title: Control vs. copper-treated cells rep1

source_name: Gracilaria tenuistipitata Chang-Xia were cultivated in seawater enriched with von Stosch solution.

value: 0.95ppm of copper (CuSO4)

value: seawater enriched with Von Stosch solution, plus 0.95ppm of copper (CuSO4).


title: MAS98.12 doxoribicin day10 mouse No62 Left Side

status: Public on Jun 01 2013

type: RNA

city: Oslo

first: Eldrid

last: Borgan

address: Ullernchausseen 70

department: Genetics

country: Norway

institute: Oslo University Hospital Radiumhospitalet

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis v5.5

scan_protocol: Agilent Technologies Microarray Scanner G2505C

data_processing: Data were extracted using Feature Extraction software (Agilent Technologies) version 10.1.1.1. The microarray data were detrended for multiplicative effects and log2 transformed. Data from control probes, probes with inferior quality for more than 20 percent of the arrays (such spots were defined as feature outliers from the FE file), and probes that were flagged as present on less than 20 percent of the arrays were omitted from the analysis. After setting spots flagged as outliers to NA, the average value of duplicate probes was used to represent each unique probe. Missing data were imputed using k-nearest neighbors with default k=1 [25], and data were normalized using quantile normalization. For transcripts (based on GeneName, as provided by Agilent Technologies) represented by multiple different probes, the probe with the highest interquartile range (IQR) was chosen to represent each transcript.

molecule: total RNA

organism: Homo sapiens

source_name: Breast Cancer Xenograft MAS98.12 doxoribicin day10

label_protocol: low-RNA input Linear Amplification RNA kit (Agilent Technologies)

growth_protocol: Two orthotopic xenograft models, MAS98.12 and MAS98.06, have been established by directly grafted orthotopic implantation of primary breast cancer tissue in SCID mice and are serially transplanted, as previously described. Locally bred athymic nude mice (NCr-Foxn1nu) were kept under pathogen-free conditions, at constant temperature (21.5 ± 0.5 °C) and humidity (55±5 %), 20 air changes/hr and a 12 hr light/dark cycle. The mice were fed RM3 diet (Scanbur BK, Norway) and distilled tap water ad libitum. The water was supplemented with 4 µg/ml 17-β-estradiol, ensuring growth in the luminal-like xenograft. Animals from the two xenograft models were randomly assigned to different treatment groups after the tumor diameter reached approximately 5 mm.

extract_protocol: Total RNA from all 60 tumor pieces was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.

tag: xenograft model

tag: mouse #

tag: side graft

value: Left Side

tag: treatment

value: Doxorubicin

tag: time (d)

tag: intrinsic subtype

value: Basal

tag: tissue

value: Basal breast cancer xenograft tumor

tag: rna extraction date

tag: rna concentration (ng/ul)

tag: rin value

tag: comment bioanalyzer

value: Bioanalyzer:looks good

tag: amplification date

tag: hybridization date

tag: donor tissue

value: primary human breast cancer


title: MAS98.06 bevacizumab day3 mouse No33 Right Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab day3

value: Right Side

value: Bevacizumab

value: Luminal

value: Luminal breast cancer xenograft tumor


title: MAS98.06 control day3 mouse No2 Right Side

source_name: Breast Cancer Xenograft MAS98.06 control day3

value: Control


title: C_30min_1

type: mixed

city: Qingdao

first: Lu

last: Lin

state: Shandong

address: 189 Songling RD

country: China

institute: QIBEBT

description: Each oligonucleotide probe had two replicates on a single slide. Additionally, six different concentrations (11, 22, 45, 90, 180 and 360 ng/ul) of genomic DNA were spotted (eight duplicates for each of the six concentrations on a single slide) as positive controls.

hyb_protocol: The Cy3 labeled genomic DNA was used as a common reference to co-hybridize the Cy5 labeled RNA samples on each slide. Hybridization was carried out using a TECAN HS4800 Pro Hybridization Station (Tecan, NC) by following the manufacturer’s instructions. This system automatically performs hybridization, washing and drying of arrays.

scan_protocol: slides were scanned using a ProScanArrayTM microarray analysis system (Perkin Elmer®, MA).

data_processing:
To determine signal intensity of fluorescence for each spot, the 16-bit TIFF scanned images were analyzed by the software ImaGene 6.1 (Biodiscovery Inc., EI Segundo, CA). Microarray data were analyzed as previously described by Mukhopadhyay et al. (Mukhopadhyay et al., 2006; He et al., 2009b). Briefly, it includes the following major steps. (i) Empty spots with SNR <2.0 (SNR, signal-to-noise ratio), and bad spots were flagged and removed before normalization. (ii) The net signal of each spot was calculated by subtracting the background signal and adding a pseudo signal of 100 to obtain a positive value. For resulting net signals of <50, a value of 50 was used. (iii) The total signal intensity of all microarray (slides) in this experiment was normalized with the genomic DNA signal (Cy3 signal), and a normalization factor was calculated for each slide. (iv) Both Cy3 and Cy5 signal intensity of each spot were adjusted by multiplying the normalization factor calculated above. Therefore, the resultant Cy5 signal of each probe presents the normalized signal intensity for each gene. (v) A ratio R of Cy5/Cy3 signal was calculated for each spot on each array. (vi) To compare genomic analysis, the control and treatment conditions were defined respectively so as to identify the control (Rc) and treatment (Rt) ratios. And then log2 R value was calculated for each gene. (vii) Finally, to access the significant change between treatment and control, a Z score was calculated via following equation: , where 0.25 is a pseudovariance term. Typically, a cutoff |Log2R|≥1.0 and |Z|≥ 2.0 was used to determine changes with significance.
The column headers for the raw data are (separated by ;): id;probe_ID;gene_ID;pos;flag;signal_mean;bg_mean;net_sig;bg_stdev;SNR;SBR;demo;sig_stdev;meta_row;meta_col;sub_row;sub_col

organism: Thermoanaerobacter sp. X514

source_name: X514 (wt) was collected at mid-log after addition ddH2O 30 minutes as control

label_protocol: Ten microgram of total RNA was reverse-transcribed using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 1 mM Cy5 dUTP (Invitrogen) according to previous  description (He et al., 2006). The purified 500 ng genomic DNA was fluorescently labeled by random priming using Klenow fragment of DNA polymerase  in the presence of 1mM Cy3 dUTP as described elsewhere (He et al., 2005).

growth_protocol: Thermoanaerobacter sp. X514 wt, Xm and Xe were grown anaerobically in defined medium supplement either with or without ethanol.

extract_protocol: Total cellular RNA was isolated using Trizol Reagent (Invitrogen). RNA samples were treated with Rnase-free DNaseI and purifed using the total RNA Isolation Kit (NucleoSpin RNAII, Macherey-Nagel Inc. Genomic DNA was isolated and purified from Thermoanaerobacter sp. X514 by CTAB (hexadecyltrimethylammonium bromide)-NaCl method (Zhou et al., 1995).

tag: strain

value: Thermoanaerobacter sp. X514

value: as the control of 0.15% ethanol treated 30 minutes

molecule: genomic DNA

source_name: pool of genomic DNA extracted from control organisms for all samples

value: control


title: 015_1h_3

source_name: X514 (wt) was collected at mid-log after addition 0.15% ethanol 1 hour

value: 0.15% ethanol treated 1 hour


title: 015_1h_2


title: wt-0%_3

source_name: X514 was collected at mid-log in the presence of  50mM glucose

value: in the absence of ethanol


title: Foxp3+ activated in vitro_Polysome-associated RNA_16

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

description:
Gene expression data from Foxp3+  cells  Activated in vitro for 36 h using RNA isolated from Polysome-associated RNA
@52002900806729121711409035233667.CEL

hyb_protocol: Samples were hybridized with the Affymetrix GeneChip Mouse Genome 430 2.0 Array according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data were extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

label: biotin

organism: Mus musculus

label_protocol: Ovation Pico WTA system (NuGEN) according to the manufacturer’s instructions.

growth_protocol: Cells isolated from lymph nodes and spleens were stained with PE conjugated CD4 antibody (GK1.5, eBioscience, San Diego, CA) and MACS purified. Thereafter TFoxp3+ and TFoxp3- cells were sorted based on CD4 and GFP-Foxp3 expression using a FACSAria to obtain cell populations of high purity (>97%). For the activated samples cells were activated for 36h with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]

extract_protocol: Cytosolic and polysome-associated RNA were prepared directly ex vivo or post-activation in vitro as described previously (Larsson O, 2007 ancer Res 67: 6814-6824). For cells isolated directly ex vivo, RNA from two experiments was pooled for each sample.

treatment_protocol: For the naïve cells all buffers and media were supplemented with cycloheximide (Sigma, St. Louis, MO) (100µg/ml). For the activated samples cells were activated for 36h with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]

tag: cell type

tag: condition

value: Activated in vitro for 36 hrs with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]

tag: isolated rna

value: Polysome-associated RNA


title: Foxp3+ activated in vitro_Cytoplasmic RNA_15

description:
Gene expression data from Foxp3+  cells  Activated in vitro for 36 h using RNA isolated from Cytoplasmic RNA
@52002900806729121711409035233670.CEL

source_name: Cells isolated from lymph nodes and spleens

value: Cytoplasmic RNA


title: 015_30min_2

source_name: X514 (wt) was collected at mid-log after addition 0.15% ethanol 30 minutes

value: 0.15% ethanol treated 30 minutes


title: wt-0%_1


title: 015_30min_3


title: Foxp3+ activated in vitro_Cytoplasmic RNA_13

description:
Gene expression data from Foxp3+  cells  Activated in vitro for 36 h using RNA isolated from Cytoplasmic RNA
@52002900806729121711409035233660.CEL


title: wt-0%_2


title: Foxp3+ activated in vitro_Polysome-associated RNA_14

description:
Gene expression data from Foxp3+  cells  Activated in vitro for 36 h using RNA isolated from Polysome-associated RNA
@52002900806729121711409035233638.CEL


title: 015_30min_1


title: Homo sapiens  SD860

type: genomic

city: Barcelona

first: Irene

last: Hernando

address: Dr Aiguader 88

country: Spain

institute: UPF/CSIC

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

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value < 0.01.  A strict filtering step  was performed to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested. We only retained those probes that had either a perfect match, or had 1 or 2 mismatches in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.

label: Cy3, Cy5

source_name: blood

label_protocol: Standard Illumina labelling protocol

extract_protocol: unknown

tag: gender

value: male

tag: organism

value: Homo sapiens

value: blood


title: Foxp3- activated in vitro_Cytoplasmic RNA_9

description:
Gene expression data from Foxp3-  cells  Activated in vitro for 36 h using RNA isolated from Cytoplasmic RNA
@52002900806613121411408986822875.CEL


title: Foxp3- ex vivo_Polysome-associated RNA_8

description:
Gene expression data from Foxp3-  cells  Ex vivo using RNA isolated from Polysome-associated RNA
YV090709CPO082-2_01.CEL

value: Ex vivo


title: Foxp3- activated in vitro_Polysome-associated RNA_12

description:
Gene expression data from Foxp3-  cells  Activated in vitro for 36 h using RNA isolated from Polysome-associated RNA
@52002900806613121411408986822861.CEL


title: Homo sapiens  SD647

value: female


title: Foxp3+ ex vivo_Cytoplasmic RNA_5

description:
Gene expression data from Foxp3+  cells  Ex vivo using RNA isolated from Cytoplasmic RNA
YV090709CPO079-2_01.CEL


title: Foxp3- activated in vitro_Polysome-associated RNA_10

description:
Gene expression data from Foxp3-  cells  Activated in vitro for 36 h using RNA isolated from Polysome-associated RNA
@52002900806613121411408986822890.CEL


title: Foxp3+ ex vivo_Polysome-associated RNA_6

description:
Gene expression data from Foxp3+  cells  Ex vivo using RNA isolated from Polysome-associated RNA
YV090709CPO080-2_01.CEL


title: Homo sapiens  SD961


title: Foxp3- activated in vitro_Cytoplasmic RNA_11

description:
Gene expression data from Foxp3-  cells  Activated in vitro for 36 h using RNA isolated from Cytoplasmic RNA
@52002900806613121411408986822851.CEL


title: Foxp3- ex vivo_Cytoplasmic RNA_7

description:
Gene expression data from Foxp3-  cells  Ex vivo using RNA isolated from Cytoplasmic RNA
YV090709CPO081-2_01.CEL


title: E9.5 embryos, Control rep 1

city: San Francisco

first: Yulei

last: Shang

state: CA

address: 513 Parnassus street

department: Pathology

country: USA

institute: UCSF

hyb_protocol: Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 oC for 5 minutes and imme diately chill on ice for 5–30 minutes. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. Set the shaker speed to 300 rpm and incubate slides for 18–24 h at 37 oC, maintaining a consistent hybridization time for comparative experiments.

scan_protocol: The arrays were then scanned on a Axon GenePix 4000B Scanner with Genepix Pro 3.0 software, Expression 5 uM for this whole genome arrays

data_processing:
The raw data were re-scaled to account for the differences in individual hybridization intensities.  Analyse quality using Codelink Expression Analysis software version 4.0.
The raw data were normalized with Median-Normalization method.
Total 300 spots for positive control and 320 spots for negative control. Therefore, a total of 620 spots data were already eliminated from the whole 35,587 spot data on the T00342 array.

source_name: E9.5 embryo

label_protocol: 1 ug of total RNA was used as a template for reverse transcriptase with MessageAmpTM II-Biotin enhanced Kit (Ambion)

growth_protocol: E9.5 control, Hipk1-/-, Hipk2-/-, Hipk1-/-;2-/- mouse embryos

extract_protocol: Total RNA was extracted from E9.5 embryos using PicoPureTM RNA Isolation Kit (Arcturus).

treatment_protocol: No treatments

value: C57B6/129svj mixed background

value: whole embryo

tag: genotype/variation


title: Homo sapiens  SD583


title: Homo sapiens  SD428


title: Foxp3+ ex vivo_Polysome-associated RNA_2

description:
Gene expression data from Foxp3+  cells  Ex vivo using RNA isolated from Polysome-associated RNA
YV090709CPO072-2_01.CEL


title: Foxp3- ex vivo_Polysome-associated RNA_4

description:
Gene expression data from Foxp3-  cells  Ex vivo using RNA isolated from Polysome-associated RNA
YV090709CPO074-2_01.CEL


title: Homo sapiens  SD249


title: Foxp3- ex vivo_Cytoplasmic RNA_3

description:
Gene expression data from Foxp3-  cells  Ex vivo using RNA isolated from Cytoplasmic RNA
YV090709CPO073-2_01.CEL


title: Gorilla beringei graueri  A967

organism: Gorilla beringei graueri

value: Gorilla beringei graueri


title: Homo sapiens  SD1067


title: Gorilla gorilla gorilla  A962

organism: Gorilla gorilla gorilla

value: Gorilla gorilla gorilla


title: Pan troglodytes troglodytes  A960

organism: Pan troglodytes troglodytes

value: Pan troglodytes troglodytes


title: Homo sapiens  SD455


title: Pan troglodytes verus  A965

organism: Pan troglodytes verus

value: Pan troglodytes verus


title: Homo sapiens  SD643


title: WT #187

city: Lund

first: Catarina

last: Rippe

address: BMC, D12

department: Experimental Sciences

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol scan_setting: Direct Hyb

data_processing: The data were quantile normalisation and background corrected using GenomeStudio software

source_name: Mouse C57/bl6

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Rneasy mini kit (Qiagen)

value: wildtype

tag: age

value: newborn 0-6 h

value: Lung


title: WT #182


title: WT #179


title: Pan troglodytes troglodytes  A958


title: Foxp3+ ex vivo_Cytoplasmic RNA_1

description:
Gene expression data from Foxp3+  cells  Ex vivo using RNA isolated from Cytoplasmic RNA
YV090709CPO071-2_01.CEL


title: Pan troglodytes troglodytes  A957


title: C_2h_3

description: Each oligonucleotide probe had two replicates on a single slide. Additionally, six different concentrations (11, 22, 45, 90, 180 and 360 ng/ul) of genomic DNA were spotted (eight duplicates for each of the six concentrations on a single slide) as positive controls.

source_name: X514 (wt) was collected at mid-log after addition ddH2O 2 hour as control

value: Thermoanaerobacter sp. X514

tag: treatment

value: as the control of 0.15% ethanol treated 2 hour

value: control


title: HsO4E-072_359108

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
Date: 2009/10/02
CPC: 1

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner Image intensity data were extracted with GenePix Pro 6.0 analysis software

data_processing:
Quantification of Cy3 and Cy5 and selection of good spots were performed using the MAIA software (Novikov E and Barillot E. Software package for automatic microarray image analysis (MAIA). The ACUITY software was then used to normalize log ratios Cy3/Cy5 with Lowess non linear normalization, to filter out genes not present in at least 3 slides out of 4, to evaluate the reproducibility of the 4 microarrays of each patient (hierarchical clustering, Self Organizing Maps). Statistical analyses to insure reproducibility was performed using Excel (correlation coefficients, ANOVA). Only slides that passed all reprocubility tests were validated.
the mean of the replicated probes

source_name: Ref

label_protocol: kit Amino Allyl MessageAmp II (Ambion). We hybridized 4 microarrays per patient using pangenomic microarrays from the "Réseau National des Génopôles" (Illkirch, France). 2 slides were hybridized with reference RNA labelled Cy5 and patient RNA labelled Cy3.Hybridation : Agilent protocol with few modifications : 750 ng of each labelled RNA were hubriddized at 60°C during 17 hours in an Aglient hybridization oven. After washings, Slides were scanned with a GenePix 4000B scanner (Molecular Devices). Image intensity data were extracted with GenePix Pro 6.0 analysis software. hybridized with reference RNA labelled Cy3 and patient RNA labelled Cy5, and 2 slides were hybridized with reference RNA labelled Cy5 and patient RNA labelled Cy3.Hybridation : Agilent protocol with few modifications : 750 ng of each labelled RNA were hubriddized at 60°C during 17 hours in an Aglient hybridization oven. After washings, Slides were scanned with a GenePix 4000B scanner (Molecular Devices). Image intensity data were extracted with GenePix Pro 6.0 analysis software.

extract_protocol: Trizol

value: Universal Reference RNA (Stratagene)

extract_protocol: Blood sample: 2.5 mL harvested in PAXgene® Blood RNA tubes (PreAnalytix). RNA extraction: PAXgene® Blood RNA kit (Qiagen). Extraction amount: 10ug

tag: tissue

value: Blood

tag: cpc


title: HsO4E-074_359110

description:
Date: 2010/01/19
CPC: 5


title: WT #188


title: HsO4E-073_359109

description:
Date: 2010/01/19
CPC: 5


title: MAS98.06 bevacizumab-without Estradiol day3 mouse No3 Left Side

source_name: Breast Cancer Xenograft MAS98.06 bevacizumab-withoutEstradiol day3

tag: xenograft model

tag: mouse #

tag: side graft

value: Left Side

value: Bevacizumab without Estradiol

tag: time (d)

tag: intrinsic subtype

value: Luminal

value: Luminal breast cancer xenograft tumor

tag: rna extraction date

tag: rna concentration (ng/ul)

value: primary human breast cancer


title: HsO4E-024_359497

description:
Date: 2009/10/02
CPC: 1


title: HsO4E-079_359152

description:
Date: 2010/01/22
CPC: 3


title: HsO4E-025_359498

description:
Date: 2009/10/02
CPC: 1


title: WT #177

tag: strain


title: HsO4E-071_359107

description:
Date: 2009/10/02
CPC: 1


title: Cavin-1/PTRF KO #238

value: Cavin-1 deficiency


title: Cavin-1/PTRF KO #235


title: HsO4E-077_359114

description:
Date: 2010/01/20
CPC: 3


title: HsO4E-078_359115

description:
Date: 2010/01/22
CPC: 3


title: HsO4E-070_359258

description:
Date: 2009/10/06
CPC: 5


title: HsO4E-069_359259

description:
Date: 2009/10/06
CPC: 5


title: Control vs. copper-treated cells rep3

city: São Paulo

first: Paulo

middle: A.

last: Zaini

state: São Paulo

address: Av. Prof. Lineu Prestes, 748 - Butantã

department: Bioquímica

country: Brazil

institute: Universidade de São Paulo

description: Biological replicate 1 of 2. Technical replicate 3 of 4 (dye swap).

hyb_protocol: AF555 and AF647 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (GE Healthcare, USA) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning, USA) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were soaked in water for 10s and dried with nitrogen gas.

scan_protocol: Scanned on a GenePix scanner (Agilent, USA). Fluorescence intensity mean and surrounding mean background from each spot were obtained with the software Array Vision 6.0 (Imaging Research, Inc., USA). Unreliable spots were manually flagged.

data_processing:
Spots presenting mean intensity below 2 times the standard deviation of its background in AF555 and AF647 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the iron stress time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((F555+F647)/2)].
Raw data files contain the platform columns listed below, plus the last two columns containing the raw data; one for channel 1 (labelled with AF647, red fluorescence) and one for channel 2 (labelled with AF555, green fluorescence).

organism: Gracilaria tenuistipitata

label_protocol: 10 µg of total RNA were used for cDNA synthesis with ImPromII Reverse Transcription System (Promega, USA) according to manufacturer's instructions. The cDNAs were labeled with the fluorophores Alexa Fluor 555 and 647 by using the kit Super Script Plus cDNA Indirect Labeling System, according to the instructions provided by the manufacturer (Invitrogen, USA).

growth_protocol: Specimens of the tetrasporophyte of Gracilaria tenuistipitata Chang-Xia were cultivated in seawater enriched with von Stosch solution (Edwards, 1970) and final ph adjusted to 7.5, at a temperature of 24ºC, with a plant density of 5 g.L-1, under a light/dark cycle of 12-h, and at an irradiance of 120 µmol photons/m-2 s-1 provided by a white fluorescent lamp (GE Healthcare, USA). The medium was renewed every six days.

extract_protocol: Total RNA extracted using Concert Plant RNA Reagent (Invitrogen, USA). Quality control of RNA was performed using a Bioanalyzer equipment (Agilent, USA)

treatment_protocol: Cells were cultured in the medium described in the growth protocol, containing 0.95ppm of copper (CuSO4) or 1ppm of cadmium (CdCl2), all from (Sigma-Aldrich, USA).

tag: growth condition

value: seawater enriched with Von Stosch solution, plus 0.95ppm of copper (CuSO4).

value: 0.95ppm of copper (CuSO4)

value: seawater enriched with Von Stosch solution.


title: HsO4E-062_359162

description:
Date: 2009/09/10
CPC: 1


title: HsO4E-061_359164

description:
Date: 2009/09/09
CPC: 1


title: HsO4E-057_359254

description:
Date: 2009/09/09
CPC: 1


title: Cavin-1/PTRF KO #157


title: Cavin-1/PTRF KO #186


title: Cavin-1/PTRF KO #192


title: HsO4E-044_359421

description:
Date: 2010/01/13
CPC: 2


title: HsO4E-043_359422

description:
Date: 2010/01/13
CPC: 2


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after rhesus rotavirus  challenge_D14_RRV_2

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Total RNA including microRNA

hyb_protocol: Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45˚C on the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneSpring GX 11.5 using RMA normalization, then normalized to the median of all samples.

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA amplified with TargetAmp1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, WI) using both the TargetAmp t7-Oligo (dT) Primer A (Epicentre, WI) and the Full Spectrum MultiStart Primers for T7 IVT (10X) (SBI System Biosciences, CA) along with SuperScript III Reverse Transcriptase (Invitrogen, CA).

growth_protocol: Balb/c mice were purchased from Charles River Laboratories (Wilmington, MA).

extract_protocol:
Extrahepatic bile ducts and gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injection and stabilized with RNAlater (QIAGEN, CA).
3 sets of samples were generated for each time point (experimental and control groups), with each set containing 2-6 extrahepatic bile ducts.
Total RNA was isolated from extrahepatic bileducts of RRV- or saline-injected mice using miRNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

treatment_protocol: Newborn mice were injected intraperitoneally with 20 μL of a solution containing 1.5x10^6 fluorescent-forming units (ffu) of type-A Rhesus Rotavirus (RRV) or 0.9% normal saline (NS; control) within 24 hours of birth.

tag: mouse strain

value: Balb/c

tag: time

value: 14 days

tag: injected agent

value: Rhesus rotavirus

tag: condition

value: experimental biliary atresia

value: Extrahepatic bileduct and gallbladder


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after normal saline injection_D14_NS_3

description: Total RNA including microRNA

value: Normal saline

value: control


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after normal saline injection_D14_NS_2

description: Total RNA including microRNA


title: HsO4E-036_359444

description:
Date: 2009/09/18
CPC: 3

value: Universal Reference RNA (Stratagene)

value: Blood


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after rhesus rotavirus  challenge_D14_RRV_3

description: Total RNA including microRNA


title: HsO4E-048_359177

description:
Date: 2009/09/10
CPC: 1


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after rhesus rotavirus  challenge_D7_RRV_3

description: Total RNA including microRNA

value: 7 days


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after normal saline injection_D14_NS_1

description: Total RNA including microRNA


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after rhesus rotavirus  challenge_D7_RRV_1

description: Total RNA including microRNA


title: Extrahepatic bileduct and gallbladder en bloc at day 14 after rhesus rotavirus  challenge_D14_RRV_1

description: Total RNA including microRNA


title: HP2_S7_iPS_minus_Mel_p8

city: New York

first: Yvonne

last: Mica

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

description: Replicate 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation in Partek Genomics Suite software.

source_name: Coriell Cell Repository (GM17890), mature melanocytes, HP2

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

growth_protocol: hESCs (WA09; passages 32-50) were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. hESC cells were grown in DMEM:F12 hESC media containing 6ng/mL FGF2 and passaged using dispase or accutase. Primary melanocytes were maintained in M254 media with HMGS supplement (Invitrogen).

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

treatment_protocol: hESCs were plated on matrigel for differentiation and grown in the presence of 100 nM LDN-193189, 10 uM SB431542, 3 uM CHIR 99021 (Stemgent), 25 ng/ml BMP4 (R&D) and 100nM EDN3 (American Peptide Company) for BE. Cells were dissociated at day 11 and replated on poly-ornithine-, laminin-, and fibronectin-coated plates in NB/Mel media. NB/Mel media was prepared by replacing the WNT3A-CM component in Mel-1 media (Fang et al., 2006) with Neurobasal (Invitrogen) medium containing 2% B27 supplement (Invitrogen), 3μM Chir, 25 ng/ml BMP4, and 500 μM dbcAMP. Cells were fed every other day and passaged weekly for maintenance and expansion.

tag: cell line

tag: cell type

value: disease-specific induced pluripotent stem cell-derived melanocytes

tag: cell stage

value: mature melanocytes

tag: genotype

tag: day of collection/passage

value: passage 8

tag: clone


title: HP2_S3_iPS_minus_Mel_p8

description: Replicate 1.


title: HsO4E-081_359208

description:
Date: 2010/01/20
CPC: 3

tag: tissue

tag: cpc


title: HsO4E-083_359160

description:
Date: 2010/01/22
CPC: 3


title: HP_S5_iPS_minus_Mel_p8

description: Replicate 2.

source_name: Coriell Cell Repository (GM14609), mature melanocytes, HP

value: HP


title: HP_S4_iPS_minus_Mel_p8

description: Replicate 1.


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after normal saline injection_D7_NS_3

description: Total RNA including microRNA


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after normal saline injection_D7_NS_2

description: Total RNA including microRNA


title: CH_S10_iPS_minus_Mel_p8

description: Replicate 3.

source_name: Coriell Cell Repository (GM02075), mature melanocytes, CH

value: CH


title: HsO4E-082_359161

description:
Date: 2010/01/20
CPC: 3


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after rhesus rotavirus  challenge_D7_RRV_2

description: Total RNA including microRNA


title: HP2_S9_iPS_minus_Mel_p8

description: Replicate 3.


title: HP_S7_iPS_minus_Mel_p8

description: Replicate 3.


title: HsO4E-037_359445

description:
Date: 2009/09/18
CPC: 3


title: HsO4E-075_359111

description:
Date: 2010/01/19
CPC: 5


title: HsO4E-080_359153

description:
Date: 2010/01/22
CPC: 3


title: C1_12_iPS_minus_Mel_p8

description: Replicate 3.

source_name: Coriell Cell Repository (GM17569), mature melanocytes, C1


title: CH_S4_iPS_minus_Mel_p8

description: Replicate 2.


title: C1_S7_iPS_minus_Mel_p8

description: Replicate 2.


title: CH_S1_iPS_minus_Mel_p8

description: Replicate 1.


title: HsO4E-063_359420

description:
Date: 2010/01/19
CPC: 5


title: HEMn_p4_i

description: Replicate 1.

source_name: Primary melanocytes, WT

value: primary melanocytes

value: melanocytes

value: WT

value: passage 4


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after rhesus rotavirus  challenge_D3_RRV_1

description: Total RNA including microRNA

value: Balb/c

value: 3 days

value: Rhesus rotavirus


title: HEMa_p_plus_3_ii

description: Replicate 2.

value: passage 3


title: HEMa_p_plus_3_i

description: Replicate 1.


title: SD27_BE_d11

description: Replicate 2.

source_name: WA09 embryonic stem cells, WT, day 11

value: ESC-derived melanocyte progenitors

value: melanocyte progenitors

value: day 11


title: HsO4E-033_359441

description:
Date: 2010/01/13
CPC: 2

value: Blood

value: Universal Reference RNA (Stratagene)


title: HEMn_p4_ii

description: Replicate 2.


title: HsO4E-068_359411

description:
Date: 2009/10/06
CPC: 5


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after normal saline injection_D3_NS_3

description: Total RNA including microRNA

value: Normal saline

value: control

value: Extrahepatic bileduct and gallbladder


title: SD25_ES_minus_Mel_p14

description: Replicate 2.

source_name: WA09 embryonic stem cells, WT, passage 14

value: ESC-derived mature melanocytes

value: mature melanocytes

value: passage 14


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after rhesus rotavirus  challenge_D3_RRV_2

description: Total RNA including microRNA

value: experimental biliary atresia


title: C1_S4_iPS_minus_Mel_p8

description: Replicate 1.

value: disease-specific induced pluripotent stem cell-derived melanocytes

value: passage 8


title: Extrahepatic bileduct and gallbladder en bloc at day 7 after normal saline injection_D7_NS_1

description: Total RNA including microRNA

value: Balb/c

value: 7 days


title: SD24_ES_minus_Mel_p14

description: Replicate 1.

value: WT


title: SD28_BE_d11

description: Replicate 3.

value: ESC-derived melanocyte progenitors


title: SD26_iPS_minus_Mel_p14

description: Replicate 3.


title: HsO4E-034_359442

description:
Date: 2009/10/06
CPC: 5


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after rhesus rotavirus  challenge_D3_RRV_3

description: Total RNA including microRNA

value: 3 days

value: Rhesus rotavirus


title: HsO4E-032_359440

description:
Date: 2010/01/13
CPC: 2

value: Blood


title: HsO4E-076_359112

description:
Date: 2010/01/20
CPC: 3

value: Universal Reference RNA (Stratagene)


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after normal saline injection_D3_NS_2

description: Total RNA including microRNA

value: Normal saline


title: Extrahepatic bileduct and gallbladder en bloc at day 3 after normal saline injection_D3_NS_1

description: Total RNA including microRNA

value: control


title: SD27_d0_b

description: Replicate 2.

source_name: WA09 embryonic stem cells, WT, day 0

value: embryonic stem cells (ESCs)

value: ESC

value: day 0


title: HsO4E-039_359447

description:
Date: 2009/09/18
CPC: 3


title: WT #142

tag: genotype/variation

value: wildtype

tag: age

value: newborn 0-6 h

value: Lung


title: HsO4E-049_359178

description:
Date: 2009/09/10
CPC: 1


title: HsO4E-038_359446

description:
Date: 2009/09/18
CPC: 3


title: Activated T cells_tripl5

city: Utrecht

first: sjoerd

last: holwerda

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Gene expression data for activated T cells

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the mouse gene 1.0st array in a GeneChip Hyb oven 640 according to manufacturer instructions. Washing was done in a GeneChip WS-system according to manufacturer instructions.

scan_protocol: Scanning was done on a geneChip scanner 7G incl. autocaroussel using affymetrix launcher software for downstream image processing

data_processing: Normalized gene expression values were calculated using robust multi-array average (RMA)

source_name: 4 days in vitro activated (aCD3+aCD28+IL2) T cells

label_protocol: Total RNA was labeled using the Affymetrix GeneChip® WT (Whole Transcript) Terminal Labeling Kit, according to manufacturers instructions

growth_protocol: Resting (B and T) cells (Day 0) were isolated directly from the spleen;Activated (B and T) cells (Day 4) were harvested after a four day in vitro activation assay

extract_protocol: Trizol was used to extract total RNA according to manufacturers instructions

treatment_protocol: RNA was extracted after one PBS wash

value: Activated T cell

value: C57Bl/6 x FVB


title: SD28HR_d8

description: Replicate 3.

source_name: WA09 embryonic stem cells, NC, day 8

growth_protocol: hESCs (WA09; passages 32-50) were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2.  hESCs were grown in DMEM:F12 hESC media containing 6ng/mL FGF2 and passaged using dispase or accutase.

treatment_protocol: hESCs were plated on matrigel for differentiation and grown in the presence of 100 nM LDN-193189 (Stemgent) and 10 uM SB431542 (Tocris) for DSi, or grown in the presence of 100 nM LDN-193189, 10 uM SB431542, and 3 uM CHIR 99021 (Stemgent) for NC, or grown in the presence of 100 nM LDN-193189, 10 uM SB431542, 3 uM CHIR 99021 (Stemgent), 25 ng/ml BMP4 (R&D) and 100nM EDN3 (American Peptide Company) for BE.

value: embryonic stem cells

tag: treatment

value: NC

tag: day of collection


title: HsO4E-058_359255

description:
Date: 2009/09/09
CPC: 1


title: Splenic T cells_tripl6

description: Gene expression data for resting T cells

source_name: mature, B220 negative splenic T cells

value: Resting T cell

tag: strain


title: SD28LSBwd_d11

description: Replicate 3.

source_name: WA09 embryonic stem cells, DSi, day 11

value: DSi


title: Activated T cells_tripl4


title: SD28LSBwd_d3

description: Replicate 3.

source_name: WA09 embryonic stem cells, DSi, day 3


title: Cavin-1/PTRF KO #237

source_name: Mouse C57/bl6

value: Cavin-1 deficiency


title: HsO4E-059_359256

description:
Date: 2009/09/09
CPC: 1

value: Blood


title: SD28BE_d8

description: Replicate 3.

source_name: WA09 embryonic stem cells, BE, day 8

value: BE


title: Splenic T cells_tripl4


title: Activated B cells_tripl3

description: Gene expression data for activated B cells

source_name: 4 days in vitro activated (aCD40+IL4) B cells

value: Activated B cell


title: HsO4E-047_359350

description:
Date: 2009/09/10
CPC: 1

source_name: Ref

value: Universal Reference RNA (Stratagene)


title: SD28BE_d11

description: Replicate 3.

source_name: WA09 embryonic stem cells, BE, day 11


title: SD28HR_d6

description: Replicate 3.

source_name: WA09 embryonic stem cells, NC, day 6


title: Activated T cells_tripl6


title: SD26_d0_b

description: Replicate 1.

value: embryonic stem cells (ESCs)

value: WT


title: Splenic T cells_tripl5


title: SD28HR_d3

description: Replicate 3.

source_name: WA09 embryonic stem cells, NC, day 3


title: HsO4D-114_359502

description:
Date: 2009/02/11
CPC: 1


title: SD28_d1

description: Replicate 3.

source_name: WA09 embryonic stem cells, day 1


title: HsO4D-119_359067

description:
Date: 2009/01/27
CPC: 4


title: SD28HR_d11

description: Replicate 3.

source_name: WA09 embryonic stem cells, NC, day 11


title: SD28LSBwd_d8

description: Replicate 3.

source_name: WA09 embryonic stem cells, DSi, day 8


title: SD28LSBwd_d6

description: Replicate 3.

source_name: WA09 embryonic stem cells, DSi, day 6


title: SD27BE_d11

description: Replicate 2.


title: HsO4D-100_351690

description:
Date: 2009/03/25
CPC: 4


title: HsO4D-098_351683

description:
Date: 2009/02/17
CPC: 1


title: SD27HR_d11

description: Replicate 2.


title: SD28_d0

description: Replicate 3.

source_name: WA09 embryonic stem cells, day 0


title: SD27LSBwd_d8

description: Replicate 2.


title: SD27BE_d8

description: Replicate 2.


title: SD27HR_d8

description: Replicate 2.


title: HsO4D-097_351684

description:
Date: 2009/02/17
CPC: 1


title: SD27HR_d3

description: Replicate 2.


title: SD27LSBwd_d11

description: Replicate 2.


title: HsO4D-113_359503

description:
Date: 2009/02/11
CPC: 1


title: Activated B cells_tripl2


title: HsO4D-106_359061

description:
Date: 2009/06/30
CPC: 2


title: Activated B cells_tripl1


title: SD27HR_d6

description: Replicate 2.


title: SD27LSBwd_d3

description: Replicate 2.


title: Splenic B cells_tripl_1

description: Gene expression data for resting B cells

source_name: mature, CD43 negative splenic B cells

value: Resting B cell


title: SD27_d1

description: Replicate 2.


title: SD27LSBwd_d6

description: Replicate 2.


title: SD27_d0

description: Replicate 2.


title: Splenic B cells_tripl_2


title: HsO4D-093_359522

description:
Date: 2009/01/19
CPC: 2


title: SD26HR_d11

description: Replicate 1.


title: SD26BE_d11

description: Replicate 1.


title: HsO4D-089_351730

description:
Date: 2009/01/19
CPC: 2


title: Ebf1-deficient CD19+ biological rep3

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Expression data from long-term Ebf1-deficient, CD19+, Bcl2tg cells

hyb_protocol: Fragmentation and hybridization were conducted on Mouse Gene 1.0 ST Array according to the Affymetrix Expression Analysis Technical Manual

scan_protocol: Affymetrix GeneChip scanner (GCS); Scanner type = M10

data_processing: Data were analyzed with R/Bioconductor. RMA expression values were calculated using affy package available with affylmGUI.

source_name: Ebf1-deficient CD19+ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng of total RNA

growth_protocol: Late Fr. C pro-B cells were adoptively transferred into sublethally irradiated Rag2-deficient and IL2rg-deficient recipients.

extract_protocol: CD19+ cells were revealed twelve weeks post injection, RNeasy minikit (Quiagen) was used to isolate RNA

treatment_protocol: In order to conditionally delete Ebf1, recipients were 4-OHT (2mg per injection) treated on day 1, 2, 4 and 7.

value: CD19+ cells


title: Ebf1-deficient CD19+ biological rep2


title: HsO4D-088_351727

description:
Date: 2009/07/16
CPC: 1


title: SD26HR_d8

description: Replicate 1.

source_name: WA09 embryonic stem cells, NC, day 8


title: SD26LSBwd_d8

description: Replicate 1.


title: HsO4D-083_351796

description:
Date: 2009/03/03
CPC: 2


title: SD26LSBwd_d11

description: Replicate 1.

source_name: WA09 embryonic stem cells, DSi, day 11


title: Ebf1-deficient CD19+ biological rep1


title: SD26HR_d6

description: Replicate 1.


title: SD26BE_d8

description: Replicate 1.


title: HsO4D-082_351797

description:
Date: 2009/02/18
CPC: 4


title: SD26_d0

description: Replicate 1.


title: SD26_d1

description: Replicate 1.


title: HsO4D-086_351726

description:
Date: 2009/07/16
CPC: 1


title: SD26HR_d3

description: Replicate 1.


title: SD26LSB_d3

description: Replicate 1.

source_name: WA09 embryonic stem cells, DSi, day 3


title: HsO4D-081_351689

description:
Date: 2009/02/18
CPC: 4


title: WT2 Day 9 Colon

city: Saint Louis

first: Ansuman

last: Satpathy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Scanner model: M10, Core software/version: AGCC ScanCom

data_processing: Data were processed using RMA Quantile Normalization with DNASTAR Arraystar software.

source_name: Notch2 f/f C57Bl/6

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

extract_protocol: The distal colon (2nd 1cm segment) was harvested and RNA prepared using the Qiagen Rneasy Mini Kit.

treatment_protocol: Mice were analyzed following infection with 2 x 10^9 C. rodentium strain DBS100 (American Type Culture Collection).

tag: infection

value: C. rodentium

value: day 9

value: colon


title: WT1 Day 9 Colon

tag: time


title: Notch2 KO2 Day 9 Colon

source_name: Notch2f/f CD11c-cre

value: Notch2 KO


title: SD26_BE_d11

description: Replicate 1.

source_name: WA09 embryonic stem cells, WT, day 11

value: ESC-derived melanocyte progenitors

value: melanocyte progenitors

value: day 11


title: HsO4D-078_352189

description:
Date: 2009/03/11
CPC: 5

source_name: Ref


title: WT2 Day 4 Colon

value: day 4


title: HsO4D-073_351891

description:
Date: 2009/04/01
CPC: 2


title: WT1 Day 4 Colon


title: HsO4D-071_351893

description:
Date: 2009/04/01
CPC: 2


title: Notch2 KO1 Day 9 Colon


title: Splenic B cells_tripl_3

value: C57Bl/6 x FVB


title: HsO4D-070_351806

description:
Date: 2009/03/31
CPC: 5

value: Blood


title: SD26LSBwd_d6

description: Replicate 1.

value: embryonic stem cells

value: DSi


title: HsO4D-077_352190

description:
Date: 2009/03/11
CPC: 5

value: Universal Reference RNA (Stratagene)


title: Batf3 KO2 Day 9 Colon

source_name: Batf3 KO

value: Batf3 KO


title: Notch2 KO2 Day 4 Colon


title: Notch2 KO1 Day 4 Colon


title: HsO4D-069_351805

description:
Date: 2009/03/31
CPC: 5


title: HsO4D-068_351807

description:
Date: 2009/03/10
CPC: 2


title: Batf3 KO1 Day 9 Colon


title: WT3 DEC205

growth_protocol: Primary splenocytes were harvested by digestion with Collagenase B and DNAse1

extract_protocol:
RNA was prepared using the RNAqueous-Micro kit (Invitrogen).
WT and Notch2f/f CD11c-cre DC Sorts: WT and Notch2 KO Splenic CD11b+ DCs were sorted as MHCII+ CD11c+ CD11b+ CD24-, WT and Notch2 KO Splenic DEC205+ DCs were sorted to as MHCII+ CD11c+ CD11b- CD24+ DEC205+

treatment_protocol: Mice were analyzed at steady-state.

value: WT

value: cDC

tag: cell type subset


title: [ER+/PR+]HER2- HEL_183

city: Helsinki

first: Xiaofeng

last: Dai

address: Haartmaninkatu 8 P.O. BOX 700

country: Finland

institute: Helsinki University Central Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: fluorescent

source_name: Breast Tumor Tissue

label_protocol: standard Illumina protocol

tag: disease subtype

tag: disease state

value: breast cancer

value: breast cancer tumor


title: TNP HEL_180

value: TNP


title: HsO4D-067_351808

description:
Date: 2009/03/10
CPC: 2


title: [ER-/PR-]HER2- HEL_182


title: [ER+/PR+]HER2- HEL_179


title: [ER+/PR+]HER2- HEL_178


title: [ER+/PR+]HER2- HEL_176


title: WT3 CD11b

tag: cell type


title: HsO4D-064_351651

description:
Date: 2009/03/04
CPC: 1


title: HsO4D-065_351809

description:
Date: 2009/03/04
CPC: 1


title: WT2 DEC205


title: [ER-/PR-]HER2- HEL_181


title: [ER+/PR+]HER2- HEL_170


title: [ER+/PR+][ER-/PR-]HER2- HEL_171


title: WT1 DEC205


title: WT1 CD11b


title: [ER+/PR+]HER2- HEL_169


title: KO3 CD11b

source_name: Notch2 f/f CD11c-cre C57Bl/6


title: [ER+/PR+]HER2- HEL_174


title: [ER+/PR+]HER2- HEL_173


title: [ER+/PR+]HER2- HEL_168


title: HsO4D-061_351652

description:
Date: 2009/07/14
CPC: 1


title: [ER+/PR+]HER2- HEL_163


title: HsO4D-059_351608

description:
Date: 2009/07/01
CPC: 3


title: [ER+/PR+]HER2- HEL_166


title: HsO4D-058_351610

description:
Date: 2009/07/01
CPC: 3


title: [ER+/PR+]HER2- HEL_162


title: HsO4D-057_351613

description:
Date: 2009/07/15
CPC: 2


title: KO3 DEC205


title: KO2 DEC205


title: [ER+/PR+]HER2- HEL_175


title: WT2 CD11b


title: HsO4D-056_351612

description:
Date: 2009/07/15
CPC: 2


title: KO2 CD11b


title: TNP HEL_164


title: prg-1 (pk2290); daf-2 (e1370) Early vs. Late

city: Cambridge

first: Eric

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

country: United Kingdom

institute: University of Cambridge

description: Comparison of total RNA expression levels between early generation lines and their late generation progeny

hyb_protocol: Hybridization was performed using NimbleGen hybridization, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using NimbleGen hybridization, following their standard operating protocol. See www.nimblegen.com. Scan parameters were specifically calibrated to capture the repeatitive elements.

data_processing: For each probe, the log2 [Cy5]/[Cy3] ratio is transformed to a z-score  by subtracting the mean log2 ratio and dividing by the standard  deviation of log2 ratios

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298); daf-2 (e1370) Late

label_protocol: Labeling was performed using NimbleGen Cy3-Cy5 Random 9mer System, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: All Caenorhabditis elegans samples were grown and propagated on NGM plates seeded with OP50 E. coli and maintained at 20ºC

extract_protocol: Total RNA was harvested using TRIzol Reagent Protocol (Life Technologies).

treatment_protocol: Unstarved worms on plates recently depleted of food were harvested using M9 buffer, rinsed with additional M9 and then used in the extraction protocol.

value: Bristol N2

value: Substitution early stop mutant prg-1, missense substitution mutant daf-2

tag: phenotype

value: Normal

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298); daf-2 (e1370) Early


title: [ER+/PR+]HER2- HEL_165


title: KO1 DEC205

value: Notch2 KO


title: HsO4D-052_351801

description:
Date: 2009/03/25
CPC: 4


title: HsO4D-063_351653

description:
Date: 2009/07/14
CPC: 1


title: [ER-/PR-]HER2- HEL_157


title: HsO4D-050_351606

description:
Date: 2009/03/17
CPC: 2


title: prg-1 (tm872); daf-2 (m41) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872); daf-2 (m41) Late

tag: genotype

value: deletion prg-1, missense substitution mutant daf-2

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872); daf-2 (m41) Early


title: TNP HEL_159


title: KO1 CD11b


title: [ER+/PR+]HER2- HEL_156


title: [ER-/PR-]HER2- HEL_155


title: [ER+/PR+]HER2- HEL_160


title: rsd-2 (yp10) Early vs. Late, 20°C

description: Comparison of total RNA expression levels between early generation lines and their late generation progeny, all grown at the nonpermissive temperature of 20°C

data_processing: For each probe, the log2 [Cy5]/[Cy3] ratio is transformed to a z-score  by subtracting the mean log2 ratio and dividing by the standard  deviation of log2 ratios. The software used for processing the data into the Matrix files: Galaxy (https://main.g2.bx.psu.edu/).

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (yp10), 20ºC Late

tag: strain/line

value: Missense substitution rsd-2

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (yp10), 20ºC Early


title: prg-1 (tm872); daf-2 (e1370) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872); daf-2 (e1370) Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872); daf-2 (e1370) Early


title: rsd-2 (yp10) Early vs. Late, 25°C

description: Comparison of total RNA expression levels between early generation lines and their late generation progeny, all grown at the nonpermissive temperature of 25°C

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (yp10), 25ºC Late

growth_protocol: All Caenorhabditis elegans samples were grown and propagated on NGM plates seeded with OP50 E. coli and maintained at 25ºC

value: progressive sterility

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (yp10), 25ºC Early


title: [ER+/PR+]HER2- HEL_158


title: HsO4D-047_352005

description:
Date: 2009/02/10
CPC: 1

value: Blood


title: prg-1 (pk2290); daf-2 (e1368) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298); daf-2 (e1368) Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298); daf-2 (e1368) Early


title: rsd-2 (pk3307) Early vs. Late, 20°C

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (pk3307), 20ºC Late

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (pk3307), 20ºC Early


title: [ER+/PR+]HER2- HEL_153


title: [ER+/PR+]HER2- HEL_152


title: HsO4D-044_352075

description:
Date: 2009/02/04
CPC: 2

source_name: Ref


title: [ER+/PR+]HER2- HEL_151

source_name: Breast Tumor Tissue


title: prg-1 (n4357) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (n4357) Late

value: deletion prg-1

source_name: Caenorhabditis elegans Bristol N2 prg-1 (n4357) Early


title: Dr_SAL/SAL_4

city: Budapest

first: Viola

last: Tamasi

address: Nagyvarad sqr 4

department: Genetic, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

hyb_protocol: 750 ng biotin labeled cRNA was hybridized onto the array according to Illumina protocols.

scan_protocol: Illumina's Bead Studio v3 sofware was used.

data_processing: Raw microarray data were processed with beadarray, preprocessCore and puma Bioconductor packages for R. Biefly, backgroundCorrect method used in the beadarray package was set to “minimum”, and “log = TRUE; n = 10” variables were used for createbeadsummaryData method. The normalization method used was the quantile normalization method in the preprocessCore package. Additionally, pumaComb, pumaDE, and write.rslts functions with default settings were used.

organism: Rattus norvegicus

source_name: dorsal raphe

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotin labeled cRNA.

extract_protocol: Trizol protocol

treatment_protocol: saline in a volume of 1 ml/kg and/or sham-operation 3 weeks prior to sacrifice; 15 mg/kg MDMA in a volume of 1 ml/kg ip. 3 weeks prior to sacrifice; 40 mg/kg venlafaxine in Alzet 2001 osmotic minipumps for 3 weeks prior to sacrifice; double treatment (venlafaxine adminstration after a single injection of MDMA, see previously)

value: vehicle

tag: gender

value: male

value: brain

value: Dark Agouti


title: Dr_SAL/SAL_3

tag: tissue


title: WT2 DEC205 ESAM+

extract_protocol:
RNA was prepared using the RNAqueous-Micro kit (Invitrogen).
WT ESAM+ and ESAM- CD11b+ DC Sorts: WT Splenic CD11b+ESAM+ DCs were sorted from Cx3cr1-gfp mice as MHCII+ CD11c+ CD11b+ CD24- ESAM+ Cx3cr1 int, WT Splenic CD11b+ ESAM- DCs were sorted from Cx3cr1-gfp mice as MHCII+ CD11c+ CD11b+ CD24- CX3CR1gfp+ ESAM-
WT ESAM+ and ESAM- DEC205+ DC Sorts: WT Splenic DEC205+ ESAM+ DCs were sorted as MHCII+ CD11c+ CD24+ CD11b- DEC205+ ESAM+, WT Splenic DEC205+ ESAM- DCs were sorted as MHCII+ CD11c+ CD24+ CD11b- DEC205+ ESAM-

value: WT

value: cDC

value: DEC205 ESAM+


title: Dr_SAL/SAL_2


title: TNP HEL_154

value: TNP

value: breast cancer

value: breast cancer tumor


title: WT1 DEC205 ESAM+


title: rsd-2 (pk3307) Early vs. Late, 25°C

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (pk3307), 25ºC Late

value: Bristol N2

source_name: Caenorhabditis elegans Bristol N2 rsd-2 (pk3307), 25ºC  Early


title: HsO4D-040_351671

description:
Date: 2009/01/28
CPC: 2

value: Universal Reference RNA (Stratagene)

tag: cpc


title: Dr_SAL/SAL_1


title: WT2 CD11b ESAM+

source_name: C57Bl/6 Cx3cr1-gfp

tag: genotype/variation

value: CD11b ESAM+


title: WT2 DEC205 ESAM-

value: DEC205 ESAM-


title: WT1 DEC205 ESAM-


title: Dr_SAL/VLX_4

value: VLX (40 mg/kg, minipump) treated


title: [ER+/PR+]HER2- HEL_148


title: [ER+/PR+]HER2- HEL_149


title: WT2 CD11b ESAM-

value: CD11b ESAM-


title: HsO4D-046_352007

description:
Date: 2009/02/10
CPC: 1

value: Blood


title: [ER+/PR+]HER2- HEL_147


title: WT1 CD11b ESAM+


title: HsO4D-039_351673

description:
Date: 2009/01/28
CPC: 2


title: [ER+/PR+]HER2- HEL_146


title: [ER+/PR+]HER2- HEL_145


title: HsO4D-038_351672

description:
Date: 2009/01/27
CPC: 4


title: rsd-6 (pk3300) Early vs. Late, 25°C

source_name: Caenorhabditis elegans Bristol N2 rsd-6 (pk3300), 25ºC Late

value: Nonsense substitution rsd-6

value: progressive sterility

source_name: Caenorhabditis elegans Bristol N2 rsd-6 (pk3300), 25ºC Early


title: prg-1 (tm872) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872) Late

value: deletion prg-1

source_name: Caenorhabditis elegans Bristol N2 prg-1 (tm872) Early


title: HsO4D-049_351607

description:
Date: 2009/03/17
CPC: 2


title: HsO4D-037_351675

description:
Date: 2009/02/04
CPC: 2


title: Dr_SAL/VLX_2

value: male

value: brain

value: Dark Agouti


title: Dr_SAL/VLX_1


title: HsO4D-036_351674

description:
Date: 2009/02/03
CPC: 1


title: [ER+/PR+]HER2- HEL_161


title: Dr_SAL/VLX_3


title: WT1 CD11b ESAM-

value: WT

value: cDC


title: HsO4D-035_351602

description:
Date: 2009/02/03
CPC: 1


title: [ER+/PR+]HER2- HEL_144

value: breast cancer


title: [ER+/PR+]HER2- HEL_141

value: breast cancer tumor


title: HsO4D-026_352024

description:
Date: 2009/01/21
CPC: 5


title: HsO4D-025_352022

description:
Date: 2009/01/21
CPC: 5


title: Dr_MDMA/SAL_1

value: MDMA (15 mg/kg) treated


title: Metastatic GC_Ovary_1 round

city: Seoul

first: Myung-Soo

last: Kang

address: 50 Irwon-dong

department: SAIHST

country: South Korea

institute: Samsung Medical Center

description:
species:human, tumor histology: gastric carcinoma, primary or meta: meta, tumor site cultured: ovary
Xenografted tumor metastasized to ovaries when human gastric carcinoma SNU-16 cells were orthotopically implanted into the stomach of the BalB/c nude mice. This is the tumor in the ovary from the first-round implantation

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Expression Console software. Convolution background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: highly tumorigenic human gastric carcinoma SNU-16 cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 µg/ml streptomycin (R10), and incubated at 37℃ in humidified air containing 5% CO2

extract_protocol: Pellets of ten millions cells of each 16S, 16O, 16SS, and 16OO cells were washed once with PBS and lysed in 1 ml of TRIzol® reagent (Invitrogen). Total RNAs were isolated as manufacturer’s instruction.

value: Xenografted tumor metastasized to ovaries from 1st round implantation


title: Dr_MDMA/SAL_3


title: Orthotopic GC_Stomach_2 round

description:
species:human, tumor histology: gastric carcinoma, primary or meta: primary, tumor site cultured: ovary
Xenografted tumor formed in the stomach when human gastric carcinoma SNU-16S cells were orthotopically implanted into the stomach of the BalB/c nude mice. This is the tumor in the stomach from the second-round implantation

value: Xenografted tumor formed in the stomach from 2nd round of implantation


title: Dr_MDMA/SAL_4


title: Metastatic GC_Ovary_2 round

description:
species:human, tumor histology: gastric carcinoma, primary or meta: meta, tumor site cultured: ovary
Xenografted tumor metastasized to the ovary when human gastric carcinoma SNU-16O cells were orthotopically implanted into the stomach of the BalB/c nude mice. This is the tumor in the stomach from the second-round implantation

value: Xenografted tumor metastasized to ovaries from 2nd round implantation


title: rsd-6 (pk3300) Early vs. Late, 20°C

source_name: Caenorhabditis elegans Bristol N2 rsd-6 (pk3300), 20ºC Late

value: Bristol N2

value: Normal

source_name: Caenorhabditis elegans Bristol N2 rsd-6 (pk3300), 20ºC Early


title: [ER+/PR+]HER2- HEL_143


title: [ER+/PR+]HER2- HEL_140


title: Dr_MDMA/VLX_2

value: MDMA (15 mg/kg) and VLX (40 mg/kg, minipump) double treated


title: HsO4D-018_351868

description:
Date: 2009/06/25
CPC: 1

value: Universal Reference RNA (Stratagene)

value: Blood


title: [ER+/PR+]HER2- HEL_139


title: HsO4D-034_351601

description:
Date: 2009/06/25
CPC: 1


title: Liver biopsy sample obtained from a deceased-donor adult_NHL11

hyb_protocol: Following chemical fragmentation of biotinylated-labeled cRNA, 10ug of cRNA were hybridized for 16hr at 45˚C on the GeneChip® Human Gene 1.0 ST Array (Affymetrix, CA). Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
Expression data (Affymetrix .CEL format) imported to GeneSpring software:
1. Normalized all data using RMA (Robust Muti-array Average) methods.
2. Performed baseline transformation to median of 7 normal control samples.
There was no other option to specifically normalize data across all samples.

source_name: Liver

extract_protocol:
Wedge liver biopsy samples were obtained from infants with biliary atresia during intraoperative cholangiogram. Wedge or needle liver biopsy samples from other causes of intrahepatic cholestasis were obtained during diagnostic procedures. Liver biopsy samples from deceased-donor children were obtained during procedure to confirm the eligibiity of the patients as a donor.
Biopsy samples were snap frozen in liquid nitrogen, and stored at -80˚C by the time of RNA isolation.
Total RNA was isolated from liver biopsy samples using RNeasy Mini Kit, according to the manufacturer’s protocol (QIAGEN, CA).
RNA integrity was verified using the Agilent 2100 Bioanalyser (Agilent Technologies, Inc., CA).

value: liver

tag: condition

value: Sample for internal control to normalize each batch of GeneChip microarray run

tag: age of biopsy


title: Liver biopsy sample obtained from a deceased-donor adult_NHL7


title: Liver biopsy sample obtained from a deceased-donor adult_NHL8


title: HsO4D-021_352016

description:
Date: 2009/01/20
CPC: 3


title: Dr_MDMA/VLX_4

tag: treatment

value: male

value: brain


title: Liver biopsy sample obtained from a deceased-donor adult_NHL9


title: [ER+/PR+]HER2- HEL_134

extract_protocol: unknown


title: [ER+/PR+][ER-/PR-]HER2- HEL_133


title: [ER+/PR+]HER2- HEL_135


title: [ER+/PR+]HER2- HEL_138


title: Orthotopic GC_Stomach_1 round

description:
species:human, tumor histology: gastric carcinoma, primary or meta: primary, tumor site cultured: stomach
Xenografted tumor formed in the stomach when human gastric carcinoma SNU-16 cells were orthotopically implanted into the stomach of the BalB/c nude mice. This is the tumor in the stomach from the first-round implantation

value: Xenografted tumor formed in the stomach from 1st round of implantation


title: HsO4D-016_351872

description:
Date: 2009/03/03
CPC: 2


title: prg-1 (pk2290) Early vs. Late

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298) Late

tag: strain

value: Substitution early stop mutant prg-1

value: progressive sterility

source_name: Caenorhabditis elegans Bristol N2 prg-1 (pk2298) Early


title: Dr_MDMA/VLX_1

value: Dark Agouti


title: Liver biopsy sample obtained from a deceased-donor adult_NHL4


title: Liver biopsy sample obtained from a deceased-donor adult_NHL6


title: Dr_MDMA/VLX_3


title: [ER+/PR+]HER2- HEL_128

source_name: Breast Tumor Tissue

value: breast cancer

value: breast cancer tumor


title: [ER+/PR+]HER2- HEL_127


title: Core Basal HEL_126

value: Core Basal


title: HsO4D-005_351910

description:
Date: 2009/06/18
CPC: 5

source_name: Ref


title: HsO4D-023_352017

description:
Date: 2009/01/20
CPC: 3


title: [ER+/PR+]HER2- HEL_125


title: HsO4D-008_351902

description:
Date: 2009/06/18
CPC: 5


title: HsO4D-003_351908

description:
Date: 2009/06/30
CPC: 2


title: Liver biopsy sample obtained from a deceased-donor adult_NHL3


title: Hp_SAL/SAL_1

source_name: hippocampus

value: vehicle


title: HsO4D-095_359505

description:
Date: 2009/02/11
CPC: 1


title: HsO4D-112_359504

description:
Date: 2009/02/11
CPC: 1


title: Hp_SAL/SAL_3


title: Liver biopsy sample obtained from a deceased-donor adult_NHL2


title: Hp_SAL/VLX_4

value: VLX (40 mg/kg, minipump) treated


title: Hp_SAL/SAL_4


title: [ER+/PR+]HER2- HEL_122


title: HsO4D-111_359418

description:
Date: 2009/02/10
CPC: 1


title: Hp_SAL/VLX_3


title: [ER+/PR+]HER2- HEL_119


title: [ER+/PR+]HER2- HEL_117


title: HsO4D-110_359065

description:
Date: 2009/02/10
CPC: 1


title: Liver biopsy sample obtained from a deceased-donor child_UC9035

value: Normal control

value: 3 years


title: Liver biopsy sample obtained from a deceased-donor adult_NHL1


title: Hp_SAL/VLX_2


title: Core Basal HEL_115


title: Liver biopsy sample obtained from a deceased-donor child_UC9011

value: 3.5 years


title: Hp_SAL/VLX_1


title: Hp_SAL/SAL_2


title: HsO4D-045_352125

description:
Date: 2009/02/04
CPC: 2

value: Blood

value: Universal Reference RNA (Stratagene)


title: Hp_MDMA/SAL_4

value: MDMA (15 mg/kg) treated


title: Liver biopsy sample obtained from a deceased-donor child_UC9101

value: liver

value: 2 years


title: HsO4D-043_352123

description:
Date: 2009/02/04
CPC: 2


title: HsO4D-029_352023

description:
Date: 2009/02/03
CPC: 1


title: [ER+/PR+]HER2- HEL_109


title: Liver biopsy sample obtained from a deceased-donor child_UC9023

value: 31 months


title: HsO4D-027_352021

description:
Date: 2009/02/03
CPC: 1


title: Hp_MDMA/SAL_3

value: male

value: brain


title: Hp_MDMA/SAL_2

value: Dark Agouti


title: HsO4D-042_352124

description:
Date: 2009/01/28
CPC: 2


title: [ER+/PR+][ER-/PR-]HER2- HEL_101

value: breast cancer


title: [ER+/PR+]HER2- HEL_113

value: breast cancer tumor


title: Liver biopsy sample obtained from a deceased-donor child_UC9009


title: HsO4D-041_352122

description:
Date: 2009/01/28
CPC: 2


title: Liver biopsy sample obtained from a deceased-donor child_UC9612


title: [ER+/PR+][ER-/PR-]HER2- HEL_100


title: [ER+/PR+]HER2- HEL_105


title: HsO4D-118_359068

description:
Date: 2009/01/27
CPC: 4


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_Cint7

value: Diseased control

value: 119 days


title: Hp_MDMA/VLX_2

value: MDMA (15 mg/kg) and VLX (40 mg/kg, minipump) double treated


title: HsO4D-117_359069

description:
Date: 2009/01/27
CPC: 4


title: HsO4D-116_359070

description:
Date: 2009/01/21
CPC: 5


title: Liver biopsy sample obtained from a deceased-donor child_UC8926

value: Normal control

value: 22 months


title: [ER+/PR+]HER2- HEL_092


title: [ER+/PR+]HER2- HEL_091


title: Hp_MDMA/SAL_1


title: Hp_MDMA/VLX_4


title: Hp_MDMA/VLX_3


title: Hp_MDMA/VLX_1


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_Cint25

value: 189 days


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_Cint5

value: 70 days


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_Cint29

value: 48 days


title: Fc_SAL/SAL_4

source_name: frontal cortex

value: vehicle


title: [ER+/PR+]HER2- HEL_086


title: Fc_SAL/SAL_3


title: HsO4D-115_359501

description:
Date: 2009/01/21
CPC: 5

value: Blood

value: Universal Reference RNA (Stratagene)


title: Fc_SAL/SAL_2


title: [ER+/PR+][ER-/PR-]HER2- HEL_085


title: [ER+/PR+]HER2- HEL_084


title: Fc_SAL/SAL_1


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_Cint16

value: liver

value: 71 days


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B93

value: 73 days


title: HsO4D-024_352019

description:
Date: 2009/01/20
CPC: 3


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B88

value: 75 days


title: HsO4D-085_351799

description:
Date: 2009/07/16
CPC: 1


title: [ER+/PR+]HER2- HEL_080

value: breast cancer


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B97

value: 157 days


title: [ER+/PR+]HER2- HEL_076

value: breast cancer tumor


title: Core Basal HEL_074

value: Core Basal


title: HsO4D-084_351798

description:
Date: 2009/07/16
CPC: 1


title: HsO4D-055_351615

description:
Date: 2009/07/15
CPC: 2


title: [ER+/PR+]HER2- HEL_071


title: HsO4D-094_359521

description:
Date: 2009/01/20
CPC: 3


title: Fc_SAL/VLX_3

value: VLX (40 mg/kg, minipump) treated

value: male

value: brain

value: Dark Agouti


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B74

value: Diseased control

value: 19 days


title: HsO4D-054_351614

description:
Date: 2009/07/15
CPC: 2


title: Fc_SAL/VLX_2


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B87

value: 41 days


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B67

value: 26 days


title: Core Basal HEL_070


title: Fc_MDMA/SAL_4

value: MDMA (15 mg/kg) treated


title: Fc_SAL/VLX_1


title: HsO4D-062_351654

description:
Date: 2009/07/14
CPC: 1

value: Blood

value: Universal Reference RNA (Stratagene)


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B62

value: liver

value: 43 days


title: [ER+/PR+]HER2- HEL_072

value: breast cancer


title: [ER+/PR+]HER2- HEL_069


title: HsO4D-053_351802

description:
Date: 2009/07/14
CPC: 1


title: HsO4D-109_359064

description:
Date: 2009/07/01
CPC: 3


title: [ER+/PR+][ER-/PR-]HER2- HEL_068


title: Fc_MDMA/SAL_3


title: Fc_MDMA/SAL_2


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint24

value: Biliary Atresia

value: 95 days


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B68

value: 54 days


title: Fc_MDMA/SAL_1


title: HsO4D-108_359063

description:
Date: 2009/07/01
CPC: 3


title: Liver biopsy sample obtained from a patient with other cause of intrahepatic cholestasis than biliary atresia_B61


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint23

value: 69 days


title: [ER+/PR+]HER2- HEL_066

value: breast cancer tumor


title: [ER+/PR+]HER2- HEL_065


title: Fc_SAL/VLX_4

value: VLX (40 mg/kg, minipump) treated

value: male

value: brain


title: HsO4D-105_359355

description:
Date: 2009/06/30
CPC: 2


title: Aphid Vat- (PMR5) library

type: SRA

city: University Park

first: Sampurna

last: Sattar

state: PA

address: 138 ASI Building

department: College of Agricultural Sciences

institute: The Pennsylvania State University

description: Aphis gossypii (cotton-melon aphid)

library_source: transcriptomic

data_processing:
sRNA sequences were extracted from raw reads
Sequenced reads were trimmed for adaptor sequence and redundant sequences were removed.
Sequenced reads were queried against ribosomal and transfer RNAs from Flybase and the matched r/tRNAs were removed.
Unique sequences with 10 or more counts were aligned against A.gossypii coding regions (EST database) for perfect matches.
Sequences were then aligned against the miRBASE with up to two mismatches to identify the conserved miRNA using Bowtie.
Sequences were then aligned against the A.gossypii EST, M. persicae EST and A. pisum with up to two mismatches using Bowtie for potential candidates for novel A. gossypii miRNAs..
Novel miRNAs were identified using the algorithm miRDeep.
Genome_build: A.gossypii EST, M. persicae EST and A. pisum
Supplementary_files_format_and_content: RT# 16587360 reference number of the pre-submission query correspondance.

organism: Aphis gossypii

source_name: whole insect tissue

growth_protocol: Aphid colony maintained on susceptible honeydew melon plants in a controlled growth chamber at 21 degree C, with a photoperiod of 16:8h (light:dark)

extract_protocol:
The total RNA was extracted using Trizol method. Enrichment for low molecular weight (LMW) RNA was performed according to Lu et al 2007 (Lu, C., Meyers, B., C., and Green, P. 2007. Construction of small RNA cDNA libraries for deep sequencing. Methods. 43: 110-117).
50 microgram of low molecular weight RNA was used for small RNA library preparation

treatment_protocol: Thrid and fourth leaves from 4 week old melon plants, both AR5 and PMR5 were used for aphid infestations. Each leaf was exposed to 50 aphids confined in a clip cage. Infestations were terminated after 48 h. Whole insects were collected and snap frozen in liq N2

tag: interaction type

value: Susceptible interaction with host plant melon

tag: feeding

value: 48 hours

tag: host plant

value: Vat- (PMR5) melon


title: Fc_MDMA/VLX_3

value: MDMA (15 mg/kg) and VLX (40 mg/kg, minipump) double treated

value: Dark Agouti


title: HsO4D-107_359062

description:
Date: 2009/06/30
CPC: 2

value: Blood

value: Universal Reference RNA (Stratagene)


title: HsO4D-007_351912

description:
Date: 2009/06/18
CPC: 5


title: Aphid Vat+ (AR5) library

description: Aphis gossypii (cotton-melon aphid)

value: Resistance interaction with host plant melon

value: Vat+ (AR5) melon


title: [ER+/PR+][ER-/PR-]HER2- HEL_061

tag: disease subtype

value: breast cancer


title: Core Basal HEL_060

value: Core Basal

tag: disease state


title: Fc_MDMA/VLX_2


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint21

value: liver

value: Biliary Atresia

value: 97 days


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint22

value: 80 days


title: HsO4D-022_352015

description:
Date: 2009/06/25
CPC: 1


title: HsO4D-006_351913

description:
Date: 2009/06/18
CPC: 5


title: Fc_MDMA/VLX_1

value: male


title: [ER+/PR+][ER-/PR-]HER2- HEL_059

value: breast cancer tumor


title: [ER+/PR+]HER2- HEL_062


title: HsO4D-001_351880

description:
Date: 2009/06/25
CPC: 1


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint19

value: 58 days


title: Liver biopsy sample obtained from a deceased-donor adult_NHL5

value: Sample for internal control to normalize each batch of GeneChip microarray run


title: HsO4D-091_359524

description:
Date: 2009/01/19
CPC: 2


title: HsO4D-092_359523

description:
Date: 2009/01/19
CPC: 2


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint10

value: 39 days


title: [ER+/PR+]HER2- HEL_056


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint9

value: 70 days


title: [ER+/PR+]HER2- HEL_055


title: HsO4D-072_351894

description:
Date: 2009/04/01
CPC: 2


title: [ER+/PR+]HER2- HEL_058


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint18

value: 75 days


title: Skin 3

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: cDNA was produced from total RNA using random primer labeling.

hyb_protocol: 600 ng labelled product was hybridized to slides usinge a NimbleGen Hybridization Kit (cat. no. 05 583 934 001) according to manufacturers protocol, then hybridized for 16 hours at 42 degrees.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data was normalized using the Robust Microarray Average (RMA) procedure implemented via the oligo package in Bioconductor

source_name: Normal Tissue

label_protocol: 600 ng total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene600

extract_protocol: On average, 50 7 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist (YY) using every 10th section stained by May-Giemsa. Careful attention was paid to the mi

tag: tissue type

value: Human Adult Normal Tissue

value: Skin

tag: supplier

value: biochain

tag: catalog number


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint11

value: 77 days


title: Kidney 3

value: Kidney


title: HsO4D-004_351911

description:
Date: 2009/04/01
CPC: 2

value: Blood

extract_protocol: Trizol

value: Universal Reference RNA (Stratagene)


title: [ER-/PR-]HER2- HEL_053

value: breast cancer


title: [ER+/PR+]HER2- HEL_054


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint6

value: liver

value: Biliary Atresia

value: 65 days


title: Liver biopsy sample obtained from a patient with biliary atresia_Cint1

value: 54 days


title: HsO4D-103_359352

description:
Date: 2009/03/31
CPC: 5

extract_protocol: Blood sample: 2.5 mL harvested in PAXgene® Blood RNA tubes (PreAnalytix). RNA extraction: PAXgene® Blood RNA kit (Qiagen). Extraction amount: 10ug


title: Bladder 3

value: Bladder


title: HsO4D-104_359354

description:
Date: 2009/03/31
CPC: 5


title: [ER+/PR+]HER2- HEL_052

value: breast cancer tumor


title: Skin 2


title: [ER+/PR+][ER-/PR-]HER2- HEL_050


title: Heart 3

value: Heart


title: Breast 3

value: Breast


title: HsO4D-102_359351

description:
Date: 2009/03/25
CPC: 4


title: Core Basal HEL_046

value: Core Basal


title: HsO4D-101_359525

description:
Date: 2009/03/25
CPC: 4


title: Liver biopsy sample obtained from a patient with biliary atresia_B101

value: 79 days


title: Liver 3

value: Human Adult Normal Tissue

value: Liver


title: HsO4D-051_351804

description:
Date: 2009/03/17
CPC: 2


title: [ER+/PR+]HER2- HEL_045


title: Colon 3

value: Colon

value: biochain


title: Core Basal HEL_051


title: Liver biopsy sample obtained from a patient with biliary atresia_B100

value: 40 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B98

value: 76 days


title: Heart 2


title: Liver biopsy sample obtained from a patient with biliary atresia_B99

value: 83 days


title: [ER+/PR+]HER2- HEL_043

value: breast cancer


title: HsO4D-048_352006

description:
Date: 2009/03/17
CPC: 2

value: Blood

value: Universal Reference RNA (Stratagene)


title: Liver biopsy sample obtained from a patient with biliary atresia_B95

value: liver

value: Biliary Atresia

value: 168 days


title: [ER+/PR+]HER2- HEL_042

value: breast cancer tumor


title: HsO4D-075_352194

description:
Date: 2009/03/11
CPC: 5


title: Brain 3

value: Brain


title: Liver biopsy sample obtained from a patient with biliary atresia_B96

value: 50 days


title: TNP HEL_041

value: TNP


title: Bladder 2

value: Human Adult Normal Tissue

value: Bladder


title: HsO4D-074_351892

description:
Date: 2009/03/10
CPC: 2


title: Prostate 3

value: Prostate


title: Liver biopsy sample obtained from a patient with biliary atresia_B94

value: 75 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B84

value: 47 days


title: HsO4D-033_351605

description:
Date: 2009/03/04
CPC: 1


title: Muscle 3

value: Muscle

value: biochain


title: Liver biopsy sample obtained from a patient with biliary atresia_B82

value: 59 days


title: [ER+/PR+]HER2- HEL_038

value: breast cancer


title: Core Basal HEL_037

value: Core Basal


title: [ER+/PR+][ER-/PR-]HER2- HEL_040


title: Lung 3

value: Lung


title: HsO4D-076_352195

description:
Date: 2009/03/11
CPC: 5

value: Blood

value: Universal Reference RNA (Stratagene)


title: Liver biopsy sample obtained from a patient with biliary atresia_B83

value: liver

value: Biliary Atresia


title: HsO4D-066_351810

description:
Date: 2009/03/10
CPC: 2


title: Prostate 2


title: HsO4D-010_352118

description:
Date: 2009/03/03
CPC: 2


title: Liver biopsy sample obtained from a patient with biliary atresia_B80

value: 51 days


title: [ER+/PR+]HER2- HEL_036

value: breast cancer tumor


title: HsO4D-019_351870

description:
Date: 2009/03/04
CPC: 1


title: Ovary 3

value: Human Adult Normal Tissue

value: Ovary


title: Liver biopsy sample obtained from a patient with biliary atresia_B79

value: 84 days


title: [ER+/PR+]HER2- HEL_035


title: HsO4D-009_351903

description:
Date: 2009/03/03
CPC: 2


title: Colon 2

value: Colon


title: [ER+/PR+]HER2- HEL_032


title: HsO4D-080_352187

description:
Date: 2009/02/18
CPC: 4


title: Liver biopsy sample obtained from a patient with biliary atresia_B77

value: 32 days


title: Brain 2

value: Brain


title: HsO4D-079_352186

description:
Date: 2009/02/18
CPC: 4


title: Liver biopsy sample obtained from a patient with biliary atresia_B73

value: 52 days


title: Breast 2

value: Breast

value: biochain


title: Liver biopsy sample obtained from a patient with biliary atresia_B75

value: 80 days


title: Ovary 2


title: Liver biopsy sample obtained from a patient with biliary atresia_B72

value: 44 days


title: [ER+/PR+]HER2- HEL_030

value: breast cancer


title: [ER+/PR+][ER-/PR-]HER2- HEL_028


title: [ER+/PR+]HER2- HEL_026


title: [ER+/PR+]HER2- HEL_025


title: [ER-/PR-]HER2- HEL_031


title: HsO4D-096_351685

description:
Date: 2009/02/17
CPC: 1

value: Blood

value: Universal Reference RNA (Stratagene)


title: HsO4D-099_351688

description:
Date: 2009/02/17
CPC: 1


title: [ER+/PR+]HER2- HEL_024


title: Kidney 2

value: Kidney


title: Liver 2

value: Liver


title: Liver biopsy sample obtained from a patient with biliary atresia_B64

value: liver

value: Biliary Atresia

value: 63 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B70

value: 106 days


title: Skin 1

value: Human Adult Normal Tissue

value: Skin


title: Muscle 2

value: Muscle


title: [ER-/PR-]HER2- HEL_023

value: breast cancer tumor


title: Liver biopsy sample obtained from a patient with biliary atresia_B59

value: 68 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B69

value: 50 days


title: Prostate 1

value: Prostate

value: biochain


title: Liver biopsy sample obtained from a patient with biliary atresia_B66

value: 97 days


title: Lung 2

value: Lung


title: Pongo abelii  A955

data_processing: The methylation value was set to null for probes with a detection p-value < 0.01.  A strict filtering step  was performed to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested. We only retained those probes that had either a perfect match, or had 1 or 2 mismatches in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.

organism: Pongo abelii

source_name: blood

value: female

tag: organism

value: Pongo abelii

value: blood


title: Liver biopsy sample obtained from a patient with biliary atresia_B52

value: liver

value: 169 days


title: [ER+/PR+]HER2- HEL_022

value: breast cancer


title: Ovary 1

value: Ovary


title: Pongo abelii  A953

tag: gender


title: Brain 1

value: Human Adult Normal Tissue

tag: tissue

value: Brain


title: [ER+/PR+]HER2- HEL_018


title: Core Basal HEL_017

value: Core Basal


title: Liver biopsy sample obtained from a patient with biliary atresia_B50

value: Biliary Atresia

value: 64 days


title: Pongo abelii  A949


title: Pongo pygmaeus  A944

organism: Pongo pygmaeus

value: male

value: Pongo pygmaeus


title: Breast 1

value: Breast

value: biochain


title: Pongo abelii  A947


title: Core Basal HEL_016

value: breast cancer tumor


title: Core Basal HEL_015


title: Liver biopsy sample obtained from a patient with biliary atresia_B49

value: 43 days


title: [ER+/PR+]HER2- HEL_011


title: Liver biopsy sample obtained from a patient with biliary atresia_B53

value: 91 days


title: Colon 1

value: Colon


title: Pongo pygmaeus  A943

value: female

value: blood


title: [ER+/PR+]HER2- HEL_008

value: breast cancer


title: Liver biopsy sample obtained from a patient with biliary atresia_B48

value: liver

value: 41 days


title: Gorilla gorilla gorilla  A937

value: Gorilla gorilla gorilla


title: Heart 1

value: Human Adult Normal Tissue

value: Heart


title: Kidney 1

value: Kidney


title: Liver biopsy sample obtained from a patient with biliary atresia_B47

value: Biliary Atresia

value: 113 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B46

value: 33 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B45

value: 71 days


title: Liver 1

value: Liver

value: biochain


title: Core Basal HEL_007

value: Core Basal

value: breast cancer tumor


title: Lung 1

value: Lung


title: Gorilla gorilla gorilla  A931

value: male

value: blood


title: Liver biopsy sample obtained from a patient with biliary atresia_B44

value: liver

value: 73 days


title: Gorilla beringei graueri  A929

value: Gorilla beringei graueri


title: Gorilla gorilla gorilla  A932

value: female

value: Gorilla gorilla gorilla


title: Muscle 1

value: Human Adult Normal Tissue

value: Muscle


title: [ER+/PR+][ER-/PR-]HER2- HEL_006

value: breast cancer


title: [ER+/PR+]HER2- HEL_005


title: TNP HEL_003

value: TNP


title: Liver biopsy sample obtained from a patient with biliary atresia_B41

value: Biliary Atresia

value: 44 days


title: Pan paniscus  A925

organism: Pan paniscus

value: Pan paniscus


title: [ER+/PR+]HER2- HEL_001


title: [ER+/PR+]HER2- HEL_002


title: MAL1 (strain containing MAK2-Q100G allele). + 1NM-PP1 (inhibiting molecule) vs + DMSO (control) repeat 4

city: Berkeley

first: Abby

last: Leeder

address: 111 Koshland Hall

institute: UC Berkeley

hyb_protocol: Hybridizations were performed using Pronto kits (Promega) according to the manufacturer's protocol and as described by Tian et al (2007 - Eukaryotic cell 6(6)1018:29)

scan_protocol: Scanned on an Axon GenePix 4000B

data_processing: Images were quantified using GenePix Pro 6 software (Molecular Devices)

organism: Neurospora crassa OR74A

source_name: MAL1 (MAK2-Q100G allele) + 1NM-PP1 (inhibiting molecule)

label_protocol: The ChipShot Indirect cDNA Synthesis and labelling protocol from Promega/Corning (Promega) was used according to the manufacturer's instructions, with the following exceptions: 10μg dried cDNA was resuspended in 9 μl 0.06 M sodium bicarbonate, and quenching was accomplished by the addition of 4.5 μl 4 M hydroxylamine

growth_protocol: N. crassa conidia were grown at 30 degrees in liquid media chambers. 20 minutes before the end of the incubation, ATP analog 1NM-PP1 (or DMSO to the contol sample) was added to the media. At the end of the incubation, cells were filtered and immediately frozen in liquid N2.

extract_protocol: RNA was extracted using Trizol

source_name: MAL1 (MAK2-Q100G allele) + DMSO (control)


title: Bladder 1

value: Bladder

value: biochain


title: MAL1 (strain containing MAK2-Q100G allele). + DMSO (control) vs + 1NM-PP1 (inhibiting molecule) repeat 3


title: MAL1 (strain containing MAK2-Q100G allele). + 1NM-PP1 (inhibiting molecule) vs + DMSO (control) repeat 3


title: MAL1 (strain containing MAK2-Q100G allele). + 1NM-PP1 (inhibiting molecule) vs + DMSO (control)  repeat 2


title: Liver biopsy sample obtained from a patient with biliary atresia_B37

value: 66 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B36

value: 22 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B35

value: 27 days


title: Pan paniscus  A919

city: Barcelona

first: Irene

last: Hernando

address: Dr Aiguader 88

institute: UPF/CSIC

value: male

value: blood


title: Pan paniscus  A920


title: MAL1 (strain containing MAK2-Q100G allele). + DMSO (control) vs + 1NM-PP1 (inhibiting molecule) repeat 1


title: Pan paniscus  A917


title: Pan paniscus  A914


title: Liver biopsy sample obtained from a patient with biliary atresia_B39

value: liver

value: 52 days


title: 72 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 3

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description:
Biological replicate 3 of 3
72 hpf MO-grnA Rep3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction (FE) Software (version10.5.1.1).

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

organism: Danio rerio

source_name: MO-grnA_72 hpf

label_protocol: Agilent's Quick Amp Labeling Kit denerates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: The zebrafish were maintained at our own facility in a controlled environment with a 14/10-h light-dark cycle at 28 °C.  The fertilized eggs were collected at the 1-cell stage.

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

treatment_protocol: An injection volume from 2-3 nl of MOs was injected into 1-cell-stage embryos.

tag: injected with

value: morpholino of zf-grna

tag: age

value: 72 hpf

value: trunk region of morphant

source_name: WT_72 hpf

value: wild type (untreated)

value: trunk region of zebrafish embryos


title: Liver biopsy sample obtained from a patient with biliary atresia_B29

tag: condition

value: Biliary Atresia

value: 73 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B31

tag: age of biopsy

value: 48 days


title: tumor metformin3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: human pancreatic cancer

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: cell line: Cells were grown in RPM I 1640 supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C. Tumor(mouse): Each mouse was inoculated with Panc1 cells (5×106 cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: cell line: Panc1 cells were treated with 10 mM metformin or without metformin for 72 h. Tumor: The metformin-treated group was injected 5 times a week intraperitoneally (i.p.) at 1 mg/body or 2 mg/body per day for 5 weeks.

tag: pancreatic cancer

value: tumor

tag: agent

value: metformin


title: MAL1 (strain containing MAK2-Q100G allele). + 1NM-PP1 (inhibiting molecule) vs + DMSO (control)  repeat 1

tag: strain


title: tumor control3

value: control


title: 72 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 2

description:
Biological replicate 2 of 3
72 hpf MO-grnA Rep 2

tag: genotype/variation


title: Pan troglodytes schweinfurthii  A910

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

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

organism: Pan troglodytes schweinfurthii

label_protocol: Standard Illumina labelling protocol

value: Pan troglodytes schweinfurthii


title: MAL1 (strain containing MAK2-Q100G allele). + DMSO (control) vs + 1NM-PP1 (inhibiting molecule) repeat 2


title: Liver biopsy sample obtained from a patient with biliary atresia_B21

organism: Homo sapiens


title: 48 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 2

description:
Biological replicate 2 of 3
48 hpf MO-grnA Rep 2

source_name: MO-grnA_48 hpf

value: 48 hpf

source_name: WT_48 hpf


title: 48 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 3

description:
Biological replicate 3 of 3
48 hpf MO-grnA Rep3


title: tumor control2


title: tumor metformin2


title: Liver biopsy sample obtained from a patient with biliary atresia_B24

source_name: Liver

value: 54 days


title: Pan paniscus  A915

value: female

value: Pan paniscus

value: blood


title: Liver biopsy sample obtained from a patient with biliary atresia_B22

value: liver

value: 68 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B28

value: 50 days


title: 72 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 1

description:
Biological replicate 1 of 3
72 hpf MO-grnA Rep 1

value: morpholino of zf-grna

value: 72 hpf

value: trunk region of morphant

value: wild type (untreated)


title: tumor control1


title: Liver biopsy sample obtained from a patient with biliary atresia_B20

value: Biliary Atresia

value: 63 days


title: tumor metformin1

value: tumor

value: metformin


title: 24 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 3

description:
Biological replicate 3 of 3
24 hpf MO-grnA Rep 3

source_name: MO-grnA_24 hpf

value: 24 hpf

source_name: WT_24 hpf

value: trunk region of zebrafish embryos


title: Liver biopsy sample obtained from a patient with biliary atresia_B19

value: 55 days


title: cell line control9

value: cell line

value: control


title: cell line metformin9


title: 24 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 2

description:
Biological replicate 2 of 3
24 hpf MO-grnA Rep 2


title: 48 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 1

description:
Biological replicate 1 of 3
48 hpf MO-grnA Rep 1

value: 48 hpf


title: ulcerative colitis colon mucosa Kelle39

city: Houston

first: R.

middle: Alan

last: Harris

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Ulcerative colitis colon mucosa sample

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: GenomeStudio software version 2010.3.0.30128

label: Cy5 and Cy3

source_name: colon mucosa Kelle39

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from colon mucosa samples using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) starting at step 5 of the Tissue Protocol following bead beating and Qiagen TissueLyser treatment. All samples were quality tested with PicoGreen prior to proceeding with the microarrays.

value: Male

tag: age (y)

value: Colon mucosa

value: ulcerative colitis


title: Liver biopsy sample obtained from a patient with biliary atresia_B15

value: liver

value: 41 days


title: cell line metformin8


title: ulcerative colitis colon mucosa Kelle37

description: Ulcerative colitis colon mucosa sample

source_name: colon mucosa Kelle37

value: Female


title: Liver biopsy sample obtained from a patient with biliary atresia_B10


title: 16 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 2

description:
Biological replicate 2 of 3
16 hpf MO-grnA Rep2

source_name: MO-grnA_16 hpf

value: morpholino of zf-grna

value: 16 hpf

value: trunk region of morphant

source_name: WT_16 hpf

value: wild type (untreated)


title: Liver biopsy sample obtained from a patient with biliary atresia_B18

value: Biliary Atresia

value: 46 days


title: Liver biopsy sample obtained from a patient with biliary atresia_B14

value: 68 days


title: 24 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 1

description:
Biological replicate 1 of 3
24 hpf MO-grnA Rep 1

value: 24 hpf

value: trunk region of zebrafish embryos


title: cell line metformin7

value: cell line

value: metformin


title: Liver biopsy sample obtained from a patient with biliary atresia_B9

value: 73 days


title: 16 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 3

description:
Biological replicate 3 of 3
16 hpf MO-grnA Rep 3


title: 16 hpf trunk region of zebrafish embryos: WT vs MO-grnA injected Replicate 1

description:
Biological replicate 1 of 3
16 hpf MO-grnA Rep 1