title: 4MH

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

institute: Forth Military Medicial University

hyb_protocol: Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.
The 4MH, Vel and JNJ group represent for the nude mice subjected with 100 μM/kg 4MH, velhicle or 100 μM/kg JNJ. The ID_REF represent for 35,923 LncRNAs and 24,881 coding transcripts that can be detected by our third-generation LncRNA microarray.

source_name: xenograft tumor of TE-2 cells in the nude mice subjected with injections of 100 μM/kg histamine H4 receptor agonist 4-methylhistamine  for 4 weeks

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: All animal procedures were performed following the National Animal Experimentation guidelines and were approved by the ethics committee of the Kunming General Hospital of Chengdu Military Region. All nu/nu mice were bred in aseptic conditions at a constant humidity and temperature with standard 12 h light-dark cycles and free access to drinking water and standard chow. TE-2 cells (1 × 107 in 100 mL of PBS) were suspended in a volume of 0.2 ml serum-free medium and injected subcutaneously into the hind flanks of the animals. At the end of the treatment, the nude rats were sacrificed and xenograft tumors were harvested for tumor volumes calculation (0.5 × length (mm) × width2 (mm2) as well as other experiments. When the subcutaneous tumors reached 20 mm3 (about 3 w), The mice were randomly assigned to one of the following four groups: (1) Vel group: nude mice received I.V. injections of vehicle (0.9% NaCl) once a day for 4 w; (2) 4MH group: nude mice received I.V. injections of 100 μM/kg H4R agonist 4MH once a day for 4 w; (3) JNJ group: nude mice received I.V. injections of 100 μM/kg H4R antagonist JNJ once a day for 4 w. At the end, the mice were sacrificed and tissue samples and cells were put into liquid nitrogen for 10 min and then into an ultra freezer at 80°C.

extract_protocol: Total RNA was extracted using the GeneJET RNA purification Kit according to the manufacturer’s instructions (Thermo Scientific). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).

tag: cell line

value: esophagus cancer TE-2 cell line

value: xenograft tumor

tag: agent

value: H4R activaiton (4MH)


title: Mouse 2 HF WT

status: Public on Sep 01 2017

type: RNA

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Total RNA isolated from Flexor digitorum  brevis muscle from WT mice. Biological replicate 2

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.1 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the 'AROMA' package (Bioconductor project) and a custom CDF from Brainarray, mouse-ENTREZG 21.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Flexor digitorum  brevismuscle, Biological replicate 2, WT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA

growth_protocol: From 7-8 weeks of age, male FVB/n mice were fed a high fat diet containing 58% fat, 25.5% carbohydrate and 16.4% protein for 8 weeks. All animals were maintained under pathogen free condition at the York University vivarium on a 12/12h light-dark cycle with food and water available ad libitum.

extract_protocol: Total RNA was using Trizol according to the manufacturer's instructions. Quality/quantity was checked using NanoDrop 2000 spectrophotometer. RNA was dissolved in 20 μl RNAse-free water with no additives.

treatment_protocol: WT C57BL/6 and TLR2-/- mice were used in this study. TLR2-/- mice were on a C57BL/6 background and were kindly provided by Dr S. Akira (Osaka University, Osaka, Japan). WT C57BL/6 mice were purchased from Charles River Laboratories (Wilminton, MA, USA). All the mice used in this study were males and more than 7 weeks old. Animals were kept and bred at Karolinska Institutet animal facility in a specific pathogen-free environment with standard room temperature and a 12-12 hour light/dark cycle. Food and water were provided ad libitum. Mice were killed by rapid neck disarticulation and the flexor digitorum brevis muscles were removed.

tag: tissue

value: Flexor digitorum  brevis

value: Skeletal muscle

tag: genotype

value: WT

tag: Sex

value: Male

tag: subject

value: Biological replicate 2


title: Mouse 3 HF TLR2-/-

description: Total RNA isolated from Flexor digitorum  brevis muscle from TLR-/- mice. Biological replicate 3

source_name: Flexor digitorum  brevismuscle, Biological replicate 3, TLR2-/-

value: Biological replicate 3


title: JNJ

country: China

organism: Homo sapiens

source_name: xenograft tumor of TE-2 cells in the nude mice subjected with injections of 100 μM/kg histamine H4 receptor antagonist JNJ7777120 for 4 weeks

treatment_protocol: All animal procedures were performed following the National Animal Experimentation guidelines and were approved by the ethics committee of the Kunming General Hospital of Chengdu Military Region. All nu/nu mice were bred in aseptic conditions at a constant humidity and temperature with standard 12 h light-dark cycles and free access to drinking water and standard chow. TE-2 cells (1 × 107 in 100 mL of PBS) were suspended in a volume of 0.2 ml serum-free medium and injected subcutaneously into the hind flanks of the animals. At the end of the treatment, the nude rats were sacrificed and xenograft tumors were harvested for tumor volumes calculation (0.5 × length (mm) × width2 (mm2) as well as other experiments. When the subcutaneous tumors reached 20 mm3 (about 3 w), The mice were randomly assigned to one of the following four groups: (1) Vel group: nude mice received I.V. injections of vehicle (0.9% NaCl) once a day for 4 w; (2) 4MH group: nude mice received I.V. injections of 100 μM/kg H4R agonist 4MH once a day for 4 w; (3) JNJ group: nude mice received I.V. injections of 100 μM/kg H4R antagonist JNJ once a day for 4 w. At the end, the mice were sacrificed and tissue samples and cells were put into liquid nitrogen for 10 min and then into an ultra freezer at 80°C.

value: H4R inhibition JNJ


title: Mouse 4 HF TLR2-/-

description: Total RNA isolated from Flexor digitorum  brevis muscle from TLR-/- mice. Biological replicate 4

source_name: Flexor digitorum  brevismuscle, Biological replicate 4, TLR2-/-

value: Biological replicate 4


title: Mouse 1 HF TLR2-/-

description: Total RNA isolated from Flexor digitorum  brevis muscle from TLR-/- mice. Biological replicate 1

source_name: Flexor digitorum  brevismuscle, Biological replicate 1, TLR2-/-

value: Biological replicate 1


title: IECs_InVivo_4day_rep1

city: Seoul

first: June Sung

last: Bae

address: 31, Ttukseom-ro 1-gil, Seongdong-gu

country: South Korea

institute: SG Medical

description:
4 days after tamoxifen injection in Mob1a f/f; Mob1b f/f; Villin-creERT2 mice
Δ 1

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: IECs_4days after tamoxifen

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Mice were backcrossed more than 6 generation to C57BL/6J and raised under SPF conditions.

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

treatment_protocol: Tamoxifen (80mg/kg per day, 2 days) was intraperitoneally injected 8 weeks after birth to induce deletion of the Mob1a/b gene in mouse IECs.

tag: strain background

tag: genotype/variation

value: conditional knockout of Mob1a/b

tag: gender

value: male

tag: age

value: 8 week old

tag: timepoint

value: 4 days after Tamoxifen injection

value: intestine

tag: cell type

value: intestinal epithelial cells (IECs)


title: IECs_InVivo_WT_rep2

description:
7 days after tamoxifen injection in Mob1a f/f; Mob1b f/f mice
WT 2

source_name: IECs_wild type

value: wild type


title: Vel

source_name: xenograft tumor of TE-2 cells in the nude mice subjected with injections of vehicle (0.9% NaCl) for 4 weeks

value: esophagus cancer TE-2 cell line

value: xenograft tumor

value: control (vehicle)


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Tamoxifen rep 3

status: Public on Aug 31 2017

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was  fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression  hybridisation buffer was added and 43ul of sample hybridised for 17 hours at  67oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays  were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1  minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray  scanner using one color scan settings for 8x60k array slides; scan area  61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid:  028005_D_F_20120201) to obtain background subtracted and spatially  detrended Processed Signal intensities.

source_name: TAM

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.1ug total RNA using the  One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012)  according to the manufacturer’s instructions, followed by RNeasy column  purification (Qiagen). Dye incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Undifferentiated spermatogonia were cultured on mitomycin-inactivated mouse embryonic fibroblast (MEF) feeder cells in StemPro-34 media (Thermo Fisher Scientific) supplemented with 10ng/ml GDNF, 10ng/ml bFGF, 20ng/ml EGF, 25μg/ml insulin and other additives as previously described (Hobbs et al., 2012).

extract_protocol: Sorted cells were lysed in TRIzol LS reagent (Thermo Fisher Scientific) then RNA was purified and DNase treated using a Direct-zol RNA Miniprep kit (Zymo Research).

treatment_protocol: Cells were treated with 0.2μM of 4-hydroxytamoxifen for 4 days then transferred to regular media for an additional 4 days before analysis. Spermatogonia were separated from contaminating MEF feeders by sorting according to EpCAM expression (Kanatsu-Shinohara et al., 2003).

value: Cultured undifferentiated spermatogonia


title: Arabidopsis_LateS_biorep2_techrep1

type: genomic

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

description:
At_Repli-chip_ratio.late.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Late S biorep2 techrep1

hyb_protocol: Th Cy dye-labeled target and reference samples were co-hybridized on a Nimblegen tiling array with a dye-swap experimental design. After the overnight hybridization, DyeSaver2 was used to minimize oxidation of Cy dyes.

scan_protocol: Hybridized arrays were scanned using a PerkinElmer ScanArray Express scanner and quantified using NimbleScan version 2.4.27.

data_processing:
Arrays were loess and quantile normalized using the limma package in R to obtain ratios of the BrdU IP data to the reference data. The variance between the biological replicates and technical replicates was similar so biological replicates were treated as technical replicates, and average of all replicates was calculated.
Bedgraph files contain Loess-smoothed ratios (BrdU/reference DNA) using a 25-kb window.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: BrdU IP DNA from late S cells

label_protocol: Amplified target and reference DNA samples were labeled with either Cy3 or Cy5 and purified using a BioPrime Array CGH Genomic Labeling System (Invitrogen)

growth_protocol: At (Col-0) cells were grown in Gamborg's B5 basal medium with minor salt, maintained on a rotary shaker at 160 rpm under constant light at 23C, and subcultured weekly.

extract_protocol: After reversing the crosslinks, newly replicated DNA was extracted from sorted nuclei using phenol/chloroform/IAA and a phase lock gel. Newly replicated DNA was isolated by immunoprecipitation to BrdU and purified with a QIAquick PCR purification kit (Qiagen).

treatment_protocol: A 7-d split culture was grown for 16 hrs and then labeled for 1 hr with 100 uM BrdU.

tag: cultivar

value: 7-d split suspension culture cells

tag: cell cycle stage

value: late S

source_name: Unsorted cells reference DNA


title: Arabidopsis_EarlyS_biorep2_techrep2

description:
At_Repli-chip_ratio.early.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Early S biorep2 techrep2

source_name: BrdU IP DNA from early S cells

value: early S


title: Arabidopsis_MidS_biorep2_techrep1

description:
At_Repli-chip_ratio.mid.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Mid S biorep2 techrep1

source_name: BrdU IP DNA from mid S cells

value: mid S


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Tamoxifen rep 2


title: Arabidopsis_EarlyS_biorep2_techrep1

description:
At_Repli-chip_ratio.early.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Early S biorep2 techrep1


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Vehicle rep 3

source_name: CTRL/VEH


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Vehicle rep 2


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Tamoxifen rep 1


title: Arabidopsis_LateS_biorep2_techrep2

description:
At_Repli-chip_ratio.late.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Late S biorep2 techrep2


title: Hepatogenic differentiation_Hepatocyte (3)

city: Taipei

first: Chien-Wei

last: Lee

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol by GeneChip® Scanner 3000 7G

data_processing: The data were analyzed by RMA normalization method of 'affy' pachage in R software.

source_name: Hepatogenic differentiation_Hepatocyte

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Mouse MSCs and MLCs were cultured in an mMSC-maintenance medium, low glucose DMEM supplemented with 10% FBS; mouse primary hepatocytes were cultured in Hep-maintenance medium, and DMEM/F12 supplemented with 10% FBS; HD 28 cells are differentiated from mMSCs by following methods.MSCs were treated with a Step-1 differentiation medium, consisting of IMDM supplemented with 20 ng/ml HGF and 10 ng/ml bFGF (R&D Systems), and nicotinamide 0.61 g/L (Sigma-Aldrich), for 7 days, then treated with a Step-2 differentiation medium, consisting of IMDM supplemented with 20 ng/ml oncostatin M (Invitrogen), 1 μmol/L dexamethasone (Sigma-Aldrich), and 50 mg/ml ITS+ premix (BD Biosciences). The medium was changed once per week to generate HD 28 cells. dHD 28 cells are derived from HD 28 cells by following methods. Hepatogenic de-differentiation was induced in HD 28 cells derived from MSCs by replacing the Step-2 medium with MSC-maintenance medium. MLCs are derived from mouse orimary hepatocytes by following method. A stepwise protocol was used for the lineage reprogramming of mouse primary hepatocytes into MLCs. Mouse primary hepatocytes were cultured in an mMSCs-maintenance medium with 10 ng/ml hTGF-β1 for 7 days, with 5 ng/ml hTGF-β1 for 7-14 days, with 1 ng/ml hTGF-β1 for 14-28 days. After 28 days, cells were maintained in an mMSCs-maintenance medium.

extract_protocol: Total RNA was extracted using a Trizol reagent (Sigma-Aldrich) according to the manufacturer’s directions.

treatment_protocol: See growth protocol

tag: status

value: Hepatocyte


title: Sall4flox/flox Ubc-CreER (Sall4TAM-KO) Vehicle rep 1


title: Hepatogenic de-differentiation_MLC cells (2)

value: MLC cells


title: Arabidopsis_MidS_biorep1_techrep1

description:
At_Repli-chip_ratio.mid.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Mid S biorep1 techrep1


title: Hepatogenic de-differentiation_MLC cells (3)


title: Hepatogenic de-differentiation_MLC cells (1)


title: Hepatogenic differentiation_MSC cells (3)

source_name: Hepatogenic differentiation_MSC cells

value: MSC cells


title: Arabidopsis_MidS_biorep1_techrep2

description:
At_Repli-chip_ratio.mid.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Mid S biorep1 techrep2


title: Hepatogenic de-differentiation_dHD28 cells (2)

value: dHD28 cells


title: Hepatogenic differentiation_MSC cells (2)


title: Arabidopsis_EarlyS_biorep1_techrep2

description:
At_Repli-chip_ratio.early.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Early S biorep1 techrep2


title: Arabidopsis_LateS_biorep1_techrep2

description:
At_Repli-chip_ratio.late.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Late S biorep1 techrep2


title: Hepatogenic de-differentiation_dHD28 cells (3)


title: Hepatogenic de-differentiation_dHD28 cells (1)


title: Hepatogenic differentiation_HD28 cells (1)

source_name: Hepatogenic differentiation_HD28 cells

value: HD28 cells


title: Hepatogenic differentiation_Hepatocyte (2)


title: Hepatogenic differentiation_MSC cells (1)


title: Arabidopsis_MidS_biorep2_techrep2

description:
At_Repli-chip_ratio.mid.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Mid S biorep2 techrep2


title: Hepatogenic differentiation_HD28 cells (3)


title: Hepatogenic differentiation_Hepatocyte (1)


title: Hepatogenic differentiation_HD28 cells (2)


title: Arabidopsis_EarlyS_biorep1_techrep1

description:
At_Repli-chip_ratio.early.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Early S biorep1 techrep1


title: Arabidopsis_LateS_biorep1_techrep1

description:
At_Repli-chip_ratio.late.ng.smooth.25kb.bedgraph
Arabidopsis Repli-chip Late S biorep1 techrep1


title: MLL_03729

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich leukemia laboratory

hyb_protocol: We used SurePrint G3 ISCA CGH+SNP Bundle, 4x180K according to manufacturer's protocol

scan_protocol: Protocol CytoCGH_0209_4x_Mar14 (Read Only) was used with CytoGenomics v 2.9.1.0 on instrument Agilent G5761A SureScan Dx Microarray Scanner System

data_processing: Unmodified Raw data provided as separate files from CytoGenomics v2.9.1.0. We have used LogRatio directly extracted from the feature extraction software (Agilent CytoGenomics).

source_name: Bone marrow/Blood

label_protocol: labeling was done with SureTag Complete DNA Labeling Kit according to manufacturer's protocol, Cy3 were used for reference sample and Cy5 for the test sample

extract_protocol: DNA was extracted on a Qiacube according to manufacturer's protocol

value: male

value: Bone marrow/Blood

tag: diagnosis

value: Chronic Lymphocytic Leukemia (CLL)

source_name: Agilent Euro Male

extract_protocol: Catalog number for Agilent male control DNA:  #5190-4370. Catalog number for Agilent female control DNA: #5190-4371.

tag: control type

value: commercially available normal genomic DNA


title: MLL_03605

value: female

source_name: Agilent Euro Female


title: MLL_03740


title: MLL_03472


title: MLL_03516


title: MLL_03578


title: MLL_03101


title: MLL_03598


title: MLL_03257


title: MLL_03724


title: MLL_03096


title: MLL_03626


title: MLL_03099


title: MLL_03517


title: MLL_03487


title: MLL_03470


title: MLL_03162


title: MLL_03527


title: MLL_03372


title: MLL_03394


title: MLL_03211


title: MLL_03163


title: MLL_03070


title: MLL_03459


title: MLL_03435


title: MLL_03107


title: MLL_03195


title: MLL_03192


title: MLL_03396


title: MLL_03264


title: MLL_03005


title: MLL_02840


title: MLL_03008


title: MLL_02946


title: MLL_02911


title: MLL_02727


title: MLL_02926


title: MLL_02704


title: MLL_02684


title: MLL_02454


title: MLL_02631


title: MLL_02688


title: MLL_02702


title: MLL_02354


title: MLL_02163


title: MLL_02189


title: MLL_02448


title: MLL_02386


title: MLL_02503


title: MLL_02501


title: MLL_02402


title: MLL_02621


title: MLL_02173


title: MLL_02059


title: MLL_02046


title: MLL_02134


title: MLL_02007


title: MLL_02102


title: MLL_02036


title: MLL_02398


title: MLL_02263


title: MLL_02027


title: MLL_01950


title: MLL_01983


title: MLL_02213


title: MLL_01948


title: MLL_01952


title: MLL_01940


title: MLL_01972


title: MLL_01856


title: MLL_01836


title: MLL_01843


title: Maresi_Roots_Control_repl1

city: Katowice

first: Miroslaw

last: Kwasniewski

state: silesia district

address: Jagiellonska 28

country: Poland

institute: University of Silesia in Katowice

description:
K_Mar_R_c_19
Gene expression in leaf of Maresi barley cultivar in drought stress

hyb_protocol: 55 µl of 2x the GE Hybridization mix (Agilent GE Hybridization Kit) was added to the fragmented cRNA and 110 was loaded onto the Agilent 4x44k Barley Array within a gasket array slide sandwich. Arrays were hybridised in a rotisserie hybridisation oven at 65°C for 17 hours (Agilent p/n G2545a Hybridization Oven). After 17 hours, the slides were removed from the oven and washed with Agilent Wash Buffers containing Triton X.

scan_protocol: After the wash, the slides were taken to be scanned on an Agilent High Resolution Scanner using the green dye channel at a resolution of a 5 µm single pass scan with no extended dynamic range.

data_processing: Scanned images were analysed using Agilent Feature extraction software version 10.7.3.1.

organism: Hordeum vulgare

source_name: Maresi, roots, control conditions, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of RNA using the the Agilent Low Input Quick Amp Kit according to the manufacturer's instructions, followed by Qiagen RNeasy Mini Kit column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two barley genotypes were used for the study: a German semidwarf cultivar Maresi and a Syrian breeding line Cam/B1/CI08887//CI05761 (CamB), adapted to dry environments. Grains of both genotypes were sterilized and sown in the pots with a dimension of 37 x 15 x 14 cm (L x W x H). The pots were filled with a mixture of sandy loam and sand (7 : 2, w/w). Initially, 15 seedlings were placed in pots, and after germination, the number of plants was reduced to 10. At this time, the seedlings were transferred to an air-conditioned greenhouse, where the temperature was maintained at 20/17°C (day/night), with the light intensity of 520 µmol(photon)m-2s-2.

extract_protocol: Total RNA was isolated using an RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. After isolation, RNA was purified using precipitation in 1M lithium chloride. Each RNA precipitate was dissolved in nuclease-free H2O. The yield and purity of the RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was checked using denaturation agarose gel electrophoresis using pre-cast gels and FlashGel RNA System (Lonza, Basel, Switzerland).

treatment_protocol: Drought stress treatment: Soil drought (3.65%, i.e. pF = 4.0) was applied to plants after the appearance of the 4th leaf and it was continued for 10 days. The substrate humidity was determined by monitoring pots weight. Plants grown in pots with 11% water content (pF = 2.8) were used as the control.

value: Roots

tag: water stress time point

value: 2 (drought stress)


title: Maresi_Leaf_Drought_repl1

description:
K_Mar_L_d_16
Gene expression in roots of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, drought stress, replicate 1

value: Leaf no. 2

value: 1 (control conditions)


title: MLL_01870


title: Maresi_Roots_Drought_repl2

description:
K_Mar_R_d_23
Gene expression in roots of Maresi barley cultivar in drought stress

source_name: Maresi, roots, drought stress, replicate 2


title: Maresi_Roots_Drought_repl1

description:
K_Mar_R_d_22
Gene expression in roots of Maresi barley cultivar in drought stress

source_name: Maresi, roots, drought stress, replicate 1


title: Maresi_Leaf_Drought_repl2

description:
K_Mar_L_d_17
Gene expression in roots of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, drought stress, replicate 2


title: Maresi_Roots_Control_repl2

description:
K_Mar_R_c_20
Gene expression in leaf of Maresi barley cultivar in drought stress

source_name: Maresi, roots, control conditions, replicate 2


title: MLL_01828


title: Maresi_Leaf_Control_repl3

description:
K_Mar_L_c_15
Gene expression in leaf of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, control conditions, replicate 3


title: Maresi_Leaf_Drought_repl3

description:
K_Mar_L_d_18
Gene expression in roots of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, drought stress, replicate 3


title: Maresi_Leaf_Control_repl2

description:
K_Mar_L_c_14
Gene expression in leaf of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, control conditions, replicate 2


title: Maresi_Roots_Control_repl3

description:
K_Mar_R_c_21
Gene expression in leaf of Maresi barley cultivar in drought stress

source_name: Maresi, roots, control conditions, replicate 3


title: CamB_Roots_Drought_repl2

description:
K_Cam_R_d_11
Gene expression in roots of CamB barley breeding line in drought stress

source_name: CamB, roots, drought stress, replicate 2


title: MLL_01824


title: MLL_01802


title: MLL_01769


title: CamB_Roots_Control_repl2

description:
K_Cam_R_c_08
Gene expression in leaf of CamB barley breeding line in drought stress

source_name: CamB, roots, control conditions, replicate 2


title: CamB_Roots_Drought_repl3

description:
K_Cam_R_d_12
Gene expression in roots of CamB barley breeding line in drought stress

source_name: CamB, roots, drought stress, replicate 3


title: Maresi_Leaf_Control_repl1

description:
K_Mar_L_c_13
Gene expression in leaf of Maresi barley cultivar in control conditions

source_name: Maresi, leaf no.2, control conditions, replicate 1


title: CamB_Roots_Drought_repl1

description:
K_Cam_R_d_10
Gene expression in roots of CamB barley breeding line in drought stress

source_name: CamB, roots, drought stress, replicate 1


title: Maresi_Roots_Drought_repl3

description:
K_Mar_R_d_24
Gene expression in roots of Maresi barley cultivar in drought stress

source_name: Maresi, roots, drought stress, replicate 3


title: CamB_Roots_Control_repl3

description:
K_Cam_R_c_09
Gene expression in leaf of CamB barley breeding line in drought stress

source_name: CamB, roots, control conditions, replicate 3


title: CamB_Roots_Control_repl1

description:
K_Cam_R_c_07
Gene expression in leaf of CamB barley breeding line in drought stress

source_name: CamB, roots, control conditions, replicate 1


title: MLL_01713

source_name: Bone marrow/Blood

source_name: Agilent Euro Male


title: CamB_Leaf_Drought_repl3

description:
K_Cam_L_d_06
Gene expression in roots of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, drought stress, replicate 3


title: MLL_01745


title: MLL_01693


title: MLL_01691

source_name: Agilent Euro Female


title: CamB_Leaf_Drought_repl2

description:
K_Cam_L_d_05
Gene expression in roots of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, drought stress, replicate 2


title: CamB_Leaf_Control_repl1

description:
K_Cam_L_c_01
Gene expression in leaf of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, control conditions, replicate 1


title: CamB_Leaf_Control_repl3

description:
K_Cam_L_c_03
Gene expression in leaf of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, control conditions, replicate 3


title: MLL_01626


title: MLL_01642


title: CamB_Leaf_Drought_repl1

description:
K_Cam_L_d_04
Gene expression in roots of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, drought stress, replicate 1


title: MLL_01666


title: MLL_01612


title: MLL_01594


title: MLL_01438


title: MLL_01486


title: MLL_01688


title: MLL_01621


title: MLL_01378


title: MLL_01437


title: MLL_01325


title: MLL_01579


title: MLL_01472


title: MLL_01502


title: MLL_01222


title: MLL_01346


title: MLL_01507


title: MLL_01417


title: MLL_01195


title: MLL_01549


title: MLL_01464


title: MLL_01151


title: MLL_00841


title: MLL_00711


title: MLL_00653


title: MLL_00682


title: MLL_00924


title: MLL_01144


title: MLL_00687


title: MLL_00958


title: CamB_Leaf_Control_repl2

description:
K_Cam_L_c_02
Gene expression in leaf of CamB barley breeding line in control conditions

source_name: CamB, leaf no.2, control conditions, replicate 2


title: TAF-MSC 1

city: Lund

first: Niels-Bjarne

last: Woods

address: BMC A12

department: Molecular Medicine and Gene Therapy

institute: Lund University

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard  scan protocol

data_processing: CEL files were normalized using the RMA method via the Oligo R package

source_name: Term amniotic fluid

label_protocol: Affymetrix standard labeling kit

growth_protocol: TAF-MSCs were cultured in media 1 and 2 for three passages and CB-Endo cells were cultured in medium 1 for five passages

extract_protocol: Total RNA was prepared using Trizol reagent and phenol-chloroform extraction method

value: TAF-MSCs


title: MLL_00935


title: CB-ENDO 2

source_name: Term umbilical cord

value: CB-Endo cells


title: CB-ENDO 1


title: MLL_00770


title: MLL_00661


title: TAF-MSC 2


title: ILN6h MPL-1

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

description: gene expression from draining ileac lymph node at 6h after immunization

hyb_protocol: RNA samples were processed for hybridization on GeneChip_ Whole Mouse Genome 430 2.0 arrays following standard procedures

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affimetrix).

data_processing: Data were normalized using gcrma in the Bioconductor suite

source_name: Ileac lymph node, MPL, 6h

extract_protocol: Total RNA was isolated by homogenizing pooled dLN in Tripure reagent (1 ml/100 mg tissue; Roche Applied Science) and then extracted with chloroform followed by RNeasy™ Minikit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the RNeasy column to avoid genomic DNA contamination. RNA was concentrated by ethanol precipitation, and quantified by RiboGreen™ (Life Technologies). 1mgof each RNA sample was used for target preparation, using a one-cycle cDNA synthesis kit.

treatment_protocol: C57BL/6 mice (6-8 weeks old) were immunized in both hind limbs, in the gastrocnemius (gcm) muscles and in a volume of 50 µl/muscle with AS01b (100mg/ml QS-21 + 100mg/ml MPL) or QS-21 (100mg/ml) or MPL (100mg/ml), all formulated in liposomes. Ileac lymph nodes were identified as draining in setup experiments. Lymph nodes were mechanically homogenized prior to RNA extraction.

value: ileac lymph node

tag: strain


title: ILN6h MPL-3

label_protocol: RNA samples were processed for hybridization on GeneChip_ Whole Mouse Genome 430 2.0 arrays following standard procedures

tag: tissue


title: ILN6h dQ-3

source_name: Ileac lymph node, QS-21, 6h


title: MLL_00865


title: ILN6h MPL-2


title: ILN6h PBS-3

source_name: Ileac lymph node, PBS, 6h


title: ILN6h dQ-2


title: ILN6h AS01b-1

source_name: Ileac lymph node, AS01b, 6h


title: ILN6h PBS-2


title: ILN6h PBS-1


title: ILN4h PBS-3

description: gene expression from draining ileac lymph node at 4h after immunization

source_name: Ileac lymph node, PBS, 4h


title: ILN6h dQ-1


title: ILN6h AS01b-3


title: ILN4h PBS-1


title: ILN6h AS01b-2


title: ILN4h MPL-1

source_name: Ileac lymph node, MPL, 4h


title: ILN4h MPL-2


title: MLL_01004

source_name: Bone marrow/Blood


title: ILN4h dQ-2

source_name: Ileac lymph node, QS-21, 4h


title: ILN4h AS01b-2

source_name: Ileac lymph node, AS01b, 4h


title: ILN4h MPL-3


title: ILN4h PBS-2


title: ILN4h AS01b-1


title: ILN2h PBS-3

description: gene expression from draining ileac lymph node at 2h after immunization

source_name: Ileac lymph node, PBS, 2h


title: ILN4h dQ-1


title: ILN4h dQ-3


title: ILN4h AS01b-3


title: ILN2h PBS-1


title: ILN2h MPL-2

source_name: Ileac lymph node, MPL, 2h


title: ILN2h dQ-3

source_name: Ileac lymph node, QS-21, 2h


title: ILN2h MPL-1


title: ILN2h PBS-2


title: ILN2h dQ-2


title: ILN2h MPL-3


title: MUC_00866

source_name: Agilent Euro Female


title: ILN2h AS01b-1

source_name: Ileac lymph node, AS01b, 2h


title: ILN2h dQ-1


title: MUC_00861

source_name: Agilent Euro Male


title: MUC_00867


title: ILN2h AS01b-2


title: ILN2h AS01b-3


title: MUC_00868


title: MUC_00862


title: MUC_00864


title: MUC_00853


title: MUC_00857


title: MUC_00595


title: MUC_00552


title: MUC_00847


title: MUC_00855


title: MUC_00854


title: MUC_00214


title: MUC_00856


title: MLL_09931


title: MLL_09900


title: MUC_00849


title: MUC_00695


title: MLL_09932


title: MLL_09891


title: Patient Derived Xenograft Serial Passage 3

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Data was imported into Partek Genomic Suite using Partek defaults as allele specific intensity which was converted to copy number.

label: Biotin

source_name: Xenograft

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Tumor growth was established in NOD/SCID mouse and tumors have been passaged serially

extract_protocol: Genomic DNA was isolated from tumor samples snap frozen in liquid nitrogen at the time of passaging. We used a Proteinase K/SDS buffer to dissociate the tissue (10 mM Tris-Cl (pH 8.0), 0.1 M EDTA (pH 8,0), 0.5% (w/v) SDS, 20mg/mL Proteinase K) overnight at 55°C. Protein extraction was achieved with Phenol-Chloroform-Isoamyl alcohol using phase lock centrifuge gels (5-Prime, Gaithersburg, USA) and DNA was precipitated with 100% ethanol and 7.5 M ammonium acetate. The pellet was washed with 75% ethanol and then dried.

tag: host strain

value: NOD/SCID mouse

tag: tissue/cell type

value: Patient-derived xenograft

tag: passage

value: passage 3


title: MLL_09901


title: MUC_00852


title: Patient Derived Xenograft Serial Passage 0

value: passage 0


title: MLL_09903


title: MLL_09878


title: MLL_09861


title: MLL_09897


title: MLL_09905


title: Clivial Chordoma Primary tumour

source_name: patient primary tumor

value: primary tumour


title: MLL_09882


title: MLL_09859

value: male


title: MLL_09895

value: Bone marrow/Blood


title: MLL_09850

value: Chronic Lymphocytic Leukemia (CLL)


title: MLL_04320

value: commercially available normal genomic DNA


title: MLL_04316


title: MLL_04315

value: female


title: MUC_00859


title: MLL_04177


title: MLL_04236


title: MLL_04173


title: MLL_04258


title: MLL_04026


title: Copper 96h treatment 2 replicate 4

city: Aachen

first: Laura

last: Sonnack

address: Forckenbeckstr. 6

institute: Fraunhofer IME

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized overnight for 17 h at 65°C

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

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and QC Metric Set GE_QCMT_Jan09) During this step the background was subtracted and outliers detected and flagged.

organism: Danio rerio

source_name: Copper 96h treatment 2 replicate 4

label_protocol: The samples were processed following the Agilent´s One-Color Microarray-Based Gene Expression Analysis Protocol (Low Input Quick Amp Labeling, Version 6.6, September 2012). The starting amount of all samples was 100 ng of total RNA.

growth_protocol: Zebrafish embryo toxicity test followig DIN EN ISO 15088; After harvest of the eggs, the embryos were quickly transferred to the wells (one embryo/well) of the plates and incubated for 48 h and 96 h at 26 ± 1°C with a 14-h photoperiod

extract_protocol: Total RNA was extracted from the frozen, pooled embryos by the Trizol-Method and homogenization with motor-driven plastic micro pistils. Subsequently, RNA was cleaned-up using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers' protocols. For all RNA samples, the absorbance ratio 260/280 was above 2.0 and 260/230 above 1.8 while the RNA integrity number was above 8.7

treatment_protocol: All metal test solutions were prepared in ISO-standard water (prepared according to OECD guideline 203, Annex 2) diluted 1:5

tag: developmental stage

value: 96hpf embryos


title: MLL_04025


title: Copper 96h treatment 2 replicate 3

source_name: Copper 96h treatment 2 replicate 3


title: MLL_04027


title: MLL_03971


title: Copper 96h treatment 1 replicate 3

source_name: Copper 96h treatment 1 replicate 3


title: MLL_03840


title: Copper 96h treatment 1 replicate 4

source_name: Copper 96h treatment 1 replicate 4


title: Copper 96h treatment 2 replicate 1

source_name: Copper 96h treatment 2 replicate 1


title: Copper 96h treatment 2 replicate 2

source_name: Copper 96h treatment 2 replicate 2


title: MLL_04097

source_name: Bone marrow/Blood


title: Copper 48h treatment 2 replicate 2

source_name: Copper 48h treatment 2 replicate 2

value: 48hpf embryos


title: MLL_03816


title: Copper 96h treatment 1 replicate 1

source_name: Copper 96h treatment 1 replicate 1


title: MLL_03782


title: MLL_03890


title: MLL_04330


title: MLL_03781


title: MLL_03786


title: Copper 96h treatment 1 replicate 2

source_name: Copper 96h treatment 1 replicate 2


title: Copper 48h treatment 2 replicate 3

source_name: Copper 48h treatment 2 replicate 3


title: MLL_03834


title: Copper 48h treatment 2 replicate 1

source_name: Copper 48h treatment 2 replicate 1


title: Cobalt 96h treatment 2 replicate 2

source_name: Cobalt 96h treatment 2 replicate 2


title: Cobalt 96h treatment 1 replicate 3

source_name: Cobalt 96h treatment 1 replicate 3


title: Copper 48h treatment 1 replicate 3

source_name: Copper 48h treatment 1 replicate 3


title: Cobalt 96h treatment 1 replicate 2

source_name: Cobalt 96h treatment 1 replicate 2


title: Cobalt 96h treatment 2 replicate 3

source_name: Cobalt 96h treatment 2 replicate 3


title: Copper 48h treatment 1 replicate 1

source_name: Copper 48h treatment 1 replicate 1


title: Cobalt 96h treatment 2 replicate 1

source_name: Cobalt 96h treatment 2 replicate 1


title: Copper 48h treatment 1 replicate 2

source_name: Copper 48h treatment 1 replicate 2


title: Cobalt 96h treatment 1 replicate 1

source_name: Cobalt 96h treatment 1 replicate 1


title: Cobalt 48h treatment 2 replicate 2

source_name: Cobalt 48h treatment 2 replicate 2


title: Cadmium 96h treatment 1 replicate 3

source_name: Cadmium 96h treatment 1 replicate 3


title: Cadmium 96h treatment 2 replicate 4

source_name: Cadmium 96h treatment 2 replicate 4


title: Cobalt 48h treatment 1 replicate 1

source_name: Cobalt 48h treatment 1 replicate 1


title: Cobalt 48h treatment 2 replicate 1

source_name: Cobalt 48h treatment 2 replicate 1


title: Cobalt 48h treatment 1 replicate 3

source_name: Cobalt 48h treatment 1 replicate 3


title: Cadmium 96h treatment 1 replicate 2

source_name: Cadmium 96h treatment 1 replicate 2


title: Cobalt 96h treatment 2 replicate 4

source_name: Cobalt 96h treatment 2 replicate 4


title: Cadmium 96h treatment 2 replicate 1

source_name: Cadmium 96h treatment 2 replicate 1


title: Cadmium 96h treatment 2 replicate 2

source_name: Cadmium 96h treatment 2 replicate 2


title: Cadmium 48h treatment 2 replicate 2

source_name: Cadmium 48h treatment 2 replicate 2


title: Cobalt 48h treatment 2 replicate 3

source_name: Cobalt 48h treatment 2 replicate 3


title: Cobalt 48h treatment 1 replicate 2

source_name: Cobalt 48h treatment 1 replicate 2


title: Cadmium 96h treatment 1 replicate 1

source_name: Cadmium 96h treatment 1 replicate 1


title: Cadmium 96h treatment 1 replicate 4

source_name: Cadmium 96h treatment 1 replicate 4


title: MLL_04288

source_name: Bone marrow/Blood

source_name: Agilent Euro Female


title: Cadmium 48h treatment 2 replicate 3

source_name: Cadmium 48h treatment 2 replicate 3


title: Cadmium 96h treatment 2 replicate 3

source_name: Cadmium 96h treatment 2 replicate 3


title: Cobalt 96h treatment 1 replicate 4

source_name: Cobalt 96h treatment 1 replicate 4


title: Cadmium 48h treatment 1 replicate 3

source_name: Cadmium 48h treatment 1 replicate 3


title: Cadmium 48h treatment 2 replicate 1

source_name: Cadmium 48h treatment 2 replicate 1


title: Cadmium 48h treatment 1 replicate 2

source_name: Cadmium 48h treatment 1 replicate 2


title: DAs004

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

description: Gene expression data from cultured MCF7 with CD24- phenotype

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Partek GS 6.4 software (St. Louis, MO) using GCRMA normalization algorithm

source_name: cultured MCF7 with CD24- phenotype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Qiagen RNA extraction kit used according to the manufacturer's protocol

treatment_protocol: MCF7 cultured cells with or without retrovirus carrying a constitutivly active RAF1 full length cDNA and xenografts from nude mice.

tag: cell line

tag: modification

value: Cell culture, CD24 -/low


title: DAs001

description: Gene expression data from cultured MCF7 with CD24+ phenotype

source_name: cultured MCF7 with CD24+ phenotype

value: Cell culture, CD24 +/high


title: DAs002


title: Sal014

description: Gene expression data from MCF7 cells harvested from visceral metastases

value: Visceral metastases


title: Sal015

source_name: MCF7 cells harvested from visceral metastases


title: DAs003


title: Cadmium 48h treatment 1 replicate 1

source_name: Cadmium 48h treatment 1 replicate 1


title: Sal013

description: Gene expression data from MCF7 cells transfected with RAF1

source_name: MCF7 cells transfected with RAF1

value: RAF1 transfected MCF7


title: Sal012


title: Sal010

description: Gene expression data from MCF7 cells harvested from lung metastases

value: Lung metastases


title: Sal009

source_name: MCF7 cells harvested from lung metastases


title: Sal006

description: Gene expression data from MCF7 cells

source_name: MCF7 cells

value: Wild type


title: RE 0,2, replicate 3

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

institute: University of Muenster

description: RE 0,2

hyb_protocol: RNA washybridized to the Affymetrix Gene 1.0 ST C. elegans Array using the Affymetrix WT PLUS Reagent Kit using the manufacturer’s recommendations

scan_protocol: Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing:
After scanning, first quality analyses were made using the Affymetrix Expression Console (Affymetrix) and Partek Genomics Suite software (Partek Inc., St. Louis, MO, USA) to check the spike-in controls. Statistical analyses of microarray data were performed using the Partek Genomics Suite. CEL-files (containing raw expression measurements) were imported to Partek GS
The robust multi-array average (RMA) algorithm was used for normalization. The array data were quantile-normalized and log-2 transformed. For each probe, Fisher's least significant difference was tested to statistically compare the difference between the means of the groups´ expression measurements. A false-discovery-rate of ≤ 0.05 was used as a threshold for significance [49]. Only genes with a fold-change of +- 2.0 were regarded as significantly changed in expression

organism: Caenorhabditis elegans

source_name: whole worm

label_protocol: RNA was labelled using the Affymetrix WT PLUS Reagent Kit using the manufacturer’s recommendations

growth_protocol: C. elegans was cultured under standard conditions (NGM agar plates supplemented with E.coli OP50 at 20°C)

extract_protocol: RNA was isolated using the Qiagen RNeasy® Mini Kit. Lysis of the worms was achieved by grinding the pellet in a total of 600 µL lysis buffer under repeated freezing in liquid nitrogen. Further isolation, including an on-column DNAse I digest (Qiagen, Germany), was performed according to the manufacturer’s instructions.

treatment_protocol: Approx. 500 - 1000 young adult worms were incubated for 6h at 20°C in M9 buffer solution containing plant extract and fraction H3 at different concentrations (0.02 to 0.2 mg/mL) or without any treatment (NK).

value: whole worm

value: adult

tag: treatment

value: extract (EtOH 50%) from Combretum mucronatum, 2 mg/mL


title: H3 0,02, replicate 3

description: H3 0,02

value: procyanidin enriched fraction, 0.02 mg/mL


title: H3 2, replicate 2

description: H3 2

value: procyanidin enriched fraction, 2 mg/mL


title: NK, replicate 3

description: NK

value: negative control


title: RE 0,2, replicate 1

description: RE 0,2


title: H3 0,2, replicate 3

description: H3 0,2

value: procyanidin enriched fraction, 0.2 mg/mL


title: Sal004

description: Gene expression data from first generation of MCF7 cells

source_name: first generation of MCF7 cells

value: First generation


title: Sal007

description: Gene expression data from MCF7 cells


title: NK, replicate 2

description: NK


title: Sal005


title: RE 0,2, replicate 2

description: RE 0,2


title: Sal008

description: Gene expression data from first generation of MCF7 cells transfected with RAF1 gene

value: RAF1 transfected first generation


title: H3 0,02, replicate 2

description: H3 0,02


title: H3 2, replicate 3

description: H3 2


title: NK, replicate 1

description: NK


title: H3 0,2, replicate 2

description: H3 0,2


title: H3 0,2, replicate 1

description: H3 0,2


title: H3 2, replicate 1

description: H3 2


title: H3 0,02, replicate 1

description: H3 0,02


title: Normal gastric mucosa, 200394970032_R02C02

status: Public on Aug 30 2017

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

description:
normal gastric mucosa from gastric cancer patient
200394970032_R02C02

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

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing: Idat files were loaded into R and analyzed with R/Bioconductor packages

label: Cy5 and Cy3

source_name: Normal gastric mucosa

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the MagAttract DNA Blood M48 kit (Qiagen, Valencia, CA) and BioRobot M48 automatic extraction equipment (Qiagen)

tag: gender

value: Male

tag: cancer status

value: Case

tag: h. pylori infection

value: Positive


title: Normal gastric mucosa, 200394970074_R03C02

description:
normal gastric mucosa from gastric cancer patient
200394970074_R03C02

value: Past infection


title: Normal gastric mucosa, 200394970074_R02C01

description:
normal gastric mucosa from healthy control
200394970074_R02C01

value: Control


title: Normal gastric mucosa, 200394970074_R02C02

description:
normal gastric mucosa from gastric cancer patient
200394970074_R02C02


title: Normal gastric mucosa, 200394870089_R04C02

description:
normal gastric mucosa from healthy control
200394870089_R04C02


title: Normal gastric mucosa, 200394970032_R05C01

description:
normal gastric mucosa from gastric cancer patient
200394970032_R05C01


title: Normal gastric mucosa, 200394870089_R03C02

description:
normal gastric mucosa from gastric cancer patient
200394870089_R03C02


title: Normal gastric mucosa, 200394870016_R05C02

description:
normal gastric mucosa from healthy control
200394870016_R05C02


title: Normal gastric mucosa, 200394970079_R05C02

description:
normal gastric mucosa from healthy control
200394970079_R05C02


title: Normal gastric mucosa, 200394970049_R05C02

description:
normal gastric mucosa from healthy control
200394970049_R05C02

value: Female


title: Normal gastric mucosa, 200394970032_R03C01

description:
normal gastric mucosa from healthy control
200394970032_R03C01


title: Normal gastric mucosa, 200394970074_R01C01

description:
normal gastric mucosa from gastric cancer patient
200394970074_R01C01


title: Normal gastric mucosa, 200394970079_R06C02

description:
normal gastric mucosa from gastric cancer patient
200394970079_R06C02


title: Normal gastric mucosa, 200394970079_R05C01

description:
normal gastric mucosa from healthy control
200394970079_R05C01


title: Normal gastric mucosa, 200394870016_R02C02

description:
normal gastric mucosa from gastric cancer patient
200394870016_R02C02


title: Normal gastric mucosa, 200394870105_R05C01

description:
normal gastric mucosa from healthy control
200394870105_R05C01


title: Normal gastric mucosa, 200394870089_R05C01

description:
normal gastric mucosa from healthy control
200394870089_R05C01


title: Normal gastric mucosa, 200394870016_R03C01

description:
normal gastric mucosa from gastric cancer patient
200394870016_R03C01


title: Normal gastric mucosa, 200394870016_R03C02

description:
normal gastric mucosa from healthy control
200394870016_R03C02


title: Normal gastric mucosa, 200394870089_R01C01

description:
normal gastric mucosa from gastric cancer patient
200394870089_R01C01


title: Normal gastric mucosa, 200394970049_R02C02

description:
normal gastric mucosa from gastric cancer patient
200394970049_R02C02


title: Normal gastric mucosa, 200394970074_R04C01

description:
normal gastric mucosa from healthy control
200394970074_R04C01


title: Normal gastric mucosa, 200394970032_R04C01

description:
normal gastric mucosa from gastric cancer patient
200394970032_R04C01


title: Normal gastric mucosa, 200394870089_R06C01

description:
normal gastric mucosa from gastric cancer patient
200394870089_R06C01


title: Normal gastric mucosa, 200394970049_R06C02

description:
normal gastric mucosa from gastric cancer patient
200394970049_R06C02


title: Normal gastric mucosa, 200394870016_R04C01

description:
normal gastric mucosa from healthy control
200394870016_R04C01


title: Normal gastric mucosa, 200394970049_R04C02

description:
normal gastric mucosa from healthy control
200394970049_R04C02


title: Normal gastric mucosa, 200394870016_R04C02

description:
normal gastric mucosa from gastric cancer patient
200394870016_R04C02


title: Normal gastric mucosa, 200394970079_R06C01

description:
normal gastric mucosa from gastric cancer patient
200394970079_R06C01


title: Normal gastric mucosa, 200394870105_R06C02

description:
normal gastric mucosa from gastric cancer patient
200394870105_R06C02


title: Normal gastric mucosa, 200394870089_R03C01

description:
normal gastric mucosa from gastric cancer patient
200394870089_R03C01


title: Normal gastric mucosa, 200394870105_R01C02

description:
normal gastric mucosa from gastric cancer patient
200394870105_R01C02


title: Normal gastric mucosa, 200394970079_R03C02

description:
normal gastric mucosa from gastric cancer patient
200394970079_R03C02


title: Normal gastric mucosa, 200394970074_R01C02

description:
normal gastric mucosa from healthy control
200394970074_R01C02


title: Normal gastric mucosa, 200394870105_R05C02

description:
normal gastric mucosa from healthy control
200394870105_R05C02


title: Normal gastric mucosa, 200394970074_R04C02

description:
normal gastric mucosa from healthy control
200394970074_R04C02


title: Normal gastric mucosa, 200394970049_R02C01

description:
normal gastric mucosa from healthy control
200394970049_R02C01


title: Normal gastric mucosa, 200394970079_R01C01

description:
normal gastric mucosa from healthy control
200394970079_R01C01


title: Normal gastric mucosa, 200394970049_R01C01

description:
normal gastric mucosa from gastric cancer patient
200394970049_R01C01


title: Normal gastric mucosa, 200394870016_R06C02

description:
normal gastric mucosa from gastric cancer patient
200394870016_R06C02


title: Normal gastric mucosa, 200394870089_R02C01

description:
normal gastric mucosa from healthy control
200394870089_R02C01


title: Normal gastric mucosa, 200394870105_R04C02

description:
normal gastric mucosa from healthy control
200394870105_R04C02


title: Normal gastric mucosa, 200394970049_R03C02

description:
normal gastric mucosa from gastric cancer patient
200394970049_R03C02


title: Normal gastric mucosa, 200394970079_R04C02

description:
normal gastric mucosa from healthy control
200394970079_R04C02


title: Normal gastric mucosa, 200394970049_R01C02

description:
normal gastric mucosa from healthy control
200394970049_R01C02


title: Normal gastric mucosa, 200394970079_R02C01

description:
normal gastric mucosa from gastric cancer patient
200394970079_R02C01


title: Normal gastric mucosa, 200394870105_R04C01

description:
normal gastric mucosa from healthy control
200394870105_R04C01

value: Negative


title: Normal gastric mucosa, 200394870016_R05C01

description:
normal gastric mucosa from gastric cancer patient
200394870016_R05C01


title: Normal gastric mucosa, 200394870016_R01C02

description:
normal gastric mucosa from healthy control
200394870016_R01C02


title: Normal gastric mucosa, 200394970074_R06C02

description:
normal gastric mucosa from healthy control
200394970074_R06C02


title: Normal gastric mucosa, 200394970074_R03C01

description:
normal gastric mucosa from gastric cancer patient
200394970074_R03C01


title: Normal gastric mucosa, 200394870016_R06C01

description:
normal gastric mucosa from healthy control
200394870016_R06C01


title: Normal gastric mucosa, 200394870105_R03C02

description:
normal gastric mucosa from gastric cancer patient
200394870105_R03C02


title: Normal gastric mucosa, 200394970032_R05C02

description:
normal gastric mucosa from gastric cancer patient
200394970032_R05C02


title: Normal gastric mucosa, 200394970032_R06C02

description:
normal gastric mucosa from healthy control
200394970032_R06C02


title: Normal gastric mucosa, 200394870016_R01C01

description:
normal gastric mucosa from healthy control
200394870016_R01C01


title: Normal gastric mucosa, 200394870105_R01C01

description:
normal gastric mucosa from healthy control
200394870105_R01C01


title: Normal gastric mucosa, 200394970032_R06C01

description:
normal gastric mucosa from healthy control
200394970032_R06C01


title: Normal gastric mucosa, 200394870105_R06C01

description:
normal gastric mucosa from gastric cancer patient
200394870105_R06C01


title: Normal gastric mucosa, 200394970049_R03C01

description:
normal gastric mucosa from healthy control
200394970049_R03C01


title: Normal gastric mucosa, 200394870089_R06C02

description:
normal gastric mucosa from healthy control
200394870089_R06C02


title: Normal gastric mucosa, 200394870089_R04C01

description:
normal gastric mucosa from healthy control
200394870089_R04C01


title: Normal gastric mucosa, 200394870089_R05C02

description:
normal gastric mucosa from gastric cancer patient
200394870089_R05C02


title: Normal gastric mucosa, 200394970032_R03C02

description:
normal gastric mucosa from healthy control
200394970032_R03C02


title: Normal gastric mucosa, 200394870016_R02C01

description:
normal gastric mucosa from gastric cancer patient
200394870016_R02C01


title: WT_P1_Hippo-8

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

description:
WT-8
Sample_2206

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma package in R. DetectionCall function in R lumi package was used to filter out probes with detection value less than 0.01. This resulted in about 13k probes left for downstream analysis.

source_name: Mouse Hippocampus

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

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

value: WT

tag: timepoints


title: WT_P30_Hippo-6

description:
WT-6
Sample_61806


title: KO_P1_Hippo-8

description:
KO-8
Sample_2306

value: KO


title: Normal gastric mucosa, 200394970049_R05C01

description:
normal gastric mucosa from gastric cancer patient
200394970049_R05C01


title: Normal gastric mucosa, 200394970032_R01C01

description:
normal gastric mucosa from gastric cancer patient
200394970032_R01C01


title: Normal gastric mucosa, 200394870105_R03C01

description:
normal gastric mucosa from gastric cancer patient
200394870105_R03C01


title: WT_P30_Hippo-7

description:
WT-7
Sample_62806


title: KO_P30_Hippo-7

description:
KO-7
Sample_61706


title: Normal gastric mucosa, 200394870089_R01C02

description:
normal gastric mucosa from gastric cancer patient
200394870089_R01C02


title: KO_P30_Hippo-3

description:
KO-3
Sample_64706


title: WT_P30_Hippo-3

description:
WT-3
Sample_62706


title: WT_P1_Hippo-5

description:
WT-5
Sample_2106


title: WT_P1_Hippo-4

description:
WT-4
Sample_3106


title: Normal gastric mucosa, 200394970049_R06C01

description:
normal gastric mucosa from healthy control
200394970049_R06C01


title: KO_P30_Hippo-6

description:
KO-6
Sample_61906


title: KO_P1_Hippo-4

description:
KO-4
Sample_2906


title: KO_P30_Hippo-5

description:
KO-5
Sample_62606


title: Normal gastric mucosa, 200394970079_R02C02

description:
normal gastric mucosa from healthy control
200394970079_R02C02


title: Normal gastric mucosa, 200394870105_R02C01

description:
normal gastric mucosa from gastric cancer patient
200394870105_R02C01


title: WT_P30_Hippo-2

description:
WT-2
Sample_62906


title: Normal gastric mucosa, 200394970032_R01C02

description:
normal gastric mucosa from healthy control
200394970032_R01C02


title: WT_P1_Hippo-1

description:
WT-1
Sample_3006


title: KO_P1_Hippo-1

description:
KO-1
Sample_2806


title: KO_P1_Hippo-2

description:
KO-2
Sample_2406


title: Normal gastric mucosa, 200394970049_R04C01

description:
normal gastric mucosa from gastric cancer patient
200394970049_R04C01


title: Normal gastric mucosa, 200394970032_R02C01

description:
normal gastric mucosa from healthy control
200394970032_R02C01


title: Normal gastric mucosa, 200394970079_R03C01

description:
normal gastric mucosa from healthy control
200394970079_R03C01


title: D2.OR BORG Biological Rep 2

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd Rm 2404

institute: Case Western Reserve University

description:
D2.OR cells expressing full length murine BORG
sch16027

hyb_protocol: Following fragmentation, cRNA was hybridized on GeneChip Mouse Gene 2.0 ST Array

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Thermo Fisher)

data_processing:
The data were analyzed with Affymetrix Expression Console, Affymetrix Transcriptome Analysis Console, and Ingenuity Pathway Analysis
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Longitudinal 3D-outgrowth was carried out by plating cells (31,500 cells/cm2) atop solidified Cultrex cushion (600 µl/well; 6 well plate) and grown in complete media supplemented with 5% Cultrex for 7 days.

extract_protocol: Cells were isolated from 3D-culture as and RNA was extracted using TRIzol reagent (Thermo Fisher) according to the manufacturer’s instructions

treatment_protocol: Cells were non-enzymatically isolated using Cultrex 3D-Culture Cell Harvesting Kit (Trevigen) and subsequently prepared for microarray analysis

value: D2.OR breast cancer cells

tag: genotype/variation

value: expressing full length murine BORG


title: Normal gastric mucosa, 200394970079_R01C02

description:
normal gastric mucosa from gastric cancer patient
200394970079_R01C02


title: D2.OR BORG/sgTRIM28 Biological Rep 1

description:
D2.OR cells expressing full length murine BORG with CRISPR/Cas9-mediated knockout of TRIM28
sch16028


title: D2.OR BORG/sgTRIM28 Biological Rep 2

description:
D2.OR cells expressing full length murine BORG with CRISPR/Cas9-mediated knockout of TRIM28
sch16029


title: A549 HCI-2509 1

city: Cologne

first: Iris

middle: Felicitas

last: Macheleidt

address: Kerpenerstr. 63

department: Institute for Pathology

institute: University Hopsital Cologne

description: Gene expression data of A549 treated with 2 µM HCI-2509 for 48 h

hyb_protocol: 4.1µg of biotinylated cDNA were hybridized for 16 hr at 45C on a huGene 2.0 St Array Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner G3000 7G

data_processing: The data were analyzed with Affymetrix ® Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: A549 treated with 2µM HCI-2509 for 48h

label_protocol: Biotinylated cDNA was prepared according the manufacturer´s protocol of Applause® WT-Amp ST System (NuGene®; San Carlos, USA) using 100ng of total RNA

growth_protocol: A549 cells were cultured in DMEM media supplemented with 10% FCS. Cells were seeded out at a density of 1.5 x 10^5.

extract_protocol: RNA was exctraced using the automated isolation kit AS-1280 (Promega) in the Maxwell-16 (Promega) according to the manufacturer´s protocol.

treatment_protocol: The next day, media was changed to either containing DMSO or 2 µM HCI-2509. After 48 h of treatement time, cells were harvested.

tag: organ

value: lung


title: Normal gastric mucosa, 200394970079_R04C01

description:
normal gastric mucosa from gastric cancer patient
200394970079_R04C01


title: A549 Ctrl 3

description: Gene expression data of A549 treated with DMSO

source_name: A549 treated with DMSO as control

value: DMSO


title: Normal gastric mucosa, 200394970074_R05C01

description:
normal gastric mucosa from healthy control
200394970074_R05C01


title: D2.OR Empty Biological Rep 1

description:
D2.OR cells expressing vector control
sch16024

source_name: D2.OR cells expressing vector control

value: control


title: D2.OR Empty Biological Rep 2

description:
D2.OR cells expressing vector control
sch16025


title: A549 HCI-2509 2


title: Normal gastric mucosa, 200394870105_R02C02

description:
normal gastric mucosa from healthy control
200394870105_R02C02


title: Normal gastric mucosa, 200394970074_R05C02

description:
normal gastric mucosa from gastric cancer patient
200394970074_R05C02


title: A549 Ctrl 1


title: A549 Ctrl 2


title: A549 HCI-2509 3


title: AD-SUM159

city: Graz

first: Martin

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

country: Austria

institute: Medical University of Graz

hyb_protocol: Affymetrix GeneChip miRNA 3.0 Array (Cat No. 902017); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0001 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); 2way-Anova Ingenuity IPA – version: 16542223

label_protocol: Afymetrix FlashTaq Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA Arrays v3, P/N 703095 Rev1, (Cat No. HSR10FTA)

growth_protocol: SUM159 cells were grown in Ham`s F12 containing 1 mmol/L L-glutamine, 2 mmol/L HEPES buffer, 5µg/ml  insulin actrapid, 1µg/ml hydrocortisone, 1% penicillin/streptomycin ( (50 units per ml of penicillin, 50μg/ml of streptomycin) and 5% FBS gold. MCF-7 cells were grown in MEM with Earle's salts containing 2 mmol/L L-Glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin and 10% FBS gold. BT474 were cultured in RPMI 1640 (with L-Glutamine), 20% FBS gold, 1% penicillin/streptomycin and 10µg/ml insulin Actrapid.  For Mammospheres, the adherent growing breast cancer cell lines were dissociated into single cells using trypsin/EDTA and 2,000 single cells per well seeded in ultra-low attachment 6-well plates using serum-free MEBM medium supplemented with 1xB27 supplement, 20 ng/ml human epidermal growth factor EGF, 10 ng/ml human basic fibroblast growth factor FGF, 20 IU/ml Heparin and 1% antibiotic/antimycotic solution containing 10,000 units/mL of penicillin, 10,000 µg/mL of streptomycin, and 25 µg/mL of Gibco Amphotericin B).  Cells were incubated in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol: miRNeasy

treatment_protocol: Comparison of standard adherent growing cells compared to mammospheres in ultra-low attachment conditions.

tag: cell type

value: breast cancer (BC) cell line

tag: growth type

value: standard adherent growing cells


title: AD-MCF7


title: D2.OR BORG Biological Rep 1

description:
D2.OR cells expressing full length murine BORG
sch16026


title: Normal gastric mucosa, 200394970032_R04C02

description:
normal gastric mucosa from gastric cancer patient
200394970032_R04C02


title: MS-SUM159

value: mammospheres in ultra-low attachment condition


title: Normal gastric mucosa, 200394970074_R06C01

description:
normal gastric mucosa from gastric cancer patient
200394970074_R06C01

value: Male


title: MS-MCF7


title: thyroid_precancerous_6

city: chengdu

first: qiheng

last: gou

address: southern people street 3rd 17

institute: sichuan university

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar). After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: precancerous lesions

label_protocol: Add 1ug of total RNA to a 1.5-mL microcentrifuge tube. Add 1.2 μL of T7 Promoter Primer. Use nuclease-free water to bring the total reaction volume to 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

value: thyroid

tag: disease state

value: precancerous lesions


title: thyroid_precancerous_147

tag: tissue


title: MS-BT474


title: thyroid_cancer_147

source_name: thyroid cancer

value: thyroid cancer


title: Normal gastric mucosa, 200394870089_R02C02

description:
normal gastric mucosa from healthy control
200394870089_R02C02

value: Control


title: AD-BT474


title: thyroid_cancer_160


title: GECS_N55 gastric normal tissue adjacent to gastric cancer GECS_T55

city: Bucuresti

first: Mihaela

last: Chivu-Economescu

state: Bucuresti

address: Mihai Bravu 285 Ave, sector 3

department: Cellular and Molecular Pathology

country: Romania

institute: Stefan S. Nicolau Institute of Virology

hyb_protocol: We used Agilent Whole Human oligonucleotid arrays type 4x44 k. Hybridization was performed at 65°C, for 17 hours.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray Scanner, which uses a laser  to excite Cy3 labeled RNA to measure fluorescence after the target sample was bound to the substrate.

data_processing: Data were extracted from the images using Agilent Technologies’ Feature Extraction software version 9.1.3.1. Normalized data in Series supplementary file.

source_name: gastric normal tissue

label_protocol: Labeling reaction input for all samples was 1000 ng of total RNA. The method uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3 labeled CTP. For labeling reaction we used Low RNA Input Linear Amplification, one-color kit (Agilent Technologies, Ca) which enable to obtain cRNA labeled with Cy3.

extract_protocol: Total cellular RNA was extracted from tissue samples using the Tri-Reagent protocol (Sigma-Aldrich, St. Louis, MO, USA)

value: gastric normal tissue

tag: tumor


title: GECS_T54 gastric cancer

source_name: gastric cancer

value: gastric cancer

value: AJCC:II; grading G3


title: GECS_T53 gastric cancer

value: AJCC:IVI; grading G3


title: GECS_T55 gastric cancer

value: AJCC:II; grading G1/G2


title: thyroid_cancer_6


title: GECS_T56 gastric cancer

value: AJCC:IV; grading G2/G3


title: GECS_T52 gastric cancer


title: GECS_N53 gastric normal tissue adjacent to gastric cancer GECS_T53


title: GECS_N56 gastric normal tissue adjacent to gastric cancer GECS_T56


title: HER2_MBC102_Resistant

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient102

hyb_protocol: The labeled RNAs were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Slides were scanned with LuxScan 10K Microarray Scanner(CapitalBio, Beijing, China)

data_processing:
Quantile normalization across multiple arrays, log 2 transformation of expression levels, and images were analyzed with GenePix Pro 6.0 software(Axon Instruments, Foster City, CA, USA)
High quality expression values was selected for analysis, then differentially expressed genes were identified.

source_name: serum sample collected from trastuzumab therapy resistant HER2 positive breast cancer

label_protocol: Total RNA extracted from 600ul serum was employed with 100 nmol/L of pCp-DY647 and 15 Units of T4 RNA ligase in a total reaction volume of 20 µL at 16°C overnight.

extract_protocol: Total RNA was extracted from 103 samples with the Plasma RNA Purification Mini Kit (51000, NorgenBiotek Corporation, Canada), following manufacturer's instructions.

value: serum

tag: trastuzumab therapy

value: resistant

tag: tissue type

value: HER2 positive metastatic breast cancer


title: HER2_MBC101_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient101


title: GECS_T50 gastric cancer


title: HER2_MBC103_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient103


title: GECS_N50 gastric normal tissue adjacent to gastric cancer GECS_T50


title: GECS_N51 gastric normal tissue adjacent to gastric cancer GECS_T51


title: GECS_N49 gastric normal tissue adjacent to gastric cancer GECS_T49


title: GECS_T51 gastric cancer


title: GECS_N47 gastric normal tissue adjacent to gastric cancer GECS_T47


title: GECS_T47 gastric cancer


title: GECS_T48 gastric cancer

value: AJCC:II; grading G2


title: HER2_MBC100_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient100


title: GECS_N52 gastric normal tissue adjacent to gastric cancer GECS_T52


title: GECS_N48 gastric normal tissue adjacent to gastric cancer GECS_T48


title: thyroid_precancerous_160


title: HER2_MBC96_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient96


title: HER2_MBC98_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient98


title: HER2_MBC95_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient95


title: GECS_T49 gastric cancer


title: HER2_MBC97_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient97


title: HER2_MBC99_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient99


title: HER2_MBC94_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient94


title: HER2_MBC77_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient77


title: HER2_MBC79_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient79


title: HER2_MBC78_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient78


title: HER2_MBC83_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient83


title: HER2_MBC82_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient82


title: HER2_MBC75_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient75


title: HER2_MBC76_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient76


title: HER2_MBC74_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient74


title: HER2_MBC80_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient80


title: HER2_MBC71_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient71


title: HER2_MBC72_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient72


title: HER2_MBC91_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient91


title: HER2_MBC87_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient87


title: HER2_MBC90_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient90


title: HER2_MBC89_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient89


title: HER2_MBC86_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient86


title: HER2_MBC84_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient84


title: HER2_MBC85_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient85


title: HER2_MBC66_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient66


title: HER2_MBC64_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient64


title: HER2_MBC65_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient65


title: HER2_MBC70_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient70


title: HER2_MBC93_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient93


title: HER2_MBC59_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient59

source_name: serum sample collected from trastuzumab therapy sensitive HER2 positive breast cancer

value: sensitive


title: HER2_MBC61_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient61


title: HER2_MBC60_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient60


title: HER2_MBC62_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient62


title: HER2_MBC73_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient73


title: HER2_MBC81_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient81


title: HER2_MBC92_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient92


title: HER2_MBC88_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient88


title: HER2_MBC54_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient54


title: HER2_MBC52_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient52


title: HER2_MBC50_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient50


title: HER2_MBC67_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient67


title: HER2_MBC68_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient68


title: HER2_MBC69_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient69


title: HER2_MBC63_Resistant

description: HER2 positive metastatic breast cancer_trastuzumab therapy resistant_serum sample_patient63


title: HER2_MBC42_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient42


title: HER2_MBC49_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient49


title: HER2_MBC45_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient45


title: HER2_MBC56_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient56


title: HER2_MBC57_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient57


title: HER2_MBC51_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient51


title: HER2_MBC58_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient58


title: HER2_MBC48_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient48


title: HER2_MBC47_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient47


title: HER2_MBC35_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient35


title: HER2_MBC37_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient37


title: HER2_MBC55_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient55


title: HER2_MBC39_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient39


title: HER2_MBC44_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient44


title: HER2_MBC32_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient32


title: HER2_MBC31_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient31


title: HER2_MBC28_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient28


title: HER2_MBC46_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient46


title: HER2_MBC43_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient43


title: HER2_MBC34_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient34


title: HER2_MBC53_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient53


title: HER2_MBC36_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient36


title: HER2_MBC23_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient23


title: HER2_MBC38_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient38


title: HER2_MBC13_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient13


title: HER2_MBC17_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient17


title: HER2_MBC19_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient19


title: HER2_MBC18_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient18


title: HER2_MBC41_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient41


title: HER2_MBC33_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient33


title: HER2_MBC30_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient30


title: HER2_MBC40_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient40


title: HER2_MBC26_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient26


title: HER2_MBC24_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient24


title: HER2_MBC20_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient20


title: HER2_MBC29_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient29


title: HER2_MBC27_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient27


title: HER2_MBC10_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient10


title: HER2_MBC12_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient12


title: HER2_MBC14_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient14


title: HER2_MBC25_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient25


title: HER2_MBC8_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient8


title: HER2_MBC1_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient1


title: HER2_MBC15_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient15


title: HER2_MBC21_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient21


title: HER2_MBC16_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient16


title: HER2_MBC22_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient22


title: HER2_MBC3_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient3


title: HER2_MBC7_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient7


title: HER2_MBC5_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient5


title: HER2_MBC6_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient6


title: Ptch mutant [090410MJA_moe430-2.0_100795-07]

status: Public on Aug 29 2017

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Academic Medical Center

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
7.090410MJA_moe430-2.0_100795-07.CEL.KO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized. The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. The Affymetrix Mouse Genome 430-2.0 Arrays are used for hybridization.

scan_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for scanning of the chips.

data_processing: The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.

source_name: Ptch mutant_whole colons

label_protocol: The Affymetrix 3’ IVT-Express labeling Kit (#901229) is used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng is used for the labeling experiments.

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

treatment_protocol: Rosa26-CreERT2-Ptch1+/+ and Rosa26-CreERT2-Ptch1fl/fl mice were intraperitoneally injected with 1 mg tamoxifen for 5 consecutive days. At day 12 animals were sacificed and colons were isolated.

tag: strain  background

value: mixed C57BL/6  X Balb/c

value: Patched1 knockout

value: whole colons

tag: timepoint

value: 12 days after the start of the induction with tamoxifen


title: HER2_MBC11_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient11


title: HER2_MBC2_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient2


title: HER2_MBC9_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient9


title: Ptch wildtype [090410MJA_moe430-2.0_100795-08]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
8.090410MJA_moe430-2.0_100795-08.CEL.WT

source_name: Ptch wildtype_whole colons

value: Patched1 wildtype


title: HER2_MBC4_Sensitive

description: HER2 positive metastatic breast cancer_trastuzumab therapy sensitive_serum sample_patient4


title: Ptch mutant [090410MJA_moe430-2.0_100795-04]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
4.090410MJA_moe430-2.0_100795-04.CEL.KO


title: Ptch wildtype [090410MJA_moe430-2.0_100795-10]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
10.090410MJA_moe430-2.0_100795-10.CEL.WT


title: HCT116 p53 minus 2Gy irradiation replicate 3

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description:
HCT116 p53 minus were irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.
HCT116_p53minus_2Gy_rep3

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Colorectal cancer HCT116 p53 minus cells non-irradiated

label_protocol: 1 μg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion). cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: Cells were cultured in RPMI-1640 cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2mM glutamine (Gibco), 100 IU/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA MiniPrep kit (ZYMO RESEARCH) according to the manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Inhibition of p53 gene expression in HCT116, a human colorectal cancer cell line was done using RNA interference (shRNA). The cell line that showed greatest reduction (85-90%) of p53 expression were treated with single (2 Gy) or fractionated (5 x 2Gy) doses of ionizing radiation.

tag: cell line/genotype

value: HCT116 p53 minus

tag: origin

value: Colorectal cancer

value: Control

source_name: Colorectal cancer HCT116 p53 minus cells irradiated with 2 Gy

value: single dose of 2Gy


title: Ptch wildtype [090410MJA_moe430-2.0_100795-05]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
5.090410MJA_moe430-2.0_100795-05.CEL.WT


title: HCT116 p53 minus 2x5Gy irradiation replicate 3

description:
HCT116 p53 minus were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.
HCT116_p53minus_5x2Gy_rep3

tag: treatment

source_name: Colorectal cancer HCT116 p53 minus cells irradiated with 5x2 Gy

value: fractionated dose of 5x2Gy


title: HCT116 wild type 5x2Gy irradiation replicate 3

description:
HCT116 wild type were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.
HCT116_wt_5x2Gy_rep3

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Whole Human Genome Microarrays 4x44k (Agilent) for 17 hours at 65°C using HS 400 hybridization station (Tecan).

source_name: Colorectal cancer HCT116 cells non-irradiated

extract_protocol: Total RNA was isolated from harvested cells using Quick-RNA MiniPrep kit (ZYMO RESEARCH) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Cell were treated with single (2 Gy) or fractionated (5x2 Gy) doses of ionizing radiation

tag: cell line

source_name: Colorectal cancer HCT116 cells irradiated with 5x2 Gy


title: Ptch wildtype [090410MJA_moe430-2.0_100795-09]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
9.090410MJA_moe430-2.0_100795-09.CEL.WT


title: HCT116 p53 minus 2x5Gy irradiation replicate 2

description:
HCT116 p53 minus were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.
HCT116_p53minus_5x2Gy_rep2


title: HCT116 wild type 5x2Gy irradiation replicate 1

description:
HCT116 wild type were irradiated with fractionated 5 x 2Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.
HCT116_wt_5x2Gy_rep1


title: Ptch mutant [090410MJA_moe430-2.0_100795-01]

description:
Gene expression data from colons that were isolated 12 days after activating the Hedgehog pathway
1.090410MJA_moe430-2.0_100795-01.CEL.KO