title: primary breast cancer, sample_1889

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

institute: Erasmus MC

data_processing: mas5 parameters from affy R package, available at www.bioconductor.org using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: primary breast cancer _Non

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

value: snap frozen primary breast tumor

tag: mutation status

value: Non


title: Th22 rep 1

status: Public on Jan 16 2017

type: RNA

city: New Lambton Heights

first: Maximilian

last: Plank

state: Australia

address: Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

hyb_protocol: Samples were hybridized using a GeneTitan® Hybridization, Wash, and Stain Kit for WT Array Plates (Affymetrix) according to manufacturer's protocol

scan_protocol: Samples were scanned on a GeneTitan® Multi-Channel (MC) Instrument (Affymetrix)

data_processing: Data was analysed using Expression Console and Transcriptome Analysis Console v3.0 (both Affymetrix)

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Sorted Th22 cells

label_protocol: Samples were labelled using a GeneChip® WT PLUS Reagent Kit (Affymetrix) according to manufacturer's protocol

growth_protocol: For the generation of effector Th cell subsets, purified naïve Th cells were stimulated in complete media (IMDM, 10% FCS, 2 mM L-glutamine, 50 µM β-mercaptoethanol, 100U/ml Penicillin-Streptomycin; Invitrogen, Australia) with plate-bound anti-CD3ε (1 μg/ml; Clone 145-2C11; BD Pharmingen, USA) and soluble anti-CD28 (4 μg/ml; Clone 37.51; BD Pharmingen, USA) for 3 days under polarizing conditions for Th0 cells (media alone), Th1 cells (10 ng/ml IL-12, 10 ng/ml IL-2, 10 μg/ml anti-IL-4), Th17 cells (10 ng/ml IL-1β, 30 ng/ml IL-6, 1 ng/ml TGF-β, 10 μg/ml anti-IL-4, 10 μg/ml anti-IFN-γ) or Th22 cells (10 ng/ml IL-1β, 30 ng/ml IL-6, 20ng/ml IL-23, 400nM FICZ, 10 μM Galunisertib (LY2157299), 10 μg/ml anti-IL-4, 10 μg/ml anti-IFN-γ), 5 μg/ml anti-TGF-β1/2/3 (Clone 1D11, RnDSystems) and 10 ng/ml TNF-α were added where indicated.

extract_protocol: For the extraction of total RNA, Trizol (Invitrogen, Australia) was used according to manufacturer’s protocol

treatment_protocol: Th17 (IL-17A+) and Th22 (IL-22+IL-17A-) cell populations were sorted to purity prior to RNA extraction

tag: strain


title: 39A_F_HDID1

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

country: USA

institute: Oregon Health and Science University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

source_name: brain striatum

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

extract_protocol: Frozen brains were slightly thawed and dissected by hand under RNAse-free conditions. Using the optic chiasm as the rostral marker, a 2-mm coronal slice of brain tissue was isolated. Following the partial cone shape of the striatum, the dissection moved dorsal 1 mm, followed by a cut to the lateral boundary of the striatum, with a final cut following the lateral-ventral boundary. The isolated tissue was immediately placed in 100 ml of Trizol  (Invitrogen, Carlsbad, CA). On average, the isolated striatal tissue samples weighed 3 mg.

treatment_protocol: Mice were euthanized, and brains were removed and immediately frozen on dry ice.

tag: sex (f=female, m=male)

value: F

tag: behavioral phenotype

value: Drinker

tag: selection


title: Th22 rep 2


title: 38A_M_HDID1

value: M


title: 94A_M_HDID2


title: Th17 rep 2

source_name: Sorted Th17 cells


title: CD133-positive (C60+)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent 8x15k miRNA microarray V19 comprised of 2006 miRNAs from Sanger miRBase (release 19) at 55°C for 20 hours.

scan_protocol: After hybridization, slides were immediately washed and scanned in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images.

data_processing: Data (intensity signal) were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15.  ''signal' is  a measure of the abundance of a transcript.

organism: Homo sapiens

label_protocol: 100 ng of total RNA from each sample were labeled with Cy3 by using Agilent miRNA labeling kit following manufacturer’s instructions.

extract_protocol: Genome wide microRNA profiling of 12 CD133high and 12 CD133low tumor samples were performed using Agilent Human miRNA Microarray (V19).  CD133 positive cells were isolated from freshly resected and physically/enzymatically dissociated tumor tissue samples using Magnetic-activated Cell Sorting (MACS) technique (Miltenyi Biotech, Bergisch Gladbach, Germany) and “EasySep Positive Selection Human PE Selection Kit (StemCell Technologies, (Vancouver, BC, Canada)” following the manufacturer’s protocol. Shortly, fresh tumor tissue samples were physically minced with a scalpel and exposed to enzymatic dissociation using 400 μg/ml Collagenase enzyme (GIBCO, New York, USA) at 37C for 3 hours. Dissociated cells were filtered using a 70-μm cell strainer to get a single cell suspension. Cells were labeled with CD133/2-PE (Miltenyi Biotech clone AC133) antibody. After magnetic sorting, CD133 enriched (CD133high) and remaining (CD133low) cell populations were immediately washed and homogenized in “Lysis/Binding Buffer” of “mirVana miRNA Isolation Kit” (Ambion, Darmstadt, Germany) for further RNA isolation.

tag: cell marker

tag: tissue

value: larynx cancer

tag: age

tag: Sex

tag: surgery

value: Partial Laryngectomy

tag: grade

value: III

tag: Stage


title: 92A_F_HDID2


title: 93A_F_HDID2


title: CD133-positive (C37+)

value: Total Laryngectomy


title: 147A_F_HSNPT

value: Control


title: CD133-positive (C64+)

value: II


title: CD133-positive (C55+)


title: CD133-positive (C16+)


title: Th17 rep 1


title: 37A_M_HDID1


title: 91A_F_HDID2


title: 35A_M_HDID1


title: CD133-positive (C14+)


title: Naive rep 2

source_name: Sorted naïve Th cells


title: Naive rep 1


title: 146A_F_HSNPT


title: 144A_M_HSNPT


title: 145A_F_HSNPT


title: 90A_F_HDID2


title: 33A_F_HDID1


title: Hmo1 TAP replicate 3

type: genomic

city: concepcion

first: matias

middle: ignacio

last: hepp

state: biobio

address: barrio universitario s/n, casilla 160-C

department: bioquimica y biologia molecular

country: Chile

institute: universidad de concepcion

description: Biological replicate 3 of 3.  hmo1 TAP IP

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc) , and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to manufacturer’s instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US45102919.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Data processed in R (version 2.12.1) using MEDIAN normalization, MA<-normalizeWithinArrays(RG,method=median).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: TAP IP

label_protocol: Briefly, 50 ng of IP or input DNA were treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4 ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate TAP-tagging proteins (50ul IgG-Sepharose 6FF per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate TAP-proteins. The immune complexes were pulled down with 50 ul of Protein G Sepharose 6FF (GE) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

tag: origin

value: Open Biosystem

tag: genotype/variation

source_name: INPUT


title: 141A_F_HSNPT


title: Nhp6B TAP replicate 3

description: Biological replicate 3 of 3.  nhp6b TAP IP


title: 88A_F_HDID2


title: 136A_F_HSNPT


title: Hmo1 TAP replicate 2

description: Biological replicate 2 of 3.  hmo1 TAP IP


title: CD133-negative (C60-)


title: Hmo1 TAP replicate 1

description: Biological replicate 1 of 3.  hmo1 TAP IP


title: 31A_F_HDID1


title: 142A_F_HSNPT


title: CD133-negative (C64-)


title: 30A_F_HDID1


title: CD133-negative (C67-)

value: Supraglottic Laryngectomy


title: 143A_M_HSNPT


title: Nhp6B TAP replicate 1

description: Biological replicate 1 of 3.  nhp6b TAP IP


title: CD133-negative (C37-)


title: 82A_M_HDID2


title: 25A_M_HDID1


title: 23A_M_HDID1


title: CD133-negative (C16-)


title: Nhp6A TAP replicate 2

description: Biological replicate 2 of 3.  nhp6a TAP IP


title: Nhp6A TAP replicate 3

description: Biological replicate 3 of 3.  nhp6a TAP IP


title: Nhp6B TAP replicate 2

description: Biological replicate 2 of 3.  nhp6b TAP IP


title: 132A_M_HSNPT


title: CD133-negative (C55-)


title: 87A_F_HDID2


title: CD133-negative (C14-)


title: 130A_M_HSNPT


title: 79A_F_HDID2


title: CD133-negative (C68-)


title: 131A_M_HSNPT


title: 17A_M_HDID1


title: 123A_M_HSNPT


title: Wildtype TAP replicate 3

description: Biological replicate 3 of 3.  Wildtype IP TAP

value: Wildtype


title: 134A_F_HSNPT


title: Wildtype TAP replicate 1

description: Biological replicate 1 of 3.  Wildtype IP TAP


title: Wildtype TAP replicate 2

description: Biological replicate 2 of 3.  Wildtype IP TAP


title: 15A_F_HDID1


title: 78A_M_HDID2


title: 121A_M_HSNPT


title: 22A_F_HDID1


title: Single hmo1 knockout replicate 3

description: Biological replicate 3 of 3.  hmo1 knockout IP snf5

source_name: Snf5 IP

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate Snf5 (2 ul αSnf5 per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate Snf5. The immune complexes were pulled down with 50 ul of Protein G Sepharose 4FF (GE) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

value: hmo1 knockout


title: Single hmo1 knockout replicate 1

description: Biological replicate 1 of 3.  hmo1 knockout IP snf5


title: Single hmo1 knockout replicate 2

description: Biological replicate 2 of 3.  hmo1 knockout IP snf5


title: Nhp6A TAP replicate 1

description: Biological replicate 1 of 3.  nhp6a TAP IP


title: 67A_F_HDID2


title: 68A_F_HDID2


title: 69A_F_HDID2


title: 66A_F_HDID2


title: 9A_F_HDID1


title: 61A_F_HDID2


title: Double nhp6 (a/b) knockout replicate 3

description: Biological replicate 3 of 3.  nhp6a/nhp6b knockout IP snf5

value: Stillman Lab

value: nhp6a/nhp6b knockout


title: 120A_M_HSNPT


title: Double nhp6 (a/b) knockout replicate 2

description: Biological replicate 2 of 3.  nhp6a/nhp6b knockout IP snf5


title: KO(cy3) vs WT(cy5) biological replicate 1 dyeswap

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version.10.5.1.1).

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

source_name: WT CD4+ T cells

label_protocol: Differentially labeled 400 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44K  ver.2 whole mouse genome arrays (Agilent Design #  026655) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

growth_protocol: CD4+CD62L+ naïve T cells were purified from spleens using an automated magnetic cell sorter.

extract_protocol: Total RNA of the CD4+CD62L+ naïve T was extracted RNeasy mini kit (Qiagen) according to the manjufacturer’s instructions.

treatment_protocol: CD4+CD62L+ naïve T cells were were cultured in RPMI medium and stimulated with anti-CD28 mAb and, plate-coated anti-CD3 mAb described previously for 5 days in the addition of 50 ng/ml IL-2, and 1 ng/ml rhTGFβ.

value: WT

source_name: Lamtor1-deficient CD4+ T cells

value: KO


title: 113A_F_HSNPT

value: F


title: Total RNA from GADD34{delta}C/{delta}C MEFs treated with poly I:C, rep2

city: Marseille cedex 09

first: Philippe

last: Pierre

address: Case 906

country: France

institute: Centre d’Immunologie de Marseille-Luminy

description: SAMPLE 11

hyb_protocol: Hybridizations were carried out following Agilent Technologies instructions for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Santa Clara, CA, USA), using SurePrint G3 Mouse Gene Expression v2 Microarrays.

scan_protocol: Images were obtained using the Agilent G2505C microarray scanner and fluorescence quantization was performed using the Agilent Feature Extraction software version 10.7.3.1 and the GE1_107_Sep09 protocol.

data_processing: Gene Expression microarray raw data were normalized using the Quantile method through the limma package in the R statistical environment.

source_name: GADD34ΔC/ΔC_MEFs_poly I:C

label_protocol: Same amounts of RNA extract (200 ng) from each replicate were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Mouse embryonic fibroblasts were cultured in DMEM supplemented with 5 % heat-inactivated fetal bovine serum and 50µM beta-mercaptoethanol. Cells were plated and culture with fresh medium the day before the experiment.

extract_protocol: Dry pellets of cells were lysed in a NP40-containing buffer (0.5%) supplemented with RNAsin (360U/ml). After short centrifugation, supernatants were collected and proteins were denaturated with 1% SDS, EDTA 10mM and proteinase K 200µg/ml during 30 min at 37°C. RNA was extracted with phenol/chloroforme pH4.5 and the aqueous phase was used to precipitate RNA with LiCl/Isopropanol at -20°C. Concentration was determined with Nanodrop and quality with Agilent Bioanalyser.

treatment_protocol: Final volume per flask was 30 ml: 24 ml of DMEM with 5 % FBS and 6 ml of lipofectamine/poly (I:C) mix, containing 100 µl of lipofectamine 2000 and 75 µg of HMW poly (I:C). Cells were treated during 6h and harvest before lysis.

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: treated with

value: 2.5µg/ml of HMW poly(I:C) for 6 hrs


title: WT(cy3) vs KO(cy5) biological replicate 1


title: 60A_M_HDID2

value: M

value: Drinker


title: 112A_F_HSNPT


title: Total RNA from GADD34{delta}C/{delta}C MEFs treated with poly I:C, rep1

description: SAMPLE 10


title: 114A_F_HSNPT


title: 7A_M_HDID1


title: Double nhp6 (a/b) knockout replicate 1

description: Biological replicate 1 of 3.  nhp6a/nhp6b knockout IP snf5


title: 111A_F_HSNPT


title: Wildtype Snf5 IP replicate 3

description: Biological replicate 3 of 3.  Wildtype IP snf5


title: Wildtype Snf5 IP replicate 1

description: Biological replicate 1 of 3.  Wildtype IP snf5


title: 6A_M_HDID1


title: 85A_F_HDID2


title: CD133-positive (C15+)

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent 8x15k miRNA microarray V19 comprised of 2006 miRNAs from Sanger miRBase (release 19) at 55o C for 20 hr.

data_processing: Data (intensity signal)  were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15. ''signal' is a measure of the abundance of a transcript.

value: larynx  cancer

value: Laryngectomy

value: III


title: CD133-positive (C9+)

value: Total Laryngectomy


title: Wildtype Snf5 IP replicate 2

description: Biological replicate 2 of 3.  Wildtype IP snf5

value: Open Biosystem


title: CD133-positive (C28+)


title: Total RNA from GADD34{delta}C/{delta}C MEFs treated with poly I:C, rep3

description: SAMPLE 12


title: 139A_M_HSNPT

value: Control


title: Total RNA from WT MEFs treated with poly I:C, rep2

description: SAMPLE 5

source_name: WT_MEFs_poly I:C

value: wild type


title: Total RNA from not treated GADD34{delta}C/{delta}C MEFs, rep2

description: SAMPLE 8

value: none (untreated)


title: 29A_F_HDID1


title: 58A_M_HDID2


title: Total RNA from WT MEFs treated with poly I:C, rep1

description: SAMPLE 4


title: Total RNA from not treated WT MEFs, rep3

description: SAMPLE 3


title: 140A_M_HSNPT


title: Total RNA from not treated GADD34{delta}C/{delta}C MEFs, rep3

description: SAMPLE 9


title: 59A_M_HDID2


title: CD133-positive (C27+)

value: II


title: Total RNA from not treated WT MEFs, rep2

description: SAMPLE 2


title: Total RNA from WT MEFs treated with poly I:C, rep3

description: SAMPLE 6


title: 86A_F_HDID2


title: Total RNA from not treated GADD34{delta}C/{delta}C MEFs, rep1

description: SAMPLE 7


title: Total RNA from not treated WT MEFs, rep1

description: SAMPLE 1


title: CD133-negative (C9-)


title: CD133-negative (C28-)


title: 138A_M_HSNPT


title: 27A_F_HDID1


title: 77A_M_HDID2


title: CD133-negative (C15-)


title: 83A_M_HDID2


title: 21A_F_HDID1


title: Liver, intermittent diet, age 12 months, replicate 4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.38.0).

source_name: Liver, intermittent diet, age 12 months

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male C57BL/6J mice (age: 7 weeks) were purchased from Janvier (Cedex, France) and were housed in pairs of two in the light and temperature (20C)-controlled animal facility of Wageningen University (12-hour light/dark cycle, lights on at 04.00). The mice received standard AIN-93G (Research Diet Services, Wijk bij Duurstede, The Netherlands) for 2 weeks upon arrival. At the start of the diet intervention, the mice were 9 weeks old, housed individually and randomly distributed into four intervention groups: 1) Control diet (C) receiving AIN-93W diet ad libitum (n=89); 2) Moderate-Fat diet (MF) receiving AIN-93W-MF ad libitum (n=127); 3) Intermittent diet (INT) receiving alternating one week AIN-93W-MF ad libitum followed by one week 60E% of the C diet based on the mean energy intake of the mice on the AIN-93W diet (n=155); and 4) Calorie Restricted diet (CR) receiving AIN-93W-CR in portions containing 70E% of the mean energy intake of the group of the control mice were provided each day at 15.30 (n=117). At the age of 12M, we created group 5) by transferring a subset of 32 randomly selected mice from the MF-intervention group to the INT diet which they received for the second part of their life (for study design see Figure 1A of the paper). With the INT dietary intervention, we intended to induce the maximal fluctuation in weight gain and weight loss that is allowed according to the regulations of our Local ethical committee for care and use of laboratory animals (that is 20% of the total body weight). AIN-93W is a variant of the AIN-93M (maintenance of adult mice) diet, which slightly differs on the fat source. The 10E% fat content in AIN-93M solely comes from soybean oil, while the fat source of AIN-93W is a mix of 6E% soybean oil and 4E% palm oil, in order to balance saturated and unsaturated fat composition. The AIN-93-W-MF contained 25E% fat, also from soybean oil and palm oil. AIN-93W-CR contained increased concentrations of vitamins and minerals in order to feed these mice the same concentrations of micronutrients as the mice receiving AIN-93W diet to avoid malnutrition. The array data from the 6-, 12- and 24-month-old mice exposed to the Control, CR and MF diet have been published before, and are available under GEO accession number: GSE84495.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

tag: gender

value: male

value: liver

value: 12 months

value: intermittent diet


title: Liver, intermittent diet, age 12 months, replicate 6


title: Liver, intermittent diet, age 24 months, replicate 2

source_name: Liver, intermittent diet, age 24 months

value: 24 months


title: CD133-negative (C27-)


title: 129A_M_HSNPT


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 8

source_name: Liver, switched from medium fat diet at age of 12 months to intermittent diet, age 24 months

value: from medium fat to intermittent diet at age of 12 months


title: 128A_F_HSNPT

value: F


title: 26A_M_HDID1

value: M

value: Drinker


title: Liver, intermittent diet, age 6 months, replicate 4

source_name: Liver, intermittent diet, age 6 months

value: 6 months


title: Liver, intermittent diet, age 24 months, replicate 1


title: Liver, intermittent diet, age 6 months, replicate 6


title: 137A_F_HSNPT


title: Liver, intermittent diet, age 24 months, replicate 7


title: 14A_F_HDID1


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 1


title: Liver, intermittent diet, age 12 months, replicate 5


title: 19A_M_HDID1


title: 73A_F_HDID2


title: 74A_F_HDID2


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 7


title: 76A_M_HDID2


title: 127A_F_HSNPT


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 6


title: 18A_M_HDID1


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 5


title: 65A_F_HDID2


title: 13A_M_HDID1


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 3


title: Liver, intermittent diet, age 24 months, replicate 4


title: Liver, intermittent diet, age 24 months, replicate 6


title: 117A_M_HSNPT


title: 116A_M_HSNPT


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 2


title: Liver, intermittent diet, age 12 months, replicate 7


title: 110A_F_HSNPT


title: 62A_F_HDID2


title: 109A_F_HSNPT


title: 57A_M_HDID2


title: Liver, medium fat diet (25% energy) to intermittent diet switch, age 24 months, replicate 4


title: Liver, intermittent diet, age 12 months, replicate 1


title: Liver, intermittent diet, age 24 months, replicate 3


title: 11A_M_HDID1


title: Liver, intermittent diet, age 6 months, replicate 5


title: 64A_F_HDID2


title: Liver, intermittent diet, age 6 months, replicate 3


title: 107A_M_HSNPT


title: Liver, intermittent diet, age 12 months, replicate 3


title: Liver, intermittent diet, age 24 months, replicate 5


title: 2A_F_HDID1


title: Liver, intermittent diet, age 12 months, replicate 2


title: 4A_F_HDID1


title: 55A_F_HDID2


title: Liver, intermittent diet, age 6 months, replicate 2


title: 53A_F_HDID2


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep10

status: Public on Jan 15 2017

city: Braine-l'Alleud

first: Jonathan

last: van Eyll

address: UCB Pharma - Building S2C

department: NewMedicines

country: Belgium

institute: UCB Pharma

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina MouseRef-8 v2 (Illumina, Inc., San Diego, CA, U.S.A.). Hybridization and washing were performed according to the Illumina Manual “Direct Hybridization Assay Guide”.

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with default settings (no background subtraction and no normalization). QC and normalization of microarray data were performed using “Lumi” package in R- Bioconductor. Briefly, samples that passed QC were Log2-transformed and normalized by quantiles between chips. Only QC passed samples are provided in this dataset.

source_name: epileptic hippocampus exposed 7 days to PLX3397 at 30 mg/kg

label_protocol: The Quality control, RNA labeling, hybridization and data extraction were performed at GenomeScan/ServiceXS B.V. (Leiden, The Netherlands). RNA concentration was measured using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, U.S.A). The RNA quality and integrity was determined using Lab-on-Chip analysis on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.). Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: All in vivo experiments were performed according to the National Rules on Animal Experiments in Belgium and to the guidelines of the European Community Council Directive 2010/63/EU. Formal approval to conduct these experiments was obtained from the local Ethical Committees.

extract_protocol: Snap frozen hippocampi were homogenized in RLT buffer (Qiagen, 74134) using precellys® system in CK14 tubes following manufacturer’s instructions. Total RNA was obtained from mouse hippocampi using RNeasy Plus Mini Kit (Qiagen, 74134) following manufacturer’s instructions. RNA concentration was measured with a NanoDrop ND-1000 Spectrophotometer. RNA quality was assessed using the Bio-Rad Experion Automated Electrophoresis System (RQI ≥ 7).

treatment_protocol: For epileptic animals, status epilepticus (SE) was initiated with a single 300 mg/kg intraperitoneal (i.p.) injection of pilocarpine (Sigma-Aldrich) in male NMRI mice, 30 min after N-methylscopolamine bromide administration (1 mg/kg; i.p.). Within 10 to 45 min after pilocarpine treatment, animals displayed generalized clonic-tonic seizures that progressed to continuous convulsive activity, i.e. status epilepticus (SE). To limit the duration of SE mice were injected with a bolus dose of diazepam (10 mg/kg; i.p.) after 3 h. The mice typically show spontaneous recurrent seizures within few days after SE and continue to display them for several weeks. For PLX3397 or vehicle administration, animals received daily injections (oral gavage) with vehicle, Csf1R inhibitor compound (PLX3397) at 3 or 30 mg/kg during 7 days.

tag: strain

value: NMRI

value: hippocampus

value: adult (>12 weeks)


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep18

source_name: epileptic hippocampus exposed 7 days to PLX3397 at 3 mg/kg


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep13


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep17


title: hippocampus_pilocarpine_vehicle_rep14

source_name: epileptic hippocampus exposed 7 days to vehicle


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep11


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep14


title: Liver, intermittent diet, age 6 months, replicate 1


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep12


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep15


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep14


title: hippocampus_pilocarpine_vehicle_rep13


title: hippocampus_pilocarpine_vehicle_rep17


title: hippocampus_Naive_vehicle_rep6

source_name: healthy hippocampus exposed 7 days to vehicle


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep16


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep8


title: hippocampus_pilocarpine_vehicle_rep15


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep11


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep10


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep13


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep12


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep9


title: hippocampus_Naive_vehicle_rep5


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep9


title: 84A_M_HDID2

source_name: brain striatum

tag: sex (f=female, m=male)


title: hippocampus_pilocarpine_vehicle_rep16


title: hippocampus_pilocarpine_vehicle_rep12


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep3


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep7


title: hippocampus_pilocarpine_vehicle_rep11


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep4


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep2


title: hippocampus_Naive_vehicle_rep4


title: 118A_M_HSNPT

tag: behavioral phenotype

value: Control


title: tumor_111

city: Shanghai

first: liu

last: BingYa

address: 197 Ruijin ER RD

department: surgery

country: China

institute: RuiJin Hospital,SJTU

description: human gastric tissues

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

data_processing: The data normalization and probe summarization were performed by Robust Multichip Analysis (RMA) using R Bioconductor software.

source_name: surgically resected from patient of gastric cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

extract_protocol: Total RNA was extracted from the tissues or cells using the Trizol reagent (Invitrogen) according to the manufacturer’s instructions. Total RNA was eluted with RNase-free water and stored at -80℃. RNA concentrations were determined by Epoch spectrophotometry.

value: gastric cancer tumor


title: P2-IL4

city: Bristol

first: Andrew

last: Newby

state: International/Other

address: Level 7 Bristol Royal Infirmary, Upper Maudlin Street

country: United Kingdom

institute: University of Bristol

description: Sample name: Sample 24

data_processing: Genespring GX12.5: Threshold: 1.0, Logbase: 2, Normalization: Shift to 75 percentile, Baseline Transformation: median of all samples, Flag Information: Lower cutoff for 'Present' call :0.8 Upper cutoff for 'Absent' call : 0.

source_name: Monocytes

label_protocol: Standard Illumina Biotin labeling protocol

extract_protocol: Total RNA was isolated using PureLinkTM RNA Mini Kit (Ambion)

treatment_protocol: Mononuclear cells were isolated using Ficoll-Paque Plus (GE Healthcare Life Sciences), red blood cells were lysed with 150 mM ammonium chloride/ 0.1% BSA and monocytes were allowed to adhere to plastic in RPMI 1640/1% human serum AB (SigmaAldrich) for an hour. Non-adherent cells were removed with warm Dulbecco’s phosphate buffered saline (D-PBS; Gibco) and the medium was replaced with RPMI 1640/ 10% foetal bovine serum (FBS; SigmaAldrich) for an hour. Monocytes were differentiated into macrophages in RPMI 1640 medium containing 10% FBS and 20 ng/mL of colony-stimulating factor-1 (human recombinant CSF-1, R & D systems), which was replenished on day 3. Differentiated macrophages were treated for 6, 18, 32 and 48h in the same medium with either 100 ng/mL of recombinant human interferon-γ (IFN-γ) (R & D systems) or 10 ng/mL of recombinant human interleukin-4 (IL-4) (R & D systems) to polarize them into M1 and M2 phenotypes, respectively

value: monocytes

tag: treatment


title: hippocampus_Naive_vehicle_rep3


title: hippocampus_pilocarpine_vehicle_rep10


title: P4-GSKJ4

description: Sample name: Sample 21


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep6


title: P3-GSKJ4

description: Sample name: Sample 22


title: tumor_108

description: human gastric tissues


title: P1-GSKJ4-IFNg

description: Sample name: Sample 23


title: tumor_110

description: human gastric tissues


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep8


title: tumor_107

description: human gastric tissues


title: P4-GSKJ4-IFNg

description: Sample name: Sample 20


title: P2-GSKJ4

description: Sample name: Sample 19


title: tumor_109

description: human gastric tissues


title: tumor_104

description: human gastric tissues


title: hippocampus_pilocarpine_vehicle_rep9


title: tumor_106

description: human gastric tissues


title: tumor_105

description: human gastric tissues


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep15


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep5


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep6


title: P4-IL4

description: Sample name: Sample 18


title: P3-IL4

description: Sample name: Sample 16


title: hippocampus_Naive_vehicle_rep2


title: tumor_102

description: human gastric tissues


title: hippocampus_Naive_vehicle_rep1


title: hippocampus_pilocarpine_vehicle_rep8


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep5


title: P4-GSKJ4-IL4

description: Sample name: Sample 14


title: P1-IFNg

description: Sample name: Sample 17

value: IFNg


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep7

value: male


title: tumor_99

description: human gastric tissues


title: tumor_98

description: human gastric tissues


title: tumor_100

description: human gastric tissues


title: tumor_96

description: human gastric tissues


title: tumor_92

description: human gastric tissues


title: tumor_97

description: human gastric tissues


title: hippocampus_pilocarpine_vehicle_rep7


title: tumor_91

description: human gastric tissues


title: tumor_95

description: human gastric tissues


title: hippocampus_pilocarpine_vehicle_rep6


title: tumor_94

description: human gastric tissues


title: P2-IFNg

description: Sample name: Sample 12


title: tumor_93

description: human gastric tissues


title: tumor_103

description: human gastric tissues


title: P4-IFNg

description: Sample name: Sample 11


title: tumor_101

description: human gastric tissues


title: P1-GSKJ4-IL4

description: Sample name: Sample 13


title: tumor_90

description: human gastric tissues


title: P1-IL4

description: Sample name: Sample 15


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep4


title: tumor_87

description: human gastric tissues


title: P3-GSKJ4-IL4

description: Sample name: Sample 10


title: P1-GSKJ4

description: Sample name: Sample 8


title: hippocampus_pilocarpine_vehicle_rep5


title: tumor_88

description: human gastric tissues


title: tumor_83

description: human gastric tissues


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep3


title: tumor_86

description: human gastric tissues


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep2


title: tumor_84

description: human gastric tissues


title: tumor_89

description: human gastric tissues


title: tumor_82

description: human gastric tissues


title: P2-GSKJ4-IFNg

description: Sample name: Sample 7


title: tumor_75

description: human gastric tissues


title: hippocampus_pilocarpine_vehicle_rep4


title: tumor_85

description: human gastric tissues


title: tumor_77

description: human gastric tissues


title: tumor_81

description: human gastric tissues


title: hippocampus_pilocarpine_vehicle_rep3


title: hippocampus_pilocarpine_vehicle_rep2


title: tumor_76

description: human gastric tissues


title: tumor_80

description: human gastric tissues


title: tumor_79

description: human gastric tissues


title: P4-DMSO

description: Sample name: Sample 9

value: DMSO


title: hippocampus_pilocarpine_PLX3397_3_mg/kg_rep1


title: P3-IFNg

description: Sample name: Sample 6


title: P2-GSKJ4-IL4

description: Sample name: Sample 4


title: tumor_78

description: human gastric tissues


title: P2-DMSO

description: Sample name: Sample 5


title: tumor_74

description: human gastric tissues


title: tumor_72

description: human gastric tissues


title: FC EDL3

city: Berlin

first: Dieter

last: Blottner

address: Phillipstrasse 12

department: Anatomy

country: Germany

institute: Charité Universitaetsmedizin Berlin

description: Gene expression data from EDL of mouse  haused in a standard animal facility (during the Bion  flight) for 30 days

hyb_protocol: 15 μg of each labeled and fragmented cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix GeneChip Mouse 430A 2.0 Array

scan_protocol: Arrays were scanned at 1.56-μm resolution using the Affymetrix GeneChip System confocal scanner 3000

data_processing:
Data analysis was performed importing cel files to the Partek® Genomics Suite® 6.6 software. Robust Multichip Average algorithm (RMA) was used for data normalization.
Annotation (Mouse430A_2.na34.annot.csv ) and cdf Files from: http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430A-20.

label_protocol: The amplification and labeling of 100 ng of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA) using the GeneChip® 3’ IVT Express Protocol.

extract_protocol: Total RNA was isolated from mouse soleus (n = 3) and EDL (n = 3) muscles of each experimental group (BF, BG and FC) using a two step isolation protocol: modified Chomczinsky extraction followed by column purification (RNeasy micro Kit, Qiagen, Hilden,Germany)

value: extensor digitorum muscle

value: Male


title: hippocampus_pilocarpine_PLX3397_30_mg/kg_rep1


title: tumor_73

description: human gastric tissues


title: P1-DMSO

description: Sample name: Sample 2


title: tumor_71

description: human gastric tissues


title: tumor_68

description: human gastric tissues


title: FC EDL2

source_name: mouse  haused in a standard animal facility (during the Bion  flight)


title: hippocampus_pilocarpine_vehicle_rep1


title: FC EDL1


title: BG EDL2

description: Gene expression data from EDL of mouse  haused for 30 days in a replicate habitat of  Bion M1 biosatellite

source_name: mouse  haused in a replicate habitat of  Bion M1 biosatellite


title: tumor_67

description: human gastric tissues


title: tumor_64

description: human gastric tissues


title: tumor_66

description: human gastric tissues


title: BG EDL1


title: P3-GSKJ4-IFNg

description: Sample name: Sample 1


title: P3-DMSO

description: Sample name: Sample 3


title: tumor_69

description: human gastric tissues


title: tumor_65

description: human gastric tissues


title: tumor_59

description: human gastric tissues


title: tumor_63

description: human gastric tissues


title: tumor_61

description: human gastric tissues


title: tumor_62

description: human gastric tissues


title: BG EDL3


title: tumor_70

description: human gastric tissues


title: tumor_57

description: human gastric tissues


title: tumor_56

description: human gastric tissues


title: tumor_60

description: human gastric tissues


title: tumor_58

description: human gastric tissues


title: BF EDL3

description: Gene expression data from EDL muscle of mouse flown 30 days aboard on Bion M3

source_name: mouse flown aboard on Bion M1


title: BF EDL1

description: Gene expression data from EDL muscle of mouse flown 30 days aboard on Bion M1


title: tumor_52

description: human gastric tissues


title: tumor_50

description: human gastric tissues


title: FC SOL1

description: Gene expression data from soleus of mouse  haused in a standard animal facility (during the Bion  flight) for 30 days

value: soleus muscle


title: tumor_53

description: human gastric tissues


title: tumor_54

description: human gastric tissues


title: tumor_55

description: human gastric tissues


title: FC SOL2


title: tumor_49

description: human gastric tissues


title: tumor_47

description: human gastric tissues


title: FC SOL3


title: tumor_48

description: human gastric tissues


title: tumor_51

description: human gastric tissues


title: #17 AX4965 (SX00837F70)

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from thin melanoma with good outcome

hyb_protocol: The amplified cDNA was quantified, fragmented, and labeled in preparation for hybridization to GeneChip™ Human Transcriptome 2.0 Arrays (Affymetrix, Santa Clara, CA) using 5.5μg of ss-cDNA product following protocols outlined in the above-mentioned user manual.

scan_protocol: Washing, staining (GeneChip® Fluidics Station 450, Affymetrix), and scanning (GeneChip® Scanner 3000, Affymetrix) were performed following protocols outlined in the GeneChip™ Expression Wash, Stain, and Scan User Manual for Cartridge Arrays.

data_processing: The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek® Genomics Suite™ ( 6.6 version 6.15.0730) and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets. Differentially expressed genes were identified using ANOVA with two factors: prognosis and scan date (random variable).

source_name: Thin melanoma, FFPE

label_protocol: RNA was amplified and labeled using the GeneChip™ WT Pico Reagent Kit (Affymetrix, Santa Clara, CA) which enables amplification and target preparation for whole transcriptome expression analysis. Amplification was performed with 10ng of total RNA input following procedures described in the WT Pico Reagent Kit user manual.

extract_protocol:
Paraffin embedded thin melanoma tissue samples were cut into 5-µm-thick sections and mounted onto PEN (polyethylene naphthalate) membrane glass slides. Regions of interest were identified by pathology on corresponding H&E slides of the tissue sections.  The stained slides were microdissected using the ArcturusXT™ Microdissection System (Molecular Devices, Sunnyvale, CA) onto CapSure® HS LCM Caps (Molecular Devices, Sunnyvale, CA).
RNA was isolated using Qiagen’s RNeasy FFPE Kit (Qiagen, Hilden, DE).  The transfer film with the attached dissected material was separated from each CapSure HS LCM Cap and placed in lysis buffer then, following the manufacturer’s protocol, RNA was purified using spin cartridge technology, quantified (Nanodrop 8000, Thermo Scientific), and then stored at -80°C.

tag: outcome

value: Good

tag: diagnosis

value: Thin melanoma


title: tumor_44

description: human gastric tissues

tag: tissue


title: tumor_46

description: human gastric tissues


title: BF EDL2

description: Gene expression data from EDL muscle of mouse flown 30 days aboard on Bion M2

tag: Sex


title: BG SOL3

description: Gene expression data from soleus of mouse  haused for 30 days in a replicate habitat of  Bion M1 biosatellite


title: tumor_42

description: human gastric tissues


title: tumor_45

description: human gastric tissues


title: tumor_43

description: human gastric tissues


title: #19 AX4964 (SX0083B9D6)


title: BF SOL3

description: Gene expression data from soleus muscle of mouse flown 30 days aboard on Bion M1


title: #15 AX4960 (SX0083C797)


title: BF SOL2


title: BG SOL1


title: BG SOL2


title: tumor_41

description: human gastric tissues


title: #16 AX4962 (SX0083CF95)


title: #14 AX4961 (SX0083533)


title: tumor_40

description: human gastric tissues


title: tumor_39

description: human gastric tissues


title: #13 AX4959 (SX0083D77)


title: 15C_PBS_day28_2

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was scanned with a Agilent G2565CA scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.5.1 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Paralichthys olivaceus

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 15 °C, 28 days

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

extract_protocol: Total RNA was extracted from fish spleen using the RNeasy Mini Kit.

treatment_protocol: Fish were treated with Edwardsiella tarda formallin-killed cells and PBS (control).

value: PBS

tag: temperature

value: 15 °C

tag: time course

value: 28 days


title: 15C_PBS_day28_1


title: #1 AX4958 (SX0083BC56)


title: #2 AX4966 (SX0083AC63)


title: #18 AX4803 (SX0083CF5F)

description: Gene expression data from thin melanoma with poor outcome

value: Poor


title: 22C_FKC_day28_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 22 °C, 28 days

value: FKC

value: 22 °C


title: #12 AX4963 (SX0083C0FD)


title: tumor_35

description: human gastric tissues


title: BF SOL1


title: 22C_FKC_day28_2


title: tumor_37

description: human gastric tissues


title: #3 AX4957 (SX00837F71)


title: 22C_PBS_day28_2

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 22 °C, 28 days


title: tumor_36

description: human gastric tissues


title: 22C_PBS_day28_3


title: tumor_33

description: human gastric tissues


title: tumor_38

description: human gastric tissues


title: #11 AX4704 (SX0083C938)


title: tumor_34

description: human gastric tissues


title: 22C_PBS_day28_1


title: DM day 5

city: Kamakura

first: Satoshi

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Rattus norvegicus

source_name: fracture callus

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: On post-fracture day 5 and 11, the newly generated specific tissues, that is, the fracture callus were harvested. All harvested tissues were stored in RNAlater (Ambion, Austin, TX) at 4°C until used. The tissue specimens from 5 different animals in each group on post-fracture day 5 and 11 respectively were pooled, and were submitted to Toray (Kamakura, Japan) for RNA isolation and microarray analysis. RNA samples were extracted from tissues using miRNesy mini kit (Quiagen) according to manufacture's protocol.

tag: blood glucose level

value: over 300 mg/dl

value: fracture callus


title: #9 AX4169 (SX0083CA65)


title: 22C_PBS_day3_3

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 22 °C, 3 days

value: 3 days


title: 15C_PBS_day28_3


title: TwinI_ALS

city: Darlinghurst

first: Paul

middle: E

last: Young

state: NSW

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

description: blood from ALS patient

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from white blood cells using the QIAmp blood kit (Qiagen)

value: blood

value: Female

tag: age (years)

tag: twin pair

tag: disease status

value: ALS


title: 22C_PBS_day3_2


title: #8 AX4182 (SX0083CA7D)


title: TwinH_Control

description: blood from control

value: Control


title: 22C_PBS_day3_1


title: tumor_32

description: human gastric tissues

value: gastric cancer tumor


title: tumor_30

description: human gastric tissues


title: #10 AX5332 (SX0083C937)


title: DM Day 11


title: Ctr Day 5

value: normal


title: tumor_31

description: human gastric tissues


title: 15C_PBS_day3_3

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 15 °C, 3 days


title: TwinJ_Control

description: blood from control


title: tumor_28

description: human gastric tissues


title: tumor_29

description: human gastric tissues


title: #5 AX5487 (SX0083CDAE)


title: #7 AX4171 (SX0083CBEF)


title: TwinG_ALS

description: blood from ALS patient


title: #6 AX4170 (SX0083CBF0)


title: TwinF_Control

description: blood from control


title: tumor_27

description: human gastric tissues


title: Ctr Day 11


title: 22C_FKC_day28_1


title: 15C_FKC_day28_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 15 °C, 28 days


title: #4 AX4684 (SX00838CF8)


title: 15C_FKC_day28_2


title: TwinE_ALS

description: blood from ALS patient


title: 15C_FKC_day28_1


title: 15C_FKC_day3_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 15 °C, 3 days


title: TwinD_Control

description: blood from control

value: Male


title: tumor_21

description: human gastric tissues


title: B6_male_astrocyte_clone#2(2)_Vector

city: Frederick

first: Karlyne

middle: M

last: Reilly

state: MD

address: West 7th St at Fort Detrick, PO Box B

department: Mouse Cancer Genetics Program

institute: National Cancer Institute, Center for Cancer Research

hyb_protocol: Labeled cDNA (4.4 ug) of each sample was hybridized to Affymetrix  mouse 430 2.0 GeneChip array at 45C for 16 hrs.  GeneChip arrays were washed on Affymetrix Fluidics Station 450 using manufacturer’s recommended scripts.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000 and data were collected using Affymetrix AGCC software.

data_processing: Data was normalized in Partek Genomics Suite v6.5 using GC-RMA.

source_name: C57BL/6J male astrocyte, vector only

label_protocol: RNA (10 ng) was amplified and labeled with Ovation Whole Blood Solution kit (Nugen, CA) following manufacturer’s protocol.

growth_protocol: Primary astrocytes were isolated from P0-P1 neonate mice and cultured in DMEM + 20% FBS + antibiotics.

extract_protocol: Total RNA was extracted from primary astrocytes using RNeasy Mini Kit (Qiagen) and treated with TURBO DNAfree (Ambion). RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

treatment_protocol: Primary astrocytes were pelleted and resuspended in transfection buffer at 2 X 10^6 cells/100 μl, transferred to a sterile 3 mm Amaxa nucleofection cuvette (Lonza) and with 5 μg pcDNA3.1-hygro CDCA7L or pcDNA3.1-hygro vector. Cells were electroporated using the T-020 mouse astrocyte program and the basic nucleofector kit for primary mammalian glial cells (Lonza, cat#VPI-1006). Nucleofected cells were then resuspended in 500 μl sterile culture medium and transferred to 6 cm plates pre-coated with poly-L-lysine, and incubated at 37 °C.

value: astrocytes

value: male

tag: cdca7l expression

value: Vector control


title: 22C_FKC_day3_1

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 22 °C, 3 days


title: B6_male_astrocyte_clone#3(5)_Vector


title: tumor_22

description: human gastric tissues

source_name: surgically resected from patient of gastric cancer


title: B6_male_astrocyte_clone#2(4)_Vector


title: TwinC_ALS

description: blood from ALS patient


title: tumor_25

description: human gastric tissues


title: tumor_24

description: human gastric tissues


title: TwinB_Control

description: blood from control


title: 129_male_astrocyte_clone#3(2)_Vector

source_name: 129S4/SvJae male astrocyte, vector only


title: 15C_PBS_day3_2

value: PBS

value: 15 °C


title: B6_male_astrocyte_clone#4(3)_Vector


title: tumor_23

description: human gastric tissues


title: 129_male_astrocyte_clone#3(1)_Vector


title: tumor_18

description: human gastric tissues


title: B6_male_astrocyte_clone#5.6(1)_Vector


title: tumor_19

description: human gastric tissues


title: 15C_PBS_day3_1


title: 129_male_astrocyte_clone#5(2)_Vector


title: tumor_20

description: human gastric tissues


title: 129_male_astrocyte_clone#5(1)_Vector


title: 15C_FKC_day3_1

value: FKC


title: 15C_PBS_6h_2

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 15 °C, 6 hours

value: 6 hours


title: tumor_17

description: human gastric tissues


title: 15C_PBS_6h_1


title: 129_male_astrocyte_clone#3(3)_Vector


title: 22C_FKC_day3_2

value: 22 °C


title: tumor_14

description: human gastric tissues


title: B6_male_astrocyte_clone#2(2)_Cdca7l

source_name: C57BL/6J male astrocyte, Cdca7l overexpressed

value: Cdca7l overexp


title: tumor_26

description: human gastric tissues


title: B6_male_astrocyte_clone#5.6(1)_Cdca7l


title: tumor_15

description: human gastric tissues


title: 22C_FKC_day3_3

value: 3 days


title: tumor_13

description: human gastric tissues


title: B6_male_astrocyte_clone#4(3)_Cdca7l


title: TwinA_ALS

description: blood from ALS patient

value: blood


title: 22C_FKC_6h_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 22 °C, 6 hours


title: B6_male_astrocyte_clone#5(3)_Cdca7l


title: 22C_FKC_6h_2


title: 129_male_astrocyte_clone#3(2)_Cdca7l

source_name: 129S4/SvJae male astrocyte, Cdca7l overexpressed


title: 22C_PBS_6h_1

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 22 °C, 6 hours


title: 15C_PBS_6h_3


title: tumor_10

description: human gastric tissues


title: tumor_11

description: human gastric tissues


title: tumor_12

description: human gastric tissues


title: 22C_PBS_6h_2


title: tumor_9

description: human gastric tissues


title: tumor_7

description: human gastric tissues


title: 129_male_astrocyte_clone#3(3)_Cdca7l


title: 129_male_astrocyte_clone#5(1)_Cdca7l


title: tumor_16

description: human gastric tissues


title: 129_male_astrocyte_clone#3(1)_Cdca7l


title: 22C_PBS_6h_3


title: 22C_PBS_day0_3

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 22 °C, 0 day

value: 0 day


title: B6_female_astrocyte_clone#2.1(1)_Vector

source_name: C57BL/6J female astrocyte, vector only

value: female


title: tumor_8

description: human gastric tissues


title: 129_male_astrocyte_clone#1(4)_Cdca7l


title: B6_female_astrocyte_clone#5.1(1)_Vector


title: 22C_PBS_day0_1


title: tumor_5

description: human gastric tissues


title: tumor_4

description: human gastric tissues


title: tumor_6

description: human gastric tissues


title: 22C_PBS_day0_2


title: 15C_PBS_day0_3

source_name: Spleen isolated from fish intraperitoneally injected with PBS, 15 °C, 0 day


title: tumor_3

description: human gastric tissues


title: 15C_FKC_6h_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 15 °C, 6 hours


title: tumor_1

description: human gastric tissues


title: B6_female_astrocyte_clone#3(3)_Vector


title: B6_female_astrocyte_clone#4(5)_Vector


title: B6_female_astrocyte_clone#6(3)_Vector


title: 22C_FKC_6h_1


title: 129_female_astrocyte_clone#1(3)_Vector

source_name: 129S4/SvJae female astrocyte, vector only


title: 129_female_astrocyte_clone#2(3)_Vector


title: 15C_FKC_6h_1


title: 15C_FKC_6h_2


title: 15C_FKC_day0_3

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 15 °C, 0 day


title: 22C_FKC_day0_1

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 22 °C, 0 day


title: normal_20

description: human gastric tissues


title: 129_female_astrocyte_clone#2(1)_Vector


title: 129_female_astrocyte_clone#4(1)_Vector


title: 15C_FKC_day0_1


title: normal_18

description: human gastric tissues


title: B6_female_astrocyte_clone#3(3)_Cdca7l

source_name: C57BL/6J female astrocyte, Cdca7l overexpressed


title: normal_19

description: human gastric tissues


title: tumor_2

description: human gastric tissues


title: B6_female_astrocyte_clone#1(4)_Cdca7l


title: normal_21

description: human gastric tissues


title: 15C_FKC_day0_2


title: normal_17

description: human gastric tissues


title: B6_female_astrocyte_clone#4(5)_Cdca7l


title: normal_16

description: human gastric tissues


title: 15C_FKC_day3_2

source_name: Spleen isolated from fish intraperitoneally injected with FKC, 15 °C, 3 days


title: 129_female_astrocyte_clone#2(1)_Cdca7l

source_name: 129S4/SvJae female astrocyte, Cdca7l overexpressed


title: 22C_FKC_day0_2


title: normal_15

description: human gastric tissues

source_name: surgically resected from patient of gastric cancer


title: 129_female_astrocyte_clone#1(3)_Cdca7l


title: 129_female_astrocyte_clone#2(3)_Cdca7l


title: 22C_FKC_day0_3


title: 129_female_astrocyte_clone#4(1)_Cdca7l


title: 15C_PBS_day0_2


title: 15C_PBS_day0_1


title: normal_13

description: human gastric tissues


title: normal_11

description: human gastric tissues


title: B6_female_astrocyte_clone#6(3)_Cdca7l


title: normal_14

description: human gastric tissues


title: normal_8

description: human gastric tissues


title: Ctr Day 5

source_name: fracture callus

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

value: fracture callus


title: normal_5

description: human gastric tissues


title: normal_12

description: human gastric tissues


title: normal_10

description: human gastric tissues


title: normal_6

description: human gastric tissues


title: B6_male_astrocyte_clone#3(5)_Cdca7l


title: DM Day 11

value: over 300 mg/dl


title: normal_9

description: human gastric tissues

value: normal


title: DM day 5


title: normal_3

description: human gastric tissues


title: normal_7

description: human gastric tissues


title: normal_1

description: human gastric tissues


title: normal_4

description: human gastric tissues


title: Ctr Day 11


title: IPF_1109, Timepoint 0

status: Public on Jan 14 2017

city: London

first: Philip

last: Molyneaux

address: Dovehouse Street

institute: Imperial College London

description: IPF, Timepoint 0

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit material.

scan_protocol: Affymetrix GeneTitan

data_processing: Data were processed using Affymetrix Power Tools. RMA background correction were applied to probe intensities, gene level expression were summarized from the intensities and then quantile normalized.

source_name: whole blood

label_protocol: Samples were fragmented and labelled using the Encore® Biotin Module Kit (NuGEN)

extract_protocol: The PAXgene Blood RNA Kit (PreAnalytiX) was used to isolate RNA according to the manufacturer’s protocol.

value: whole blood

tag: disease state

value: Idiopathic Pulmonary Fibrosis

tag: survival (months)

tag: fvc

tag: dlco


title: normal_2

description: human gastric tissues


title: IPF_1096, Timepoint 0

description: IPF, Timepoint 0

tag: gender


title: IPF_1065, Timepoint 0

description: IPF, Timepoint 0

value: male


title: IPF_1098, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1100, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1085, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1059, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1063, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1057, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1055, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1050, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1049, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1092, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1047, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1060, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1045, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1046, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1045, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1053, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1043, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1044, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1045, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1044, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1076, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1042, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1043, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1041, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1042, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1042, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1041, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1041, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1040, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1040, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1040, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1038, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1039, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1036, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1038, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1039, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1040, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1037, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1038, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1038, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1039, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1039, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1038, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1037, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1037, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1040, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1036, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1034, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1034, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1035, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1035, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1036, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1031, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1031, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1031, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1034, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1037, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1033, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1031, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1031, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1028, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1028, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1029, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1029, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1030, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1029, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1028, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1028, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1030, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1030, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1029, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1030, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1027, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1028, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1030, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1026, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1026, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1024, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1025, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1026, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1026, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1029, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1027, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1019, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1023, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1019, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1025, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1025, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1025, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1024, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1016, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1018, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1024, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1024, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1023, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1018, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1020, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1023, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1014, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1014, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1020, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1019, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1019, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1014, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1018, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1013, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1013, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1018, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1020, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1018, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1014, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1014, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1011, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1013, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1012, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1013, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1013, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1012, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1011, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1011, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1007, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1007, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1011, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1012, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1011, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1009, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1007, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1009, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1007, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1006, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1004, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1008, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1007, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1010, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1010, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1006, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1006, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1005, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1004, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1004, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1008, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1003, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1003, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1004, Timepoint 1

description: IPF, Timepoint 1


title: IPF_1001, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1003, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1001, Timepoint 3

description: IPF, Timepoint 3


title: IPF_1004, Timepoint 2

description: IPF, Timepoint 2


title: IPF_1001, Timepoint 0

description: IPF, Timepoint 0


title: IPF_1003, Timepoint 4

description: IPF, Timepoint 4


title: IPF_1003, Timepoint 1

description: IPF, Timepoint 1


title: Control_7, Timepoint 0

description: Control, Timepoint 0

value: control


title: Control_18, Timepoint 0

description: Control, Timepoint 0


title: Control_6, Timepoint 0

description: Control, Timepoint 0


title: Control_15, Timepoint 0

description: Control, Timepoint 0


title: Control_17, Timepoint 0

description: Control, Timepoint 0


title: Control_2, Timepoint 0

description: Control, Timepoint 0


title: Control_3, Timepoint 0

description: Control, Timepoint 0


title: Control_11, Timepoint 0

description: Control, Timepoint 0


title: Control_8, Timepoint 0

description: Control, Timepoint 0


title: Control_4, Timepoint 0

description: Control, Timepoint 0


title: Control_20, Timepoint 0

description: Control, Timepoint 0


title: Control_13, Timepoint 0

description: Control, Timepoint 0


title: Control_12, Timepoint 0

description: Control, Timepoint 0


title: Control_5, Timepoint 0

description: Control, Timepoint 0


title: Control_19, Timepoint 0

description: Control, Timepoint 0


title: 2-2

city: Ningbo

first: Junming

last: Guo

address: Jiangbei District Fenghua Road No. 818

institute: Ningbo University School of Medicine

description: This sample is plasma from healthy person

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned at 5 µm/pixel resolution using a GenePix 4000B scanner piloted by GenePix Pro 6.0 software (Axon Instruments, Union City, CA). Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and raw intensity extraction.

data_processing:
The raw microarray data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.
Platform GPL19978 has 5396 probes, but only 1751 probes were detected because the quantity of RNA extracted from human plasma samples was relatively low. As a result some circRNAs couldn’t be analyzed by probes effectively. All of the analyzed probes and their normalized data are provided in the Sample Data tables.

source_name: Healthy control

label_protocol: CircRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted by using TRIzol -LS (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrohoresis.

value: Healthy control

value: plasma


title: 2-1

description: This sample is plasma  from a patient with gastric cancer  before operation

source_name: Gastric cancer plasma

value: Gastric cancer


title: 3-1


title: 3-2


title: Control_1, Timepoint 0

description: Control, Timepoint 0


title: 1-1


title: Control_9, Timepoint 0

description: Control, Timepoint 0


title: 1-2


title: Control_14, Timepoint 0

description: Control, Timepoint 0


title: Control_10, Timepoint 0

description: Control, Timepoint 0


title: Control_16, Timepoint 0

description: Control, Timepoint 0


title: Pcgf6KO+ Pcgf6_flag

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

description: gene expression in Pcgf6KO+ Pcgf6_flag mouse embryonic stem cell

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by quantile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: ES cells were cultured with mouse embryonic fibroblasts (MEFs) inactivated with mitomycin-C in DMEM supplemented with15% fetal calf serum , leukemia inhibitory factor , L-glutamine , non-essential amino acids , 0.1 mM betamercaptoethanol , and penicillin/streptomycin. All ES cell lines were maintained at 37°C in 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Pcgf6KO ES cells were generated by Cas9 technology. Pcgf6KO_Pcgf6_flag ES cells were established by lentiviral infection technology.

tag: cell type

value: embryonic stem cell

tag: genotype

value: Pcgf6KO+ Pcgf6_flag


title: MIST1-LSL Mouse Liver p2 (27583)

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

description: Gene expression data from MIST1-LSL liver 1 extraction 2

hyb_protocol: Total RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 WT Arrays according to manufacturers instructions

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.  Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files imported into Partek were normalized using RMA.

source_name: Excised Liver 2

label_protocol: Total RNA extracted and amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences)

extract_protocol: Total RNA was extracted, purified by RNEasy Mini Kit, and RNA integrity verified on Agilent Bioanalyzer

value: Liver

value: AAV8-TBG-iCre; MIST1-LSL;mTmG

tag: age

value: 9 Weeks

tag: background strain

value: mixed background, but backcrossed ~10 generations to C57/B6


title: Control Mouse Liver p2 (27581)

description: Gene expression data from control liver extraction 2

tag: tissue

value: AAV8-TBG-iCre; mTmG


title: Control Mouse Liver p2 (27582)


title: Pcgf6KO

description: gene expression in Pcgf6KO mouse embryonic stem cell


title: Control Mouse Liver p1 (27579)

description: Gene expression data from control liver extraction 1

source_name: Excised Liver 1


title: wildtype

description: gene expression in wildtype mouse embryonic stem cell

value: wildtype


title: MIST1-LSL Mouse Liver p1 (27580)

description: Gene expression data from MIST1-LSL liver 1 extraction 1


title: EM_P18 of pregnancy_1

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description: Gene expression in EM Pregnant p18

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

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

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

organism: Bos taurus

source_name: Pregnant EM p18

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the endometrium using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Endometrium

tag: study

value: In vivo

tag: group

value: Pregnancy p18

tag: phase


title: EM_P18 of pregnancy_2

description: Gene expression in EM Pregnant p18


title: EM_D18 of the estrous cycle_3

description: Gene expression in EM cyclic d18

source_name: Cyclic EM d18

value: Non pregnant d18


title: aneurysm

city: Kyoto

first: Tomohiro

last: Aoki

address: Konoe-cho, Yoshida, Sakyo-ku

institute: Kyoto University

hyb_protocol: Gene Expression Hybridization Kit

scan_protocol: Agilent Feature Extraction

data_processing: normalization method

source_name: aneurysm lesion at 3 weeks after the induction

label_protocol: Low Input Quick Amp Labeling Kit, one-color

extract_protocol: Rneasy Fibrous Tissue Kit

value: aneurysm


title: EM_P18 of pregnancy_4

description: Gene expression in EM Pregnant p18


title: EM_D18 of the estrous cycle_2

description: Gene expression in EM cyclic d18


title: EM_P18 of pregnancy_3

description: Gene expression in EM Pregnant p18


title: EM_D18 of the estrous cycle_4

description: Gene expression in EM cyclic d18


title: EM_P15 of pregnancy_3

description: Gene expression in EM Pregnant p15

source_name: Pregnant EM p15

value: Pregnancy p15


title: EM_P15 of pregnancy_1

description: Gene expression in EM Pregnant p15


title: EM_D18 of the estrous cycle_1

description: Gene expression in EM cyclic d18


title: EM_P15 of pregnancy_2

description: Gene expression in EM Pregnant p15


title: EM_D15 of the estrous cycle_2

description: Gene expression in EM cyclic d15

source_name: Cyclic EM d15

value: Non pregnant d15


title: PC14 E+CD133+

city: Kaohsiung

first: Chao-Ju

last: Chen

state: Kaohsiung

address: No.100 , Tzyou 1st Road Kaohsiung 807 , Taiwan, 11F department of laboratory medicine

department: Laboratory medicine

country: Taiwan

institute: Kaohsiung Medical University Hospital

description: Gene expression data from epithelial type CD133+ stem-like cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: biotin

growth_protocol: Cells were cultured in 5% CO2 incubator at 37C

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 4 subpopulations cells from the non-small-cell lung cancer (PC14) cell line according to the E-cadherin and CD133 expression level by FACS

tag: cell line

value: NSCLC PC14 cell line

tag: cell subpopulation


title: PC14 E-CD133+

description: Gene expression data from mesenchymal type CD133+ stem-like cells


title: EM_D15 of the estrous cycle_3

description: Gene expression in EM cyclic d15


title: PC14 E+CD133-

description: Gene expression data from epithelial type CD133- non-stem like cells


title: EM_D15 of the estrous cycle_1

description: Gene expression in EM cyclic d15


title: control arterial wall

source_name: intracranial aeterial walls without treatment

value: normal


title: Control Mouse Liver p1 (27578)


title: EM_D15 of the estrous cycle_4

description: Gene expression in EM cyclic d15


title: control endometrial stromal cells of patient 6

status: Public on Jan 13 2017

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description:
TB7576
Bisulfite treated genomic DNA

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

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

data_processing:
Genome Studio software
Normalized Average Beta (background correction and normalization to internal controls using Genome Studio) and detection p-value

source_name: CESC 2

growth_protocol: Primary stromal cells were cultured on fibronectin-collagen (Gibco, Grand Island, NY) coated dishes in DMEM-F12 without phenol red (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine (Gibco) and 1% antibiotics –antimycotic (Gibco) up to passage 3. To exclude influences of the serum derived steroid hormones on DNA methylation and expression in the cultures, the cells were grown in culture medium containing 10% charcoal stripped fetal bovine serum (CS-FBS; Gibco).

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

tag: individual

value: patient 6

value: control

tag: site

value: Endometrial stroma

value: cell culture of endometrial stromal cells


title: PC14 E-CD133-

description: Gene expression data from mesenchymal type CD133- non-stem-like cells


title: control endometrial stromal cells of patient 7

description:
TB7577
Bisulfite treated genomic DNA

source_name: CESC 3

value: patient 7

tag: disease state


title: endometriotic stromal cells from ovarian ectopic sites of patient 4

description:
TB9107
Bisulfite treated genomic DNA

source_name: OESC 4

value: patient 4

value: endometriosis

value: Ectopic endometriotic stroma :ovary

value: cell culture of endometriotic stromal cells


title: endometriotic stromal cells from ovarian ectopic sites of patient 3

description:
TB7580
Bisulfite treated genomic DNA

source_name: OESC 3

value: patient 3


title: endometriotic stromal cells from ovarian ectopic sites of patient 2

description:
TB7579
Bisulfite treated genomic DNA

source_name: OESC 2

value: patient 2


title: control endometrial stromal cells of patient 5

description:
TB7575
Bisulfite treated genomic DNA

source_name: CESC 1

value: patient 5


title: RKO.UHRF1.d4

city: Baltimore

first: Stephen

middle: B

last: Baylin

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

hyb_protocol: standard as recommended by Illumina

scan_protocol: standard as recommended by Illumina

data_processing: Preprocessed by Bioconductor Minfi package. Computed normalized average beta with minfi.

label: standard as recommended by Illumina

label_protocol: standard as recommended by Illumina

growth_protocol: standard as recommended by ATCC

extract_protocol: standard pheno-chloroform method

value: RKO

value: colorectal cancer cells


title: HCT116_Uhrf1_10nM_DAC


title: 3AB12_MT1sh51_D10

description: HCT116_3Aknockout_3Bknockout_1/2DNMT1_DNMT1shRNA#51_day10


title: control endometrial stromal cells of patient 9

description:
TB9112
Bisulfite treated genomic DNA

source_name: CESC 5

value: patient 9


title: control endometrial stromal cells of patient 8

description:
TB9110
Bisulfite treated genomic DNA

source_name: CESC 4

value: patient 8


title: HCT116_10nM_DAC


title: MT3AB12


title: HCT116.UHRF1.d4


title: endometriotic stromal cells from ovarian ectopic sites of patient 1

description:
TB7578
Bisulfite treated genomic DNA

source_name: OESC 1

value: patient 1


title: DKO8_NS

description: HCT116 double knockout cells #8 (DNMT1hypomorph, DNMT3Bknockout)


title: HCT116.UHRF1.d14


title: HCT116_2.5_DNMT1_KD

description: HCT116_3Aknockout_3Bknockout_1/2DNMT1_DNMT1shRNA#49


title: 3AB12_MT1sh51_D9

description: HCT116_3Aknockout_3Bknockout_1/2DNMT1_DNMT1shRNA#51_day9


title: RKO.UHRF1.d14


title: DKO4

description: HCT116 double knockout cells #4 (DNMT1hypomorph, DNMT3Bknockout)


title: DKO3

description: HCT116 double knockout cells #3 (DNMT1hypomorph, DNMT3Bknockout)


title: HCT116_10nM_DAC_day2


title: HCT116_1um_DAC_day2


title: HCT116_100nm_DAC_day2


title: CM7F040P06.pl35

city: Saint Paul

first: Robert

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: Fast-neutron mutant/ wild-type parent comparison

hyb_protocol: Arrays are hybridized at 67C for approximately 72 hours at a rotation speed of 20rpm. Arrays are washed in Wash Buffer 1 for 5 minutes at room temperature, Wash Buffer 2 for 1.5 minutes at 37C, followed by a 1minute wash in room temperature Acetonitrile. All other processing follow Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

scan_protocol: Arrays are immediately and individually scanned using Roche NimbleGen MS200 array scanner using NimbleGen MS200 v1.2 acquisition software. The array is inserted “active side up” with a Scan Resolution of 2micons, Gain at 100% for both channels, Laser Intensity at 100% for both channels, Autogain is deselected and a Multi Tiff File Setting.

data_processing: Image extraction and grid alignment is done using Agilent Feature Extraction (FE) 12.0.0.7.  The CGH module portion of Agilent Genomic Workbench (AWB) 7.0.4.0 software is used to generate data.  Analysis settings include: Aberration Algorithm is ADM-2, Threshold is 6.0, Fuzzy Zero is selected, GC correction is selected with a window size of 2 Kb, Legacy is selected with a bin size of 10, Diploid Peak is deselected, Manually Reassign Peaks is deselected and Combine Intra-Array Replicates is selected. The Aberration Filter is set to call amplification or deletion as having 2 consecutive probes with an absolute log ratio greater or equal to +/- 1.

organism: Glycine max

label_protocol: Individual reactions with 500ng of Soybean DNA are labeled with Cy3 and Cy5 following Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

extract_protocol: Soybean DNA is extracted from approximately 90 mg of fresh, young tissue disrupted with mortar and pestle and liquid nitrogen. The tissue is processed using Qiagen DNeasy Plant Mini Kit catalog number 69106. The Qiagen protocol is followed with 2 elution’s of DNA from the column using 60uL – 50% AE / 50% Water.

value: Leaf


title: CM7F040P06.pl45


title: HCT116_3BcKO


title: 11553

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: subcutaneous adipose tissue

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

value: subcutaneous adipose tissue

value: male

tag: bmi

tag: whr

tag: ffmass

tag: totfa

tag: matsuda

tag: gfr

tag: homair

tag: systbp

tag: diastbp


title: 11614

tag: tissue

tag: gender

tag: age


title: 11485


title: 11596


title: 11441


title: MT3BKO_3A_cKO_2

tag: cell line

tag: cell type


title: MT3BKO_3A_cKO_1


title: CM7F040P05.pl15


title: 11436


title: 11404


title: MT1hypo.MT1sh51.d12


title: 11401


title: 11658


title: 11445


title: 11418


title: 11295


title: HCT116_3B_KO


title: RKO.MT1sh51.d11


title: RKO.MT1sh51.d5


title: DKO2_NS

description: HCT116 double knockout cells #2 (DNMT1hypomorph, DNMT3Bknockout)


title: 11123


title: HCT116.MT1sh49.d12


title: HCT116_3A_KO_2


title: MT1hypo.MT1sh49.d12


title: RKO.NS

description: RKO

source_name: RKO


title: 11381


title: HCT116.NS


title: MT1hypo.NS


title: 11113


title: 11054


title: CM7F040P05.pl39


title: 11027


title: HCT116.MT1sh51.d12


title: 11047


title: 11000


title: 10995


title: 11008


title: 11260


title: 11063


title: 10929


title: 10974


title: 11138


title: 10896


title: 11010


title: HCT116.MT1sh51.d4


title: 11132


title: HCT116_3A_KO_1


title: 10875


title: 10830


title: 10888


title: 10790


title: 10805


title: 10886


title: 10829


title: 11003


title: 10781


title: 10738


title: 10715


title: 10786


title: 10732


title: 10754


title: 10706


title: 10697


title: 10704


title: 10685


title: 10691


title: 10682


title: 10675


title: 10662


title: 10624


title: 10665


title: 10437


title: 10548


title: 10631


title: 10409


title: 10420


title: 10451


title: 10472


title: 10534


title: 10450


title: 10575


title: 10425


title: 10486


title: 10419


title: 10510


title: 10390


title: 10618


title: 10417


title: 10664


title: 10551


title: 10463


title: 10565


title: 10567


title: 10598


title: 10521


title: 10389


title: 10525


title: 10385


title: 10365


title: 10743


title: 10377


title: 10277


title: 10322


title: 10309


title: 10177


title: 10348


title: 10381


title: 10217


title: 10211


title: 10267


title: 10100


title: 10292


title: 10243


title: 10373


title: 10156


title: 10314


title: 10247


title: 10271


title: 10276


title: 10190


title: 10133


title: 10245


title: 10252


title: 10070


title: 10112


title: 10122


title: 10063


title: 10061


title: 10012


title: 8286


title: 8244


title: 8120


title: 10050


title: 7997


title: 8280


title: 10039


title: 8119


title: 8133


title: 8167


title: 7948


title: 7927


title: 8229


title: 8006


title: 8126


title: 7996


title: 7988


title: 7856


title: 7894


title: 7954


title: 8067


title: 8324


title: 7985


title: 7955


title: 7866


title: 7863


title: 7811


title: 7797


title: 7848


title: 7769


title: 7801


title: 7707


title: 7717


title: 7768


title: 7791


title: 7675


title: 7626


title: 7742


title: 7624


title: 7672


title: 7611


title: 7530


title: 7657


title: 7517


title: 7600


title: 7573


title: 7501


title: 7651


title: 7491


title: 7498


title: 7471