title: Testis_trcp(1;14)_1

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

department: Animal Genetics

institute: INRA

description: Gene expression analysis in infertile boars

hyb_protocol: Microarray hybridation oven according to manufacturer's instruction

scan_protocol: Image analysis using the Feature Extraction software (Agilent).

data_processing: Data were filtered to keep only spots of sufficient intensity and quality for at least 2 out of 3 technical replicates. Intensity values were log-transformed and normalized by the quantile normalization method. Differential analysis was then performed using the Limma package (Bioconductor). Threshold parameters were defined as follow: maximal adjusted p-value (Benjamini& Hochberg) of 0.01 and minimal log-fold change (lfc) of 2.

organism: Sus scrofa

source_name: Testicular biopsy

label_protocol: Label, hybridation , scan and data extraction were performed by the GeT-Biopuces platform following manufacturer's intruction. Samples were then marked by Cyanine-3 fluorochrome and converted in cDNA before hybridization on the 60K customized chip from Agilent (Voillet et al., 2014).

extract_protocol: Total RNA from three independant testicular biopsies was extracted  using the Nucleospin RNA kit (Macherey-Nagel). Quantity and quality of RNA was evaluated by NanoDrop dosage and Bioanalyser analysis (Agilent Technologies).

tag: semen parameters

value: Oligo-astheno-teratospermic

tag: chromosomal status


title: wild type HBE_No2

status: Public on Jun 30 2016

type: RNA

city: Nanjing

first: Xiaobo

last: Li

address: Dingjiaqiao 87

country: China

institute: Southeast University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant miRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated miRNAs.

molecule: total RNA

organism: Homo sapiens

source_name: HBE cells

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: cell line

value: human bronchial epithelial (HBE) cell line

tag: treatment

value: control


title: Nucleus pulposus_degenerated_2_miRNA

city: Xi'an

first: Hai-Qiang

last: Wang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

description:
Sample name: R2
Same sample as in GSM1354770.

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA microRNA Array, 7th generation (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.The intensity of green signal is calculated after background subtraction and four replicated spots of each probe on the same slide have been averaged. We use Median Normalization Method to obtain Normalized Data, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

source_name: Nucleus pulposus tissue, degenerated

label_protocol: The miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) was used according to the manufacturer’s guideline for miRNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity were measured by using NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: All the specimens were collected from intervertebral discs of cadaveric donors or patients within 3 hours after anatomy or surgery, respectively. Following rinse with phosphate-buffered saline, the nucleus pulposus tissue was carefully collected under stereoscopic microscope.

tag: tissue

value: nucleus pulposus

tag: condition

value: degenerated

tag: idd related disease

value: intervertebral disc herniation

tag: degeneration grading

value: V

tag: disc level

tag: gender

value: male

tag: age

value: 38 years


title: PPCD Affected Individual 1

type: genomic

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

country: USA

institute: Stein Eye Institute, UCLA

description: Affected 1

hyb_protocol: As per manufacturer's instructions. Protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling for Blood Cells or Tissues - Version 6,3, October 2010.

scan_protocol: Agilent Feature Extraction V 11.5.1.

data_processing: Agilent CytoGenomics 3.0.1.1 software. Genome build hg19. Default Analysis Method - CGH+SNP v2. Normalization: GC correction and Diploid Peak Centralization.

molecule: genomic DNA

source_name: blood leukocytes, affected

extract_protocol: Genomic DNA was isolated using the FlexiGene DNA kit as per manufacturer's recommendations.

tag: disease status

value: posterior polymorphous corneal dystrophy 1 (PPCD1)

tag: cell type

value: blood leukocytes

value: female

source_name: Human reference DNA (Agilent 5190-4371)

tag: sample type

value: reference


title: Nucleus pulposus_control_5_miRNA

description:
Sample name: N5
Same sample as in GSM1354768.

source_name: Nucleus pulposus tissue, normal

value: no

value: I

value: 52 years


title: Testis_Oligospermic_3

country: France

value: Oligospermic


title: Testis_Oligospermic_2


title: Testis_Control_3

value: Control


title: 12hGX_7.8pM_rep2

city: Oslo

first: Knut Erik

last: Tollefsen

address: Gaustadallèen 21

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: Gene expression after 12 h in 7.8 pM emamectin benzoate exposed Daphnia magna replicate 2

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 50 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies).

growth_protocol: OECD Test Guideline 202

extract_protocol: Total RNA was extracted from pooled Daphnia using Zymo Tissue&Insect RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/280>1.8, yield >50 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Daphnia magna were exposed 5 concentrations of emamectin benzoate for 12h. After exposure, the organisms were pooled and sampled in RNALater (Qiagen, Hilden, Germany) and stored in -80°C until further use.

value: Whole organism

tag: developmental stage

value: <24h juvenile


title: Nucleus pulposus_control_4_miRNA

description:
Sample name: N4
Same sample as in GSM1354767.

value: nucleus pulposus

value: control

value: 43 years


title: 12hGX_7.8pM_rep1

source_name: Gene expression after 12 h in 7.8 pM emamectin benzoate exposed Daphnia magna replicate 1


title: 12hGX_Control_rep4

source_name: Gene expression after 12 h in control Daphnia magna repicate 4


title: Nucleus pulposus_control_1_miRNA

description:
Sample name: N1
Same sample as in GSM1354764.

value: 33 years


title: 12hGX_Control_rep3

source_name: Gene expression after 12 h in control Daphnia magna replicate 3


title: Nucleus pulposus_control_3_miRNA

description:
Sample name: N3
Same sample as in GSM1354766.

value: male

value: 41 years


title: Nucleus pulposus_control_2_miRNA

description:
Sample name: N2
Same sample as in GSM1354765.

value: 35 years


title: Testis_Control_1


title: Testis_trcp(1;14)_3

value: Oligo-astheno-teratospermic


title: Testis_Oligospermic_1


title: Testis_trcp(1;14)_2


title: 12hGX_Control_rep2

source_name: Gene expression after 12 h in control Daphnia magna replicate 2


title: Testis_Control_2


title: 12hGX_Control_rep1

source_name: Gene expression after 12 h in control Daphnia magna replicate 1


title: 4T1_lung metastasis foci_rep2

status: Public on Jun 29 2016

city: Córdoba

first: Cristobal

last: Fresno

state: Córdoba

address: Av. Armada Argentina 3555

department: UA AREA CS. SOC. Y HUM

country: Argentina

institute: CONICET-Universidad Católica de Córdoba

description: Biological replicate 2 of 4. 30 days old lung metastasis foci from 4T1-SCR-bearing mouse

hyb_protocol: 60 pmol of reference aRNA (pool of all samples) labeled with Alexa 647 and 60 pmol of each experimental sample aRNA labeled with Alexa 555 were diluted in  50 ul of hybridization buffer (5x SSC , 50% formamide, 0,1% SDS , 0.01% Salmon Sperm DNA ). The mix was heated for 2 minutes at 95°C and then hibridized to microarrays for 16 hours at 42°C. After hybridization, slides were washed sequential

scan_protocol: An Axon Genepix 4000b array scanner was used to scan the arrays and detect the presence, location, and amount of bound target on the probe array. Raw data were collected using Genepix Pro 6.1software.

data_processing:
Expression levels for each chip where within-normalized using limma with the following parameters: “printtiploess” method, weighted according to Genepix Pro 6.1 software values, “normexp” background correction and an intensity offset of 50.
Only gene-coding probes with valid Entrez Gene IDs according to manufacturer annotation and present in The Database for Annotation, Visualization and Integrated Discovery (DAVID) and above noise levels were kept for further analysis. BetweenArrayNormalization:scale.

label: Alexa 647

organism: Mus musculus

source_name: Total RNA from pooled samples

label_protocol: Total RNA amplification and cRNA labeling was performed using SuperScript Indirect RNA Amplification System (Invitrogen)

growth_protocol: Stably transduced 4T1 cells were cultured on plastic dishes in RPMI medium supplemented with 10% (v/v) FBS (Natocor, Cordoba, Argentina)  and 250 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA). 200.000 cells were injected in the mammary fat pad of 6-8 weeks old female Balb/c mice.

extract_protocol: Total RNA was obtained from 2 days-old tumors or 30 days old 4T1-SCR lung foci using the RNeasy mini kit (Qiagen).

treatment_protocol: 4T1 cell were transduced with a pRNATin-H1.4 lentiviral vector (Genscript) encoding a siRNA targeted to the 437bp to 455bp sequence of murine SPARC mRNA or a scramble sequence. The lentiviarl vector were generated according to GenScript guidelines, using ViraPower Packaging mix (Invitrogen). The cells were selected with 500 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA). The stable clone 4T1-C18 was obtained by limiting dilution of the stable cell culture bulks.

tag: passage

tag: strain

value: BALB/c

value: Female

tag: tumor stage

value: 30 days old lung foci

tag: origin of cells

value: ATCC® CRL-2539™

label: Alexa 555

source_name: Lung metastasis foci of 4T1-SCR tumor-bearing mouse


title: 4T1_control primary tumor_rep4

description: Biological replicate 4 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a scramble sequence.

tag: cell line

value: 2 days-old tumors

source_name: Primary tumors generated from a 4T1 cell line stably expressing a scramble sequence


title: 4T1_lung metastasis foci_rep1

description: Biological replicate 1 of 4. 30 days old lung metastasis foci from 4T1-SCR-bearing mouse


title: 4T1_lung metastasis foci_rep3

description: Biological replicate 3 of 4. 30 days old lung metastasis foci from 4T1-SCR-bearing mouse


title: 4T1_SPARC knock down_rep4

description: Biological replicate 4 of 4. 4T1 cells stably expressing a siRNA against SPARC, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a siRNA against SPARC. Hybridization day 3

extract_protocol: Total RNA was obtained from cells using the RNeasy mini kit (Qiagen).

tag: origin

tag: treatment protocol

value: 4T1 cell were transduced with a pRNATin-H1.4 lentiviral vector (Genscript) encoding a siRNA targeted to the 437bp to 455bp sequence of murine SPARC mRNA, which was generated according to GenScript guidelines, using ViraPower Packaging mix (Invitrogen). The cells were selected with 500 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA). The stable clone 4T1-C18 was obtained by limiting dilution of the stable cell culture bulks.

tag: growth protocol

value: 4T1-C18 cells were cultured on plastic dishes in RPMI medium supplemented with 10% (v/v) FBS (Natocor, Cordoba, Argentina)  and 250 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA).

value: Cells were cultured on plastic dishes in RPMI medium supplemented with 10% (v/v) FBS (Natocor, Cordoba, Argentina)  and 250 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA).


title: 4T1_control primary tumor_rep2

description: Biological replicate 2 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a scramble sequence.


title: 4T1_control_rep1

description: Biological replicate 1 of 4. 4T1 cells stably expressing a scramble sequence, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a scramble sequence. Hybridization day 1

value: 4T1 cell were transduced with a pRNATin-H1.4 lentiviral vector (Genscript) carrying the scramble sequence, which was generated according to GenScript guidelines, using ViraPower Packaging mix (Invitrogen). The cells 4T1-SCR were selected with 500 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA).

value: 4T1-SCR cells were cultured on plastic dishes in RPMI medium supplemented with 10% (v/v) FBS (Natocor, Cordoba, Argentina)  and 250 µg/ml Geneticin® (Invitrogen, Carlsbad, CA, USA).


title: 4T1_control_rep4

description: Biological replicate 4 of 4. 4T1 cells stably expressing a scramble sequence, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a scramble sequence. Hybridization day 3


title: 4T1_SPARC knock down_rep2

description: Biological replicate 2 of 4. 4T1 cells stably expressing a siRNA against SPARC, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a siRNA against SPARC. Hybridization day 2


title: 4T1_control_rep3

description: Biological replicate 3 of 4. 4T1 cells stably expressing a scramble sequence, harvested after 25 passages.


title: 4T1_control_rep2

description: Biological replicate 2 of 4. 4T1 cells stably expressing a scramble sequence, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a scramble sequence. Hybridization day 2


title: 4T1_control primary tumor_rep3

description: Biological replicate 3 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a scramble sequence.


title: 4T1_lung metastasis foci_rep4

description: Biological replicate 4 of 4. 30 days old lung metastasis foci from 4T1-SCR-bearing mouse


title: 4T1_SPARC knock down primary tumor_rep4

description: Biological replicate 4 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a siRNA against SPARC.

source_name: Primary tumors generated from a 4T1 cell line stably expressing a siRNA against SPARC


title: 4T1_control primary tumor_rep1

description: Biological replicate 1 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a scramble sequence.


title: 4T1_SPARC knock down primary tumor_rep3

description: Biological replicate 3 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a siRNA against SPARC.


title: 4T1_SPARC knock down_rep1

description: Biological replicate 1 of 4. 4T1 cells stably expressing a siRNA against SPARC, harvested after 25 passages.

source_name: 4T1 cell line stably expressing a siRNA against SPARC. Hybridization day 1


title: 4T1_SPARC knock down primary tumor_rep2

description: Biological replicate 2 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a siRNA against SPARC.


title: 4T1_SPARC knock down primary tumor_rep1

description: Biological replicate 1 of 4. 2 days-old primary tumor generated from 4T1 cells stably expressing a siRNA against SPARC.


title: 35D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_500mM_NaCl_replicate_3

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

description: Gene expression for 1 week 500 mM NaCl salt-acclimated Yukon rosette leaves. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G2514F; DesignID 031554) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for AgilentHD_GX for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 031554_D_F_20101207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Eutrema salsugineum

source_name: 35-day-old hydroponic grown rosette leaves, 1-week 500 mM NaCl salt-acclimated

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

growth_protocol: For cold acclimation experiments, seeds of Arabidopsis thaliana accessions were stratified at 4°C for 1 week and grown on soil at 20°C for 3 weeks under 8 hrs light/16 hrs dark cycle at growth chamber. Seedlings plants were continued grown at 20°C for 2 weeks under 16 hrs light/8 hrs dark cycle at greenhouse. Tuva seeds were stratified at 4°C for 1 week and grown on soil at 20°C for 8 weeks under 16 hrs light/8 hrs dark cycle at greenhouse. For salt stress experiments, seeds of Col-0 and Yukon accessions were  stratified at 4°C for 1 week and grown at 20°C on non sterile hydroponic trays for 3 weeks and 26 days, respectively  under 16 hrs light/8 hrs dark cycle at greenhouse.

extract_protocol: Total RNA was isolated and on-column DNA digestion was performed with the RNeasy Plant mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: For the cold acclimation experiments, soil grown 6-week-old Arabidopsis plants were cold acclimated at 4°C for 2 weeks. Soil grown 8-week-old Tuva plants were cold acclimated at 4°C for 2 weeks. For the salt stress experiments, both hydroponic grown  24-day-old Col-0 and 29-day-old Yukon plants were salt acclimated at 200 mM NaCl for one week. Additionally, hydroponic grown 35-day-old Yukon plants were salt acclimated at 500 mM NaCl for one week. Control plants were 3-week-old for Col-0 and 26-day-old for Yukon and continue grown for additional one week before sampled for RNA extraction.

tag: tissue

value: rosette leaves


title: 35D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_500mM_NaCl_replicate_2


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma10

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

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

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software V2011.1 was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

value: Male

tag: location

value: Mt

tag: tumor (clinical diagnosis) uicc 6th

tag: n

tag: m

tag: cstage

value: III


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma8

tag: gender

tag: age

value: IIB


title: 33D_old_hydroponic_grown_rosette_leaves_control_replicate_3

description: Gene expression for contorl Yukon rosette leaves. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

source_name: 33-day old hydroponic grown rosette leaves control plants


title: 29D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_3

description: Gene expression for 1 week 200 mM NaCl salt-acclimated Yukon rosette leaves. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

source_name: 29-day-old hydroponic grown rosette leaves, 1-week 200 mM NaCl salt-acclimated


title: 29D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_2


title: A21

city: Darlinghurst

first: Stuart

last: Tangye

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

description: naïve CD4+ T cells NEMO X-linked hemizygous loss of function mutation #1

hyb_protocol: 3 µg fragmented, biotin labelled ss-cDNA was hybridised to Affymetrix Human Gene Array version 2.1ST. Samples were hybridised to arrays for 16 hours at 45°C in the Affymetrix GeneTitan Instrument

scan_protocol: Arrays were washed and scanned on the Affymetrix GeneTitanand Affymetrix GC3000 scanner instrument as per manufacturers protocol

data_processing: R/Bioconductor

label: biotin

label_protocol: 1 ng of total RNA was used as input for the amplification and labelling of samples using the Affymetrix WT Pico Kit

growth_protocol: Analysis was performed on freshly isolated primary human immune cells (ie no culture)

extract_protocol: RNA was isolated from sorted populations of human naïve and memory CD4+ T cells using QIAGEN RNA isolation kits.

treatment_protocol: Analysis was performed on freshly isolated primary human immune cells (ie no treatment was performed)

tag: cell type

value: CD4+ T cells


title: A22

description: naïve CD4+ T cells NEMO X-linked hemizygous loss of function mutation #2


title: 29D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_1


title: A16

description: naïve CD4+ T cells IL-12RB1 biallelic loss of function mutation #2


title: 4T1_SPARC knock down_rep3

description: Biological replicate 3 of 4. 4T1 cells stably expressing a siRNA against SPARC, harvested after 25 passages.

tag: passage


title: A18

description: naïve CD4+ T cells IFNGR1 heterozygous loss of function mutation #1


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma7

value: Ut


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma9

value: IVB


title: A23

description: naïve CD4+ T cells IL21R homozygous loss of function mutation


title: A17

description: naïve CD4+ T cells BTK (Bruton's tyrosine kinase) X-linked hemizygous mutation #1


title: 35D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_500mM_NaCl_replicate_1


title: 33D_old_hydroponic_grown_rosette_leaves_control_replicate_1


title: A24

description: naïve CD4+ T cellsCD40L X-linked hemizygous loss of function mutation #2


title: 33D_old_hydroponic_grown_rosette_leaves_control_replicate_2


title: A20

description: naïve CD4+ T cells CD40L X-linked hemizygous loss of function mutation #1


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma6


title: A19

description: Heathy control naïve CD4+ T cells #3

source_name: Heathy control naïve CD4+ T cells


title: A11

description: naïve CD4+ T cells STAT1 heterozygous loss of function mutation #1


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma4


title: A14

description: naïve CD4+ T cells IFNGR1 heterozygous loss of function mutation #2


title: A15

description: naïve CD4+ T cells ICOS homozygous mutation #1


title: A13

description: naïve CD4+ T cells IL-12RB1 biallelic loss of function mutation #1


title: A8

description: naïve CD4+ T cells BTK (Bruton's tyrosine kinase) X-linked hemizygous mutation #2


title: A9

description: naïve CD4+ T cells IL-10R bi-allelic (compund heterozygous) loss of function mutation #1


title: A4

description: naïve CD4+ T cells STAT1 heterozygous loss of function mutation #2


title: A10

description: naïve CD4+ T cells Heathy control #2

source_name: naïve CD4+ T cells Heathy control


title: 24D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_3

description: Gene expression for 1 week 200 mM NaCl salt-acclimated Col-0 rosette leaves. RNA was hybridized on  Agilent Arabidopsis thaliana expression array

organism: Arabidopsis thaliana

source_name: 24-day-old hydroponic grown rosette leaves, 1-week 200 mM NaCl salt-acclimated


title: 24D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_1


title: 4W_old_hydroponic_grown_rosette_leaves_control_replicate_3

description: Gene expression for contorl Col-0 rosette leaves. RNA was hybridized on  Agilent Arabidopsis thaliana expression array

source_name: 4-week-old hydroponic grown rosette leaves, control plants


title: A3

description: naïve CD4+ T cells STAT3 heterozygous dominant negative mutation #1


title: A6

description: naïve CD4+ T cells STAT3 heterozygous dominant negative mutation #2


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma2

value: Ce


title: A5

description: Heathy control naïve CD4+ T cells #4


title: A2

description: naïve CD4+ T cells STAT1 heterozygous gain of function mutation #1


title: 24D_old_hydroponic_grown_rosette_leaves_1W_acclimated_at_200mM_NaCl_replicate_2


title: 4W_old_hydroponic_grown_rosette_leaves_control_replicate_1


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma5

value: Lt


title: TSCM-enriched Donor#4

city: Bethesda

first: Luca

last: Gattinoni

address: 9000 Rockville Pike

department: Experimental Transplantation and Immunology Branch

institute: NCI - National Cancer Institute

description: TSCM-enriched cell culture from Donor#4

hyb_protocol: Samples were hybridized to WT Human Gene 1.0 ST arrays using Affymetrix hybridization kit materials, according to the manufacturrer's instructions. Sample cocktails were heated at 99°C for 5 minutes, then 45°C for 5 minutes, centrifuged at max speed for 1 minute. Eighty microliters of hybridization solution was transferred to each array, and hybridized 17 hours at 45°C at 60rpm. Fluidics washing protocol used was FS450_0007.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
In all processing steps, samples were processed at the same time as a single batch. The obtained Affymetrix .CEL files were imported into the Genomics Suite software (Partek, St. Louis, MO, USA). The imported data were analyzed at the gene-level, with exons summarized to genes, using the median expression of all the exons of a gene. Background correction was carried out using the robust multiarray average (RMA) algorithm, with quantile normalization, median polish probe summarization, and log2 probe transformation. Differentially expressed genes (DEGs) were identified by Two-Way ANOVA.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: TSCM-enriched

label_protocol: WT expression kit (Ambion), WT Terminal Labeling Kit (Affymetrix), according to the manufatcturer's instructions

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from lymphocyte-enriched apheresis blood (provided by the NIH Blood Bank) according to standard techniques. For TSCM-enriched cells generation,  CD8+CD62L+CD45RA+ T cells enriched by serial positive selection with Streptamer-Fab technology (Stage Cell Therapeutics, Göttingen, Germany) were stimulated with anti-CD3/CD28 beads (ratio 1:1) in the presence of IL-7 (5ng/ml), IL-21 (30ng/ml) and TWS119 (glycogen synthase-3β inhibitor, 5uM). Two days after the initial stimulation, cells were transduced with PG-13-CD19-H3 (CD19 CAR) retroviral vector for two consecutive days (day 2 and 3). Beads were removed on day 4 and cells were then expanded in culture until day 9 to meet dose requirement.  CD19 CAR Standard cell cultures were obtained by stimulating PBMCs with the anti-CD3 monoclonal antibody OKT3 (50ng/mL) and IL-2 (40IU/mL). Two days after the stimulation, cells were transduced with PG-13-CD19-H3 (CD19 CAR) retroviral vector for two consecutive days (day 2 and 3) and then cultured in complete media containing 300IU/mL IL-2 for 9 days.  Peripheral blood mononuclear cells (PBMCs) were isolated from lymphocyte-enriched apheresis blood (provided by the NIH Blood Bank) according to standard techniques. For TSCM-enriched cells generation,  CD8+CD62L+CD45RA+ T cells enriched by serial positive selection with Streptamer-Fab technology (Stage Cell Therapeutics, Göttingen, Germany) were stimulated with anti-CD3/CD28 beads (ratio 1:1) in the presence of IL-7 (5ng/ml), IL-21 (30ng/ml) and TWS119 (glycogen synthase-3β inhibitor, 5uM). Two days after the initial stimulation, cells were transduced with PG-13-CD19-H3 (CD19 CAR) retroviral vector for two consecutive days (day 2 and 3). Beads were removed on day 4 and cells were then expanded in culture until day 9 to meet dose requirement.  CD19 CAR Standard cell cultures were obtained by stimulating PBMCs with the anti-CD3 monoclonal antibody OKT3 (50ng/mL) and IL-2 (40IU/mL). Two days after the stimulation, cells were transduced with PG-13-CD19-H3 (CD19 CAR) retroviral vector for two consecutive days (day 2 and 3) and then cultured in complete media containing 300IU/mL IL-2 for 9 days.

extract_protocol: miRNeasy Mini Kit (Qiagen), according to manufatcturer's instructions

treatment_protocol: CD8+CD62L+CD45RA+ enriched T cells from healthy donor  stimulated with anti-CD3/CD28 beads in the presence of IL-7, IL-21 and TWS119, transduced with CD19 CAR retroviral vector and then expanded in culture for 9 days

tag: cell population

value: CD8+CD62L+CD45RA+ T cells

tag: donor


title: A7

description: naïve CD4+ T cells STAT1 heterozygous gain of function mutation #2


title: Standard Donor#3

description: CD19 CAR Standard cell culture from Donor#3

source_name: Standard PBMCs

treatment_protocol: PBMCs from healthy human donor stimulated with the anti-CD3 monoclonal antibody OKT3 and IL-2, transduced with CD19 CAR retroviral vector and cultured in complete media containing IL-2

value: Peripheral blood mononuclear cells (PBMCs)


title: TSCM-enriched Donor#1

description: TSCM-enriched cell culture from Donor#1


title: Standard Donor#1

description: CD19 CAR Standard cell culture from Donor#1


title: A1

description: Heathy control naïve CD4+ T cells #1


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma1


title: TSCM-enriched Donor#3

description: TSCM-enriched cell culture from Donor#3


title: 4W_old_hydroponic_grown_rosette_leaves_control_replicate_2


title: Standard Donor#4

description: CD19 CAR Standard cell culture from Donor#4


title: Genomic DNA from biopsy of esophageal squamouse cell carcinoma3


title: HNF6KO_ZT10_Liver_Microarray 2

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

description: Gene expression data from HNF6KO ZT10 mouse liver

hyb_protocol: Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Array images were captured on a GCS3000 laser scanner (Affymetrix) and analyzed by the Penn Microarray Core using Partek Genomics Suite.

data_processing: Data analysis was done using BioConductor packages  (Oligo)

source_name: liver

label_protocol: GeneChIP WT terminal labeling

growth_protocol: C57BL/6 mice were grown on normal chow on normal light/dark schedule

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

treatment_protocol: no specific treatment was performed

tag: genotype/variation

value: liver

tag: strain

value: 12 weeks

tag: Sex

value: male


title: WT_ZT10_Liver_Microarray 3

description: Gene expression data from WT ZT10 mouse liver

value: WT


title: HNF6KO_ZT10_Liver_Microarray 1


title: WT_ZT10_Liver_Microarray 4


title: WT_ZT10_Liver_Microarray 1


title: HNF6KO_ZT10_Liver_Microarray 3


title: HNF6KO_ZT10_Liver_Microarray 4


title: WT_ZT10_Liver_Microarray 2


title: Liver from streptozotocin/bezafibrate-treated mice, biological replicate 4

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
STZ_BEZ_46
Type I diabetes induced by streptozotocin.
Gene expression data from liver tissue of streptozotocin/bezafibrate-treated mice, biological replicate 4.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol (GeneChip Scanner 3000 7G).

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation.

source_name: Liver tissue from streptozotocin/bezafibrate-treated mice

label_protocol: WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Animals housed under spf conditions.

extract_protocol: miRNeasy Mini Kit (Qiagen) including DNase treatment.

treatment_protocol: To induce type 1 diabetes, 65 mg/kg of streptozotocin (STZ) was injected i.p. into 10-16 weeks-old mice on 5 consecutive days while respective controls were mock-injected with citrate buffer. BEZ treatment for 8 weeks started 2 weeks after STZ injection. BEZ (B7273, Sigma-Aldrich) was mixed to standard mouse chow in 0.25% or 0.5% (w/w) concentration (BEZ food) by the supplier (R/M-H, Ssniff, Germany); control animals received untreated placebo food (standard diet, SD food).

tag: strain/background

value: wildtype

value: 5-6 months

tag: treatment

value: streptozotocin/bezafibrate


title: Liver from streptozotocin/bezafibrate-treated mice, biological replicate 3

description:
STZ_BEZ_45
Type I diabetes induced by streptozotocin.
Gene expression data from liver tissue of streptozotocin/bezafibrate-treated mice, biological replicate 3.

tag: tissue


title: Liver from streptozotocin/bezafibrate-treated mice, biological replicate 5

description:
STZ_BEZ_49
Type I diabetes induced by streptozotocin.
Gene expression data from liver tissue of streptozotocin/bezafibrate-treated mice, biological replicate 5.


title: Liver from streptozotocin/bezafibrate-treated mice, biological replicate 2

description:
STZ_BEZ_44
Type I diabetes induced by streptozotocin.
Gene expression data from liver tissue of streptozotocin/bezafibrate-treated mice, biological replicate 2.


title: 585A1-ActivinA_100

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description:
Sample 8
Human iPSC line (585A1) cultured with 100 ng/ml Activin A for 7 days.

hyb_protocol: Manufacturer's protocol.

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX12.1. Signals were normalized to the 75th percentile.

source_name: iPSCs, 4 ng/ml bFGF + 100 ng/ml Activin A, 7 days

label_protocol: Manufacturer's protocol.

growth_protocol: The human induced pluripotent stem cells were cultured on SNL-feeder cells with Primate ESC medium (ReproCELL) supplemented with basic FGF and Activin A at 37 ºC in a humidified incubator with 5% CO2. In Samples 1-4, the cells were cultured with different concentrations of basic FGF (0, 4, 20, and 100 ng/ml) and without Activin A. In Samples 5-8, the cells were cultured with 4 ng/ml basic FGF and with different concentrations of Activin A (0, 4, 20, and 100 ng/ml).

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: induced pluripotent stem cells

value: 4 ng/ml basic FGF (bFGF) + 100 ng/ml Activin A for 7 days


title: 585A1-ActivinA_0

description:
Sample 5
Human iPSC line (585A1) cultured with no Activin A for 7 days.

source_name: iPSCs, 4 ng/ml bFGF + 0 ng/ml Activin A, 7 days

value: 4 ng/ml basic FGF (bFGF) + 0 ng/ml Activin A for 7 days


title: 585A1-ActivinA_4

description:
Sample 6
Human iPSC line (585A1) cultured with 4 ng/ml Activin A for 7 days.

source_name: iPSCs, 4 ng/ml bFGF + 4 ng/ml Activin A, 7 days

value: 4 ng/ml basic FGF (bFGF) + 4 ng/ml Activin A for 7 days


title: 585A1-ActivinA_20

description:
Sample 7
Human iPSC line (585A1) cultured with 20 ng/ml Activin A for 7 days.

source_name: iPSCs, 4 ng/ml bFGF + 20 ng/ml Activin A, 7 days

value: 4 ng/ml basic FGF (bFGF) + 20 ng/ml Activin A for 7 days


title: 585A1-bFGF_20

description:
Sample 3
Human iPSC line (585A1) cultured with 20 ng/ml basic FGF (bFGF) for 7 days.

source_name: iPSCs, 20 ng/ml bFGF, 7 days

value: 20 ng/ml basic FGF (bFGF) for 7 days


title: 585A1-bFGF_4

description:
Sample 2
Human iPSC line (585A1) cultured with 4 ng/ml basic FGF (bFGF) for 7 days.

source_name: iPSCs, 4 ng/ml bFGF, 7 days

value: 4 ng/ml basic FGF (bFGF) for 7 days


title: 585A1-bFGF_100

description:
Sample 4
Human iPSC line (585A1) cultured with 100 ng/ml basic FGF (bFGF) for 7 days.

source_name: iPSCs, 100 ng/ml bFGF, 7 days

value: 100 ng/ml basic FGF (bFGF) for 7 days


title: khES3_ActivinA_100

description: Human ESC line (khES3) cultured with 100 ng/ml Activin A and 4 ng/ml bFGF for 7 days

hyb_protocol: Manufature's protocol

data_processing: GeneSpring (Agilent). Signals were normalized to the 75th percentile.

label_protocol: Manufature's protocol

growth_protocol: Human pluripotent stem cells were culture on mitomycin C-treated SNL feeder cells in Primate ES cell medium (ReproCELL) containing 4 ng/mL recombinant bFGF (Wako) unless otherwise stated.

treatment_protocol: For hematopoietic differentiation, we performed hematopoietic differentiation of human iPSCs by using StemPro-34 (Invitrogen) based media. Cytokines or a chemical compound were utilized as follows during differentiation: on day 0-1, human BMP4 (hBMP4; 10 ng/ml) and Rock-inhibitor (Y27632, 10 μM); on day 1-4, hBMP4 (10 ng/ml) and human basic fibroblast growth factor (hbFGF, 5 ng/ml); on day 4-8, human vascular endothelial growth factor (hVEGF, 10 ng/mL), hbFGF (1 ng/mL), human interleukin-6 (hIL-6, 10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), human stem cell factor (hSCF, 100 ng/mL), and human Fms-like tyrosine kinase 3 ligand (hFlt3L, 100 ng/mL); and on Day 8-20, hVEGF (10 ng/mL), hIL-6 (10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), hSCF (100 ng/mL), hFlt3L (100 ng/mL), human erythropoietin (hEPO, 4U/ml), and human thrombopoietin (hTPO, 50 ng/mL). For neural differentiation, we used embryoid body formation method. After embryoid body formation of dissociated human iPS/ESCs using low-binding culture dish, the cells were cultured in the medium which consisted of DMEM/F-12 (Gibco), 1% MEM Non-Essential Amino Acids Solution (Gibco), 5% Knockout Serum Replacement (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 10 M Y-27632, 2 M dorsomorphin (Sigma), and 10 M SB431542 (Sigma). In sample 744A2-IGF2(+), IGF2 was forced to express in iPSC line (744A2)  by doxycycline-inducible system for 7 days (control: 744A2-IGF2(-), doxycycline-negative condition).

value: Human ESCs cultured with 100 ng/ml Activin A


title: Liver from streptozotocin/bezafibrate-treated mice, biological replicate 1

description:
STZ_BEZ_43
Type I diabetes induced by streptozotocin.
Gene expression data from liver tissue of streptozotocin/bezafibrate-treated mice, biological replicate 1.


title: 744A2-IGF2(-)

description: Human iPSC line (744A2) control

value: Human iPSCs (control)


title: khES3_ActivinA_20

description: Human ESC line (khES3) cultured with 20 ng/ml Activin A and 4 ng/ml bFGF for 7 days

value: Human ESCs cultured with 20 ng/ml Activin A


title: 585A1-bFGF_0

description:
Sample 1
Human iPSC line (585A1) cultured with no basic FGF (bFGF) for 7 days.

source_name: iPSCs, 0 ng/ml bFGF, 7 days

value: 0 ng/ml basic FGF (bFGF) for 7 days


title: khES3-bFGF0

description: Human ESC line (khES3) cultured with no basic FGF(bFGF) for 7 days

value: Human ESCs cultured with no basic FGF(bFGF)


title: khES3-bFGF100

description: Human ESC line (khES3) cultured with 100 ng/ml bFGF for 7 days

value: Human ESCs cultured with 100 ng/ml bFGF


title: khES3-bFGF4

description: Human ESC line (khES3) cultured with 4 ng/ml bFGF for 7days

value: Human ESCs cultured with 4 ng/ml bFGF


title: khES3_ActivinA_0

description: Human ESC line (khES3) cultured with no Activin A but with 4 ng/ml bFGF for 7 days

value: Human ESCs cultured with no Activin A


title: khES3_ActivinA_4

description: Human ESC line (khES3) cultured with 4 ng/ml Activin A and 4 ng/ml bFGF for 7days

value: Human ESCs cultured with 4 ng/ml Activin A


title: Cira82-erythroblast

description: Magnetically sorted CD235a (+) erythroblasts differentiated from human iPSCs

source_name: human iPS/ESC derived-erythroblasts

growth_protocol: We differentiated human induced pluripotent stem cell lines by using StemPro-34 (Invitrogen) based media. Cytokines or a chemical compound were utilized as follows during differentiation: on day 0-1, human BMP4 (hBMP4; 10 ng/ml) and Rock-inhibitor (Y27632, 10 μM); on day 1-4, hBMP4 (10 ng/ml) and human basic fibroblast growth factor (hbFGF, 5 ng/ml); on day 4-8, human vascular endothelial growth factor (hVEGF, 10 ng/mL), hbFGF (1 ng/mL), human interleukin-6 (hIL-6, 10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), human stem cell factor (hSCF, 100 ng/mL), and human Fms-like tyrosine kinase 3 ligand (hFlt3L, 100 ng/mL); on day 8-20, hVEGF (10 ng/mL), hIL-6 (10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), hSCF (100 ng/mL), hFlt3L (100 ng/mL), human erythropoietin (hEPO, 4U/ml), and human thrombopoietin (hTPO, 50 ng/mL); on day 20-28, hEPO (4U/ml), hSCF (100 ng/mL), and hIL-3 (5 ng/mL); on day 28-35, hEPO (4U/ml) and hSCF (100 ng/mL). On day 35, erythroblasts were subject to the microarray analysis.

treatment_protocol: iPS/ESC-derived CD235a (Glycophorin A)+ erythroblasts were purified by CD235a -MicroBeads (Miltenyi Biotec, 120-000-308) and autoMACS (Miltenyi biotech).


title: 751B4-hematopoietic differentiation day2

description: Human iPSC line (751B4) after 2 days of hematopoietic differentiation

value: Human iPSCs after 2 days of hematopoietic differentiation


title: 751B4-hematopoietic differentiation day4

description: Human iPSC line (751B4) after 4 days of hematopoietic differentiation

value: Human iPSCs after 4 days of hematopoietic differentiation


title: khES3-bFGF20

description: Human ESC line (khES3) cultured with 20 ng/ml bFGF for 7 days

value: Human ESCs cultured with 20 ng/ml bFGF


title: 751B4-neural differentiaiton day4

description: Human iPSC line (751B4) after 4 days of neural differentiation

source_name: 751B4-neural differentiaiton day4

value: Human iPSCs after 4 days of neural differentiation


title: khES3-erythroblast

description: Magnetically sorted CD235a (+) erythroblasts differentiated from human ESCs


title: 692D2-erythroblast

value: Magnetically sorted CD235a (+) erythroblasts differentiated from human iPSCs


title: 744A2-IGF2(+)

description: Human iPSC line (744A2) forced to express IGF2 gene for 7 days

value: Human iPSCs forced to express IGF2 gene


title: TIG1204F1-erythroblast


title: 744A2-erythroblast


title: Keratinocyte#1 [parental_lines_expression]

description:
MN001_004
Human Keratinocyte, parental tissue of iPSC lines used for the study.

hyb_protocol: Hybridized to Agilent-028004 arrays according to the manufacturer's protocol.

data_processing: GeneSpring (Agilent). Signals were normalized to percentile.

source_name: Human keratinocyte

growth_protocol: The human fibroblasts were cultured with Dulbecco's Modified Eagle Medium with 10% fetal bovine serum. The peripheral blood mononuclear cells were freshly drawn from a volunteer, and subject to the analysis. The keratinocyte was purchased from ATCC, and cultured with Keratinocyte-SFM (1X), Liquid (Life Technologies).

value: keratinocyte


title: PBMN-SF91 [parental_lines_expression]

description:
MN001_005
Human peripheral blood mononuclear cells, parental tissue of iPSC lines used for the study.

value: peripheral blood mononuclear cells


title: HDF-1437 [parental_lines_expression]

description:
MN001_003
Human dermal fibroblast, parental tissue of iPSC lines used for the study.

source_name: Human dermal fibroblast

value: dermal fibroblast


title: 610B1-erythroblast


title: HDF-TIG107 [parental_lines_expression]

description:
MN001_001
Human dermal fibroblast, parental tissue of iPSC lines used for the study.


title: HDF-BJ [parental_lines_expression]

description:
MN001_002
Human foreskin fibroblast, parental tissue of iPSC lines used for the study.

source_name: Human foreskin fibroblast

value: foreskin fibroblast


title: H1-HPC

description: FACS-sorted Hematopoietic precursor cells differentiated from human pluripotent stem cells on day 15

data_processing: GeneSpring GX. Signals were normalized to percentile.

growth_protocol: We differeniated human pluripotent stem cell lines by using StemPro-34 (Invitrogen) based media for 15 days.Cytokines or a chemical compound were utilized as follows during differentiation: on day 0-1, human BMP4 (10 ng/ml) and Rock-inhibitor (Y27632) (10 μM); on day 1-4, human BMP4 (10 ng/ml) and human basic fibroblast growth factor (bFGF; 5 ng/ml); on day 4-8, human vascular endothelial growth factor (hVEGF; 10 ng/mL), hbFGF (1 ng/mL), human interleukin-6 (hIL-6; 10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), human stem cell factor (hSCF; 100 ng/mL), and human Fms-like tyrosine kinase 3 ligand (hFlt3L; 100 ng/mL); and on Day 8-15, hVEGF (10 ng/mL), hIL-6 (10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), hSCF (100 ng/mL), hFlt3L (100 ng/mL), human erythropoietin (hEPO; 4U/ml), and human thrombopoietin (50 ng/mL)

treatment_protocol: CD34+CD38-CD43+lineage marker- cells, which were differentiated from human pluripotent stem cells, were sorted by flow cytometer (Aria2).

value: Human pluripotent stem cells-derived hematopoietic precursor cells (CD34+CD38-CD43+lineage marker -)


title: KRV1-HPC

source_name: Human pluripotent stem cells-derived hematopoietic precursor cells


title: 751B4-erythroblast

source_name: Human pluripotent stem cells-derived erythroblasts

growth_protocol: We differeniated human induced pluripotent stem cell lines by using StemPro-34 (Invitrogen) based media. Cytokines or a chemical compound were utilized as follows during differentiation: on day 0-1, human BMP4 (hBMP4; 10 ng/ml) and Rock-inhibitor (Y27632, 10 μM); on day 1-4, hBMP4 (10 ng/ml) and human basic fibroblast growth factor (hbFGF, 5 ng/ml); on day 4-8, human vascular endothelial growth factor (hVEGF, 10 ng/mL), hbFGF (1 ng/mL), human interleukin-6 (hIL-6, 10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), human stem cell factor (hSCF, 100 ng/mL), and human Fms-like tyrosine kinase 3 ligand (hFlt3L, 100 ng/mL); and on Day 8-20, hVEGF (10 ng/mL), hIL-6 (10 ng/mL), hIL-3 (40 ng/mL), hIL-11 (5 ng/mL), hSCF (100 ng/mL), hFlt3L (100 ng/mL), human erythropoietin (hEPO, 4U/ml), and human thrombopoietin (hTPO, 50 ng/mL). For erythroid differentiation, we differentiated PSCs by the aforementioned method for 20 days and changed the medium to erythroid differentiation medium, which contained hEPO (4U/ml), hSCF (100 ng/mL), and hIL-3 (5 ng/mL). On day 28, hIL-3 was discontinued. On day 35, erythroblasts were subject to the microarray analysis.

treatment_protocol: CD34+CD38-CD43+lineage marker- cells, which were differentiated from human pluripotent stem cells, were sorted by flow cytometer (Aria2) on day 15. iPSC-derived erythroblasts were purified by CD235a (Glycophorin A)-MicroBeads (Miltenyi Biotec, 120-000-308) and autoMACS (Miltenyi biotech) on day 35.


title: KEP1-HPC


title: khES3-HPC


title: H9-HPC


title: 457C1-HPC


title: khES1-HPC


title: 454E2-HPC


title: 451F3-HPC


title: 744A2-HPC


title: 665A7-HPC


title: 610B1-HPC


title: Cira24-HPC


title: 606A1-HPC


title: 744B9-HPC


title: 648A1-HPC


title: 692D2-HPC


title: 751B4-HPC


title: 585B1-HPC


title: 648B1-HPC


title: 751A3-HPC


title: 821B1

description:
SAMPLE 12
Human induced pluripotent stem cells derived from dental pulp cells.

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard recommended Illumina scanner setting protocol using BeadArray Reader.

data_processing: Illumina GenomeStudio software and GeneSpring (Agilent Technologies).

source_name: iPSCs derived from dental pulp cells

label_protocol: Standard Illumina protocol.

growth_protocol: Human pluripotent stem cells were cultured on mitomycin C-treated SNL feeder cells in Primate ES cell medium (ReproCELL) containing 4 ng/mL recombinant bFGF (Wako).

extract_protocol: Genomic DNA lysates were extracted with DNeasy(R) blood and tissue kit (QIAgen) in accordance with manufacturer's protocol.

value: human induced pluripotent stem cells

tag: derivation

value: dental pulp cells


title: 798B2

description:
SAMPLE 10
Human induced pluripotent stem cells derived from dental pulp cells.


title: 585A1-HPC


title: Cira23-HPC


title: 427F1-HPC


title: Cira22-HPC


title: 821A1

description:
SAMPLE 11
Human induced pluripotent stem cells derived from dental pulp cells.


title: 409B2-HPC


title: 404C2-HPC


title: 711A5

description:
SAMPLE 8
Human induced pluripotent stem cells derived from cord blood.

source_name: iPSCs derived from cord blood

value: cord blood


title: TIG1204F1-HPC


title: 798A3

description:
SAMPLE 9
Human induced pluripotent stem cells derived from dental pulp cells.


title: 363G1

description:
SAMPLE 5
Human induced pluripotent stem cells derived from dermal fibroblasts.

source_name: iPSCs derived from dermal fibroblasts

value: dermal fibroblasts


title: 622C1

description:
SAMPLE 6
Human induced pluripotent stem cells derived from peripheral T cells.

source_name: iPSCs derived from peripheral T cells

value: peripheral T cells


title: 346F1

description:
SAMPLE 4
Human induced pluripotent stem cells derived from dermal fibroblasts.


title: 346E1

description:
SAMPLE 2
Human induced pluripotent stem cells derived from dermal fibroblasts.


title: 428C2 [iPSCs_methylation]

description:
SAMPLE 8
Human induced pluripotent stem cells derived from dermal fibroblast.

data_processing:
Illumina GenomeStudio software and GeneSpring (Agilent Technologies).
Unmethylated (Signal_A) and methylated (Signal_B) signal intensities are in the 'unmethylated_methylated_signals.txt' file, which is linked to the Series record as a supplementary file.

source_name: Human iPSCs derived from dermal fibroblast

value: induced pluripotent stem cells


title: TIG1074F1-HPC


title: 1488-4F1 [iPSCs_methylation]

description:
SAMPLE 5
Human induced pluripotent stem cells derived from dermal fibroblast.


title: 453C2 [iPSCs_methylation]

description:
SAMPLE 4
Human induced pluripotent stem cells derived from dental pulp cell.

source_name: Human iPSCs derived from dental pulp cell

value: dental pulp cell


title: 1687-4F2 [iPSCs_methylation]

description:
SAMPLE 6
Human induced pluripotent stem cells derived from dermal fibroblast.


title: 346D1

description:
SAMPLE 1
Human induced pluripotent stem cells derived from dermal fibroblasts.


title: 346E2

description:
SAMPLE 3
Human induced pluripotent stem cells derived from dermal fibroblasts.


title: 414C2 [iPSCs_methylation]

description:
SAMPLE 9
Human induced pluripotent stem cells derived from dermal fibroblast.


title: 622E1

description:
SAMPLE 7
Human induced pluripotent stem cells derived from peripheral T cells.


title: 454D1 [iPSCs_methylation]

description:
SAMPLE 3
Human induced pluripotent stem cells derived from dental pulp cell.


title: 253G4-HPC

description: FACS-sorted Hematopoietic precursor cells differentiated from human pluripotent stem cells on day 15


title: 201B6-HPC


title: 201B7-HPC


title: 421C1 [iPSCs_methylation]

description:
SAMPLE 7
Human induced pluripotent stem cells derived from dermal fibroblast.


title: 454B1 [iPSCs_methylation]

description:
SAMPLE 2
Human induced pluripotent stem cells derived from dental pulp cell.


title: 253G1-HPC


title: 751A3

description: Human induced pluripotent stem cells derived from dermal fibroblasts

source_name: Human induced pluripotent stem cells

growth_protocol: The human induced pluripotent stem cells were culruted on SNL-feeder cells with Primate ESC medium (ReproCELL) supplemented with 4 ng/ml bFGF at 37 ºC in a humidified incubator with 5% CO2.

value: Human induced pluripotent stem cells


title: 7KE2

description: Human induced pluripotent stem cells derived from keratinocytes


title: Keratinocyte#2

description: SAMPLE 15

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard recommended Illumina scanner setting protocol using BeadArray Reader

data_processing: Illumina GenomeStudio software  Unmethylated(Signal_A) and methylated(Signal_B) signal intensities

source_name: Parental lines of human iPSC lines

extract_protocol: GenomicDNA lysates were extracted with DNeasy(R) blood and tissue kit (QIAgen) in accordance with manufacture's protocol.

value: human keratinocyte


title: DP74

description: SAMPLE 16

value: human dental pulp cells


title: Kereratinocyte#1

description: SAMPLE 14


title: 751B4


title: 744B9

description: Human induced pluripotent stem cells derived from peripheral blood


title: 744A2


title: PBMN-SF91

description: SAMPLE 13

value: human peripheral blood mononuclear cells


title: 692D2


title: KRV-1


title: KEP1


title: 648B1


title: 648A1


title: Cira83


title: PBMN#1

description: SAMPLE 11


title: PBMN#2

description: SAMPLE 12


title: Cira24


title: Cira82


title: Cira29


title: Cira23


title: HDF_1437

description: SAMPLE 7

value: human dermal fibroblasts


title: Cira27


title: CB-CD34#2

description: SAMPLE 10

value: human cord blood CD34 (+) cells


title: HDF_TIG107

description: SAMPLE 6


title: Cira22


title: 457C1

description: Human induced pluripotent stem cells derived from denatal pulp cells


title: HDF- 0995PD

description: SAMPLE 4


title: 451F3


title: 453F2 [iPSCs_methylation]

description:
SAMPLE 1
Human induced pluripotent stem cells derived from dental pulp cell.


title: 454 E2


title: 427F1


title: CB-CD34#1

description: SAMPLE 9


title: HDF-TIG120

description: SAMPLE 2


title: HDF-0982PD

description: SAMPLE 3


title: 409B2


title: HDF-SF91

description: SAMPLE 5


title: HDF1388

description: SAMPLE 1


title: 404C2


title: khES1

description:
human embryonic stem cells
SAMPLE 36

data_processing: Illumina GenomeStudio software and GeneSpring (Agilent Techonologies)  Unmethylated(Signal_A) and methylated(Signal_B) signal intensities

source_name: human embryonic stem cells

growth_protocol: Human pluripotent stem cells were culture on mitomycin C-treated SNL feeder cells in Primate ES cell medium (ReproCELL) containing 4 ng/mL recombinant bFGF (Wako)

value: human embryonic stem cells


title: H9

description:
human embryonic stem cells
SAMPLE 39


title: khES3

description:
human embryonic stem cells
SAMPLE 37


title: Kep1

description:
human induced pluripotent stem cells derived from kerationocyte
SAMPLE 33

source_name: human induced pluripotent stem cells


title: HDF_BJ

description: SAMPLE 8

value: human dermal fibroblasts from naonatal foreskin


title: 7KE2

description:
human induced pluripotent stem cells derived from kerationocyte
SAMPLE 35


title: UO-31

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

description: SAMPLE 60

data_processing: Raw Cq-values were filtered based on a detection threshold of 28 PCR cycles, excluding measurements with Cq > 28. The median Cq-value of triplicate measurements per gene was subsequently used to calculate a sample-specific normalization factor, applying the global mean normalization strategy.  Briefly, each Cq-value was normalized by subtracting the mean Cq-value per sample. Normalized Cq-values were multiplied by -1 such that higher values represent higher expression levels.

label: SYBR Green

source_name: cell line

label_protocol: Labeling with SYBR Green

growth_protocol: cell pellets were obtained from the National Cancer Institute (Developmental Therapeutics Program)

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

tag: cancer type

value: Renal


title: KRV1

description:
human induced pluripotent stem cells derived from kerationocyte
SAMPLE 34


title: 751B4

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 32


title: 6289N

description: Heathy control naïve CD4+ T cells #7

source_name: Heathy control naïve CD4+ T cells

value: CD4+ T cells


title: H1

description:
human embryonic stem cells
SAMPLE 38


title: 5547N

description: Heathy control naïve CD4+ T cells #6


title: 6289M

description: Heathy control memory CD4+ T cells #7

source_name: Heathy control memory CD4+ T cells


title: 744B9

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 30

value: human induced pluripotent stem cells


title: 744A2

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 29


title: 585B1

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 27


title: UACC-257

description: SAMPLE 58

value: Melanoma


title: 5547M

description: Heathy control memory CD4+ T cells #6


title: UACC-62

description: SAMPLE 59


title: U251

description: SAMPLE 57

value: Central Nervous System


title: 665A7

description:
human induced pluripotent stem cells derived from cord blood
SAMPLE 23


title: 751A3

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 31


title: 692D2

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 28


title: 648B1

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 25


title: 720M

description: Heathy control memory CD4+ T cells #5


title: 585A1

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 26


title: TK-10

description: SAMPLE 56


title: T-47D

description: SAMPLE 55

value: Breast


title: Cira83

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 20


title: Cira24

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 19


title: 648A1

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 24


title: Cira22

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 17


title: 606A1

description:
human induced pluripotent stem cells derived from cord blood
SAMPLE 21


title: Cira29

description:
human induced pluripotent stem cells derived from peripheral blood
SAMPLE 15


title: Cira27

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 14


title: 610B1

description:
human induced pluripotent stem cells derived from cord blood
SAMPLE 22


title: Cira82

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 16


title: SF-539

description: SAMPLE 48


title: RXF-393

description: SAMPLE 47


title: SK-MEL-5

description: SAMPLE 49


title: SN12C

description: SAMPLE 51


title: SR

description: SAMPLE 54

value: SR

value: Leukemia


title: 720RN

description: Heathy control naïve CD4+ T cells #5


title: OVCAR-5

description: SAMPLE 44

value: Ovarian


title: SNB-19

description: SAMPLE 52


title: OVCAR-8

description: SAMPLE 45


title: RPMI-8226

description: SAMPLE 46


title: Cira23

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 18


title: 457C1

description:
human induced pluripotent stem cells derived from dental pulp cell
SAMPLE 13


title: SNB-75

description: SAMPLE 53


title: SK-OV-3

description: SAMPLE 50


title: 454_E2

description:
human induced pluripotent stem cells derived from dental pulp cell
SAMPLE 12


title: 451F3

description:
human induced pluripotent stem cells derived from dental pulp cell
SAMPLE 11


title: NCI-H522

description: SAMPLE 43

value: Non Small Cell Lung


title: TIG1204F1

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 9


title: NCI-H322M

description: SAMPLE 41


title: 427F1

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 10


title: NCI-H460

description: SAMPLE 42


title: 409B2

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 7


title: NCI-H23

description: SAMPLE 40


title: NCI-H226

description: SAMPLE 39


title: pstA1A2KOKO_rep3

city: Aurora

first: Martin

middle: I

last: Voskuil

state: CO

department: Microbiology

institute: University of Colorado Denver

description: Biological replicate 3 of 3

hyb_protocol: Arrays were prehybridized in water, SSC, BSA, and SDS. Labeling reaction was concentrated to 5ul in a microcon 10 filter tube, added to tRNA, SSC, formamide, and SDS, and heated to 98 C for two minutes. Samples were hybridzed overnight at 50 C.

scan_protocol: Scanned on Molecular Device's Genepix 4000B

data_processing: ArrayStar5 software was used for microarray analysis. Experiments performed in triplicate were loaded into ArrayStar and normalized using RMA (Quantile).  Statistical significance was determined using the Moderated t-test with Benjamini Hochberg testing correction.

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

source_name: total RNA from aerobic cultures

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for two minutes at 98 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 30 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNAse treated. Fur further purification, Quiagen RNeasy kit was used according to the manufacturer's instructions.

tag: growth

value: logarithmic phase aerobic cultures, OD600 of 0.2

tag: genotype

value: M. tuberculosis Erdman

value: M. tuberculosis Erdman strain ΔpstA1A2


title: pstA1A2KOKO_rep2

description: Biological replicate 2 of 3


title: pstA2KO_rep1

description: Biological replicate 1 of 3

value: M. tuberculosis Erdman strain ΔpstA2


title: TIG1074F1

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 8


title: 253G1

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 4


title: pstA1A2KOKO_rep1

description: Biological replicate 1 of 3


title: pstA2KO_rep3

description: Biological replicate 3 of 3


title: 404C2

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 6


title: EC1118_70_a

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

description: Gene expression in sample from EC1118 strain, biological rep a , at 70 g/L released CO2

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7

data_processing: Data normalization and statistical analysis were performed using R 3.1.1 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

source_name: EC1118_70 repetition a

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: The cells were growing in a medium containing 200 g/l of sugars, 330 mg/l of assimilable nitrogen (amino acids and ammonium) and 8 mg/l of phytosterolsat 24°C.

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: 109 cells were harvested by centrifugation at 1000 g for 5 min at 4°C and the cell pellets were washed with DEPC-treated water and then frozen in methanol at -80°C.

tag: released co2 (g/l)

tag: array

tag: block


title: 253G4

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 5

tag: cell type


title: MDA-MB-468

description: SAMPLE 37


title: Cira28

description:
human iPS cells generated from peripheral blood
SAMPLE 5

source_name: human induced pluripotent stem cell

value: human induced pluripotent stem cell


title: 201B7

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 2


title: ECA5_70_b

description: Gene expression in sample from ECA5 strain, biological rep b , at 70 g/L released CO2

source_name: ECA5_70 repetition b


title: Cira26

description:
human iPS cells generated from dermal fibroblast
SAMPLE 4


title: ES06

description:
human ES cells
SAMPLE 6

source_name: human ES cells

value: human ES cells


title: MDA-MB-435

description: SAMPLE 36


title: BMM_Capn6-Wt

city: Tokyo

first: Takuro

last: Miyazaki

address: 1-5-8 Hatanodai, Shinagawa-ku

department: Biochemistry

institute: Showa University School of Medicine

description: Gene expression at day3 in culture.

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Feature Extraction software

source_name: Bone marrow-derived macropahges, day4

label_protocol: standard Agilent protocol

growth_protocol: Murine bone marrow cells were collected by flushing femoral bone marrow with culture medium; subsequently, the cells were incubated in Dulbecco’s Modified Eagle’s medium (Sigma-Aldrich Corp., St Louis, MO, USA) supplemented with 10% serum, penicillin–streptomycin–amphotericin B (Wako Pure Chemical Industries, Ltd., Osaka, Japan), and M-CSF (50 ng/mL) for differentiation into macrophages in the presence  of TNF-α (10 ng/mL). Unbound cells were removed by washing with medium; the culture medium was changed every other day.

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

treatment_protocol: Cell were cultured in the presence of M-CSF at 50 ng/mL and TNF-a at 10 ng/mL.

value: Cultured bone marrow cells

tag: gender

value: Male


title: 246G1

description:
human induced pluripotent stem cells derived from dermal fibroblast of neonatal foreskin
SAMPLE 3


title: ECA5_35_b

description: Gene expression in sample from ECA5 strain, biological rep b , at 35 g/L released CO2

source_name: ECA5_35 repetition b


title: MALME-3M

description: SAMPLE 35


title: ECA5_70_a

description: Gene expression in sample from ECA5 strain, biological rep a , at 70 g/L released CO2

source_name: ECA5_70 repetition a


title: pstA2KO_rep2

description: Biological replicate 2 of 3


title: 201B6

description:
human induced pluripotent stem cells derived from dermal fibroblast
SAMPLE 1


title: M14

description: SAMPLE 34


title: IGR-OV1

description: SAMPLE 33


title: BMM_Capn6-Ko

description: Gene expression at day3 in culture.


title: EC1118_35_b

description: Gene expression in sample from EC1118 strain, biological rep b , at 35 g/L released CO2

source_name: EC1118_35 repetition b


title: ECA5_70_c

description: Gene expression in sample from ECA5 strain, biological rep c , at 70 g/L released CO2

source_name: ECA5_70 repetition c


title: EC1118_70_c

description: Gene expression in sample from EC1118 strain, biological rep c , at 70 g/L released CO2

source_name: EC1118_70 repetition c


title: 418C1

description:
human iPS cells generated from dermal fibroblast
SAMPLE 1


title: EC1118_35_a

description: Gene expression in sample from EC1118 strain, biological rep a , at 35 g/L released CO2

source_name: EC1118_35 repetition a


title: 604A1

description:
human iPS cell generated from cord blood cells
SAMPLE 2


title: EC1118_70_b

description: Gene expression in sample from EC1118 strain, biological rep b , at 70 g/L released CO2

source_name: EC1118_70 repetition b


title: ECA5_35_a

description: Gene expression in sample from ECA5 strain, biological rep a , at 35 g/L released CO2

source_name: ECA5_35 repetition a


title: Cira25

description:
human iPS cells generated from peripheral blood
SAMPLE 3


title: HL-60

description: SAMPLE 32

source_name: cell line


title: 610B1-HPC

description: SAMPLE 9

data_processing: Illumina GenomeStudio Software

source_name: human PSC-derived hematopoietic precursor cells

value: Pluripotent-stem cell derived hematopoietic precursor cells


title: HCT-15

description: SAMPLE 31

value: Colon


title: 648A1-HPC

description: SAMPLE 8


title: khES3-HPC

description: SAMPLE 10


title: EKVX

description: SAMPLE 30

value: EKVX


title: CAKI-1

description: SAMPLE 29

value: Renal


title: ACHN

description: SAMPLE 27

value: ACHN


title: LOXIMVI

description: SAMPLE 26

value: LOXIMVI

value: Melanoma


title: 457C1-HPC

description: SAMPLE 6


title: 692D2-HPC

description: SAMPLE 7


title: BT-549

description: SAMPLE 28

value: Breast


title: KM12

description: SAMPLE 25


title: HOP-92

description: SAMPLE 23

value: Non Small Cell Lung


title: HT29

description: SAMPLE 24


title: Cstb-/- primary mouse microglia, biological rep 1

city: Helsinki

first: Inken

last: Körber

address: Haartmaninkatu 8

department: Neuroscience Center

country: Finland

institute: Folkhälsan Institue of Genetics / University of Helsinki

description:
Gene-level expression data from Cstb-/- primary mouse microglia.
KO_2

hyb_protocol: The sample preparation and hybridization of each cRNA to Affymetrix Mouse Exon 1.0 ST Array was performed based on the manufacturer's instructions.

scan_protocol: The quality of each microarray was controlled using the Affymetrix GeneChip Operating Software (GCOS) v1.4.

data_processing:
The raw data were imported into GeneSpring GX 12.6 software and the gene-level expression analysis was performed using the 'core' probe sets, which were normalized by RMA16 algorithm. The background is adjusted on a per-chip basis and the normalization on probe level is performed by quantile normalization. Per gene normalization is performed by baseline transformation.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.csv

source_name: Cstb-/- primary mouse microglia

label_protocol: The cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cstb-/- and control mice were grown under standard conditions in animal facilities. Mixed glia cultures were prepared from dissected, meninges-free cerebellar cortices of postnatal day 5 mice. The cortices were incubated with 20% trypsin and 20 µg DNase I at 37C for 20 minutes and triturated. The generated cells were grown in DMEM/2 mM L-glutamine/10%FCS/1% penicillin-streptomycin until confluency. Then microglia were shaken off (3 h, 225 rpm, 37C) and cultured for an additional 24h before RNA collection. Purity of cultures was verified by F4/80 and GFAP immunostaining.

extract_protocol: Total RNA was extracted from pooled cells of two mice using the PerfectPure RNA Cultured Cell kit (5 PRIME) and RNA quality was controlled by chip-based capillary electrophoresis (Bioanalyzer 2100, Agilent).

tag: strain background

value: Cstb-/-

value: cultured primary microglia


title: Cstb-/- primary mouse microglia, biological rep 2

description:
Gene-level expression data from Cstb-/- primary mouse microglia.
KO_3

tag: genotype/variation


title: control primary mouse microglia, biological rep 4

description:
Gene-level expression data from wild-type primary mouse microglia.
WT_4

source_name: control primary mouse microglia

value: wild-type


title: TIG1204F1-HPC

description: SAMPLE 5


title: Cstb-/- primary mouse microglia, biological rep 3

description:
Gene-level expression data from Cstb-/- primary mouse microglia.
KO_4


title: control primary mouse microglia, biological rep 1

description:
Gene-level expression data from wild-type primary mouse microglia.
WT_1


title: control primary mouse microglia, biological rep 3

description:
Gene-level expression data from wild-type primary mouse microglia.
WT_3


title: TIG1074F1-HPC

description: SAMPLE 4


title: RCCPDX23 model at passage P5

city: Strasbourg

first: Thierry

last: Massfelder

address: 11 rue Humann

institute: INSERM

description: Gene expression data from tumor tissue

hyb_protocol: Arrays were washed, stained (fluidics: FS450 with FS450_0001 protocol).

scan_protocol: Scanned using a GeneArray scanner (GeneChip® Scanner 3000)

data_processing: Scans were processed with Affymetrix GeneChip® Command Console (AGCC 3.2.3) (INS GEN/0036*). The scanned images were converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix MAS 5.0 files. Image QCs were performed by visual inspection (INS GEN/0008). Array QC metrics were determined using the QC tool (R script created from historical data and Affymetrix recommendations) with the following thresholds:  “Z”-parameter (Z-BG, Z-Scale, Z-Present, Z-Actin, Z-GAPDH, Z-Deg): A Z-score is calculated for each QC metrics as follows [Z = (x – mean) / standard deviation]. The Z-score provide a way to assess “outlier” behaviour (too good or too bad relative to the mean).

label: Biotin

source_name: Tumor tissue of the RCCPDX23 model at P5

label_protocol: The 3’IVT protocol underwent reverse transcription, primed with T7 oligo(dT) primer, of total RNA to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA was then converted into a double-stranded DNA template for transcription. The second-strand cDNA synthesis converted the single-stranded cDNA into a double stranded DNA template for transcription. The reaction employed DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesized aRNA and incorporated a biotin-conjugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin‑labeled aRNA prepared the sample for hybridization onto Affymetrix GeneChip® arrays (U133 Plus 2.0). The quality of fragmented PCR products was checked on 1% agarose gel.

growth_protocol: Fresh tumor tissue were harvested at P0 (primary tumor) directly after surgery, and at the different passages in anesthetized mice (gazeous anesthesia)as indicated in the Samples section and prior to mice euthanasia.

extract_protocol: Total RNA from patients’ primary tumors and from corresponding tumors at passage ranging from P1 to P8 was obtained using Qiagen RNAeasy mini columns according to manufacturer’s protocol. The concentration and integrity/purity of each RNA sample were measured using RNA 6000 LabChip kit (Agilent) and the Agilent 2100 bioanalyzer.

treatment_protocol: There were no prior treatment.

value: CCC human tumor

tag: passages


title: HCT-116

description: SAMPLE 21


title: Hs-578T

description: SAMPLE 22


title: Macrophage_M2_Ctrl_rep1

description: Gene expression data from alveolar macrophages, M2 population, derived from wildtype mice

hyb_protocol: Standard Illumina hybridization protocol including minor modification as suggested by Nugen

scan_protocol: Standard Illumina scanning protocol (HiScan)

data_processing: Data including background subtraction (GenomeStudioV2011.1 software, gene expression module version 1.9.0), removal of negative values by introducing an offset, quantile normalisation

source_name: Alveolar macrophages, M2 population, derived from wildtype mice

label_protocol: Ovation PicoSL WTA System V2 in combination with the Encore Biotin IL Module (Nugen)

growth_protocol: Animals housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: As described in the paper. Briefly, primary alveolar macrophages were isolated from the lungs of mice by bronchoalveolar lavage (BAL) with 8 washes of 1 ml PBS at room temperature. Polarization towards the M2 phenotype was done with IL-4  (20 ng/ml, Immunotool) treatment for up to 24 h. Unpolarized cells (M0) served as controls.

tag: age

value: 8-12 weeks

tag: strain

value: Alveolar macrophage

tag: cell population


title: Macrophage_M2_Ctrl_rep2


title: RCCPDX18 model at passage P6

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P6

tag: tissue


title: 404C2-HPC

description: SAMPLE 3


title: Macrophage_M2_Ctrl_rep3


title: RCCPDX23 model at passage P4

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX23 model at P4


title: RCCPDX23 model at passage P2

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX23 model at P2


title: RCCPDX18 model at passage P8

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P8


title: Primary tumor of RCCPDX23 model

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX23 model at P0


title: RCCPDX23 model at passage P1

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX23 model at P1


title: 409B2-HPC

description: SAMPLE 2


title: 253G4-HPC

description: SAMPLE 1


title: CCRF-CEM

description: SAMPLE 19

tag: cell line

value: CCRF-CEM

value: Leukemia


title: HCC-2998

description: SAMPLE 20


title: SW-620

description: SAMPLE 18


title: SK-MEL-28

description: SAMPLE 17


title: SK-MEL-2

description: SAMPLE 16


title: SF-295

description: SAMPLE 15

value: Central Nervous System


title: RCCPDX18 model at passage P2

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P2


title: Macrophage_M0_Ctrl_rep1

description: Gene expression data from alveolar macrophages, M0 population, derived from wildtype mice

source_name: Alveolar macrophages, M0 population, derived from wildtype mice


title: Macrophage_M2_Lmp7ko_rep3

description: Gene expression data from alveolar macrophages, M2 population, derived from Lmp7 k.o. mice

source_name: Alveolar macrophages, M2 population, derived from Lmp7 k.o. mice


title: Macrophage_M2_Lmp7ko_rep1


title: PC-3

description: SAMPLE 13

value: Prostate


title: SF-268

description: SAMPLE 14


title: RCCPDX18 model at passage P4

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P4


title: Primary tumor of RCCPDX18 model

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P0


title: Macrophage_M0_Ctrl_rep3


title: Macrophage_M2_Lmp7ko_rep2


title: RCCPDX18 model at passage P1

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX18 model at P1


title: NCI/ADR-RES

description: SAMPLE 38

source_name: cell line

value: NCI/ADR-RES

value: Ovarian


title: Macrophage_M0_Ctrl_rep2


title: RCCPDX16 model at passage P5

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX16 model at P5


title: OVCAR-3

description: SAMPLE 11


title: Macrophage_M0_Lmp7ko_rep3

description: Gene expression data from alveolar macrophages, M0 population, derived from Lmp7 k.o. mice

source_name: Alveolar macrophages, M0 population, derived from Lmp7 k.o. mice


title: Macrophage_M0_Lmp7ko_rep2


title: Primary tumor of RCCPDX16 model

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX16 model at P0


title: RCCPDX16 model at passage P4

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX16 model at P4


title: MOLT-4

description: SAMPLE 10


title: control primary mouse microglia, biological rep 2

description:
Gene-level expression data from wild-type primary mouse microglia.
WT_2

source_name: control primary mouse microglia


title: Cstb-/- primary mouse microglia, biological rep 4

description:
Gene-level expression data from Cstb-/- primary mouse microglia.
KO_5

source_name: Cstb-/- primary mouse microglia


title: OVCAR-4

description: SAMPLE 12


title: DKO 2

city: DaeJon

first: Da-Hye

last: Lee

address: 335 Gwahangno

department: Biological science

country: South Korea

institute: KAIST

description: replicate 2

hyb_protocol: Illumina standard hybridization protocol

scan_protocol: Illumina standard scanning protocol

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

source_name: Neonatal liver

label_protocol: Biotinylated cDNA was obtained by Illumina TotalPrep RNA Amplification Kit

growth_protocol: Neonatal mice were obtained from the same pregnant mice

extract_protocol: Total mRNA was extracted with QIAGEN RNeasy Mini kit according to manufaturer's protocol

value: B6;129 mixed

value: postnatal day 1

value: liver

value: female


title: RCCPDX15 model at passage P2

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX15 model at P2


title: MDA-MB-231

description: SAMPLE 9

value: Breast


title: DKO 1

description: replicate 2


title: RCCPDX15 model at passage P4

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX15 model at P4


title: MCF-7

description: SAMPLE 8


title: K562

description: SAMPLE 7


title: Macrophage_M0_Lmp7ko_rep1


title: Primary tumor of RCCPDX15 model

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX15 model at P0


title: DU145

description: SAMPLE 5


title: COLO-205

description: SAMPLE 4

value: Colon


title: HOP-62

description: SAMPLE 6

value: Non Small Cell Lung


title: CON group_Calf No. 14_Rumen epithelial RNA

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: ruman epithelium

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 500 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the rumen epithelium using Trizo (Invitrogen) according to the manufacturer's instructions.

value: Rumen epithelium

tag: feeding group

value: Forage non-provision group

tag: calf number


title: RCCPDX13 model at passage P5

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX13 model at P5

value: CCC human tumor


title: RCCPDX15 model at passage P1

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX15 model at P1


title: A549ATCC

description: SAMPLE 3

tag: cancer type


title: Control 2

description: replicate 1

tag: genotype

value: wild type


title: CON group_Calf No. 8_Rumen epithelial RNA


title: CON group_Calf No. 11_Rumen epithelial RNA


title: CON group_Calf No. 12_Rumen epithelial RNA


title: HAY group_Calf No. 13_Rumen epithelial RNA

value: Forage provision group


title: RCCPDX13 model at passage P1

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX13 model at P1


title: 786-0

description: SAMPLE 1

value: Renal


title: A498

description: SAMPLE 2


title: TBTO_48h_exp3

status: Public on Jun 28 2016

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: To adjust the volume to 200 μl, nuclease free water was added to the labeled samples. Thereafter 200 μl hybridization buffer provided in miRCURY LNA™ microRNA Array, 5th generation kit (Exiqon, Denmark) was added. In a total volume of 400 μl the sample was denatured for 2 minutes at 95ºC, incubated on ice for at least 15 minutes and then spun down. Manual hybridization was performed using an Agilent hybridization SureHyb chamber kit and gasket slide kit at 56 °C for 16h in a hybridization oven with rotation. Following manual hybridization the arrays were automatically washed in a Tecan HS4800 Pro Hybridization station according to Exiqon instructions. For each biological experiment, one hybridization per time point was conducted and one sample per array.

scan_protocol: After washing, the arrays were scanned using the GenePix 4000A scanner (Axon Instruments, Foster City, CA).

data_processing: To quantify the signals, the images were processed in to GPR (5th) and TXT (7th) files through the GenePix Pro Sofware Suite version 3.0 by using the GAL file for probe annotation, as obtained from Exiqon. The GAL file is based on miRBase version 20.0. These GPR or TXT files were then imported in to R 2.11.0, for quality control and statistical analysis. First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were deviated technically. During data analysis the spot intensities were background-corrected and then filtered for low signals (i.e. intensity < 10). Only the mouse microRNA reporter intensities (661 unique reporters x 4 technical replicates) were used for further analyses. If for a reporter less than 3 of the 4 technical replicates were left, then the reporter intensity on that specific reporter was set to NA. The data were log2 transformed, followed by a quantile normalization and a summarization step. In the summarization step, the median intensity from the remaining technical replicates per condition was calculated. Finally, for each reporter a cut-off filtering was applied using the median of the three biological replicates. Only reporters that had a median intensity ≥50 for at least one condition of the 9 compounds tested, or their respective controls, passed this filtering per time point. After filtering, log2 ratios were calculated between average intensities of the treatment of its respective control.

label_protocol: The miRCURYTM locked-nuclei acid array (LNA), 5th and 7th generation (Exiqon, Denmark) contains probes that detect mature forms of all microRNAs present in miRBase 20.0 (http://www.mirbase.org/) (Griffiths-Jones et al, 2008). The Exiqon platform has been validated and is shown to reliably detect microRNA expression. The 5th and 7th generation microarray contains 9,360 and 14,708 reporters, which represent several control probes and sequences of mature human/mouse/rat specific microRNA (4 technical replicates). In our analysis, 661 unique mouse reporters (measurable on both generation arrays) were used. cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye (single color) using the mercury LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 12.5 μl.

growth_protocol: PMH were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates as described before.

extract_protocol: At the end of treatment the medium was removed and PMH were harvested in Qiazol (QIAGEN Benelux B.V., Venlo, The Netherlands). Total RNA was isolated using a miRNeasy Mini Kit (QIAGEN Benelux B.V., Venlo, The Netherlands) according to the manufacturer’s protocol and followed by DNase I (Qiagen, Inc) treatment. Following purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8 were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After a recovery period of 40-42h, the Dulbecco's Modified Eagle's (Gibco BRL, Breda, The Netherlands) culture medium was replaced by culture medium containing either one of the 21 compounds or a vehicle control (0.5% of DMSO, PBS, EtOH). Seventeen chemicals were obtained through Sigma-Aldrich, TCDD through Cerilliant, DMBA through ICN, E2 through Steraloids Inc. and PhB through Brocacef Intramuraal bv. A dose causing minimal cytotoxicity after 24h of exposure thus resulting in ±80% viability, was established by the MTT assay (Mosmann, 1983). Next, cells were treated with an IC20-24h dose of di(2-ethylhexyl)phthalate(DEHP), 4-Acetylaminofluorene(4AAF), Curcumin(Cur), Phenobarbital(PhB), Reserpine(Res), 7,12-Dimethylbenzanthracene (DMBA), Resorcinol(Resorcinol), Para-cresidine(pCres), Phenacetin(Phen), Diclofenac(diclo), Wy 14643(Wy), Tributyltinoxide(TBTO), Benzo[a]pyrene(BaP), 8-Hydroxyquinoline [AKA 8-quinolinol](8HQ), 17-b-estradiol(E2), ampicillin(AmpC), cisplatin(CisPl), Aflatoxin B1(AFB1), Cyclosporin A(CsA), 2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD), Quercetin(Que) for 24 or 48 h before being harvested. Independent biological experiments (at least in triplicate) with hepatocytes from different mice were obtained for every time point.

tag: studymainsource

value: Mouse liver


title: TBTO_48h_exp1


title: TBTO_48h_exp2


title: RCCPDX13 model at passage P2

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX13 model at P2


title: TBTO_24h_exp3


title: HAY group_Calf No. 10_Rumen epithelial RNA


title: Control 1

description: replicate 1


title: HAY group_Calf No. 9_Rumen epithelial RNA


title: RCCPDX13 model at passage P4

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX13 model at P4


title: RCCPDX16 model at passage P2

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX16 model at P2


title: TBTO_24h_exp1


title: MDA-MB-231 cells expressing KDM3Ash

city: Los Angeles

first: Cun-Yu

last: Wang

state: California(CA)

address: 10833 Le Conte Avenue

department: Division of Oral Biology and Medicine

institute: UCLA School of Dentistry

description: Gene expression data

hyb_protocol: Following fragmentation, cRNA were hybridized with an Affymetrix Human Genome Plus 2.0 Array.

scan_protocol: The arrays were scanned with a GeneArray scanner (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

source_name: ATCC

label_protocol: Biotin labelled cRNA were prepared by standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Hunam breast cancer cell line, MDA-MB-231 was cultured by standard protocl using DMEM with 10% FBS and antibiotics

extract_protocol: RNA was extracted using RNeasy kit (quagen) following manufacturers protocol

treatment_protocol: The cells were transfected with scramble or KDM3A shRNA. After puromycin (1 mcg/ml) selection, cells were used.

tag: infection

value: KDM3A shRNA

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: Epithelial

value: Derived from 51 years old female


title: Resorcinol_48h_exp2


title: Primary tumor of RCCPDX13 model

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX13 model at P0


title: RCCPDX16 model at passage P1

description: Gene expression data from tumor tissue

source_name: Tumor tissue of the RCCPDX16 model at P1


title: MDA-MB-231 cells expressing Scrsh

description: Gene expression data

value: scramble shRNA

value: Mammary gland/breast; derived from metastatic site:pleural effusion


title: Resorcinol_48h_exp1


title: Reserpine_48h_exp3


title: Resorcinol_24h_exp1


title: Resorcinol_24h_exp2


title: Reserpine_48h_exp2


title: Reserpine_48h_exp1


title: Reserpine_24h_exp3


title: Reserpine_24h_exp1


title: Reserpine_24h_exp2


title: Resorcinol_48h_exp3


title: Que_24h_exp3


title: Que_48h_exp1


title: Que_24h_exp2


title: Resorcinol_24h_exp3


title: Phen_48h_exp3


title: Que_24h_exp1


title: Phen_48h_exp1


title: PhB_48h_exp3


title: Phen_48h_exp2


title: Que_48h_exp3


title: PhB_48h_exp2


title: PhB_48h_exp1


title: Phen_24h_exp3


title: Que_48h_exp2


title: PhB_24h_exp3


title: Phen_24h_exp2


title: PhB_24h_exp2


title: TBTO_24h_exp2


title: PhB_24h_exp1


title: Paracres_48h_exp1


title: Paracres_24h_exp3


title: E2_48h_exp3


title: Paracres_24h_exp2


title: Paracres_48h_exp3


title: Paracres_24h_exp1


title: Paracres_48h_exp2


title: E2_48h_exp2


title: E2_24h_exp1


title: DMBA_48h_exp3


title: E2_24h_exp2


title: E2_24h_exp3


title: Phen_24h_exp1


title: DMBA_48h_exp2


title: DMBA_48h_exp1


title: diclo_48h_exp2


title: diclo_48h_exp3


title: DMBA_24h_exp2


title: DMBA_24h_exp1


title: diclo_24h_exp3


title: DEHP_48h_exp3


title: diclo_48h_exp1


title: diclo_24h_exp2


title: E2_48h_exp1


title: DEHP_48h_exp1


title: DEHP_48h_exp2