title: HDF_OSK+let-7_inh_TRA(+)_day11

city: San Francisco

first: Kathleen

middle: A

last: Worringer

state: CA

address: 1650 Owens St.

institute: Gladstone Institutes

description:
Gene expression after 11 days of reprogramming
OSK+let-7 Inh US94000320_252800419216_S01_GE1_107_Sep09_2_2

hyb_protocol: Manufacturer's protocol

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

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: TRA-1-60+ cells 11 days post-infection with OSK + let-7 inhibitor

label_protocol: Manufacturer's protocol

growth_protocol: DMEM containing 10% fetal bovine serum (days 0-7) or Primate ESC medium (ReproCELL) supplemented with 4ng/mL bFGF (days 8-11 and hESCs) at 37 deg C in a humidified incubator with 5% CO2.

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

treatment_protocol: Human dermal fibroblasts were transduced with the indicated combinations of GFP, OCT4, SOX2, KLF4, cMYC, and LIN-41 retroviruses (day 0). On days 1 and 6, OSK+control or OSK+let-7inh plates were transfected with control or let-7 inhibitor, respectively. On day 11, TRA-1-60 positive cells were collected.

value: human dermal fibroblasts (HDFs)

tag: transfected with

value: OSK + let-7 inhibitor


title: Breast control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep4

status: Public on Nov 20 2013

type: RNA

city: Tucson

first: Vincent

last: Gardeux

state: AZ

address: 1657 East Helen Street, PO Box 210240

department: Medicine

country: USA

institute: University of Arizona

description: Gene expression data

hyb_protocol: Hybridization were performed following Affymetrix protocols

scan_protocol: standard Affymetrix protocol

data_processing: The raw data were normalized according to the Robust Multiple-array Average (RMA) technique using Affymetrix Power Tools (APT).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer cell line MDA-MB231

label_protocol: Labeling of cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine in a humid environment at 37°C, with 5% CO2.

extract_protocol: For each of the cell lines, MDA-MB231 and A2780, total RNAs were extracted from four biological replicates of PTBP1-depleted cells, PTBP1-KD (4× PTBP1/+DOX) and eight biological replicates control cells (4× PTBP1/-DOX and 4× LUCshRNA/+DOX) by Direct-zol RNA kit (Zymo Research, Irvine, CA) . All paired samples consist of PTBP1-depleted cells (PTBP1-KD) and matched control cells. Qualities of RNA were assessed based on the RNA quality indicator (RQI ≥ 8) using Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA).

treatment_protocol: In order to analyze the effect of PTBP1 depletion, two consecutive viral transductions were performed in both MDA-MB231 and A2780 cell lines. Cells were plated on 24-well plate (10-20×104 cells/well), maintained in culture for 16 hours, and then medium containing LV-tTR/KRAB-Red lentiviral particles was added. Following 16 h of incubation, cells were transduced a second time by LV-THM/PTBshRNA or LV-THM/LUCshRNA lentiviral particles. Clones expressing both red and green fluorescent protein (dsRED and GFP respectively) were selected and expanded. Following 16 h of incubation, cells were washed and split in two subcultures, one without doxycycline (PTBP1/-DOX; Control , express PTBP1 WT) and the other with Doxycycline (DOX) at a final concentration of 1 μg/ml (PTBP1/+DOX; PTBP1-KD). Doxycycline was prepared according to the manufacturer’s recommendations (Sigma-Aldrich, St. Louis, MO). Five days later, cells were analyzed by fluorescence microscopy, and PTBP1 gene expression was assessed using PCR and Western Blotting (data not shown). The cells that were transduced by LV-LUCshRNA express PTBP1 regardless of the presence of DOX (LUCshRNA/+DOX). Constructs and lentivirus preparation were performed as previously described

tag: tissue

value: Epithelial, breast adenorcinoma

tag: cell line

value: Breast cancer cell line MDA-MB231

tag: age

value: derived from breast adenocarcinoma of female 51 years adult

tag: treatment


title: TRAIL R2 siRNA R2si_40h_1

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: miRNA expression profiles from cell culture

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: Panc1 cells, treated with TRAIL R2 siRNA for 40h

growth_protocol: Cells were cultured as previously described (Trauzold et al., 2001). For transient transfections DharmaFECT1 transfection reagent (Thermo Scientific, Dharmacon Epsom, UK; Panc1, MDA-MB-231, HCT116 cells) or NeoFX (Ambion, Applied Biosystems, Germany; Panc89 cells) were used. The in vitro differentiation assay of A818-6 cells was performed as described (Lehnert et al., 2001).

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: Panc1 cells were treated for 40h with siRNA (On-Targetplus® smart pool siRNA; Dharmacon) against TRAIL-R2 or with control siRNA in experimental setups with 5 biological replicates per group.

value: TRAIL R2 siRNA


title: Breast control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep1

description: Gene expression data


title: HDF_OSKM_TRA(+)_day11

description:
Gene expression after 11 days of reprogramming
OSKM US94000320_252800419243_S02_GE1_107_Sep09_2_3

source_name: TRA-1-60+ cells 11 days post-infection with OSKM

tag: cell type

value: OSKM


title: HDF_OSK+control_inh_TRA(+)_day11

description:
Gene expression after 11 days of reprogramming
OSK+Control Inh US94000320_252800419216_S01_GE1_107_Sep09_2_1.txt

source_name: TRA-1-60+ cells 11 days post-infection with OSK + control inhibitor

value: OSK + control inhibitor


title: Breast control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep3

description: Gene expression data


title: H1_hESC

description:
human embryonic stem cell 1 gene expression
H1 hESC US94000320_252800419217_S01_GE1_107_Sep09_1_1

source_name: human embryonic stem cell 1

value: pluripotent human embryonic stem cells (hESCs)


title: HDF_OSK+LIN-41_TRA(+)_day11

description:
Gene expression after 11 days of reprogramming
OSK+LIN41 US94000320_252800419243_S02_GE1_107_Sep09_2_4

source_name: TRA-1-60+ cells 11 days post-infection with OSK + LIN-41

value: OSK + LIN-41


title: Breast control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep2

description: Gene expression data


title: HIP1

type: SRA

city: Lausanne

first: Marion

last: LELEU

address: Station 15

country: Switzerland

institute: EPFL

description:
Primer name: HIP1_4C_seq_R
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT GTAGTGAGCGGGGGCATT
Primer name: HIP1_4C_seq_F
Sequence: CAAGCAGAAGACGGCATACGAGTTGGGCACCTGCTTCAT

library_source: genomic

data_processing:
Reads were normalized to the total number of reads. Smoothed data were obtained by applying a running mean algorithm with 19 fragments per window.As the data from the three replicated viewpoints were strongly correlated,  we used the average of each fragments for these experiments.
We used a domainogram algorithm to detect significantly interacting regions without imposing a fixed window size as suggested in [de Wit et al, Global chromatin domain organization of the Drosophila genome, PLoS Genet. 2008 Mar 28;4(3)]. The positive signals were ranked per chromosome and Bricks (Blocks of Regulators In Chromosomal Kontext) were called based on a FDR threshold of 0.1 for “short-range” interactions, defined as interactions within 2.5 Mb up- and downstream of GBAS and MDH2, the first and last viewpoint, respectively (HSA7 coordinates: 53,532,296-78,116,172; about 25 Mb around the WBSCR). Genomic space outside of these borders was called the “long-range” region. As interactions in this long-range region are more subject to random interactions, we used a more stringent FDR threshold of 0.001. To determine differentially interacting regions between the WBS and Ctrl cells, we first computed the log2 ratio of WBS over Ctrl of the smoothed profile corrected data and selected ratio Bricks (as described above) that were specific to either WBS or Ctrl.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: The 2 "smoothed" files correspond to smoothed data for 2 conditions (WT and WBS), while file "ratios_selectedBricks.bedGraph" is a list of significantly interacting regions obtained as described above.

molecule: genomic DNA

source_name: EBV transformed mononuclear cells from peripheral blood

growth_protocol: Lymphoblastoid cell lines were grown in RPMI1640 medium supplemented with 10% FCS and 1% PS

extract_protocol:
50 million exponentially growing cells were harvested and crosslinked with 1% formaldehyde, lysed and cut with the restriction enzyme BglII. After ligation and reversal of the crosslinks, the DNA was purified to obtain the 3C library. This 3C library was further digested with NlaIII and circularized to obtain a 4C library. The inverse PCR primers to make the 4C-seq templates were designed to contain the Illumina adaptor tails, as well as the bait-specific sequences for each of the six loci we interrogated. 4C libraries were multiplexed (three samples per mulitplex), libraries were prepared according to Illumina's instructions for ChIP-seq but without size selection and sequenced on Illumina GAIIxl (76-mer single end tags)
Instrument model: Illumina GAIIxl
library_strategy: 4C-seq

value: Lymphoblastoid cells

tag: control lymphoblastoid cell line id

tag: wbs lymphoblastoid cell line id

tag: interrogated locus


title: PGK-233

city: Seville

first: Purificacion

last: Estevez-Garcia

state: Seville

address: Manuel Siurot avenue

department: Molecular Oncology

country: Spain

institute: Institute of Biomedicine

description: test

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: colorectal cell fraction

label_protocol: FAM.

extract_protocol: All colorectal tissue samples were maintained at -80ºC until RNA extraction and grinded under liquid nitrogen. Homogenization was achieved using QIAshredder homogenizers and total RNA was extracted using RNeasy Mini kit (both kits from Qiagen Inc; Valencia, CA, USA).

tag: response to chemotherapy

value: NON-RESPONDER

value: colorectal cancer tumor


title: KCTD7

description:
Primer name: KCTD7_4C_seq_F
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT CT TTCAGAGCTCACCAAGGTTTG
Primer name: KCTD7_4C_seq_R
Sequence: CAAGCAGAAGACGGCATACGACCAGCCACGTACTCTGAAAA


title: PGK-229

description: test


title: PGK-231

description: test

value: RESPONDER


title: Breast control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep3

description: Gene expression data


title: PGK-225

description: test


title: HDF_GFP(+)_day11

description:
Gene expression after 11 days of reprogramming
HDF+GFP US94000320_252800419217_S01_GE1_107_Sep09_1_2

source_name: GFP-positive cells 11 days after infection with GFP

value: GFP alone


title: Breast control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep1

description: Gene expression data


title: Breast control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep2

description: Gene expression data


title: ASL

description:
Primer name: ASL_4C_seq_F3
Sequence: CAAGCAGAAGACGGCATACGA GCTCCAGTGATCAGGACCAG
Primer name: ASL_4C_seq_R3
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT TGGGTTGAATGAGCAACAGT

value: ASL


title: PGK-223

description: test


title: PGK-219

description: test


title: PGK-221

description: test


title: PGK-217

description: test


title: PGK-215

description: test


title: PGK-213

description: test


title: Breast control Luc, PTBP1 wildtype,Dox treated, biological rep3

description: Gene expression data

value: control Luc, PTBP1 wildtype, Dox treated


title: PGK-211

description: test


title: PGK-209

description: test


title: PGK-203

description: test


title: Switchgrass_rep3

city: Amherst

first: Jeffrey

middle: L

last: Blanchard

state: MA

address: 203 Morrill Science Center IVN

department: Biology

institute: University of Massachusetts Amherst

hyb_protocol: The labeled cDNA samples were hybridized on the arrays according to Affymetrix guidelines.

scan_protocol: The hybridized arrays were scanned with a GeneChip Scanner 3000.

data_processing: The resulting raw spot image data files were processed into pivot and quality report files using Microarray Suite version 5.0.   Expression values were calculated using the Custom Array Analysis Software (CAAS) package (http://www.sourceforge.net/projects/caas-microarray/) that implements the Robust Multichip Average method.  The quality of the microarray datasets were analyzed using probe-level modeling procedures provided by the affyPLM package in BioConductor.  No image artifacts due to array manufacturing or processing were observed.  In summary, all quality control checks indicated that the RNA purification, cDNA synthesis, labeling and hybridization procedures adapted for use in C. phytofermentans resulted in high quality data.

organism: Lachnoclostridium phytofermentans

label_protocol: Ten μg total RNA from each sample was used as template to synthesize labeled cDNAs using Affymetrix GeneChip DNA Labeling Reagent Kits.

growth_protocol: C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20]. Growth on anaerobic medium derived from GS-2 containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH. This medium was supplemented with 0.3% (wt/vol) of the specific substrate added as a filter-sterilized solution to the sterile medium. Broth cultures were incubated at 30˚C under anaerobic conditions (100% N2) as described in by Hungate. RNA was purified from mid-exponential phase cultures.

extract_protocol: RNA was isolated from three replicates of each type of culture at mid exponential phase.  Briefly, cells were flash-frozen by immersion in liquid nitrogen, harvested by centrifugation for 5 min at 8,000 rpm at 4°C and re-suspended in 100 µl in TE buffer pH 8 (EMD Chemicals) containing 2 mg/ml lysozyme (Sigma-Aldrich) and incubated at 37°C for 40 min.  Total RNA was isolated using the RNeasy RNA purification kit (QIAGEN) according to the manufacturer’s instructions.  Contaminating DNA in total RNA preparations was removed with RNase-free DNase I (QIAGEN).

tag: culture condition

value: Switchgrass


title: Corn_stover_rep2


title: PGK-199

description: test


title: Corn_stover_rep3


title: Switchgrass_rep1


title: GBAS

description:
Primer name: GBAS_4C_seq_F
Sequence: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT TTCTAAGCGGACATTTTCCT
Primer name: GBAS_4C_seq_R
Sequence: CAAGCAGAAGACGGCATACGAgtgtggtgattcatccctgt

value: GBAS


title: Switchgrass_rep2


title: Corn_stover_rep1


title: Breast control Luc, PTBP1 wildtype,Dox treated, biological rep4

description: Gene expression data

value: Epithelial, breast adenorcinoma


title: Ovarian control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep2

description: Gene expression data

source_name: Ovarian carcinoma cell line A2780

value: Epithelial, ovarian carcinoma

value: Ovarian carcinoma cell line A2780

value: derived fromtumour tissue of an untreated patient (age and gender not available)


title: Ovarian control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep3

description: Gene expression data


title: HT29 miR-146a rep_2

city: Taipei

first: Wei-Lun

last: Hwang

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

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 Plus 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: RMA through R-based affy module.

label: Biotin

source_name: colon cancer cells, miR-146a expression

label_protocol: Biotinylated cRNA was generated using standard Affymetrix protocols.

growth_protocol:
The medium for this cell line is 10% FBS-DMEM.
atmosphere: air, 95%; carbon dioxide (CO2), 5%
temperature: 37.0°C

extract_protocol: Total RNA were extracted by the RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected to reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.

treatment_protocol: HT29 cells were transduced with an miR-146a expression construct using a lentivirus system.

tag: transduction

value: miR-146a expression construct


title: Ovarian control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep3

description: Gene expression data


title: Breast control Luc, PTBP1 wildtype,Dox treated, biological rep2

description: Gene expression data

value: Breast cancer cell line MDA-MB231

value: derived from breast adenocarcinoma of female 51 years adult


title: Breast control Luc, PTBP1 wildtype,Dox treated, biological rep1

description: Gene expression data


title: Ovarian control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep1

description: Gene expression data


title: Ovarian control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep4

description: Gene expression data


title: HT29 miR-146a rep_1


title: PGK-197

description: test


title: HT29-vector

source_name: colon cancer cells, control

treatment_protocol: HT29 cells were transduced with an empty vector using a lentivirus system.

value: empty vector


title: PGK-205

description: test


title: Ovarian control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep2

description: Gene expression data


title: Ovarian control PTB shRNA, PTBP1 wildtype, no Dox treated, biological rep1

description: Gene expression data


title: Ovarian control PTB shRNA, PTBP1 knockdown, Dox treated, biological rep4

description: Gene expression data


title: Glucose_rep3

value: Glucose


title: Ovarian control Luc, PTBP1 wildtype,Dox treated, biological rep4

description: Gene expression data


title: Glucose_rep2


title: CO-149

description: test


title: CO-143

description: test

value: NON-RESPONDER


title: CO-141

description: test

value: colorectal cancer tumor


title: Glucose_rep1


title: CO-139

description: test

value: RESPONDER


title: CO-156

description: test


title: Xylose_rep1

growth_protocol: C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20]. Growth on single carbon-source utilized anaerobic medium derived from GS-2CB and containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH. This medium was supplemented with 0.3% (wt/vol) of the specific substrate added as a filter-sterilized solution to the sterile medium. Broth cultures were incubated at 30˚C under anaerobic conditions (100% N2) as described in by Hungate [30]. Growth was determined spectrophotometrically by monitoring changes in optical density at 660 nm. RNA was purified from mid-exponential phase cultures.

extract_protocol: RNA was isolated from two replicates of each type of culture at mid exponential phase.  Briefly, cells were flash-frozen by immersion in liquid nitrogen, harvested by centrifugation for 5 min at 8,000 rpm at 4°C and re-suspended in 100 µl in TE buffer pH 8 (EMD Chemicals) containing 2 mg/ml lysozyme (Sigma-Aldrich) and incubated at 37°C for 40 min.  Total RNA was isolated using the RNeasy RNA purification kit (QIAGEN) according to the manufacturer’s instructions.  Contaminating DNA in total RNA preparations was removed with RNase-free DNase I (QIAGEN).

tag: carbohydrate source

value: Xylose


title: TAMs sorted from imatinib resistant human GIST_HG113

city: New York

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. The data were analyzed with MAS 5.0 algorithm using Affymetrix Gene Expression Console.

source_name: TAMs sorted from imatinib resistant GIST

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: Tumors were obtained freshly from the operating room from consenting patients using an IRB approved protocol.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) was used to isolate RNA.

treatment_protocol: Tumors were obtained from humans diagnosed with GIST that were untreated, or sensitive to imatinib, or resistant to imatinib based on RECIST criteria.

value: gastrointestinal stromal tumor (GIST)

value: freshly sorted tumor associated macrophages (TAMs)


title: CO-71

description: test


title: Pectin_rep2

value: Pectin


title: Xylose_rep2


title: TAMs sorted from imatinib resistant human GIST_HG108


title: CO-144

description: test


title: Ovarian control Luc, PTBP1 wildtype,Dox treated, biological rep2

description: Gene expression data

value: control Luc, PTBP1 wildtype, Dox treated


title: Xylan_rep1

value: Xylan


title: TAMs sorted from imatinib resistant human GIST_HG106


title: Xylan_rep2


title: Ovarian control Luc, PTBP1 wildtype,Dox treated, biological rep3

description: Gene expression data

value: Epithelial, ovarian carcinoma


title: TAMs sorted from imatinib sensitive human GIST_HG119

source_name: TAMs sorted from imatinib sensitive GIST


title: Ovarian control Luc, PTBP1 wildtype,Dox treated, biological rep1

description: Gene expression data

value: Ovarian carcinoma cell line A2780


title: TAMs sorted from imatinib sensitive human GIST_HG128


title: TAMs sorted from imatinib sensitive human GIST_HG114


title: TAMs sorted from imatinib sensitive human GIST_HG133


title: TAMs sorted from imatinib sensitive human GIST_HG112


title: TAMs sorted from imatinib resistant human GIST_HG130


title: CO-69

description: test


title: treated group, biological rep3

city: Xiamen

first: Tingwu

last: Liu

address: Siming Road 422

country: China

institute: Xiamen university

description: simulated acid rain group

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

scan_protocol: Image processing was performed using Affymetrix GeneChip Operating System (GCOS).

data_processing: Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using RMA implemented in R language using standard settings. Statistical testing for differential expression was performed with logic-t analysis.

organism: Arabidopsis thaliana

source_name: simulated acid rain treated group, biological rep3

label_protocol: Double-stranded cDNA was synthesized from 5 μg of template total RNA using the One-Cycle cDNA Synthesis kit (Affymetrix), and biotin labeled cRNA was synthesized using the IVT Labeling kit (Affymetrix).

growth_protocol: Seeds of Arabidopsis thaliana, ecotype Columbia-0 (Col-0) were planted in the mixed matrix with vermiculite and cover soil (2:1) after vernalization. Then, plants were grown in controlled growth chamber with a light/dark regime of 16/8 hr, temperature of 23/20°C and a light intensity of 150 μmol m-2 s-1 photosynthetically active radiation (PAR).

extract_protocol: 20 mg of total RNA from leaves of Arabidopsis with or without AR treatment was extracted using the RNeasy plant mini kit (Qiagen), and the product was used to make biotin-labeled cRNA targets.

treatment_protocol: The seedlings were sprayed by simulated acid rain (AR, pH 3.0) at 5 ml per seedling, meanwhile, the seedlings were sprayed with control solution (CK, pH 5.6) which had the same ion composition as AR. The AR solution was prepared from H2SO4 and HNO3 in the ratio of 5 to 1 by chemical equivalents, which represents the average ion composition of rainfall in South China

tag: ecotype

tag: genotype

value: wild-type


title: Pectin_rep1


title: treated group, biological rep2

description: simulated acid rain group

source_name: simulated acid rain treated group, biological rep2


title: TAMs sorted from untreated human GIST_HG138

source_name: TAMs sorted from untreated GIST


title: CO-65

description: test


title: treated group, biological rep1

description: simulated acid rain group

source_name: simulated acid rain treated group, biological rep1


title: Mannose_rep2

value: Mannose


title: CO-61

description: test


title: Mannose_rep1


title: CO-59

description: test


title: CO-53

description: test


title: Galactose_rep2

value: Galactose


title: Control group, biological rep2

description: control group

source_name: Control group, biological rep2


title: Galactose_rep1


title: TAMs sorted from untreated human GIST_HG135


title: Control group, biological rep1

description: control group

source_name: Control group, biological rep1


title: TAMs sorted from untreated human GIST_HG132#1


title: Control group, biological rep3

description: control group

source_name: Control group, biological rep3


title: CO-48

description: test


title: CO-49

description: test


title: Cellulose_rep2

value: Cellulose


title: Cellulose_rep1


title: CO-47

description: test


title: CO-45

description: test


title: Cellobiose_rep2

value: Cellobiose


title: TAMs sorted from untreated human GIST_HG120


title: Cellobiose_rep1


title: CO-43

description: test


title: TAMs sorted from untreated human GIST_HG127


title: TAMs sorted from untreated human GIST_HG117


title: induced delta 1

city: Cambridge

first: Weida

last: Li

address: 7 Divninity Avenue

institute: Harvard University

description: replicate 1

hyb_protocol: Hyb protocol for Illumina MouseRef-8 v2.0 expression beadchip

scan_protocol: Scan protocol for Illumina MouseRef-8 v2.0 expression beadchip

data_processing: The raw signal was  quantile-normalized across samples in R.

organism: Mus musculus

source_name: Pancreas

label_protocol: label protocol for Illumina MouseRef-8 v2.0 expression beadchip

growth_protocol: Rag1-/- were obtained from Jackson Labs.  For delta- cell induction, 100ul (>1x 109 pfu) of purified adenovirus was directly injected into the splenic lobe of the dorsal pancreas.

extract_protocol: Cherry+  induced beta cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience), RNA samples were extracted by Trizol

treatment_protocol: Pancreata were perfused through the common bile duct.  After removing endogenous islets, the acinar fraction was digested with liberase and Elastase. Roche) into single cells.

value: Pancreas


title: CO-41

description: test

value: NON-RESPONDER


title: TAMs sorted from untreated human GIST_HG132#2


title: 12 Bladder healthy tissue

city: Moscow

first: Anastasia

last: Zabolotneva

address: Miklukho-Maklaya 16/10

country: Russia

institute: Intitute of Bioorganic chemistry

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Bladder healthy tissue

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

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

tag: Sex

value: male

tag: disease state

value: Healthy bladder tissue


title: Brachypodium_distachyon_rep2


title: CO-35

description: test

value: colorectal cancer tumor


title: CO-39

description: test


title: induced delta 2

description: replicate 2


title: Brachypodium_distachyon_rep1


title: TAMs sorted from untreated human GIST_HG129

value: gastrointestinal stromal tumor (GIST)


title: L-Arabinose_rep2

value: L-Arabinose


title: TAMs sorted from untreated human GIST_HG101

value: freshly sorted tumor associated macrophages (TAMs)


title: 2.2. Bladder cancer tissue

source_name: Bladder cancer tissue

value: II stage, T2bNxM0, G2/G3, reccurence


title: 10 Bladder healthy tissue


title: 11 Bladder healthy tissue


title: TAMs sorted from untreated human GIST_HG110


title: induced delta 3

description: replicate 3


title: TAMs sorted from untreated human GIST_HG100


title: 7. Bladder cancer tissue

value: III/IV stage, T4aNxMx, G3, reccurence + renal cancer IV stage T3N2M0, G3


title: CO-34

description: test

source_name: colorectal cell fraction

value: RESPONDER


title: 6. Bladder cancer tissue

value: III stage, T3aN0M0, G1/G2, reccurence


title: 8. Bladder cancer tissue

value: IV stage, T4aN2M0, G3, reccurence


title: 5. Bladder cancer tissue

value: IV stage, T4aN1M0, G3


title: Experimental Evolution founder

source_name: Experimental Evolution founder

growth_protocol: C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20]. Growth on cellobiose utilized anaerobic medium derived from GS-2CB and containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH. This medium was supplemented with 0.3% (wt/vol) of the specific substrate added as a filter-sterilized solution to the sterile medium. Broth cultures were incubated at 30˚C under anaerobic conditions (100% N2) as described in by Hungate [30]. Growth was determined spectrophotometrically by monitoring changes in optical density at 660 nm. RNA was purified from mid-exponential phase cultures.

value: founder


title: Butyrate_rep2

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

scan_protocol: Affymetrix Gene ChIP Scanner G3000

data_processing: Data were processed using RMA algorithm with R package Bioconductor.

source_name: C57BL/6 Splenic CD4+ Naïve T cells

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

growth_protocol: RPMI1640 supplemented with 10%FCS, antibiotics, IL-2 and TGF-beta

extract_protocol: QIAGEN Rneasy micro

treatment_protocol: 0.1 mM Butyrate

tag: strain

tag: genotype/variation

value: Wild type

value: Splenic CD4+ Naïve T cells

tag: culture conditions

value: Treg-inducing condition

tag: agent

value: Butyrate


title: Butyrate_rep1


title: CO-33

description: test

tag: tissue


title: TAMs sorted from untreated human GIST_HG98

tag: cell type


title: 4. Bladder cancer tissue

value: male

tag: age

value: III stage, T4aNxM0, G3, reccurence


title: CO-32

description: test

value: NON-RESPONDER

value: colorectal cancer tumor


title: Experimental Evolution line C

source_name: Experimental Evolution line C

value: line C


title: L-Arabinose_rep1

value: L-Arabinose


title: CO-31

description: test


title: Experimental Evolution line B

source_name: Experimental Evolution line B

value: line B


title: Experimental Evolution line A

source_name: Experimental Evolution line A

value: line A


title: CO-30

description: test

value: RESPONDER


title: Control_rep2

value: Control


title: Control_rep1


title: 3. Bladder cancer tissue

value: II stage, T2N0M0, G2


title: 2. Bladder cancer tissue

value: female

value: I stage, T1N0M0, G3


title: CO-27

description: test


title: CO-29

description: test


title: CO-26

description: test


title: CO-21.1-3

description: test


title: CO-25

description: test


title: CO-28

description: test


title: CO-22.1

description: test


title: ZR-75-1 Cells with shGFP #2

city: Seoul

first: Han-Woong

last: Lee

address: Yonsei university, Yonseiro 50

department: Biochemistry

country: South Korea

institute: Yonsei University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were processed using Affymetrix GCOS software and normalized with RMA method. RMA files were imported into GeneSpring 7.3 software (Agilent Technologies) and further analyzed.

source_name: ZR-75-1 with shGFP

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Cells were grown in RPMI 1640 with 10% FBS, 5% penicillin/streptomycin

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen).

treatment_protocol: No Chemicalls were treated

tag: treatment

value: shGFP

tag: cell line

value: ZR-75-1 Breast Cancer Cells


title: CO-15.1

description: test

tag: response to chemotherapy


title: TAMs sorted from vehicle control tumors, biological replicate#2

description: SAMPLE 2

source_name: TAMs sorted from vehicle control tumors

growth_protocol: GIST mice were maintained under standard specific pathogen free conditions.

treatment_protocol: Some mice were treated with imatinib 600 mg/L in the drinking water.

value: gastrointestinal stromal tumor (GIST)

value: freshly sorted tumor associated macrophages (TAMs)


title: CO-14.2-3

description: test


title: ZR-75-1 Cells with shGFP #1


title: TAMs sorted from imatinib treated tumors, biological replicate#2

description: SAMPLE 4


title: CO-18.1

description: test


title: TAMs sorted from vehicle control tumors, biological replicate#1

description: SAMPLE 1


title: ZR-75-1 Cells with shEI24 #2-2

source_name: ZR-75-1 with shEI24


title: 1.2. Bladder cancer tissue

value: male

value: III stage, T3bN0M0, G2


title: E12.5 XY GFP sort control rep3

city: Cincinnati

first: Tony

last: DeFalco

state: OH

address: 3333 Burnet Avenue, MLC 7045

department: Division of Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from E12.5 control intersitial cells/macrophages

hyb_protocol: Hybridization was performed via standard Affymetrix protocols by the Duke IGSP Microarray Core Facility.

scan_protocol: GeneChips were scanned by the Duke IGSP Microarray Core Facility.

data_processing: The data were analyzed with Affymetrix Expression Console Version 1.1, using 3' Expression array standard/default RMA methods.

source_name: control interstitial cells/macrophages

label_protocol: RNA was submitted to the Duke IGSP Microarray Core Facility for the standard Affymetrix protocol from approximately 100-200ng total RNA.

growth_protocol: E12.5 control;Mafb-GFP and c-Maf-/-;Mafb-GFP gonads+mesonephroi were dissected in PBS.

extract_protocol: Total RNA was extracted via Qiagen RNeasy Micro Kit as per manufacturer's instructions.

treatment_protocol: Samples were trypsinized to single cell suspension and subjected to FACS sorting. See Jameson et al., 2012. PLoS Genet. 8(3):e1002575. PMID: 22438826.

value: GFP+ FACS-sorted gonad/mesonephros cells

value: c-Maf+/-;Mafb-GFP+/-

tag: genetic background

value: mixed background of mostly C57BL/6 with some potential BALB/c and CD-1


title: Parental ZR-75-1 Cells #2

source_name: Parental ZR-75-1


title: Nr14_gl11_v5

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

description: enriched guard cell fraction of Arabidopsis thaliana

hyb_protocol: Samples were hybridized on an Agilent Platform using the Agilent Arabidopsis V4 (design number 021169) microarray chips (http://www.agilent.com) with one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006).

scan_protocol: Agilent Microarray Scanner,extended dynamic range (XDR) at high resolution (5 µm)

data_processing: Data sets were extracted by the feature extraction software package (v9.5.3.1/ Agilent Technologies) using a standard protocol. Subsequently data were normalized using quantile-quantile as normalization method (bioconductor package "preprocessCore").

source_name: gl1-1; replicate 2

label_protocol: One-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)

growth_protocol: Arapidopsis thaliana  plants were grown in soil and cultivated in a greenhouse under short-day conditions (8 h light/16 h darkness, 22°C/16°C) with illumination by 100 µmol m-2 sec-1 white light. Samples were collected after 5h of illumination.

extract_protocol: RNeasy Plant Mini Kit, according to the manufacturers protocol


title: CO-13.1-2

description: test

value: colorectal cancer tumor


title: TAMs sorted from imatinib treated tumors, biological replicate#1

description: SAMPLE 3


title: ZR-75-1 Cells with shEI24 #1-2


title: Nr15_gl11

source_name: gl1-1; replicate 3


title: ZR-75-1 Cells with shEI24 #1-1


title: E12.5 XY GFP sort control rep2


title: E12.5 XY GFP sort c-Maf mutant rep3

description: Gene expression data from E12.5 c-Maf mutant intersitial cells/macrophages

source_name: c-Maf mutant interstitial cells/macrophages

value: c-Maf-/-;Mafb-GFP+/-


title: ZR-75-1 Cells with shEI24 #2-1


title: CO-10.1-4

description: test


title: E12.5 XY GFP sort c-Maf mutant rep1


title: Parental ZR-75-1 Cells #1


title: Nr13_gl11_v5

source_name: gl1-1; replicate 1


title: CO-11-2

description: test


title: CO-12-2

description: test

value: NON-RESPONDER


title: CO-6.2-2

description: test

value: RESPONDER


title: E12.5 XY GFP sort c-Maf mutant rep2


title: CO-5.2-2

description: test


title: CO-4.2

description: test


title: SW480-Vector control cells

hyb_protocol: Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA) were hybridized to arrays with Phalanx hybridization buffer. After 16 hrs hybridization at 37C, non-specificc binding targets were washed away by three different washing steps (Wash 1 37C 5 mins; Wash 2 37C 5 mins, 25C 5mins; Wash 3 rinse 20 times), and the slides were dried by centrifugation and scanned for data acquisition.

scan_protocol: Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) was applied for scanning. The Cy5 fluorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: The signal intensity of each spot was process by R program. We filtered out spots that the flag <0. Spots that passed the criteria were normalized by 75% media scaling normalization method. Normalized spot intensities were exported for analysis.

source_name: SW480-Vector control cells

label_protocol: Kreatech's ULS microRNA Labeling Kit was applied for labeling and labeling efficiency more than 15 was used for hybridization. The labeling efficiency are calculated by the concentration of CyDye and RNA measured by NanoDrop ND-1000. Each of the arrays submitted (SW480-vec and SW480-Snail) is labeled only with Cy5 for hybridization. Cy3 is not labeled onto our sample and considered as negative control in scanning.

extract_protocol: The total RNA was extracted by TRIzol reagent (invitrogen) according to the manufacture's guideline. Only quality RNA (260/280>1.8, 260/230>1.8, RIN>8) was used for further experiments. Optical density was measured by NanoDrop ND-1000, RIN score was given by Agilent RNA 6000 Nano Assay.

value: Colon cancer

tag: transfection

value: vector control


title: Nr11_slac15

source_name: slac1-3; replicate 2


title: SW480-Snail transfected cells

source_name: SW480-Snail transfected cells

value: Snail transfection


title: Muscle Large 2 vs. Small 2 [neomale]

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

state: Ontario

address: Science Complex, University of Guelph

department: Intergrative Biology

country: Canada

institute: University of Guelph

description: mRNA pooled from 5 fish.

hyb_protocol: cDNA was hybridized according to Preventing Ozone Related Problems version of the the hybridization protocol described in Two-Color Microarray-Based Gene Expression Analysis (Agilent Technologies) in Agilent hybridization chambers.

scan_protocol: Images were scanned on a GenePix 4200A scanner. Images were quantified using Genepix Pro software (version 6.1).

data_processing: GeneSpring GX (v. 7.3.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 647

organism: Oncorhynchus mykiss

source_name: muscle from small fish

label_protocol: cDNA was prepared from 0.5 ug mRNA using a SuperScript® Plus Direct cDNA Labeling System with Alexa Fluor® aha-dUTPs and labelled with either Alexa Fluor 555 or Alexa Fluor 647 according to the manufacturer's instructions.

growth_protocol: Rainbow trout from the Lyndon strain were reared at Alma Aquaculture Research Station and fed ad libitum.

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions.
mRNA was extracted from total RNA using μMACS mRNA Isolation Kits – Small Scale according to the manufacturer's instructions.

tag: strain/background

value: Lyndon

tag: parentage

value: neomale offspring

value: muscle

tag: size

value: small

label: Alexa Fluor 555

source_name: muscle from large fish

value: large


title: Nr10_slac15

source_name: slac1-3; replicate 1


title: Nr7_ler

source_name: ler; replicate 3

value: ler


title: CO-2.1-2

description: test

source_name: colorectal cell fraction


title: Muscle Large 1 vs. Small 1 [neomale]

description: mRNA pooled from 5 fish.


title: Nr12_slac15

source_name: slac1-3; replicate 3


title: Muscle Small 2 vs. Large 2 [neomale]

description: mRNA pooled from 5 fish.


title: E12.5 XY GFP sort control rep1

tag: genotype


title: Muscle Small 1 vs. Large 1 [neomale]

description: mRNA pooled from 5 fish.


title: Nr5_ler

source_name: ler; replicate 1


title: Nr4_ost12

source_name: ost1-2; replicate 2


title: Liver Large 2 vs. Small 2 [neomale]

description: mRNA pooled from 5 fish.

source_name: liver from small fish

value: liver

source_name: liver from large fish


title: Lin28B MO injected zebrafish embryos

status: Public on Nov 19 2013

city: Kasugai

first: Yasuo

last: Ouchi

state: Aichi

address: 1200 Matsumoto-cho

department: Department of Biomedical Sciences

institute: Chubu University

description: blends equal amounts of each samples

hyb_protocol: Labeled RNA was hybridized to the microarray slide for 16-20 hr at 56 degrees.

scan_protocol: Hybridization signals were detected by DNA microarray scanner(G2505C, Agilent)

data_processing: Hy3 (samples) signal was normalized with division used Hy5 (Universal reference) signal. Filtering parameter (CV%<50) was applied to the data.

organism: Danio rerio

source_name: Lin28B MO injected zebrafish embryos at 5 hpf

label_protocol: 250 ug of total RNA was labeled with miRCURY LNA microRNA Power Labeling kit (Exiqon) according to manufacture's protocol.

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

tag: developmental stage

value: embryo

tag: injected with

value: Lin28B MO

source_name: Universal Reference

tag: sample type

value: Universal Reference


title: 6W T. salsuginea rosette leaves 2W cold acclimated replicate 3

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

description: Gene expression for 2 weeks cold acclimated Col-0 rosette leaves at 4 °C. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

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

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

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

organism: Eutrema salsugineum

source_name: 6-week-old rosette leaves, 2-week cold-acclimated

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

growth_protocol: Col-0 seeds were stratified at 4°C for 1 week and grown on soil at 20°C for 3 weeks under 8 hrs light/16 hrs dark cycle at growth chamber. Col-0 plants were continued grown at 20°C for 2 weeks under 16 hrs light/8 hrs dark cycle at greenhouse. Yukon seeds were stratified at 4°C for 1 week and grown on soil at 20°C for 8 weeks under 16 hrs light/8 hrs dark cycle at greenhouse.

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

treatment_protocol: Soil grown 6-week-old Col-0 plants were cold acclimated at 4°C for 2 weeks. Soil grown 8-week-old Yukon plants were cold acclimated at 4°C for 2 weeks.

value: rosette leaves

value: 2-week cold-acclimated

tag: species

value: Thellungiella salsuginea

tag: cultivar

value: Yukon


title: 6W T. salsuginea rosette leaves non acclimated replicate 1

description: Gene expression for non acclimated Col-0 rosette leaves. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

source_name: 6-week-old rosette leaves, non-acclimated

tag: tissue

value: non-acclimated


title: 8W T. salsuginea rosette leaves non acclimated replicate 3

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

source_name: 8-week-old rosette leaves, non-acclimated


title: Liver Small 1 vs. Large 1 [neomale]

description: mRNA pooled from 5 fish.


title: Nr1_ost12

description: enriched guard cell fraction of Arabidopsis thaliana,

source_name: ost1-2; replicate 1

tag: genotype/variation


title: Nr6_ler

source_name: ler; replicate 2


title: Lin28A MO injected zebrafish embryos

description: blends equal amounts of each samples

source_name: Lin28A MO injected zebrafish embryos at 5 hpf

value: Lin28A MO


title: Control MO injected zebrafish embryos

description: blends equal amounts of each samples

source_name: Control MO injected zebrafish embryos at 5 hpf

value: Control MO


title: Liver Small 2 vs. Large 2 [neomale]

description: mRNA pooled from 5 fish.

value: Lyndon


title: 8W T. salsuginea rosette leaves 2W cold acclimated replicate 2

description: Gene expression for 2 weeks cold acclimated Yukon rosette leaves at 4 °C. RNA was hybridized on custom made Agilent Thellungiella salsuginea expression array

source_name: 8-week-old rosette leaves, 2-week cold-acclimated

tag: age


title: 6W T. salsuginea rosette leaves 2W cold acclimated replicate 2

tag: treatment


title: 8W T. salsuginea rosette leaves non acclimated replicate 2


title: 8W T. salsuginea rosette leaves 2W cold acclimated replicate 1


title: 6W T. salsuginea rosette leaves non acclimated replicate 2


title: 8W T. salsuginea rosette leaves non acclimated replicate 1


title: 6W T. salsuginea rosette leaves non acclimated replicate 3


title: 8W T. salsuginea rosette leaves 2W cold acclimated replicate 3


title: Liver Large 1 vs. Small 1 [neomale]

description: mRNA pooled from 5 fish.

value: neomale offspring


title: 6W T. salsuginea rosette leaves 2W cold acclimated replicate 1


title: HT29 monolayers were placed in contact with PRL2010 cells for 4 h_T4_II

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C.  5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95°C. Hybridization was performed at 45Â°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner. Laser was set at 33% power and PMT at 650.

data_processing: Data extraction was carried out using CombiMstrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software. All teh procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com).

source_name: Modulation of HT29 gene expression by PRL2010_T4

label_protocol: Reverse transcription and amplification of 500 ng of total RNA was performed with ImProm-IITM Reverse Transcriptase (Promega, Madison, USA) according to the manufacturer’s instructions. 5 µg of RNA was then labelled with ULS Labelling kit for Combimatrix arrays with Cy5 (Kreatech, The Netherlands)

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C. HT29 cells were grown in DMEM medium (high glucose, HEPES) medium supplemented with 10% heat-inactivated fetal bovine serum (LifeTechnologies, Italy), penicillin (100 U/ml), streptomycin (0·1 mg/ml) and amphotericin B (0.25 µg/ml) and 4 mM L- glutamine were seeded into the upper compartments of a six-well transwell plate.

extract_protocol: Total RNA from the pellet was isolated using the RNeasy mini kit (Qiagen, Italy) according to the manufacturer's instructions, including an RNase-free DNase I (Qiagen, Italy) digestion step.

tag: cell type

value: HT29 cell monolayers

tag: inoculation

value: B. bifidum PRL2010 cells

tag: time


title: 1mM indole,30 min exposure, replicate 3

city: Ulsan

middle: J.

last: Mitchell

address: 50 UNIST-gil

department: School of Life Sciences

institute: Ulsan National Institute of Science and Technology (UNIST)

description: Gene expression after  30 min of incubation at 30 °C in HEPES buffer supplemented with 1 mM indole

hyb_protocol: Hybridization was done using Gene Expression Hybridization kit according to Agilent instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k HD microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 034490_D_F_20110525) to obtain background subtracted and spatially detrended Processed Signal intensities. The processed signals from each array were normalized through dividing the data from each array by the 75 percentile median of all control probes for that array according to Agilent recommendations. The outlier probes which were more than 3-fold away from the average for each gene were then removed.

organism: Bdellovibrio bacteriovorus HD100

source_name: B. bacteriovorus attack phase, 30 min, 1 mM, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Agilent Low input Quick Amp WT One-color Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, USA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: B. bacteriovorus was cultured using E. coli MG1655 as a prey in 150 ml of HEPES buffer. Three subcultures were prepared and after 24 h of incubation, they were filtered through 0.45 µm filters and concentrated 10 times through centrifugation.

extract_protocol: RNA was extracted after that using Trizol / chloroform extraction method . RNA purification was done using RNeasy Mini kit (Qiagen, USA). The RNA concentration was then measured using a NanoDrop spectrophotometer. The RNA quality was assessed in Agilent 2100 bioanalyzer using RNA Nano-Chips (Agilent, USA).

treatment_protocol: From each of these concentrated cultures, three 4 ml aliquots were taken and mixed with indole at a concentration of 0, 1, and 2 mM. These cultures were then incubated for 30 min at 30°C with continuous shaking.

tag: cell stage

value: Attack phase cells


title: 1mM indole,30 min exposure, replicate 1

source_name: B. bacteriovorus attack phase, 30 min,1 mM, replicate 1


title: 0 mM indole,30 min exposure, replicate 3

description: Gene expression after  30 min of incubation at 30 °C in HEPES buffer supplemented with 0 mM indole

source_name: B. bacteriovorus attack phase, 30 min, 0 mM, replicate 3


title: Fetus liver Pool-Control reference DNA (Cy5) x methylated DNA (Cy3)

type: genomic

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Mouse Fetus Liver N=6

hyb_protocol: Agilent Oligo aCGH Hybridization Kit

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 10.5.1.1

source_name: Liver Pool Control Immunoprecipitated DNA (methylated DNA)

label_protocol: Manual: Agilent Genomic Labeling kit PLUS (Agilent Technologies, Santa Clara, CA, USA)

growth_protocol: C57BL/6J mice were purchased from Japan SLC Co. Ltd. (Hamamatsu, Japan). The animals were housed at the Animal Institution in Showa University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum. As per the supplier’s (CLEA) information, CE-2 includes 51.4% nitrogen free extracts, 24.9% crude protein, 8.6% moisture, 6.7% crude ash, 4.6% crude fat, and 3.7% crude fiber. The physiological fuel value is 346.7 kcal per 100 g chow.

extract_protocol: Blood & Cell Culture DNA Kit Mini (Qiagen, Valencia, CA, USA)

treatment_protocol: All animal experiments were started after a period of acclimation of at least one week. Pregnant animals were obtained by housing females with males (1-2 females/male). The day the vaginal plug was observed was designated embryonic day 0 (ED0) and gestation day 0 (GD0). Pregnant mice were exposed to 50% food restriction (FR) from GD 10 to 17 and caesarean section was performed between 10:00-12:00 AM on GD18. Amount of CE-2 chow supplied FR group was calculated as 50% of CE-2 consumed by control group each gestation day. Control group was supplied with chow ad libitum.

tag: strain

value: fetal liver

source_name: Liver Pool Control total genomic DNA (reference DNA)


title: Fetus liver Pool-Treatment FR reference DNA (Cy5) x methylated DNA (Cy3)

description:
Mouse Fetus Liver N=6
Dye-swap

source_name: Liver Pool Treatment FR Immunoprecipitated DNA (methylated DNA)

source_name: Liver Pool Treatment FR total genomic DNA (reference DNA)


title: Fetus liver Pool-Control reference DNA (Cy3) x methylated DNA (Cy5)

description: Mouse Fetus Liver N=6


title: 0 mM indole,30 min exposure, replicate 2

first: Robert

source_name: B. bacteriovorus attack phase, 30 min, 0 mM, replicate 2


title: 1mM indole,30 min exposure, replicate 2

source_name: B. bacteriovorus attack phase, 30 min, 1 mM, replicate 2


title: HT29 monolayers were placed in contact with PRL2010 cells for 4 h_T4_I


title: HT29 monolayers were placed in contact with PRL2010 cells for 2 h_T2_II

source_name: Modulation of HT29 gene expression by PRL2010_T2


title: Fetus liver Pool-Treatment FR reference DNA (Cy3) x methylated DNA (Cy5)

description:
Mouse Fetus Liver N=6
Dye-swap


title: HT29 monolayers were placed in contact with PRL2010 cells for 0 h_T0_II

source_name: Modulation of HT29 gene expression by PRL2010_T0

value: control


title: 2mM indole,30 min exposure, replicate 2

description: Gene expression after  30 min of incubation at 30 °C in HEPES buffer supplemented with 2 mM indole

source_name: B. bacteriovorus attack phase, 30 min,2 mM, replicate 2


title: 2mM indole,30 min exposure, replicate 1

source_name: B. bacteriovorus attack phase, 30 min,2 mM, replicate 1


title: 0 mM indole,30 min exposure, replicate 1

source_name: B. bacteriovorus attack phase, 30 min, 0 mM, replicate 1


title: HT29 monolayers were placed in contact with PRL2010 cells for 1 h_T1_II

source_name: Modulation of HT29 gene expression by PRL2010_T1


title: D4_miR27a_2

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description: SGBS preadipocyte cells originate from male patient with SGB syndrome and are cultured 2 days in serum-free OF medium prior to differentiation. Subsequently QuickDiff medium is added for the first 4 days of differentiation and then changed for 3FC medium. Please see Wabitsch M. et al. Int J Obes Relat Metab Disord. 2001 for more details. To identify microRNA target genes MiRNA mimics (Thermo Scientific Dharmacon, Colorado, USA) or a scrambled double-stranded siRNA sequence as control (siControl) (Eurogentec, Liège, Beligium) were introduced into zero or four days differentiated SGBS adipocytes using Lipofectamine RNAiMAX reagent (Invitrogen, Halle, Belgium) according to manufacturer’s instructions. The first differentiation medium was replaced by the transfection mixture and incubated for 2 hours prior to changing to the second differentiation medium (see above). 24 h post-transfection the cells were collected for RNA extraction.

hyb_protocol: Hybridized as recommended by manufacturer

scan_protocol: Scanned as recommended by manufacturer

data_processing: R/Bioconductor lumi package with vst transformation and rsn normalization. (control probe values in separate table, subtracted prior to vst transformation using lumiB method bgAdjust)

source_name: SGBS preadipocyte cell line undergoing differentiation for 4 days and transfected for additional 24 h

label_protocol: Labelled as recommended by manufacturer

growth_protocol: SGBS cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/Nutrient Mix F12 (Gibco) containing 8 mg/l biotin, 4 mg/l pantothenate, 0.1 mg/mg streptomycin and 100 U/ml penicillin (OF medium) supplemented with 10% FBS in a humidified 95%air/5%CO2 incubator. The cells were seeded into culture medium flasks or plates, which were coated with a solution of 10 microL/ml fibronectin and 0.05% gelatine in phosphate-buffered saline. Confluent cells were cultured in serum-free OF medium for 2 days followed by stimulation to differentiate with OF media supplemented with 0.01 mg/ml human transferrin, 200 nM T3, 100 nM cortisol, 20 nM insulin, 500 microM IBMX and 100 nM rosiglitazone (Cayman Chemicals). After day 4, the differentiating cells were kept in OF media supplemented with 0.01 mg/ml human transferrin, 100 nM cortisol and 20 nM insulin.

extract_protocol: Total RNA was extracted using TriSure (Bioline). 1 mL of TriSure was added per a confluent 6-well to lyse the cells. RNA extracted with 200 uL chloroform and precipitated from the aqueous phase with 400 uL isopropanol by incubating at -20C overnight.

tag: time of transfection

value: day 4

tag: transfection


title: D4_miR27a_3

treatment_protocol: To identify microRNA target genes MiRNA mimics (Thermo Scientific Dharmacon, Colorado, USA) or a scrambled double-stranded siRNA sequence as control (siControl) (Eurogentec, Liège, Beligium) were introduced into zero or four days differentiated SGBS adipocytes using Lipofectamine RNAiMAX reagent (Invitrogen, Halle, Belgium) according to manufacturer’s instructions. The first differentiation medium was replaced by the transfection mixture and incubated for 2 hours prior to changing to the second differentiation medium (see above). 24 h post-transfection the cells were collected for RNA extraction


title: HT29 monolayers were placed in contact with PRL2010 cells for 2 h_T2_I


title: D4_miR29a_2


title: D4_miR222_3


title: D4_miR222_2


title: HT29 monolayers were placed in contact with PRL2010 cells for 0 h_T0_I


title: D4_miR222_1


title: D4_siCtrl_3

value: siCtrl


title: D4_miR27a_1


title: D4_miR29a_3


title: D0_siLamin_2

source_name: Confluent preadipocyte SGBS cell line collected 24 h after transfection

value: day 0

value: siLamin


title: D0_siLamin_1


title: D0_miR30a_3


title: D0_miR30a_2


title: D0_miR422a_1


title: D4_miR29a_1


title: 8W A. thaliana rosette leaves 2W cold acclimated replicate 2

description: Gene expression for 2 weeks cold acclimated Yukon rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array

source_name: 8-week-old rosette leaves, 2-week cold-acclimated

value: rosette leaves

value: 2-week cold-acclimated

value: Arabidopsis thaliana


title: D0_miR422a_3


title: D4_siCtrl_1


title: D0_miR30a_1


title: D0_siCtrl_1


title: 8W A. thaliana rosette leaves non acclimated replicate 3

description: Gene expression for non acclimated Yukon rosette leaves. RNA was hybridized on Agilent Arabidopsis expression array

source_name: 8-week-old rosette leaves, non-acclimated

value: non-acclimated


title: D0_siCtrl_2


title: 8W A. thaliana rosette leaves non acclimated replicate 2


title: 8W A. thaliana rosette leaves 2W cold acclimated replicate 3


title: 8W A. thaliana rosette leaves non acclimated replicate 1


title: D4_siCtrl_2


title: ACA_plasma_sample_1

city: Budapest

first: Diana

middle: Rita

last: Szabo

address: Szentkirályi u. 46

country: Hungary

institute: Semmelweis University

description: miRNA expression profiling after plasma isolation from adrenocortical adenoma patient

hyb_protocol: Hybridization, washing and staining steps were performed using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Chip was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: Results were analyzed using GeneSpring software 10.1 (Agilent Technologies Inc., Santa Clara, CA, USA) following the instructions of the manufacturer. Raw data were filtered on the level of expression (raw expression is higher than 20 percentile in the 100% of samples in at least one group) and fold change filter was set to 2- or 3-fold between ACA and ACC groups.

source_name: human plasma, adrenocortical adenoma, sample_1

label_protocol: Total RNA (100 ng) was labelled using FlashTag Biotin HSR Labeling Kit (Genisphere, Hatfield, PA, USA).

extract_protocol: EDTA-anticoagulated blood was collected from ACA and ACC patients and centrifuged at 3000rpm for 20min at 4°C. Total RNA was isolated from 200μl plasma with Qiagen miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's protocol Purification of total RNA, including small RNAs, from serum or plasma using the miRNeasy Mini Kit with minor modifications: 5μl of 5nm Syn-cel-miR-39 miScript miRNA Mimic and 2μl Glycogen were added. RNA concentration was measured by NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) in all samples and the concentration of RNA extracted from plasma ranged from 3.3 to 26.9 ng/μl.

value: plasma sample

tag: disease status

value: adrenocortical adenoma


title: 8W A. thaliana rosette leaves 2W cold acclimated replicate 1


title: ACC_plasma_sample_1

description: miRNA expression profiling after plasma isolation from adrenocortical carcinoma patient

source_name: human plasma, adrenocortical carcinoma, sample_1

value: adrenocortical carcinoma


title: D0_siCtrl_3


title: 6W A. thaliana rosette leaves non acclimated replicate 1

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

source_name: 6-week-old rosette leaves, non-acclimated


title: ACC_plasma_sample_3

source_name: human plasma, adrenocortical carcinoma, sample_3


title: ACC_plasma_sample_4

source_name: human plasma, adrenocortical carcinoma, sample_4


title: 6W A. thaliana rosette leaves non acclimated replicate 2


title: 6W A. thaliana rosette leaves 2W cold acclimated replicate 1

description: Gene expression for 2 weeks cold acclimated Col-0 rosette leaves at 4 °C. RNA was hybridized on Agilent Arabidopsis expression array

source_name: 6-week-old rosette leaves, 2-week cold-acclimated


title: 6W A. thaliana rosette leaves non acclimated replicate 3


title: ACA_plasma_sample_3

source_name: human plasma, adrenocortical adenoma, sample_3


title: ACA_plasma_sample_4

source_name: human plasma, adrenocortical adenoma, sample_4


title: ACA_plasma_sample_2

source_name: human plasma, adrenocortical adenoma, sample_2


title: ACC_plasma_sample_2

source_name: human plasma, adrenocortical carcinoma, sample_2


title: 6W A. thaliana rosette leaves 2W cold acclimated replicate 2


title: MGHU3 Cells_TAK1 siRNA_Biological Replicate 1

city: Irvine

first: Leslie

last: Thompson

address: Biological Sciences III

institute: University of California, Irvine

description: SAMPLE 10

hyb_protocol: 2 ug of the labeled, fragmented single-stranded cDNA was then hybridized to probe sets on a Human AffymetrixGeneChip 1.0ST array.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.

data_processing: Data were imported into Partek Genomics Suite Version 6.6 software with the following operations being done to prepare the data for statistical analysis: 1) RMA Background Correction, 2) Quantile Normalization, 3) Log base 2 transformation, and 4) Summary of Probe sets using mean value. Statistical analysis consisted of one-way ANOVA with a single categorical variable, and gene lists were generated for those genes with fold-change magnitude > 2 and p-value with a false discovery rate (FDR) <.05.

source_name: MGHU3 Cells_TAK1 siRNA

label_protocol: The Ambion WT expression kit (Life Technologies) was used to prepare RNA samples for whole transcriptome microarray analysis per manufacturer's instructions

growth_protocol: MGHU3 cells were propagated at 37°C in RPMI 1640 (Hyclone; Thermo Scientific, Rockford, IL) supplemented with 10% FBS (Invitrogen).

extract_protocol: Total RNA was processed as recommended by Affymetrix, Inc. Briefly, RNA was isolated using TRIzol (Life Technologies) and passed through RNeasy spin columns (Life Technologies) for further clean up.

treatment_protocol: Cells were transfected using the Neon system (Life Technologies).  Following the manufacturer’s procedure, 1x10^6 cells were suspended in 100µl suspension solution containing 5 µg siRNA (Dharmacon) or plasmid and pulsed under program 3 for cells

tag: cell line

value: malignant urothelial cells

value: FGFR3 Y375C mutation

tag: transfected with

value: 5ug TAK1 siRNA


title: control 2

city: Tokushima

first: Naozumi

last: Ishimaru

address: 3-18-15 Kuramoto

department: Department of Oral Molecular Pathology

institute: Institute of Health Biosciences The University of Health Biosciences

description: control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php.For the normalization housekeeping genes:ACTB.
Fold Change worksheet reports test.control(i.e. average of test sample1-3/agerage of control sample 4-6 ) ratios

label: SYBR

source_name: ear tissue

label_protocol: Total RNA was reverse-transcrived into cDNA using a PrimeScript II 1st tsrand cDNA Synthesis Kit (Takara). Transript levels were measured using a 7300 real-time PCR systetem (Applied Biosystems) with SYBR Premix Ex Taq (Takara)

extract_protocol: Total RNA was isolated from the ear tissue using ISOGEN (Wako Puew Chemical).

treatment_protocol: In order to induce delayed-type hypersensitivity with nickel, NiCl2 together with imcomplete Freund's adjuvant was intraperitoneally injected to female C58BL/6J mice. Two weeks later, Nickel with complete Freund's adjuvant was intradermally injected into the ear skin. At 48h after the 2nd challenge, total RNA was isolated from the ear tissues. ProSOne,6(4);e19017,2011

tag: tisuue

value: ear


title: control 3

description: control


title: control 1

description: control


title: MGHU3 Cells_TAK1 siRNA + PD173074_Biological Replicate 2

description: SAMPLE 8

source_name: MGHU3 Cells_TAK1 siRNA + PD173074

tag: treated with


title: MGHU3 Cells_TAK1 siRNA + PD173074_Biological Replicate 3

description: SAMPLE 9


title: MGHU3 Cells_TAK1 siRNA_Biological Replicate 3

description: SAMPLE 12


title: Ni treated 2

description: test

value: Ni


title: Ni treated 3

description: test

source_name: eat tissue


title: Ni treated 1

description: test


title: MGHU3 Cells_Control siRNA + PD173074_Biological Replicate 3

description: SAMPLE 6

source_name: MGHU3 Cells_Control siRNA + PD173074

value: 5ug Control siRNA


title: MGHU3 Cells_Control siRNA_Biological Replicate 3

description: SAMPLE 3

source_name: MGHU3 Cells_Control siRNA


title: MGHU3 Cells_TAK1 siRNA_Biological Replicate 2

description: SAMPLE 11


title: MGHU3 Cells_Control siRNA + PD173074_Biological Replicate 2

description: SAMPLE 5


title: MGHU3 Cells_Control siRNA_Biological Replicate 2

description: SAMPLE 2


title: MGHU3 Cells_Control siRNA + PD173074_Biological Replicate 1

description: SAMPLE 4


title: MGHU3 Cells_Control siRNA_Biological Replicate 1

description: SAMPLE 1


title: 48hr

city: Tallahassee

first: Jonathan

middle: Hancock

last: Dennis

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: The Florida State University

hyb_protocol: The labeled DNA was precipitated with 1 volume isopropanol, and hybridized according to manufacturer's protocols. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on a Nimblegen scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan CGH arrays.

source_name: iSLK.219 cells

label_protocol: 1 µg of mononucleosomally protected and genomic DNA was directly labeled by Klenow (Nimblegen) random priming with Cy3 and Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: iSLK.219 (clone 10), derived from iSLK, was latently infected with a recombinant rKSHV.219 virus (Vieira and O'Hearn, 2004) and cultured and maintained as described previously (Myoung and Ganem, 2011).  One day before induction of KSHV reactivation, 5 × 106 cells were seeded into a 150-mm dish.  The next day, the medium was replaced with DMEM containing 1% FBS, and doxycycline was added to a final concentration of 0.2 µg/ml.  Cells were harvested at the designated times after doxycycline addition.  The 0 hours was treated identically to the 6 hours except that doxycycline was not added.  iSLK.219 cell lines were harvested at 2.5 × 107 cells.  The cells were cross-linked in 1% formaldehyde in PBS and incubated at room temperature for 10 min.  The cross-linking reaction was stopped with 125 mM glycine.  The nuclei were then isolated in nucleus isolation buffer (0.3 M sucrose, 2 mM MgOAc2, 1 mM CaCl2, 1% Nonidet P-40, 10 mM HEPES, pH 7.8) by centrifiguation at 1000 X g for 5 minutes at 4°C.  All MNase nucleosome mapping experiments were performed with two biological replicates from completely independent growths and treatments of cells (Supp. Fig. 19).  iSLK.219 nuclei or in vitro assembled nucleosomes were digested with a titration of MNase (Worthington Biochemical Corp.) for nucleosome-distribution experiments.  The concentrations for the MNase titration were 4 U/ml, 2 U/ml, 1 U/ml, and 0.05 U/ml of MNase in MNase cleavage buffer:  5 mM KCl, 4 mM MgCl2, 1 mM CaCl2, 12.5% glycerol, and 50 mM Tris-Cl (pH 7.4).  The MNase reaction occurred at a titration of MNase concentration to ensure equivalent representation of the early and late digesting fractions of the genome.  These reactions were performed at 37°C for 5 min, and the reactions were stopped with 50 mM EDTA.  We then treated the MNase-digested nuclei with 0.2 μg/μl proteinase K,1% sodium dodecyl sulfate, and incubated overnight at 60°C to reverse the protein-DNA cross-links. Following the separation of nucleosomal ladder on a 2% agarose gel, mononucleosomally protected DNA (~150 bp) was isolated by excision of the specific sample’s band, and the DNA was purified by electroelution.  For each sample, mononucleosomally protected DNA of all MNase concentrations were combined.  Mononucleosomal DNA was extracted with phenol-chloroform, precipitated with alcohol, and dissolved in TE (10 mM Tris-Cl. pH 8.0, 0.1 mM EDTA).  Bare genomic DNA (reference) was isolated from iSLK and iSLK.219 by resuspension of the cells in a 0.2-μg/μl proteinase K and 1% SDS solution and incubated at 55°C overnight.

value: iSLK.219 cells

tag: material

value: Mononucleosomal protected DNA

value: bare genomic DNA


title: 12hr


title: 6hr


title: SGBS_T0901317_2

description: SGBS preadipocyte cells originate from male patient with SGB syndrome and are cultured 2 days in serum-free OF medium prior to differentiation. Subsequently QuickDiff medium is added for the first 4 days of differentiation and then changed for 3FC medium. Please see Wabitsch M. et al. Int J Obes Relat Metab Disord. 2001 for more details. To identify LXR target genes, the day 10 differentiated adipocytes were stimulated with the synthetic LXR agonist 1 microM T0901317 for 4 h, control cells received solvent (DMSO at final concentration 0.1%)

source_name: Day 12 differentiated SGBS adipocyte cell line

treatment_protocol: Day 10 differentiated adipocytes were stimulated with the synthetic LXR agonist 1 microM T0901317 for 4 h, control cells received solvent (DMSO at final concentration 0.1%)


title: Pdx1-deficient cell 1

city: Philadelphia

first: Tao

last: Gao

state: PA

address: 421 Curie Blvd, BRB II/III, Room 527

institute: University of Pennsylvania

hyb_protocol: A total of 1.5 μg of biotinylated cRNAs was hybridized to the Mouse Gene 1.0ST microarray.

scan_protocol: After staining with streptavidin-phycoerythrin and biotinylated anti-streptavidin, samples were scanned  and data were collected by using GCS3000 laser scanner.

data_processing:
All statistical analysis was performed using Ingenuity Pathway Analysis database and under the R language environment. A heat map of expression was generated by Treeview.
affymetrix-algorithm-name = rma-gene-default; affymetrix-algorithm-version = 1.0
program-name = Expression Console; program-version = 1.1.2800.19935

source_name: Pdx1-deficient cell

label_protocol: Five hundred nanograms of total RNA were used for the synthesis of cDNA, followed by amplification and biotin labeling.

growth_protocol: RNA was isolated from islet cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from islet cells by using an RNeasy total RNA isolation Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Single-stranded cDNA was generated, labeled, and  hybridized with Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned  was performed according to the manufacturer's instruction (Affymetrix).

tag: strain background

value: mixed background of B6 and BALB/C

value: Pdx1-deficient (PKO)

value: pancreatic islet

tag: cell subtype

value: reprogrammed cells


title: Pdx1-deficient cell 2

tag: genotype/variation


title: Islet alpha cell 1

source_name: Islet alpha cell

value: RIP-CreER; Pdx1fl/+, RosaYFP

value: normal α-cells


title: Islet beta cell 5

source_name: Islet beta cell

value: glucagon-Cre; RosaYFP

value: normal islet β-cells


title: Pdx1-deficient cell 3


title: Pdx1-deficient cell 4


title: Islet alpha cell 2


title: Pdx1-deficient cell 5


title: Islet alpha cell 3


title: Islet alpha cell 4


title: Islet alpha cell 5


title: Islet beta cell 3


title: SGBS_dmso_2

tag: treatment

value: solvent (DMSO) 4 h


title: Islet beta cell 2

tag: cell type


title: 24hr


title: SGBS_dmso_3


title: Islet beta cell 1


title: SGBS_T0901317_3


title: HT29 monolayers were placed in contact with PRL2010 cells for 1 h_T1_I

source_name: Modulation of HT29 gene expression by PRL2010_T1

value: HT29 cell monolayers

tag: inoculation

value: B. bifidum PRL2010 cells


title: 0hr


title: Islet beta cell 4


title: SGBS_T0901317_1


title: D0_miR422a_2

source_name: Confluent preadipocyte SGBS cell line collected 24 h after transfection

value: day 0


title: SGBS_dmso_1


title: SGBS_day3_3

description: SGBS preadipocyte cells originate from male patient with SGB syndrome and are cultured 2 days in serum-free OF medium prior to differentiation. Subsequently QuickDiff medium is added for the first 4 days of differentiation and then changed for 3FC medium. Please see Wabitsch M. et al. Int J Obes Relat Metab Disord. 2001 for more details

source_name: SGBS cell line undergoing differentiation

treatment_protocol: See growth protocol for induction of differentiation.

value: SGBS

tag: time

value: day 3


title: SGBS_day12_3

value: day 12


title: SGBS_day3_1


title: SGBS_day12_2


title: SGBS_day3_2


title: SGBS_8h_1

value: 8 h


title: SGBS_12h_2


title: SGBS_12h_1


title: Transcriptomic profile of PRL2010 colonization in murine model_T1_I

source_name: Modulation of mouse gene expression after PRL2010 colonization_test

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C. Bacterial colonization was established by five consecutive daily administrations using a micropipette tip placed immediately behind the incisors.

value: BALB/c

tag: gender

value: female

tag: age

value: 3 months old

tag: tissue

value: caecum


title: SGBS_day1_1

value: day 1


title: SGBS_4h_2

value: 4 h


title: SGBS_day1_3


title: Transcriptomic profile of PRL2010 colonization in murine model_T2_II

tag: strain


title: SGBS_day1_2


title: SGBS_8h_3


title: Transcriptomic profile of PRL2010 colonization in murine model_C1_I

source_name: Modulation of mouse gene expression after PRL2010 colonization_control

value: control


title: SGBS_8h_2


title: SGBS_4h_3


title: Transcriptomic profile of PRL2010 colonization in murine model_C2_II


title: SGBS_day0_1

source_name: Confluent SGBS cell line

value: 0 h


title: SGBS_day0_3


title: SGBS_4h_1


title: 6W A. thaliana rosette leaves 2W cold acclimated replicate 3

source_name: 6-week-old rosette leaves, 2-week cold-acclimated

value: rosette leaves

value: 2-week cold-acclimated

tag: species

value: Arabidopsis thaliana

tag: cultivar


title: 180866

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description: Functional Studies in AML and MDS

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2/Mouse 430 2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06

data_processing: The data were analyzed with Affymetrix GeneChip Command Console using Affymetrix default analysis settings for MAS5 algorithm and a target intensity of 1500 was used for global scaling as normalization method

source_name: trisomy 8 t-AML

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  (Expression Analysis Technical Manual, 2008, Affymetrix)

growth_protocol: Not applicable

extract_protocol: Trizol according to manufacture's instructions.

treatment_protocol: Not applicable

value: Bone marrow

value: trisomy 8 t-AML


title: SGBS_day0_2

tag: cell line

value: SGBS


title: 189941

description: Functional Studies in AML and MDS

source_name: non-trisomy 8 t-AML

value: non-trisomy 8 t-AML


title: MG-treated ST2

city: Toon

first: Sohei

last: Kitazawa

state: Ehime

address: Shitsukawa

department: Molecular Pathology

institute: Ehime University

hyb_protocol: Standard

scan_protocol: GenePix4000B scanner (Axon Instruments)

data_processing: Array-Pro Analyzer Ver.4.5

source_name: Continuous cultured experimental samples after 48h MG treatment

label_protocol: RNA Transcript SureLABEL Core Kit

growth_protocol: Mouse bone marrow stromal cell-line ST2 (RIKEN, Tsukuba, Japan) was cultured in α-MEM (Sigma, St. Louis, MO) supplemented with 10% FBS (Sigma), 100 μg/ ml penicillin/ streptomycin (ICN Biomedicals, Inc., Aurora, OH) and 100 μM methylglyoxal (MG), and maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: RNAeasy

treatment_protocol: Cells were treated with either 100 μM methylglyoxal (MG-treated ST2) or vehicle (non-treated ST2), and maintained at 37°C in a humidified atmosphere with 5% CO2 for 48 hours.

value: bone marrow stromal cell-line

value: MG-treated


title: non-treated ST2

source_name: Continuous cultured experimental samples after 48h without MG treatment


title: 548417

description: Functional Studies in AML and MDS


title: 180365

description: Functional Studies in AML and MDS


title: 751407

description: Functional Studies in AML and MDS


title: 982895

description: Functional Studies in AML and MDS


title: GATA2CKO renal CD

city: Sendai

first: Takashi

last: Moriguchi

address: Seiryo

institute: Tohoku University

description: Gene expression of GATA2CKO CD cells

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model US82800151.

data_processing: The data were analyzed and normalized with GeneSpring software. After normalization, the data was baseline transformed to the median of all samples.

source_name: GATA2CKO mouse renal collecting duct cells

label_protocol: 50 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Adult kidney collecting duct cells were purified by DBA-lectin and magnetic beads, total RNA was extracted from purified cells by ISOGEN (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Gata2 renal tubule specific knockout was induced by feeding 4 weeks old mice with additional 4 weeks doxycycline solution

value: Mixed

tag: genotype

value: 8 weeks


title: ZH1407_ALL

city: Lyon

first: Nicolas

last: Picard

address: 7 passage du Vercors

country: France

institute: CNRS

description: Gene expression in ALL Tubules

hyb_protocol: Target cRNA Samples (100μl) were hybridized to Whole mouse Genome 4x44k OligoMicroarrays (Agilent) for 17h at 65°C. Arrays were then washed using Agilent GE Wash Buffers 1 and 2, according to the manufacturer instructions

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)

data_processing: GeneSpring 10 (Agilent Technologies, USA)

source_name: Renal Tubules

label_protocol: Cy3-labelled nucleotides using a Low RNA Input Linear Amp Kit+Cy dye, one-color kit (Agilent)

extract_protocol: Ambion microRNA extraction kit

tag: sample type

value: ALL

tag: mouse

value: Male


title: WT renal CD

description: Gene expression of WT CD cells

source_name: Wild type mouse renal collecting duct cells

value: Wild type


title: 476204

description: Functional Studies in AML and MDS


title: ZH1406_ALL

description: Gene expression in ALL Tubules

value: Female


title: Id3KO at Stage 2, biological rep 1

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

description: Gene expression data from mouse Id3KO Stage 2 iNKT cells

hyb_protocol: 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Sorted Tet+CD24-CD44+NK1.1- iNKT cells from Id3KO thymus

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix two-cycle cDNA sunthesis.

growth_protocol: Mice were housed at the Univeristy of Chicago Animal Resource Center, following the guidelines of The University of Chicago Institutional Animal Care and Use Committee.

extract_protocol: RNA was prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

treatment_protocol: Thymocyte single cell suspensions were surface stained and FACS sorted into RLT-containing (Qiagen) eppendorf tubes, before freezing in dry ice. Cells were stored in -80oC until RNA extraction was performed.

value: Thymus

value: 6 weeks old


title: Id3KO at Stage 2, biological rep 2

value: Sorted Tet+CD24-CD44+NK1.1- iNKT cells from Id3KO thymus


title: ZH1407_EGFP+

description: Gene expression in EGFP+ Tubules

value: EGFP+


title: ZH1406_EGFP-

description: Gene expression in EGFP- Tubules

value: EGFP-


title: Id3KO at Stage 1, biological rep 2

description: Gene expression data from mouse Id3KO Stage 1 iNKT cells

source_name: Sorted Tet+CD24-CD44-NK1.1- iNKT cells from Id3KO thymus


title: Id3KO at Stage 1, biological rep 1

value: Sorted Tet+CD24-CD44-NK1.1- iNKT cells from Id3KO thymus


title: ZH1405_EGFP-

description: Gene expression in EGFP- Tubules


title: Id3KO at Stage 2, biological rep 3


title: ZH1406_EGFP+

description: Gene expression in EGFP+ Tubules


title: ZH1405_ALL

description: Gene expression in ALL Tubules


title: 514901

description: Functional Studies in AML and MDS

value: Bone marrow


title: 779828

description: Functional Studies in AML and MDS


title: 864484

description: Functional Studies in AML and MDS


title: MGHU3 Cells_TAK1 siRNA + PD173074_Biological Replicate 1

description: SAMPLE 7

source_name: MGHU3 Cells_TAK1 siRNA + PD173074

value: malignant urothelial cells

value: FGFR3 Y375C mutation

tag: transfected with

value: 5ug TAK1 siRNA

tag: treated with


title: WT at stage 2 iNKT, biological rep 1

description: Gene expression data from mouse WT Stage 2 iNKT cells

source_name: Sorted Tet+CD24-CD44+NK1.1- iNKT cells from WT thymus

value: WT


title: ZH1407_EGFP-

description: Gene expression in EGFP- Tubules


title: WT at stage 2 iNKT, biological rep 3

value: Sorted Tet+CD24-CD44+NK1.1- iNKT cells from WT thymus


title: 377512

description: Functional Studies in AML and MDS

value: trisomy 8 t-AML


title: ZH1408_ALL

description: Gene expression in ALL Tubules

value: ALL


title: WT at stage 2 iNKT, biological rep 2


title: ZH1405_EGFP+

description: Gene expression in EGFP+ Tubules

value: Male


title: 856024

description: Functional Studies in AML and MDS

value: non-trisomy 8 t-AML


title: ZH1408_EGFP+

description: Gene expression in EGFP+ Tubules

value: Female


title: ZH1408_EGFP-

description: Gene expression in EGFP- Tubules


title: WT HFD_RPWAT_vehicle_Day 5_REP05

status: Public on Nov 18 2013

city: Boston

first: eric

last: muise

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_Veh_d5_5

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: RPWAT

label_protocol: The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cDNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: genotype/variation

value: 8 weeks

tag: diet

value: HFD

tag: treatment protocol

value: twice daily with vehicle (saline)

value: 6 hrs post last dose (5day time point)

value: retroperitoneal white adipose tissue


title: WT at stage 1 iNKT, biological rep 2

description: Gene expression data from mouse WT Stage 1 iNKT cells

source_name: Sorted Tet+CD24-CD44-NK1.1- iNKT cells from WT thymus

tag: cell type

value: Thymus

value: 6 weeks old


title: WT HFD_RPWAT_vehicle_Day 5_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_Veh_d5_1

tag: time


title: 942008

description: Functional Studies in AML and MDS

value: Bone marrow


title: 501254

description: Functional Studies in AML and MDS


title: WT HFD_RPWAT_vehicle_Day 5_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_Veh_d5_2


title: WT HFD_RPWAT_vehicle_Day 2_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_Veh_d2_4

value: 6 hrs post last dose (2day time point)


title: WT HFD_RPWAT_FGF21_Day 5_REP05

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_wtFGF21_d5_5


title: WT HFD_RPWAT_vehicle_Day 2_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_Veh_d2_3


title: WT HFD_RPWAT_FGF21_Day 5_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_wtFGF21_d5_4


title: WT at stage 1 iNKT, biological rep 1

value: Sorted Tet+CD24-CD44-NK1.1- iNKT cells from WT thymus


title: WT HFD_RPWAT_vehicle_Day 2_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_Veh_d2_2

value: WT


title: WT HFD_RPWAT_FGF21_Day 2_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_wtFGF21_d2_3


title: WT HFD_RPWAT_FGF21_Day 5_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_wtFGF21_d5_1


title: WT HFD_RPWAT_FGF21_Day 5_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_wtFGF21_d5_3


title: SGBS_day12_1

source_name: SGBS cell line undergoing differentiation

value: SGBS

value: day 12


title: WT HFD_RPWAT_FGF21_Day 2_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_wtFGF21_d2_4


title: WT HFD_RPWAT_vehicle_Day 2_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_Veh_d2_1


title: WT HFD_RPWAT_vehicle_Day 5_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_Veh_d5_4


title: WT HFD_RPWAT_FGF21_Day 2_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_C57HFD_wtFGF21_d2_2


title: WT HFD_RPWAT_vehicle_Day 5_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_Veh_d5_3


title: WT HFD_RPWAT_FGF21_Day 5_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from C57BL6 mice on HFD diet treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
RPWAT_C57HFD_wtFGF21_d5_2