title: Fetus 611_LWMS_D110

city: Castanet tolosan

first: Laurence

last: Liaubet

address: chemin de borde rouge

department: Animal Genetic

country: France

institute: INRA

description: Gene expression at 110 days of gestation in LWMS fetal intestin (jejunum)

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 44368 rows each corresponding to a unique ProbeName (provided as data Matrix) and 61 columns (individuals).

organism: Sus scrofa

source_name: jejunum (intestin)

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

extract_protocol: An aliquot of 200mg of intestinal tissue was processed for total RNA isolation and purification using Trizol (Invitrogen, France) according to the manufacturer instructions. The method included a DNase digestion step to remove contaminating DNA. The extracted total RNA was eluted in 100-200µl of RNase-free water and stored at -80°C.

treatment_protocol: After laparotomy, a middle-segment of jejunum was placed into RNAlater (Applied Biosystems) at 4℃ for 24 h and then maintained at -20℃ until later RNA extraction.

tag: days of gestation

tag: fetus genotype

value: LWMS

tag: maternal genotype

value: MS

tag: paternal genotype

value: LW


title: WT-CD4+T cells-Day2-rep

status: Public on Jun 01 2017

type: RNA

city: Houston

first: wenhao

last: chen

state: TX

address: 6670 Bertner Street, R7-216

country: USA

institute: Houston Methodist Research Institute

description: Gene expression of activated wt CD4+ T cells at day2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (074809) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner(G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_jul11 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Mus musculus

source_name: wt,spleen,activatedCD4+ T cells,Day2

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

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

treatment_protocol: CD4+ T cells was cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 50 uM 2-ME. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: tissue

value: Spleen

tag: gender

value: male

tag: cell type

value: CD4+ T cells

tag: genotype

value: wildtype

tag: background strain


title: Fetus 401_MSMS_D110

description: Gene expression at 110 days of gestation in MSMS fetal intestin (jejunum)

value: MSMS


title: Fetus 895_LWLW_D90

description: Gene expression at 90 days of gestation in LWLW fetal intestin (jejunum)

value: LWLW


title: Fetus 622_LWMS_D110


title: Fetus 485_MSLW_D90

description: Gene expression at 90 days of gestation in MSLW fetal intestin (jejunum)

value: MSLW


title: Fetus 632_MSMS_D110


title: Fetus 670_LWLW_D110

description: Gene expression at 110 days of gestation in LWLW fetal intestin (jejunum)


title: Fetus 455_MSLW_D90


title: Fetus 954_LWMS_D90

description: Gene expression at 90 days of gestation in LWMS fetal intestin (jejunum)


title: Fetus 854_LWLW_D110


title: Fetus 900_MSLW_D90


title: Fetus 509_LWMS_D90


title: Fetus 533_LWMS_D90


title: Fetus 902_MSLW_D90


title: Fetus 500_LWLW_D90


title: Fetus 633_LWMS_D110


title: Fetus 874_LWMS_D110


title: Fetus 405_LWMS_D110


title: Fetus 520_LWMS_D90


title: Fetus 525_LWMS_D90


title: Fetus 484_LWLW_D90


title: WT-CD4+T cells-Day2


title: Fetus 572_LWLW_D110


title: Fetus 827_MSMS_D90

description: Gene expression at 90 days of gestation in MSMS fetal intestin (jejunum)


title: Fetus 766_MSMS_D90


title: Fetus 409_MSMS_D110


title: Fetus 575_LWLW_D110


title: Fetus 894_LWLW_D90


title: Fetus 688_MSLW_D110

description: Gene expression at 110 days of gestation in MSLW fetal intestin (jejunum)


title: Fetus 481_MSLW_D110


title: Fetus 826_MSMS_D90


title: Fetus 504_LWMS_D90


title: Fetus 508_LWMS_D90


title: Fetus 557_LWLW_D110


title: Fetus 411_LWMS_D110


title: Fetus 559_LWLW_D110


title: Fetus 952_MSMS_D90


title: Fetus 899_MSLW_D90


title: Fetus 498_MSLW_D90


title: Fetus 578_MSLW_D110


title: Fetus 871_MSMS_D110


title: Fetus 736_LWLW_D90


title: Fetus 851_MSLW_D110


title: Fetus 462_LWLW_D90


title: Fetus 458_LWLW_D90


title: Fetus 852_LWLW_D110


title: Fetus 609_LWMS_D110


title: Fetus 476_MSLW_D110


title: Fetus 469_LWLW_D110


title: Fetus 449_LWLW_D90


title: Fetus 407_MSMS_D110


title: Fetus 560_MSLW_D110


title: Fetus 524_MSMS_D90


title: Fetus 738_MSLW_D90


title: Fetus 872_LWMS_D110


title: SQUU-B

city: Fukuoka

first: Yuma

last: Hashiguchi

address: 3-1-1, Maidashi, Higashi-ku

department: Division of Maxillofacial Diagnostic and Surgical Sciences

country: Japan

institute: Kyushu University Faculty of Dental Science

hyb_protocol: biotin labeled miRNA was hybridized to Affymetrix GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing:
The data were analyzed with  with median polish summarization and quantile normalization by Affymetrix® Expression Console 1.4.1 Software, and obtained normalized intensity values.
After the normalization, the probes designed for Human were extracted from normalized data for the purposes of our study.

label: biotin

organism: Homo sapiens

source_name: SQUU-B (OSCC) cells with transfected empty vector

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

growth_protocol: All cell lines were maintained in a humidified atmosphere of 5% CO2 at 37°C, and cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Life Technologies, CA, USA) supplemented with 10% fetal bovine serum (FBS) and 100 units/ml penicillin/streptomycin.

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: tongue

tag: cell line

value: oral squamous cell carcinoma (OSCC) cell line

tag: genotype/variation

value: control


title: SQUU-B EL

source_name: SQUU-B cells with low expression of E-cadherin

value: low expression of E-cadherin


title: Fetus 887_LWLW_D90


title: Fetus 627_MSMS_D110


title: Fetus 823_LWMS_D90


title: SQUU-B Over

source_name: SQUU-B (OSCC) cells with transfected ΔNp63β overexpressing vector

value: overexpressing {delta}Np63{beta}


title: Fetus 532_MSMS_D90


title: ECA5 vs. EC1118 replicate 1

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

description: Biological replicate 1 of 4 of ECA5 vs. Biological replicate 2 of 4 of EC1118.

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: print-tip-loess witinh-array normalization, quantile between-array normalization. R 2.9.2 software and limma bioconductor package used.

organism: Saccharomyces cerevisiae

source_name: Total RNA of ECA5 strain

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

growth_protocol: Cultures were performed on MS medium (Bely et al., 1990) containing 240g/L glucose and a nitrogen source composed of 28 mg/L nitrogen from amonium and 96.3 mg/L from amino acids. 5x109 cells were collected when CO2 production reached 45g/l.h and were kept for RNA extraction

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: strain

tag: biological replicate

source_name: Total RNA of EC1118 strain


title: Fetus 450_MSLW_D90


title: 1205LU shILEI 5 replicate 3

city: Charleston

first: Philip

middle: H

last: Howe

state: South Carolina

address: 173 Ashley Avenue

department: Biochemistry

institute: Medical University of South Carolina

hyb_protocol: Fragmented cRNA samples were hybridized overnight at 45°C to Affymetrix GeneChip Primeview Human Gene Expression Array.

scan_protocol: Post hybridization washing, phycoerythrin-streptavidin staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer's protocols.

data_processing: Hybridization data (CEL files) were normalized by RMA algorithm using Affymetrix Expression Console software; detection calls were obtained by Affymetrix MAS5 algorithm. Expression data were compared using dChip software.

label: Biotin

source_name: 1205Lu melanoma cell line

label_protocol: cDNA synthesis from 100 ng total RNA, in vitro transcription of biotin-labeled cRNA by 3'IVT Express Plus kit (Affymetrix),  and fragmentation of cRNAs were performed following established Affymetrix procedures.

growth_protocol: All cell lines were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum, puromycin (1000 ng/ml for WM9 derivatives and 125 ng/ml for 1205Lu derivatives) and 1% antibiotic/antimycotic solution (penicillin G, streptomycin, amphotericin B).

extract_protocol: RNA was extracted with TRIzol/chloroform and precipitated with isopropanol.

value: FAM3C shRNA vector


title: Fetus 825_LWMS_D90


title: EC1118 vs. ECA5 replicate 1

description: Biological replicate 1 of 4 of EC1118 vs. Biological replicate 2 of 4 of ECA5.


title: Fetus 850_LWLW_D110


title: EC1118 vs. ECA5 replicate 2

description: Biological replicate 3 of 4 of EC1118 vs. Biological replicate 4 of 4 of ECA5.


title: 1205LU shILEI 5 replicate 2


title: Fetus 623_MSMS_D110


title: Fetus 402_LWMS_D110


title: 1205LU SCR replicate 1

value: Control shRNA vector


title: 1205LU shILEI 5 repliate 1


title: WM9 shILEI 4 replicate 3

source_name: WM9 melanoma cell line


title: 1205LU shILEI 3 replicate 3


title: WM9 shILEI 4 replicate 1


title: WM9 shILEI 3 replicate 3


title: WM9 SCR replicate 1


title: 1205LU SCR replicate 2


title: 1205LU SCR replicate 3


title: liver tumour in mouse 5 at W5, biological rep5

city: Shanghai

first: Meiyi

last: Li

address: No.320 Yueyang Road

country: China

institute: Institute of Biochemistry and Cell Biology

description: Gene expression data from human hepatic tumour in mouse at the fifth week after orthotopic implantation

hyb_protocol: Following fragmentation, Biotinylated cRNA were hybridized for 16 hr at 45C on Affymetrix human primerview microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared with 3' IVT express kit according to the standard Affymetrix protocol

extract_protocol: Rneasy mini protocol for RNA cleanup was used according to the manufacturer's instructions.

value: Human HCCLM3 cell line labelled with a stable fluorescent protein


title: WM9 SCR replicate 3


title: liver tumour in mouse 4 at W5, biological rep4

source_name: human hepatic tumour in mouse at the fifth week after orthotopic implantation


title: liver tumour in mouse 5 at W4, biological rep5

description: Gene expression data from human hepatic tumour in mouse at the fourth week after orthotopic implantation


title: WM9 shILEI 3 replicate 2


title: 1205LU shILEI 3 replicate 1


title: WM9 shILEI 4 replicate 2


title: WM9 shILEI 3 replicate 1


title: liver tumour in mouse 1 at W5, biological rep1


title: liver tumour in mouse 5 at W3, biological rep5

description: Gene expression data from human hepatic tumour in mouse at the third week after orthotopic implantation


title: liver tumour in mouse 3 at W4, biological rep3

source_name: human hepatic tumour in mouse at the fourth week after orthotopic implantation


title: 1205LU shILEI 3 replicate 2


title: liver tumour in mouse 4 at W3, biological rep4

source_name: human hepatic tumour in mouse at the third week after orthotopic implantation


title: liver tumour in mouse 2 at W4, biological rep2


title: liver tumour in mouse 3 at W3, biological rep3


title: WM9 SCR replicate 2


title: liver tumour in mouse 4 at W2, biological rep4

description: Gene expression data from human hepatic tumour in mouse at the second week after orthotopic implantation


title: liver tumour in mouse 2 at W5, biological rep2


title: liver tumour in mouse 1 at W4, biological rep1


title: liver tumour in mouse 3 at W5, biological rep3


title: liver tumour in mouse 1 at W3, biological rep1


title: Mus Musculus_MMC 4h 1

city: Maastricht

first: Kasper

last: Derks

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

hyb_protocol: Labeled materials were hybridized to Custom Exiqon LNA probes for 16 hours at 60°C, subsequently washed and scanned

scan_protocol: Samples were finally scanned using the ScanArray Express HT (Tecan). Image generation and feature extraction were performed using Imagene 6.0.

data_processing: The raw microRNA data, median signal minus median background, were normalized using quantile normalization. The quality control discarded an array as outlier when the intensity distribution after background substraction was deviating from the control samples. Duplicate spots on the array were averaged and the normalized values were analyzed for differentially expressed microRNAs using a linear model (bioconductor package Limma; Smyth 2005) and corrected for multiple testing (Benjamini and Hochberg 1995) was applied.

source_name: embryonic stem cell_MMC 4h 1

label_protocol: Total RNA was labeled using the Createch Cy3 label kit (Createch), 1ug of total RNA was used.

growth_protocol: Mouse embryonic stem cells were thawed and grown on feeder coated plates for 2 passages. Subsequently plated on gelatin coated plates and treated for 4h,8h and 12h with a GTXC, NGTXC, Ox or Mock treated with corresponding dissolvent. After exposure total RNA was isolated with miRNEasy kit (Qiagen) and stored at -80.

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. All samples passed RNA quality control using capillary gel electrophoresis (RIN > 9) (Bioanalyzer 2100; Agilent Technologies, Amstelveen, the Netherlands). MicroRNA profiling was performed as previously described (Pothof et al. 2009).

treatment_protocol: For the chemicals used in this study, appropriate dosages were derived from previously performed clonogenic survival (G. Hendruks, unpublished data). In short, mouse embrynoic stem cells were exposed to chemicals, using multiple dosages based on literature or expert advice. The number of colony's formed by the cells after exposure compared to the mock-treated was used as a read-out for survival.

tag: compound

value: MMC

tag: class

value: GTXC

tag: exposure time

value: embryonic stem cell

tag: clone


title: liver tumour in mouse 3 at W2, biological rep3

source_name: human hepatic tumour in mouse at the second week after orthotopic implantation


title: liver tumour in mouse 5 at W2, biological rep5


title: liver tumour in mouse 2 at W2, biological rep2


title: liver tumour in mouse 4 at W4, biological rep4


title: Mus Musculus_PBS 8h 2

source_name: embryonic stem cell_PBS 8h 2

value: PBS

value: Control


title: Mus Musculus_MMS 4h 1

source_name: embryonic stem cell_MMS 4h 1

value: MMS


title: Mus Musculus H2O2 12h 4

source_name: embryonic stem cell H2O2 12h 4

value: Ox


title: Mus Musculus_DEM 8h 3

source_name: embryonic stem cell_DEM 8h 3

value: DEM


title: Mus Musculus_Dox 4h 1

source_name: embryonic stem cell_Dox 4h 1

value: Dox


title: Mus Musculus_CSA 12h 3

source_name: embryonic stem cell_CSA 12h 3

value: CSA

value: NGTXC


title: Mus Musculus_DEM 12h 4

source_name: embryonic stem cell_DEM 12h 4


title: Mus Musculus_DMSO 12h 3

source_name: embryonic stem cell_DMSO 12h 3

value: DMSO


title: Mus Musculus_DES 4h 3

source_name: embryonic stem cell_DES 4h 3

value: DES


title: MDA-MB-231_LncRNA

city: Beijing

first: Wanjin

address: No. 38, Xueyuan road.

institute: Peking University Health Science Center

description: The Genome-wide lncRNA expression in MDA-MB-231 cells.

hyb_protocol: Amplified/Cy3-labeled  cDNAs  were  hybridized  onto   oligonucleotide  microarrays  containing  40,916  probes of  lncRNAs  (CapitalBio  Human   lncRNA 4.0 Array).

scan_protocol: The pictures in tiff were scaned and values were extracted by Feature Extraction software.

data_processing: The data was analzed by GeneSpring software.

source_name: MDA-MB-231 Cells

extract_protocol: RNAs were eluted and extracted with TRIzol (Invitrogen).


title: Mus Musculus_Cispt 8h 2

source_name: embryonic stem cell_Cispt 8h 2

value: Cispt


title: liver tumour in mouse 1 at W2, biological rep1


title: liver tumour in mouse 2 at W3, biological rep2


title: Mus Musculus H2O2 4h 1

source_name: embryonic stem cell H2O2 4h 1


title: Mus Musculus_MMS 8h 4

source_name: embryonic stem cell_MMS 8h 4


title: ECA5 vs. EC1118 replicate 2

description: Biological replicate 3 of 4 of ECA5 vs. Biological replicate 4 of 4 of EC1118.

source_name: Total RNA of ECA5 strain

source_name: Total RNA of EC1118 strain


title: Mus Musculus_PBS 8h 1

source_name: embryonic stem cell_PBS 8h 1


title: MCF7_LncRNA

description: The Genome-wide lncRNA expression in MCF-7 cells.

source_name: MCF-7 Cells


title: Mus Musculus_Wy 8h 4

source_name: embryonic stem cell_Wy 8h 4

value: Wy


title: Mus Musculus H2O2 12h 1

source_name: embryonic stem cell H2O2 12h 1


title: Mus Musculus_DES 12h 3

source_name: embryonic stem cell_DES 12h 3


title: Mus Musculus_DES 8h 2

source_name: embryonic stem cell_DES 8h 2


title: Mus Musculus_DEM 4h 4

source_name: embryonic stem cell_DEM 4h 4


title: Mus Musculus_MMS 12h 1

source_name: embryonic stem cell_MMS 12h 1


title: Mus Musculus_CSA 8h 2

source_name: embryonic stem cell_CSA 8h 2


title: Mus Musculus_DES 4h 4

source_name: embryonic stem cell_DES 4h 4


title: Mus Musculus_MEN 4h 4

source_name: embryonic stem cell_MEN 4h 4

value: MEN


title: Mus Musculus_Arsenite 8h 3

source_name: embryonic stem cell_Arsenite 8h 3

value: Arsenite


title: Mus Musculus_MMS 4h 3

source_name: embryonic stem cell_MMS 4h 3


title: Mus Musculus_DEM 12h 3

source_name: embryonic stem cell_DEM 12h 3


title: Mus Musculus_MEN 8h 4

source_name: embryonic stem cell_MEN 8h 4


title: Mus Musculus_Dox 4h 3

source_name: embryonic stem cell_Dox 4h 3


title: Mus Musculus H2O2 8h 2

source_name: embryonic stem cell H2O2 8h 2


title: MR820 3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

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

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

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

source_name: Mouse small intestine

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

growth_protocol: Primary cells

extract_protocol: RNA was isolated using magnetic beads from 2000 cels. Library preparation and amplification were performed as described by Gonzalez et al., 2010. Amplification was performed for 22 cycles.

treatment_protocol: Untreated

tag: population

value: Mex3a Neg Lgr5 High

tag: strip


title: CBPΔ/Δ x EµBcl2, rep 3

first: Michael

middle: R

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: Overnight hybridization according to Affymetrix Protocol

scan_protocol: Scanned with Affymetrix GeneChip Scanner 3000 and GCOS software

data_processing: Cel files were RMA normalized using the 'ExpressionFileCreator' module of GenePattern.

source_name: Splenic B-cells

label_protocol: Biotin labeling according to Affymetrix Protocol

growth_protocol: Spleens were disaggregated and cells viably cryopreserved.

extract_protocol: RNA and DNA were extracted using Qiagen AllPrep Micro Kit, according to the manufacturer's protocol.

treatment_protocol: Cryopreserved cells were thawed, washed twice in PBS, and B-cells isolated using Dynabeads Mouse CD43 Untouched B-cells (Life Technologies)

value: Crebbp-deleted


title: MR820 5

value: Mex3a Low Lgr5 Low


title: WD4847-2 miR-193b rep3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
miR193-3
replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Total RNA was isolated with Direct-zol RNA miniprep Kit (Zymo).

value: WD4847-2 liposarcoma cells

tag: treatment


title: MR820 1

value: Mex3a High Lgr5 High


title: WD4847-2 miR-193b rep1

description:
miR193-1
replicate 1


title: Mus Musculus_PBS 8h 4

source_name: embryonic stem cell_PBS 8h 4

value: PBS

value: Control

value: embryonic stem cell


title: WD4847-2 Control miRNA rep3

description:
NS3
replicate 3

source_name: Control miRNA, WD4847-2

value: Control miRNA


title: Mus Musculus_Wy 4h 2

source_name: embryonic stem cell_Wy 4h 2


title: WD4847-2 Control miRNA rep2

description:
NS2
replicate 2


title: MR820 2

value: Mex3a Low Lgr5 High


title: WD4847-2 miR-193b rep2

description:
miR193-2
replicate 2


title: MK082-31

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: single replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control results were within expected range. The data were normalized using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, GBA N370S donor MK082, clone 31

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: male

tag: donor

value: GBA N370S donor

tag: culture conditions

value: mTeSR-1 + matrigel

value: induced pluripotent stem cells derived from dermal fibroblasts


title: CBPΔ/Δ x EµBcl2, rep 2


title: JR053-1

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor JR053, clone 1

tag: gender

value: control donor


title: CBPF/F x EµBcl2, rep 3

value: Crebbp-floxed


title: MK088-7

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, GBA N370S donor MK088, clone 7

tag: cell type


title: OX2-28

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor OX2, clone 28


title: JR053-6

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor JR053, clone 6


title: WD4847-2 Control miRNA rep1

description:
NS1
replicate 1


title: Mus Musculus_MMC 4h 3

source_name: embryonic stem cell_MMC 4h 3

value: MMC

value: GTXC


title: MR793 3

value: Mex3a Neg Lgr5 High


title: MR820 6

value: Mex3a Neg Lgr5 Low


title: MR820 4

value: Mex3a High Lgr5 Low


title: Mus Musculus_DMSO 8h 1

source_name: embryonic stem cell_DMSO 8h 1

value: DMSO


title: CBPΔ/Δ x EµBcl2, rep 1

value: Crebbp-deleted


title: Mus Musculus_MMC 8h 3

source_name: embryonic stem cell_MMC 8h 3


title: MR793 6


title: Mus Musculus_DMSO 4h 3

source_name: embryonic stem cell_DMSO 4h 3

value: Control


title: Mus Musculus_Dox 4h 2

source_name: embryonic stem cell_Dox 4h 2

value: Dox

value: embryonic stem cell


title: Mus Musculus_Cispt 4h 2

source_name: embryonic stem cell_Cispt 4h 2

value: Cispt


title: MR793 5

value: Mex3a Low Lgr5 Low


title: MR793 2

value: Mex3a Low Lgr5 High


title: MR793 4


title: DD8817 miR-193b rep3

description:
DD_m193b_3
replicate 3

value: DD8817 liposarcoma cells


title: CBPF/F x EµBcl2, rep 1


title: DD8817 miR-193b rep2

description:
DD_m193b_2
replicate 2


title: Mus Musculus_DMSO 8h 3

source_name: embryonic stem cell_DMSO 8h 3


title: MR793 1

source_name: Mouse small intestine

value: Mex3a High Lgr5 High


title: Mus Musculus_DMSO 4h 4

source_name: embryonic stem cell_DMSO 4h 4


title: Mus Musculus_Arsenite 4h 3

source_name: embryonic stem cell_Arsenite 4h 3

value: Arsenite

value: Ox


title: Mus Musculus_Arsenite 12h 4

source_name: embryonic stem cell_Arsenite 12h 4


title: DD8817 Control miRNA rep3

description:
DD_NS_3
replicate 3

source_name: Control miRNA, DD8817

value: Control miRNA


title: Baurle_562-8_Col_52h_Rep2_ATH1

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

description: Col 52h Rep2

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content.

organism: Arabidopsis thaliana

source_name: 8 Col 52h Rep2

label_protocol: Total RNA was labelled according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Arabidopsis thaliana plants were grown in GM medium (1% [w/v] glucose) at 23°C/ 21°C in 16-h-light/8-h-dark cycles unless otherwise indicated. ago1-25 were obtained from N. Baumberger.

extract_protocol: For microarray analysis, RNA from three biological replicates per genotype and treatment (4 h after acclimation, 52 h after acclimation and 4 h non-treated control) was purified over an RNeasy Plant RNA extraction column (Qiagen) and processed for hybridization of Affymetrix ATH1 GeneChips (NASC microarray facility).

treatment_protocol: HS treatments were performed in a water bath or incubator. For the priming HS (ACC), 4-d-old seedlings were subjected to a heat regime of 1 h, 37°C; 1.5 h, 23°C; and 45 min, 44°C. All priming treatments were started 6 h after dawn to ensure comparability and minimize diurnal effects.

tag: genotype

value: Col

value: 52 hr after acclimation


title: Baurle_562-6_Col_4h_Rep3_ATH1

description: Col 4h Rep3

source_name: 6 Col 4h Rep3

value: 4 hr after accilimation


title: Mus Musculus_PBS 12h 1

source_name: embryonic stem cell_PBS 12h 1

value: PBS


title: Mus Musculus_PhenB 12h 2

source_name: embryonic stem cell_PhenB 12h 2

value: PhenB

value: NGTXC


title: Baurle_562-7_Col_52h_Rep1_ATH1

description: Col 52h Rep1

source_name: 7 Col 52h Rep1


title: Baurle_562-4_Col_4h_Rep1_ATH1

description: Col 4h Rep1

source_name: 4 Col 4h Rep1


title: HEK293_CEBPA_3

city: Singapore

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted at the probe level with no background correction using Illumina's BeadStudio software.  Date was quantile normalized and log2 transformed in  R 2.15.2/Bioconductor.

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: All the HEK293 cell lines were maintained in DMEM, 10% HI-FBS, kept between 10% and 90% confluency in a 37˚C, 5% C02 tissue culture incubator

extract_protocol: RNA was extracted from monocytes using an RNAasy Mini Kit (Qiagen) as per manufacturers specifications. Extracted RNA was quantified on a Bioanalyser (Agilent) for quality control and used subsequently in microarray assay.

tag: transfected with

value: lentiviral vector containing CEBPA


title: Baurle_562-3_Col_contr_Rep3_ATH1

description: Col contr Rep3

source_name: 3 Col contr Rep3

value: control


title: DD8817 miR-193b rep1

description:
DD_m193b_1
replicate 1

tag: cell line


title: Xpa_24hr

city: Kobe

first: Makoto

last: Kunisada

address: 7-5-2 Kusunoki-cho

department: Dermatology

institute: Kobe university of medicine

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4400A.

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: Xpa_24hr UVB 1kJ/m^2 exposed

extract_protocol: using Trizol, chloroform, isopropanol, ethanol

treatment_protocol: No UV or UVB 1kJ/m^2 exposed

value: hairless albino

tag: genotype/variation

value: Xpa mutant


title: Baurle_562-9_Col_52h_Rep3_ATH1

description: Col 52h Rep3

source_name: 9 Col 52h Rep3


title: Mus Musculus_MMC 12h 2

source_name: embryonic stem cell_MMC 12h 2

value: MMC

value: GTXC

value: embryonic stem cell


title: HEK293_control_3

scan_protocol: According to beadchip array manufacturer's protocol

value: none (uninfected control)


title: Baurle_562-5_Col_4h_Rep2_ATH1

description: Col 4h Rep2

source_name: 5 Col 4h Rep2


title: HEK293_CEBPA_1


title: Xpa_3hr

source_name: Xpa_3hr UVB 1kJ/m^2 exposed

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

tag: strain


title: HEK293_CEBPA_2


title: Mus Musculus_DES 4h 2

source_name: embryonic stem cell_DES 4h 2

value: DES

tag: biological replicate


title: Mus Musculus H2O2 4h 4

source_name: embryonic stem cell H2O2 4h 4

tag: compound

value: Ox


title: DD8817 Control miRNA rep1

description:
DD_NS_1
replicate 1

value: DD8817 liposarcoma cells

value: Control miRNA


title: Baurle_562-2_Col_contr_Rep2_ATH1

description: Col contr Rep2

source_name: 2 Col contr Rep2

value: Col


title: Mus Musculus_DEM 8h 4

source_name: embryonic stem cell_DEM 8h 4

value: DEM

tag: class


title: DD8817 Control miRNA rep2

description:
DD_NS_2
replicate 2

source_name: Control miRNA, DD8817


title: WT_3hr

source_name: WT_3hr, UVB 1kJ/m^2 exposed

value: wild type


title: HEK293_control_1


title: Mus Musculus_PhenB 5h 4

source_name: embryonic stem cell_PhenB 5h 4

value: PhenB

tag: exposure time


title: HEK293_control_2


title: Baurle_562-1_Col_contr_Rep1_ATH1

description: Col contr Rep1

source_name: 1 Col contr Rep1


title: Baurle_562-27_ago1_52h_Rep3_ATH1

description: ago1 52h Rep3

source_name: 27 ago1 52h Rep3

value: 52 hr after acclimation


title: WT_no UV

source_name: WT_no UV


title: WT_24hr

source_name: WT_24hr UVB 1kJ/m^2 exposed


title: Mus Musculus_DEM 12h 2

source_name: embryonic stem cell_DEM 12h 2

tag: clone


title: 102: FS_beads_rep4

city: Oslo

first: Bjørn

last: Skålhegg

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: CD4+ human Th0 cells at 21% O2 Rep 4

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

source_name: Buffy coat

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

growth_protocol: CD4+ T cells from buffy coats were isolated by positive selection using magnetic beads. T cells were cultured in RPMI-1640 medium with 10% heat inactivated calf serum, 1% penicillin/streptavidin and 2% L-glutamin. Cells were plated in 12 well plates (0.2x106 per well) and stimulated by anti-CD3/CD28 beads (Dynal/Fisher) with 1:2 bead-to-cell ratio for 7 days in atmosphere of 5% CO2 or 5%CO2 and 1%O2. Th17 populations were polarized per protocol from Multenyi Biotec by addition of IL-1alpha (20ng/mL), IL-6 (30ng/mL), IL-23 (30ng/mL), TGF-beta (2,25ng/mL) and neutralizing antibodies to anti-IFN-gamma (1 µg/mL) and anti-IL-4 (2,5 µg/mL). CSE treatment was performed together with Th17 polarization.

extract_protocol: total RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: oxygen

value: CD4+ T helper cell


title: Mus Musculus_Cispt 12h 2

source_name: embryonic stem cell_Cispt 12h 2

value: Cispt


title: 64: B_ThCSE_rep4

description: CD4+ human Th17 cells CSE treated at 1% O2 Rep 4


title: LXC5 plus RA - biological rep A

city: Buffalo

first: Stefano

last: Rossetti

address: Elm and Carlton Streets

department: Cancer Genetics

institute: Roswell Park Cancer Institute

description: Control T47D cells stably transfected with an empty pLXSN vector, treated with 1 microM retinoic acid for 72h

hyb_protocol: 11 micrograms of cRNA were then fragmented in fragmentation buffer (Affymetrix) at 95 °C for 35 min. and hybridized for 16h at 45 °C onto U133A microarrays (Affymetrix).

scan_protocol: After washing and staining, the chips were scanned in a Hewett-Packard/Affymetrix scanner at 570 nm.

data_processing: Array data files were processed using the MAS5.0 algorithm in the affy R library within Bioconductor suite to generate expression summary values for each probe set. MAS5.0 based “present calls” was used to filter out probe sets whose expression intensities were close to background noise across all samples (that is, without “present” status in all samples including both treatments and controls), and  probe sets whose “present calls” was inconsistent within the biological replicates in any of  the four conditions. Further quality control included the usage of latest affy annotation package to filter out probes sets without any known gene assignment. The Limma program in the Bioconductor package under R computing environment was used to calculate the level of differential gene expression. Briefly, a linear model was fit to the data (i.e., two-factor design with cell means corresponding to the different conditions and a random effect for array).

source_name: LXC5 treated with 1 microM Retinoic Acid 72h

label_protocol: Double stranded cDNA was generated from 5 microg of RNA using Superscript ds cDNA synthesis kit (Life Technologies) and T7-oligo(dT) primers. The cDNA was purified with GeneChip Sample Cleanup Module (Affymetrix) and used to synthesized biotin-labeled cRNA with Enzo RNA transcript Labeling Kit (Enzo Life Sciences).

growth_protocol: Cells were grown in DMEM plus 5% FBS.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen)

treatment_protocol: Cells were seeded in equal amounts, let attach ovrenight, and treated either with 1 micorM RA or vehicle (Ethanol) for 72h, replacinf the drug-containing medium every 24 h. Treatments were performed under dim yellow light conditions

value: 1 microM Retinoic Acid 72h

value: T47D breast cancer cell line

tag: stable transfection

value: Empty pLXSN vector


title: DNC8 plus RA - biological rep A

description: T47D cells stably transfected with pLXSN-RARA403 (RARA dominant netaive), treated with 1 mcroM retinoic acid for 72h

source_name: DNC8 treated with 1 microM Retinoic Acid 72h

tag: treatment


title: Baurle_562-26_ago1_52h_Rep2_ATH1

description: ago1 52h Rep2

source_name: 26 ago1 52h Rep2


title: LXC5 plus RA - biological rep B


title: DNC8 plus RA - biological rep B


title: Mus Musculus_MEN 12h 3

source_name: embryonic stem cell_MEN 12h 3

value: MEN


title: DNC8 minus RA - biological rep B

description: T47D cells stably transfected with pLXSN-RARA403 (RARA dominant netaive), treated with vehicle (Ethanol) for 72h

source_name: DNC8 treated with vehicle, 72h

value: vehicle, 72h


title: Baurle_562-21_ago1_contr_Rep3_ATH1

description: ago1 contr Rep3

source_name: 21 ago1 contr Rep3

value: control


title: Baurle_562-23_ago1_4h_Rep2_ATH1

description: ago1 4h Rep2

source_name: 23 ago1 4h Rep2

value: 4 hr after accilimation


title: Baurle_562-25_ago1_52h_Rep1_ATH1

description: ago1 52h Rep1

source_name: 25 ago1 52h Rep1


title: Mus Musculus_Arsenite 4h 1

source_name: embryonic stem cell_Arsenite 4h 1

value: Arsenite

value: Ox

value: embryonic stem cell


title: Mus Musculus_Dox 8h 3

source_name: embryonic stem cell_Dox 8h 3

value: Dox

value: GTXC


title: Baurle_562-24_ago1_4h_Rep3_ATH1

description: ago1 4h Rep3

source_name: 24 ago1 4h Rep3


title: 122: B_beads_rep4

description: CD4+ human Th0 cells at 1% O2 Rep 4


title: DNC8 minus RA - biological rep A


title: 34: FS_ThCSE_rep4

description: CD4+ human Th17 cells CSE treated at 21% O2 Rep 4


title: LXC5 minus RA - biological rep A

description: Control T47D cells stably transfected with an empty pLXSN vector, treated with vehicle (Ethanol) for 72h

source_name: LXC5 treated with vehicle, 72h


title: LXC5 minus RA - biological rep B


title: CBPF/F x EµBcl2, rep 2

source_name: Splenic B-cells

value: Crebbp-floxed


title: 52: B_beads_rep3

description: CD4+ human Th0 cells at 1% O2 Rep 3


title: Mus Musculus_CSA 4h 2

source_name: embryonic stem cell_CSA 4h 2

value: CSA

value: NGTXC


title: 22: FS_beads_rep3

description: CD4+ human Th0 cells at 21% O2 Rep 3

value: CD4+ T helper cell


title: Baurle_562-22_ago1_4h_Rep1_ATH1

description: ago1 4h Rep1

source_name: 22 ago1 4h Rep1


title: Baurle_562-20_ago1_contr_Rep2_ATH1

description: ago1 contr Rep2

source_name: 20 ago1 contr Rep2


title: Mus Musculus_DES 8h 1

source_name: embryonic stem cell_DES 8h 1

value: DES


title: Mus Musculus_DMSO 4h 2

source_name: embryonic stem cell_DMSO 4h 2

value: DMSO

value: Control


title: Mus Musculus_CSA 12h 2

source_name: embryonic stem cell_CSA 12h 2


title: Mus Musculus_MEN 4h 2

source_name: embryonic stem cell_MEN 4h 2


title: 63: B_Th_rep4

description: CD4+ human Th17 cells at 1% O2 Rep 4

source_name: Buffy coat


title: 94: FS_ThCSE_rep3

description: CD4+ human Th17 cells CSE treated at 21% O2 Rep 3


city: Neuherberg

first: Sebastian

middle: Gerhard

last: Doll

address: Ingolstädter Landstraße 1

department: Institute of developmental genetics

institute: Helmholtz Zentrum München

description: Gene expression data from Ferroptosis-resistant cell clones cB4, biological replicate 3

data_processing: Data including background subtraction (GenomeStudioV2010.1 software, gene expression module version 1.6.0), removal of negative values by introducing an offset, quantile normalisation

source_name: Mouse embrionic fibroblasts

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and cultured in a 37°C incubator with humidified atmosphere of 5% CO2 (Binder)

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

tag: tissue

value: Mouse embrionic fibroblasts

tag: age

value: Passage (>100)

value: female


description: Gene expression data from Ferroptosis-resistant cell clones cB7, biological replicate 2

tag: gender


title: Baurle_562-19_ago1_contr_Rep1_ATH1

description: ago1 contr Rep1

source_name: 19 ago1 contr Rep1

value: control


title: 44: B_ThCSE_rep2

description: CD4+ human Th17 cells CSE treated at 1% O2 Rep 2

tag: cell type


title: 54: B_ThCSE_rep1

description: CD4+ human Th17 cells CSE treated at 1% O2 Rep 1


title: GBM-CancerTissue-49

first: Lin

last: Feng

address: Panjiayuan nanli 17#

institute: Peiking union medical school

description: glioblastoma multiforme tissue

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data was normalized using the quantile method from the limma R package.

source_name: glioblastoma multiforme tissue sample49

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: All samples were snap-frozen in liquid nitrogen and stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied.

tag: patient

value: M

tag: overall survival (months)

tag: events (dead = 1)


description: Gene expression data from Ferroptosis-resistant cell clones cB1, biological replicate 3


title: 33: FS_Th_rep4

description: CD4+ human Th17 cells at 21% O2 Rep 4


title: 14: FS_ThCSE_rep2

description: CD4+ human Th17 cells CSE treated at 21% O2 Rep 2


description: Gene expression data from Ferroptosis-resistant cell clones cB7, biological replicate 3


title: 114: B_ThCSE_rep3

description: CD4+ human Th17 cells CSE treated at 1% O2 Rep 3


title: GBM-CancerTissue-50

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample50


title: 113: B_Th_rep3

description: CD4+ human Th17 cells at 1% O2 Rep 3


title: Mus Musculus_Cispt 12h 4

source_name: embryonic stem cell_Cispt 12h 4

value: Cispt

tag: cell line


title: Mus Musculus H2O2 12h 2

source_name: embryonic stem cell H2O2 12h 2

value: Ox


title: Mus Musculus H2O2 8h 4

source_name: embryonic stem cell H2O2 8h 4

value: embryonic stem cell


title: GBM-CancerTissue-45

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample45

value: F


title: 43: B_Th_rep2

description: CD4+ human Th17 cells at 1% O2 Rep 2


description: Gene expression data from Ferroptosis-resistant cell clones cB1, biological replicate 2

tag: strain


description: Gene expression data from Ferroptosis-resistant cell clones cB4, biological replicate 2


description: Gene expression data from Ferroptosis-resistant cell clones cB4, biological replicate 1


description: Gene expression data from Ferroptosis-resistant cell clones cB7, biological replicate 1


title: Mus Musculus_CSA 12h 4

source_name: embryonic stem cell_CSA 12h 4

tag: biological replicate


description: Gene expression data from TAM-inducible Gpx4 k.o. cell line, biological replicate 3


title: Mus Musculus_DEM 4h 3

source_name: embryonic stem cell_DEM 4h 3

tag: compound

value: DEM


title: 112: B_beads_rep2

description: CD4+ human Th0 cells at 1% O2 Rep 2


title: 92: FS_beads_rep2

description: CD4+ human Th0 cells at 21% O2 Rep 2


title: 13: FS_Th_rep2

description: CD4+ human Th17 cells at 21% O2 Rep 2


title: GBM-CancerTissue-46

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample46


title: 93: FS_Th_rep3

description: CD4+ human Th17 cells at 21% O2 Rep 3


title: GBM-CancerTissue-42

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample42


title: GBM-CancerTissue-43

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample43


title: GBM-CancerTissue-48

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample48


title: 53: B_Th_rep1

description: CD4+ human Th17 cells at 1% O2 Rep 1


title: Mus Musculus_DES 4h 1

source_name: embryonic stem cell_DES 4h 1

tag: class


title: GBM-CancerTissue-47

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample47


title: 23: FS_Th_rep1

description: CD4+ human Th17 cells at 21% O2 Rep 1

source_name: Buffy coat


title: Mus Musculus_DMSO 4h 1

source_name: embryonic stem cell_DMSO 4h 1

tag: exposure time


title: Mus Musculus_PBS 4h 3

source_name: embryonic stem cell_PBS 4h 3

value: PBS

tag: clone


description: Gene expression data from TAM-inducible Gpx4 k.o. cell line, biological replicate 2

source_name: Mouse embrionic fibroblasts


title: 12: FS_beads_rep1

description: CD4+ human Th0 cells at 21% O2 Rep 1

tag: oxygen


title: GBM-CancerTissue-39

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample39


description: Gene expression data from Ferroptosis-resistant cell clones cB1, biological replicate 1


title: Mus Musculus H2O2 8h 1

source_name: embryonic stem cell H2O2 8h 1


title: GBM-CancerTissue-44

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample44


title: Mus Musculus_Dox 12h 4

source_name: embryonic stem cell_Dox 12h 4

value: Dox

value: GTXC


title: Mus Musculus_PBS 12h 2

source_name: embryonic stem cell_PBS 12h 2


description: Gene expression data from TAM-inducible Gpx4 k.o. cell line, biological replicate 1


title: 24: FS_ThCSE_rep1

description: CD4+ human Th17 cells CSE treated at 21% O2 Rep 1

value: CD4+ T helper cell


title: Mus Musculus_DMSO 8h 4

source_name: embryonic stem cell_DMSO 8h 4


title: Mus Musculus_MMS 12h 2

source_name: embryonic stem cell_MMS 12h 2

value: MMS


title: wild type mouse 1 left ventricle

city: Muenster

first: Ilaria

last: Piccini

address: Albert-Schweitzer-Campus 1

institute: UKM

description: biological replicate 1

data_processing: The data were normalised using cubic spline normalization with Geome Studio Software (Illumina, 2010).Differential gene expression was assessed  employing the Illumina custom algorithm

source_name: Mouse left ventricle

growth_protocol: 12 months old mice

extract_protocol: RNA was extracted with Rneasy fibrous tissue  mini ki (Qiagen with DNase I treatment on column) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: wild type

tag: genetic background

value: Swiss Agouti

value: 12 months

value: Left ventricle + Septum


title: Mus Musculus_Wy 4h 1

source_name: embryonic stem cell_Wy 4h 1

value: Wy

value: NGTXC


title: GBM-CancerTissue-35

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample35


title: GBM-CancerTissue-36

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample36


title: Mus Musculus_Wy 8h 2

source_name: embryonic stem cell_Wy 8h 2


title: Mus Musculus_DES 8h 4

source_name: embryonic stem cell_DES 8h 4

value: DES


title: 42: B_beads_rep1

description: CD4+ human Th0 cells at 1% O2 Rep 1

source_name: Buffy coat


title: wild type mouse 4 left ventricle

description: biological replicate 4

tag: tissue


title: Mus Musculus_Cispt 12h 1

source_name: embryonic stem cell_Cispt 12h 1

value: Cispt


title: GBM-CancerTissue-40

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample40

value: M

tag: age


title: Scn5adelta/+ mouse 1 left ventricle

description: biological replicate 1


title: Mus Musculus_DES 8h 3

source_name: embryonic stem cell_DES 8h 3

value: embryonic stem cell


title: Scn5adelta/+ mouse 3 left ventricle

description: biological replicate 3


title: wild type mouse 2 left ventricle

description: biological replicate 2


title: GBM-CancerTissue-41

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample41

tag: gender

value: F


title: Mus Musculus_CSA 8h 3

source_name: embryonic stem cell_CSA 8h 3

value: CSA


title: Scn5adelta/+ mouse 4 left ventricle

description: biological replicate 4


title: GBM-CancerTissue-37

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample37


title: GBM-CancerTissue-32

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample32


title: Mus Musculus_MMS 12h 3

source_name: embryonic stem cell_MMS 12h 3


title: GBM-CancerTissue-34

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample34


title: GBM-CancerTissue-33

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample33


title: GBM-CancerTissue-38

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample38


title: Scn5adelta/+ mouse 2 left ventricle

description: biological replicate 2

source_name: Mouse left ventricle


title: GBM-CancerTissue-31

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample31


title: Mus Musculus_MMC 8h 1

source_name: embryonic stem cell_MMC 8h 1

value: MMC


title: Mus Musculus_MEN 8h 1

source_name: embryonic stem cell_MEN 8h 1

value: MEN

value: Ox


title: GBM-CancerTissue-27

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample27


title: GBM-CancerTissue-29

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample29


title: Mus Musculus_MMS 8h 1

source_name: embryonic stem cell_MMS 8h 1

value: GTXC


title: Mus Musculus_DES 12h 4

source_name: embryonic stem cell_DES 12h 4


title: wild type mouse 3 left ventricle

description: biological replicate 3


title: GBM-CancerTissue-28

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample28


title: GBM-CancerTissue-26

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample26


title: GBM-CancerTissue-24

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample24


title: GBM-CancerTissue-30

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample30


title: Mus Musculus_Cispt 12h 3

source_name: embryonic stem cell_Cispt 12h 3


title: Mus Musculus_MEN 8h 3

source_name: embryonic stem cell_MEN 8h 3


title: Mus Musculus_PhenB 4h 2

source_name: embryonic stem cell_PhenB 4h 2

value: PhenB


title: GBM-CancerTissue-25

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample25


title: Mus Musculus_MMS 8h 3

source_name: embryonic stem cell_MMS 8h 3

value: MMS


title: GBM-CancerTissue-21

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample21


title: GBM-CancerTissue-22

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample22


title: Mus Musculus_PBS 4h 1

source_name: embryonic stem cell_PBS 4h 1

value: PBS

value: Control


title: Mus Musculus_DMSO 8h 2

source_name: embryonic stem cell_DMSO 8h 2

value: DMSO


title: Mus Musculus_PBS 8h 3

source_name: embryonic stem cell_PBS 8h 3


title: GBM-CancerTissue-18

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample18


title: GBM-CancerTissue-16

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample16


title: GBM-CancerTissue-19

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample19


title: GBM-CancerTissue-17

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample17


title: Mus Musculus_Wy 12h 4

source_name: embryonic stem cell_Wy 12h 4

value: Wy


title: Mus Musculus_Wy 8h 3

source_name: embryonic stem cell_Wy 8h 3

value: NGTXC


title: GBM-CancerTissue-14

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample14


title: Mus Musculus_CSA 4h 4

source_name: embryonic stem cell_CSA 4h 4


title: Mus Musculus_Arsenite 8h 1

source_name: embryonic stem cell_Arsenite 8h 1

value: Arsenite


title: GBM-CancerTissue-13

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample13


title: GBM-CancerTissue-23

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample23


title: Mus Musculus_CSA 8h 4

source_name: embryonic stem cell_CSA 8h 4


title: Mus Musculus_Wy 8h 1

source_name: embryonic stem cell_Wy 8h 1


title: GBM-CancerTissue-20

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample20


title: Mus Musculus H2O2 12h 3

source_name: embryonic stem cell H2O2 12h 3


title: Mus Musculus_PhenB 12h 1

source_name: embryonic stem cell_PhenB 12h 1


title: Mus Musculus_Dox 4h 4

source_name: embryonic stem cell_Dox 4h 4

value: Dox


title: Mus Musculus_PhenB 8h 2

source_name: embryonic stem cell_PhenB 8h 2


title: GBM-CancerTissue-10

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample10


title: GBM-CancerTissue-07

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample07

value: M


title: GBM-CancerTissue-09

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample09


title: GBM-CancerTissue-11

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample11


title: GBM-CancerTissue-08

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample08


title: GBM-CancerTissue-15

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample15


title: GBM-CancerTissue-12

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample12


title: Mus Musculus_MMS 12h 4

source_name: embryonic stem cell_MMS 12h 4

value: embryonic stem cell


title: Mus Musculus_Cispt 8h 4

source_name: embryonic stem cell_Cispt 8h 4

value: Cispt


title: GBM-CancerTissue-06

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample06


title: Mus Musculus_DEM 8h 2

source_name: embryonic stem cell_DEM 8h 2

value: DEM


title: GBM-CancerTissue-04

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample04


title: Mus Musculus_MMC 8h 2

source_name: embryonic stem cell_MMC 8h 2

value: MMC


title: Mus Musculus_Arsenite 8h 2

source_name: embryonic stem cell_Arsenite 8h 2


title: Mus Musculus_Dox 8h 2

source_name: embryonic stem cell_Dox 8h 2


title: Mus Musculus_Arsenite 12h 3

source_name: embryonic stem cell_Arsenite 12h 3


title: Mus Musculus_Arsenite 4h 2

source_name: embryonic stem cell_Arsenite 4h 2


title: Mus Musculus_Cispt 8h 1

source_name: embryonic stem cell_Cispt 8h 1


title: Mus Musculus_Cispt 4h 4

source_name: embryonic stem cell_Cispt 4h 4


title: GBM-CancerTissue-02

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample02

value: F


title: DSS vs Control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Biological replicate one of one

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: DSS+

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Atoh1-CrePGR mice were crossed with Rosa26-LSL-tdTomato mice, to generate Atoh1-crePGR/Rosa26-tdTomato mice.  Those mice were treated with 3% DSS or distilled water for 5 consecutive days, followed by tdTomato-labeling of Atoh1+ve cells and their descendants by the induction of Cre-mediated gene recombination for another 5 days. After 6 days from Cre induction, tdTomato+ve cell population was collected from the mice colonic epithelium by fluorescence activated cell sorting (FACS).

extract_protocol: Total RNA was isolated from sorted cells using RNeasy Micro kit (QIAGEN).

treatment_protocol: 3% DSS or distilled water was administrated to the  Atoh1-crePGR/Rosa26-tdTomato mice for 5 consecutive days. RU486 was injected intraperitoneally for another 5 consecutive days.

tag: treated with

value: 3% DSS for 5 days

value: colon

tag: cell type

value: Atoh1+ve  epithelial cells

source_name: DSS-

value: distilled water for 5 days


title: Mus Musculus_DEM 12h 1

source_name: embryonic stem cell_DEM 12h 1

value: Ox


title: EGFP+ve tdTomato+ve vs. EGFP+ve tdTomato-ve

description:
Biological replicate one of one.
Normalized log2 ratio (Tmt+GFP+ ([2])/ Tmt-GFP+ ([1]))

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries, Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries, Inc., Tokyo, Japan).

source_name: Tmt-GFP+

label_protocol: cDNA and Amino Allyl aRNA were synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: Atoh1-CrePGR mice were crossed with Lgr5-EGFP-IRES-CreERT2 mice and Rosa26-LSL-tdTomato mice, to generate Atoh1-crePGR/Lgr5-EGFP-IRES-creERT2/Rosa26-tdTomato mice. Atoh1+ve cells and their descendants were labeled with tdTomato by the induction of Cre-mediated gene recombination for 5 days. After 20 days from Cre recombination, [1] EGFP+ve/tdTomato-ve, [2] EGFP+ve/tdTomato+ve and [3] EGFP-ve/tdTomato+ve cells were collected from the mouse small intestinal epithelium by fluorescence-activated cell sorting (FACS).

extract_protocol: Total RNA was isolated from sorted cells using RNeasy Mini kit (QIAGEN).

treatment_protocol: RU486 was injected intraperitoneally for 5 consecutive days for Cre-mediated gene recombination.

tag: genotype/variation

value: small intestinal epithelium

tag: cell population

value: EGFP+ve/tdTomato-ve

source_name: Tmt+GFP+

value: EGFP+ve/tdTomato+ve


title: GBM-CancerTissue-01

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample01

tag: patient

tag: overall survival (months)

tag: events (dead = 1)


title: GBM-CancerTissue-03

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample03


title: GBM-CancerTissue-05

description: glioblastoma multiforme tissue

source_name: glioblastoma multiforme tissue sample05


title: EGFP-ve tdTomato+ve vs. EGFP+ve tdTomato-ve

description:
Biological replicate one of one.
Normalized log2 ratio (Tmt+GFP- ([3])/ Tmt-GFP+ ([1]))

source_name: Tmt+GFP-

value: EGFP-ve/tdTomato+ve


title: Mus Musculus_DEM 4h 1

source_name: embryonic stem cell_DEM 4h 1

tag: compound

tag: biological replicate

tag: cell line


title: scramble control replicate 2 HCE [siKLF7_undifferentiated]

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

hyb_protocol: 2ug of the labeled, fragmented single stranded cDNA is hybridized at 45C with rotation for 17 hours (Affymetrix GenechIP Hybridization Oven 640) to probe sets present on an Affymetrix GeneChIP 1.0ST array. The GeneChIP arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007)

scan_protocol: Arrays were scanned using GeneChIP Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHIP). The settings used were algorithm-PLIER v2.0; quantification scale-Linear;quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.
Raw values lower than 200 were not considered expressed

source_name: HCE

label_protocol: The Ambion WT expression kit (Life Technologies) was used to prepare RNA samples for whole transcriptome microarray analysis

growth_protocol: HCE were grown in Occulife media (LifeLine Technologies)

extract_protocol: Cells were collected and lysed in Trizol, followed by Chloroform extraction. RNA was extracted from the aqueous phase. RNA concentration and quality were quantified on a NanoDrop

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 20nM control (Dharmacon ON-TARGETplus Control pool, D-001810-10-05) or KLF7 (Dharmacon L-019540-00-0005). They were collected 48 hours after transfection

value: undifferentiated cells

value: HCE


title: Mus Musculus H2O2 8h 3

source_name: embryonic stem cell H2O2 8h 3

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. All samples passed RNA quality control using capillary gel electrophoresis (RIN > 9) (Bioanalyzer 2100; Agilent Technologies, Amstelveen, the Netherlands). MicroRNA profiling was performed as previously described (Pothof et al. 2009).

tag: class

tag: exposure time

tag: clone


title: scramble control replicate 1 HCE [siKLF7_undifferentiated]


title: Mus Musculus_PhenB 12h 3

source_name: embryonic stem cell_PhenB 12h 3

value: PhenB

value: NGTXC


title: Mus Musculus_MMC 12h 3

source_name: embryonic stem cell_MMC 12h 3

value: GTXC

value: embryonic stem cell


title: scramble control replicate 2 HCE [siKLF4_undifferentiated]

hyb_protocol: 2ug of the labeled, fragmented single stranded cDNA is hybridized at 45C with rotation for 17 hours (Affymetrix GenechIP Hybridization Oven 640) to probe sets present on an Affymetrix GeneChIP 2.0ST array. The GeneChIP arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007)

growth_protocol: HCE were grown in CNT-prime media (Cell-n-Tech, #CNT-PR)

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 20nM control (Dharmacon ON-TARGETplus Control pool, D-001810-10-05) or KLF4 (Qiagen SI00463253, S103176733). They were collected 48 hours after transfection


title: Mus Musculus_Cispt 4h 1

source_name: embryonic stem cell_Cispt 4h 1

value: Cispt


title: siKLF7 replicate 2 HCE [siKLF7_undifferentiated]


title: Mus Musculus_PhenB 4h 1

source_name: embryonic stem cell_PhenB 4h 1


title: Mus Musculus_MMC 4h 2

source_name: embryonic stem cell_MMC 4h 2

value: MMC


title: siKLF4 replicate 2 HCE [siKLF4_undifferentiated]


title: Mus Musculus_Arsenite 12h 1

source_name: embryonic stem cell_Arsenite 12h 1

value: Arsenite


title: Mus Musculus_MMS 4h 4

source_name: embryonic stem cell_MMS 4h 4

value: MMS


title: Mus Musculus H2O2 4h 3

source_name: embryonic stem cell H2O2 4h 3


title: Mus Musculus_DMSO 12h 2

source_name: embryonic stem cell_DMSO 12h 2

value: DMSO

value: Control


title: siKLF4 replicate 1 HCE [siKLF4_undifferentiated]


title: siKLF7 replicate 1 HCE [siKLF7_undifferentiated]


title: 80306

type: protein

city: Tempe

first: Benjamin

last: Katchman

state: AZ

address: 727 E. Tyler St.

institute: Arizona State University

description:
The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.
This sample did not pass QA/QC; omitted from the study

hyb_protocol: Plasma hybridization was performed on TECAN HS 4800 Pro. 1. Protein arrays were blocked with 5% milk PBST (0.2% Tween) for 1 hour at RT; 2. 150ul 1:50 diluted serum was applied to each slide with medium agitation 16 hours at 4oC; 3. Slides were incubated with 150ul 1:500 dilution of Dylight 649-linked anti-human secondary antibodies (Jackson Immunoresearch) in milk PBST.

scan_protocol: Slides were scanned by TECAN PowerScanner at 50% gain, 50% laser and 10µm resolution.

data_processing: 1. The background signal estimated by the 25th percentile of the negative control; 2. Normalize the array by the median.

label: Serum samples are not labeled

molecule: protein

source_name: Peripheral Blood

label_protocol: No lable was performed on the serum sample

extract_protocol: Peripheral blood samples were drawn from the antecubital vein and serum was prepared according to a standardized protocol before freezing serum aliquots at -80oC

value: Serum

tag: type

value: Serous Ovarian Cancer

tag: array batch

value: GST1 - 4; FLAG


title: 80302

description: The serum was applied on the protein array, secondary anti-human IgG antibody used for detection.

tag: tissue


title: Mus Musculus_MEN 12h 4

address: P. Debyelaan 25

institute: Maastricht University Medical Center

data_processing: The raw microRNA data, median signal minus median background, were normalized using quantile normalization. The quality control discarded an array as outlier when the intensity distribution after background substraction was deviating from the control samples. Duplicate spots on the array were averaged and the normalized values were analyzed for differentially expressed microRNAs using a linear model (bioconductor package Limma; Smyth 2005) and corrected for multiple testing (Benjamini and Hochberg 1995) was applied.

source_name: embryonic stem cell_MEN 12h 4

value: MEN

value: Ox


title: 70181

value: Healthy Control


title: Mus Musculus_Wy 12h 1

source_name: embryonic stem cell_Wy 12h 1

value: Wy


title: 70254


title: Mus Musculus_Dox 8h 1

source_name: embryonic stem cell_Dox 8h 1

value: Dox


title: 70001


title: 80175


title: 80301


title: 50547


title: Mus Musculus_CSA 8h 1

source_name: embryonic stem cell_CSA 8h 1

value: CSA

value: NGTXC


title: Mus Musculus_Arsenite 8h 4

source_name: embryonic stem cell_Arsenite 8h 4

value: embryonic stem cell


title: Mus Musculus_MMC 12h 1

source_name: embryonic stem cell_MMC 12h 1

value: GTXC


title: 50511


title: Mus Musculus_DES 12h 2

source_name: embryonic stem cell_DES 12h 2

value: DES


title: 80014


title: Mus Musculus_PBS 12h 4

source_name: embryonic stem cell_PBS 12h 4

value: PBS


title: Mus Musculus_MEN 4h 1

source_name: embryonic stem cell_MEN 4h 1


title: Mus Musculus_DEM 8h 1

source_name: embryonic stem cell_DEM 8h 1

value: DEM


title: 50822


title: Mus Musculus_MMS 4h 2

source_name: embryonic stem cell_MMS 4h 2

value: MMS


title: scramble control replicate 1 HCE [siKLF4_undifferentiated]

source_name: HCE

value: undifferentiated cells

value: HCE


title: 50273

value: Serum


title: 50314

value: GST1 - 4; FLAG


title: 50382


title: Control tissue at 0 min, biological rep3

city: Bar Harbor

first: Vishnu

last: Hosur

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

hyb_protocol: Hybridized onto 1.0 ST GeneChip (Affymetrix) arrays.

scan_protocol: GeneChips were scanned and quantified using GeneChip Scanner 3000 and GCOS 1.0 software, respectively.

data_processing: Average signal intensities for each probe set within arrays were calculated and exported using Affymetrix’s Expression Console (Version 1.1) software. Probes were summarized into probe sets using the RMA (Robust Multi-Array Average) method, which incorporates convolution background correction, sketch quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.

source_name: Control tissue at 0 min

label_protocol: Following cDNA synthesis, total RNA was amplified, labeled with biotinylated nucleotides.

extract_protocol:
Frozen in RNAlater
TRIzol (ThermoFisher Scientific) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were wounded using a surgical ear punch device to make 2-mm through-and-through holes in the center of the ears. At the indicated times, mice were euthanized and a 3-mm biopsy punch was used to collect 1-mm of tissue adjacent to the 2-mm through-and-through holes. Skin tissue was then washed with PBS and stored in RNAlater solution.

value: Ear pinna tissue

tag: strain

tag: genotype

tag: treatment

value: control

tag: time

value: 0 hours

tag: age


title: Mutant tissue at 0 min, biological rep3

source_name: Mutant tissue at 0 min


title: Mus Musculus_Dox 12h 1

first: Kasper

last: Derks

hyb_protocol: Labeled materials were hybridized to Custom Exiqon LNA probes for 16 hours at 60°C, subsequently washed and scanned

source_name: embryonic stem cell_Dox 12h 1

label_protocol: Total RNA was labeled using the Createch Cy3 label kit (Createch), 1ug of total RNA was used.


title: 50009

value: Healthy Control


title: 7237


title: Mus Musculus_Wy 12h 3

source_name: embryonic stem cell_Wy 12h 3

value: Wy


title: Mus Musculus_MEN 12h 1

source_name: embryonic stem cell_MEN 12h 1

value: MEN

value: Ox


title: Mus Musculus_Cispt 4h 3

source_name: embryonic stem cell_Cispt 4h 3

value: Cispt

value: embryonic stem cell


title: 50460

source_name: Peripheral Blood


title: Mutant tissue at 0 min, biological rep2


title: 50814


title: 50240


title: Mus Musculus_PBS 12h 3

source_name: embryonic stem cell_PBS 12h 3

value: Control


title: 5733


title: Control tissue at 0 min, biological rep1


title: 50456


title: Mus Musculus_DES 12h 1

source_name: embryonic stem cell_DES 12h 1

value: DES

value: NGTXC


title: Mutant tissue at 0 min, biological rep1


title: Control tissue at 0 min, biological rep2


title: Mutant tissue at 2h, biological rep2

source_name: Mutant tissue at 2h

value: ear punch

value: 2 hours


title: 5714


title: Mutant tissue at 2h, biological rep1


title: Mus Musculus_DMSO 12h 1

source_name: embryonic stem cell_DMSO 12h 1

value: DMSO


title: Mus Musculus_PhenB 8h 4

source_name: embryonic stem cell_PhenB 8h 4

value: PhenB


title: Mutant tissue at 24h, biological rep1

source_name: Mutant tissue at 24h

value: 24 hours


title: 5679

value: Serum

value: GST1 - 4; FLAG


title: Mutant tissue at 24h, biological rep2

value: Ear pinna tissue


title: 5791

value: Healthy Control


title: 5753


title: 5418


title: Mus Musculus H2O2 4h 2

source_name: embryonic stem cell H2O2 4h 2


title: Mus Musculus_CSA 12h 1

source_name: embryonic stem cell_CSA 12h 1

value: CSA


title: Mus Musculus_Dox 12h 3

source_name: embryonic stem cell_Dox 12h 3

value: Dox

value: GTXC


title: 5594


title: Mutant tissue at 15 min, biological rep3

source_name: Mutant tissue at 15 min

value: 15 minutes


title: 5372


title: 5097


title: 5069


title: 5072


title: 5384


title: Mus Musculus_Wy 12h 2

source_name: embryonic stem cell_Wy 12h 2

value: Wy

value: embryonic stem cell


title: Mutant tissue at 2h, biological rep3


title: Mutant tissue at 24h, biological rep3


title: 5062


title: Mutant tissue at 15 min, biological rep2


title: 5357


title: Mus Musculus_CSA 4h 3

source_name: embryonic stem cell_CSA 4h 3


title: Mus Musculus_PhenB 8h 1

source_name: embryonic stem cell_PhenB 8h 1


title: 2589

value: Serous Ovarian Cancer


title: Control tissue at 24h, biological rep1

source_name: Control tissue at 24h


title: Control tissue at 2h, biological rep1

source_name: Control tissue at 2h


title: Control tissue at 2h, biological rep3


title: Control tissue at 24h, biological rep2


title: 2227


title: Control tissue at 2h, biological rep2


title: Control tissue at 15 min, biological rep1

source_name: Control tissue at 15 min


title: Control tissue at 24h, biological rep3


title: 2593

source_name: Peripheral Blood


title: 2600


title: 2586


title: 1800


title: 1678


title: 1768


title: 1666


title: 50511


title: 50822


title: 50547


title: 50814


title: 70001


title: 70181


title: 80301


title: 80302


title: 80175


title: 70254


title: 80014


title: 80306


title: 2224


title: 1923


title: 1895


title: 2100


title: 2025


title: 1985


title: 2039


title: 2198


title: 2080


title: 2073


title: 1660


title: 50460


title: Control tissue at 15 min, biological rep3


title: 50456


title: 50314


title: 50382


title: 1547


title: Control tissue at 15 min, biological rep2


title: 1545


title: 1521


title: 50009


title: 80306


title: 80302


title: 1571


title: 80301


title: 80014


title: 5733


title: 50240


title: 5714


title: 70254


title: 50261


title: 1494


title: 5791


title: 50273


title: 7237


title: 5594


title: 70181


title: 80175


title: 5384


title: 5418


title: 5753


title: 5679


title: 50814


title: 50456


title: 50460


title: 70001


title: 50511


title: 5357


title: 5097


title: 50547


title: 50273


title: 50261


title: 2589


title: 2593


title: 50314


title: 50240


title: 2586


title: 5062


title: 5072


title: 5791


title: 50009


title: 2224


title: 5372


title: 5069


title: 2600


title: 2227


title: 5679


title: 2039


title: 2080


title: 5418


title: 2100


title: 5384


title: 50822


title: 50382


title: 7237


title: 5733


title: 2073


title: 5097


title: 5594


title: 5753


title: 2198


title: 1678


title: 1800


title: 2025


title: 1985


title: 1571


title: 1768


title: 5714


title: 5357


title: 2600


title: 5069


title: 5072


title: 1923


title: 5062


title: 1547


title: 1666


title: 2586


title: 1660


title: 1895


title: 2593


title: 2589


title: 1521


title: 2224


title: 1545


title: 2080


title: 2227


title: 2198


title: 2100


title: 1985


title: 1923


title: 1494


title: 2039


title: 2025


title: 2073


title: 1678


title: 1768


title: 1660


title: 1666


title: 1800


title: 1571


title: 1521


title: 80306


title: 1547


title: 1545


title: 50547


title: 80301


title: 70254


title: 80175


title: 50511


title: 70181


title: 50460


title: 50456


title: 50814


title: 50314


title: 50240


title: 70001


title: 50822


title: 50382


title: 50261


title: 50009


title: 80302


title: 50273


title: 80014


title: 5791


title: 5753


title: 7237


title: 5418


title: 5357


title: 5097


title: 5714


title: 5733


title: 5072


title: 5372


title: 5069


title: 5062


title: 5384


title: 5594


title: 2593


title: 2600


title: 2589


title: 2517


title: 2580


title: 5679


title: 2417


title: 2586


title: 2227


title: 2404


title: Enriched Environment Mouse 1

city: London

first: Fulvio

last: D'Acquisto

address: Charterhouse square

department: William Harvey Research Institute

institute: Queen Mary University of London, Barts and The London School of Medicine and Dentistry

description: Gene expression data from animals housed in an enriched vs standard lab environment

hyb_protocol: samples were hybridised on Affymetrix GeneChip Mouse Gene v2.0ST arrays for 16 hours at 45°C with constant rotation. (Detailed protocols can be found in the Affymetrix WT Terminal Labelling and Hybridisation User Manual edition 5.)

scan_protocol: scanning of the arrays was performed on an Affymetrix GeneChip Fluidics station 450 and GCS3000 Affymetrix scanner respectively according to the manufacturer’s recommendations

data_processing: Relevant genes were filtered by excluding those without an Entrez ID and those with low expression levels less than 100 by non-logged value. T-statistics were applied across the data set using the Bioconductor package Limma, and differentially expressed genes were identified by p<0.05 (non-adjusted p-value) and fold change > 2.

source_name: Blood from a CD1 mouse housed in an enriched lab environment

label_protocol: sense strand cDNA was prepared from total RNA ready for fragmentation and labelling using the Genechip ® WT Terminal Labelling Kit

growth_protocol: Male CD1 mice were housed for 2 weeks in a standard or enriched enclosure

extract_protocol: RNA was then extracted using an RNeasy Animal Blood RNA Mini Kit (Qiagen) adhering to the manufacturer’s instructions (RNeasy Handbook 06/2012). Quality checking of each RNA sample was carried out by spectrophotometric analysis using a Nandrop (ND-1000. Thermo-Scientific) and microfluidic analysis via Agilent 2100 Bioanalyser (Agilent Technologies)

treatment_protocol: At the end of the two weeks period whole blood was extracted from animals by cardiac puncture

tag: gender

value: Male

value: 9 weeks


title: 80461


title: 2224


title: Standard Environment mouse 2

source_name: Blood from a CD1 mouse housed in a standard lab environment


title: Standard Environment mouse 3


title: 80306


title: 1769


title: 2198


title: Enriched Environment Mouse 2


title: 80302


title: 1916


title: 2100


title: 80301


title: Enriched Environment Mouse 3


title: Standard Environment mouse 1


title: 2022


title: v-Hras transduced mouse epidermal keratinocytes + Xbp1 ShRNA lentivirus biol replicate 2

city: University Park

first: Adam

middle: B.

last: Glick

state: PA

address: 101 Life Sciences Bld

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

hyb_protocol: Samples were hybridized according to manufacturer's instructions using the GeneChip Hybridization Wash and Stain Kit  and Affymetrix GeneChip Hybridization Oven 640. Arrays were washed and stained using the  Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’s protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using ArrayStar 11 software. RMA background correction was applied to probe intensities. Gene level expression were summarized from the corrected intensities and quantile normalized.
MoGene-2_0-st.pgf
MoGene-2_0-st-v1.na33.mm10.transcript.csv

source_name: primary mouse epidermal keratinocyte

label_protocol: cDNA was generated from 100 ng of total RNA from each sample using the Ambion WT Expression Kit according to the manufacturer’s protocol. The sense strand cDNA was fragmented and labelled using the Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer’s instructions

growth_protocol: Primary mouse keratinocytes were isolated from newborn FVB/n mice according to standard protocols and cultured in EMEM media with 8% chelexed serum, antibiotics and 0.05 mM calcium chloride. Keratinocytes were co-infected with a high titer v-Hras retrovirus on day 2 of culture and either scrambled control ShRNA, Ire1a ShRNA or Xbp1 ShRNA lentiviruses and after 48 hrs selected for 2 days in puromycin. Total RNA was isolated from triplicate cultures on day 5 after virus transduction. Primary keratinocytes without v-HRas were transduced with the scrambled control ShRNA lentivirus, selected in puromycin and Total RNA  isolated from these cells at the same total time in culture as virus transduced keratinocytes.

extract_protocol: Total RNA was isolated keratinocyte cultures using Ribozol on day xx after lentiviral transduction and selection. RNA quality assesed using Agilent Bioanalyzer.

tag: protocol

value: yes v-Hras retrovirus

tag: shRNA

value: Xbp1 ShRNA

value: FVB/n


title: 2080


title: JR053-1

type: genomic

description: single replicate

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file and manifest HumanCytoSNP-12v2-1_H provided by Illumina for GPL13829, and humanomniexpress_24v1-1_a for GPL19699. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

molecule: genomic DNA

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor JR053, clone 1

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: male

tag: donor

value: control donor

tag: culture conditions

value: mTeSR-1 + matrigel

tag: cell type

value: induced pluripotent stem cells derived from dermal fibroblasts


title: v-Hras transduced mouse epidermal keratinocytes + Xbp1 ShRNA lentivirus biol replicate 1


title: JR053-6

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor JR053, clone 6


title: 80014

value: Serum

value: GST1 - 4; FLAG


title: 80175


title: MK088

description: single replicate

source_name: human dermal fibroblasts, GBA N370S donor MK088

value: GBA N370S donor

value: ADMEM + 10% FCS

value: dermal fibroblasts


title: 2513


title: OX2

description: single replicate

source_name: human dermal fibroblasts, control donor OX2


title: 2025


title: 2039


title: 1636


title: 1923


title: 80497


title: 2184


title: 1985


title: MK082

description: single replicate

source_name: human dermal fibroblasts, GBA N370S donor MK082


title: 70001

value: Healthy Control


title: 70254


title: 50822


title: MK088-7

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor MK088, clone 7


title: 50814


title: v-Hras transduced mouse epidermal keratinocytes + control ShRNA lentivirus biol replicate 2

value: scrambled ShRNA


title: 50547


title: v-Hras transduced mouse epidermal keratinocytes + Xbp1 ShRNA lentivirus biol replicate 3


title: MK082-31

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor MK082, clone 31


title: v-Hras transduced mouse epidermal keratinocytes + control ShRNA lentivirus biol replicate 3


title: 1800

value: Serous Ovarian Cancer


title: v-Hras transduced mouse epidermal keratinocytes + Ire1a ShRNA lentivirus biol replicate 1

value: Ire1a ShRNA


title: v-Hras transduced mouse epidermal keratinocytes + Ire1a ShRNA lentivirus biol replicate 2


title: 50511


title: JR053

description: single replicate

source_name: human dermal fibroblasts, control donor JR053


title: 1895


title: 1768


title: 80382


title: 1666


title: 1878


title: v-Hras transduced mouse epidermal keratinocytes + control ShRNA lentivirus  biol replicate 1


title: 80005


title: 1789


title: 50460


title: 80569


title: 1678


title: 1547


title: v-Hras transduced mouse epidermal keratinocytes + Ire1a ShRNA lentivirus biol replicate 3


title: 50456


title: 1660


title: 2073


title: 80731


title: 1545


title: 80684


title: 80036


title: 50273


title: 80264


title: 50382


title: 50314


title: 1571


title: 80620


title: 1494


title: siKLF7 replicate 2 HCE [siKLF4-siKLF7_differentiation]

source_name: HCE

growth_protocol: HCE were grown in CNT-prime media (Cell-n-Tech, #CNT-PR), and were induced to differentiate by switching to CNT-prime 2D Diff media (Cell-n-Tech, #CNT-PR-D)

treatment_protocol: 100,000 cells were plated in each well of a 12 well plate, and were transfected with 30nM control (Dharmacon ON-TARGETplus Control pool, D-001810-10-05), KLF7 (L-019540-00-0005), or KLF4 (Qiagen SI00463253, S103176733). They were induced to differentiate switching to differentiation media 24 hours after transfection, and collected an additional 24 hours later.

value: differentiated

tag: cell line

value: HCE


title: siKLF4 replicate 1 HCE [siKLF4-siKLF7_differentiation]


title: 50261


title: 1521


title: 50240


title: 50009


title: 5791


title: Mouse epidermal keratinocytes + control ShRNA lentivirus biol replicate 2

value: no v-Hras retrovirus


title: 2432


title: 80218


title: Mouse epidermal keratinocytes + control ShRNA lentivirus biol replicate 1

value: FVB/n


title: 7237


title: scramble control replicate 2 HCE [siKLF4-siKLF7_differentiation]


title: 1564


title: 5714


title: 5594


title: 5679


title: scramble control replicate 1 HCE [siKLF4-siKLF7_differentiation]


title: 5753


title: 80633


title: siKLF4 replicate 2 HCE [siKLF4-siKLF7_differentiation]


title: 5357


title: 5418


title: Mouse epidermal keratinocytes + control ShRNA lentivirus biol replicate 3


title: 80178


title: 50014


title: 2480


title: 70057


title: siKLF7 replicate 1 HCE [siKLF4-siKLF7_differentiation]


title: 50427


title: 80551


title: 5527


title: 50562


title: 70181


title: 5733


title: 50325


title: 5384


title: 5372


title: 5069


title: 50360


title: 2586


title: 2227


title: 2593


title: 5033


title: NTO-3000ppm-2

city: Vicksburg

first: Ping

last: Gong

state: Mississippi

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: U.S Army Engineer Research and Development Center

description: Labeled cRNA was hybridized to the genome-wide microarray to profile global gene expression.

hyb_protocol: The labeled cDNA was hybridized to the C. elegans-specific 44K-olig array (one sample/array) at 65°C for 17 hrs using Agilent’s Gene Expression Hybridization Kits. A total of 48 samples (3 chemicals × 4 treatments per chemical × 4 replicates per treatment) were hybridized to six 8 × 44K-array slides in a randomized fashion to reduce systematic errors.

scan_protocol: An Agilent high-resolution DNA Microarray Scanner Model G2565CA was used to scan microarray images (resolution = 3 microns per pixel).

data_processing: Raw microarray gene expression data were extracted from acquired array images as spot and background signal intensity using Agilent’s Feature Extraction software v10.7. A spot was flagged out if its raw signal intensity was below its background level, or if it was saturated. A gene was flagged out if over 50% of the 48 samples had missing values for this gene. The filtered data was background subtracted and log-transformed. The spike-in RNA mix with known composition and RNA copy numbers was used to construct standard linear regression curves, from which the unknown worm RNA concentrations were derived. The derived RNA concentrations were normalized to the median value per array (sample).

organism: Caenorhabditis elegans

source_name: Wild type C. elegans var. Bristol strain N2

label_protocol: One hundred ng of total RNA was first reverse-transcribed into cDNA, followed by cDNA labeling using Low Input Quick Amp Labeling Kits (Agilent, Palo Alto, CA) in the presence of cyanine 3-CTP dye.

growth_protocol: The wild-type C. elegans var. Bristol, strain N2, was maintained at 20°C on NGM agar plates seeded with Escherichia coli OP50 bacteria. The culture was synchronized at the first larval stage (L1) by bleaching with a 5% sodium hypochlorite solution. Worms were harvested by gentle rinsing with K Medium in late L3 stage which were determined by both length and age (Donkin and Williams 1995; Altun and Hall 2005).

extract_protocol: After the 24-hr exposure, all 400 worms per well were collected into a cryogenic vial and spun at 1150 x g for 2.5 min. Supernatant was removed and the vial were flash frozen in liquid nitrogen and stored at -80°C.  Total RNA was extracted from each vial using RNeasy mini kits (Qiagen, Valencia, CA) and treated as one biological replicate. Four of the five replicates (total RNA samples) per treatment were chosen for further microarray hybridization.

treatment_protocol: After harvesting from agar plates, worms were spun at 1150 x g for 2.5 min and re-suspended in a given volume of K Medium. Twenty µL of worms were deposited on a microscope slide containing a grid sticker and worms were counted. The number of worms/mL was then calculated. Wide-bore pipet tips or transfer pipets were always used to avoid shearing of worms. Worms were exposed in 24-well tissue-culture treated (TC) plates for 24 hours to DNAN, NTO, or NQ. All test solutions were prepared in K medium except that acetone was used to dissolve DNAN, resulting in 5% carrier in the final solution. Each weel in the TC plates contained 400 worms and 1 ml of K medium or test solution. The nominal concentrations were: Vehicle control, 1.9, 15.5, 62 mg DNA/L, Blank control, 187, 750, 3000 mg NTO/L, and Blank control, 83, 666, 2667 mg NQ/L. Each treatment had 5 replicates.

value: Pooled somatic tissue of approx. 400 nematodes

value: hermaphrodite

tag: developmental stage

value: Late L3 stage grown from synchronized culture

tag: 24-hr acute treatment

value: NTO

tag: concentration

tag: replicate


title: NTO-750ppm-4

tag: tissue


title: 50263

value: Serum

tag: type


title: 5062

tag: array batch

value: GST1 - 4; FLAG


title: 50200


title: NTO-187ppm-4


title: 70261


title: NTO-Control-2

value: Control


title: NQ-Control-4

value: NQ


title: 2600


title: 50408


title: 70363


title: 2589


title: 5241


title: NQ-Control-2


title: 50208


title: 5097


title: 5072


title: NQ-2667ppm-1


title: 2224


title: NTO-187ppm-1


title: 2198


title: 5701


title: 70193


title: 2080


title: 5330


title: 50095


title: 5386


title: 2100


title: 2073


title: NTO-750ppm-1


title: NTO-CON-3

value: CON


title: 2039


title: 1630


title: 70045

value: Healthy Control


title: NQ-83ppm-4


title: 7319


title: DNAN-1.9ppm-3

value: DNAN


title: 50045


title: 2025

value: Serous Ovarian Cancer


title: Oral epithelial cells-15-week-3 [gene-level]

city: Shenyang

first: Fengxue

last: Geng

state: Liaoning

address: Nanjing North St. 117, Heping District

department: Periodontics

institute: China Medical University

description:
RNA2-2
test-3
Gene expression data from cells with bacterial infection.

hyb_protocol: Preprocessed hybridization solution (the final dilution of DNA was 25ng/μl) was added on the GeneChip and centrifuged for 16 h at 45℃ (60 rpm).

scan_protocol: GeneChip was scanned with Affymetrix scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Expression Console (version 1.3.1, Affymetrix) software offered RMA normalization for both gene- and exon-level analysis. Differential exon or junction identified through splicing index as well as P value calculated with One-Way Between-Subject ANOVA (Unpaired). The threshold was splicing index >= 2.0 or < = -2.0 and a P value<= 0.05.

source_name: immortalized oral epithelial cells infected with P. gingivalis for 15 wks

label_protocol: Biotinylated cDNAs were prepared according to the manufacturer's standard protocols (Ambion® WT Expression Kit).

growth_protocol: Human immortalized oral epithelial cells (HIOECs) were cultured in Defined Keratinocyte-SFM (GibcoTM, Thermo Fisher Scientific Inc., MA, USA) with growth supplement; P. gingivalis ATCC 33277 (American Type Culture Collection, Manassas, VA, USA) was routinely cultured.

extract_protocol: Total RNAs of HIOECs and HIOECs infected for 15 weeks were extracted with RNAiso Plus kit (TaKaRa, Dalian, China).

treatment_protocol: HIOECs were persistently infected with Porphyromonas gingivalis for up to 15 weeks. Cells without infection were cultured as the control.

value: HIOEC

value: human immortalized oral epithelial cells

tag: treatment

value: Porphyromonas gingivalis infection for 15 weeks


title: Oral epithelial cells-15-week-2 [gene-level]

description:
RNA2-1-2
test-2
Gene expression data from cells with bacterial infection.


title: DNAN-62.5ppm-5


title: 1985


title: 1923


title: Oral epithelial cells-15-week-1 [gene-level]

description:
RNA2-1-1
test-1
Gene expression data from cells with bacterial infection.


title: 5346


title: DNAN-1.9ppm-2


title: NQ-Control-3


title: 50533


title: 1895


title: DNAN-Control-4


title: 5645


title: Oral epithelial cells-non-infected-3 [gene-level]

description:
RNA1-3
control-3
Gene expression data from cells without bacterial infection.

source_name: immortalized oral epithelial cells, not infected


title: 1768


title: DNAN-Control-2


title: Oral epithelial cells-non-infected-2 [gene-level]

description:
RNA1-2
control-2
Gene expression data from cells without bacterial infection.


title: NQ-666ppm-2


title: 50179


title: 1800


title: 1678


title: NTO-Control-1


title: 1666


title: Oral epithelial cells-15-week-3 [exon-level]


title: Oral epithelial cells-15-week-2 [exon-level]


title: Oral epithelial cells-non-infected-1 [gene-level]

description:
RNA1-1
control-1
Gene expression data from cells without bacterial infection.


title: 2617

value: Benign Ovarian Disease


title: 2081