title: wt-Blood-78-weeks-3

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4

hyb_protocol: 60rpm, 18h, 45 centigrade in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: blood

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 24h IVT

growth_protocol: Maintained under normal mouse chow / SPF conditions (12h light-dark cycle)

extract_protocol: Qiagen RNEasy Lipid Tissue Mini Kit, Standardprotocol

treatment_protocol: Mouse blood was drawn by heart puncture into EDTA buffer, erythrocytes were lyzed, total blood cells were centrifuged, and taken up in Trizol.

tag: gender

value: male

value: 78 weeks

value: blood


title: patient 26 HN2227ms

status: Public on Oct 30 2013

type: RNA

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

description: training set

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data were processed using Robust Multi-Array (RMA) analysis, BRB arraytools sofware

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: fresh frozen laryngeal tumor

label_protocol: RNA was labelled using the Roche Microarray cDNA Synthesis

growth_protocol: Tumor specimens, collected from patients at the time of surgery, were immediately frozen in liquid nitrogen and then stored in -80˚C until RNA isolation

extract_protocol: RNeasy Mini Protocol, (Qiagen, CA, USA)

tag: dfs (months)

tag: dfs status (1 = recurred)

tag: grade

tag: age

tag: tissue

value: fresh frozen laryngeal tumor

tag: group

value: training set


title: stimulation with aNKp44 and IL-1/IL-7/IL-23, biological rep2

city: Berlin

first: Johannes

last: Meisig

address: Chariteplatz 1

department: Institut für Pathologie

country: Germany

institute: Charite Universitätsmedizin

description: Gene expression of RORγt+ ILCs after stimulation with aNKp44 and IL-1/IL-7/IL-23

hyb_protocol: Three replicates of biotinylated cRNA (15 ug) per group were fragmented and hybridized to 12 Affymetrix HG U133 plus 2.0 GeneChips using standard Affymetrix protocols.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Data was read in using the R/bioconductor affy package using the summary method medianpolish and normalization method rma. For annotation the bioconductor chip annotation package hgu133plus2 was used. The presence/absence algorithm implemented in mas5calls (bioconductor affy package) Was used to exclude weakly expressed genes, filtering out 60% of the genes.

source_name: RORγt+ ILCs

label_protocol: Labelling was performed using the Enzo RNA Transcript Labeling kit (Affymetrix).

extract_protocol: RNA was extracted from FACS sorted tonsil derived CD3-, CD14-, CD19-, CD56+, CD94-, CD127+ cells using the RNeasy Mini Kit (Qiagen) following manfacturer´s instructions. cDNA was synthesized from 100 ng total RNA (Ambion).

treatment_protocol: The FACS sorted cells were stimulated in RPMI+10%hAb serum with aNKp44, IL-1/IL-7/IL-23 or aNKp44/ IL-1/IL-7/IL-23 for 3.5 h at 37°C. The recombinant cytokines were applied at a concentration of each 50ng/ml and the stimulation beads at a bead-cell ratio of 5:1.

value: tonsil

tag: cell type

value: RORγt+ ILC

tag: treatment protocol


title: stimulation with aNKp44 and IL-1/IL-7/IL-23, biological rep3


title: Group B_E_9 m_rep2

type: genomic

city: Shanghai

last: Zhang

address: 1347 West Guangfu Rd.

country: China

institute: Institute of Forensic Science, Ministry of Justice

description:
Normal blood sample used for longitudinal study
#r-1

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

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

data_processing: The signal intensities and detection P values were extracted using GenomeStudio with no background subtraction or control normalization. The probes located on the X and Y chromosomes, probes containing SNP(s) or non-CpG loci, and probes with a detection P value exceeding 0.05 or missing β-values in any of the samples were removed from all individuals in the same group. After removal of these probes, 77.3% (375,324) and 76.0% (369,187) of the 485,577 CpG probes were tested for Groups A and B, respectively. The data were processed using the Bioconductor lumi package (version 2.12) and BMIQ (version 1.0) written in the R programming language. Color-bias adjustment (Col.Adj) and quantile normalization (QN) were carried out on the signal intensities in the Bioconductor lumi package to remove the batch effect from the experiment; subsequently, the probe type-bias adjustment was performed on the β-values using BMIQ. The β-values were transformed into M-values.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Peripheral blood, Group B, longitudinal study, unrelated individual

label_protocol: standard Illumina protocol

growth_protocol: Eleven monozygous twin pairs and 6 unrelated volunteers from China were recruited for the study . All participants had no health problems or diseases according to their self-reported health history records. Group A contained 10 pairs of MZ twins. Group B included a pair of MZ (male) twins and 6 unrelated individuals. Except subject H, all participants in Group B were recalled every 3 months for 9 months (0, 3, 6, and 9 m). Subject H was studied only at 0, 6, and 9 months.

extract_protocol: Buffy coat was extracted from peripheral blood, and genomic DNA was isolated using the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Four-milliliter EDTA-blood samples were collected at every visit and used for the genome-wide analysis of DNA methylation. For MZ 5B and E9 m, 5 and 6 independent whole blood samples were assessed for DNA methylation, respectively.

value: Female

value: Peripheral blood

tag: disease state

value: Normal


title: Group B_H_9 m

description:
Normal blood sample used for longitudinal study
#H-4


title: patient 25 HN2226ms

description: training set


title: stimulation with aNKp44 and IL-1/IL-7/IL-23, biological rep1


title: Group B_E_9 m_rep4

description:
Normal blood sample used for longitudinal study
#r-3


title: Group B_E_9 m_rep1

description:
Normal blood sample used for longitudinal study
#E-4


title: wt-Blood-78-weeks-1

organism: Mus musculus

tag: strain


title: patient 24 HN2225ms

description: training set


title: wt-Blood-78-weeks-2


title: stimulation with aNKp44, biological rep3

description: Gene expression of RORγt+ ILCs after stimulation with aNKp44

value: stimulation with aNKp44


title: wt-Blood-32-weeks-2

value: 32 weeks


title: wt-Blood-32-weeks-3


title: Group B_H_6 m

description:
Normal blood sample used for longitudinal study
#H-3


title: Group B_H_0 m

description:
Normal blood sample used for longitudinal study
#H-1


title: patient 23 HN2224ms

description: training set


title: wt-Blood-32-weeks-1


title: Group B_E_6 m

description:
Normal blood sample used for longitudinal study
#E-3


title: Group B_E_9 m_rep3

description:
Normal blood sample used for longitudinal study
#r-2


title: Group B_E_9 m_rep6

description:
Normal blood sample used for longitudinal study
#r-5


title: patient 22 HN2223ms

description: training set


title: Group B_E_0 m

description:
Normal blood sample used for longitudinal study
#E-0


title: stimulation with aNKp44, biological rep1


title: Group B_E_9 m_rep5

description:
Normal blood sample used for longitudinal study
#r-4


title: patient 21 HN2222ms

description: training set


title: apoE-Blood-78-weeks-3


title: patient 19 HN2220ms

description: training set


title: stimulation with IL-1/IL-7/IL-23, biological rep1

description: Gene expression of RORγt+ ILCs after stimulation with IL-1/IL-7/IL-23

value: stimulation with IL-1/IL-7/IL-23


title: patient 18 HN2219ms

description: training set


title: apoE-Blood-32-weeks-3


title: Group B_E_3 m

description:
Normal blood sample used for longitudinal study
#E-1


title: patient 20 HN2221ms

description: training set


title: stimulation with IL-1/IL-7/IL-23, biological rep3


title: stimulation with IL-1/IL-7/IL-23, biological rep2


title: apoE-Blood-78-weeks-1


title: apoE-Blood-78-weeks-2


title: Group B_G_6 m

description:
Normal blood sample used for longitudinal study
#G-3

value: Male


title: Group B_G_9 m

description:
Normal blood sample used for longitudinal study
#G-4


title: stimulation with aNKp44, biological rep2


title: ex-vivo, biological rep2

description: Gene expression of RORγt+ ILCs ex vivo

value: ex-vivo


title: apoE-Blood-32-weeks-2

description: Staining with Fluidic Station 400 Protocol: EukGe-WS2v4


title: patient 17 HN2218ms

description: training set


title: apoE-Blood-32-weeks-1


title: patient 16 HN2217ms

description: training set


title: Group B_G_3 m

description:
Normal blood sample used for longitudinal study
#G-2


title: ex-vivo, biological rep1

description: Gene expression of RORγt+ ILCs ex vivo


title: Group B_F_9 m

description:
Normal blood sample used for longitudinal study
#F-4


title: wt-Spleen-78-weeks-3

source_name: spleen

treatment_protocol: excised, rinsed with cold PBS (2mM EDTA)

value: spleen


title: patient 15 HN2216ms

description: training set


title: wt-Spleen-78-weeks-2


title: Group B_F_6 m

description:
Normal blood sample used for longitudinal study
#F-3


title: abi5-1 PEG treated radicles Replicate 3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Seeds were scarified with sand paper and imbibed on filter paper at 20°C in the dark

extract_protocol: Total RNAs were extracted from the frozen grinded seeds lots using the NucleoSpin Extract II, Total RNA Purification kit (Macherey-Nagel, GmbH & Co. KG, Germany) following manufacturer’s instructions

treatment_protocol: Germinated seeds with a protruded radicle length of  2.7 mm were selected and submitted to an osmotic treatment by incubation in a PEG 8000 solution (-1.7 MPa) at 10°C in the dark. After 72h, seeds were removed from the PEG solution and rinsed thoroughly. Three replicates of 50 radicles before and after PEG treatment from WT and abi5 mutants were excised and frozen for RNA extraction.

value: radicles

tag: genetic background

value: abi5-1 in R108

tag: treatment

value: PEG

tag: developmental stage

value: 2.7 mm radicles

tag: harvest date


title: patient 14 HN2215ms

description: training set

value: fresh frozen laryngeal tumor


title: patient 13 HN2214ms

description: training set

value: training set


title: patient 12 HN2213ms

description: training set


title: Group B_F_0 m

description:
Normal blood sample used for longitudinal study
#F-1


title: abi5-1 PEG treated radicles Replicate 1


title: Group B_G_0 m

description:
Normal blood sample used for longitudinal study
#G-1


title: abi5-1 control radicles Replicate 1

value: Control


title: wt-Spleen-78-weeks-1

value: male

value: 78 weeks


title: patient 11 HN2211ms

description: training set


title: abi5-1 control radicles Replicate 2


title: Group B_F_3 m

description:
Normal blood sample used for longitudinal study
#F-2

value: Peripheral blood


title: abi5-1 control radicles Replicate 3


title: wt-Spleen-32-weeks-3


title: Group B_D_9 m

description:
Normal blood sample used for longitudinal study
#D-4

value: Female

value: Normal


title: wt-Spleen-32-weeks-1

value: 32 weeks


title: Group B_D_6 m

description:
Normal blood sample used for longitudinal study
#D-3


title: MDA-MB-435 CREB3L1 HA ChIP

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

description:
435hMS1chip/435hMS1con
Chip-chip MDA-MB-435 CREB3L1 cells HA (CREB3L1)

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction software at Nimblegen.
The ratio_peaks.gff is the ratio of signal for each transcript on the chip between the ChIP sample and the input, which is used to determine if a positive signal is unique to the ChIP sample. The 'ratio_peaks_mapToFeatures_All_Peaks.txt' file contains data with the identity of the feature on it e.g. name and accession number.

source_name: CREB3L1 (HA) ChIP DNA from MDA-MB-435 CREB3L1 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 or Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Chromatin Immunoprecipitation (ChIP) assay was performed using an EpiQuick™ Chromatin Immunoprecipitation Kit (Epigentek™) and a HA-X (F-7) antibody (Santa Cruz).  All procedures were carried out according to the manufacturer’s specifications.  The ChIP DNA was then amplified using a GenomePLex Whole Genome Amplification Kit -4 (WGA-4) (Sigma), according to the manufacturer’s specifications.  The amplified DNA was then purified using a QIAquick® PCR purification kit (Qiagen).

tag: cell line

value: human breast adenocarcinoma cells

tag: chip antibody

value: HA-X (F-7) antibody

value: Santa Cruz

source_name: Input DNA from MDA-MB-435 CREB3L1

tag: sampe type

value: input DNA


title: patient 10 HN2210ms

description: training set

tag: dfs (months)


title: R108 PEG treated radicles Replicate 3

value: radicles


title: patient 9 HN2209ms

description: training set

tag: dfs status (1 = recurred)


title: apoE-Spleen-78-weeks-3

tag: gender

value: spleen


title: R108 control radicles Replicate 3


title: Group B_C_3 m

description:
Normal blood sample used for longitudinal study
#C-2

tag: age

value: Male


title: apoE-Spleen-78-weeks-2

tag: tissue


title: patient 8 HN2208ms

description: training set

tag: grade

tag: group


title: Group B_D_3 m

description:
Normal blood sample used for longitudinal study
#D-2


title: wt-Spleen-32-weeks-2


title: patient 6 HN2206ms

description: training set


title: apoE-Spleen-78-weeks-1


title: apoE-Spleen-32-weeks-3


title: Group B_MZ pair_#11_B_9 m

description:
Normal blood sample used for longitudinal study
#B-4

source_name: Peripheral blood, Group B, longitudinal study, MZ twin pair


title: R108 control radicles Replicate 1

value: 2.7 mm radicles


title: apoE-Spleen-32-weeks-2


title: Group B_C_9 m

description:
Normal blood sample used for longitudinal study
#C-4


title: patient 5 HN2205ms

description: training set

value: fresh frozen laryngeal tumor


title: Group B_D_0 m

description:
Normal blood sample used for longitudinal study
#D-1


title: abi5-2 PEG treated radicles Replicate 2

value: abi5-2  in R108

value: PEG


title: Group B_C_0 m

description:
Normal blood sample used for longitudinal study
#C-1


title: apoE-Spleen-32-weeks-1

value: male


title: R108 PEG treated radicles Replicate 2


title: R108 control radicles Replicate 2

value: Control


title: Group B_C_6 m

description:
Normal blood sample used for longitudinal study
#C-3

value: Peripheral blood


title: patient 7 HN2207ms

description: training set

value: training set


title: patient 4 HN2203ms

description: training set


title: Group B_MZ pair_#11_B_6 m

description:
Normal blood sample used for longitudinal study
#B-3

value: Normal


title: patient 3 HN2202ms

description: training set


title: Group B_MZ pair_#11_B_3 m

description:
Normal blood sample used for longitudinal study
#B-2


title: Group B_MZ pair_#11_B_0 m

description:
Normal blood sample used for longitudinal study
#B-1


title: patient 2 HN2201a

description: training set


title: abi5-2 PEG treated radicles Replicate 3


title: NC-8

city: Beijing

first: Ling-fei

last: Jia

address: 22 Zhongguancun Avenue South, Haidian District

institute: Peking University School and Hospital of Stomatology

description:
SAMPLE 16
adjacent histological normal tissues of TSCC-8

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

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

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

source_name: Human tongue tissues

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

growth_protocol: No growth protocol, all paired primary TSCC samples from anterior portions of the tongue and adjacent histological normal tissues were obtained from 9 patients who were admitted to the Department of Oral and Maxillofacial Surgery of Peking University School of Stomatology between May 2008 and August 2011.

extract_protocol: Total RNA was isolated from tumor and normal samples by using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA)

treatment_protocol: No treatment

tag: individual

value: patient 8

value: TSCC


title: S_treatment_rep6_pair6

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Gene expression in IUGR rabbits

hyb_protocol: Then, 1650 g of RNA obtained from each labelled sample was hybridized with an Agilent's Rabbit Microarray Kit 4x44k, P/N G2519F (Agilent Microarray Design ID 020908), for 17 hours at 65ºC

scan_protocol: Finally, each microarray was scanned (Axon 4000B scanner), at 5 m resolution in order to detect and quantify the hybridization

data_processing: Data extraction was done using Genepix Pro 6.0. Data was standardized using Robust Multi-array Average method (Bolstad, Irizarry, Astrand, & Speed, 2003) and quantile normalization from Bioconductor and R packages.

organism: Oryctolagus cuniculus

source_name: IUGR, replicate 6, pair 6

label_protocol: Next, 500 ng of total RNA from each sample was labelled with the Quick Amp One-color Labelling kit (Agilent) and  fluorochrome Cy3. Efficiency of labelling (Cy3pmol/g) was analyzed using a Nanodrop spectrophotometer to check that values were above the minimum requirements (>1.65 g and > 9.0 pmols Cy3/ g). Additionally, RNA 6000 Nano mRNA assay in the Bioanalyzer 2100 was done in order to assess that all the samples show a comparable profile and fragments size was as expected (200-2000 bp).

extract_protocol: Extraction protocol was a combination of TRIzol reagent and RNeasy Mini kit (Qiagen). RNA concentration and quality was determined in a Nanodrop spectrophotometer at 260/280 and 260/230 ratios. For every samples included in the study total amount of RNA was always above 25 g with homogenous profile, showing RNA integrity Number between 9.3 to 9.9 (analyzed with RNA 6000 Nano and Bioanalizer 2100; Agilent)

treatment_protocol: Fetal heart ventricles were immediately snap frozen and stored at -80ºC until the moment of use. FGR-gene expression profile was analyzed with a gene expression microarray containing 43,803 probes sequences obtained from the rabbit genome.  All probe sequences included in the microarray were based on rabbit (Oryctolagus cuniculus) public transcript data. Although the microarray provides information from the whole rabbit genome, in this study special interest was paid on the expression profile of the contractile machinery of the cardiomyocyte, the sarcomere.

tag: pair


title: TSCC-9

description:
SAMPLE 17
TSCC samples from anterior portions of the tongue of patient#9

value: patient 9

value: NC


title: NC-9

description:
SAMPLE 18
adjacent histological normal tissues of TSCC-9


title: TSCC-8

description:
SAMPLE 15
TSCC samples from anterior portions of the tongue of patient#8


title: abi5-1 PEG treated radicles Replicate 2

value: abi5-1 in R108


title: Group B_MZ pair_#11_A_9 m

description:
Normal blood sample used for longitudinal study
#A-4

tag: disease state


title: S_control_rep6_pair6

description: Gene expression in control rabbits

source_name: control, replicate 6, pair 6


title: abi5-2 control radicles Replicate 3

value: radicles

tag: genetic background


title: NC-7

description:
SAMPLE 14
adjacent histological normal tissues of TSCC-7

value: patient 7


title: Group B_MZ pair_#11_A_6 m

description:
Normal blood sample used for longitudinal study
#A-3

value: Male


title: abi5-2 control radicles Replicate 1

tag: treatment

value: 2.7 mm radicles


title: abi5-2 PEG treated radicles Replicate 1

tag: developmental stage


title: Group A_MZ pair_ #10_B

description:
Normal blood sample from MZ twins
#1085-177b

source_name: Peripheral blood, Group A, MZ twin pair


title: patient 1 HN2200a

description: training set

value: fresh frozen laryngeal tumor


title: R108 PEG treated radicles Replicate 1

tag: harvest date


title: Group B_MZ pair_#11_A_3 m

description:
Normal blood sample used for longitudinal study
#A-2


title: S_treatment_rep5_pair5

description: Gene expression in IUGR rabbits

source_name: IUGR, replicate 5, pair 5


title: TSCC-7

description:
SAMPLE 13
TSCC samples from anterior portions of the tongue of patient#7


title: S_control_rep4_pair4

description: Gene expression in control rabbits

source_name: control, replicate 4, pair 4


title: Group B_MZ pair_#11_A_0 m

description:
Normal blood sample used for longitudinal study
#A-1


title: S_treatment_rep4_pair4

description: Gene expression in IUGR rabbits

source_name: IUGR, replicate 4, pair 4


title: NC-6

description:
SAMPLE 12
adjacent histological normal tissues of TSCC-6

value: patient 6


title: TSCC-5

description:
SAMPLE 9
TSCC samples from anterior portions of the tongue of patient#5

value: patient 5


title: TSCC-6

description:
SAMPLE 11
TSCC samples from anterior portions of the tongue of patient#6


title: S_control_rep5_pair5

description: Gene expression in control rabbits

source_name: control, replicate 5, pair 5


title: S_treatment_rep3_pair3

description: Gene expression in IUGR rabbits

source_name: IUGR, replicate 3, pair 3


title: NC-5

description:
SAMPLE 10
adjacent histological normal tissues of TSCC-5


title: NC-4

description:
SAMPLE 8
adjacent histological normal tissues of TSCC-4

value: patient 4


title: S_control_rep2_pair2

description: Gene expression in control rabbits

source_name: control, replicate 2, pair 2


title: S_control_rep3_pair3

description: Gene expression in control rabbits

source_name: control, replicate 3, pair 3


title: Group A_MZ pair_ #9_B

description:
Normal blood sample from MZ twins
#1023-132b

value: Female


title: Group A_MZ pair_ #10_A

description:
Normal blood sample from MZ twins
#1084-177a

value: Peripheral blood


title: Group A_MZ pair_ #9_A

description:
Normal blood sample from MZ twins
#1022-132a


title: S_treatment_rep2_pair2

description: Gene expression in IUGR rabbits

source_name: IUGR, replicate 2, pair 2


title: Group A_MZ pair_ #8_B

description:
Normal blood sample from MZ twins
#999-113b


title: NC-3

description:
SAMPLE 6
adjacent histological normal tissues of TSCC-3

value: patient 3


title: S_treatment_rep1_pair1

description: Gene expression in IUGR rabbits

source_name: IUGR, replicate 1, pair 1


title: S_control_rep1_pair1

description: Gene expression in control rabbits

source_name: control, replicate 1, pair 1


title: Group A_MZ pair_ #8_A

description:
Normal blood sample from MZ twins
#998-113a

value: Normal


title: Group A_MZ pair_ #7_B

description:
Normal blood sample from MZ twins
#987-107b


title: TSCC-4

description:
SAMPLE 7
TSCC samples from anterior portions of the tongue of patient#4


title: TSCC-3

description:
SAMPLE 5
TSCC samples from anterior portions of the tongue of patient#3


title: TSCC-2

description:
SAMPLE 3
TSCC samples from anterior portions of the tongue of patient#2

value: patient 2


title: abi5-2 control radicles Replicate 2

value: abi5-2  in R108

value: Control


title: Rat mammary gland lactancy day 12, biological replicate 2

city: Cuernavaca

first: Sergio

middle: Manuel

last: Encarnación

state: Morelos

address: Av. Universidad S/N

department: Centro de Ciencias Genomicas

country: Mexico

institute: Universidad Nacional Autonoma de México

description: Biological replicate 2 of 3.

hyb_protocol: Using hybridization solution UniHyb (TeleChem International Inc., California, USA), equal quantities of labeled cDNA were hybridized to the M22K_01 microarray for 14 h at 42 °C. Each hybridization assay was carried out by triplicate. Dye swapping was carried out in separate experiments to eliminate any variation that might result from differences in fluorescence dye intensities.

scan_protocol: Acquisition and quantification of array images were performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% photomultiplier tube (PMT) gain, 70% to 75% laser power, and 10 μm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro® Analyzer from Media Cybernetics.

data_processing: Background correction, lowest normalization, intensity filter, variance analysis of replicates and selection of differentially expressed genes were performed with GenArise software (http://www.ifc.unam.mx/genarise/). The software identifies differential expressed genes by calculating an intensity-dependent z-score that measures the number of standard deviations (SD) a data point is from the mean [zi=(Ri-mean(R))/sd(R)].

organism: Rattus norvegicus

source_name: Total RNA from pooled whole inguinal mammary glands harvested from parous or virgin Sprague Dawley female rats (n = 3).

label_protocol: 10 μg of total pooled RNA were reversed transcribed into cDNA incorporating dUTP-Cy3 or dUTP-Cy5 and employing the CyScribe First-Strand cDNA labeling kit (Amersham Biosciences, New Jersey, USA). A dye-swap experiment was performed for each time point sample. Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Cy3 and 655 nm for Cy5.

growth_protocol: Female Sprague Dawley rats were obtained from the Animal Care Facility of Centro Médico Nacional Siglo XXI, Mexican Institute of Social Security (IMSS), in Mexico City. Animals were housed at 22 ± 2°C with a 12-h light/dark cycle with free access to water. From weaning until 8 weeks of age, rats were fed with a Chow 5008 commercial diet (Agribrands Purina, Mexico, DF, Mexico). When rats reached 8 weeks of age, a purified diet was provided ad libitum for a period of 6 weeks with an adequate quantity of all nutrients.

extract_protocol: Inguinal mammary glands were collected on the indicated day of adulthood (virgin), pregnancy or lactation. Frozen mammary gland was pulverized and total RNA was isolated from tissue (0.2 g) using TRIzol (Invitrogen, California, USA) according to the manufacturer's instructions. Total RNA from mammary tissue was isolated from three different animals of each physiological period and it was pooled and kept in aliquots for later determination of its purity and integrity.

tag: strain

value: Sprague Dawley

value: > 14 weeks

value: Parous or virgin

value: Mammary gland

source_name: Total RNA from pooled whole inguinal mammary glands harvested from Sprague Dawley female rats at lactancy day 12.

value: Lactancy day 12


title: Group A_MZ pair_ #7_A

description:
Normal blood sample from MZ twins
#986-107a

value: Male


title: NC-2

description:
SAMPLE 4
adjacent histological normal tissues of TSCC-2

value: TSCC


title: PC9:TGF-β-

city: Tokyo

first: Kazuhiro

last: Kitamura

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pulmonary Medicine and Oncology, Graduate School of Medicine

country: Japan

institute: Nippon Medical School

description: SAMPLE 7

hyb_protocol: 5 μg of total RNA was employed for hybridization on miRNA microarray chips containing 667 probes with the TaqMan® Array Human MicroRNA A + B Cards Set v2.0 (Life Technologies, Carlsbad, CA) on a 7900 Real Time PCR System (Applied Biosystems, Foster City, CA).

scan_protocol: Processed slides were scanned with a PerkinElmer ScanArray XL5K Scanner.

data_processing:
Experimental data were analyzed by DataAssist™ Software (Life Technologies) using RNU44 and RNU48 as endogenous controls. Ct values were provided from all miRNAs represented on the cards and fold changes in expression were calculated using the delta delta Ct (ddCt) method. Expression levels of MammU6  on the array card were defined as positive controls for the purpose of ddCt calculation.
sample data table reports -ΔCt, where -ΔCt = -[ΔCttarget -ΔCt avarage MammU6].
normalized_calibrated.txt reports  2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtsample1].  SAMPLE1 was arbitrarily designated as the calibrator sample.
fold_change.txt reports test/control (i.e., A549:TGF-β+/A549:TGF-β-) ratios in each cell line.

label: FAMTM

source_name: lung adenocarcinoma cell line_after TGF-β1 exposure

label_protocol: PCR assays were performed using TaqMan® MicroRNA Assays (Life Technologies, Carlsbad, CA) following the Manufacturer’s instructions. Reverse transcription reaction was performed using  TaqMan® MicroRNA Reverse Trabnscription Kit (Life Techn.ologies). Quantitative real-time PCR were performed with cycling condition of 95゜C  for 10 min (followed by 95゜C for 15 sec and 60゜C for 60 sec ) for a total of 40 cycles.

growth_protocol: These four cell lines have been obtained from 2003 to 2011, were amplified and frozen, and one aliquot of each was thawed for this project, although no authentication was done by the authors. All cells were routinely screened for the absence of mycoplasma. These cell lines were maintained in RPMI 1640 medium (GIBCO, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted from the four lines with TRIzol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol: Four cell lines were treated with 5ng/ml of TGF-β1 for 72hr.

tag: cell line

tag: cell type

value: lung adenocarcinoma cell line

tag: treated with

value: none (control)


title: Group A_MZ pair_ #6_A

description:
Normal blood sample from MZ twins
#959-83a


title: Rat mammary gland lactancy day 12, biological replicate 1

description: Biological replicate 1 of 3.


title: Rat mammary gland lactancy day 1, biological swap replicate 3

description: Biological replicate 3 of 3.

source_name: Total RNA from pooled whole inguinal mammary glands harvested from Sprague Dawley female rats at lactancy day 1.

value: Lactancy day 1


title: Group A_MZ pair_ #1_A

description:
Normal blood sample from MZ twins
#44-24a

value: Female


title: WT no sugar, replica 2 (14309140)

city: Montreal

first: Daniel

last: Dignard

state: QC

address: 6100, Royalmount

department: HHT

institute: NRC

description: Sample name: 14309140.txt Sc

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done in a "SlideBooster" chamber (Advalytik)

scan_protocol: ScanArray Gx scanner (Perkin Elmer) at 10-µm resolution

data_processing: Expression array data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Saccharomyces cerevisiae

source_name: [test] S288c

label_protocol: Indirect labeling with Cy3 and Cy5 was performed. For expression profiling experiment, 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of amino-allyl-dUTP (Sigma A-410) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB cat.70054Z) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The cDNAs were purified with QIAquick PCR Purification Kit (Qiagen) with 5mM potassium phosphate pH8.5 replacing the tris in the wash and elution buffers. The cDNAs were labeled with mono-reactive dyes (GE-Healthcare/ Amersham: cy3 cat. PA23001, cy5 cat. PA25001). The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

growth_protocol: For S.cerevisiae microarrays, starter cultures of S288c strain were in raffinose medium (SR) as carbon source, and grown at 30C to an OD600 of 0.7 - 0.8. The cells were then washed with sterile water. The cell pellet was resuspended in S-based medium (no sugar) and an equal amount of cells transferred in no sugar (S) or xylose (SX) medium for experiments samples or in glucose (SD) medium for the reference samples. The cultures was incubated for ~2h until an increase in the OD600 was observed for the reference culture in glucose. For C.albicans microarrays, starter culture of SC5314 was in SD (glucose) medium. The overnight culture was washed with water and used to inoculate xylose (SX) or glucose (SD) medium at an OD600 of 0.1 and grown at 30C for ~5-6 h to an OD600 of ~0.8 .

extract_protocol: Total RNA was extracted by mechanical disruption of the cells with glass beads using the FastPrep-24 (MP Biomedical). Thereafter, total RNA was isolated and purified with the Rneasy kit (Qiagen cat.74104).

tag: genotype/variation

value: WT

tag: carbon source

value: no sugar (S)

source_name: [reference] S288c

value: glucose (SD)


title: PC3:TGF-β+

description: SAMPLE 6

source_name: lung adenocarcinoma cell line_before TGF-β1 exposure

value: 5ng/ml of TGF-β1 for 72hr


title: Rat mammary gland lactancy day 12, biological swap replicate 3

description: Biological replicate 3 of 3.

tag: gender

tag: age


title: WT no sugar, replica 1, dye-swap (14309104)

description: Sample name: 14309104.txt Sc


title: PC9:TGF-β+

description: SAMPLE 8


title: TSCC-1

description:
SAMPLE 1
TSCC samples from anterior portions of the tongue of patient#1

source_name: Human tongue tissues

value: patient 1

tag: tissue

value: NC


title: Rat mammary gland pregnancy day 14, biological swap replicate 3

description: Biological replicate 3 of 3.

value: Sprague Dawley

source_name: Total RNA from pooled whole inguinal mammary glands harvested from Sprague Dawley female rats at pregnancy day 14.

value: Pregnancy day 14


title: Rat mammary gland lactancy day 1, biological replicate 2

description: Biological replicate 2 of 3.

value: > 14 weeks

value: Parous or virgin


title: Group A_MZ pair_ #6_B

description:
Normal blood sample from MZ twins
#960-83b

source_name: Peripheral blood, Group A, MZ twin pair

value: Peripheral blood

value: Normal


title: Group A_MZ pair_ #5_B_rep5

description:
Normal blood sample from MZ twins
#127-34d

value: Male


title: Rat mammary gland lactancy day 1, biological replicate 1

description: Biological replicate 1 of 3.

value: Mammary gland


title: NC-1

description:
SAMPLE 2
adjacent histological normal tissues of TSCC-1

value: TSCC


title: hESC_H1_PacBio

type: SRA

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
Illumina reads were aligned to reference genome hg19 by SpliceMap
PacBio reads were corrected by LSC
Gene isoforms were identified by IDP
Gene/transcript abundance was estimated by rSeq (optimized and integrated into IDP)
Genome_build: hg19
Supplementary_files_format_and_content: gtf and fasta file

molecule: polyA RNA

source_name: Human embryonic stem cell, H1

growth_protocol: Male human Embryonic Stem cells (H1) were used for our study. The cells were routinely cultured in feeder free conditions on Matrigel (BD) and in mTeSR1 (Stem Cell technologies). RNA seq was performed on cells between passage 50 and 55. The undifferentiated state of the hESCs was assayed by immunofluorescence for transcription factors OCT4 and NANOG and for the surface markers SSEA4, TRA-1-60 and TRA-1-81 (Figure S9). Pluripotency, assessed by teratoma assay, revealed the capacity of hESCs to form in vivo derivatives of the three germ layers

extract_protocol:
Total RNA was prepared by TRIzol extraction (Ambion; http://www.ncbi.nlm.nih.gov/pubmed/2440339) and treated with RNase-free DNase I to degrade contaminating gDNA. This was followed by a second extraction with acid-phenol-chloroform and the RNA was precipitated in 0.5M ammonium acetate and 2.5 volumes of ethanol. The integrity of the RNA was tested by a Bioanalyzer RNA Nano assay (Agilent). PolyA RNA was purified from the total RNA (>100 µg) using magnetic oligo-dT beads (Dynal) according to the manufacturer’s recommended protocol.
Two different manufacturer’s kits and accompanying protocols for generating full-length cDNAs were employed; Clontech SMARTer PCR and Invitrogen Superscript Full-Length cDNA kit. Each utilizes a retroviral reverse transcriptase to initiate cDNA synthesis at the 3’ polyA tail, but the two kits use different mechanisms to capture the 5’ end information. The Clontech method relies upon template-switching to an exogenous tag oligonucleotide when the reverse transcriptase reaches the 5’ end of the molecule. The Invitrogen method employs an RNase I digestion and subsequent 7-methyl-guanosine affinity step to purify the RNA-DNA hybrids that represent a full copy of the transcript. This is followed by an RNA ligase step to add a defined sequence to the 5’ ends of the polyA RNAs, prior to reverse transcription. For each method, 1 µg of polyA RNA served as the input material into the recommended protocol and the manufacturer methods were followed up through second strand cDNA synthesis. At this point, PCR (12-15 cycles; Phusion DNA polymerase. New England Biolabs) was used to amplify the double-stranded cDNA by using specific primers directed to the defined sequences present at the 5’ and 3’ ends of the cDNAs. Long extension times of 3.5 minutes ensure that longer molecules can be captured as well. The cDNA libraries were assayed by fluorimetry and Bioanalyzer assays. Both of Clontech and Invitrogen kits are reproducible. For example, housekeeping genes at different sizes (ACTB, 1808bp; GADPH, 1310bp; SARS 2291bp; IARS, NM_002161, 4406bp and NM_013417, 4510bp) are detected by full length long reads from the two preps .

value: Human embryonic stem cells

tag: passage


title: Group A_MZ pair_ #5_B_rep3

description:
Normal blood sample from MZ twins
#127-34b


title: Group A_MZ pair_ #5_B_rep2

description:
Normal blood sample from MZ twins
#127-34a


title: Group A_MZ pair_ #5_B_rep1

description:
Normal blood sample from MZ twins
#127-34


title: Group A_MZ pair_ #4_B

description:
Normal blood sample from MZ twins
#121-28


title: Group A_MZ pair_ #1_B

description:
Normal blood sample from MZ twins
#45-24b

value: Female


title: wt-RLN-78-weeks-2

description: Staining with Fluidic Station 450 Protocol: Midi-euk2v3_450

source_name: Lymph node renal

label_protocol: T7-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY) with an IVT of 68h

growth_protocol: ApoE-/- and wild-type mice on the C57BL/6J background were from The Jackson Laboratories (Bar Harbor, Maine). Mice were housed in SPF conditions with standard chow diet and were euthanized by carbon dioxide inhalation.

extract_protocol: RNA was extracted using a phenol/chloroform extraction according to the manufacturer's structions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Micro-kit (Qiagen, Hilden, Germany).

treatment_protocol: The abdominal aorta was exposed, perfused in situ with ice-cold PBS/2mM EDTA and was removed inclusive of paraaortal lymph nodes, adipose and connective tissue. The isolated abdominal aorta was cut in half and embedded in Tissue Tec (Sakura Finetek, Zoeterwoude, NL) and was frozen at -80 centigrade. 200 unstained 10 micrometer cryo-sections of the associated renal lymph node were microdissected with a Palm MicroBeam laser system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) and pooled in Trizol (Invitrogen, Carlsbad, CA)(according to published procedures: Laser-Capture Microdissection of Hyperlipidemic/ApoE-/- Mouse Aorta Atherosclerosis. Methods Mol Biol. 2011;755:417-28).

value: Lymph node renal

value: male

value: 78 weeks


title: LC2/ad:TGF-β+

description: SAMPLE 4

value: lung adenocarcinoma cell line

value: 5ng/ml of TGF-β1 for 72hr


title: WT no sugar, replica 1 (14309081)

description: Sample name: 14309081.txt Sc

value: WT

value: no sugar (S)

value: glucose (SD)


title: Rat mammary gland pregnancy day 14, biological replicate 2

description: Biological replicate 2 of 3.

value: Sprague Dawley

value: > 14 weeks

value: Pregnancy day 14


title: WT in xylose, replica 2, dye-swap (14309137)

description: Sample name: 14309137.txt Sc

value: xylose (SX)


title: Group A_MZ pair_ #4_A

description:
Normal blood sample from MZ twins
#120-27

value: Male

value: Peripheral blood

value: Normal


title: Group A_MZ pair_ #5_A

description:
Normal blood sample from MZ twins
#126-33


title: PC3:TGF-β-

description: SAMPLE 5

value: none (control)


title: A549:TGF-β+

description: SAMPLE 2


title: WT in xylose, replica 2 (14308823)

description: Sample name: 14308823.txt Sc


title: Group A_MZ pair_ #5_B_rep4

description:
Normal blood sample from MZ twins
#127-34c


title: WT in xylose, replica 1, dye-swap (14309078)

description: Sample name: 14309078.txt Sc


title: LC2/ad:TGF-β-

description: SAMPLE 3


title: apoE-RLN-78-weeks-3


title: wt-RLN-78-weeks-3


title: Rat mammary gland pregnancy day 5, biological swap replicate 3

description: Biological replicate 3 of 3.

value: Female

value: Parous or virgin

value: Mammary gland

source_name: Total RNA from pooled whole inguinal mammary glands harvested from Sprague Dawley female rats at pregnancy day 5.

value: Pregnancy day 5


title: Rat mammary gland pregnancy day 5, biological replicate 2

description: Biological replicate 2 of 3.


title: A549:TGF-β-

description: SAMPLE 1

value: lung adenocarcinoma cell line


title: Group A_MZ pair_ #2_B

description:
Normal blood sample from MZ twins
#54-57b


title: Group A_MZ pair_ #3_A

description:
Normal blood sample from MZ twins
#100-7


title: WT in xylose, replica 1 (14308825)

description: Sample name: 14308825.txt Sc


title: 15C, 1h, Replicate 1

status: Public on Oct 29 2013

city: University of Helsinki

first: Elias

last: Dahlsten

address: P.O. Box 66

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

hyb_protocol: Agilent (Agilent, Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing: Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: background subtraction with normexp and offset 50. Log-ratio was calculated between KO-mutant and WT and normalized with loess.

organism: Clostridium botulinum A str. ATCC 3502

label_protocol: A total of 2 µg of each RNA sample was reverse-transcribed into cDNA and simultaneously labeled with fluorescent dyes. In brief, each 30-µl labeling reaction contained 0.2 µg/µl of random hexamers (Invitrogen), 0.01 M DTT (Invitrogen), 1.3 U/µl ribonuclease inhibitor (Invitrogen), 0.5 µM dATP, dTTP and dGTP, 0.2 µM dCTP, 1.7 nmol of Cy-3 or Cy-5 labeled dCTP (GE Healthcare, Pittsburgh, PA), 13 U/µl of SuperScript III reverse transcriptase (Invitrogen), and appropriate buffer (1 x First Strand Buffer, Invitrogen) and was incubated at 46 °C for 3 h. RNA hydrolysis and reaction inactivation were performed by addition of 10 µl of 0.1 M NaOH and 0.5 mM EDTA and incubation at 70 °C for 15 min. The reactions were subsequently neutralized by addition of 10 µl of 0.1 M HCl. The cDNA was purified with QIAquick PCR Purification Kit (Qiagen), with final elution volume of 40 µl. The cDNA concentration of each sample was measured with NanoDrop.

growth_protocol: TPGY, anaerobic, 37 °C, up to OD600=1.0 (5-7 hours), then subjected to temperature downshift to 15 °C and thereafter incubated at 15 °C

extract_protocol: Five-ml samples from three replicate C. botulinum ATCC 3502 wild type or cbo365 KO-mutant cultures were collected at mid-logarithmic growth phase at 37 °C and 1 h after temperature downshift to 15 °C. The samples were collected into sterile plastic tubes containing ice-cold ethanol-phenol (9:1) solution (Sigma Aldrich, St. Louis, MO, USA), mixed thoroughly, and incubated on ice for 30 min. Cells were harvested by centrifugation (4 °C, 8000 x G) for 5 min. The cell pellets were immediately frozen to -70 °C until RNA extraction. The cell pellets were thawed on ice for 5 min and used for RNA extraction with the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. The cells were lysed with a solution containing 25 mg/ml lysozyme (Sigma Aldrich, St. Louis, MO, USA) and 250 IU/ml mutanolysin (Sigma Aldrich) in Tris-EDTA buffer (pH 8.0, Fluka BioChemica, Buchs, Switzerland) and agitated at 37 °C for 30 min. The final elution volume of RNAse free water was 300 µl. To confirm efficient removal of all genomic DNA, an additional DNase treatment was carried out using the DNA-free Kit (Ambion, Austin, TX, USA) according to manufacturer’s instructions. The RNA yield and purity (A260/A280) were checked using the NanoDrop ND-1000 device (NanoDrop Technologies, Wilmington, DE, USA). The RNA purity ratio was >2.0 for all samples. Integrity of RNA was confirmed using a miniatyrized gel electrophoresis in the Agilent Bioanalyzer (Agilent Technologies, Waldbronn, Germany). The RNA integrity number was >9.2 for all RNA samples.

value: ATCC 3502

value: Wild Type

tag: temperature

value: 15 °C

source_name: ATCC 3502, CBO0365 KO mutant, 15C

value: CBO0365 KO mutant


title: apoE-RLN-78-weeks-2

value: Lymph node renal

value: male

value: 78 weeks


title: 15C, 1h, Replicate 2


title: Rat mammary gland pregnancy day 14, biological replicate 1

description: Biological replicate 1 of 3.

value: Sprague Dawley

value: > 14 weeks

value: Pregnancy day 14


title: 37C, Replicate 2

source_name: ATCC 3502, CBO0365 KO mutant, 37C

value: 37 °C


title: 15C, 1h, Replicate 3


title: Group A_MZ pair_ #3_B

description:
Normal blood sample from MZ twins
#101-8

value: Male

value: Peripheral blood

value: Normal


title: Rat mammary gland pregnancy day 5, biological replicate 1

description: Biological replicate 1 of 3.

value: Female

value: Parous or virgin

value: Mammary gland

source_name: Total RNA from pooled whole inguinal mammary glands harvested from Sprague Dawley female rats (n = 3) at pregnancy day 5 .


title: Group A_MZ pair_ #2_A

description:
Normal blood sample from MZ twins
#54-57a


title: wt-RLN-78-weeks-1


title: FCHL-CHD patient 11 [GPL95]

city: London

first: Carol

last: Shoulders

address: Charterhouse Square

department: Centre for Endocrinology

country: United Kingdom

institute: QMUL

description: Gene expression data from upper abdominal subcutaneous adipose tissue of CHD patient with FCHL

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix Genechips for 16 hr at 45°C and GeneChips were washed and stained in an Affymetrix Fluidics Station according to standard Affymetrix protocols.

scan_protocol: Performed according to standard Affymetrix protocols.

data_processing: Image-files were analysed with Bioconductor in R using the pmonly and rma algorithms implemented in expresso. Normalisation of chip sets was performed by the ‘quantiles’ approach and probe sets summarised using ‘median polish’. Probes were labelled ‘absent’ or ‘present’ according to the Affymetrix Microarray Suite 5.0 algorithm. Probes returning absent calls in all cel files were removed. Differences in probe values were detected by the Significance Analysis of Microarray (SAM) procedure at specified false detection rates (FDR).

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 11

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

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

treatment_protocol: Tissue was excised from upper abdominal subcutaneous region and immediately snap-frozen in the operating room.

tag: chd status

value: CHD:patient undergoing coronary artery bypass surgery

tag: fchl status

value: FCHL

tag: tg rsponse to statins status

value: not classified


title: apoE-RLN-78-weeks-1


title: FCHL-CHD patient 10 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 10


title: 37C, Replicate 1

value: ATCC 3502

value: Wild Type

value: CBO0365 KO mutant


title: 37C, Replicate 3


title: NONCHD-NONFCHL patient 1 [GPL95]

description: Gene expression data from upper abdominal subcutaneous adipose tissue of heart valve replacement surgery patient without FCHL

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 1

value: non-CHD:patient undergoing heart valve replacement surgery

value: non-FCHL


title: NONCHD-NONFCHL patient 4 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 4


title: FCHL-CHD patient 12 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 12

value: non-reduced TG


title: NONCHD-NONFCHL patient 5 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 5


title: FCHL-CHD patient 9 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 9

value: reduced TG


title: NONCHD-NONFCHL patient 2 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 2


title: CHD-NONFCHL patient 6 [GPL95]

description: Gene expression data from upper abdominal subcutaneous adipose tissue of non-FCHL CHD patient

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 6


title: FCHL-CHD patient 8 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 8


title: NONCHD-NONFCHL patient 3 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 3


title: FCHL-CHD patient 13 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 13


title: FCHL-CHD patient 4 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4


title: CHD-NONFCHL patient 5 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 5


title: FCHL-CHD patient 7 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 7


title: FCHL-CHD patient 6 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 6


title: FCHL-CHD patient 5 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5


title: FCHL-CHD patient 3 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 3


title: CHD-NONFCHL patient 3 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 3


title: CHD-NONFCHL patient 4 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 4


title: FCHL-CHD patient 2 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 2


title: FCHL-CHD patient 1 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 1


title: NONCHD-NONFCHL patient 4 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 4


title: CHD-NONFCHL patient 2 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 2


title: CHD-NONFCHL patient 1 [GPL95]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 1


title: NONCHD-NONFCHL patient 2 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 2


title: FCHL-CHD patient 11 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 11


title: FCHL-CHD patient 10 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 10


title: FCHL-CHD patient 13 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 13


title: FCHL-CHD patient 12 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 12


title: FCHL-CHD patient 9 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 9


title: FCHL-CHD patient 8 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 8


title: CHD-NONFCHL patient 6 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 6


title: NONCHD-NONFCHL patient 3 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 3


title: NONCHD-NONFCHL patient 5 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 5


title: FCHL-CHD patient 4 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4


title: FCHL-CHD patient 7 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 7


title: CHD-NONFCHL patient 4 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 4


title: FCHL-CHD patient 5 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5


title: FCHL-CHD patient 3 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 3


title: skeletal muscle_non-treated_rep3

city: Nagoya

first: Madoka

last: Iida

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology department

institute: Nagoya University

description: Gene expression data from skeletal muscle of non-treated AR-97Q mice

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven, following the manufacturers instructions. After hybridization, microarrays were washed and scanned.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).

source_name: non-treated AR-97Q mouse skeletal muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.

growth_protocol: These mice were fed under 12L12D at 25℃ condition.

extract_protocol: RNA from the total spinal cord and skeletal muscle was isolated from three mice of each group using Trizol reagent (Life Technologies corporation, Carlsbad, CA) according to the manufacturer’s specifications. The RNA samples were purified over RNeasy columns (Qiagen, Germantown, MA).

treatment_protocol: PG was administered to AR-97Q mice at concentration of 0.02% in the food from 6 weeks of age until they are anatomized.

value: male

value: skeletal muscle

tag: treatment

value: non-treated


title: NONCHD-NONFCHL patient 1 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 1


title: CHD-NONFCHL patient 3 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 3


title: CHD-NONFCHL patient 5 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 5


title: skeletal muscle_PG-treated_rep2

description: Gene expression data from skeletal muscle of PG-treated AR-97Q mice

source_name: PG-treated AR-97Q mouse skeletal muscle

value: 0.02% pioglitazone (PG) treatment


title: skeletal muscle_PG-treated_rep3


title: spinal cord_PG-treated_rep3

description: Gene expression data from spinal cord of PG-treated AR-97Q mice

source_name: PG-treated AR-97Q mouse spinal cord

value: spinal cord


title: FCHL-CHD patient 6 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 6


title: skeletal muscle_non-treated_rep2


title: skeletal muscle_PG-treated_rep1


title: FCHL-CHD patient 2 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 2


title: skeletal muscle_non-treated_rep1


title: spinal cord_PG-treated_rep2


title: FCHL-CHD patient 1 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 1


title: CHD-NONFCHL patient 2 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 2


title: spinal cord_non-treated_rep1

description: Gene expression data from spinal cord of non-treated AR-97Q mice

source_name: non-treated AR-97Q mouse spinal cord


title: spinal cord_PG-treated_rep1


title: CHD-NONFCHL patient 1 [GPL93]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 1


title: spinal cord_non-treated_rep3


title: spinal cord_non-treated_rep2


title: hepatocyte 3

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

description: hepatocyte

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: hepatocyte

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

treatment_protocol: untreated for each sample condition

value: hepatocyte


title: hepatocyte 2

description: hepatocyte


title: hepatocyte 1

description: hepatocyte


title: ITS clone 6.6.2

description: ITS

source_name: ITS clone 6.6

value: ITS

tag: clone


title: mES 3

description: mES

source_name: mES

value: mES


title: ITS clone 6.6.3

description: ITS


title: mES 2

description: mES


title: ITS clone 6.6.1

description: ITS


title: ITS clone 3.8.2

description: ITS

source_name: ITS clone 3.8


title: ITS clone 3.8.1

description: ITS


title: mES 1

description: mES


title: DU145-LN4

city: Boston

first: Jacqueline

last: Banyard

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Childrens Hospital

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using rank-in-variant normalization

source_name: Human prostate cancer cell line

label_protocol: Labeling performed according to manufacturer instructions

extract_protocol: Total RNA was extracted from cells using RNeasy mini columns (Qiagen)

value: 4 rounds of lymph node metastasis from prostate xenograft


title: DU145ivLU4

description: replicate 1

value: 4 rounds of lung metastasis from tail vein injection


title: DU145-LN2

description: replicate 1

value: 2 rounds of lymph node metastasis from prostate xenograft


title: DU145ivLU3

description: replicate 1

value: 3 rounds of lung metastasis from tail vein injection


title: ITS clone 3.8.3

description: ITS


title: DU145ivLU1

description: replicate 1

value: 1 round of lung metastasis from tail vein injection


title: NONCHD-NONFCHL patient 4 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 4

value: non-CHD:patient undergoing heart valve replacement surgery


title: NONCHD-NONFCHL patient 5 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 5

value: non-FCHL


title: 32-cell_b6.5

city: Kyoto

first: Yutaka

last: Satou

state: Kyoto

address: Kitashirakawa Oiwake-tyo, Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

hyb_protocol: Hybridization and washing were performed using GE Hybridization kit (Agilent) and GE Washing Buffer (Agilent), according to the manufacture’s instructions.

scan_protocol: The slides after washing were scanned on an Agilent G2505C Microarray Scanner (Agilent Technologies) using default settings. The scanned file option, TIFF file dynamic range was set to 20-bit.

data_processing: The scanned images were quantified by Feature Extraction Software ver.10.7( Agilent Technologies) using default parameters.

organism: Ciona intestinalis

source_name: blastomere, b6.5

label_protocol: 50ng total RNA was labeled using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacture’s instructions (www.agilent.com/).

growth_protocol: Wild Ciona intestinalis adults were used.

extract_protocol: The total RNA was extracted using RNeasy Mini Kit (QIAGEN). The quality of extracted RNA was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) using Agilent RNA 6000 Pico Kit (Agilent). The RNA yield was measured with Quant-iT RNA Assay Kit (Invitrogen).

treatment_protocol: Unfertilized eggs and sperm of C.intestinalis were obtained by dissection. After insemination, eggs were dechorionized and developed in Millipore-filtered seawater at 18℃.Each blastomere was isolated by a fine glass needle under a stereomicroscope and transferred into RNAlater (Ambion), immediately.

tag: developmental stage


title: DU145ivLU2

description: replicate 1

value: 2 rounds of lung metastasis from tail vein injection


title: FCHL-CHD patient 11 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 11

value: CHD:patient undergoing coronary artery bypass surgery

value: FCHL

value: not classified


title: DU145

description: replicate 1

value: DU145 (ATCC)


title: FCHL-CHD patient 12 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 12

value: non-reduced TG


title: 32-cell_b6.8

source_name: blastomere, b6.8


title: 32-cell_b6.7

source_name: blastomere, b6.7


title: DU145-LN1

description: replicate 1

value: 1 round of lymph node metastasis from prostate xenograft


title: FCHL-CHD patient 13 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 13

value: reduced TG


title: 32-cell_a6.5

source_name: blastomere, a6.5


title: NONCHD-NONFCHL patient 3 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 3


title: FCHL-CHD patient 10 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 10


title: 32-cell_B6.2

source_name: blastomere, B6.2


title: 32-cell_a6.8

source_name: blastomere, a6.8


title: 16-cell_b5.4

source_name: blastomere, b5.4


title: 16-cell_b5.3

source_name: blastomere, b5.3


title: 32-cell_B6.3

source_name: blastomere, B6.3


title: 32-cell_A6.1

source_name: blastomere, A6.1


title: FCHL-CHD patient 9 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 9


title: NONCHD-NONFCHL patient 1 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 1


title: NONCHD-NONFCHL patient 2 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 2


title: FCHL-CHD patient 8 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 8


title: CHD-NONFCHL patient 5 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 5


title: CHD-NONFCHL patient 6 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 6


title: FCHL-CHD patient 7 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 7


title: 32-cell_A6.2

source_name: blastomere, A6.2


title: CHD-NONFCHL patient 3 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 3


title: CHD-NONFCHL patient 4 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 4


title: 16-cell_a5.3

source_name: blastomere, a5.3


title: FCHL-CHD patient 6 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 6


title: 16-cell_a5.4

source_name: blastomere, a5.4


title: FCHL-CHD patient 5 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5


title: CHD-NONFCHL patient 2 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 2


title: FCHL-CHD patient 4 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4


title: CHD-NONFCHL patient 1 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 1


title: NONCHD-NONFCHL patient 5 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 5


title: FCHL-CHD patient 1 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 1


title: FCHL-CHD patient 2 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 2


title: FCHL-CHD patient 3 [GPL92]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 3


title: 16-cell_B5.1

source_name: blastomere, B5.1


title: 8-cell_a4.2

source_name: blastomere, a4.2


title: FCHL-CHD patient 10 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 10


title: FCHL-CHD patient 13 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 13


title: 16-cell_A5.1

source_name: blastomere, A5.1


title: 8-cell_b4.2

source_name: blastomere, b4.2


title: NONCHD-NONFCHL patient 2 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 2


title: FCHL-CHD patient 12 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 12


title: NONCHD-NONFCHL patient 3 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 3


title: FCHL-CHD patient 11 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 11


title: NONCHD-NONFCHL patient 1 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 1


title: 8-cell_B4.1

source_name: blastomere, B4.1


title: NONCHD-NONFCHL patient 4 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 4


title: CHD-NONFCHL patient 5 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 5


title: FCHL-CHD patient 7 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 7


title: 32-cell_whole

source_name: whole embryo


title: CHD-NONFCHL patient 6 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 6


title: FCHL-CHD patient 6 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 6


title: FCHL-CHD patient 8 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 8


title: FCHL-CHD patient 5 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5


title: FCHL-CHD patient 4 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4


title: CHD-NONFCHL patient 4 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 4


title: CHD-NONFCHL patient 3 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 3


title: FCHL-CHD patient 3 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 3


title: FCHL-CHD patient 2 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 2


title: FCHL-CHD patient 9 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 9


title: FCHL-CHD patient 1 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 1


title: CHD-NONFCHL patient 1 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 1


title: CHD-NONFCHL patient 2 [GPL94]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 2


title: 8-cell_A4.1

source_name: blastomere, A4.1


title: 16-cell_whole


title: 8-cell_whole


title: Fertilized Egg_50min

value: 50min after fertilization


title: Fertilized Egg_20min

value: 20min after fertilization


title: Unfertilized egg_244K

source_name: Unfertilized egg

value: unfertilized egg


title: 4-cell_whole


title: NONCHD-NONFCHL patient 5 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 5


title: 2-cell_whole

source_name: whole embryo


title: NONCHD-NONFCHL patient 3 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 3


title: FCHL-CHD patient 13 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 13


title: FCHL-CHD patient 11 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 11


title: NONCHD-NONFCHL patient 4 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 4


title: NONCHD-NONFCHL patient 1 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 1


title: FCHL-CHD patient 10 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 10


title: CHD-NONFCHL patient 6 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 6


title: CHD-NONFCHL patient 5 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 5


title: NONCHD-NONFCHL patient 2 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue nonFCHL-nonCHD patient 2


title: FCHL-CHD patient 8 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 8


title: FCHL-CHD patient 9 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 9


title: UFE_batch i

hyb_protocol: Hybridization and washing were performed using GE Hybridization kit (Agilent) and GE Washing Buffer (Agilent) according to the manufacture’s instructions.

source_name: Unfertilized eggs from individual i

extract_protocol: The total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacture’s protocols. The quality of extracted RNA was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) using Agilent RNA 6000 Nano Kit (Agilent). The RNA yield was measured with Quant-iT RNA Assay Kit (Invitrogen).

treatment_protocol: Unfertilized eggs of C.intestinalis were obtained by dissection from one individual and dechorionized. After insemination, fertilized eggs were incubated in Millipore-filtered seawater at 18℃, and 8-, 16- and 32-cell embryos were sampled.

tag: individual

value: i


title: FCHL-CHD patient 7 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 7


title: UFE_batch d2

source_name: Unfertilized eggs from individual d, technical replicate

value: d


title: UFE_batch l

source_name: Unfertilized eggs from individual l

value: l


title: UFE_batch j

source_name: Unfertilized eggs from individual j

value: j


title: UFE_batch k

source_name: Unfertilized eggs from individual k

value: k


title: UFE_batch c

source_name: Unfertilized eggs from individual c

value: c


title: FCHL-CHD patient 6 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 6


title: UFE_batch h

source_name: Unfertilized eggs from individual h

value: h


title: FCHL-CHD patient 5 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 5

value: CHD:patient undergoing coronary artery bypass surgery


title: UFE_batch c_Dup

source_name: Unfertilized eggs from individual c, technical replicate


title: FCHL-CHD patient 4 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 4

value: FCHL


title: FCHL-CHD patient 2 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 2


title: CHD-NONFCHL patient 3 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 3

value: non-FCHL


title: UFE_batch m

source_name: Unfertilized eggs from individual m

value: m


title: UFE_batch d

source_name: Unfertilized eggs from individual d


title: FCHL-CHD patient 3 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 3


title: CHD-NONFCHL patient 4 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 4


title: 8cell_batch g

source_name: whole 8-cell embryos from individual g

value: 8-cell embryo

value: g


title: 32cell_batch g

source_name: whole 32-cell embryos from individual g

value: 32-cell embryo


title: UFE_batch n

source_name: Unfertilized eggs from individual n

value: n


title: 16-cell_B5.2

source_name: blastomere, B5.2


title: FCHL-CHD patient 12 [GPL8300]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 12

value: non-reduced TG


title: ASC_N-cadherin(+)_rep1

city: Tsukuba

first: Hisako

last: Ishimine

state: Japan Ibaraki

address: higashi1-1-1 Tsukuba central 4

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of N-cadherin(+) ASCs

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4122F) 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile,  then dried immediately.

scan_protocol: Slides were scanned immediately after washing with the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100430) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

label_protocol: RNA was labeled using the ‘Agilent Quick-Amp Labeling Kit’ (Agilent Technologies) following the manufacturer's protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: The ASCs were expanded using MesenPRO RSTM Medium.

extract_protocol: Total RNA were isolated from MSCs using ISOGEN (Nippon Gene) according to the manufactureres’ recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Immunomagnetic separation of N-cadherin+ cells was performed with autoMACSTMPro system(Miltenyi biotec) according to the manufacturers' recommendation.

value: adipose

value: ASCs (Adipose-drived Stem Cells)


title: ASC_rep1

description: Gene expression of ASCs

source_name: ASC


title: 32cell_batch f

source_name: whole 32-cell embryos from individual f

value: f


title: 16cell_batch g

source_name: whole 16-cell embryos from individual g

value: 16-cell embryo


title: 8cell_batch f

source_name: whole 8-cell embryos from individual f


title: 16cell_batch f

source_name: whole 16-cell embryos from individual f


title: Naïve_H9_hESC

city: Rehovot

first: Yair

middle: S

last: Manor

address: 234 Hertzel st.

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data of the indicated cell line

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Matlab software and its Bioinformatics toolbox, using RMA method.

label: Biotin

source_name: Naïve H9 hESC

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Isolating and expanding naïve human pluripotent cells: The following serum free defined conditions, termed WIS-NHSM (Weizmann Institute of Science Naïve Human Stem cell Medium) were used to isolate, generate, derive and stabilize naïve human pluripotent stem cells (iPSCs and ESCs) with the unique biological properties described in this study. WIS-NHSM media was generated by including: 475 ml Knockout DMEM  (Invitrogen 10829), 5gr AlbuMAX (Invitrogen 11020-021), 5 ml N2 supplement (Invitrogen 17502048), 10 µg of recombinant human LIF (Peprotech), 8ng/ml recombinant bFGF (Peprotech) and 1ng/ml recombinant TGFβ1 (Peprotech), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), Penicillin-Streptomycin (Invitrogen) and small molecule inhibitors: PD0325901 (1 µM, ERK1/2i, AXON MEDCHEM); CHIR99021 (3µM, GSK3bi, AXON MEDCHEM); SB203580 (5µM, p38i, TOCRIS);  SP600125 (10µM, JNKi, TOCRIS). Throughout the study Naïve hESCs/hiPSCs were grown on 0.2% gelatin + 1ng/ml vitronectin coated plates for at least 1 hour in 37oC. Cells were passage by single cell trypsinization (0.25% or 0.05% Trysin+EDTA) every 3-4 days. Although not essential, enhanced single cell cloning efficiency can be obtained with WIS-NHSM supplementation with ROCK pathway inhibitor Y-27632 (5 µM, ROCKi Axon Medchem) for 24 hours before and after cell passaging. Culture of conventional/primed human ESCs and iPSCs:The following already established conventional human ESCs and iPSC lines were used (indicated passage number of the cell line taken for conversion into naïve pluripotency is indicated in parentheses): Human induced pluripotent stem cells C1 (P21) and C2 (P9) hiPSC lines 15 and the human embryonic stem cell (hESC) lines BGO1 (P35) (National Institutes of Health ID code BG01; BresaGen], H1 (P40), H9 (P37), WIBR1 (P13), WIBR3 (P11) hESCs were maintained in 20% pO2 conditions (unless indicated otherwise) on irradiated mouse embryonic fibroblast (MEF) feeder layers or Gelatin/vitronectin coated plates,  in hESC medium: (425ml Knockout-DMEM – Invitrogen 10829) supplemented with 15% Knockout Serum Replacement (Invitrogen 10828-028), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), and 8 ng/mL bFGF  (Peprotech) and 1 ng/ml recombinant human TGF β 1 (Peprotech). Cultures were passaged every 5–7 days either manually or, or by trypsinization (24 hour pre and 24hour after addition of ROCK inhibitor at 10nM concentration).

extract_protocol: mRNA was extracted byTRIZOL reagent (invitogene) according to manufacturer's instructions

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction

value: hESC

tag: pluripotent state

value: Naïve


title: Primed_WIBR3_hESC

source_name: Primed WIBR3 hESC

tag: cell type

value: Primed


title: Naïve_C1_hiPSC

source_name: Naïve C1 hiPSC


title: Naïve_BGO1_hESC

source_name: Naïve BGO1 hESC


title: Primed_H9_hESC

source_name: Primed H9 hESC


title: Re-Primed_WIBR3_hESC

source_name: Re-Primed WIBR3 hESC


title: UFE_batch f

source_name: Unfertilized eggs from individual f

value: unfertilized egg


title: ASC_N-cadherin(-)_rep1

description: Gene expression of N-cadherin(-) ASCs


title: UFE_batch g

source_name: Unfertilized eggs from individual g


title: 32cell_batch e

source_name: whole 32-cell embryos from individual e

value: e


title: Naïve_WIBR3_hESC_2

source_name: Naïve WIBR3 hESC


title: 16cell_batch e

source_name: whole 16-cell embryos from individual e


title: Naïve_WIBR3_hESC_1


title: Naïve_C2_hiPSC

source_name: Naïve C2 hiPSC


title: Naïve_Wis1_hESC

source_name: Naïve Wis1 hESC


title: bone marrow_case_rep4

city: Shanghai

first: xiaoqin

last: wang

address: 12 wulumuqi road central

institute: Huashan  hospital

description: gene expression in cases

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: case 4

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, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

value: bone marrow

value: male

tag: disease state

value: myelodysplastic syndrome


title: bone marrow_case_rep1

description: gene expression in cases

source_name: case 1


title: bone marrow_case_rep2

description: gene expression in cases

source_name: case 2

value: female


title: bone marrow_control_rep2

description: gene expression in controls

source_name: control 2

value: normal


title: UFE_batch e

source_name: Unfertilized eggs from individual e


title: Naïve_WIS2_hESC

source_name: Naïve WIS2 Hesc


title: UFE_batch b_Dup

source_name: Unfertilized eggs from individual b, technical replicate

value: b


title: bone marrow_case_rep3

description: gene expression in cases

source_name: case 3


title: bone marrow_control_rep3

description: gene expression in controls

source_name: control 3


title: UFE_batch b

source_name: Unfertilized eggs from individual b


title: mouse tracheal epithelial cells_wild type

first: Jiong

last: Deng

state: Shanghai

address: 280 South Chongqing Road, 2-801

department: Department of Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

description: MTEC_wild type

hyb_protocol: A hybridization cocktail including 5.5 μg of fragmented, and end-labeled ssDNA was applied to GeneChip Mouse Exon 1.0 ST arrays. Hybridization was performed using GeneChip hybridization oven 645 and wash and stain script on the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Probeset intensities were calculated from the CEL files of the 2 samples using the RMA algorithm with default settings at both the gene level and the probeset level in Expression Console, using the core probe sets as defined by Affymetrix.

source_name: MTECs from wild type mouse

label_protocol: Generate the sense-strand cDNA using  the Ambion® WT Expression Kit from 250ng  total  RNA for fragmentation and labeling using the Affymetrix GeneChip® WT Terminal Labeling Kit.

growth_protocol: The mouse tracheal epithelial cells were cultured in K-SFM supplemented with epidermal growth factor (EGF; 5 ng/ml) and bovine pituitary extract (50 μg/ml; Invitrogen) and the cells were cultured at exponential phase.

extract_protocol: Total RNA was isolated using the QIAGEN miRNeasy Mini kit and DNA was digested using the QIAGEN RNase-Free DNase Set according to the manufacturer's directions.

treatment_protocol: no treatment

tag: strain background

tag: genotype/variation

value: wild type control (Gprc5a+/+)

value: 3 weeks

value: mouse tracheal epithelial cells (MTECs)


title: DU145ivLU4 cells

description: Common reference ppol

hyb_protocol: Hybridized to miRCURY LNA array version 11.0 (Exiqon, Denmark) according to array manual using Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: scanned using Agilent G2565BA Microarray scanner system (Agilent Technologies), image analysis using ImaGene 8.0 software (BioDiscovery Inc, USA)

data_processing: LOESS normalized, background correction using Normexp with offset value 10 (Convolution model from Richie, ME, Bioinformatics, 2007, Vol 23 , no 20, 2700-2707)

source_name: DU145ivLU4 cells

label_protocol: 0.5ug RNA labeled using miRCURY miRNA array  Power labeling kit (Exiqon, Denmark)

extract_protocol: Total RNA was purfied using Trizol followed by Rneasy MinElute clean up kit, according to manufacturers instructions

tag: cell line

value: DU145 cells cycled four times by in vivo lung metastasis from tail vein injection to lungs

source_name: Common reference

tag: reference

value: Reference pool made from all samples


title: 8cell_batch e

source_name: whole 8-cell embryos from individual e

value: 8-cell embryo


title: bone marrow_control_rep4

description: gene expression in controls

source_name: control 4

tag: tissue

tag: gender

tag: age


title: CHD-NONFCHL patient 2 [GPL91]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 2

tag: chd status

value: CHD:patient undergoing coronary artery bypass surgery

value: non-FCHL


title: UFE_batch a

source_name: Unfertilized eggs from individual a

value: a


title: DU145ivLU2 cells

description: Common reference ppol

source_name: DU145ivLU2 cells

value: DU145 cells cycled twice by in vivo lung metastasis from tail vein injection to lungs


title: DU145-LN4 cells

description: Common reference ppol

source_name: DU145-LN4 cells

value: DU145 cells cycled four times in vivo from prostate xenograft to lymph node


title: CHD-NONFCHL patient 1 [GPL91]

source_name: subcutaneous, upper abdominal adipose tissue non-FCHL-CHD patient 1

tag: fchl status


title: FCHL-CHD patient 1 [GPL91]

source_name: subcutaneous, upper abdominal adipose tissue FCHL-CHD patient 1

value: FCHL

tag: tg rsponse to statins status

value: reduced TG


title: UFE_batch a_Dup

source_name: Unfertilized eggs from individual a, technical replicate

value: unfertilized egg


title: bone marrow_control_rep1

description: gene expression in controls

source_name: control 1

value: bone marrow

value: female


title: Naïve_H1_hESC

source_name: Naïve H1 hESC

value: hESC

value: Naïve


title: BRAF activated + ZEB1 in the  murine melanocytic melan-a cell line

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

institute: Inserm U590

hyb_protocol: According to  manufacturer's instructions  (Affymetrix)

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

data_processing: CHP files were processed using MAS5 analysis algorithm with Affymetrix Expression Console software 1.1

source_name: murine melanocytes

extract_protocol: Total RNA were extract with with Trizol (Sigma), then 100 ng of total RNA were amplified using Kit GeneChip 3’ IVT Express (Affymetrix)

value: Melan-a [derived from normal epidermal melanoblasts from inbred C57BL/6 embryos (Bennett et al., Int J. Cancer, 1987)]

value: BRAF activated + ZEB1


title: mouse tracheal epithelial cells_Gprc5a KO

source_name: MTECs from Gprc5a kock out mouse

value: Gprc5a knockout (Gprc5a−/−)

value: 3 weeks

value: mouse tracheal epithelial cells (MTECs)


title: BRAF activated + SNAIL2 in the  murine melanocytic melan-a cell line

label_protocol: According to  manufacturer's instructions  (Affymetrix)

value: BRAF activated + SNAIL2


title: DU145-LN2 cells

description: Common reference ppol

source_name: DU145-LN2 cells

value: DU145 cells cycled twice in vivo from prostate xenograft to lymph node

value: Reference pool made from all samples


title: parental DU145 cells

description: Common reference ppol

source_name: parental DU145 cells

value: DU145 cells


title: DU145-LN1 cells

description: Common reference ppol

source_name: DU145-LN1 cells

value: DU145 cells cycled once in vivo from prostate xenograft to lymph node


title: BRAF activated + TWIST1 in the  murine melanocytic melan-a cell line

value: BRAF activated + TWIST1


title: BRAF activated + ZEB2 in the  murine melanocytic melan-a cell line

value: BRAF activated + ZEB2


title: HepaRG_Hep_1

status: Public on Oct 28 2013

city: Rennes

first: Hélène

last: Dubois-Pot-Schneider

address: Hopital Pontchaillou, rue Henri Le Guilloux

institute: INSERM UMR 991

description: Gene expression of HepaRG-hepatocyte (30 days of normal culture conditions)

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (profile Agilent G3-GX-1color).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol GE_1-107_sep09_ssSurogates and Grid: 028004_D_F_20110325. Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by flag and signal intensity was applied. Briefly, were retained only the entities in which at least 100% of the values in at least one condition  had a detected flag (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which 100% of the values in at least one condition were within the range of interest (i.e. 20-100th percentile).

source_name: HepaRG, Hepatocyte, day30, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labelling 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 (Thermo Fischer Scientific, Waltham, MA).  amplification yield was 4.04 ± 0.53 µg cRNA and specific activity was 11.97 ± 0.98 pmol Cy3 per µg cRNA.

extract_protocol: RNA extractions were performed with RNeasy mini kit (Qiagen)  following the manufacturer's recommendations. RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

treatment_protocol: hESC (WA09, WiCell) were maintained on irradiated mouse embryonic fibroblast feeder cells, in DMEM/F12 medium supplemented with 20% knockout serum replacement, 1mM L-glutamine, 1% non essential amino acids, 0.1 mM beta-mercaptoethanol, and 4 ng/ml bFGF.

tag: origin cell line

value: HepaRG

tag: differentiation state

value: Hepatocyte

tag: time

value: 30 days


title: HepaRG_Hep_4

source_name: HepaRG, Hepatocyte, day30, replicate4


title: HepaRG_Hep_3

source_name: HepaRG, Hepatocyte, day30, replicate3


title: BRAF activated in the  murine melanocytic melan-a cell line

value: BRAF activated


title: HepaRG_cHep_3

description: Gene expression of HepaRG-committed hepatocyte (10 days of normal culture conditions)

source_name: HepaRG, committed Hepatocyte, day10, replicate3

value: committed hepatocyte


title: bone marrow_case_rep3 [10572]

description: patient bone marrow

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

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

data_processing: BeadStudio software 2011.1

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purifiedusing QIAamp DNA Mini Kit according to standard instructions

value: male

value: bone marrow

value: myelodysplastic syndrome


title: BRAF non activated in the  murine melanocytic melan-a cell line

value: Melan-a [derived from normal epidermal melanoblasts from inbred C57BL/6 embryos (Bennett et al., Int J. Cancer, 1987)]

value: BRAF non activated


title: HepaRG_Chol_4

description: Gene expression of HepaRG-cholangiocyte (10 days of culture)

source_name: HepaRG, Cholangiocyte, day10, replicate4

value: Cholangiocyte

value: 10 days


title: HepaRG_Hep_2

source_name: HepaRG, Hepatocyte, day30, replicate2


title: HepaRG_Chol_1

source_name: HepaRG, Cholangiocyte, day10, replicate1


title: HepaRG_HB_4

description: Gene expression of HepaRG-hepatoblast (4 days of culture)

source_name: HepaRG, Hepatoblast, day4, replicate4

value: Hepatoblast

value: 4 days