient 335 [335N]

description: Colon biopsy

source_name: Colon biopsy sample 335


title: human pluripotent stem cells, primed, control, 1


title: human pluripotent stem cells, naïve, shPOU5F1, 2


title: Genomic DNA from patient 674 [674N]

description: Colon biopsy

source_name: Colon biopsy sample 674

value: Caecum


title: Genomic DNA from patient 357 [357N]

description: Colon biopsy

source_name: Colon biopsy sample 357


title: Genomic DNA from patient 599 [599N]

description: Colon biopsy

source_name: Colon biopsy sample 599


title: human pluripotent stem cells, naïve, shNANOG, 2


title: Genomic DNA from patient 469 [469N]

description: Colon biopsy

source_name: Colon biopsy sample 469


title: Genomic DNA from patient 654 [654N]

description: Colon biopsy

source_name: Colon biopsy sample 654


title: human pluripotent stem cells, naïve, control, 1


title: Genomic DNA from patient 703 [703N]

description: Colon biopsy

source_name: Colon biopsy sample 703

value: Sigmoid


title: Genomic DNA from patient 627 [627N]

description: Colon biopsy

source_name: Colon biopsy sample 627

value: Normal


title: Genomic DNA from patient 638 [638N]

description: Colon biopsy

source_name: Colon biopsy sample 638


title: Genomic DNA from patient 612 [612N]

description: Colon biopsy

source_name: Colon biopsy sample 612

value: Descending


title: Genomic DNA from patient 592 [592N]

description: Colon biopsy

source_name: Colon biopsy sample 592


title: Genomic DNA from patient 597 [597N]

description: Colon biopsy

source_name: Colon biopsy sample 597


title: Patient_OPL_OC 1555

city: Navi Mumbai

first: Manoj

middle: Balkrishna

last: Mahimkar

state: Maharashtra

address: Sector-22, Owe Village, Kharghar Node

institute: Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre

description: Leukoplakia- Oral Precancerous lesion

hyb_protocol: 1.65 µg of labeled cRNA sample were fragmented at 60ºC and hybridized on to microarray slides. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies; 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Scanned using an Agilent Scanner (Agilent Technologies, G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

source_name: Leukoplakia- Oral Precancerous lesion

label_protocol: 500ng of samples were labeled with fluorochromes Cy3 using Agilent Quick-Amp labeling Kit (Agilent Technologies, 5190-0442). Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000

extract_protocol: RNA was extracted using AllPrep® DNA/RNA/miRNA Universal kit, QIAGEN. RNA quantification was performed on Nanodrop-1000 spectrophotometer (Thermo Scientific: 1000). The RNA integrity was evaluated using Agilent RNA 6000 Nano Chip, Bioanalyzer (Agilent: 2100)

treatment_protocol: Freshly collected oral tissues from oral leukoplakia, oral cancer patients and healty indivduals were kept at -80°C till RNA was extracted.

value: Female

tag: site

value: Gingivobuccal complex

tag: Stage

value: Oral Precancer


title: Patient_OPL_OC 2067

description: Leukoplakia- Oral Precancerous lesion

value: Male


title: Genomic DNA from patient 610 [610N]

description: Colon biopsy

source_name: Colon biopsy sample 610


title: Genomic DNA from patient 580 [580N]

description: Colon biopsy

source_name: Colon biopsy sample 580


title: Patient_OPL_OC 2061

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OPL_OC 1565

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OSCC_OC1891

description: Oral Tumor Tissue

source_name: Oral Tumor Tissue


title: Genomic DNA from patient 470 [470N]

description: Colon biopsy

source_name: Colon biopsy sample 470


title: Genomic DNA from patient 564 [564N]

description: Colon biopsy

source_name: Colon biopsy sample 564


title: Genomic DNA from patient 402 [402N]

description: Colon biopsy

source_name: Colon biopsy sample 402


title: Patient_OSCC_OC1910

description: Oral Tumor Tissue


title: Genomic DNA from patient 446 [446N]

description: Colon biopsy

source_name: Colon biopsy sample 446

value: Transverse


title: Genomic DNA from patient 471 [471N]

description: Colon biopsy

source_name: Colon biopsy sample 471

value: Recto-sigmoid


title: Genomic DNA from patient 464 [464N]

description: Colon biopsy

source_name: Colon biopsy sample 464


title: Genomic DNA from patient 604 [604N]

description: Colon biopsy

source_name: Colon biopsy sample 604


title: Genomic DNA from patient 466 [466N]

description: Colon biopsy

source_name: Colon biopsy sample 466


title: Genomic DNA from patient 508 [508N]

description: Colon biopsy

source_name: Colon biopsy sample 508


title: Genomic DNA from patient 520 [520N]

description: Colon biopsy

source_name: Colon biopsy sample 520


title: Genomic DNA from patient 459 [459T]

description: Colon biopsy

source_name: Colon biopsy sample 459

value: Tumour


title: Genomic DNA from patient 529 [529N]

description: Colon biopsy

source_name: Colon biopsy sample 529


title: Genomic DNA from patient 443 [443T]

description: Colon biopsy

source_name: Colon biopsy sample 443

value: Hepatic flexure


title: Patient_OSCC_OC1984

description: Oral Tumor Tissue


title: Patient_OSCC_OC1983

description: Oral Tumor Tissue


title: Patient_OSCC_OC1965

description: Oral Tumor Tissue


title: Genomic DNA from patient 614 [614N]

description: Colon biopsy

source_name: Colon biopsy sample 614


title: Genomic DNA from patient 331 [331N]

description: Colon biopsy

source_name: Colon biopsy sample 331


title: Genomic DNA from patient 570 [570T]

description: Colon biopsy

source_name: Colon biopsy sample 570


title: Genomic DNA from patient 593 [593T]

description: Colon biopsy

source_name: Colon biopsy sample 593


title: Genomic DNA from patient 328 [328N]

description: Colon biopsy

source_name: Colon biopsy sample 328


title: Genomic DNA from patient 526 [526T]

description: Colon biopsy

source_name: Colon biopsy sample 526


title: Genomic DNA from patient 436 [436T]

description: Colon biopsy

source_name: Colon biopsy sample 436


title: Genomic DNA from patient 548 [548T]

description: Colon biopsy

source_name: Colon biopsy sample 548


title: Patient_OSCC_OC1896

description: Oral Tumor Tissue

source_name: Oral Tumor Tissue


title: Genomic DNA from patient 435 [435T]

description: Colon biopsy

source_name: Colon biopsy sample 435


title: Patient_OSCC_OC1932

description: Oral Tumor Tissue


title: Patient_OSCC_OC1846

description: Oral Tumor Tissue


title: Patient_OPL_OC 1884

description: Leukoplakia- Oral Precancerous lesion

source_name: Leukoplakia- Oral Precancerous lesion


title: Patient_OSCC_OC1844

description: Oral Tumor Tissue


title: Patient_OSCC_OC1845

description: Oral Tumor Tissue


title: Patient_OPL_OC1377

description: Leukoplakia- Oral Precancerous lesion


title: Genomic DNA from patient 539 [539T]

description: Colon biopsy

source_name: Colon biopsy sample 539


title: Genomic DNA from patient 391 [391T]

description: Colon biopsy

source_name: Colon biopsy sample 391


title: Control_N97

description: Oral Normal Tissue

source_name: Oral Normal Tissue

value: Control


title: Patient_OSCC_OC1914

description: Oral Tumor Tissue


title: Patient_OSCC_OC1986

description: Oral Tumor Tissue


title: Patient_OSCC_OC1947

description: Oral Tumor Tissue


title: Genomic DNA from patient 334 [334N]

description: Colon biopsy

source_name: Colon biopsy sample 334


title: Patient_OPL_OC1952

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OPL_OC1435

description: Leukoplakia- Oral Precancerous lesion


title: Genomic DNA from patient 535 [535T]

description: Colon biopsy

source_name: Colon biopsy sample 535


title: Genomic DNA from patient 459 [459N]

description: Colon biopsy

source_name: Colon biopsy sample 459


title: Genomic DNA from patient 593 [593N]

description: Colon biopsy


title: Patient_OSCC_OC1791

description: Oral Tumor Tissue


title: Patient_OPL_OC2202

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OPL_OC2201

description: Leukoplakia- Oral Precancerous lesion


title: Genomic DNA from patient 543 [543T]

description: Colon biopsy

source_name: Colon biopsy sample 543


title: Genomic DNA from patient 429 [429T]

description: Colon biopsy

source_name: Colon biopsy sample 429


title: Genomic DNA from patient 370 [370T]

description: Colon biopsy

source_name: Colon biopsy sample 370


title: Genomic DNA from patient 517 [517T]

description: Colon biopsy

source_name: Colon biopsy sample 517


title: Genomic DNA from patient 526 [526N]

description: Colon biopsy


title: Genomic DNA from patient 617 [617T]

description: Colon biopsy

source_name: Colon biopsy sample 617


title: Genomic DNA from patient 583 [583N]

description: Colon biopsy

source_name: Colon biopsy sample 583


title: Genomic DNA from patient 458 [458T]

description: Colon biopsy

source_name: Colon biopsy sample 458


title: Patient_OPL_OC2303

description: Leukoplakia- Oral Precancerous lesion


title: Genomic DNA from patient 443 [443N]

description: Colon biopsy

source_name: Colon biopsy sample 443


title: Patient_OPL_OC2209

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OSCC_OC2184

description: Oral Tumor Tissue

source_name: Oral Tumor Tissue


title: Patient_OPL_OC2293

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OPL_OC2299

description: Leukoplakia- Oral Precancerous lesion


title: Genomic DNA from patient 583 [583T]

description: Colon biopsy


title: Patient_OPL_OC2300

description: Leukoplakia- Oral Precancerous lesion


title: Patient_OSCC_OC2185

description: Oral Tumor Tissue


title: Genomic DNA from patient 391 [391N]

description: Colon biopsy


title: Genomic DNA from patient 435 [435N]

description: Colon biopsy

source_name: Colon biopsy sample 435


title: Genomic DNA from patient 548 [548N]

description: Colon biopsy

source_name: Colon biopsy sample 548


title: Patient_OSCC_OC2109

description: Oral Tumor Tissue