title: 2F-BA-3 [G3_2]

city: Taichung

first: Ling-Chu

last: Chang

state: -- select state --

address: 6F, No. 350, Jingmao 1st Road, Beitun Dist.,

department: Center for Molecular Medicine

country: Taiwan

institute: China Medical University Hospital

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Fluorinated betulinic acid-treated MCF-7 cells

label_protocol: 5 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: MCF-7 cells were cultured in DMEM/F12 medium supplemented with 10% (v/v) FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Cells were treated with 40 uM betulinic acid or 40 uM fluorinated betulinic acid for 24 h.

tag: cell type

value: human breast cancer cells

tag: treated with

value: 40 uM fluorinated betulinic acid for 24hr


title: HCC6046-T5

status: Public on Mar 03 2017

type: genomic

city: Los Angeles

first: Huy

middle: Q

last: Dinh

state: California

address: 8700 Beverly Blvd

department: Center for Bioinformatics and Functional Genomics

country: USA

institute: Cedars Sinai Medical Center

description: Tumor

hyb_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform

data_processing: Methylumi Bioconductor package: https://www.bioconductor.org/packages/release/bioc/html/methylumi.html

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Frozen tissues

growth_protocol: Frozen tissues

extract_protocol: DNA was extracted using Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions

treatment_protocol: No treatment

tag: tissue

value: Tumor


title: HCC6046-T1

description: Tumor

scan_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform


title: HCC8257-T5

description: Tumor

label_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform


title: HCC5647-T1

description: Tumor


title: D. shibae_wt_30_min_NOstress_rep1

type: RNA

city: Braunschweig

first: Matthias

last: Ebert

address: Spielmannstraße 7

department: Institute of Microbiology

country: Germany

institute: Technical University Braunschweig

description: Gene expression of D. shibae after 30 min of nitrosative stress, Biological replicate 1 of 3.

hyb_protocol: 600 ng of labeled RNA were pooled, fragmented and hybridized according to the “one-color microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing:
Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). For analyses only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.
Data was normalized within the array and between array slides and background corrected.

molecule: total RNA

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: Dinoroseobacter shibae, anaerob,+NO

label_protocol: Two µg of isolated total cellular RNA was labeled with Cy3, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: For the nitrosative stress experiment Dinoroseobacter shibae DFL12T wild type and corresponding mutant strains were grown in artificial saltwater minimal medium (SWM) supplemented with 16.9 mM succinate. For aerobic cultivation 125 ml of cell culture was inoculated with a grown pre-culture to an OD578 nM of 0.05 in a baffled flasks shaking at 200 rpm at 30°C in dark. After reaching an OD578 nM of 0.5 cells were shifted to serum flasks with rubber stoppers and 25 mM pyruvate was added. Incubation occurred at 100 rpm and 30°C in dark, to avoid aerobic anoxygenic photosynthesis of D. shibae during the experiment. After 30 min of anaerobic starvation a final concentration of 50 nM of NO saturated water was added in a Coy anaerobic chamber.

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was analyzed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: An anaerobic shift was performed after reaching an OD578 nM of 0.5 by shifted cells to serum flasks. Oxygen was consumed within 30 min by D. shibae itself. The investigated time points were directly before injection of 50 nM of NO and 30 min after injection.

tag: strain

tag: growth phase

value: exponential phase

tag: genotype/variation

value: wt

tag: stress

value: NO stress


title: D. shibae_ΔdnrD_anaerob_rep1

description: Gene expression of D. shibae ΔdnrD, anaerob, Biological replicate 1 of 3.

source_name: Dinoroseobacter shibae,ΔdnrD, anaerob

value: {delta}dnrD

value: anaerob


title: D. shibae_wt_30_min_NOstress_rep3

description: Gene expression of D. shibae after 30 min of nitrosative stress, Biological replicate 3 of 3.


title: D. shibae_wt_30_min_NOstress_rep2

description: Gene expression of D. shibae after 30 min of nitrosative stress, Biological replicate 2 of 3.


title: D. shibae_wt_anaerob_rep2

description: Gene expression of D. shibae, anaerob, Biological replicate 2 of 3.

source_name: Dinoroseobacter shibae, anaerob


title: BA-2 [G2_2]

source_name: Betulinic acid-treated MCF-7 cells

tag: cell line

value: 40 uM betulinic acid  for 24 hr


title: D. shibae_wt_anaerob_rep1

description: Gene expression of D. shibae, anaerob, Biological replicate 1 of 3.


title: D. shibae_wt_anaerob_rep3

description: Gene expression of D. shibae, anaerob, Biological replicate 3 of 3.


title: C. elegans with 500μg/ml anatase TiO2_rep3

city: Hsinchu

first: Chun-Chih

last: Hu

address: 101, Sec. 2, Kuang-Fu Road

department: Materials Science and Engineering

institute: National Tsing Hua University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Rosetta Resolver System (Rosetta Biosoftware, Seattle, WA, USA) (Weng et al., 2006) and Transcriptome Analysis Console (TAC) Software (Sugnet et al., 2004) (Affymetrix, Waltham, MA, USA).

label: biotin

organism: Caenorhabditis elegans

source_name: C. elegans with 500μg/ml anatase TiO2

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

growth_protocol: C. elegans wild type (N2) strains were maintained on NGM (nematode growth medium) agar plates seeded with (uracil auxotroph) E. coli OP50 (serving as a food source) at 20°C according to standard methods (Brenner, 1974).

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

treatment_protocol: Synchronized worms were exposed to anatase TiO2 NPs prepared in S-medium (worm liquid growth medium) (Lewis and Fleming, 1995) in the dark.

value: wild type

tag: exposed to

value: 500μg/ml anatase TiO2


title: BA-2 [G2_1]


title: C. elegans without anatase TiO2_rep3

source_name: C. elegans without anatase TiO2

value: none (control)


title: CTL-1 [G1_1]

source_name: Control


title: HCC6046-T2

description: Tumor


title: HCC8010-T5

description: Tumor


title: JEG-3-R5

city: Boston

first: Kevin

middle: Meyer

last: Elias

state: MA

address: 75 Francis Street

department: OB/GYN

institute: Brigham and Women's Hospital

description: Gene expression data from chemotherapy resistant cell line

hyb_protocol: The fragmented cRNA was hybridized to a HG U133 Plus 2.0 array at 45°C, overnight, in the presence of several biotinylated control oligonucleotides (for quality control)

scan_protocol: Read using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: The microarray data were analyzed using ArrayStar v.11.2 (DNASTAR, Madison, WI).  Robust Multiarray Analysis (RMA) was used for background correction followed by quantile normalization and median polish summarization. A pre-analysis filter used signal intensity as the method of determining probe set inclusion. Probe sets that had a group mean of log2 signal >5 were kept for further analysis.

source_name: Choriocarcinoma cell line, resistant to 10^-5 M Methotrexate

growth_protocol: Cell lines were grown in a tissue culture incubator at 37° C with 5% CO2 in Eagle’s Minimum Essential Medium (ATCC), supplemented with 10% fetal bovine serum (ATCC) and 1% L-glutamine- penicillin-streptomycin (Sigma-Aldrich, Saint Louis, MO).

extract_protocol: Total RNA was isolated by TRIzol® (Thermo Fisher Scientific, Cambridge, MA) and then further purified by clean-up over RNeasy Micro columns (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: The cell lines were serially passaged in complete medium supplemented with each cell line’s respective IC50 concentration of methotrexate until the cell lines were able to proliferate normally.

value: placenta cell line

tag: behavior

value: malignant


title: CTL-1 [G1_2]


title: JEG-3-R6

source_name: Choriocarcinoma cell line, resistant to 10^-6 M Methotrexate


title: JEG-3-R7

source_name: Choriocarcinoma cell line, resistant to 10^-7 M Methotrexate


title: HCC8010-T3

description: Tumor


title: HCC8010-T4

description: Tumor


title: JEG-3

description: Gene expression data from parent cell line

source_name: Choriocarcinoma parent cell line

value: JEG-3 - ATCC


title: 3A-Sub E

source_name: Normal placenta parent cell line

value: CRL-1584 (3A-Sub E) - ATCC

value: benign


title: NP-R7

source_name: Normal placenta cell line, resistant to 10^-7 M Methotrexate


title: HCC8010-N

description: Normal liver tissue

value: Normal liver tissue


title: HCC8010-T1

description: Tumor


title: HCC8213-N

description: Normal liver tissue


title: 2F-BA-3 [G3_1]

value: human breast cancer cells

value: 40 uM fluorinated betulinic acid for 24hr


title: atg12_conditional_knockout4

city: San Francisco

first: Emmanuelle

last: Passegue

state: CA

address: 35 Medical Center Way, RMB-1017, Box 0667

department: Department of Medicine, Hem/Onc Division

institute: The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco

description: Gene expression data from freshly isolated Atg12flox/flox:Mx1-Cre conditional knockout HSCs

hyb_protocol: Hybridized on Affymetrix Gene ST 1.0 microarrays according to manufacturers’ instructions.

scan_protocol: The signal intensity fluorescent images produced during the Affymetrix GeneChip hybirdizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: Gene expression was first measured at the probe set level (n = 241,619) using the RMA (Robust Multi-array Average) methodology followed by quantile normalization. Quality of the data was assessed using principal component analysis (PCA) as well as unsupervised hierarchical clustering. Probe set annotation for the MoGene1.0st v1 array was downloaded from Affymetrix's website and the 241,619 probe sets were mapped to the 28,853 main transcript set (excluding controls). This data set was used for all analyses. We used a family of generalized, linear models  implemented with the R package, LIMMA, to assess differential expression between groups of interest.

organism: Mus musculus

source_name: Freshly isolated Atg12flox/flox:Mx1-Cre conditional knockout HSCs

label_protocol: Sense-strand complementary DNA targets were generated using the NuGEN WT-Ovation Exon Module, fragmented and biotinylated using the Encore Biotin Module.

growth_protocol: freshly double sorted HSCs from mice

extract_protocol: Arcturus PicoPure RNA Isolation Kit, amplified using Ovation Pico WTA System V2

value: bone marrow

value: hematopoietic stem cell

tag: genotype

value: atg12f/f cre

tag: age

value: 3-4 months

tag: cell markers


title: HCC8010-T2

description: Tumor

value: Tumor


title: control2

description: Gene expression data from freshly isolated Atg12flox/flox HSCs

source_name: Freshly isolated Atg12flox/flox HSCs


title: 19.1

city: Guelph

first: Tamas

last: Revay

state: ON

address: 50 Stone Rd E

department: Biomedical Sci

country: Canada

institute: University of Guelph

hyb_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada

data_processing:
This work analysed DNA copy number variations only. The starting points were the GenomeStudio project files (.bsc) provided by DNAL Landmarks. The LogR data was  exported from GenomeStudio using the GoldenHelix SVS exporter. Copy number analysis was done in SNP and Variation Suite ver. 7.7.8. (SVS, GoldenHelix Inc.)
The illumina defined cluster positions were applied to all samples and LogR values were calculated in GenomeStudio (Illumina).

label: C-Bio and A-DNP

organism: Bos taurus

source_name: gDNA from blood

growth_protocol: Primary fibroblast cell lines were established by using standard culture techniques 30 from ear notch samples of three unrelated Holstein bulls. Briefly, the samples were digested in 0.5% collagenase type 1 for 6h at 38oC then cultured in DMEM with 10% FBS, 1% PenStrep (Invitrogen Canada Inc. Burlington, ON, Canada) and 2mM L-glutamine (Sigma-Aldrich Canada Ltd, Oakville, ON, Canada). The primary fibroblasts were sequentially cultured (seeded at 3x104 cells/25cm2 flask and harvested at ~1.5x105 cells/flask, ~2.5 population doubling/passage) and sampled at passage 5, 15 and 25 (P5, P15, P25) for DNA extraction.

extract_protocol: Genomic DNA was extracted using a standard Proteinase K and phenol/chlorophorm method.

tag: breed

value: Holstein

value: blood


title: control4


title: control1


title: atg12_conditional_knockout2


title: atg12_conditional_knockout3


title: 19.4

scan_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada


title: control3


title: 28.4

label_protocol: The protocol followed the manufacturers recommendations by the service provider DNA Landmarks, Quebec, Canada


title: atg12_conditional_knockout1


title: 14.4


title: VL_post_id136

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

hyb_protocol: Samples were hybridised to Human Gene 1.0 ST Arrays (Affymetrix) following the manufacturer’s instructions

scan_protocol: After washing, arrays were scanned using a GS 3000 scanner (Affymetrix)

data_processing: GeneSpring was used for quality control and pre-processing of the raw data.  Data were normalised using the RMA16 algorithm in GeneSpring.

source_name: inguinal lymph node aspirates, post-treatment

label_protocol: Aliquots of total RNA (200ng) were labelled using Affymetrix’s WT sense Target labelling kit

growth_protocol: Aspirates were directly injected into 700uL of RLT buffer (RNeasy Micro Kit; QIAGEN, UK), and stored in liquid nitrogen until RNA was extracted in a single batch.

extract_protocol: Aspirates were directly injected into 700uL of RLT buffer (RNeasy Micro Kit; QIAGEN, UK), and RNA prepared using these kits in accordance with the manufacturer´s instruction.  RNA integrity and purity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano and Pico LabChip kit (Agilent Technologies, Massy, France).  All samples had RNA integrity (RIN) values >7.

treatment_protocol: Aspirates were directly injected into 700uL of RLT buffer (RNeasy Micro Kit; QIAGEN, UK), and RNA prepared using these kits in accordance with the manufacturer´s instruction.  Samples in RLT buffer were stored in liquid nitrogen and RNA was extracted in a single batch. RNA integrity and purity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano and Pico LabChip kit (Agilent Technologies, Massy, France).


title: VL_pre_id137

source_name: inguinal lymph node aspirates, pre-treatment


title: 17.6


title: 14.1


title: 17.1


title: 19.6


title: 13.4


title: VL_pre_id136


title: 28.6


title: 28.1


title: 14.6


title: 13.6


title: 15w3

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

country: Japan

institute: National Institute of Radiological Sciences

description: Lung adenocarcinoma from rat irradiated at 15 weeks old (#3/3)

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 40 hours at 65°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 (Protocol v.7.1) in an ozone-depleted hood.

scan_protocol: The slides were scanned in an Agilent DNA Microarray scanner (G2565CA)

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for computing ratios

organism: Rattus norvegicus

source_name: Lung adenomcarcinoma

label_protocol: 1 μg of RNase-treated DNA (test or reference) was labelled using the Agilent SureTag DNA labeling kit (Protocol v.7.1), following all instructions for a 2x105K array.

extract_protocol: Frozen tumour tissue was cut into sections of 20 micron thickness and mounted on micoscope slides. Slides were stained with Cresol violet to identify regions of adenocarcinoma, which were then scraped from the slides using a needle into a collection tube. The tumour specimens were then extracted using the QIAGEN QIAamp Micro DNA extraction kit. Reference DNA was extracted directly from frozen ear skin tissue.

treatment_protocol: Lung tumour lesions were excised at autopsy, and a portion of the tumour mass snap-frozen in liquid nitrogen before long-term storage at -80°C.

value: Wistar

tag: Sex

value: Female

source_name: Ear skin


title: VL_post_id134


title: 15w2

description: Lung adenocarcinoma from rat irradiated at 15 weeks old (#2/3)


title: 11.6


title: 17.4


title: 13.1


title: VL_pre_id134


title: VL_post_id130


title: 11.1


title: 15w1

description: Lung adenocarcinoma from rat irradiated at 15 weeks old (#1/3)


title: 10.6


title: 5w2

description: Lung adenocarcinoma from rat irradiated at 5 weeks old (#2/3)


title: 5w1

description: Lung adenocarcinoma from rat irradiated at 5 weeks old (#1/3)


title: VL_post_id111


title: VL_post_id115


title: VL_pre_id115


title: VL_post_id119


title: VL_pre_id119


title: 1w3

description: Lung adenocarcinoma from rat irradiated at 1 week old (#3/3)


title: 1w2

description: Lung adenocarcinoma from rat irradiated at 1 week old (#2/3)


title: VL_post_id137


title: 10.1


title: 1w1

description: Lung adenocarcinoma from rat irradiated at 1 week old (#1/3)


title: VL_pre_id111


title: 1.1


title: 1.6


title: 1.4


title: 10.4


title: VL_post_id127


title: VL_post_id110


title: A P05

source_name: gDNA from fibroblast

value: ear fibroblast

tag: passage


title: Spo2

description: Lung adenocarcinoma from unirradiated rat (#2/3)


title: VL_pre_id127


title: VL_pre_id110


title: Spo3

description: Lung adenocarcinoma from unirradiated rat (#3/3)


title: SW480_NC

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

country: China

institute: Second Military Medical University

description: Expression profiles of SW480 without exposure to radiation.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: All probes were mapped to human genome 38 from Ensembl database by SeqMap and probes perfectly and uniquely matched to the exons of the Ensembl annotation database were subject to the further analyses. Background correction and quantile normalization were performed by “rma.background.correct” and “normalize.quantiles.robust” functions in the preprocessCore package. Preprocessed data then was transformed into log2 scale. Probes with intensity low signials were filtered.  Median intensity of multiple probes annotating to the same gene was calculated to generate the gene-level data.

source_name: SW480 cells without exposure to radiation.

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA).

growth_protocol: All cell lines were maintained in Dulbecco’s Modified Eagle Medium (Hyclone, Thermo Fisher Scientific, Pittsburgh, PA, USA) supplemented with 10% heat-inactivated fetal bovine serum (GIBCO, Grand Island, Life Technologies, NY, USA), 100 units/ml penicillin and 100mg/ml streptomycin at 37℃ in a 5% CO2 humidified atmosphere.

extract_protocol: The purity and concentration of total RNA were assessed using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Lovo, RKO and SW480 cell lines were exposure to 2Gy dose of radation for 0.5 min, while samples of control group were untreated.


title: A P15


title: RKO_RA

description: Expression profiles of RKO with exposure to radiation.

source_name: RKO cells with exposure to radiation.

value: RKO


title: SW480_RA

description: Expression profiles of SW480 with exposure to radiation.

source_name: SW480 cells with exposure to radiation.


title: A P25


title: Spo1

description: Lung adenocarcinoma from unirradiated rat (#1/3)


title: RKO_NC

description: Expression profiles of RKO without exposure to radiation.

source_name: RKO cells without exposure to radiation.


title: 11.4


title: exosome_adult human_rep2

city: fuzhou

first: liping

last: fan

state: fujian

address: xinquan road NO.29 gulou district

department: blood transfusion

institute: fujian medical university union hospital

description: Human blood donor were female and free

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

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

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: human suspended red blood cell unit with leukocyte reduced

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All human blood donors were free.Whole blood were collected in the donation room.Whole blood were made into suspended red blood cell unit with leukocyte reduced within 6 hours.Suspended red blood cell unit stored at 2-6℃ for 2 weeks.

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

treatment_protocol: Supernatant from suspended red blood cell unit with leukocyte reduced were seperated by centrifugation.Exosome were extracted by ExoQuick reagent bought from SBI company and stored at -80℃.

value: exosome

tag: gender

value: female


title: exosome_adult human_rep3

description: Human blood donor were male and free

value: male


title: Colon_IBS patient#3_mice

status: Public on Mar 02 2017

city: Hamilton

first: Premysl

last: Bercik

address: 1280 Main Street West

department: Medicine

institute: McMaster University

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P3

scan_protocol: Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule.

data_processing:
After collection, the RCC files that were generated by the digital analyzer and contained the counts of each samples were imported into the nSolver software fo further anlysis. After checking the quality scores for each sample, a Positive Control Normalization and a Reference (Housekeeping) Gene Normalization. was performed for each sample.
Fields of view counted

label: color-coded barcode technology

source_name: Colonic sections_tissue

label_protocol: The protocol followed was according to manufacturer's intructions (color-coded barcode technology)

extract_protocol: Total RNA extractions were conducted with the RNeasy Mini Kit (Qiagen, Toronto, Canada) according to the manufacturer’s instructions. DNase digestion during purification was carried out using the RNase-free DNase (Qiagen).

value: NIH Swiss

value: 10-12 weeks (at colonization)

tag: human donor of fecal sample

value: IBS patient#3_P3

value: Colonic tissue from mice colonized with P3


title: exosome_adult human_rep1

description: Human blood donor were male and free


title: Colon_IBS patient#6_mice

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P6

hyb_protocol: The protocol followed was according to manufacturer's intructions

value: IBS patient#6_P6

value: Colonic tissue from mice colonized with P6


title: Colon_Healthy volunteer#5_mice

description: Colonic tissue from germ-free NIH swiss mice (10-12 weeks) colonized with H5

value: Healthy volunteer#5_H5

value: Colonic tissue from mice colonized with H5


title: Colon_IBS patient#4_mice

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P4

value: IBS patient#4_P4

value: Colonic tissue from mice colonized with P4


title: VL_pre_id130


title: Colon_IBS patient#5_mice

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P5

value: IBS patient#5_P5

value: Colonic tissue from mice colonized with P5


title: M2 P15

value: Holstein

value: ear fibroblast


title: Colon_IBS patient#2_mice

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P2

value: IBS patient#2_P2

value: Colonic tissue from mice colonized with P2


title: M2 P25


title: 5w3

description: Lung adenocarcinoma from rat irradiated at 5 weeks old (#3/3)

value: Wistar

value: Female


title: Colon_IBS patient#1_mice

description: Colonic tissue from germ free NIH swiss mice (10-12 weeks) colonized with P1

value: NIH Swiss

value: 10-12 weeks (at colonization)

value: IBS patient#1_P1

value: Colonic tissue from mice colonized with P1


title: Colon_Healthy volunteer#4_mice

description: Colonic tissue from germ-free NIH swiss mice (10-12 weeks) colonized with H4

value: Healthy volunteer#4_H4

value: Colonic tissue from mice colonized with H4


title: Colon_Healthy volunteer#1_mice

description: Colonic tissue from germ-free NIH swiss mice (10-12 weeks) colonized with H1

value: Healthy volunteer#1_H1

value: Colonic tissue from mice colonized with H1


title: Colon_Healthy volunteer#2_mice

description: Colonic tissue from germ-free NIH swiss mice (10-12 weeks) colonized with H2

value: Healthy volunteer#2_H2

value: Colonic tissue from mice colonized with H2


title: LOVO_NC

description: Expression profiles of Lovo without exposure to radiation.

source_name: Lovo cells without exposure to radiation.

value: Lovo


title: M2 P05

value: Holstein


title: LOVO_RA

description: Expression profiles of Lovo with exposure to radiation.

source_name: Lovo cells with exposure to radiation.


title: M3 P05

value: ear fibroblast


title: F12/GDV1-GFP-DDON generation 1 40-48hpi

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

country: Switzerland

institute: Swiss Tropical and Public Health Institute

hyb_protocol: Microarray hybridizations were carried out as described in (Painter HJ, Altenhofen LM, Kafsack BF, Llinás M: Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol Biol. 2013;923:213-9). In short, 400ng Cy5-labeled test cDNA and 400ng Cy3-labeled reference pool cDNA were hybridized on a P. falciparum 8x15K Agilent gene expression microarray (GEO platform ID GPL15130) for 16 hours at 65°C in an Agilent hybridisation oven (G2545A).

scan_protocol: Microarrays were scanned as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: The raw microarray data representing relative transcript abundance ratios between each test sample and the reference pool (Cy5/Cy3 log2 ratios) were subjected to lowess normalization and background filtering as implemented by the Acuity 4.0 program (Molecular Devices). Flagged features and features with either Cy3 or Cy5 intensities lower than two-fold the background were discarded.

organism: Plasmodium falciparum

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 1 at 40-48hpi

label_protocol: Labeling was carried out as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]

growth_protocol: F12/GDV1-GFP-DDOFF parasites were synchronized twice 16 hrs apart to obtain an eight hour growth window (16-24hpi). After re-invasion parasites were synchronised again at 0-8hpi. At 4-12 hpi the culture was split into two populations of which one half was maintained in absence of Shield-1 (F12/GDV1-GFP-DDOFF) and one half was cultured in presence of Shield-1 (F12/GDV1-GFP-DDON). For both populations, total RNA was isolated in the same cell cycle (generation 1) from trophozoites (T1; 28-36 hpi), early schizonts (ES1; 36-44 hpi), late schizonts (LS1; 44-04 hpi), and after re-invasion (generation 2) from early ring stages (ER2; 8-16hpi), late ring stages (LR2; 16-24hpi), trophozoites (T2; 24-32 hpi), early schizonts (ES2; 32-40 hpi).

extract_protocol: Total RNA was extracted using Ribozol (Amresco) following manufacturer's instructions.

tag: clone background

value: conditional mutant F12/GDV1-GFP-DD

tag: culture conditions

value: 4nM WR99210; 312nM Shield-1

tag: time point

value: 40-48 hours post-invasion (hpi)

tag: generation

value: whole organism

organism: Plasmodium falciparum 3D7

source_name: reference pool RNA

value: wild type

tag: sample type

value: cDNA reference pool extracted from wild type parasites (8-48hpi)


title: F12/GDV1-GFP-DDON generation 2 24-32hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 2 at 24-32hpi

tag: genotype/variation

value: 24-32 hours post-invasion (hpi)

tag: tissue


title: F12/GDV1-GFP-DDOFF generation 2 8-16hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 2 at 8-16hpi

value: 8-16 hours post-invasion (hpi)


title: F12/GDV1-GFP-DDOFF generation 2 24-32hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 2 at 24-32hpi


title: F12/GDV1-GFP-DDON generation 2 8-16hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 2 at 8-16hpi


title: F12/GDV1-GFP-DDOFF generation 2 32-40hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 2 at 32-40hpi

value: 32-40 hours post-invasion (hpi)


title: F12/GDV1-GFP-DDON generation 2 16-24hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 2 at 16-24hpi

value: 16-24 hours post-invasion (hpi)


title: F12/GDV1-GFP-DDON generation 2 32-40hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 2 at 32-40hpi


title: F12/GDV1-GFP-DDOFF generation 2 16-24hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 2 at 16-24hpi


title: 3D7/GDV1-GFP-DDON generation 2 24-32hpi

hyb_protocol: Microarray hybridizations were carried out as described in (Painter HJ, Altenhofen LM, Kafsack BF, Llinás M: Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol Biol. 2013;923:213-9). In short, 500ng Cy5-labeled test cDNA and 500ng Cy3-labeled reference pool cDNA were hybridized on a P. falciparum 8x15K Agilent gene expression microarray (GEO platform ID GPL15130) for 16 hours at 65°C in an Agilent hybridisation oven (G2545A).

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 2 at 24-32hpi

growth_protocol: 3D7/GDV1-GFP-DDOFF parasites were synchronized twice 16 hrs apart to obtain an eight hour growth window (16-24hpi). After re-invasion parasites were synchronised again at 0-8hpi. At 4-12 hpi the culture was split into two populations of which one half was maintained in absence of Shield-1 (3D7/GDV1-GFP-DDOFF) and one half was cultured in presence of Shield-1 (3D7/GDV1-GFP-DDON). For both populations, total RNA was isolated in the same cell cycle (generation 1) from trophozoites (T1; 24-32 hpi), early schizonts (ES1; 32-40 hpi), late schizonts (LS1; 40-48 hpi), and after re-invasion (generation 2) from early ring stages (ER2; 8-16hpi), late ring stages (LR2; 16-24hpi), trophozoites (T2; 24-32 hpi), early schizonts (ES2; 32-40 hpi).

value: conditional mutant 3D7/GDV1-GFP-DD


title: F12/GDV1-GFP-DDOFF generation 1 32-40hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 1 at 32-40hpi


title: 3D7/GDV1-GFP-DDON generation 2 32-40hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 2 at 32-40hpi


title: F12/GDV1-GFP-DDON generation 1 32-40hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 1 at 32-40hpi


title: F12/GDV1-GFP-DDOFF generation 1 40-48hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 1 at 40-48hpi


title: M3 P25

source_name: gDNA from fibroblast


title: F12/GDV1-GFP-DDON generation 1 24-32hpi

source_name: RNA extracted from F12/GDV1-GFP-DDON parasites in generation 1 at 24-32hpi


title: F12/GDV1-GFP-DDOFF generation 1 24-32hpi

source_name: RNA extracted from F12/GDV1-GFP-DDOFF parasites in generation 1 at 24-32hpi


title: 3D7/GDV1-GFP-DDON generation 2 16-24hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 2 at 16-24hpi

source_name: reference pool RNA


title: 3D7/GDV1-GFP-DDON generation 1 32-40hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 1 at 32-40hpi


title: 3D7/GDV1-GFP-DDON generation 1 40-48hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 1 at 40-48hpi


title: 3D7/GDV1-GFP-DDON generation 2 8-16hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 2 at 8-16hpi


title: 3D7/GDV1-GFP-DDON generation 1 24-32hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDON parasites in generation 1 at 24-32hpi


title: 3D7/GDV1-GFP-DDOFF generation 2 32-40hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 2 at 32-40hpi


title: 3D7/GDV1-GFP-DDOFF generation 2 24-32hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 2 at 24-32hpi


title: 3D7/GDV1-GFP-DDOFF generation 2 16-24hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 2 at 16-24hpi


title: 3D7/GDV1-GFP-DDOFF generation 2 8-16hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 2 at 8-16hpi


title: 3D7/GDV1-GFP-DDOFF generation 1 32-40hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 1 at 32-40hpi


title: 3D7/GDV1-GFP-DDOFF generation 1 24-32hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 1 at 24-32hpi


title: 3D7/GDV1-GFP-DDOFF generation 1 40-48hpi

source_name: RNA extracted from 3D7/GDV1-GFP-DDOFF parasites in generation 1 at 40-48hpi


title: fMG Replicate 1

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: SAMPLE 13

hyb_protocol: Labeled cDNA was hybridized, washed and stained to separate Affymetrix GeneChip Human 2.0 ST Arrays by sample according to the protocols described by Affymetrix (Affymetrix, Inc). Per staining, streptavidin phycoerythrin solution was used (Molecular Probes, Carlsbad, CA) and enhanced by an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: The Affymetrix GeneChip Scanner 3000 was used to scan each Affymetrix GeneChip Human 2.0 ST Array. After, gene probe intensities were generated using the Affymetrix AGCC software (Affymetrix, Inc).

data_processing: CEL files were imported into the Partek Genomics Suite v2 (www.partek.com) using option "RMA" under default settings. RMA background correction and quantile normalization was performed upon import; generating 53,981 log2 median polished gene probe expression values per CEL file. Probe values representing spike-in and hybridization controls were next filter-removed and the remaining probe values (n=53,617) exported for interrogation and analysis in R (https://cran.r-project.org/).

label: Biotin

source_name: fMG

label_protocol: 200 nanograms of total RNA per sample was used in conjunction with the Affymetrix recommended protocol for the GeneChip Human 2.0 ST Array (Affymetrix, Inc).

growth_protocol: NCRM-5 and iNC-012 hiPSCs were maintained as feeder-free on matrigel (BD)-coated 6-well plates and split every 3 days. The cells were split 1:6 or 1:12 using EDTA (0.5mM in Ca2+ and Mg2+ free PBS with 1.8mg/ml NaCl). Essential 8 (Invitrogen) medium was utilized for growth and maintenance of NCRM-5 hiPSC, and maintained in humidified 37°C incubator with 5% CO2 and 21% O239. mTESR (StemCell Technologies) media was used for iNC-012 cells.

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

tag: cell type

value: fMG


title: iMG (iNC-012) Replicate 1

description: SAMPLE 10

source_name: iMG (iNC-012)

value: iMG (iNC-012)


title: DC Replicate 3

description: SAMPLE 18

source_name: DC

value: DC


title: Mac Replicate 3

description: SAMPLE 21

source_name: Mac

value: Mac


title: iMG (iNC-012) Replicate 3

description: SAMPLE 12


title: Mac Replicate 2

description: SAMPLE 20


title: iMG (iNC-012) Replicate 2

description: SAMPLE 11


title: Mac Replicate 1

description: SAMPLE 19


title: iMG (NCRM-5) Replicate 3

description: SAMPLE 6

source_name: iMG (NCRM-5)

value: iMG (NCRM-5)


title: DC Replicate 1

description: SAMPLE 16


title: fMG Replicate 3

description: SAMPLE 15


title: iNC-012 Replicate 2

description: SAMPLE 8


title: NCRM-5 Replicate 1

description: SAMPLE 1


title: iMG (NCRM-5) Replicate 1

description: SAMPLE 4


title: iMG (NCRM-5) Replicate 2

description: SAMPLE 5


title: fMG Replicate 2

description: SAMPLE 14


title: NCRM-5 Replicate 2

description: SAMPLE 2


title: DC Replicate 2

description: SAMPLE 17


title: OWT

city: Taipei

first: Wei-Lun

last: Hwang

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

department: Department of Biotechnology and Laboratory Science in Medicine

institute: National Yang Ming Chiao Tung University

description: The gene expression data of parental, OECM-1 cells

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: RMA through R based affy modulea

source_name: Parental HNSCC cells (OECM-1)

label_protocol: Standard Affymetrix procedures

growth_protocol: Cells were cultured under 10% FBS-containing medium in a humidified chamber at 37'C.

treatment_protocol: Cells were cultered in the presence 300ug/ml of Cetuximab for 4 weaks followed by 1000ug/ml of Cetiximab until 30 cell passages to establish the Cetuximab resistant clone. The ecqual amount of PBS were treated in parental OECM-1 cells as the experimental control.

value: head-and-neck squamous carcimoma

tag: treatment

value: PBS treatment


title: iNC-012 Replicate 1

description: SAMPLE 7


title: ExVivoBlood_rep11

first: Lin

last: Fan

address: Zhengmin Road 507#

department: Tuberculosis

institute: Shanghai Pulmonary hospital

description: microarray hybridization after RNA abstraction from whole blood

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2. Equilibrate water bath to 60°C. 3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:4. Mix well but gently on a vortex mixer. 5. Incubate at 60°C for exactly 30 minutes to fragment RNA.  6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9. Place sample on ice and load onto the array as soon as possible.  10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. 12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.  13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14. Hand-tighten the clamp onto the chamber. 15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17. Hybridize at 65°C for 17 hours.

scan_protocol: Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Procedure: 1. Open the Agilent Feature Extraction (FE) software. 2. Add the images (.tif) to be extracted to the FE Project. 3. Set FE Project Properties. 4. Check the Extraction Set Configuration. 5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. 6. Select Project > Start Extracting and export data to txt..

source_name: whole blood

label_protocol: Procedure: 1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.  2. Add 1.2 μL of T7 Promoter Primer.  3. Use nuclease-free water to bring the total reaction volume to 11.5 μL. 4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. 5. Place the reactions on ice and incubate for 5 minutes. 6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. 8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. 9. Incubate samples at 40°C in a circulating water bath for 2 hours. 10. Move samples to a 65°C circulating water bath and incubate for 15 minutes. 11. Move samples to ice. Incubate for 5 minutes. 12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. 13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. 15. Incubate samples in a circulating water bath at 40°C for 2 hours. Purify the labeled/amplified RNA and labeled cRNA QC Kit and instrument: RNeasy Mini Kit (Qiagen p/n 74104) NanoDrop ND-1000  Procedure: 1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL. 2. Add 350 μL of Buffer RLT and mix well by pipetting. 3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge. 4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube. 5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube. 6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube. 7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. 8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column. 9. Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”). * From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50. * Blank the instrument with 1.5 μL of 1x labeling solution. * Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3). * The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation: (Concentration of Cy3) Specific Activity =——————————————— = pmol Cy3 per μg cRNA (Concentration of cRNA) * 1000 * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

growth_protocol: freshed blood samples taken from peripheral venous blood , then remained at  -80°C for no more than two weeks.

extract_protocol: 1. Homogenization a. Tissues a) Cryopulverization of tissue using the Biopulverizer * Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen. * Place prefrozen tissue in the well of the mortar. * Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS). * Empty the powdered contents for subsequent homogenization or extraction procedures. Cells Grown in Monolayer:Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. . Cells Grown in Suspension Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of animal, plant or yeast cells, or per 1 × 107 bacterial cells. Washing cells ,before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.2. Phase Separation Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.3. RNA Precipitation Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. 4. RNA Wash Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. 5. Redissolving the RNA At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. Step 2 Total RNA Clean-up and RNA QC Kits and Reagents: RNasey Mini Kit(Qiagen p/n 74104):   Buffer RPE Buffer RLT RNeasy Mini spin column NanoDrop ND-1000 Baseline-ZERO DNase(EPICENTRE, Cat. Nos. DB0711K)  Things to do before starting: 1. Buffer RPE is supplied as a concentrate. Before using for the first time, add 4 volumes of ethanol (96–100%) as indicated on the bottle to obtain a working solution.  Procedure: 1. Mix the following in a microcentrifuge tube: Redissolved RNA ≤85ul 10×Reaction buffer 10ul Baseline-ZERO DNase 5ul RNase-free water X ul Total volume 100ul 2. Incubate at 37°C for 30 minutes. 3. Add 350 μl Buffer RLT, and mix well. 4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5. 5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through. 6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through. 7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane. 8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min. 9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA. 10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

treatment_protocol: Procedure: 1. Homogenization a. Tissues a) Cryopulverization of tissue using the Biopulverizer * Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen. * Place prefrozen tissue in the well of the mortar. * Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS). * Empty the powdered contents for subsequent homogenization or extraction procedures.b) Homogenization using the Mini-Bead-Beater-16 * Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.  * Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten. * Set the timer depending on the type of sample. Start the machine.

value: female


title: ExVivoBlood_rep9

value: male


title: NCRM-5 Replicate 3

description: SAMPLE 3


title: OER

description: The gene expression data of trained Cetuximab resistant OECM-1 cells.

source_name: The Cetuximab resistant cells (OECM-1 ER)

value: 300-1000ug/ml Cetuximab treatment for 30 passages


title: ExVivoBlood_rep10


title: M3 P15

source_name: gDNA from fibroblast

value: Holstein

value: ear fibroblast


title: ExVivoBlood_rep7


title: ExVivoBlood_rep8


title: ExVivoBlood_rep1


title: ExVivoBlood_rep5


title: ExVivoBlood_rep6


title: ExVivoBlood_rep2


title: ExVivoBlood_rep3


title: ExVivoBlood_rep4


title: BY4743, fhl1/+ vs. WT

city: Nagahama

first: Yukio

last: Mukai

state: Shiga

address: 1266 Tamura-cho

department: Department of Bioscience

institute: Nagahama Institute of Bio-Science and Technology

hyb_protocol: Hybridization was performed for 16 h at 37°C with rotary shake (250 rpm).

scan_protocol: The hybridized array was scanned with a 3D-Gene Scanner 3000 (Toray).

data_processing: The average intensity of the background was subtracted from the detected signals, then the sample values were determined by the global normalization method (Cy3/Cy5 ratio median=1).

organism: Saccharomyces cerevisiae

source_name: fhl1/+ diploid cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, #1753). CyDye labeling was performed using Cy3 Mono-Reactive Dye (GE, #PA23001) and Cy5 Mono-Reactive Dye (GE, #PA25001). Antisense RNA was synthesized and labeled with Cy3 for the fhl1/FHL1 mutant and with Cy5 for the wild type.

growth_protocol: Cells of wild-type and fhl1/FHL1 yeast strains were exponentially grown in YPD medium at 30°C.

extract_protocol: Total RNAs were isolated from the yeast cells using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: strain

source_name: wild-type diploid cells


title: BMM Replicate 2

description: bm-Mac Replicate 2

hyb_protocol: Labeled cDNA was hybridized, washed and stained to separate Affymetrix GeneChip Mouse Gene 1.0 ST Arrays by sample according to the protocols described by Affymetrix (Affymetrix, Inc).  Per staining, streptavidin phycoerythrin solution was used (Molecular Probes, Carlsbad, CA) and enhanced by an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: The Affymetrix Gene Chip Scanner 3000 was used to scan each Affymetrix GeneChip Mouse Gene 1.0 ST Array.  After, gene probe intensities were generated using the Affymetrix AGCC software (Affymetrix, Inc).

data_processing: CEL files were imported into the Partek Genomics Suite v2 (www.partek.com) using option "RMA" under default settings. RMA background correction and quantile normalization was performed upon import; generating 35,556 log2 median polished gene probe expression values per CEL file. After, probe values were exported for interrogation and analysis in R (https://cran.r-project.org/).

source_name: bm-Mac

label_protocol: 200 nanograms of total RNA per sample was used in conjunction with the Affymetrix recommended protocol for the GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Inc).

growth_protocol: iPSC were maintained on a mitotically inactivated C57Bl/6 background mouse embryonic fibroblast feeder layer using Knockout DMEM with 10% ES-qualified fetal bovine serum (FBS), non-essential amino acids, sodium pyruvate, 2-mercaptoethanol, penicillin/streptomycin, and leukemia inhibitory factor. gMG were maintained in DMEM/F12 media  with 10% defined FBS, 2 mM 2-mercaptoethanol, 2 mM Glutamax, non-essential amino acids, 20 ng/mL recombinant murine GM-CSF, 20 ng/mL recombinant murine M-CSF, 20 ng/mL recombinant murine IL-3, and penicillin/streptomycin.  All other cells were maintained in DMEM/F12 media with 10% defined FBS, 2 mM Glutamax and penicillin/streptomycin.

value: bm-Mac

tag: age

value: adult


title: Colon_Healthy volunteer#3_mice

description: Colonic tissue from germ-free NIH swiss mice (10-12 weeks) colonized with H3

source_name: Colonic sections_tissue

value: NIH Swiss

value: 10-12 weeks (at colonization)

value: Healthy volunteer#3_H3

value: Colonic tissue from mice colonized with H3


title: iPS-MG Replicate 3

description: iPS-MG Replicate 3

source_name: iPS-MG

value: C57BL/6NCr - Cx3cr1gfp/+

value: iPS-MG


title: BMM Replicate 3

description: bm-Mac Replicate 3


title: DC Replicate 3

description: DC Replicate 3

value: DC


title: NSC Replicate 1

description: NSC Replicate 1

source_name: NSC

value: NSC


title: PM Replicate 3

description: p-Mac Replicate 3

source_name: p-Mac

value: p-Mac


title: PM Replicate 1

description: p-Mac Replicate 1


title: nMG Replicate 2

description: neo-MG Replicate 2

source_name: neo-MG

value: neo-MG


title: nMG Replicate 1

description: neo-MG Replicate 1


title: BMM Replicate 1

description: bm-Mac Replicate 1


title: iPS-MG Replicate 2

description: iPS-MG Replicate 2


title: aMG Replicate 1

description: ad-MG Replicate 1

source_name: ad-MG

value: ad-MG


title: DC Replicate 1

description: DC Replicate 1


title: NSC Replicate 2

description: NSC Replicate 2


title: DC Replicate 2

description: DC Replicate 2


title: aMG Replicate 2

description: ad-MG Replicate 2


title: PM Replicate 2

description: p-Mac Replicate 2


title: NSC Replicate 3

description: NSC Replicate 3


title: iPS-MG Replicate 1

description: iPS-MG Replicate 1


title: nMG Replicate 3

description: neo-MG Replicate 3


title: aMG Replicate 3

description: ad-MG Replicate 3


title: iPSC Replicate 2

description: iPSC Replicate 2

source_name: iPSC

value: iPSC


title: E746-E750 0.1% Oxygen F2

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
5983368021_L
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and normalized using MBCB algorythm

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit

growth_protocol: HBECs were grown at 37°C and 5% CO2 in keratinocyte serum-free medium (Invitrogen/Life Technologies) supplemented with 0.2 ng/mL recombinant human EGF and 30 μg/mL bovine pituitary extract

extract_protocol: Total RNA was extracted from cells using Qiagen RNeasy Mini Kit according to manufacturer’s instruction. Quality control was performed with Bio-rad Experion system

tag: cell line

value: HBEC

tag: stress

value: hypoxic


title: iPSC Replicate 1

description: iPSC Replicate 1


title: E746-E750 0.1% Oxygen F1

description:
5983368021_K
replicate 1


title: L858R 0.1% Oxygen E1

description:
5983368021_I
replicate 1

source_name: L858R 0.1% Oxygen


title: iPSC Replicate 3

description: iPSC Replicate 3


title: WT 0.1% Oxygen D2

description:
5983368021_H
replicate 2

source_name: WT 0.1% Oxygen

value: WT


title: L858R 21% Oxygen B2

description:
5983368021_D
replicate 2

source_name: L858R 21% Oxygen

value: aerobic


title: L858R 0.1% Oxygen E2

description:
5983368021_J
replicate 2


title: L858R 21% Oxygen B1

description:
5983368021_C
replicate 1


title: WT 0.1% Oxygen D1

description:
5983368021_G
replicate 1


title: E746-E750 21% Oxygen C1

description:
5983368021_E
replicate 1


title: E746-E750 21% Oxygen C2

description:
5983368021_F
replicate 2


title: WT 21% Oxygen A2

description:
5983368021_B
replicate 2

source_name: WT 21% Oxygen


title: WT 21% Oxygen A1

description:
5983368021_A
replicate 1


title: Control_C6

status: Public on Mar 01 2017

city: Huddinge

first: Haleh

last: Davanian

state: Stockholm

address: Alfred Nobels Allé 8

department: Department of dental medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 6 ug of terminal labeled ds DNA was hybridized 16-18 hr at 47C in Affymetrix hybridization oven.

scan_protocol: Arrays were scanned in Affymetrix GeneChip Scanner 3000 7G.

data_processing: Gene level analysis was performed in Affymetrix Expression Console Software using the RMA method.

source_name: Non-tumour control

label_protocol: Sensation Plus FFPE Amplification and WT labeling kit.

growth_protocol: No treatment

extract_protocol: Qiagen- AllPrep DNA/RNA FFPE kit with Deparaffinization Solution (Qiagen).

value: control


title: iNC-012 Replicate 3

description: SAMPLE 9


title: Control_15


title: Tumour_41

source_name: Tumour

value: ameloblastoma


title: Control_C7


title: treated with PM2.5, biological rep3

city: Shanghai,

first: Feng

middle: jun

last: lin

state: xvhuiqv

address: 2Institute of Health Sciences

department: Department of Pathophysiology

institute: 1Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

treatment_protocol:
Human myocardial cells AC16 treated with PM2.5 for 24h.
After the human myocardial cells AC16 treated with PM2.5 for 24 h with a range of concentrations, the dosage which selected was 50 μg/mL of PM2.5 for following microarray analysis.

value: myocardial cell line

value: PM2.5 for 24h


title: 6A - baseline for subject 6

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/ml), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences). Heat 65oC for 5 mins, 99oC for 5 mins, 45oC for 5 mins, centrifuge top speed for 5 mins. Hybridize 16hours at 45o at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC

data_processing: RMA

source_name: vastus lateralis baseline

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

extract_protocol: Extraction of total RNA was performed using Norgen kit according to the manufacturer's instructions.

treatment_protocol: Baseline for Subject id: 6

value: vastus lateralis

tag: subject id


title: control, biological rep3

source_name: AC16, control

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


title: Tumour_23


title: Control_16


title: 4A - baseline for subject 4

treatment_protocol: Baseline for Subject id: 4


title: treated with PM2.5, biological rep2


title: control, biological rep2


title: Tumour_71


title: Tumour_24


title: 7A - baseline for subject 7

treatment_protocol: Baseline for Subject id: 7


title: 7B - post supplementation for subject 7

source_name: vastus lateralis after supplementation

treatment_protocol: 8 weeks of PrimaVie Shilajit (250mg b.i.d) Supplementation for Subject id: 7


title: control, biological rep1


title: treated with PM2.5, biological rep1


title: 4B - post supplementation for subject 4

treatment_protocol: 8 weeks of PrimaVie Shilajit (250mg b.i.d) Supplementation for Subject id: 4


title: Tumour_34


title: Tumour_28


title: 6B - post supplementation for subject 6

treatment_protocol: 8 weeks of PrimaVie Shilajit (250mg b.i.d) Supplementation for Subject id: 6


title: 60 day_rep 2

city: New Delhi

first: Subeer

middle: S

last: Majumdar

state: Delhi

address: Aruna Asaf Ali Marg, JNU Complex

country: India

institute: National Institute of Immunology

hyb_protocol: The labeled aRNA samples were hybridized on to a Rat Gene Expression Array 4x44k    (AMADID: 14879 ). 1650 ng of cy3 labeled  samples were  fragmented and hybridized .  Fragmentation of labeled aRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Data extraction from Images was done using Agilent Feature Extraction software and 75th percentile shift Normalization of the data was done in GeneSpring GX

source_name: Sertoli cells_60 days old

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. aRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled aRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Sertoli cells were isolated from testis and maintained in culture for four days with defined growth factor medium.

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit as per the manufacturer’s protocol

treatment_protocol: Sertoli Cells were treated with 50ng/ml oFSH and 10-7 M Testosterone in a pulsatile manner for 11hrs.

tag: age of rat

value: 60 days old

value: Testis

value: Sertoli cells (Sc)


title: 5 day_rep 1

source_name: Sertoli cells_5 days old

value: 5 days old


title: 12 day_rep 1

source_name: Sertoli cells_12 days old

value: 12 days old


title: Mm_CD1_Q50_F_wk12_hyb8192

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: gene expression mouse striatum

hyb_protocol: Hybridized to Agilent-028005 SurePrint G3 8x60k Mouse Microarrays [GPL10787]

scan_protocol: Agilent Technologies Scanner G2505C

data_processing:
performed quantile normalization and log2-transformation. We used ComBat (Johnson et al., 2007) to remove batch effects related to the date on which microarrays were hybridized. Linear models were fit using the limma R package (Smyth, 2005)
Expression levels were extracted from Agilent microarray image files. Data were reduced by taking the mean expression value of duplicate probes within each array. Expression levels were then quantile normalized across arrays and log-transformed. For each array, we calculated a quality score (Q), using the formula: Q = sqrt((IRC/10)^2+Rho^2)/sqrt(2) where IRC is the count of in-range features on this array and Rho is the Spearman rank correlation coefficient comparing the rank-order of probe-level expression on this array to the median rank-ordering of probes across all arrays. We removed low quality arrays at a threshold of Q < 0.8, determined by manual inspection of the data.

source_name: Q50 mouse striatum 12 weeks old

label_protocol: 50 ng of total RNA was labeled with Agilent Low Input QuickAmp kit

growth_protocol: Heterozygous males of six different strains (129S2/SvPasCrl.HttQ111/+, FVB/NCrl.HttQ111/+, CD-1.HttQ111/+, C57BL/6J.HttQ92/+, C57BL/6J.HttQ50/+, C57BL/6J.Htt Q111/+) were crossed with wild type females of corresponding background strains in order to generate cohorts of age-matched heterozygous pups and WT controls for the time-course assigned tissue harvests. A tail snip was acquired at weaning (2-4-weeks) to determine the CAG repeat length of each mouse. One heterozygous animal and one age-matched wild type control animal from each strain were harvested three times weekly from 4 to 20 weeks of age. The sex of mice harvested at these times was randomized. An additional 5 female and 5 male heterozygous animals from the B6 Htt Q111 and CD1 Htt Q111 strains were harvested at 4, 8, 12, 16, and 21 weeks of age. Time of day of harvest was randomized within the hours of light in the mouse room, typically ≥3 hours after lights came on and ≥3 hours before lights went off.

extract_protocol: Total RNA extracted from individual mouse striata using Trizol following manufacturer's instructions

treatment_protocol: The right hemisphere of each animal's brain was microdissected.  Tissues were snap frozen and stored at -80°C.  The right hemisphere striata of each animal was used for isolation of RNA for transcriptional profiling.

tag: sample id

tag: mouse id

tag: allele nominal

tag: allele actual

tag: date harvest

tag: time harvest

tag: date hyb

tag: Sex

value: F

tag: age (weeks)

value: striatum


title: 60 day_rep 1

tag: tissue

tag: cell type


title: 5 day_rep 3


title: 5 day_rep 2


title: Mm_CD1_Q50_F_wk12_hyb4785

description: gene expression mouse striatum

tag: strain


title: 12 day_rep 3


title: 60 day_rep 3


title: Mm_CD1_Q50_F_wk12_hyb9235

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk15_hyb1724

description: gene expression mouse striatum

source_name: Q50 mouse striatum 15 weeks old


title: Mm_CD1_Q50_F_wk12_hyb5518

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk12_hyb8424

description: gene expression mouse striatum


title: 12 day_rep 2


title: Mm_CD1_Q50_F_wk13_hyb3364

description: gene expression mouse striatum

source_name: Q50 mouse striatum 13 weeks old


title: Mm_CD1_Q50_F_wk20_hyb5300

description: gene expression mouse striatum

source_name: Q50 mouse striatum 20 weeks old


title: Mm_CD1_Q50_F_wk20_hyb6133

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk16_hyb0649

description: gene expression mouse striatum

source_name: Q50 mouse striatum 16 weeks old


title: Mm_CD1_Q50_F_wk15_hyb5695

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk16_hyb3434

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk18_hyb0229

description: gene expression mouse striatum

source_name: Q50 mouse striatum 18 weeks old


title: Mm_CD1_Q50_F_wk14_hyb5834

description: gene expression mouse striatum

source_name: Q50 mouse striatum 14 weeks old


title: Mm_CD1_Q50_F_wk16_hyb1967

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk20_hyb6077

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk16_hyb0993

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk20_hyb6298

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk16_hyb9249

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk13_hyb5601

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk4_hyb4704

description: gene expression mouse striatum

source_name: Q50 mouse striatum 4 weeks old


title: Mm_CD1_Q50_F_wk20_hyb6668

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk19_hyb3130

description: gene expression mouse striatum

source_name: Q50 mouse striatum 19 weeks old


title: Mm_CD1_Q50_F_wk5_hyb8471

description: gene expression mouse striatum

source_name: Q50 mouse striatum 5 weeks old


title: Mm_CD1_Q50_F_wk7_hyb3501

description: gene expression mouse striatum

source_name: Q50 mouse striatum 7 weeks old


title: Mm_CD1_Q50_F_wk4_hyb5025

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk4_hyb2049

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk8_hyb8051

description: gene expression mouse striatum

source_name: Q50 mouse striatum 8 weeks old


title: Mm_CD1_Q50_F_wk6_hyb2867

description: gene expression mouse striatum

source_name: Q50 mouse striatum 6 weeks old


title: Mm_CD1_Q50_F_wk6_hyb5241

description: gene expression mouse striatum


title: Mm_CD1_Q50_F_wk8_hyb3917

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk12_hyb3988

description: gene expression mouse striatum

value: M


title: Mm_CD1_Q50_M_wk12_hyb2187

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk14_hyb1704

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk12_hyb8897

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk19_hyb9929

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk12_hyb7415

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk10_hyb7053

description: gene expression mouse striatum

source_name: Q50 mouse striatum 10 weeks old


title: Mm_CD1_Q50_M_wk17_hyb9247

description: gene expression mouse striatum

source_name: Q50 mouse striatum 17 weeks old


title: Mm_CD1_Q50_M_wk16_hyb0723

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk16_hyb6399

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk16_hyb7778

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk20_hyb1473

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk18_hyb8402

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb4458

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk17_hyb6316

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk20_hyb9024

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk20_hyb0681

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk20_hyb7479

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk16_hyb9050

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb4597

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb3221

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb4277

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk8_hyb7746

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb6248

description: gene expression mouse striatum


title: CSE3

city: Kyoto

first: Takehiro

last: Iki

address: 53, Shogoin-Kawahara cho, Sakyo

department: Clinical Application Department

institute: Center for iPS cell research and application, Kyoto University

hyb_protocol: According to manufature's protocol.

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

data_processing: A three-stage data processing procedure was applied to raw signal intensities. First, a background correction was performed with the ‘backgroundCorrect’ function in the ‘limma’ package of R. Then, the quantile normalization was performed to remove the technical bias using the ‘normalizeBetweenArrays’ function in the ‘limma’ package of R. Finally, to filter out control probes and low expression probes, the 95th percentiles of the negative control probes on each array were computed, and probes that were at least 10% brighter than the negative controls on at least three arrays were stored.

source_name: mouse cochlear sensory epithelia, replicate3

label_protocol: 50 or 100 ng of total RNA were used to prepare Cy3-labelled target cRNA with the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol:
Undifferentiated ESCs were maintained in gelatin-coated dishes without feeder cells in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Gibco), 0.1 mM 2-mercaptoethanol (Wako), 0.1 mM nonessential amino acids (Gibco), and 1,000 U/ml of LIF (Wako).
Primary otospheres were cultured for four or five days. For expansion, the otospheres were dissociated using 0.125% trypsin/EDTA for 15 minutes at 37°C, followed by mechanical dissociation involving 40 cycles of pipetting with plastic pipette tips (10-200 μl). Then, the cell suspension was filtered through a 100 μm cell strainer (BD Falcon), and the cells were replated in a six-well low attachment plate and cultured for four or five days to obtain secondary otospheres.

extract_protocol: Each specimen was soaked in TRIzol® (Thermo Scientific) and degraded completely. Genomic DNA was degraded by aspirating the specimen with a 22 G needle, and was removed by collecting the supernatants after centrifugation. Chloroform and glycogen (Sigma) were added to the supernatants to obtain an aqueous phase, which included RNA. Total RNA was isolated from the solution via isopropanol precipitation and was washed with 70% ethanol. To prevent DNA contamination, DNase treatment of the extracted RNA was performed with TURBO™ DNase (Ambion). The isolated RNA was dissolved in 50 μl of RNase-free water, after which the concentration of total RNA was measured using a Nanodrop2000 (Thermo Scientific) and the quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol:
Four batches of CSE were transferred into 100 μl of 0.125% trypsin/EDTA in phosphate-buffered saline (PBS) and incubated for 15 minutes at 37°C. Enzymatic digestion was then blocked by adding 100 μl of a 5 mg/ml trypsin inhibitor (Sigma) and a 0.6 mg/ml DNase I solution (Sigma) in the sphere culture medium consisting of Dulbecco's modified Eagle’s medium/F12 mixed 1:1 (DMEM-F12) supplemented with N2 and B27 (Thermo scientific), basic fibroblast growth factor (bFGF; 10 ng/mL), mouse insulin-like growth factor-1 (IGF1; 50 ng/mL, all growth factors obtained from R&D Systems), heparan sulfate (50 ng/mL, Sigma) and ampicillin (50 μg/ml). The tissues were carefully triturated by pipetting 40 times with plastic pipette tips (10-200 μl; Greiner). The cell suspension was filtered through a 70 μm cell strainer (BD Falcon) into the wells of a six-well low attachment plate (Greiner). The remaining cells present on the first dish were washed out with 900 μl of sphere culture medium, and this medium was passed through the cell strainer into the same well of the second plate. The same manipulation was repeated with another 900 μl of medium. The cell suspension was cultured in an incubator at 37°C with 5% CO2.
After being anesthetized and washed with 100% ethanol, the mice were decapitated and the temporal bones were dissected. Twenty cochleae were excised and the whole cochlear ducts were exposed by removing the bony capsule. The CSE was isolated by separating the spiral ligament and stria vascularis, and the isolated organs were transferred to a sterile dish containing cold Hanks’ Balanced Salt Solution (HBSS).

value: Institution of Cancer Research (ICR) mice

value: cochlear sensory epithelia


title: Mm_CD1_Q50_M_wk7_hyb1747

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk8_hyb4939

description: gene expression mouse striatum


title: Mm_CD1_Q50_M_wk4_hyb7891

description: gene expression mouse striatum


title: OS6

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate6

value: otospheres


title: Mm_CD1_Q50_M_wk4_hyb6276

description: gene expression mouse striatum


title: CSE1

source_name: mouse cochlear sensory epithelia, replicate1


title: CSE2

source_name: mouse cochlear sensory epithelia, replicate2


title: Mm_CD1_Q50_M_wk5_hyb1457

description: gene expression mouse striatum


title: OS5

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate5


title: OS2

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate2


title: OS4

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate4


title: OS3

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate3


title: ES2

source_name: Cultured cells, mouse ES cells, D3, Passage13

value: embryonic stem cells (ESCs)


title: OS1

source_name: Suspension-cultured cells, dissociated mouse cochlear cells, Passage1,replicate1


title: AK4-WT

first: Jun-An

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

institute: Academia Sinica

description: Gene expression in wt EB after RA treated two days

hyb_protocol: 825 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4858A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software10.5.1 (Agilent) using default parameters (protocol GE1-105_D08 and Grid: 028005_D_F_20110711) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: EB after two day RA induction

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA isolation by Trizol, DNase treated by TURBO DNA-free Kit (Life Technology), and checked with Bioanalyzer 2100 (Agilent) for RIN > 9.

treatment_protocol: To get the time series samples from ES cell to motor neurons, RA/Shh were applied from day 2 to day 5 during the differention process.

value: embryoid bodies

tag: gender

value: male


title: AK3-WT

description: Gene expression in wt EB after RA treated one days

source_name: EB after one day RA induction


title: ES-WT

description: Gene expression in wt ES cells

source_name: wild type ES cell

value: embryonic stem cells


title: Mm_CD1_WT_M_wk9_hyb9980

description: gene expression mouse striatum

data_processing: performed quantile normalization and log2-transformation. We used ComBat (Johnson et al., 2007) to remove batch effects related to the date on which microarrays were hybridized. Linear models were fit using the limma R package (Smyth, 2005). Expression levels were extracted from Agilent microarray image files. Data were reduced by taking the mean expression value of duplicate probes within each array. Expression levels were then quantile normalized across arrays and log-transformed.For each array, we calculated a quality score (Q), using the formula: Q = sqrt((IRC/10)^2+Rho^2)/sqrt(2) where IRC is the count of in-range features on this array and Rho is the Spearman rank correlation coefficient comparing the rank-order of probe-level expression  on this array to the median rank-ordering of probes across all arrays. We removed low quality arrays at a threshold of Q < 0.8, determined by manual inspection of the data.

source_name: WT mouse striatum 9 weeks old

growth_protocol: Heterozygous males of six different strains (129S2/SvPasCrl.HttQ111/+, FVB/NCrl.HttQ111/+, CD-1.HttQ111/+, C57BL/6J.HttQ92/+, C57BL/6J.HttQ50/+, C57BL/6J.Htt Q111/+) were crossed with wild type females of corresponding background strains in order to generate cohorts of age-matched heterozygous pups and WT controls for the time-course assigned tissue harvests. A tail snip was acquired at weaning (2-4-weeks) to determine the CAG repeat length of each mouse. One heterozygous animal and one age-matched wild type control animal from each strain were harvested three times weekly from 4 to 21 weeks of age. The sex of mice harvested at these times was randomized. An additional 5 female and 5 male heterozygous animals from the B6 Htt Q111 and CD1 Htt Q111 strains were harvested at 4, 8, 12, 16, and 21 weeks of age. Time of day of harvest was randomized within the hours of light in the mouse room, typically ≥3 hours after lights came on and ≥3 hours before lights went off.

value: WT


title: Mm_CD1_Q111_F_wk14_hyb9873

description: gene expression mouse striatum

source_name: Q111 mouse striatum 14 weeks old


title: Mm_B6_WT_M_wk16_hyb9877

description: gene expression mouse striatum

source_name: WT mouse striatum 16 weeks old


title: Mm_FVB_Q111_M_wk19_hyb9939

description: gene expression mouse striatum

source_name: Q111 mouse striatum 19 weeks old

value: FVB


title: AK7-WT

description: Gene expression in wt EB after RA treated five days

source_name: MN after five day RA induction


title: RA 8hr-WT

description: Gene expression in wt EB after RA treated 8hrs

source_name: EB after 8hrs RA induction


title: Mm_B6_WT_F_wk13_hyb9990

description: gene expression mouse striatum

source_name: WT mouse striatum 13 weeks old


title: Mm_129_WT_M_wk16_hyb9951

description: gene expression mouse striatum


title: ES1

source_name: Cultured cells, mouse ES cells, G4-2, Passage13


title: Mm_B6_WT_M_wk6_hyb9994

description: gene expression mouse striatum

source_name: WT mouse striatum 6 weeks old


title: Mm_B6_Q92_F_wk4_hyb9848

description: gene expression mouse striatum

source_name: Q92 mouse striatum 4 weeks old


title: Mm_B6_Q111_M_wk4_hyb9861

description: gene expression mouse striatum

source_name: Q111 mouse striatum 4 weeks old


title: Mm_CD1_Q111_F_wk20_hyb9779

description: gene expression mouse striatum

source_name: Q111 mouse striatum 20 weeks old


title: Mm_CD1_WT_F_wk19_hyb9801

description: gene expression mouse striatum

source_name: WT mouse striatum 19 weeks old


title: Mm_B6_Q111_F_wk16_hyb9798

description: gene expression mouse striatum

source_name: Q111 mouse striatum 16 weeks old


title: Mm_B6_WT_M_wk9_hyb9841

description: gene expression mouse striatum


title: Mm_FVB_Q111_M_wk6_hyb9780

description: gene expression mouse striatum

source_name: Q111 mouse striatum 6 weeks old


title: Mm_B6_Q92_F_wk19_hyb9772

description: gene expression mouse striatum

source_name: Q92 mouse striatum 19 weeks old


title: Mm_129_Q111_M_wk11_hyb9763

description: gene expression mouse striatum

source_name: Q111 mouse striatum 11 weeks old


title: Mm_B6_Q50_M_wk16_hyb9682

description: gene expression mouse striatum

source_name: Q50 mouse striatum 16 weeks old


title: Mm_B6_WT_M_wk20_hyb9778

description: gene expression mouse striatum

source_name: WT mouse striatum 20 weeks old


title: Mm_B6_Q111_F_wk4_hyb9712

description: gene expression mouse striatum


title: Mm_CD1_WT_F_wk9_hyb9698

description: gene expression mouse striatum

source_name: WT mouse striatum 9 weeks old


title: Mm_B6_Q50_F_wk8_hyb9644

description: gene expression mouse striatum

source_name: Q50 mouse striatum 8 weeks old


title: Mm_CD1_Q111_F_wk12_hyb9725

description: gene expression mouse striatum

source_name: Q111 mouse striatum 12 weeks old


title: Mm_B6_WT_M_wk6_hyb9535

description: gene expression mouse striatum


title: Mm_129_WT_F_wk18_hyb9499

description: gene expression mouse striatum

source_name: WT mouse striatum 18 weeks old


title: Mm_FVB_WT_F_wk20_hyb9495

description: gene expression mouse striatum


title: Mm_CD1_Q111_M_wk17_hyb9428

description: gene expression mouse striatum

source_name: Q111 mouse striatum 17 weeks old


title: Mm_FVB_Q111_M_wk5_hyb9450

description: gene expression mouse striatum

source_name: Q111 mouse striatum 5 weeks old


title: Mm_129_WT_F_wk5_hyb9547

description: gene expression mouse striatum

source_name: WT mouse striatum 5 weeks old


title: Mm_FVB_WT_F_wk14_hyb9809

description: gene expression mouse striatum

source_name: WT mouse striatum 14 weeks old


title: Mm_B6_WT_M_wk10_hyb9452

description: gene expression mouse striatum

source_name: WT mouse striatum 10 weeks old


title: Mm_129_WT_M_wk4_hyb9427

description: gene expression mouse striatum

source_name: WT mouse striatum 4 weeks old


title: Mm_CD1_Q111_F_wk12_hyb9405

description: gene expression mouse striatum


title: Mm_CD1_WT_F_wk18_hyb9697

description: gene expression mouse striatum


title: Mm_129_Q111_F_wk17_hyb9310

description: gene expression mouse striatum


title: Mm_CD1_WT_M_wk17_hyb9304

description: gene expression mouse striatum

source_name: WT mouse striatum 17 weeks old


title: Mm_CD1_Q111_F_wk20_hyb9631

description: gene expression mouse striatum

source_name: Q111 mouse striatum 20 weeks old


title: Mm_B6_Q111_F_wk20_hyb9598

description: gene expression mouse striatum


title: Mm_CD1_Q111_M_wk11_hyb9624

description: gene expression mouse striatum


title: Mm_129_WT_F_wk20_hyb9701

description: gene expression mouse striatum


title: Mm_B6_Q111_F_wk20_hyb9488

description: gene expression mouse striatum


title: Mm_B6_WT_M_wk19_hyb9354

description: gene expression mouse striatum

source_name: WT mouse striatum 19 weeks old


title: Mm_B6_WT_F_wk13_hyb9424

description: gene expression mouse striatum

source_name: WT mouse striatum 13 weeks old


title: Mm_B6_WT_M_wk9_hyb9373

description: gene expression mouse striatum


title: Mm_B6_Q92_M_wk12_hyb9460

description: gene expression mouse striatum

source_name: Q92 mouse striatum 12 weeks old


title: Mm_B6_WT_M_wk20_hyb9365

description: gene expression mouse striatum


title: Mm_CD1_WT_F_wk16_hyb9672

description: gene expression mouse striatum

source_name: WT mouse striatum 16 weeks old


title: Mm_B6_WT_F_wk6_hyb9303

description: gene expression mouse striatum

source_name: WT mouse striatum 6 weeks old


title: Mm_B6_Q92_M_wk5_hyb9295

description: gene expression mouse striatum

source_name: Q92 mouse striatum 5 weeks old


title: Mm_129_Q111_F_wk7_hyb9286

description: gene expression mouse striatum

source_name: Q111 mouse striatum 7 weeks old


title: Mm_FVB_Q111_M_wk19_hyb9289

description: gene expression mouse striatum

source_name: Q111 mouse striatum 19 weeks old


title: Mm_CD1_WT_M_wk6_hyb9290

description: gene expression mouse striatum


title: Mm_CD1_Q111_M_wk8_hyb9212

description: gene expression mouse striatum

source_name: Q111 mouse striatum 8 weeks old


title: Mm_CD1_WT_F_wk14_hyb9258

description: gene expression mouse striatum


title: Mm_B6_Q111_M_wk14_hyb9187

description: gene expression mouse striatum

source_name: Q111 mouse striatum 14 weeks old


title: Mm_B6_Q50_M_wk14_hyb9197

description: gene expression mouse striatum

source_name: Q50 mouse striatum 14 weeks old


title: Mm_CD1_WT_F_wk10_hyb9181

description: gene expression mouse striatum


title: Mm_B6_WT_M_wk8_hyb9159

description: gene expression mouse striatum

source_name: WT mouse striatum 8 weeks old


title: Mm_B6_Q111_M_wk15_hyb9147

description: gene expression mouse striatum

source_name: Q111 mouse striatum 15 weeks old


title: Mm_B6_WT_F_wk8_hyb9144

description: gene expression mouse striatum


title: Mm_B6_WT_M_wk18_hyb9140

description: gene expression mouse striatum

source_name: WT mouse striatum 18 weeks old


title: Mm_FVB_Q111_F_wk19_hyb9044

description: gene expression mouse striatum


title: Mm_CD1_Q111_M_wk7_hyb9250

description: gene expression mouse striatum


title: Mm_B6_Q111_M_wk12_hyb9133

description: gene expression mouse striatum

source_name: Q111 mouse striatum 12 weeks old


title: Mm_CD1_WT_M_wk4_hyb9051

description: gene expression mouse striatum

source_name: WT mouse striatum 4 weeks old


title: Mm_CD1_WT_F_wk13_hyb9116

description: gene expression mouse striatum


title: Mm_CD1_Q111_M_wk20_hyb9130

description: gene expression mouse striatum

source_name: Q111 mouse striatum 20 weeks old


title: Mm_B6_Q111_F_wk10_hyb9094

description: gene expression mouse striatum

source_name: Q111 mouse striatum 10 weeks old


title: Mm_FVB_WT_M_wk8_hyb9081

description: gene expression mouse striatum


title: Mm_CD1_WT_F_wk6_hyb9100

description: gene expression mouse striatum


title: Mm_CD1_Q111_F_wk4_hyb9083

description: gene expression mouse striatum

source_name: Q111 mouse striatum 4 weeks old


title: Mm_129_Q111_F_wk13_hyb9027

description: gene expression mouse striatum

source_name: Q111 mouse striatum 13 weeks old


title: Mm_129_WT_M_wk6_hyb9003

description: gene expression mouse striatum


title: Mm_B6_Q50_M_wk4_hyb9038

description: gene expression mouse striatum

source_name: Q50 mouse striatum 4 weeks old


title: Mm_CD1_Q111_F_wk17_hyb8991

description: gene expression mouse striatum

source_name: Q111 mouse striatum 17 weeks old


title: Mm_B6_WT_M_wk12_hyb8998

description: gene expression mouse striatum

source_name: WT mouse striatum 12 weeks old


title: Mm_B6_Q111_M_wk4_hyb9732

description: gene expression mouse striatum


title: Mm_129_WT_F_wk16_hyb8975

description: gene expression mouse striatum

source_name: WT mouse striatum 16 weeks old


title: Mm_B6_WT_M_wk19_hyb8911

description: gene expression mouse striatum

source_name: WT mouse striatum 19 weeks old


title: Mm_CD1_WT_M_wk12_hyb8893

description: gene expression mouse striatum


title: Mm_B6_WT_F_wk4_hyb8811

description: gene expression mouse striatum


title: Mm_B6_Q92_M_wk6_hyb8851

description: gene expression mouse striatum

source_name: Q92 mouse striatum 6 weeks old


title: Mm_B6_Q111_F_wk8_hyb8822

description: gene expression mouse striatum

source_name: Q111 mouse striatum 8 weeks old


title: Mm_129_WT_F_wk5_hyb8827

description: gene expression mouse striatum

source_name: WT mouse striatum 5 weeks old


title: Mm_CD1_WT_M_wk5_hyb8925

description: gene expression mouse striatum


title: Mm_CD1_Q111_F_wk8_hyb8912

description: gene expression mouse striatum


title: Mm_B6_WT_M_wk15_hyb9002

description: gene expression mouse striatum

source_name: WT mouse striatum 15 weeks old


title: Mm_B6_WT_M_wk18_hyb8908

description: gene expression mouse striatum


title: Mm_129_WT_F_wk15_hyb8798

description: gene expression mouse striatum


title: Mm_129_Q111_M_wk17_hyb8793

description: gene expression mouse striatum


title: Mm_CD1_Q111_F_wk13_hyb8784

description: gene expression mouse striatum


title: Mm_CD1_WT_M_wk15_hyb8764

description: gene expression mouse striatum


title: Mm_B6_Q92_M_wk10_hyb8722

description: gene expression mouse striatum

source_name: Q92 mouse striatum 10 weeks old


title: Mm_B6_Q50_M_wk13_hyb8809

description: gene expression mouse striatum

source_name: Q50 mouse striatum 13 weeks old


title: Mm_B6_Q50_M_wk4_hyb8760

description: gene expression mouse striatum


title: Mm_CD1_WT_F_wk16_hyb8781

description: gene expression mouse striatum


title: Mm_B6_WT_F_wk16_hyb8755

description: gene expression mouse striatum


title: Mm_CD1_WT_M_wk8_hyb8737

description: gene expression mouse striatum

source_name: WT mouse striatum 8 weeks old


title: Mm_B6_WT_M_wk12_hyb8694

description: gene expression mouse striatum


title: Mm_B6_WT_F_wk11_hyb8689

description: gene expression mouse striatum

source_name: WT mouse striatum 11 weeks old


title: Mm_B6_Q50_F_wk14_hyb8905

description: gene expression mouse striatum

source_name: Q50 mouse striatum 14 weeks old


title: Mm_129_Q111_F_wk20_hyb8671

description: gene expression mouse striatum

source_name: Q111 mouse striatum 20 weeks old


title: Mm_FVB_WT_M_wk13_hyb8667

description: gene expression mouse striatum

source_name: WT mouse striatum 13 weeks old


title: Mm_CD1_WT_M_wk16_hyb8651

description: gene expression mouse striatum