title: YY116 leaf vs YY7 leaf set1

city: Guangzhou

first: Xiaoping

last: Chen

address: 18# Jinying West 2nd Street

institute: Crops Research Institute, Guangdong Academy of Agricultural Sciences

description: Comparison of gene expression profiles of YY116 and YY7 leaf tissues

hyb_protocol: Standard hybridization protocol of CapitalBio Corporation, National Engineering Research Center for Beijing Biochip Technology,

scan_protocol: All microarrays were scanned with a LuxScan 10 KA scanner using LuxScan 4.0 software (CapitalBio, Beijing)

data_processing: The LOWESS normalization method  was used for data analysis, Expression ratios were collected only on those spots with signal intensity ≥800 in at least one dye channel on the microarray slides.

organism: Arachis hypogaea

source_name: YY116 leaf

label_protocol: Standard label protocol of CapitalBio Corporation, National Engineering Research Center for Beijing Biochip Technology.

growth_protocol: Plants were field grown under normal irrigation.

extract_protocol: Total RNA samples were prepared from 2 g peanut pods and leaves using a CTAB-based protocol and further purified using Qiagen RNeasy Plant Mini Kit.

value: leaf

tag: variety

source_name: YY7 leaf


title: immature dendritic cells donor SVH 4762

status: Public on Jun 19 2012

type: RNA

city: Leiden

first: Marieke

last: Griffioen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

description: female healthy individual

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: immature dendritic cells cultured from CD14+ monocytes with GM-CSF and IL-4 for 7 days

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

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

tag: source tissue

value: peripheral blood

tag: gender

value: female

tag: disease state

value: healthy individual

tag: individual

value: donor SVH 4762

tag: cell type

value: immature dendritic cells


title: Lmna ko

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

country: USA

institute: Ut Southwestern Medical Center

hyb_protocol: Direct Hybridization Assay Protocols in Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide

scan_protocol: illumina HiScan®SQ System User Guide

data_processing: Raw data were generated by GenomeStudioTM Gene Expression Module v1.0 without background subtraction and normalization

organism: Mus musculus

source_name: Lmna ko

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit protocol

growth_protocol: DMEM high glucose with 10% FBS, 5% CO2 at 37C

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: mouse embryonic fibroblast (MEF)

tag: genotype/variation

value: Lmna-/-


title: STHdhQ111/Q111 no treatment rep3

city: Cambridge

first: Laura

last: Riva

state: MA

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

hyb_protocol: hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (MOE430v2) following standard techniques.

scan_protocol: Scanned with GeneChIP scanner 3000 7G using the standard protocol

data_processing: Expression data were analyzed using R and Bioconductor (http://www.bioconductor.org/). We normalized gene expression data using Robust Multichip Average (RMA) algorithm.

source_name: STHdhQ111/Q111 striatal cells, no treatment

label_protocol: As recommended by manufacturer

growth_protocol: STHdhQ7/Q7 and STHdhQ111/Q111 striatal cells derived from wild type HdhQ7/Q7 and HdhQ111/Q111 knock-in embryonic mice were used in this study. Cells were grown at 5% CO2 at 33°C in Dulbecco’s modified Eagle’s medium (DMEM, from CellGro, Manassas, VA) with 10% fetal bovine serum (HyClone, Logan, UT), Pen/Strep/Glutamine and 400 μg/ml G418 (both from CellGro). The cells were only used up to passage 15.

extract_protocol: Total RNA was isolated and purified using Rneasy columns (Qiagen Rneasy plus Mini kit, catalogue no. 74134)

treatment_protocol: Cells were heat-shocked at 42°C for six hours

value: striatal cells derived from  HdhQ111/Q111 knock-in embryonic mice

tag: treatment

value: no treatment

tag: genotype


title: STHdhQ111/Q111 no treatment rep2


title: SY523 leaf vs YY7 leaf set2 (dye-swap)

country: China

description: Comparison of gene expression profiles of SY523 and YY7 leaf tissues

tag: tissue

source_name: SY523 leaf


title: YY116 leaf vs YY7 leaf set2 (dye-swap)


title: STHdhQ7/Q7 no treatment rep3

source_name: STHdhQ7/Q7 striatal cells, no treatment

value: striatal cells derived from wild type HdhQ7/Q7 embryonic mice


title: SY523 leaf vs YY7 leaf set1


title: STQ leaf vs YY7 leaf set1

description: Comparison of gene expression profiles of STQ and YY7 leaf tissues

source_name: STQ leaf

value: Shitouqi


title: hematopoietic stem cells donor JTD 5000

description: male healthy individual

source_name: hematopoietic stem cells isolated by flowcytometry based on CD34 surface expression

value: G-CSF mobilized peripheral blood

value: male

value: donor JTD 5000

value: hematopoietic stem cells


title: FHS leaf vs YY7 leaf set2 (dye-swap)

description: Comparison of gene expression profiles of FHS and YY7 leaf tissues

source_name: FHS leaf

value: Fuhuasheng


title: Lmna wt

source_name: Lmna wt

value: Lmna+/+


title: STQ leaf vs YY7 leaf set2 (dye-swap)

value: leaf


title: FHS leaf vs YY7 leaf set1


title: hematopoietic stem cells donor URS 5321

description: female/male healthy individual

value: unknown

value: donor URS 5321


title: SY523 pod vs YY7 pod set1

description: Comparison of gene expression profiles of SY523 and YY7 pod tissues

source_name: SY523 pod

value: pod

source_name: YY7 pod


title: STHdhQ7/Q7 no treatment rep1


title: YY7 leaf vs YY7 leaf set2 (self-to-self)

description: Self-to-self hybridizations of genes from leaf tissues of YY7 to confirm reproducibility of array data


title: YY7 leaf vs YY7 leaf set1 (self-to-self)


title: T-cells donor SVH 4762

description: female healthy individual

source_name: T-cells isolated by flowcytometry based on CD3 surface expression

value: peripheral blood

value: female

value: healthy individual

value: donor SVH 4762

value: T-cells


title: STQ pod vs YY7 pod set2 (dye-swap)

description: Comparison of gene expression profiles of STQ and YY7 pod tissues

source_name: STQ pod


title: YY116 pod vs YY7 pod set1

description: Comparison of gene expression profiles of YY116 and YY7 pod tissues

source_name: YY116 pod


title: SY523 pod vs YY7 pod set2 (dye-swap)


title: hematopoietic stem cells donor AFD 5381

description: female/male healthy individual

value: donor AFD 5381


title: YY116 pod vs YY7 pod set2 (dye-swap)


title: T-cells patient MRJ 3087

description: female patient with chronic myeloid leukemia in remission prior to transplantation with allogeneic hematopoietic stem cells

value: patient MRJ 3087


title: STHdhQ111/Q111 Heat Shock rep2

source_name: STHdhQ111/Q111 striatal cells, Heat Shock

value: striatal cells derived from  HdhQ111/Q111 knock-in embryonic mice

value: cells were heat-shocked at 42°C for six hours


title: FHS pod vs YY7 pod set2 (dye-swap)

description: Comparison of gene expression profiles of FHS and YY7 pod tissues

source_name: FHS pod


title: STHdhQ111/Q111 Heat Shock rep3


title: STHdhQ7/Q7 no treatment rep2

value: striatal cells derived from wild type HdhQ7/Q7 embryonic mice

value: no treatment


title: STHdhQ111/Q111 Heat Shock rep1


title: YY7 pod vs YY7 pod set2 (self-to-self)

description: Self-to-self hybridizations of genes from pod tissues of YY7 to confirm reproducibility of array data


title: STHdhQ111/Q111 no treatment rep1


title: FHS pod vs YY7 pod set1

value: Fuhuasheng


title: YY7 pod vs YY7 pod set1 (self-to-self)


title: monocytes donor SVH 4762

description: female healthy individual

source_name: monocytes isolated by flowcytometry based on CD14 surface expression

value: monocytes


title: T-cells donor USQ 5957

description: male healthy individual

value: male

value: donor USQ 5957


title: STHdhQ7/Q7 Heat Shock rep2

source_name: STHdhQ7/Q7 striatal cells, Heat Shock


title: EfaR_repsA,B,C

city: Oeiras

first: Marta

middle: Coelho

last: Abrantes

address: Av. da República - EAN

country: Portugal

institute: ITQB-UNL

description:
EfaR_A: Biological replicate 1 of 3
EfaR_B: Biological replicate 2 of 3
EfaR_C: Biological replicate 3 of 3
Each slide: EfaR_A, EfaR_B, EfaR_C,  has three replicates of each gene (genes were spotted in triplicate on each slide).

hyb_protocol: Labelled cDNA was mixed and hybridized on glass slides. Hybridization was performed at 45ºC for 16h, with Ambion Slide Hyb #1 hybridization buffer

scan_protocol: Slides were scanned in a GeneTac LS IV confocal laser scanner

data_processing:
Slide images were analyzed using GenePix Pro 6.0 software. Processing and normalization (LOWESS spotpin-based) was done with MicroPrep software.
The processed/normalized data reported in the table below represents the mean of:
EfaR_A-1, EfaR_A-2, EfaR_A-3, EfaR_B-1, EfaR_B-2, EfaR_B-3, EfaR_C-1, EfaR_C-2, EfaR_C-3.
Processed/normalized data table for the individual reps is linked as a supplementary file on the Series record.

organism: Enterococcus faecalis

source_name: [reference] E. faecalis VE14089 cells

label_protocol: cDNA synthesis and indirect labelling with Cy-3-dCTP and Cy-5-dCTP were performed as described elsewhere (Kloosterman et al. 2006)

growth_protocol: E. faecalis VE14089 and VE14089 efaR::tet cells were grown until mid-exponential phase in M17 medium + 0.5% glucose

extract_protocol: Initial steps of RNA isolation were performed as described elsewhere (Kloosterman et al. 2006). Isolation was completed with Roche High Pure RNA isolation kit, following the manufacturer's instructions.

tag: strain

source_name: [test] E. faecalis VE14089 efaR::tet cells

value: VE14089 efaR::tet


title: B-cells donor SVH 4762

description: female healthy individual

source_name: B-cells isolated by flowcytometry based on CD19 surface expression

value: B-cells


title: TGF-beta stimulated vs. control IEC-6 cell replicate 2

city: Davis

first: Bo

last: Lonnerdal

state: CA

address: 1 Shields Ave.

department: Nutrition

institute: University of California, Davis

hyb_protocol: Hybridization SureHyb chamber kit and Gasket slide kit (Agilent) were used to hybridize the labeled RNA for 18 h to Exiqon miRCURY LNA miRNA array V.11.0 (miRBase Sequence Database, http://microrna.sanger.ac.uk/sequences, release 11.0).

scan_protocol: Arrays were scanned on an Axon GenePix 4000B scanner

data_processing: GPR files containing fluorescent ratios (sample/control) were generated using GenePix Pro 6.0 software. GPR files were read into R/Bioconductor [19] using the marray package. GenePix flagged spots were removed from subsequent analysis, and only unflagged human, mouse and rat probes were used for normalization and subsequent analysis. M (log2 ratios) of Cy5 to Cy3 signals were calculated for each array, and normalized by print tip loess normalization using only unflagged spots.

organism: Rattus norvegicus

source_name: IEC-6 cells treated with 50ng/ml TGF-beta

label_protocol: 300 ng of each sample was labeled with Cy5/Cy3 using miRCURY LNA microRNA array Power Labeling kit (Exiqon).

extract_protocol: Total RNA extracted with miRNeasy Mini Kit (Qiangen) according to the manufacturer's instructions

tag: passage

value: passage 4-passage 10 at 1:4 passage ratio, cells are used within 14 times population doubling upon received from ATCC

tag: sample type

value: rat small intestinal crypt cell line IEC-6

tag: cell line

tag: treatment protocol

value: 50ng/ml TGF-beta (R&D Systems)

tag: growth protocol

value: IEC-6 cells were grown in growth media (DMEM with 4 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate and 4.5 g/L glucose and supplemented with 0.1 Unit/ml bovine insulin, 90%; fetal bovine serum, 10%; and maintained at 37.0°C, 5% CO2.)

source_name: IEC-6 cells

value: untreated


title: TGF-beta stimulated vs. control IEC-6 cell replicate 1


title: STQ pod vs YY7 pod set1

value: pod

value: Shitouqi


title: TGF-beta stimulated vs. control IEC-6 cell replicate 3


title: STHdhQ7/Q7 Heat Shock rep1


title: monocytes donor USQ 5957

description: male healthy individual

value: peripheral blood

value: healthy individual


title: monocytes patient MRJ 3087

value: female

value: patient with chronic myeloid leukemia in remission prior to transplantation with allogeneic hematopoietic stem cells

value: patient MRJ 3087


title: SIV negative p18 5859990048_G

city: Port St. Lucie

first: Xiaoyong

last: Sun

state: FL

address: 9801 SW Discovery Way

institute: VGTI, FL

description:
Monkey Tfh
5859990048_G

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

organism: Macaca mulatta

source_name: Sorted cells-pellet

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: Tfh

value: Spleen


title: STHdhQ7/Q7 Heat Shock rep3

value: striatal cells derived from wild type HdhQ7/Q7 embryonic mice

value: cells were heat-shocked at 42°C for six hours


title: B-cells donor JTD 5000

description: male healthy individual

value: male

value: donor JTD 5000

value: B-cells


title: SIV negative p17 5859990048_B

description:
Monkey Tfh
5859990048_B


title: Chronic SIV infection p18 5859990048_D

description:
Monkey Tfh
5859990048_D

value: chronic SIV infection


title: PAO1_LBN+B12

status: Public on Jun 18 2012

city: Seoul

first: Sang Sun

last: Yoon

address: 250 Seongsanno, Seodaemun-gu

country: South Korea

institute: Yonsei University College of Medicine

description: PAO1 anaerobically grown in LBN+vitamin B12

hyb_protocol: Following fragmentation and end-labeling, 5 ug of cDNA were hybridized for 16 hr at 50C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: Biotin

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1, anaerobic, LBN+vitamin B12

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Prokaryote Target Preparation, P/N 702232 Rev. 2, Affymetrix).

growth_protocol: Bacterial cells were grown anaerobically in LBN or LBN supplemented with 1 microM vitamin B12 for 12 hrs.

extract_protocol: Total bacterial RNA was isolated from each of three independent cultures per growth condition. RNA was extracted using TRIzol reagent (Invitrogen, Burlington, ON) following the manufacturer’s instructions and extracted RNA was further purified by using an RNAeasy kit (Qiagen). Purified RNA samples were then pooled together and processed for downstream process.

treatment_protocol: Two different growth media, LBN and LBN+vitamin B12, are used to grow P. aeruginosa strain PAO1.


title: B-cells donor USQ 5957

description: male healthy individual

value: donor USQ 5957


title: SIV negative p17 5859990048_H

description:
Monkey Tfh
5859990048_H


title: Chronic SIV infection p18 5859990046_J

description:
Monkey Tfh
5859990046_J


title: SIV negative p17 5645692024_D

description:
Monkey Tfh
5645692024_D


title: Chronic SIV infection p18 5859990046_L

description:
Monkey Tfh
5859990046_L


title: Chronic SIV infection p18 5645692024_C

description:
Monkey Tfh
5645692024_C


title: SIV negative p18 5859990048_C

description:
Monkey Tfh
5859990048_C


title: SIV negative p17 5645692024_E

description:
Monkey Tfh
5645692024_E


title: SIV negative p18 5645692023_F

description:
Monkey Tfh
5645692023_F


title: SIV negative p18 5645692023_J

description:
Monkey Tfh
5645692023_J


title: SIV negative p18 5645692024_B

description:
Monkey Tfh
5645692024_B


title: SIV negative p17 5645692023_G

description:
Monkey Tfh
5645692023_G


title: Chronic SIV infection p18 5645692023_L

description:
Monkey Tfh
5645692023_L


title: Chronic SIV infection p18 5645692023_B

description:
Monkey Tfh
5645692023_B


title: Bladder tumor UC_0566_1_aCGH_h1

type: genomic

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: Differentially labeled DNA was pooled, mixed with 100 microgram Human Cot-1 DNA (Invitrogen), and lyophilized prior to resuspension in 55 microliter hybridization solution (50% formamide, 10% dextran sulfate, 2x SSC, 2% SDS, 10 mg/ml yeast tRNA). Probes were heated at 70°C for 15 minutes and at 37°C for 30 minutes before hybridization to micro arrays for 48-72 hours at 37°C. Prior to hybridization, micro arrays were UV-cross linked at 500 mJ/cm2 and pretreated using the Universal Micro array Hybridization Kit (Corning, Acton, MA) according to the manufacturer's instructions. The slides were washed in 2 x SSC, 0.1% SDS for 15 min, followed by 2 x SSC, 50% formamide (pH 7.0) for 15 min at 45°C, 2 x SSC, 0.1% SDS for 30 min at 45°C, and 0.2 x SSC for 15 min at room temperature.

scan_protocol: Fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies). Image analysis on scanned arrays was performed with GenePix 4.0 (Axon Instruments)

data_processing: Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad/missing or saturated during image analysis were removed. Poorly measured features with Ch1 or Ch2 signal to noise ratio (SNR) <5 were removed. Data was normalized using the popLowess method (Staaf, et al, BMC Genomics, 2007, 8:382)

molecule: genomic DNA

source_name: bladder tumor UC_0566_1

label_protocol: 1.5 microgram sample and reference genomic DNA was labeled with Cy5-dCTP or with Cy3-dCTP (Amersham Biosciences) using random primer labeling (Bioprime array CGH genomic Labeling module, Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).

extract_protocol: Genomic DNA was extracted using the Dneasy Tissue kit (Qiagen)

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resecrtions at hospitals within the southern healthcare region of Sweden

tag: histology

value: Urothelial carcinoma

tag: tumor stage

tag: tumor grade

value: bladder cancer tumor

source_name: Reference male DNA

value: Reference male DNA


title: sip8-TGFb-24h

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation, using a human oligonucleotide array U133 Plus 2.0 (Genechip, Affymetrix). After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003).

source_name: Panc-1 Nupr1-depleted cells (sip8), incubated for 24 hrs before TGFβ1 treatment

label_protocol: Fifteen micrograms of total RNA were reverse transcribed into cDNA using Superscripts reverse transcriptase (Invitrogen) and T7-oligo-d(T)24 (Geneset) as a primer. Second-strand synthesis was performed using T4 DNA polymerase and E.Coli DNA ligase, and then phosphorylated blunt ends were generated using T4 polynucleotide kinase. cDNA was purified by phenol-chloroform extraction using phase lock gels (Brinkmann). Then, cDNAs were in vitro transcribed for 16 hrs at 37°C by using the IVT Labelling Kit (Affymetrix) to produce biotinylated cRNAs. Labelled cRNA was purified using the RNeasy Mini Kit column (QIAGEN). Purified cRNA was fragmented to 200-30mers using a fragmentation buffer. The quality of total RNA, cDNA synthesis, cRNA amplification and fragmentation was monitored by capillary electrophoresis (Bioanalyzer 2100, Agilent Technologies).

growth_protocol: Panc-1 cells were cultured in Glutamax-containing DMEM(Invitrogen) and BxPC3 in RPMI (Invitrogen), both supplemented with 10% FBS (PAA Laboratories). All cells were maintained at 37°C, 5% CO2, H2O saturated.

extract_protocol: Total RNAs were extracted using Trizol reagent (Invitrogen, Burlington, ON, Canada). Total RNA was purified on RNeasy mini kit column (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Panc-1 cells were seeded in 6-wells plates to reach 30% to 50% confluence. Twenty-four hours later, a mix containing 2.2 pmoles of siRNA and 8 μl of the transfection reagent INTERFERIN (Polyplus Transfection) was added to the culture medium according to manufacturer’s instructions. Panc-1 Nupr1-depleted cells (sip8), and controls cells (siCtrl) were further incubated for 7 or 24 hrs before TGFβ1 treatment without change of medium.

tag: time (incubation)

value: 24 hrs

tag: agent


title: siCtrl-Mock

source_name: Panc-1 controls cells (siCtrl), incubated without TGFβ1 (Mock)

value: control

value: mock-treated


title: Bladder tumor UC_0610_1_aCGH_h1

source_name: bladder tumor UC_0610_1


title: Bladder tumor UC_0518_1_aCGH_h1

source_name: bladder tumor UC_0518_1


title: Bladder tumor UC_0522_1_aCGH_h1

source_name: bladder tumor UC_0522_1


title: Bladder tumor UC_0552_1_aCGH_h1

source_name: bladder tumor UC_0552_1


title: Bladder tumor UC_0513_1a_aCGH_h1

source_name: bladder tumor UC_0513_1a


title: Bladder tumor UC_0488_2_aCGH_h1

source_name: bladder tumor UC_0488_2


title: Bladder tumor UC_0543_1_aCGH_h1

source_name: bladder tumor UC_0543_1


title: Bladder tumor UC_0539_1_aCGH_h1

source_name: bladder tumor UC_0539_1


title: sip8-TGFb-7h

source_name: Panc-1 Nupr1-depleted cells (sip8), incubated for 7 hrs before TGFβ1 treatment

value: 7 hrs


title: Bladder tumor UC_0516_1_aCGH_h1

source_name: bladder tumor UC_0516_1


title: Bladder tumor UC_0455_1_aCGH_h1

source_name: bladder tumor UC_0455_1

value: Tis


title: Bladder tumor UC_0589_1_aCGH_h1

source_name: bladder tumor UC_0589_1


title: Bladder tumor UC_0533_1_aCGH_h1

source_name: bladder tumor UC_0533_1


title: Bladder tumor UC_0527_1_aCGH_h1

source_name: bladder tumor UC_0527_1

value: Ta


title: Bladder tumor UC_0399_1_aCGH_h1

source_name: bladder tumor UC_0399_1

label_protocol: 1.5 microgram sample and reference genomic DNA was fluorescently labeled with Cy3-dCTP and Cy5-dCTP (Amersham Biosciences), respectively, using the Array CGH labeling kit (Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).

source_name: Reference male DNA


title: Bladder tumor UC_0528_1_aCGH_h1

source_name: bladder tumor UC_0528_1


title: Bladder tumor UC_0507_1_aCGH_h1

source_name: bladder tumor UC_0507_1


title: siCtrl-TGFb-24h

source_name: Panc-1 controls cells (siCtrl), incubated for 24 hrs before TGFβ1 treatment


title: Bladder tumor UC_0400_1b_aCGH_h1

source_name: bladder tumor UC_0400_1b


title: sip8-Mock

source_name: Panc-1 Nupr1-depleted cells (sip8), incubated without TGFβ1 (Mock)


title: Bladder tumor UC_0519_1_aCGH_h1

source_name: bladder tumor UC_0519_1


title: Bladder tumor UC_0545_1_aCGH_h1

source_name: bladder tumor UC_0545_1


title: siCtrl-TGFb-7h

source_name: Panc-1 controls cells (siCtrl), incubated for 7 hrs before TGFβ1 treatment


title: Bladder tumor UC_0394_1_aCGH_h1

source_name: bladder tumor UC_0394_1


title: Bladder tumor UC_0521_1_aCGH_h1

source_name: bladder tumor UC_0521_1


title: Bladder tumor UC_0410_1b_aCGH_h1

source_name: bladder tumor UC_0410_1b


title: Bladder tumor UC_0551_1_aCGH_h1

source_name: bladder tumor UC_0551_1


title: Bladder tumor UC_0386_1_aCGH_h1

source_name: bladder tumor UC_0386_1


title: Bladder tumor UC_0378_1_aCGH_h1

source_name: bladder tumor UC_0378_1


title: Bladder tumor UC_0384_1_aCGH_h1

source_name: bladder tumor UC_0384_1


title: Bladder tumor UC_0376_1_aCGH_h1

source_name: bladder tumor UC_0376_1


title: Bladder tumor UC_0349_2_aCGH_h1

source_name: bladder tumor UC_0349_2

source_name: Reference male DNA


title: Bladder tumor UC_0335_1_aCGH_h1

source_name: bladder tumor UC_0335_1


title: Bladder tumor UC_0322_2_aCGH_h1

source_name: bladder tumor UC_0322_2


title: Bladder tumor UC_0343_1_aCGH_h1

source_name: bladder tumor UC_0343_1


title: Bladder tumor UC_0339_1_aCGH_h1

source_name: bladder tumor UC_0339_1


title: Bladder tumor UC_0372_1_aCGH_h1

source_name: bladder tumor UC_0372_1


title: PAO1_LBN

description: PAO1 anaerobically grown in LBN

source_name: PAO1, anaerobic, LBN


title: Bladder tumor UC_0361_1_aCGH_h1

source_name: bladder tumor UC_0361_1


title: Bladder tumor UC_0329_1_aCGH_h1

source_name: bladder tumor UC_0329_1


title: Bladder tumor UC_0368_1_aCGH_h1

source_name: bladder tumor UC_0368_1


title: Bladder tumor UC_0301_1_aCGH_h1

source_name: bladder tumor UC_0301_1


title: Bladder tumor UC_0333_1_aCGH_h1

source_name: bladder tumor UC_0333_1


title: Bladder tumor UC_0342_1_aCGH_h1

source_name: bladder tumor UC_0342_1


title: Bladder tumor UC_0299_1_aCGH_h1

source_name: bladder tumor UC_0299_1


title: Bladder tumor UC_0327_1_aCGH_h1

source_name: bladder tumor UC_0327_1


title: Bladder tumor UC_0312_1_aCGH_h1

source_name: bladder tumor UC_0312_1


title: Bladder tumor UC_0302_1_aCGH_h1

source_name: bladder tumor UC_0302_1


title: Bladder tumor UC_0287_1_aCGH_h1

source_name: bladder tumor UC_0287_1

source_name: Reference male DNA


title: Bladder tumor UC_0284_1_aCGH_h1

source_name: bladder tumor UC_0284_1


title: Bladder tumor UC_0274_1_aCGH_h1

source_name: bladder tumor UC_0274_1


title: Bladder tumor UC_0321_1_aCGH_h1

source_name: bladder tumor UC_0321_1


title: Bladder tumor UC_0265_1_aCGH_h1

source_name: bladder tumor UC_0265_1


title: Bladder tumor UC_0267_3_aCGH_h1

source_name: bladder tumor UC_0267_3


title: Bladder tumor UC_0242_1_aCGH_h1

source_name: bladder tumor UC_0242_1


title: Bladder tumor UC_0283_1_aCGH_h1

source_name: bladder tumor UC_0283_1


title: Bladder tumor UC_0240_1_aCGH_h1

source_name: bladder tumor UC_0240_1


title: Bladder tumor UC_0249_1_aCGH_h1

source_name: bladder tumor UC_0249_1

value: Tx


title: Bladder tumor UC_0290_1_aCGH_h1

source_name: bladder tumor UC_0290_1


title: Bladder tumor UC_0235_1_aCGH_h1

source_name: bladder tumor UC_0235_1


title: Bladder tumor UC_0223_1_aCGH_h1

source_name: bladder tumor UC_0223_1


title: Bladder tumor UC_0214_1_aCGH_h1

source_name: bladder tumor UC_0214_1


title: Bladder tumor UC_0208_1_aCGH_h1

source_name: bladder tumor UC_0208_1


title: Bladder tumor UC_0263_1_aCGH_h1

source_name: bladder tumor UC_0263_1


title: Bladder tumor UC_0213_1_aCGH_h1

source_name: bladder tumor UC_0213_1


title: Bladder tumor UC_0231_1_aCGH_h1

source_name: bladder tumor UC_0231_1

source_name: Reference male DNA


title: Bladder tumor UC_0215_1_aCGH_h1

source_name: bladder tumor UC_0215_1


title: Bladder tumor UC_0230_1_aCGH_h1

source_name: bladder tumor UC_0230_1


title: Bladder tumor UC_0226_1_aCGH_h1

source_name: bladder tumor UC_0226_1


title: Bladder tumor UC_0207_1_aCGH_h1

source_name: bladder tumor UC_0207_1


title: Bladder tumor UC_0209_1_aCGH_h1

source_name: bladder tumor UC_0209_1


title: Bladder tumor UC_0196_1_aCGH_h1

source_name: bladder tumor UC_0196_1


title: Bladder tumor UC_0237_1_aCGH_h1

source_name: bladder tumor UC_0237_1


title: Bladder tumor UC_0218_2_aCGH_h1

source_name: bladder tumor UC_0218_2


title: Bladder tumor UC_0199_1_aCGH_h1

source_name: bladder tumor UC_0199_1


title: Bladder tumor UC_0224_1_aCGH_h1

source_name: bladder tumor UC_0224_1


title: Bladder tumor UC_0192_1_aCGH_h1

source_name: bladder tumor UC_0192_1

extract_protocol: Genomic DNA was extracted using Trizol reagent (Invitrogen) and further purified using the Wizard kit (Promega)

source_name: Reference female DNA

value: Reference female DNA


title: Bladder tumor UC_0200_1_aCGH_h1

source_name: bladder tumor UC_0200_1


title: Bladder tumor UC_0195_1_aCGH_h1

source_name: bladder tumor UC_0195_1


title: Bladder tumor UC_0187_1_aCGH_h1

source_name: bladder tumor UC_0187_1


title: Bladder tumor UC_0203_1_aCGH_h1

source_name: bladder tumor UC_0203_1


title: Bladder tumor UC_0185_1_aCGH_h1

source_name: bladder tumor UC_0185_1

source_name: Reference male DNA


title: Bladder tumor UC_0173_1_aCGH_h1

source_name: bladder tumor UC_0173_1


title: Bladder tumor UC_0176_2_aCGH_h1

source_name: bladder tumor UC_0176_2


title: Bladder tumor UC_0162_1_aCGH_h1

source_name: bladder tumor UC_0162_1


title: Bladder tumor UC_0172_1_aCGH_h1

source_name: bladder tumor UC_0172_1


title: Bladder tumor UC_0166_1_aCGH_h1

source_name: bladder tumor UC_0166_1


title: Bladder tumor UC_0165_1_aCGH_h1

source_name: bladder tumor UC_0165_1


title: Bladder tumor UC_0152_1_aCGH_h1

source_name: bladder tumor UC_0152_1


title: Bladder tumor UC_0159_1_aCGH_h1

source_name: bladder tumor UC_0159_1


title: Bladder tumor UC_0169_1_aCGH_h1

source_name: bladder tumor UC_0169_1


title: Bladder tumor UC_0170_1_aCGH_h1

source_name: bladder tumor UC_0170_1


title: Bladder tumor UC_0145_1_aCGH_h1

source_name: bladder tumor UC_0145_1


title: Bladder tumor UC_0122_1_aCGH_h1

source_name: bladder tumor UC_0122_1

source_name: Reference female DNA


title: Bladder tumor UC_0114_1_aCGH_h1

source_name: bladder tumor UC_0114_1


title: Bladder tumor UC_0129_1_aCGH_h2

source_name: bladder tumor UC_0129_1


title: Bladder tumor UC_0149_1_aCGH_h1

source_name: bladder tumor UC_0149_1


title: Bladder tumor UC_0110_1_aCGH_h1

source_name: bladder tumor UC_0110_1


title: Bladder tumor UC_0132_1_aCGH_h1

source_name: bladder tumor UC_0132_1


title: Bladder tumor UC_0147_1_aCGH_h1

source_name: bladder tumor UC_0147_1


title: Bladder tumor UC_0134_1_aCGH_h1

source_name: bladder tumor UC_0134_1


title: Bladder tumor UC_0130_1_aCGH_h2

source_name: bladder tumor UC_0130_1


title: Bladder tumor UC_0115_1_aCGH_h1

source_name: bladder tumor UC_0115_1

source_name: Reference male DNA


title: Bladder tumor UC_0137_1_aCGH_h1

source_name: bladder tumor UC_0137_1


title: Bladder tumor UC_0111_1_aCGH_h1

source_name: bladder tumor UC_0111_1


title: Bladder tumor UC_0112_1_aCGH_h1

source_name: bladder tumor UC_0112_1


title: Bladder tumor UC_0096_1_aCGH_h1

source_name: bladder tumor UC_0096_1


title: Bladder tumor UC_0095_1_aCGH_h1

source_name: bladder tumor UC_0095_1


title: Bladder tumor UC_0117_1_aCGH_h1

source_name: bladder tumor UC_0117_1


title: Bladder tumor UC_0120_1_aCGH_h2

source_name: bladder tumor UC_0120_1

source_name: Reference female DNA


title: Bladder tumor UC_0138_1_aCGH_h1

source_name: bladder tumor UC_0138_1


title: Bladder tumor UC_0093_1_aCGH_h1

source_name: bladder tumor UC_0093_1


title: Bladder tumor UC_0106_1_aCGH_h1

source_name: bladder tumor UC_0106_1


title: Bladder tumor UC_0097_1_aCGH_h3

source_name: bladder tumor UC_0097_1


title: Bladder tumor UC_0086_1_aCGH_h1

source_name: bladder tumor UC_0086_1


title: Bladder tumor UC_0101_1_aCGH_h2

source_name: bladder tumor UC_0101_1


title: Bladder tumor UC_0080_1_aCGH_h1

source_name: bladder tumor UC_0080_1


title: Bladder tumor UC_0078_1_aCGH_h1

source_name: bladder tumor UC_0078_1


title: Bladder tumor UC_0076_1_aCGH_h1

source_name: bladder tumor UC_0076_1


title: Bladder tumor UC_0077_1_aCGH_h2

source_name: bladder tumor UC_0077_1

source_name: Reference male DNA


title: Bladder tumor UC_0075_1_aCGH_h1

source_name: bladder tumor UC_0075_1


title: Bladder tumor UC_0089_1_aCGH_h2

source_name: bladder tumor UC_0089_1


title: Bladder tumor UC_0066_3_aCGH_h1

source_name: bladder tumor UC_0066_3


title: Bladder tumor UC_0069_1_aCGH_h1

source_name: bladder tumor UC_0069_1


title: Bladder tumor UC_0057_1_aCGH_h1

source_name: bladder tumor UC_0057_1


title: Bladder tumor UC_0073_1_aCGH_h1

source_name: bladder tumor UC_0073_1

source_name: Reference female DNA


title: Bladder tumor UC_0059_1_aCGH_h1

source_name: bladder tumor UC_0059_1


title: Bladder tumor UC_0045_4_aCGH_h1

source_name: bladder tumor UC_0045_4


title: Bladder tumor UC_0040_1_aCGH_h1

source_name: bladder tumor UC_0040_1


title: Bladder tumor UC_0070_1_aCGH_h1

source_name: bladder tumor UC_0070_1


title: Bladder tumor UC_0053_1_aCGH_h2

source_name: bladder tumor UC_0053_1


title: Bladder tumor UC_0033_2_aCGH_h1

source_name: bladder tumor UC_0033_2


title: Bladder tumor UC_0041_2_aCGH_h1

source_name: bladder tumor UC_0041_2


title: Bladder tumor UC_0029_1_aCGH_h1

source_name: bladder tumor UC_0029_1


title: Bladder tumor UC_0051_1_aCGH_h2

source_name: bladder tumor UC_0051_1


title: Bladder tumor UC_0060_1_aCGH_h1

source_name: bladder tumor UC_0060_1


title: Bladder tumor UC_0034_1_aCGH_h1

source_name: bladder tumor UC_0034_1

source_name: Reference male DNA


title: Bladder tumor UC_0025_1_aCGH_h1

source_name: bladder tumor UC_0025_1


title: Bladder tumor UC_0047_1_aCGH_h2

source_name: bladder tumor UC_0047_1


title: Bladder tumor UC_0007_1_aCGH_h1

source_name: bladder tumor UC_0007_1


title: Bladder tumor UC_0002_1_aCGH_h1

source_name: bladder tumor UC_0002_1


title: Bladder tumor UC_0021_1_aCGH_h1

source_name: bladder tumor UC_0021_1

source_name: Reference female DNA


title: Bladder tumor UC_0008_1_aCGH_h1

source_name: bladder tumor UC_0008_1


title: Bladder tumor UC_0043_1_aCGH_h1

source_name: bladder tumor UC_0043_1


title: Bladder tumor UC_0061_1_aCGH_h1

source_name: bladder tumor UC_0061_1


title: Bladder tumor UC_0017_1_aCGH_h1

source_name: bladder tumor UC_0017_1


title: Bladder tumor UC_0009_1_aCGH_h1

source_name: bladder tumor UC_0009_1


title: Bladder tumor UC_0067_1_aCGH_h1

source_name: bladder tumor UC_0067_1


title: primary neuroblastoma, SD_164

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

hyb_protocol: Following fragmentation, ~5 ug of cDNA were hybridized for 16 hr at 45°C on Affymetrix Human Exon 1.0 ST arrays (Affymetrix Part No. 900 651). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update.

data_processing:
In order to obtain expression information per gene, exon data was merged by transcript clusters (hg18/core exons). Exon array data was normalized according to the RMA algorithm using Genomics Suite (Partek).

Probe group file: HuEx-1 0-st-v1.r2.pgf
Meta-probeset file: HuEx-1 0-st-v2.r2.dt1.hg18.core.mps

source_name: neuroblastoma tumor

label_protocol: Biotinylated cDNA was prepared according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 5) from 1000 ng total RNA, including the rRNA reduction step.

growth_protocol: Primary human samples from surgery. No experimental conditions.

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

treatment_protocol: No treatment.

value: primary neuroblastoma


title: Bladder tumor UC_0023_1_aCGH_h1

source_name: bladder tumor UC_0023_1


title: primary neuroblastoma, SD_165


title: primary neuroblastoma, SD_161


title: primary neuroblastoma, SD_163


title: primary neuroblastoma, SD_131


title: primary neuroblastoma, SD_159


title: Bladder tumor UC_0001_1_aCGH_h1

source_name: bladder tumor UC_0001_1


title: primary neuroblastoma, SD_130


title: primary neuroblastoma, SD_160


title: primary neuroblastoma, SD_162


title: primary neuroblastoma, SD_153


title: primary neuroblastoma, SD_114


title: primary neuroblastoma, SD_132


title: primary neuroblastoma, SD_113


title: primary neuroblastoma, SD_134


title: primary neuroblastoma, SD_158


title: primary neuroblastoma, SD_155


title: primary neuroblastoma, SD_144


title: primary neuroblastoma, SD_118


title: primary neuroblastoma, SD_152


title: primary neuroblastoma, SD_142


title: primary neuroblastoma, SD_126


title: primary neuroblastoma, SD_125


title: primary neuroblastoma, SD_127


title: primary neuroblastoma, SD_129


title: primary neuroblastoma, SD_110


title: primary neuroblastoma, SD_124


title: primary neuroblastoma, 106_SD


title: primary neuroblastoma, SD_115


title: primary neuroblastoma, SD_119


title: primary neuroblastoma, 105_SD


title: primary neuroblastoma, 107_SD


title: primary neuroblastoma, 101_SD


title: primary neuroblastoma, 100_SD


title: primary neuroblastoma, 109_SD


title: primary neuroblastoma, 95_SD


title: primary neuroblastoma, 104_SD


title: primary neuroblastoma, 98_SD


title: primary neuroblastoma, 102_SD


title: primary neuroblastoma, 96_SD


title: primary neuroblastoma, 92_SD


title: primary neuroblastoma, 90_SD


title: primary neuroblastoma, 91_SD


title: primary neuroblastoma, 94_SD


title: primary neuroblastoma, 99_SD


title: primary neuroblastoma, 93_SD


title: primary neuroblastoma, 89_SD


title: primary neuroblastoma, 103_SD


title: primary neuroblastoma, 83_SD


title: primary neuroblastoma, 81_SD


title: primary neuroblastoma, 88_SD


title: primary neuroblastoma, 97_SD


title: primary neuroblastoma, 82_SD


title: primary neuroblastoma, 87_SD


title: primary neuroblastoma, 75_SD


title: primary neuroblastoma, 76_SD


title: primary neuroblastoma, 77_SD


title: primary neuroblastoma, 72_SD


title: primary neuroblastoma, 78_SD


title: primary neuroblastoma, 71_SD


title: primary neuroblastoma, 80_SD


title: primary neuroblastoma, 70_SD


title: primary neuroblastoma, 79_SD


title: primary neuroblastoma, 66_SD


title: primary neuroblastoma, 57_SD


title: primary neuroblastoma, 60_SD


title: primary neuroblastoma, 61_SD


title: primary neuroblastoma, 55_SD


title: primary neuroblastoma, 69_SD


title: primary neuroblastoma, 67_SD


title: primary neuroblastoma, 59_SD


title: cgh-1(RNAi) 2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description: SAMPLE 5

hyb_protocol: hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix)

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing:
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probe group file: probeId_to_tr_min10probes.tab

organism: Caenorhabditis elegans

source_name: young adult cytoplasmic extracts

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)

growth_protocol: Worms were grown until the young adult stage.

extract_protocol: RNA was Trizol extracted

treatment_protocol: Cytoplasmic extracts were prepared as described in Wright et al, 2010

value: wild type

tag: developmental stage

value: young adult

tag: RNAi construct

value: whole worm lysate


title: cgh-1(RNAi) 1

description: SAMPLE 4

tag: genotype/variation


title: cgh-1(RNAi) 3

description: SAMPLE 6


title: primary neuroblastoma, 62_SD

tag: treatment


title: primary neuroblastoma, 65_SD


title: Mock RNAi 3

description: SAMPLE 3

value: Mock RNAi


title: primary neuroblastoma, 56_SD


title: primary neuroblastoma, 58_SD


title: primary neuroblastoma, 51_SD


title: primary neuroblastoma, 54_SD


title: Mock RNAi 2

description: SAMPLE 2


title: primary neuroblastoma, 52_SD


title: Mock RNAi 1

description: SAMPLE 1


title: gld-1_polysomal_3

description: SAMPLE 15

data_processing:
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probe group file : probeId_to_tr_min10probes.tab

source_name: gld-1_polysomal RNA

growth_protocol: Worms were grown until the young adult stage, washed in cold M9, and washed and frozen in washing buffer.

extract_protocol: RNA from total and polysomal sucrose fractions was extracted using Trizol

treatment_protocol: Worm lysates were prepared in extraction buffer and subjected to sucrose density gradient ultracentrifugation; the gradients were fractionated into 12 samples

value: gld-1 (q485) mutant


title: gld-1_polysomal_2

description: SAMPLE 14


title: gld-1_polysomal_4

description: SAMPLE 16


title: primary neuroblastoma, 64_SD


title: primary neuroblastoma, 53_SD


title: primary neuroblastoma, 63_SD


title: wt_polysomal_4

description: SAMPLE 12

source_name: wt_polysomal RNA


title: wt_polysomal_3

description: SAMPLE 11


title: primary neuroblastoma, 47_SD


title: primary neuroblastoma, 48_SD


title: wt_polysomal_2

description: SAMPLE 10


title: primary neuroblastoma, 46_SD


title: primary neuroblastoma, 74_SD


title: gld-1_total RNA_4

description: SAMPLE 8

source_name: gld-1_total RNA


title: gld-1_total RNA_1

description: SAMPLE 5


title: wt_total RNA_4

description: SAMPLE 4

source_name: wt_total RNA


title: gld-1_total RNA_2

description: SAMPLE 6


title: gld-1_total RNA_3

description: SAMPLE 7


title: wt_polysomal_1

description: SAMPLE 9


title: wt_total RNA_2

description: SAMPLE 2


title: primary neuroblastoma, 2_SD


title: wt_total RNA_3

description: SAMPLE 3


title: primary neuroblastoma, 45_SD


title: cgh-1_1

description: SAMPLE 7

hyb_protocol: Hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix).

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)/

extract_protocol: RNA from gonads was extracted using the PicoPure Kit.

treatment_protocol: Gonads were dissected in M9.

value: cgh-1 (tn691) mutant

value: dissected gonads


title: wt_total RNA_1

description: SAMPLE 1


title: cgh-1_2

description: SAMPLE 8


title: gld-1_3

description: SAMPLE 6


title: cgh-1_3

description: SAMPLE 9


title: primary neuroblastoma, 68_SD


title: gld-1_polysomal_1

description: SAMPLE 13


title: GLD-1 IP_3

description:
The anti-GLD-1 antibody was also raised by the in house facility: Scheckel et al., submitted.
SAMPLE 6

source_name: GLD-1 IP

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

growth_protocol: Worms were grown until the young adult stage, and washed and frozen in M9.

extract_protocol: RNA from was extracted using Trizol.

treatment_protocol: Worm lysates were prepared in extraction buffer and subjected to IP.

tag: ip antibody


title: wild-type_1

description: SAMPLE 1

source_name: wild-type

tag: tissue


title: wild-type_3

description: SAMPLE 3


title: gld-1_1

description: SAMPLE 4


title: GLD-1 IP_2

description:
The anti-GLD-1 antibody was also raised by the in house facility: Scheckel et al., submitted.
SAMPLE 5


title: gld-1_2

description: SAMPLE 5


title: MYC IP_2

description:
The anti-myc 9E10 antibody was used as a cell culture supernatant obtained by growing the 9E10 hybridoma cell line by the in house facility: Wright et al., 2011.
SAMPLE 2

source_name: MYC IP

value: anti-myc 9E10


title: GLD-1 IP_1

description:
The anti-GLD-1 antibody was also raised by the in house facility: Scheckel et al., submitted.
SAMPLE 4


title: MYC IP_1

description:
The anti-myc 9E10 antibody was used as a cell culture supernatant obtained by growing the 9E10 hybridoma cell line by the in house facility: Wright et al., 2011.
SAMPLE 1


title: MYC IP_3

description:
The anti-myc 9E10 antibody was used as a cell culture supernatant obtained by growing the 9E10 hybridoma cell line by the in house facility: Wright et al., 2011.
SAMPLE 3


title: wild-type_2

description: SAMPLE 2


title: Bladder tumor UC_0488_2.RNA.e1.a1.lbe1

hyb_protocol: According to the manufacturers specifications

data_processing:
Raw intensity values representing mean bead pool intensity values for each probe were background corrected, negative intensities were capped to zero, followed by addition of an intensity constant of 30 to all probe intensities. Data was normalized using a quantile normalization algorithm as implemented in the BASE software (Saal, L.H. et al. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol 3, 2002.).
Matrix normalized: The final reporter intensity values (unlogged) that was used for data analyses. Matrix non-normalized :Background corrected intensity values prior normalization and filtering.

source_name: Bladder tumor UC_0488_2

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp RNA Amplification kit according to the manufacturers specifications

extract_protocol: Total RNA was extracted using Trizol reagent followed by purification on RNeasy micro columns (Qiagen) according to the manufacturers recommendations

value: bladder cancer tumor


title: Bladder tumor UC_0566_1.RNA.e1.a1.lbe1

scan_protocol: According to the manufacturers specifications

source_name: Bladder tumor UC_0566_1


title: Bladder tumor UC_0349_2.RNA.e1.a1.lbe2

source_name: Bladder tumor UC_0349_2


title: Bladder tumor UC_0528_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0528_1


title: Bladder tumor UC_0545_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0545_1


title: Bladder tumor UC_0343_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0343_1


title: Bladder tumor UC_0522_1.RNA.e1.a2.lbe1

source_name: Bladder tumor UC_0522_1


title: Bladder tumor UC_0551_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0551_1


title: Bladder tumor UC_0519_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0519_1


title: Bladder tumor UC_0533_1.RNA.e2.a1.lbe1

source_name: Bladder tumor UC_0533_1


title: Bladder tumor UC_0410_1b.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0410_1b


title: Bladder tumor UC_0342_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0342_1


title: Bladder tumor UC_0386_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0386_1


title: Bladder tumor UC_0516_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0516_1


title: Bladder tumor UC_0372_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0372_1


title: Bladder tumor UC_0376_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0376_1


title: Bladder tumor UC_0368_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0368_1


title: Bladder tumor UC_0539_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0539_1


title: Bladder tumor UC_0610_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0610_1


title: Bladder tumor UC_0400_1b.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0400_1b


title: Bladder tumor UC_0507_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0507_1


title: Bladder tumor UC_0513_1a.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0513_1a


title: Bladder tumor UC_0589_1.RNA.e1.a2.lbe1

source_name: Bladder tumor UC_0589_1


title: Bladder tumor UC_0361_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0361_1


title: Bladder tumor UC_0521_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0521_1


title: Bladder tumor UC_0394_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0394_1


title: Bladder tumor UC_0384_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0384_1


title: Bladder tumor UC_0399_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0399_1


title: Bladder tumor UC_0552_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0552_1


title: Bladder tumor UC_0333_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0333_1


title: Bladder tumor UC_0290_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0290_1


title: Bladder tumor UC_0267_3.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0267_3


title: Bladder tumor UC_0335_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0335_1


title: Bladder tumor UC_0284_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0284_1


title: Bladder tumor UC_0283_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0283_1


title: Bladder tumor UC_0302_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0302_1


title: Bladder tumor UC_0240_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0240_1


title: Bladder tumor UC_0263_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0263_1


title: Bladder tumor UC_0322_2.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0322_2


title: Bladder tumor UC_0249_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0249_1


title: Bladder tumor UC_0301_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0301_1


title: Bladder tumor UC_0321_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0321_1


title: Bladder tumor UC_0226_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0226_1


title: Bladder tumor UC_0299_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0299_1


title: Bladder tumor UC_0327_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0327_1


title: Bladder tumor UC_0339_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0339_1


title: Bladder tumor UC_0265_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0265_1


title: Bladder tumor UC_0274_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0274_1


title: Bladder tumor UC_0287_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0287_1


title: Bladder tumor UC_0231_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0231_1


title: Bladder tumor UC_0242_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0242_1


title: Bladder tumor UC_0224_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0224_1


title: Bladder tumor UC_0329_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0329_1


title: Bladder tumor UC_0312_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0312_1


title: Bladder tumor UC_0237_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0237_1


title: Bladder tumor UC_0235_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0235_1


title: Bladder tumor UC_0230_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0230_1


title: Bladder tumor UC_0196_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0196_1


title: Bladder tumor UC_0207_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0207_1


title: Bladder tumor UC_0218_2.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0218_2


title: Bladder tumor UC_0195_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0195_1


title: Bladder tumor UC_0223_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0223_1


title: Bladder tumor UC_0200_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0200_1


title: Bladder tumor UC_0208_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0208_1


title: Bladder tumor UC_0173_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0173_1


title: Bladder tumor UC_0215_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0215_1


title: Bladder tumor UC_0185_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0185_1


title: Bladder tumor UC_0187_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0187_1


title: Bladder tumor UC_0209_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0209_1


title: Bladder tumor UC_0162_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0162_1


title: Bladder tumor UC_0518_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0518_1


title: Bladder tumor UC_0130_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0130_1


title: Bladder tumor UC_0137_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0137_1


title: Bladder tumor UC_0166_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0166_1


title: Bladder tumor UC_0152_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0152_1


title: Bladder tumor UC_0199_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0199_1


title: Bladder tumor UC_0213_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0213_1


title: Bladder tumor UC_0159_1.RNA.e2.a1.lbe1

source_name: Bladder tumor UC_0159_1


title: Bladder tumor UC_0214_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0214_1


title: Bladder tumor UC_0192_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0192_1


title: Bladder tumor UC_0147_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0147_1


title: Bladder tumor UC_0203_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0203_1


title: Bladder tumor UC_0170_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0170_1


title: Bladder tumor UC_0169_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0169_1


title: Bladder tumor UC_0176_2.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0176_2


title: Bladder tumor UC_0129_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0129_1


title: Bladder tumor UC_0106_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0106_1


title: Bladder tumor UC_0145_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0145_1


title: Bladder tumor UC_0120_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0120_1


title: Bladder tumor UC_0095_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0095_1


title: Bladder tumor UC_0138_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0138_1


title: Bladder tumor UC_0117_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0117_1


title: Bladder tumor UC_0112_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0112_1


title: Bladder tumor UC_0086_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0086_1


title: Bladder tumor UC_0114_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0114_1


title: Bladder tumor UC_0101_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0101_1


title: Bladder tumor UC_0122_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0122_1


title: Bladder tumor UC_0075_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0075_1


title: Bladder tumor UC_0093_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0093_1


title: Bladder tumor UC_0073_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0073_1


title: Bladder tumor UC_0067_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0067_1


title: Bladder tumor UC_0059_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0059_1


title: Bladder tumor UC_0115_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0115_1


title: Bladder tumor UC_0069_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0069_1


title: Bladder tumor UC_0077_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0077_1


title: Bladder tumor UC_0070_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0070_1


title: Bladder tumor UC_0089_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0089_1


title: Bladder tumor UC_0066_3.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0066_3


title: Bladder tumor UC_0080_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0080_1


title: Bladder tumor UC_0051_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0051_1


title: Bladder tumor UC_0097_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0097_1


title: Bladder tumor UC_0111_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0111_1


title: Bladder tumor UC_0057_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0057_1


title: Bladder tumor UC_0060_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0060_1


title: Bladder tumor UC_0053_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0053_1


title: Bladder tumor UC_0043_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0043_1


title: Bladder tumor UC_0034_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0034_1


title: Bladder tumor UC_0047_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0047_1


title: Bladder tumor UC_0029_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0029_1


title: Bladder tumor UC_0040_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0040_1


title: Bladder tumor UC_0025_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0025_1


title: Bladder tumor UC_0021_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0021_1


title: Bladder tumor UC_0033_2.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0033_2


title: Bladder tumor UC_0007_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0007_1


title: Bladder tumor UC_0008_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0008_1


title: Bladder tumor UC_0023_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0023_1


title: Bladder tumor UC_0001_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0001_1


title: Bladder tumor UC_0041_2.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0041_2


title: CTCF_CP190-2

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

description:
CTCF-CP-2
Gene expression in Kc cells with CTCF and CP190 knockdowns.

hyb_protocol: Hybridization was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), using Partek® software, version 6.5.

organism: Drosophila melanogaster

source_name: KC cells, CTCF and CP190 KDs

label_protocol: Labeling was performed by the FSU-NimbleGen Microarray Facility, following the NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Drosophila Kc cells culture was conducted as per the Drosophila RNAi Screening Center (DRSC) protocol (Armknecht et al. 2005 (PMID 15644175)).

extract_protocol: RNA was isolated from Kc cells using the Qiagen RNeasy kit following the manufacturer's protocol. cDNA synthesis was then performed using the Applied Biosystems High Capacity cDNA Reverse Transcription Kit.

treatment_protocol: RNAi knockdown was conducted as per the Drosophila RNAi Screening Center (DRSC) protocol (Armknecht et al. 2005) with the exception that dsRNA was added every day for 3 days and the cells were then collected on the 4th day.

value: Kc

value: CTCF and CP190 knockdowns


title: CTCF_CP190-1

description:
CTCF-CP-1
Gene expression in Kc cells with CTCF and CP190 knockdowns.


title: CTCF-2

description:
CTCF-2
Gene expression in Kc cells with CTCF knockdown.

source_name: KC cells, CTCF KD

value: CTCF knockdown


title: SuHw-1

description:
SuHw-1
Gene expression in Kc cells with SuHw knockdown.

source_name: KC cells, SuHw KD

value: SuHw knockdown


title: SuHw-2

description:
SuHw-2
Gene expression in Kc cells with SuHw knockdown.


title: SuHw_CP190-1

description:
SuHw-CP-1
Gene expression in Kc cells with SuHw & CP190 knockdowns.

source_name: KC cells, SuHw and CP190 KDs

value: SuHw and CP190 knockdowns


title: WT-1

description: Gene expression in wild type KC cells with B-gal KD's

source_name: wild type KC cells with B-gal KD's

value: KC cells

value: Wild type


title: CTCF-1

description:
CTCF-1
Gene expression in Kc cells with CTCF knockdown.


title: Bladder tumor UC_0017_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0017_1

value: Ta


title: SuHw_CP190-2

description:
SuHw-CP-2
Gene expression in Kc cells with SuHw & CP190 knockdowns.


title: BEAF_CTCF-2

description:
BEAF-CT-2
Gene expression in Kc cells with BEAF and CTCT0 knockdowns.

source_name: KC cells, BEAF and CTCF KDs

value: BEAF and CTCF knockdowns


title: BEAF_CTCF-1

description:
BEAF-CT-1
Gene expression in Kc cells with BEAF and CTCT0 knockdowns.


title: Bladder tumor UC_0002_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0002_1


title: WT-2


title: CP190-1

description: Gene expression in KC cells with CP190 KD's

source_name: KC cells with CP190 KD's

value: CP190 KD's


title: BEAF-1

description: Gene expression in KC cells with BEAF KD's

source_name: KC cells with BEAF KD's

value: BEAF KD's


title: BEAF_CP190-1

description:
BEAF-CP-1
Gene expression in Kc cells with BEAF and CP190 knockdowns.

source_name: KC cells, BEAF and CP190 KDs

value: BEAF and CP190 knockdowns


title: BEAF-2


title: CP190-2


title: Bladder tumor UC_0009_1.RNA.e1.a1.lbe1

source_name: Bladder tumor UC_0009_1


title: BEAF_CP190-2

description:
BEAF-CP-2
Gene expression in Kc cells with BEAF and CP190 knockdowns.


title: liver_EHL_newborn_male_rep1_mRNA

city: Nanjing

first: Runsheng

last: Li

state: Jiangsu

department: Nanjing Agricultural University

institute: Nanjing Agricultural University

description: This sample is of Erhualian liver. It is a pooled total RNA sample of two littermate piglets.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Sus scrofa

source_name: porcine liver ,newborn,male,Erhualian breed

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

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Concentration of the extracted RNA was measured using NanoDrop ND-1000 Spectrophotometer. RNA integrity was confirmed by denaturing agarose electrophoresis, and DNA contamination was evaluated by PCR using isolated RNA as template with the primer of GAPDH (primer sequence was shown in table S4). High quality RNA samples were then stored at -70°C till further use.

tag: breed

value: Erhualian

tag: gender

value: male

tag: age

value: newborn

value: liver


title: liver_EHL_newborn_male_rep2_mRNA


title: liver_LW_newborn_male_rep1_mRNA

description: This sample is of Large White liver. It is a pooled total RNA sample of two littermate piglets.

source_name: porcine liver ,newborn,male,Large White breed

value: Large White


title: liver_EHL_newborn_male_rep3_mRNA


title: wt-matA_5h_nbr29-a

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain

tag: genetic modification

value: refpool

tag: time

value: reference

source_name: wt-matA 5h

value: 5 h

value: glucose depletion

value: wt-matA 5h


title: wt-matA_60min_nbr029-a

source_name: wt-matA 60min

value: 60 min

value: wt-matA 60min


title: liver_LW_newborn_male_rep3_mRNA


title: wt-matA_7.5min_nbr029-a

source_name: wt-matA 7.5min

value: 7.5 min

value: wt-matA 7.5min


title: wt-matA_7.5min_nbr029-b

value: wt-matA


title: wt-matA_3min_nbr029-a

source_name: wt-matA 3min

value: 3 min

value: wt-matA 3min


title: wt-matA_3min_nbr029-b


title: wt-matA_60min_nbr029-b


title: wt-matA_5h-nbr29-b


title: wt-matA_2.5h-nbr29-b

source_name: wt-matA 2.5h


title: wt-matA_30min_nbr029-b

source_name: wt-matA 30min

value: 30 min


title: wt-matA_110min_nbr029-b

source_name: wt-matA 110min

value: 110 min


title: wt-matA_15min_nbr029-a

source_name: wt-matA 15min

value: 15 min

value: wt-matA 15min


title: wt-matA_2.5h_nbr29-a

value: wt-matA 2.5h


title: wt-matA_0min_nbr029-b

source_name: wt-matA 0min

value: 0 min

value: refpool


title: liver_LW_newborn_male_rep2_mRNA

value: Large White

value: male

value: newborn

value: liver


title: wt-matA_110min_nbr029-a

value: reference

value: glucose depletion

value: wt-matA 110min


title: wt-nbr030-a

source_name: wt

value: wt


title: wt-matA_0min_nbr029-a

value: wt-matA


title: wt-nbr030-b


title: wt-nbr042-a


title: wt-matA_15min_nbr029-b


title: wt-lpa005-b

hyb_protocol: Hybridization protocol v2.2

label_protocol: aminoallyl labeling v2.1.1


title: wt-matA_30min_nbr029-a

value: wt-matA 30min


title: wt-nbr042-b


title: wt-lpa005-a


title: wt-htp65-b

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: wt-htp131-b


title: wt-htp135-b


title: wt-htp10-c


title: wt-htp65-a


title: wt-htp10-a


title: wt-htp15-b


title: Liver_Female_CF_rep3

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

institute: CWRU

description: lipid synthesis, nutrition, adipose storage

hyb_protocol: cRNA was hybridized to Beadchips following Illumina's instructions

scan_protocol: Beadchips were scanned using Illumina BeadArray Reader

data_processing: Data was initially processed with Illumina GenomeStudio software to assess quality control. Raw data was transferred to Integromics Biomarker Discovery for TIBCO Spotfire software (IBD, Madrid, Spain) where data was normalized using Illumina normalization: forcePositive as background correction, log2 as variance stabilization method, and quantile as the normalization method. Wild type group was used as the reference group.

source_name: Whole liver

label_protocol: Samples were labeled with Cy3 following Illumina's protocol

growth_protocol: At 21 days of age, mice were weaned onto an enriched diet (9F Sterilizable Rodent Diet 7960, Harlan Teklad, Madison, WI) and were provided a Colyte solution (peg-3350 & electrolytes for oral solution – Schwarz Pharma, Milwaukee, WI) in place of water at half-strength since at full strength it causes adverse effects in non-CF mice. Mice were sacrificed at 23 days.

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc, Valencia, CA. DNase treatment was performed in the column prior to elution. Biotin labeled cRNA was prepared uisng Illumina TotalPrep RNA Amplification kit (Applied Biosystems/Ambion, Austin, TX).

tag: Sex

value: Female

value: 3-weeks old

tag: genotype

value: CF


title: wt-htp10-b


title: Liver_Female_CF_rep4


title: wt-ea041-a


title: wt-ea043-a


title: Liver_Female_WT_rep4

value: WT


title: wt-gam002-b


title: wt-htp07-a


title: wt-htp07-b


title: Liver_Female_CF_rep1


title: wt-ea043-b


title: wt-htp131-a


title: Liver_Female_WT_rep3


title: Liver_Female_CF_rep2


title: Liver_Female_WT_rep1


title: wt-ea040-a


title: wt-gam002-a


title: wt-ea039-1-a


title: wt-ea038-1-b


title: wt-ea038-1-a


title: wt-ea039-1-b


title: wt-ea035-b


title: wt-ea040-b


title: Liver_Female_WT_rep2


title: wt-ea034-1-b


title: wt-ea034-1-a


title: wt-ea032-a


title: wt-ea026-1-b


title: wt-ea028-1-a


title: wt-ea031-1-a


title: wt-ea025-1-a


title: wt-ea032-b


title: wt-ea035-a


title: wt-ea021-1-a


title: wt-ea024-1-ab


title: wt-ea027-1-a


title: wt-ea023-1-b


title: wt-ea022-1-b


title: wt-ea024-1-a


title: wt-ea021-1-b


title: wt-ea019-a


title: wt-ea031-1-b


title: wt-ea027-1-b


title: wt-ea020-1-b


title: wt-ea028-1-b


title: wt-ea016-1-b


title: wt-ea023-1-a


title: wt-ea020-1-a


title: wt-ea022-1-a


title: wt-ea019-b


title: wt-ea026-1-a


title: wt-ea015-1-b


title: wt-ea015-1-a


title: wt-ea014-1-a


title: wt-ea014-1-b


title: SK-LU-1

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell type

value: lung cancer cell line

tag: cell line

tag: atcc alias

tag: histology

value: Adenocarcinoma

tag: race

value: Caucasian

value: F


title: Hop-92

value: Large Cell


title: HCC4018


title: wt-ea016-1-a

value: refpool


title: HCC4019

value: M


title: HCC4006


title: wt-ea010-1-a


title: wt-ea010-1-b


title: HCC4017


title: HCC3051

value: Black


title: HCC4011


title: PC-9

value: Asian


title: HCC2935


title: wt-ea013-1-a


title: Non-irradiated unsorted intestinal epithelial cells replicate 7

city: Chapel Hill

first: P. Kay

last: Lund

state: NC

address: 6336 MBRB CB 7545 111 Mason Farm Road

department: Cell and Molecular Physiology

institute: UNC at Chapel Hill

description: Biological replicate 7/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit (5188-5242, Santa Clara, CA) and the Agilent Microarray Hybridization Chamber Kit (G2534A, Santa Clara, CA)

scan_protocol: Slides were scanned using Agilent Microarray Scanner and Agilent Scan Control software (Santa Clara, CA)

data_processing: Scanned images were analyzed, data were processed and LogRatio analysis was perfomed using Agilent Feature Extraction Software version 10.7.3.1 (Santa Clara, CA)

source_name: Unsorted intestinal epithelial cells

label_protocol: 0.1-1µg ot total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit, Two-Color (5190-2306, Santa Clara, CA) - Cy5 for samples and Cy3 for reference

growth_protocol: Sox9-EGFP BAC transgenic mice used between 6-10 weeks old

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit (Qiagen, Venlo, The Netherlands) following manufacturer's instructions

treatment_protocol: Sox9-EGFP transgenic mice were given a single dose of 14Gy abdominal irradiation using an XRAD320 (Precision X-Ray, East Haven, CT - Filter: 2mm, Al; 47cm ; 320kV/s, 10mA; 2.8Gy/min). Mice were euthanized at day 5 post-radiation, jejunum was collected and processed for single cell dissociation. Cells expressing either Negative, Sublow, Low or HIgh levels of the Sox9-EGFP transgene were isolated by FACS. Non-irradiated control mice were included in the same run of FACS and gating was defined using EGFP intensity profile of the non-irradiated controls.

tag: developmental stage

value: adult

value: male

tag: source tissue

value: small intestine - jejunum

tag: mouse model

value: Sox9-EGFP BAC transgenic mice

tag: level of expression of the sox9-egfp reporter gene

value: non-applicable (unsorted)

value: non-irradiated (control)

value: Unsorted intestinal epithelial cells

source_name: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: HCC2450

value: Squamous


title: Non-irradiated unsorted intestinal epithelial cells replicate 6

description: Biological replicate 6/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

tag: treatment

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: wt-ea013-1-b

value: wt


title: Pool of non-sorted intestinal epithelial cells from non-irradiated mice

description: Biological replicate 8/8; pool of unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

tag: gender


title: wt-ea009-1-a


title: wt-ea009-1-b


title: HCC2814

value: lung cancer cell line

tag: age

value: Caucasian


title: Non-irradiated unsorted intestinal epithelial cells replicate 5

description: Biological replicate 5/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

tag: strain


title: HCC2429

value: NSCLC (poorly diff)

value: F


title: HCC2374

value: Large Cell Neuroendocrine


title: wt-ea008-1-b

tag: genetic modification

value: refpool


title: HCC2279

value: Adenocarcinoma

value: Asian


title: Non-irradiated unsorted intestinal epithelial cells replicate 3

description: Biological replicate 3/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: male


title: HCC1897

value: Black

value: M


title: Non-irradiated unsorted intestinal epithelial cells replicate 4

description: Biological replicate 4/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

value: small intestine - jejunum

value: Sox9-EGFP BAC transgenic mice

value: non-applicable (unsorted)

value: non-irradiated (control)


title: HCC2108


title: wt-ea008-1-a

value: wt


title: HCC1359

value: lung cancer cell line

value: Large Cell


title: HCC1171

value: NSCLC (poorly diff)

value: Caucasian


title: wt-ea006-1-b


title: Non-irradiated unsorted intestinal epithelial cells replicate 2

description: Biological replicate 2/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

value: Unsorted intestinal epithelial cells

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: HCC1438


title: wt-ea006-1-a

value: refpool


title: wt-ea007-1-b


title: HCC1195

value: Adenocarcinoma (mixed)


title: Irradiated Sox9-EGFP High replicate 3

description: Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

source_name: Sorted intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene

value: adult

value: High

value: irradiated


title: HCC1833

value: Adenocarcinoma

value: F


title: HCC970

value: SCLC

value: unknown

value: M


title: wt-ea005-1-b

value: wt


title: Non-irradiated unsorted intestinal epithelial cells replicate 1

description: Biological replicate 1/8; unsorted intestinal epithelial cells from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: Sox9-EGFP BAC transgenic mice

value: non-applicable (unsorted)

value: non-irradiated (control)


title: HCC515

value: lung cancer cell line

value: Caucasian


title: HCC827

value: Adenocarcinoma (BAC features)


title: wt-ea005-1-a

value: refpool


title: HCC1313

value: Squamous


title: Irradiated Sox9-EGFP High replicate 2

description: Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: High

value: irradiated

value: Sorted intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: wt-ea003-1-a


title: HCC461

value: Adenocarcinoma

value: M


title: HCC364


title: HCC95


title: HCC78


title: Irradiated Sox9-EGFP High replicate 1

description: Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: male


title: wt-ea003-1-b

value: wt


title: Irradiated Sox9-EGFP Low replicate 3

description: Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

source_name: Sorted intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene

value: small intestine - jejunum

value: Sox9-EGFP BAC transgenic mice

value: Low


title: HCC44

value: lung cancer cell line

value: F


title: wt-ea002-1-b

source_name: refpool


title: HCC33

value: SCLC

value: Caucasian


title: Irradiated Sox9-EGFP Low replicate 2

description: Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: Sorted intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene

value: non-applicable (unsorted)

value: non-irradiated (control)


title: HCC193


title: wt-ea002-1-a

value: refpool


title: HCC366

value: Adenosquamous

value: unknown


title: wt-ea001-1-b


title: Irradiated Sox9-EGFP Sublow replicate 3

description: Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

source_name: Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene

value: adult

value: Sublow

value: irradiated

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: Irradiated Sox9-EGFP Low replicate 1

description: Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum


title: wt-ea001-1-a

value: wt


title: HCC15

value: lung cancer cell line

value: Squamous

value: Black

value: M


title: Irradiated Sox9-EGFP Sublow replicate 2

description: Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: Sox9-EGFP BAC transgenic mice

value: Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene


title: H3122

value: NSCLC


title: wt-HTP136-b

value: refpool


title: H2405

value: Adenocarcinoma

value: Caucasian


title: Irradiated Sox9-EGFP Sublow replicate 1

description: Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: non-applicable (unsorted)

value: non-irradiated (control)


title: H2887


title: wt-HTP136-a


title: Irradiated Sox9-EGFP Negative replicate 2

description: Biological replicate 2/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

source_name: Sorted intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene

value: Negative

value: irradiated

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: H2291


title: H2882

value: F


title: Irradiated Sox9-EGFP Negative replicate 3

description: Biological replicate 3/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: Sorted intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene


title: H2342

value: lung cancer cell line

value: M


title: wt-EA050-b

value: wt


title: H2258


title: wt-EA050-a


title: wt-EA044-b


title: H2228


title: H2227

value: SCLC


title: Non-irradiated Sox9-EGFP High replicate 7

description: Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: Sox9-EGFP BAC transgenic mice

value: High

value: Sorted intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene


title: H2172

value: NSCLC


title: Irradiated Sox9-EGFP Negative replicate 1

description: Biological replicate 1/3; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: non-applicable (unsorted)


title: H2250

value: Adenocarcinoma

value: Caucasian


title: wt-EA044-a

value: refpool


title: H2195


title: H2171


title: H2126


title: HOP-62

value: F


title: wt-EA037-b


title: H2141


title: H2170

value: Squamous


title: Non-irradiated Sox9-EGFP High replicate 4

description: Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: non-irradiated (control)

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: Non-irradiated Sox9-EGFP High replicate 5

description: Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H2122

value: lung cancer cell line


title: Non-irradiated Sox9-EGFP High replicate 6

description: Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: wt-EA037-a

value: wt


title: H2107

value: SCLC

value: Black

value: M


title: H2106

value: Large Cell Neuroendocrine


title: Non-irradiated Sox9-EGFP High replicate 2

description: Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: Sox9-EGFP BAC transgenic mice

value: High

value: Sorted intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene


title: H2087

value: Adenocarcinoma

value: Caucasian


title: wt-EA036-a

value: refpool


title: wt-EA036-b


title: H3255

value: F


title: Non-irradiated Sox9-EGFP High replicate 3

description: Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: non-applicable (unsorted)


title: H2086

value: lung cancer cell line


title: Non-irradiated Sox9-EGFP Low replicate 5

description: Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: Low

value: non-irradiated (control)

value: Sorted intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: Non-irradiated Sox9-EGFP High replicate 1

description: Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing High levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H2052

value: Mesothelioma

value: M


title: H2085


title: H2073


title: H2009


title: tsl1-del-2-b


title: tps3-del-1-a


title: H1975


title: Non-irradiated Sox9-EGFP Low replicate 6

description: Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: Sox9-EGFP BAC transgenic mice


title: tps3-del-1-b


title: H2023


title: Non-irradiated Sox9-EGFP Low replicate 7

description: Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: tps2-del-1-b


title: Non-irradiated Sox9-EGFP Low replicate 4

description: Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H2030


title: H1944


title: tps2-del-1-a


title: H1869

value: Squamous


title: H1819

value: Adenocarcinoma


title: H1838


title: tps2-del+ram1-del-1-b


title: H1793


title: Non-irradiated Sox9-EGFP Low replicate 3

description: Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H1781

value: Caucasian


title: Non-irradiated Sox9-EGFP Low replicate 1

description: Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H1792


title: Non-irradiated Sox9-EGFP Low replicate 2

description: Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Low levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: tsl1-del-2-a

value: refpool


title: tps2-del+gpr1-del-1-a


title: H1755

value: F


title: H1693


title: H1672

value: SCLC


title: tps2-del+gpr1-del-1-b


title: tpk2-del-3-b


title: H1650


title: H1734


title: H1703

value: Adenosquamous


title: Non-irradiated Sox9-EGFP Sublow replicate 5

description: Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: Sublow

value: Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene

value: non-applicable (unsorted)


title: Non-irradiated Sox9-EGFP Sublow replicate 4

description: Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: non-irradiated (control)

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: H1666

value: lung cancer cell line


title: tps2-del+ram1-del-1-a(2)


title: H1648

value: Black

value: M


title: Non-irradiated Sox9-EGFP Sublow replicate 7

description: Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: Sox9-EGFP BAC transgenic mice


title: H1993

value: Adenocarcinoma

value: Caucasian


title: Non-irradiated Sox9-EGFP Sublow replicate 6

description: Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H1651


title: tpk2-del-3-a

value: refpool


title: tco89-del-1-a


title: Non-irradiated Sox9-EGFP Sublow replicate 1

description: Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: H1570

value: Large Cell


title: H1607

value: SCLC


title: H2347

value: F


title: Non-irradiated Sox9-EGFP Sublow replicate 3

description: Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum


title: tco89-del-1-b


title: H1568


title: Non-irradiated Sox9-EGFP Sublow replicate 2

description: Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: Sublow

value: Sorted intestinal epithelial cells expressing Sublow levels of a Sox9-EGFP reporter gene


title: ste14-del-2-a


title: Non-irradiated Sox9-EGFP Negative replicate 7

description: Biological replicate 7/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: Negative

value: non-irradiated (control)

value: Sorted intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene

value: non-applicable (unsorted)


title: H1573

value: lung cancer cell line


title: H1437

value: M


title: Non-irradiated Sox9-EGFP Negative replicate 6

description: Biological replicate 6/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult

value: Sox9-EGFP BAC transgenic mice

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: H1238

value: Caucasian


title: H1355

value: Adenocarcinoma


title: Non-irradiated Sox9-EGFP Negative replicate 5

description: Biological replicate 5/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice


title: std1-del-2-a

value: refpool


title: H1563


title: H1395

value: F


title: H1514

value: SCLC


title: H1373

value: Black


title: H1385

value: Squamous


title: sok2-del-1-b


title: H1299

value: Large Cell Neuroendocrine


title: ste14-del-2-b


title: Non-irradiated Sox9-EGFP Negative replicate 3

description: Biological replicate 3/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: male

value: small intestine - jejunum

value: Negative


title: H920


title: H1184


title: sok2-del-1-a


title: std1-del-2-b


title: H889


title: snf4-del-1-b


title: H969


title: Non-irradiated Sox9-EGFP Negative replicate 2

description: Biological replicate 2/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: non-irradiated (control)

value: Sorted intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene

value: non-applicable (unsorted)


title: Non-irradiated Sox9-EGFP Negative replicate 4

description: Biological replicate 4/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: adult


title: H865

value: lung cancer cell line


title: Non-irradiated Sox9-EGFP Negative replicate 1

description: Biological replicate 1/7; FACS-isolated intestinal epithelial cells expressing Negative levels of a Sox9-EGFP reporter gene from non-irradiated Sox9-EGFP BAC transgenic mice

value: Sox9-EGFP BAC transgenic mice

value: Pool of non-sorted intestinal epithelial cells from non-irradiated mice


title: H1155

value: Caucasian

value: M


title: H838

value: Adenocarcinoma


title: H841

value: SCLC


title: sip2-del-1-a

value: refpool


title: H748

value: Black


title: H661

value: Large Cell


title: H720

value: Carcinoid, atypical


title: H727

value: Carcinoid

value: F


title: sip1-del-1-a


title: snf3-del-1-a


title: H820


title: sip2-del-1-b


title: shr5-del-3-b


title: H647

value: Adenosquamous


title: sip1-del-1-b


title: H526