title: BrdU-HU

city: Milan

first: Federica

last: Castellucci

address: via Adamello 16

institute: IFOM-IEO Campus

description: wt cells able to incorporate BrdU were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.2M and BrdU for 90 minutes

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

source_name: ChIP

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YPD

extract_protocol: Extraction was performed as described in Bermejo et al., 2009.

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml). For MMS experiments, G1-arrested cells were released in YPD containing methyl-methan-sulphonate (MMS) 0.033% for 60 minutes; for HU experiments, cells were released in hydroxyurea (HU) 0.2M for 90 minutes

tag: antibody

value: anti-BrdU MI-11-3 (MBL)

value: W303 ura3::URA3/GPD-TK(7X)

tag: growth protocol

value: cells were grown in YPD

value: HU 0.2M 90 minutes

source_name: supernate


title: Rfa1-HU

status: Public on Jan 28 2014

type: genomic

country: Italy

description: Rfa1-PK cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing HU 0.2M and BrdU for 90 minutes

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

value: V5 tag antibody (anti-PK) (AbD Serotec)

tag: strain

tag: genotype

value: W303 Rfa1-PK

tag: treatment


title: genomic DNA from pituitary macroadenoma Sample 9

city: Los Angeles

first: Chao

last: Ling

state: California

address: 1501 San Pablo street

department: Zilkha Neurogenetic Institute

country: USA

institute: University of Southern California

description:
d0079
female, noninvasive, pituitary

hyb_protocol: One microgram of bisulphite converted DNA per sample was used for genome-scale DNA methylation profiling, which was performed in the USC Epigenome Center using the Illumina Infinium HumanMethylation450 (HM450) Beadchip platform,

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

organism: Homo sapiens

source_name: pituitary macroadenoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA purification was processed using DNeasy Blood & Tissue kit (Qiagen) according to the standard protocols of the manufacturer.

tag: tissue

value: pituitary macroadenoma

tag: subtype

value: GH-TSH

tag: knosp grade

tag: age

tag: gender

value: female

tag: tumor type

value: noninvasive


title: Rfa1_MMS

description: Rfa1-PK cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing MMS 0.033% for 60 minutes

value: MMS 0.033% 60 minutes


title: Etanercept-8w-2

type: RNA

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

description:
Biological replicate
New Zealand White rabbits were infected with Mtb HN878 at about 3.2log10 (on day 0).  One group of rabbits were treated with Etanercept, starting at 4 weeks post-infection, for 4 or 8 weeks (i.e, 8 or 12 weeks post infection).

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for applied genomics of the Public Health Research Institute of Rutgers university was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing: Microarray data from the scanned images were extracted using the software from Agilent technologies and downstream analysis was performed using commercial software.

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers and purified through a Qiagen RNA kit.

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Mtb HN878-infected

value: Etanercept

value: lung

tag: time

value: 8 wks post infection


title: Untreated-8w-1

value: untreated


title: Hmo1_MMS

description: Hmo1-PK cells were arrested in G1 with alfa-factor (2μg/ml) and then released in media containing MMS 0.033% for 60 minutes

value: W303 Hmo1-PK


title: Etanercept-8w-1


title: genomic DNA from pituitary macroadenoma Sample 14

description:
d0666
female, invasive, pituitary

value: NFA

value: invasive


title: Maize_Δtin2_4day_rep1

city: Marburg

first: Regine

last: Kahmann

address: Karl-von-Frisch-Strasse 10

department: Organismic Interactions

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

description: Gene expression data from maize leaves infected with U. maydis SG200Δtin2

hyb_protocol: Affymetrix protocols (GeneChip® Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)

scan_protocol: Affymetrix protocols (scanning on Affymetrix GSC3000G)

data_processing: Partek Genomics Suite® version 6.12. Expression values were normalized using the RMA method.

organism: Zea mays

source_name: Maize seedling leaves inoculated with U. maydis SG200Δtin2

label_protocol: Affymetrix protocols (GeneChip® Hybridization Wash and Stain Kit)

growth_protocol: Maize plants (Early Golden Bantam) were grown in a phytochamber in a 15 h/9 h light/dark cycle; light period started/ended with 1 h ramping of light intensity. Temperature was 28 and 20 °C, relative humidity 40% and 60% during light and dark periods, respectively, with 1 h ramping for both values. Plants were inoculated with H2O (mock), SG200 and SG200Δtin2

extract_protocol: Fungus infected or water-inoculated tissue from 20 plants per experiment was harvested at 4 dpi by excising a section of the third leaf between 1 and 3 cm below the injection holes. For RNA extraction, material was pooled, ground to powder under liquid nitrogen and RNA was extracted with Trizol reagent (Invitrogen). RNA was purified applying the RNeasy kit (Qiagen).

treatment_protocol: 7-day-old maize young seedlings were infected with U. maydis cell suspensions (OD600=3.0).

value: Maize leaves of young seedlings


title: Maize_SG200_4day_rep3

description: Gene expression data from maize leaves infected with U. maydis SG200

source_name: Maize seedling leaves inoculated with U. maydis SG200


title: Maize_SG200_4day_rep2


title: Maize_SG200_4day_rep1


title: Maize_Mock_4day_rep3

description: Gene expression data from maize leaves inoculated with H2O

source_name: Maize seedling leaves inoculated with H2O


title: Untreated-8w-2


title: E. coli treated with w/o microemulsion

city: Hangzhou

first: Cai

last: Haiying

address: #866 Yuhangtang Road

country: China

institute: Zhejiang Universtiy

description: cells in exponential phase

hyb_protocol: Labeled cDNA were hybridized using the Nimblegen Hybridization System to Nimblegen Escherichia coli O157:H7 Genechip Microarrays (Roche NimbleGen Inc., USA), which contains 65,280 probes for the detection of 5,440 genes expression and some control probes used to evaluate system performance.

scan_protocol: Microarray images were scanned by Axon Instruments Gene Pix 4000B scanner (Molecular Devices, USA)，and subsequently quantified and corrected for background using GenePix Pro6.0 software (Molecular Devices, USA).

data_processing: Raw microarray intensity data were normalized per chip to the same mean value, which is recommended by the manufacturer.

organism: Escherichia coli

source_name: cells

label_protocol: Fluorescently labeled cDNA was synthesized using the Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, USA)

growth_protocol: The strain E. coli CMCC(B) 44102, was provided by Institute of Microbiology, Chinese Academy of Sciences and preserved at the Department of Food Science and Nutrition, Zhejiang University. The strain was maintained in nutrient agar medium (NA, Hangzhou Microbiological Agents Co., Ltd., China) at 37 °C, and cultured in tryptic soy broth (TSB, Qingdao Hope Biotechnology Co., Ltd., China) at pH 7.0 and transferred every 20-24 h with incubation at 37 °C.

extract_protocol: Total RNA from cells of the microemulsion-treated E. coli was extracted in duplicate using an RNAiso Plus (Cat. # 908, Takara, Japan) according to the manufacturer’s instructions,

treatment_protocol: 5 ml bacterial cultures with a known inoculum of E. coli cells (1.0 × 109 cfu/ml) was added at 1:1 (v/v) to the microemulsion and incubated on a tube rotator at 200 rpm for 4 h at 37 °C for the subsequent DNA microarray analysis. In the preliminary experiment, a complete loss of E. coli viability was achieved after 8 h by the aforementioned treatment. The prepared microemulsion has an oil phase of glycerol monolaurate (5.5% w/w of the total emulsion), ethanol (5.5%), and a surfactant phase of Tween 20 (43%). Mixtures of the surfactant-oil phase were prepared in stoppered flasks and kept in a 25 °C water bath. Subsequently, the water phase was added, and the mixture was treated in an ultrasonic bath until the system became optically clear, and allowed to equilibrate at 25 °C for at least 24 h to guarantee steady-state conditions.

value: water in oil


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 6, technical rep. left

status: Public on Jan 27 2014

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

institute: Technical University Munich

description: Sample 6a

hyb_protocol: Differently labeled samples derived from one RNA set were combined. The volume was reduced to 30 μl in a SpeedVac Concentrater 5301 (Eppendorf).  Then, 6 μl 20 x SSC and 4 μl 1 % SDS were added. Reaction mix was incubated 1 min at 94 °C and subsequently put on ice. Then, the reaction mix was applied to the microarray slide and the slide was covered with a cover slip. Hybridization was performed over night at 64 °C.

scan_protocol: Slides were scanned with the GenePix 4000B scanner (MDS Analytical Technologies) and data were analyzed via the GenePix 6.0 software (MDS Analytical Technologies).

data_processing: For normalization, the arithmetic mean of the ratios was set to one (GenePix Pro 6.0 software). In general, only spots with a fluorescence signal bigger than the local background plus one standard deviation were included in the final analysis. Spots with irregular morphology were in general excluded from the interpretation when the ratio of medians, the ratio of means and the regression ratio differed more than 30 %. To minimize the possibility of incorrect exclusion of spots due to automated interpretation, raw data of spots with a log2 ratio of medians ≥ 1 or ≤ -1 were further analyzed. If either the Cy5 or the Cy3 fluorescence intensity reached at least 50 % of the intensity averages of all spots of the respective array, the spot was included in the final analysis. As each experiment included technical duplicates, 12 data points were received for the calculation of the expression level of each gene. Genes were treated as up- or down-regulated, if (i) the log2 RTL was calculated based on at least 8 valid spots, each with a log2 ratio of medians (anaerobic/aerobic) ≤ -1.0 or ≥ 1.0 and (ii) the arithmetic mean of the log2 ratio of medians of valid spots was ≤ -1.0 or ≥ 1.0.

organism: Listeria monocytogenes EGD

source_name: anaerobically grown cells

label_protocol: 30 μg of bacterial RNA were mixed with the reverse transcription reaction mix (1 μl Superscript III Reverse Transcriptase (200 U/μl), 8 μl 5 x reaction buffer, 4 μl DTT (0.1 M) (Invitrogen), 3 µl random nonamer oligonucleotides (GE Healthcare), and 1 μl dNTP mix (20 mM dATP, 20 mM dGTP, 20 mM dTTP, and 16 mM dCTP (Fermentas)). Volume was adjusted to 38 μl with DEPC treated water, and 2 μl of a Cy3- or Cy5-labelled dCTP analogue were used for fluorescent labeling of the cDNA. Samples were incubated at 42 °C for 2 h. Then, 2 μl DNase-free RNase (> 30 U/mg, Roche Diagnostics) were added and the sample was incubated for 45 min at 37 °C and cDNA was purified using the QIAquick® PCR-Purification Kit (Qiagen) and eluted in 40 μl dH2O.

growth_protocol: 500 µl of an L. monocytogenes EGD overnight culure was used for inoculation of 50 ml BHI medium. The cultures were grown at 37 °C to an OD 600 of 0.70-0.75 either aerobically or anaerobically.

extract_protocol: The cell pellet was resuspendet in 1 ml TRIzol/TRI Reagent (Invitrogen/Sigma) and transferred into a 2 ml shredder-tube (Sarstedt) containing silic beads (diameter 0.1 mm). Solution was incubated at room temperature for 1 min, before cell walls were disrupted mechanically in a FastPrep cell disrupter. Silica beads were removed by centrifugation, RNA was extracted with chloroforme extraction, precipitated with isopropanol and the pellet was washed with 70 % EtOH. Residual DNA was removed by DNaseI digestion (Promega) according to manufacturer´s instructions. RNA was purified again follwoing the RNA clean-up protocol from the RNeasy Mini Kit (Quiagen), and an additional on column DNA digest was performed.

treatment_protocol: After reaching the final OD, cells were collected by centrifuging and the cell pellet was shock frozen immediately in liquid nitrogen. The cell pellet was stored at - 80 °C untill further processing.

tag: od600 at harvest

source_name: aerobically grown cells


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 6, technical rep. right

description: Sample 6b


title: Maize_Mock_4day_rep1


title: genomic DNA from pituitary macroadenoma Sample 15

description:
d8485
female, invasive, pituitary


title: E. coli treated with bicontinious microemulsion

description: cells in exponential phase

value: bicontinious microemulsion


title: E. coli without microemulsion treatment

description:
this sample is used as control, it is not treated by any material
cells in exponential phase

value: control


title: Maize_Mock_4day_rep2


title: genomic DNA from pituitary macroadenoma Sample 11

description:
d1426
female, noninvasive, pituitary

value: pituitary macroadenoma

value: GH


title: E. coli treated with o/w microemulsion

description: cells in exponential phase

value: oil in water


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 5, technical rep. right

description: Sample 5b


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 5, technical rep. left

description: Sample 5a


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 3, technical rep. right

description: Sample 3b


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 4, technical rep. right

description: Sample 4b


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 2, technical rep. left

description: Sample 2a


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 2, technical rep. right

description: Sample 2b


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 3, technical rep. left

description: Sample 3a


title: HbV LIVER1

city: roma

first: antonella

last: minutolo

address: viale del policlinico

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes:ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes BETA ACTIN).
Fold Change worksheet reports test/control ratios average.

label: SYBR Green

source_name: fresh liver

label_protocol: Human Adipogenesis RT² Profiler™ PCR Array SAbiosciences Qiagen

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment THERMO SCIENTIFIC

tag: phenotype

value: HbV+ liver

value: liver biopsy


title: genomic DNA from pituitary macroadenoma Sample 7

description:
d0298
male, noninvasive, pituitary

value: GH-LH

value: male

value: noninvasive


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 1, technical rep. right

description: Sample 1b


title: genomic DNA from pituitary macroadenoma Sample 8

description:
d8312
female, noninvasive, pituitary

value: female


title: genomic DNA from pituitary macroadenoma Sample 6

description:
d1438
male, noninvasive, pituitary


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 1, technical rep. left

description: Sample 1a


title: genomic DNA from pituitary macroadenoma Sample 4

description:
d0500
male, noninvasive, pituitary


title: genomic DNA from pituitary macroadenoma Sample 3

description:
d0261
female, noninvasive, pituitary


title: genomic DNA from pituitary macroadenoma Sample 5

description:
d1055
male, noninvasive, pituitary


title: Diffuse large B-cell lymphoma 69

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470A) for 18-20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 9.5.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 50% missing values across the samples were included in the further analysis.

source_name: Tumor biopsies from transformed-DLBCL specimens

label_protocol: 120 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.Labeled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221)

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manufacturer.

value: tumor biopsies from transformed-DLBCL specimens

tag: sample type

value: Fresh frozen tissue


title: Diffuse large B-cell lymphoma 67

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 66

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 70

description: miRNA expression profile


title: genomic DNA from pituitary macroadenoma Sample 2

description:
d0116
female, noninvasive, pituitary

value: NFA


title: Diffuse large B-cell lymphoma 63

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 64

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 62

description: miRNA expression profile


title: L. monocytogenes EGD, aerobic vs. anaerobic, biological rep. 4, technical rep. left

description: Sample 4a


title: Diffuse large B-cell lymphoma 61

description: miRNA expression profile


title: Gnmt_KO_1

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description: Sciatic nerves from GNMT-WT mice_Replicate 1_Gene Expression Array

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package. The data were normalised using quantile normalisation with lumi in R.

label: Biotin

organism: Mus musculus

source_name: Sciatic nerves from GNMT-WT mice

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Cat.Num. TAN07924)

growth_protocol: Sciatic nerves from post natal day 90 GNMT (wt and KO)  mice of either sex were dissected and pooled together.

extract_protocol: RNA was extracted from pooled nerves using Trizol reagent

value: GNMT WT

tag: developmental stage

value: Post natal day 90


title: Gnmt_WT_2

description: Sciatic nerves from GNMT-KO mice_Replicate 2_Gene Expression Array

source_name: Sciatic nerves from GNMT-KO mice

value: GNMT KO


title: Gnmt_WT_1

description: Sciatic nerves from GNMT-KO mice_Replicate 1_Gene Expression Array


title: P60_1

description: Sciatic nerves from P60 mice_Replicate 1_Gene Expression Array

source_name: Sciatic nerves from P60 mice

growth_protocol: Sciatic nerves from C57Bl6J mice of either sex, were dissected and pooled together at different developmental stages.


title: Diffuse large B-cell lymphoma 59

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 60

description: miRNA expression profile


title: Gnmt_KO_2

description: Sciatic nerves from GNMT-WT mice_Replicate 2_Gene Expression Array


title: NB_2

description: Sciatic nerves from new-born mice_Replicate 2_Gene Expression Array

source_name: Sciatic nerves from new-born mice

value: New born


title: NB_1

description: Sciatic nerves from new-born mice_Replicate 1_Gene Expression Array


title: P10_3

description: Sciatic nerves from P10 mice_Replicate 3_Gene Expression Array

source_name: Sciatic nerves from P10 mice


title: P60_3

description: Sciatic nerves from P60 mice_Replicate 3_Gene Expression Array


title: P60_2

description: Sciatic nerves from P60 mice_Replicate 2_Gene Expression Array


title: genomic DNA from pituitary macroadenoma Sample 1

description:
d9986
male, noninvasive, pituitary

value: Silent ACTH


title: Diffuse large B-cell lymphoma 58

description: miRNA expression profile


title: P10_1

description: Sciatic nerves from P10 mice_Replicate 1_Gene Expression Array


title: P10_2

description: Sciatic nerves from P10 mice_Replicate 2_Gene Expression Array


title: Diffuse large B-cell lymphoma 31

description: miRNA expression profile

source_name: Tumor biopsies from De novo-DLBCL specimens

value: tumor biopsies from De novo-DLBCL specimens


title: Diffuse large B-cell lymphoma 32

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 30

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 28

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 27

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 23

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 24

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 26

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 25

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 21

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 57

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 19

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 11

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 13

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 14

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 12

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 16

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 18

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 10

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 22

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 15

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 20

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 29

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 6

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 7

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 9

description: miRNA expression profile


title: NB_3

description: Sciatic nerves from new-born mice_Replicate 3_Gene Expression Array


title: Diffuse large B-cell lymphoma 17

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 8

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 5

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 4

description: miRNA expression profile


title: dorn1-1 Root 100 mM ATP 30 min rep3

city: Columbia

first: Gary

last: Stacey

state: MO

address: 1201 East Rollins street C. Bond Life Sciences center R202

department: Division of Plant Sciences

institute: University of Missouri

description: Wild type plants carring the EMS mutation in the Lectin receptor kinase I.9 were used.

hyb_protocol: GeneChip Hybridization, Wash and Stain kit from Affymetrix was used to make the hybridization mixture containing 10 microgram of the biotin-cRNA.  The Genechip was hybridized for 18 hours at 45 C and 60 rpm.  The chip was washed and stained with protocol FS_450_0004 on GeneChip Fluidics Station 450.

scan_protocol: The array images were acquired using Affymetrix GeneChip Scanner 7G using AGCC 3.1 software. These data were imported into GeneSpring 7.0 (Silicon Genetics, Redwood City, CA, USA). To remove chip-to-chip signal variation, each measurement was divided by the 50.0th percentile of all measurements in that sample.

data_processing: The raw intensities of the Affymetrix data were preprocessed using the rma function of the R Affy package, which does probe-specific correction of the perfect match (PM) probes using a model based on observed intensity being the sum of signal and noise, normalizing the corrected PM probes using quantile normalization and then calculating the expression measure using median polish. The resultant gene expression values were transformed to a log base 2 scale.

organism: Arabidopsis thaliana

source_name: Root, 100 mM ATP, 30 min

label_protocol: A total of 500 ng of RNA was used to synthesize double stranded cDNA.  The biotin-labeled cRNA was synthesized by T7 RNA polymerase-assisted in vitro transcription of the cDNA according to the MesssageAmp Primer RNA Amplification Kit protocol from Ambion (Austin, TX)

growth_protocol: Arabidopsis seeds were sown onto half strength Murashige and Skoog (MS) media containing 1% (w/v) sucrose, 1% (w/v) agar, and 0.5% (w/v) MES (pH 5.7). After cold treatment for three days, the plates were placed vertically in a growth chamber (16 h light/8 h dark cycle, 22°C, 100 μE cm-2sec-1 light intensity) and plants were grown for 5 days.

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions followed by chloroform-based purification. Genomic DNA was removed by Turbo DNase (Ambion) treatment .The DNA-free RNA was further purified with Qiagen RNeasy mini columns.

treatment_protocol: For each replicate, 120 seedlings were pooled and incubated in a single well of a 24-well plate containing 1 mL buffer (2 mM MES pH 5.7, 10 mM CaCl2) overnight at room temperature in dark. Root tissues were selectively harvested and frozen in liquid nitrogen 30 min after treatment with 100 μM ATP and 2 mM MES buffer.

tag: ecotype

tag: genotype/variation

value: dorn1-1 mutant

value: Roots of 5 day-old seedlings


title: dorn1-1 Root 100 mM ATP 30 min rep2


title: Lymph node 10

description: miRNA expression profile

source_name: Non-neoplastic lymphatic tissue

value: non-neoplastic lymphatic


title: Diffuse large B-cell lymphoma 1

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 3

description: miRNA expression profile


title: Diffuse large B-cell lymphoma 2

description: miRNA expression profile


title: Col-0 Root 100 mM ATP 30 min rep2

description: Transgenic Arabidopsis expressing calcium reporter protein, aequorin, were used as wild-type Col-0.

value: wild type


title: Col-0 Root 100 mM ATP 30 min rep3


title: dorn1-1 Root MES buffer 30 min rep2

source_name: Root, 2mM MES buffer, 30min


title: dorn1-1 Root MES buffer 30 min rep3


title: Col-0 Root MES buffer 30 min rep3


title: dorn1-1 Root 100 mM ATP 30 min rep1


title: dorn1-1 Root MES buffer 30 min rep1


title: Col-0 Root 100 mM ATP 30 min rep1


title: Col-0 Root MES buffer 30 min rep2


title: Lymph node 9

description: miRNA expression profile


title: Lymph node 7

description: miRNA expression profile


title: Lymph node 4

description: miRNA expression profile


title: Lymph node 2

description: miRNA expression profile


title: Col-0 Root MES buffer 30 min rep1


title: Lymph node 1

description: miRNA expression profile


title: Lymph node 8

description: miRNA expression profile


title: Lymph node 6

description: miRNA expression profile


title: Lymph node 5

description: miRNA expression profile


title: CD4+_CD4(cre)Raptor(fl/fl)_24hStimulation_rep4

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six (6) micrograms of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system.

scan_protocol: HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5.

source_name: CD4+ T-cells from CD4(cre)Raptor(fl/fl) mouse, stimulated for 24h with anti CD3/CD28 antibodies

label_protocol: Twenty (20) nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module.

growth_protocol: Lymphocytes were isolated from the spleen and peripheral lymph nodes of mice, and naïve T cells (CD4+CD62LhiCD44loCD25-) were sorted by flow cytometry.

extract_protocol: RNA was extracted using Qiagen's RNeasy kit, with on-column DNase digestion included.

treatment_protocol: Sorted naïve T cells (CD4+CD62LhiCD44loCD25-) were used directly, or stimulated for 8 hours or 24 hours by plate-bound anti-CD3/CD28 antibodies.

tag: cell type

value: T cells (CD4+CD62LhiCD44loCD25-)

value: stimulation with anti-CD3/CD28 antibodies

tag: treatment duration


title: Lymph node 3

description: miRNA expression profile


title: CD4+_CD4(cre)Raptor(fl/fl)_24hStimulation_rep3

tag: treatment


title: CD4+_WT_24hStimulation_rep2

source_name: CD4+ T-cells from WT mouse, stimulated for 24h with anti CD3/CD28 antibodies

tag: strain/background

value: WT


title: CD4+_WT_24hStimulation_rep4


title: CD4+_WT_24hStimulation_rep3


title: CD4+_CD4(cre)Raptor(fl/fl)_24hStimulation_rep2


title: CD4+_CD4(cre)Raptor(fl/fl)_8hStimulation_rep3

source_name: CD4+ T-cells from CD4(cre)Raptor(fl/fl) mouse, stimulated for 8h with anti CD3/CD28 antibodies


title: CD4+_CD4(cre)Raptor(fl/fl)_24hStimulation_rep1


title: CD133a

city: barcelona

first: marianna

last: vitaloni

address: dr aiuguader 88,7

institute: centre of regenerative medicine of barcelona

hyb_protocol: Sample was hybridized to Affymetrix Multispecies miRNA 3.0 Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing:
The data were RMA normalized in R (v 2.15.0) using aroma.affymetrix (v 2.7.0) and then LIMMA was applied to calculate significant differential expression between samples
RMA, Log FC of 2 was selected as a threshold for the selection of differentially expressed miRNAs between conditions

source_name: cord blood_CD133+

label_protocol: 500 ng of total RNA were amplified and labeled using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix)

extract_protocol: miRNeasy Kit QIAGEN

tag: tissue

value: cord blood

value: CD133+ cells isolated from Cord blood


title: CD4+_WT_8hStimulation_rep4

source_name: CD4+ T-cells from WT mouse, stimulated for 8h with anti CD3/CD28 antibodies


title: CD4+_CD4(cre)Raptor(fl/fl)_8hStimulation_rep2


title: FiPS

value: fibroblast

tag: cell line

value: FiPS

value: induced pluripotent stem cell lines derived from fibroblas

tag: passage number

value: high (more than 25)


title: CD4+_WT_24hStimulation_rep1


title: CD133b


title: CBiPS b_L

value: CD133+cord blood cells

value: CBiPS b

value: induced pluripotent stem cell lines derived from CD133+cord blood cells using OCT4,SOX2,KLF4,c-Myc

value: low (between 5 and 10)


title: CBiPS b_H

value: induced pluripotent stem cell lines derived from CD133+cord blood cells using OCT4,SOX2,KLF4,c-M


title: ES

source_name: embryonic stem cells

value: ES

value: embryonic stem cell lines


title: Diffuse large B-cell lymphoma 65

description: miRNA expression profile

value: tumor biopsies from transformed-DLBCL specimens

value: Fresh frozen tissue


title: CD4+_WT_8hStimulation_rep3

value: T cells (CD4+CD62LhiCD44loCD25-)

value: stimulation with anti-CD3/CD28 antibodies


title: CD4+_CD4(cre)Raptor(fl/fl)_8hStimulation_rep1


title: CD4+_WT_8hStimulation_rep2

value: WT


title: CD4+_WT_8hStimulation_rep1


title: CD4+_WT_NoStimulation_rep3

source_name: CD4+ T-cells from WT mouse, unstimulated

value: naïve T cells (CD4+CD62LhiCD44loCD25-)


title: CD4+_CD4(cre)Raptor(fl/fl)_8hStimulation_rep4


title: CD4+_WT_NoStimulation_rep4


title: CD4+_CD4(cre)Raptor(fl/fl)_NoStimulation_rep4

source_name: CD4+ T-cells from CD4(cre)Raptor(fl/fl) mouse, unstimulated


title: CD4+_WT_NoStimulation_rep1


title: CD4+_CD4(cre)Raptor(fl/fl)_NoStimulation_rep2


title: CD4+_WT_NoStimulation_rep2


title: CD4+_CD4(cre)Raptor(fl/fl)_NoStimulation_rep3


title: siRNA 2-3

status: Public on Jan 26 2014

city: Tokyo

first: Michiko

last: Nakamura

address: 2-10-1 Ohkura Setagaya-ku

department: Molecular Endocrinology

country: Japan

institute: National Research Institute for Child Health and Development

description: Gene expression after 48hr in mouse Leydig tumor cells with siRNA2 against Mamld1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, 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 to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse Leydig tumor cells with siRNA2 against Mamld1, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using Agilent One-Color Microarray-Based Gene Expression (Quick Amp Labeling) (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MLTCs were maintained in RPMI 1640 supplemented with 10% fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (Qiagen)、 DNase free (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: MLTCs were transiently transfected with two siRNAs against Mamld1 or with non-targeting control RNA (4611G) (final concentration 20 nM), using Lipofectamine RNAiMAX (Life Technologies) and 48h later, total RNA was extracted.

value: Leydig tumor cells

tag: sirna transfection

value: siRNA 2

value: Mamld1 knockdown


title: siRNA 1-4

description: Gene expression after 48hr in mouse Leydig tumor cells with siRNA1 against Mamld1

source_name: mouse Leydig tumor cells with siRNA1 against Mamld1, replicate 4

value: siRNA 1


title: siRNA 2-2

source_name: mouse Leydig tumor cells with siRNA2 against Mamld1, replicate 2


title: siRNA 1-2

source_name: mouse Leydig tumor cells with siRNA1 against Mamld1, replicate 2


title: CD4+_CD4(cre)Raptor(fl/fl)_NoStimulation_rep1


title: siRNA 1-3

source_name: mouse Leydig tumor cells with siRNA1 against Mamld1, replicate 3


title: negative control 4

description: Gene expression after 48hr in mouse Leydig tumor cells with non-targeting RNA

source_name: mouse Leydig tumor cells with non-targeting RNA, replicate 4

value: non-targeting control RNA (4611G)

value: control


title: myrAkt CD34- 3

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Signal intensity was obtained using MAS 5.0

source_name: myrAkt CD34- 3

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

growth_protocol: K5-myrAkt(L84) transgenic mice were described in Segrelles C. et al., Cancer Res (2007) 67:10879-88. Keratinocytes were isolated from the back skin of K5myrAkt transgenic mice, labelled with anti-CD34 and isolated using magnetic beads as described in as described in Lorz C. et al., Methos Mol Biol (2010) 585:1-11.

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

tag: strain

value: K5-myrAkt(L84) mice

value: CD34(-) hair follicle stem cells


title: myrAkt CD34+ 3

source_name: myrAkt CD34+ 3

value: CD34(+) hair follicle stem cells


title: T_Ctrl_biological rep1

city: Shanghai

first: Xiang

last: Yu

address: 320 Yue Yang Road

department: Institute of Neuroscience and State Key Laboratory of Neuroscience

institute: Chinese Academy of Sciences

description: Gene expression in P14 Ctrl thalamus & hypothalamus

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Thalamus, Hypothalamus, Control, biological replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa  Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Control mice were housed in standard plastic cages (32.5 × 21 × 18.5 cm) with corn bedding, ad libitum access to food and water and on a 12:12 light cycle. For dark-rearing (DR), the pregnant dams were placed in a cage completely covered by thick black plastic 1-4 days prior to delivery, and mice were cared for under dim red light. Mice were kept in the DR condition until time of experiment.

value: thalamus, hypothalamus

tag: age


title: siRNA 2-1

source_name: mouse Leydig tumor cells with siRNA2 against Mamld1, replicate 1


title: negative control 2

source_name: mouse Leydig tumor cells with non-targeting RNA, replicate 2


title: myrAkt CD34+ 4

source_name: myrAkt CD34+ 4


title: myrAkt CD34+ 2

source_name: myrAkt CD34+ 2


title: myrAkt CD34- 5

source_name: myrAkt CD34- 5


title: myrAkt CD34- 4

source_name: myrAkt CD34- 4


title: myrAkt CD34+ 1

source_name: myrAkt CD34+ 1


title: myrAkt CD34+ 5

source_name: myrAkt CD34+ 5


title: negative control 3

source_name: mouse Leydig tumor cells with non-targeting RNA, replicate 3


title: negative control 1

source_name: mouse Leydig tumor cells with non-targeting RNA, replicate 1


title: myrAkt CD34- 1

source_name: myrAkt CD34- 1


title: myrAkt CD34- 6

source_name: myrAkt CD34- 6


title: myrAkt CD34- 2

source_name: myrAkt CD34- 2


title: T_Ctrl_biological rep2

source_name: Thalamus, Hypothalamus, Control, biological replicate 2


title: siRNA 1-1

source_name: mouse Leydig tumor cells with siRNA1 against Mamld1, replicate 1


title: T_DR_biological rep1

description: Gene expression in P14 DR thalamus & hypothalamus

source_name: Thalamus, Hypothalamus, Dark rearing, biological replicate 1


title: miPSC-EC from DIO mouse1

status: Public on Jan 25 2014

city: Stanford

first: Nicholas

last: Mordwinkin

state: CA

address: 265 Campus Drive, G1105

institute: Stanford University

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were normalized, annotated and analyzed using AltAnalyze.

source_name: miPSC-EC from diet-induced obesity (DIO) mouse

label_protocol: Affymetrix 3'IVT Express protocol was used to generate biotinylated cRNA from 50-500 ngs of total RNA.

growth_protocol: miPSC-ECs were grown in endethelial cell medium at 37 degrees Celsius.

extract_protocol: Total RNA was isolated from biological duplicates of control and diet-induced obesity murine iPSC-ECs using the Qiagen Rneasy Mini Plus Kit according to the manufacturer instructions.

treatment_protocol: Cells were trypsinized before harvesting the RNA.

value: iPSC

value: 24 weeks


title: N_HP-,S07-31543

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,S07-31543

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression Blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s Human miRNA Microarray (60K, Release 16.0) and hybridized at 55 °C for 20 h with 20 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner.

data_processing: Feature Extraction software (version 10.10.1.1) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. Background intensity and feature nonuniform outliers were removed by standard procedures. Data visualization and analysis were performed with GeneSpring GX (version 7.3) software (Agilent Technologies). Signal cut-off measurements were less than 5, and normalized to 75th percentile of signal intensity to standardize each chip for cross-array comparison. Differentially expressed miRNAs were identified using a Student’s two-sample t-test with p values cut off by 0.05 and fold change more than 2.0. One-way ANOVO was used to analyze the correlation between the expression levels of miRNAs and clinic-pathological features of the patients.

source_name: H. pylori-negative FFPE specimen

label_protocol: 400 ng of total RNA was labeled with cyanine 3-pCp using the Agilent miRNA Complete Labeling kit and hybridized to the array according to the manufacturer’s protocol.

growth_protocol: Sixteen gastric cancer patients matched for age, sex and H. pylori status, who received curative operation at Seoul National University Bundang Hospital, were included for microarray study.

extract_protocol: After manual dissection under microscopic guidance avoiding the contamination of inflammatory cells and stromal cells, H&E stained sections 50 μm in thickness from cancerous and non-cancerous regions of intestinal type of gastric cancer FFPE samples were reviewed by one pathologist (H.S.L). Each section was incubated in xylene and total RNA was extracted using a RecoverAllTM Total Nucleic Acid Isolation kit (Life Technologies, CA, USA).

treatment_protocol: All subjects of this study received gastroscopy for gastric cancer screening and conformation of histological gastric adenocarcinoma diagnosis.

tag: disease

value: FFPE specimen


title: N_HP-,S07-28675

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,S07-28675


title: miPSC-EC from control mouse2

source_name: miPSC-EC from healthy (control) mouse


title: N_HP-,S09-24505

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,S09-24505


title: N_HP-,s10-37703

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,s10-37703


title: N_HP-,S10-18586

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,S10-18586


title: N_HP-,s09-29443

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,s09-29443


title: miPSC-EC from control mouse1


title: N_HP-,s07-33646

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,s07-33646


title: T_DR_biological rep2

source_name: Thalamus, Hypothalamus, Dark rearing, biological replicate 2


title: SKNSH MECP2_e1 3

city: Toronto

first: john

last: vincent

state: ON

address: 250 College Street

department: Neuroscience Research

country: Canada

institute: Centre for Addiction & Mental Health

hyb_protocol: performed as service through the UHN Microarray Centre, Toronto, ON (www.microarrays.ca)

scan_protocol: Scanner Model G2565C DNA Scanner

data_processing: Feature Extraction Version 10.7; Extraction protocol GE2_107_Sept07

source_name: SK-N-SH cell line infected with MECP2_e1 lenti

growth_protocol: Cells were grown in Eagle's Minimal Essential Medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Wisent, St. Bruno, QC, Canada) and Penicillin-Streptomycin (Invitrogen, Carlsbad, CA, USA). Neuronal differentiation of infected SK-N-SH cells was achieved by treatment of cells with retinoic acid (Cedarlane Laboratories, Burlington, ON, Canada) and herbimycin A (Cedarlane Laboratories, Burlington, ON, Canada), using a modification of the protocol previously described (Preis et al., 1988). Retinoic acid was added to the medium at 10 uM concentration seven days post-infection, and cells were grown in the presence of retinoic acid for 96 h, with medium being replaced with fresh retinoic-acid containing medium every two days. Retinoic acid treatment increases the number of neuronally committed cells in the SK-N-SH culture (Preis et al. 1988). After 96 hours, herbimycin A was added to the growth medium at 236 nM concentration, and cells were grown in the presence of both herbimycin A and retinoic acid for 72 hours, with medium being replaced with fresh medium after 48 hours. Herbimycin A was used to clear the undifferentiated cells from the culture(Preis et al., 1988).

extract_protocol: RNA was isolated from stably infected neuronally differentiated cells and from stably infected primary mouse fibroblasts using TRIzol (Invitrogen, Carlsbad, CA, USA), in accordance with the manufacturer’s protocol. The concentration of total RNA was determined by NanoDrop® spectrophotometry. Isolated RNA was stored at -80°C. The reverse transcription was performed using 2 mg of total RNA, SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) and random primers (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions

treatment_protocol: Recombinant lentiviruses that we used to infect subconfluent SK-N-SH cells were described previously by Rastegar et al.(Rastegar et al., 2009). These are self-inactivating lentiviruses encoding either MECP2_e1, MECP2_e2 or eGFP under the control of the EF1a promoter.

value: SK-N-SH

tag: lentivirus isoform

tag: lentivirus

source_name: human reference RNA (Stratagene)

value: reference


title: SKNSH MECP2_e1 INS 1

source_name: SK-N-SH cell line infected with MECP2_e1 with 9bp INS mutation lenti

value: Mut

tag: sample type


title: SKNSH MECP2_e1 2

value: WT


title: miPSC-EC from DIO mouse2


title: SKNSH MECP2_e1 INS 2


title: wxl micro

first: Xiaoling

last: WAN

address: 320 Yue-yang road, Shanghai

institute: Institut pasteur of Shanghai, Chinese Academy of Sciences

description: gene expression data in E14 cells after Mll2 knockdown

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: Slides were scanned by Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies,Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: E14 cells were infected with lentiviruses expressing short hairpin RNA (shRNA) for Mll2  for 24 hours, and then puromycin was added at 2mg/ml to select for 5 days. Then collet samples of control and Mll2 knockdown E14 cells for RNA extraction and hybridization on Affymetrix microarrays.

value: short hairpin RNA (shRNA) for Mll2

value: E14 cell line, mouse embryonic stem cell


title: SKNSH eGFP2

source_name: SK-N-SH cell line infected with eGFP lenti

value: eGFP


title: SKNSH MECP2_e2 2

source_name: SK-N-SH cell line infected with MECP2_e2 lenti


title: SKNSH eGFP1


title: SKNSH MECP2_e1 1


title: SKNSH eGFP3


title: SKNSH MECP2_e2 1


title: N_HP-,s10-12710

description: miRNA expression in the H. pylori-negative FFPE specimen (non-cancerous region), N_HP-,s10-12710


title: SKNSH MECP2_e2 3


title: SKNSH MECP2_e1 INS 3


title: N_HP+,s09-7311

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,s09-7311

source_name: H. pylori-positive FFPE specimen


title: plka1 micro

description: gene expression data in E14 cells

source_name: E14 cells infected with lentivirus expressing control short hairpin RNA (shRNA)

value: control short hairpin RNA (shRNA)


title: N_HP+,s08-21812

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,s08-21812


title: C_HP+_S08-5858

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+_S08-5858


title: N_HP+,s07-1287

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,s07-1287


title: C_HP-,s10-37703

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,s10-37703


title: C_HP-,S10-18586

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,S10-18586


title: C_HP-,S07-28675

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,S07-28675


title: C_HP-,S09-24505

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,S09-24505


title: C_HP-,s07-33646

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,s07-33646


title: C_HP-,s10-12710

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,s10-12710


title: C_HP-,s09-29443

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,s09-29443


title: Malignant pleural mesothelioma, extrapleural pneumonectomy, patient 5, vinorelbine/cis-platin

city: Copenhagen

first: Morten

last: Andersen

address: Frederik V's vej 11

department: Department of Pathology, section 5432

country: Denmark

institute: Rigshospitalet

description:
Sample 15
Test

data_processing:
The normalization and all data analysis were performed according to the manufacturer's instructions using specifically adapted GenEx software (version 2.5): http://www.exiqon.com/qpcr-software .
For the normalization, the average of all assays (global mean) detected in all samples was used. 153 assays were detected in all samples.
Target microRNA assays normalized to global mean using the formula: 2^-deltaCq, where deltaCq=assay Cq - Cq(n=153).
The specifically adapted GenEx software provided by the manufacturer performs all 2^-deltadeltaCq based fold-change calculations.

Non-normalized matrix: Reports raw Cq values for all detected assays.
Fold-change matrix: Reports patient-matched test/control (i.e., Diagnostic biopsy/non-neoplastic pleura and surgical MPM tissue/non-neoplastic pleura) ratios for each patient.

source_name: Malignant pleural mesothelioma, vinorelbine/cis-platin treated

label_protocol: For cDNA synthesis, total RNA samples was diluted to 5 ng/µl. RNA was reverse transcribed using the miRCURY LNA Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit (prod. no. 203301, Exiqon, vedbaek, DK) according to the instructions of the manufacturer (http://www.exiqon.com/mirna-pcr-kits). The thermocycling profile for reverse transcription was: 60 min. at 42° C, 5 min. at 95° C, immediate cooling and storage at 4° C. Real-time PCR amplification was performed using cDNA template at 80x dilution and exiLENT SYBR green master mix (prod. no. 203420, Exiqon) according to the manufacturer's instructions. Real-time PCR amplification was performed on a Roche LightCycler LC480 instrument (F. Hoffmann-La Roche ltd., Basel, Switzerland) with the thermal cycling parameters: 10 min. at 95° C, 45 cycles at 95° C (10 s), 60° C (1 min.). Ramp rate: 1.6° C/s.

extract_protocol: Total RNA was extracted from formalin-fixed paraffin-embedded tissues with RecoverAll Total Nucleic Acid Isolation Kit, Ambion (AM1975).

treatment_protocol: Prior to surgical extraction of tissue specimens, all patients were treated with 1-3 series of vinorelbine/cis-platin. Diagnostic biopsies are untreated.

value: malignant pleural mesothelioma

value: vinorelbine/cis-platin

tag: gender

value: male

tag: age (years)

tag: tumor stage (ptnm)

value: III

tag: histology

value: epithelioid

tag: patient


title: N_HP+,S06-8880

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,S06-8880


title: C_HP-,S07-31543

description: miRNA expression in the H. pylori-negative FFPE specimen (cancerous region), C_HP-,S07-31543


title: N_HP+,S08-34041

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,S08-34041


title: N_HP+,S08-5858

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,S08-5858


title: C_HP+_S08-34041

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+_S08-34041


title: C_HP+_S06-8880

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+_S06-8880


title: C_HP+,s08-21812

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+,s08-21812


title: C_HP+,s07-1287

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+,s07-1287


title: C_HP+,s08-15511

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+,s08-15511


title: C_HP+,s09-7311

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+,s09-7311


title: N_HP+,s08-15511

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,s08-15511


title: N_HP+,S11-3539

description: miRNA expression in the H. pylori-positive FFPE specimen (non-cancerous region), N_HP+,S11-3539


title: C_HP+,S11-3539

description: miRNA expression in the H. pylori-positive FFPE specimen (cancerous region), C_HP+,S11-3539


title: Malignant pleural mesothelioma, extrapleural pneumonectomy, patient 3, vinorelbine/cis-platin

description:
Sample 13
Test

tag: treatment

value: II


title: mouse ko fibroblast MECP2_e1 INS 2

source_name: Fibroblast; Mecp2tm1.1Bird/J

growth_protocol: Cells were grown in Minimal Essential Medium (Invitrogen, Carlsbad, CA, USA) supplemented with 20% FBS and Penicillin-Streptomycin. Cells were kept at 37°C in humid atmosphere with 5% CO2

treatment_protocol: Recombinant lentiviruses that we used to infect fibroblasts were described previously by Rastegar et al.(Rastegar et al., 2009). These are self-inactivating lentiviruses encoding either MECP2_e1, MECP2_e2 or eGFP under the control of the EF1a promoter. The infections were performed in the presence of 100 ug/ml polybrene (Sigma-Aldrich). Three independent infections with each lentiviral construct were performed for each cell line, providing three biological replicates for each treatment. Three days after infection the virus-containing medium was removed and replaced with fresh growth medium.

tag: isoform

source_name: mouse reference RNA (Stratagene)

value: mouse reference RNA (Stratagene)


title: Malignant pleural mesothelioma, extrapleural pneumonectomy, patient 1, vinorelbine/cis-platin

description:
Sample 11
Test

tag: tissue

value: female

value: IV


title: Malignant pleural mesothelioma, extrapleural pneumonectomy, patient 2, vinorelbine/cis-platin

description:
Sample 12
Test


title: Non-neoplastic pleura, extrapleural pneumonectomy, patient 5, vinorelbine/cis-platin

description:
Sample 10
Control

source_name: Pleura visceralis, vinorelbine/cis-platin treated

value: non-neoplastic pleura


title: Non-neoplastic pleura, extrapleural pneumonectomy, patient 4, vinorelbine/cis-platin

description:
Sample 9
Control


title: Non-neoplastic pleura, extrapleural pneumonectomy, patient 3, vinorelbine/cis-platin

description:
Sample 8
Control


title: mouse ko fibroblast MECP2_e1 INS 1

tag: cell line


title: Passive SIgA negative, active SIgA negative, DSS positive, biological rep2

city: Lexington

first: Charlotte

last: Kaetzel

state: KY

address: 800 Rose St.

department: Microbiology, Immunology & Molecular Genetics

institute: University of Kentucky

hyb_protocol: 2 µg of biotnylated cDNA were hybridized for 16hr at 45C on Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed using Affymetrix RMA default analysis settings and global scaling as normalization method.

source_name: Passive SIgA negative_active SIgA negative_DSS positive

label_protocol: An aliquot of 250 ng of RNA from each pool was used to generate reverse-transcribed cDNA, of which 2 µg were biotnylated according to the GeneChip® Whole Transcript Sense Target Labeling Assay Protocol, Affymetrix.

growth_protocol: A breeding scheme was used that involved crosses between mouse dams and sires that were deficient or sufficient for expression of the polymeric immunoglobulin receptor (Pigr), a protein that is required for transport of secretory IgA (SIgA) into external secretions. Offspring of these crosses were genotyped for Pigr alleles, and littermate offspring were distributed into 4 groups based on early exposure to passive  SIgA in mother's milk (P-yes and P-no) and ability to carry out Pigr-mediated endogenous transport of active SIgA (A-yes and A-no).

extract_protocol: RNA was isolated using the MagNA Pure Compact RNA Isolation Kit and automated LightCycler System (Roche Applied Science, Indianapolis, IN). RNA concentration and purity were analyzed using the Agilent 2100 Expert Eukaryotic Total RNA Nanodrop System (Agilent Technologies, Santa Clara, CA). Only samples with an RNA Integrity Number of 8.5 or greater were used for microarray analysis. Two independent pooled RNA samples were made from each treatment group of 6 mice, by combining equal amounts of RNA from 3 individual mice, thereby generating 2 biological replicates per treatment.

treatment_protocol: Colonic epithelial cells were isolated from 70-day-old gender-matched Pigr+/- and Pigr-/- offspring of Pigr+/- and Pigr-/-  dams.

tag: strain background

tag: dam genotype

value: Pigr-/-

tag: offspring genotype

tag: passive siga in mother's milk

value: no

tag: ability to carry out pigr-mediated endogenous transport of active siga

tag: treated with

value: 2% dextran sulfate sodium (DSS) in drinking water for 8 days

tag: colitis

value: colitis

tag: cell type

value: Colonic epithelial cells


title: Passive SIgA negative, active SIgA negative, DSS positive, biological rep1


title: mouse ko fibroblast MECP2_e1 3

tag: strain

tag: lentivirus

value: WT

tag: sample type


title: mouse ko fibroblast MECP2_e1 INS 3

value: Mut


title: Passive SIgA negative, active SIgA positive, DSS positive, biological rep2

source_name: Passive SIgA negative_active SIgA positive_DSS positive

value: Pigr+/-

value: yes


title: Passive SIgA negative, active SIgA negative, DSS negative, biological rep1

source_name: Passive SIgA negative_active SIgA negative_DSS negative

value: none (untreated)

value: normal


title: mouse ko fibroblast MECP2_e1 2


title: mouse ko fibroblast eGFP3


title: mouse ko fibroblast MECP2_e2 1


title: mouse ko fibroblast MECP2_e1 1


title: Passive SIgA positive, active SIgA negative, DSS positive, biological rep2

source_name: Passive SIgA positive_active SIgA negative_DSS positive


title: mouse ko fibroblast MECP2_e2 2


title: Passive SIgA negative, active SIgA positive, DSS negative, biological rep1

source_name: Passive SIgA negative_active SIgA positive_DSS negative


title: Passive SIgA negative, active SIgA negative, DSS negative, biological rep2


title: Passive SIgA negative, active SIgA positive, DSS positive, biological rep1


title: mouse ko fibroblast MECP2_e2 3


title: Passive SIgA negative, active SIgA positive, DSS negative, biological rep2


title: Non-neoplastic pleura, extrapleural pneumonectomy, patient 1, vinorelbine/cis-platin

description:
Sample 6
Control

value: vinorelbine/cis-platin

tag: gender

tag: age (years)

tag: tumor stage (ptnm)

tag: histology


title: Malignant pleural mesothelioma, extrapleural pneumonectomy, patient 4, vinorelbine/cis-platin

description:
Sample 14
Test

tag: tissue

value: malignant pleural mesothelioma

tag: treatment

value: III

value: epithelioid

tag: patient


title: mouse ko fibroblast eGFP2

tag: cell line

value: mouse reference RNA (Stratagene)


title: Malignant pleural mesothelioma, diagnostic biopsy, patient 4, untreated

description:
Sample 4
Test

source_name: Malignant pleural mesothelioma, untreated

value: female


title: Malignant pleural mesothelioma, diagnostic biopsy, patient 5, untreated

description:
Sample 5
Test

value: male


title: Malignant pleural mesothelioma, diagnostic biopsy, patient 3, untreated

description:
Sample 3
Test

value: II


title: Malignant pleural mesothelioma, diagnostic biopsy, patient 2, untreated

description:
Sample 2
Test


title: Endogenous small RNAs from A. thaliana col-0_WT_rosette leaves_1

type: SRA

city: Poznan

first: Wojciech

middle: M.

last: Karlowski

address: Umultowska 89

country: Poland

institute: Adam Mickiewicz University

description: one RNA isolation, two independent small RNA seq

library_source: transcriptomic

data_processing:
data processing step included quality filtering, adaptor trimming and size selection for 18-24 nt fragments (in-house developed Python and Perl scripts)
gdh-1.txt

source_name: 35-day-old plant rosette leaves

growth_protocol: Plants were grown under 16 h day (150–200 µmol m-2s-1), constant temperature 22°C and humidity of 70% in ‘Jiffy soil' (Jiffy International AS, Kristiansand, Norway) in a growth chamber.

extract_protocol: RNA (35 µg per sample) was sent to BC Cancer Agency (Canada)  under 96% EtOH and Na-acetate (final concentration = 0.3M). cDNA library was constructed at BC Cancer Agency according to their protocol.

tag: ecotype

tag: genotype/variation

value: wild type

value: rosette leaves

tag: age

value: 35-day-old (fully developed)


title: Passive SIgA positive, active SIgA negative, DSS negative, biological rep1

source_name: Passive SIgA positive_active SIgA negative_DSS negative

tag: strain background

tag: dam genotype

tag: offspring genotype

value: Pigr-/-

tag: passive siga in mother's milk

tag: ability to carry out pigr-mediated endogenous transport of active siga

value: no

tag: treated with

value: Colonic epithelial cells


title: Malignant pleural mesothelioma, diagnostic biopsy, patient 1, untreated

description:
Sample 1
Test

tag: gender

value: IV


title: mouse ko fibroblast eGFP1

tag: strain

tag: sample type


title: Passive SIgA positive, active SIgA negative, DSS positive, biological rep1

value: Pigr+/-

value: yes

value: 2% dextran sulfate sodium (DSS) in drinking water for 8 days

tag: colitis

value: colitis

tag: cell type


title: A549_Embelin_15μM_4h_2

city: Hyderabad

first: Shasi

middle: Vardhan

last: Kalivendi

state: Andhra Pradesh

address: Uppal Road, Tarnaka

department: Center for Chemical Biology

country: India

institute: CSIR - Indian Institute of Chemical Technology

description: Gene expression after 4hr in 15μM Embelin treated A549 cells

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: The hybridized, washed microarray slides were scanned on a G2505C scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

source_name: A549 cells, Embelin 15μM, 4h, Replicate 2

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added to the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: A549 cells were obtained from ATCC, USA. Cells were grown in Minimum essential media (MEM) supplemented with 10% FBS, 100units/ml penicillin and 100units/ml streptomycin in humidified atmosphere with 5% CO2 at 37 ° C

extract_protocol: RNA isolation was performed using QIAGEN's RNAeasy  mini kit as per manufacturer's instructions. The concentration and purity of RNA extracted were evaluated using Nanodrop and integrity of the extracted RNA was confirmed by Bioanalyzer (Agilent; 2100).

treatment_protocol: Twelve hours before the treatment cell culture media was replace to MEM containing 2% FBS.

value: A549 cells

tag: treatment

value: Embelin


title: Passive SIgA positive, active SIgA positive, DSS positive, biological rep2

source_name: Passive SIgA positive_active SIgA positive_DSS positive


title: Passive SIgA positive, active SIgA positive, DSS positive, biological rep1


title: Passive SIgA positive, active SIgA negative, DSS negative, biological rep2

value: none (untreated)

value: normal


title: A549_Embelin_15μM_4h_1

source_name: A549 cells, Embelin 15μM, 4h, Replicate 1


title: Passive SIgA positive, active SIgA positive, DSS negative, biological rep1

source_name: Passive SIgA positive_active SIgA positive_DSS negative


title: Passive SIgA positive, active SIgA positive, DSS negative, biological rep2


title: A549_Embelin_0μM_4h_2

description: Gene expression after 4hr in untreated A549 cells

source_name: A549 cells, Untreated controls, 4h, Replicate 2

value: untreated


title: Non-neoplastic pleura, extrapleural pneumonectomy, patient 2, vinorelbine/cis-platin

description:
Sample 7
Control

tag: tissue

value: non-neoplastic pleura

value: vinorelbine/cis-platin

value: male

tag: age (years)

tag: tumor stage (ptnm)

tag: histology

tag: patient


title: A549_Embelin_0μM_4h_1

source_name: A549 cells, Untreated controls, 4h, Replicate 1

tag: cell line


title: LP mouse Lung squamous cell carcinoma stroma cell, biological rep3

status: Public on Jan 24 2014

city: Boston

first: Chunxiao

last: Xu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data from LP mouse  Lung squamous cell carcinoma stroma cell

hyb_protocol: 1. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 2. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. 3. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. 4. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: The data were analyzed in R (v 3.0.1) using the oligo package in which RMA normalization was applied.

growth_protocol: Mouse cohorts of Lkb1fl/fl/Ptenfl/fl, LSL:KrasG12D and wild type mice were all maintained in virus-free conditions on a mixed 129/FVB background.

extract_protocol: Trizol reagent followed by additional purification using RNeasy from Qiagen

treatment_protocol: Tumors were dissected from the lungs of primary mice and tumor tissue was prepared as description below:  Briefly, tumors were isolated, minced, digested rotating for 1h at 37°C with 2mg/ml Dispase (Roche) and then filtered twice (100 μm, then 40 μm) after a 5 minute incubation with 0.025 mg/mL DNase (SIGMA). Cell lines were trypsinized and then filtered (40 μm). For analyzing immune cell populations, cells were isolated with Collagenase type IV and DNase as described. Single cell suspensions were stained using rat-anti-mouse-Antibodies. Epithelial cells were gated as EpCAM+/CD45-/CD31-; stroma cells were cells were gated as EpCAM-/CD45+/CD31+.

value: mixed 129/FVB

value: lung

value: stroma

tag: genotype

value: Lkb1 -/- Pten-/-

tag: developmental stage

value: Adult


title: Kras G12D mouse Lung Adenocarcinoma stroma cell, biological rep1

description: Gene expression data from Kras G12D mouse Lung Adenocarcinoma stroma cell

value: Kras G12D


title: Kras G12D mouse Lung Adenocarcinoma stroma cell, biological rep3


title: LP mouse Lung squamous cell carcinoma stroma cell, biological rep2


title: Kras G12D mouse Lung Adenocarcinoma epithelial cell, biological rep2

description: Gene expression data from Kras mouse lung adenocarcinoma  epithelial cells

value: epithelial


title: normal epithelial cell, biological rep1

description: Gene expression data from normal lung epithelial cells

source_name: normal lung epithelial cells-1

value: wild type


title: Kras G12D mouse Lung Adenocarcinoma stroma cell, biological rep2


title: normal epithelial cell, biological rep2

source_name: normal lung epithelial cells-2


title: Kras G12D mouse Lung Adenocarcinoma epithelial cell, biological rep1


title: LP mouse Lung squamous cell carcinoma epithelial cell, biological rep3

description: Gene expression data from LP mouse lung squamouse cell carcinoma epithelial cells


title: LP mouse Lung squamous cell carcinoma stroma cell, biological rep1


title: normal epithelial cell, biological rep3

source_name: normal lung epithelial cells-3


title: LP mouse Lung squamous cell carcinoma epithelial cell, biological rep2


title: heart from DM1-induced mouse (72hr) #2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
heart from DM1-induced mouse (72hr)
EpA960 (72h)-2

hyb_protocol: According to Illumina protocol.  500ng of cRNA were applied to Illumina Mouse WG-6 v2 Whole-Genome Expression Beadchips.

scan_protocol: According to Illumina protocol. Following hybridization, washing and detection, chips were scanned using the Illumina 500GX scanner at the Genomics and Proteomics Core Laboratory at Texas Children’s hospital.

data_processing:
Expression data were quantile normalized, using custom code originally provided by Kerby Shedden at the University of Michigan. The actual code used (in C++) is provided as a Series supplementary file [normalize2.Cpp.txt].
Note: 'ProbeID' column in raw data files contains Illumina platform 'Array_Address_Id' identifiers.

source_name: heart from DM1-induced mouse (72hr)

label_protocol: According to Illumina protocol. Total RNA was amplified and labeled using the Illumina Total Prep RNA Amplification Kit  (catalog AMIL1791, Ambion).

growth_protocol: Tamoxifen (Tam)-inducible and heart-specific EpA960/MCM DM1 mouse model was described previously (PMID:17823658). All experiments were conducted in accordance with the NIH Guide for the Use and Care of Laboratory Animals and approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine.

extract_protocol: According to Illumina protocol. Total RNA was prepared using RNeasy Kit (Qiagen) and the RNA quality was tested with Agilent Bioanalyzer 2100.

treatment_protocol: CUGexp RNA was induced in 2-4 month old EpA960/MCM bitransgenic animals with a single or five consecutive daily intra-peritoneal injections of 20 mg/kg Tam (Sigma-Aldrich).

value: FVB

value: adult

tag: genotype/variation

value: EpA960/MCM DM1 induced to express CUGexp

tag: time

value: heart


title: heart from untreated mouse #2

description:
heart from untreated mouse
MCM-2

source_name: heart from untreated mouse

value: untreated (MCM control)


title: heart from DM1-induced mouse (1wk) #2

description:
heart from DM1-induced mouse (1wk)
EpA960 (1wk)-2-R

source_name: heart from DM1-induced mouse (1wk)


title: heart from untreated mouse #1

description:
heart from untreated mouse
MCM-1


title: Kras G12D mouse Lung Adenocarcinoma epithelial cell, biological rep3


title: heart from DM1-induced mouse (72hr) #1

description:
heart from DM1-induced mouse (72hr)
EpA960 (72h)-1


title: mouse adult heart #1

description:
mouse adult heart
Adult-1

source_name: mouse adult heart

value: wildtype


title: heart from untreated mouse #3

description:
heart from untreated mouse
MCM-3


title: heart from DM1-induced mouse (1wk) #1

description:
heart from DM1-induced mouse (1wk)
EpA960 (1wk)-1-R


title: mouse adult heart #2

description:
mouse adult heart
Adult-2


title: SssI

city: Zurich

first: Mark

last: Robinson

state: ZH

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description:
5775446076_R04C02
SAMPLE 2

hyb_protocol: The bead arrays were run according to the protocol provided by Illumina

data_processing: R (v3.0.2)/Bioconductor 'minfi' package (minfi_1.8.9) using preprocessIllumina with default settings to get beta values (See http://imlspenticton.uzh.ch/robinson_lab/BayMeth/ for more details)

source_name: SssI-treated DNA

label_protocol: Cy5 and Cy3

growth_protocol: 37 deg C with 5% CO2

extract_protocol: Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). Genomic DNA was treated with sodium bisulfite.

treatment_protocol: Native DNA was used

value: fetal lung fibroblast

tag: treated with

value: SssI to methylate CpGs


title: heart from DM1-induced mouse (72hr) #3

description:
heart from DM1-induced mouse (72hr)
EpA960 (72h)-3


title: LP mouse Lung squamous cell carcinoma epithelial cell, biological rep1


title: hsi-stage2-rC

city: Saskatoon

first: Pierre

last: Fobert

address: 110 Gymnasium Place

institute: National Research Council Canada

hyb_protocol: Two µg  of Cy5 and 2 µg of Cy3 labeled cRNA were fragmented and hybridized using the Agilent Gene Expression Hybridization Kit following the manufacturer's instructions. Each sample co-hybridized consisted of rosette leaves from four plants. Slides were washed using the Agilent Stabilization and Drying Solution following Agilent procedures.

scan_protocol: Scanned on GenePix Scanner 4000B following the manufacturer's instructions

data_processing: GeneSpring GX10 was used to normalize array data using Lowess method and to identify significantly differntially expressed genes, following a t-test.

source_name: hsi2-2, stage 2

label_protocol: One µg  of total RNA was labeled using Agilent's QuickAmp labeling kit for two colour microarrays following the manufacturer’s protocol and incorporated a dye swap design.

growth_protocol: Plants were grown in Sunshine #4 potting mix in growth chambers with a 16-h photoperiod (200 μmol m-2s-1) at 22/20°C (day/night). Plants were watered as needed to maintain the soil moisture near field capacity and fertilized weekly with 20N:20P:20K until three-week-old.

extract_protocol: Total RNA was extracted using Qiagen RNAeasy Plant Mini Kit. Each sample co-hybridized consisted of rosette leaves from four plants.

treatment_protocol: Stage 0 material was collected from plants grown under normal wtering regime to maintain soil moisture to field capacity. Stage 1 material was collected from plants with dry soil following withholding watering but before visible wilting, and stage 2 drought was collected when visible wilting observed.

tag: drought stage

tag: plant line


title: heart from DM1-induced mouse (1wk) #3

description:
heart from DM1-induced mouse (1wk)
EpA960 (1wk)-3-R

tag: strain


title: IMR-90

description:
5775446076_R01C01
SAMPLE 1

scan_protocol: The bead arrays were run according to the protocol provided by Illumina

source_name: IMR-90 cell line


title: hsi-stage2-rB

source_name: col0, stage 2


title: hsi-stage2-rA


title: hsi-stage1-rB

source_name: col0, stage 1

source_name: hsi2-2, stage 1


title: 12R-Pancreas-Diploid

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to 400k CGH arrays (Agilent Technologies, Santa Clara, CA) for 40 hours in a rotating 65°C oven. All hybridizations were done with a pooled commercial 46,XX reference (Promega, Madison WI GSM540609).

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 10.7 using default settings.

data_processing: The aCGH data was assessed with a series of QC metrics,dye  normalized and centralized, then analyzed using an aberration detection algorithm (ADM2) which is included in Agilent Genomic Workbench 6.5 software. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average ). Series supplementary files include Log2(Cy5/Cy3) data.

source_name: Fresh frozen tissue

label_protocol: Extracted fresh frozen sourced genomic DNA was amplified using the phi29 based Illustra GenomiPhi V2 Amplification kit from GE Healthcare Bio-sciences Corp (Piscataway,NJ) according to our published protocols18.  A 100 ng aliquot of pooled 46,XX DNA (Promega, Madison, WI) was amplified with the matching amplification protocol to generate a suitable reference for each aCGH experiment using amplified DNA template.  In all cases the quality of the amplification product was assessed by gel electrophoresis.    Fresh frozen phi29 amplified and FFPE non-amplified DNAs were treated with DNAse 1 prior to Klenow based labeling. High molecular weight phi29 templates were digested for 30 minutes while the smaller fragmented FFPE samples were digested for only 1 minute. In each case 1ul of 10x DNase 1 reaction buffer and 2ul of DNase 1 dilution buffer were added to 7ul of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1.  In contrast the amplified FFPE sourced DNAs do not require DNase 1 treatment prior to Klenow-based labeling. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols

extract_protocol: DNA from sorted nuclei was extracted using an amended protocol from QIAamp® DNA Micro Kit from Qiagen (Valencia, CA).  Briefly each sorted sample was resuspended in 180ul buffer ATL and 20ul proteinase K then incubated for 3 hours at 56°C for complete lysis.  Samples were bound and washed according to QIAamp® DNA Micro Kit instructions, eluted into 50ul of H20, then precipitated overnight with 5ul 3 M sodium acetate and 180 ul 100% EtOH.  Each sample was then centrifuged for 30 minutes at 20,000 x g, washed in 1 ml of 70% EtOH for 30 minutes at 20,000 x g. The samples were carefully decanted and the DNA pellet was dried by speed vacuum then resuspension in a small volume (e.g. 10-50ul) of H20 for final concentrations suitable for accurate quantification.

value: Pancreas

tag: phenotype

value: Pancreatic Ductal Adenocarcinoma

source_name: Reference pooled 46XX

tag: gender

value: female

value: normal


title: hsi-stage0-rA

source_name: hsi2-2, stage 0

source_name: col0, stage 0


title: hsi-stage1-rA


title: hsi-stage0-rD


title: hsi-stage0-rB


title: WAT CD14+ from Obese [71]

city: Paris

first: Michele

last: Guerre-Millo

address: 91 Boulevard de l'Hopital

country: France

institute: INSERM

description:
Visceral Adipose tissue from patient unergoing gastric bypass surgery
Human subject

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI using Genome Studio (Illumina software)

source_name: WAT CD14+ cells

label_protocol: Biotinylated cRNA were prepared with the Ovation picoSL V2 and  Biotin IL from NuGen Inc  for Illumina arrays

extract_protocol: Total RNA extracted using Qiagen Rneasy miKIT with DNASE treatment

treatment_protocol: Adipocytes and cells of the stroma vascular fraction (SVF) were obtained by collagenase digestion of adipose tissue . SVF cells were resuspended in endotoxin-free PBS supplemented with 2% FCS and 1 mM EDTA. Isolation of CD14+ using positive selection magnetic beads (Stemcell technologies).

tag: cell type

value: WAT CD14+ cells

tag: group

value: Non Diabetic


title: WAT CD14+ from Obese [67]


title: WAT CD14+ from Obese [74]

value: Diabetic


title: WAT CD14+ from Obese [72]


title: hsi-stage1-rC


title: WAT CD14+ from Obese [73]


title: WAT CD14+ from Obese [68]


title: hsi-stage0-rC


title: WAT CD14+ from Obese [49]


title: WAT CD14+ from Obese [57]


title: WAT CD14+ from Obese [59]


title: WAT CD14+ from Obese [56]


title: WAT CD14+ from Obese [54]


title: breast cancer cell line_ZR75.1 native (parental cell line)_rep3

first: Marsela

last: Braunstein

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

data_processing: Raw data was normalized with the lumi package under R 3.0.0 using Simple Scaling Normalization and the 10% most variable probes were retained for differential analysis using the genefilter package. Differentially expressed probes were then identified using limma with a Benjamini-Hochberg corrected P-value cutoff of 0.05.

source_name: ZR75.1 native (parental cell line)

label_protocol: Illumina Gene Expression protocols feature a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides.

growth_protocol: Cell lines were grown in vitro in DMEM (MDA-MB-231, MCF7 and ZR75-1) or RPMI media (SKBR3) supplemented with 10% heat-inactivated FBS and 1% L-glutamine

extract_protocol: Total RNA was extracted using the RNeasy Mini kit according to the manufacturer’s recommendations

treatment_protocol: Antracycline-resistant cell lines were developed over a period of 10-12 months by exposing parental cell lines to increasing concentrations of the drug. Once the resistant cell lines were established, they were maintained in the maximum tolerated dose of anthracycline.

value: breast adenocarcinoma; epithelial cells

tag: drug phenotype

value: epirubicin sensitive (parental)


title: breast cancer cell line_MCF7 native (parental cell line)_rep1

source_name: MCF7 native (parental cell line)


title: breast cancer cell line_SKBR3 native (parental cell line)_rep3

source_name: SKBR3 native (parental cell line)


title: breast cancer cell line_ZR75.1 native (parental cell line)_rep1


title: breast cancer cell line_MCF7 native (parental cell line)_rep3


title: WAT CD14+ from Obese [55]


title: breast cancer cell line_MCF7 native (parental cell line)_rep2


title: breast cancer cell line_MDA-MB-231native (parental cell line)_rep3

source_name: MDA-MB-231 native (parental cell line)


title: breast cancer cell line_ZR75.1 native (parental cell line)_rep2


title: breast cancer cell line_SKBR3 native (parental cell line)_rep2


title: breast cancer cell line_ZR75.1epirubicin 10nM-resistant_rep3

source_name: ZR75.1epirubicin 10nM-resistant

value: epirubicin 10nM-resistant


title: breast cancer cell line_SKBR3 epirubicin 15nM-resistant_rep3

source_name: SKBR3 epirubicin 15nM-resistant

value: epirubicin 15nM-resistant


title: breast cancer cell line_MDA-MB-231native (parental cell line)_rep2


title: breast cancer cell line_MCF7 epirubicin 30nM-resistant_rep3

source_name: MCF7 epirubicin 30nM-resistant

value: epirubicin 30nM-resistant


title: breast cancer cell line_ZR75.1epirubicin 10nM-resistant_rep1


title: breast cancer cell line_MDA-MB-231native (parental cell line)_rep1


title: breast cancer cell line_SKBR3 epirubicin 15nM-resistant_rep1


title: breast cancer cell line_ZR75.1epirubicin 10nM-resistant_rep2


title: Brain_SHRSP_6w-biological rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

organism: Rattus norvegicus

source_name: whole brains derived from 6 week-old SHRSP rat strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole brains stored in RNA later (Ambion), derived from WKY, SHR and SHRSP rats using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

tag: tissue

value: whole brain

tag: age

value: 6 weeks

value: SHRSP


title: breast cancer cell line_SKBR3 epirubicin 15nM-resistant_rep2


title: Brain_SHRSP_6w-biological rep2


title: breast cancer cell line MDA-MB-231_epirubicin 25nM-resistant_rep3

source_name: MDA-MB-231_epirubicin 25nM-resistant

value: epirubicin 25nM-resistant


title: Brain_SHR_6w-biological rep3

source_name: whole brains derived from 6 week-old SHR rat strain

value: SHR


title: Brain_SHR_6w-biological rep2


title: breast cancer cell line_MCF7 epirubicin 30nM-resistant_rep1


title: breast cancer cell line_SKBR3 native (parental cell line)_rep1


title: Brain_SHRSP_6w-biological rep3


title: Brain_SHR_6w-biological rep1


title: Brain_WKY_6w-biological rep3

source_name: whole brains derived from 6 week-old WKY rat strain

value: WKY


title: Brain_WKY_6w-biological rep1


title: breast cancer cell line_MCF7 epirubicin 30nM-resistant_rep2


title: Brain_WKY_6w-biological rep2


title: Brain_SHRSP_3w-biological rep3

source_name: whole brains derived from 3 week-old SHRSP rat strain

value: 3 weeks


title: breast cancer cell line MDA-MB-231_epirubicin 25nM-resistant_rep2


title: Brain_SHRSP_3w-biological rep1


title: breast cancer cell line MDA-MB-231_epirubicin 25nM-resistant_rep1


title: Brain_SHR_3w-biological rep3

source_name: whole brains derived from 3 week-old SHR rat strain


title: Brain_SHR_3w-biological rep1


title: Brain_WKY_3w-biological rep2

source_name: whole brains derived from 3 week-old WKY rat strain


title: MCF-10A sh53BP1-2 replicate 2 [set 5]

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

data_processing: The data were log2 transformed and normalized using quantile normalization with BRB array tool (developed by Biomertric Research Branch of Division of Cancer Treatment and Diagnosis of National Cancer Institute)

label_protocol: Biotinylated cRNA were prepared with illumina TotalPrep RNA Amplification Kit

growth_protocol: All cell were cultured in MCF-10A medium

extract_protocol: total RNA was extracted with ambion mirVara miRNA isolation kit.

treatment_protocol: shRNA stable knockdown

value: mammary epithelial cells

tag: transfected with


title: Brain_SHRSP_3w-biological rep2


title: Brain_WKY_3w-biological rep3


title: Brain_SHR_3w-biological rep2


title: MCF-10A sh53BP1-2 replicate 3 [set 5]

tag: cell line


title: MCF-10A shCHK2-2 replicate 3 [set 5]


title: MCF-10A shRad51 replicate 1 [set 3]

data_processing: The data is not normalized

source_name: MCF-10A shRad51


title: MCF-10A shBRCA1 replicate 2 [set 3]

source_name: MCF-10A shBRCA1


title: MCF-10A sh53BP1-2 replicate 1 [set 5]


title: MCF-10A shBRCA1 replicate 1 [set 3]


title: MCF-10A shBRCA1 replicate 3 [set 3]


title: MCF-10A sh53BP1-1 replicate 2 [set 5]


title: MCF-10A shRad51 replicate 4 [set 3]


title: MCF-10A shBRCA1 replicate 4 [set 3]


title: MCF-10A shRad51 replicate 2 [set 3]


title: mouse embryonic heart (day 14)

description:
mouse embryonic heart (day 14)
E14

source_name: mouse embryonic heart (day 14)

value: FVB

value: embryonic day 14

value: wildtype

value: heart


title: Brain_WKY_3w-biological rep1


title: MCF-10A shRad51 replicate 3 [set 3]


title: 12R-Lung-Aneuploid

source_name: Fresh frozen tissue

value: Lung

value: Pancreatic Ductal Adenocarcinoma

source_name: Reference pooled 46XX

value: female

value: normal


title: MCF-10A sh53BP1-1 replicate 3 [set 5]


title: MCF-10A shCHK2-2 replicate 1 [set 5]


title: 12R-Omentum-Aneuploid

value: Omentum


title: MCF-10A shControl replicate 4 [set 3]

description: Control 4

source_name: MCF-10A shControl

value: shControl


title: 12R-Pancreas-Aneuploid

value: Pancreas


title: MCF-10A shCHK2-1 replicate 3 [set 5]


title: MCF-10A shCHK2-2 replicate 2 [set 5]


title: MCF-10A shControl replicate 3 [set 3]

description: Control 3


title: MCF-10A shControl replicate 2 [set 3]

description: Control 2


title: MCF-10A sh53BP1-1 replicate 1 [set 5]


title: MCF-10A shCHK1-4 replicate 1 [set 5]


title: MCF-10A shCHK1-3 replicate 3 [set 5]


title: MCF-10A shCHK2-1 replicate 1 [set 5]


title: MCF-10A shCHK1-4 replicate 2 [set 5]


title: MCF-10A shCHK2-1 replicate 2 [set 5]


title: MCF-10A shCHK1-4 replicate 3 [set 5]


title: MCF-10A shControl replicate 1 [set 3]

description: Control 1


title: MCF-10A shCHK1-3 replicate 2 [set 5]


title: MCF-10A shCHK1-3 replicate 1 [set 5]


title: MCF-10A shPTEN shBRCA1 replicate 2 [Set 2]

description: PTENBRCA1 42

source_name: MCF-10A shPTEN shBRCA1

value: shPTEN shBRCA1


title: MCF-10A shPTEN shBRCA1 replicate 4 [Set 2]

description: PTENBRCA1 54


title: MCF-10A shPTEN shBRCA1 replicate 3 [Set 2]

description: PTENBRCA1 43


title: MCF-10A shATR-4 replicate 2 [set 5]


title: MCF-10A shATR-3 replicate 3 [set 5]


title: MCF-10A shATR-4 replicate 1 [set 5]


title: MCF-10A shATR-3 replicate 2 [set 5]


title: MCF-10A shATR-4 replicate 3 [set 5]


title: MCF-10A shPTEN shBRCA1 replicate 1 [Set 2]

description: PTENBRCA1 41


title: MCF-10A shBRCA1 replicate 3 [Set 2]

description: BRCA1 44


title: MCF-10A shBRCA1 replicate 2 [Set 2]

description: BRCA1 43


title: MCF-10A shBRCA1 replicate 4 [Set 2]

description: BRCA1 53


title: MCF-10A shATR-3 replicate 1 [set 5]


title: MCF-10A shBRCA1 replicate 1 [Set 2]

description: BRCA1 42


title: MCF-10A shPTEN replicate 4 [Set 2]

description: PTEN 24

source_name: MCF-10A shPTEN

value: shPTEN