title: wild type,replicate 3

source_name: WT

value: WT


title: Pro [9253995035_D]

status: Public on Jul 23 2014

type: RNA

city: Zeist

first: Guus

last: Roeselers

address: Utrechtseweg 48

department: Microbiology & Systems Biology

country: Netherlands

institute: TNO

hyb_protocol: Total mRNA was amplified, biotinylated and randomly hybridized to MouseRef-8 v2 Expression bead arrays (Illumina, Inc., San Diego, CA, U.S.A.) following standard Illumina hybridization protocol.

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

data_processing: Data were extracted using GenomeStudio. Quality control and normalization of microarray data was performed in ArrayAnalyzer (www.arrayanalyzer.org). Non-expressed genes were removed by filtering on detection value (p value ≥0.99 in at least one sample). This resulted in gene expression values for 25,697 probes. For differential expression analysis Limma software was used. Subsequently, expression data of the transcriptomics were log-transformed (base 2).  Probes were used for biological interpretation if the p value threshold of <0.01 was passed and if the fold change between two conditions was |1.5|.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pro

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

extract_protocol: Cultured organoids were pooled, approximately 300 individual organoids per sample, and RNA was isolated using Trizol (Invitrogen, Breda, the Netherlands), followed by purification using the RNeasy Kit (Qiagen). Samples were assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and NanoDrop Spectrophotometer (NanoDrop, Wilmington, DE).

tag: strain

tag: gender

value: male

tag: tissue

value: intestinal organoids

tag: exposed to

value: propionate


title: wild type,replicate 2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

hyb_protocol: Hybridized to Illumina MouseRef-8 v2.0 expression beadchip.

scan_protocol: not provided

data_processing: raw data were processed using the R/Bioconductor package limma for background correction and quantile normalization

label_protocol: not provided

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

treatment_protocol: MiR-21-/- (21KO) mice on C57BL/6 background were kindly provided by Dr. Eric Olson (Patrick, et al. J Clin Invest. 2010;120:3912-3916.). The miR-21-/- mice do not develop spontaneous colitis.  Gene expression profiles were established for normal miR-21-/- mice and wild type c57BL/6 mice (WT) from Taconic Farm Inc. (Hudson, NY)

value: colon mucosa

tag: genotype

value: wild type

tag: group


title: wild type,replicate 1


title: MiR-21 knockout replicate 3

value: MiR-21 knockout


title: MiR-21 knockout replicate 1


title: Con [9253995035_H]

source_name: Con

value: standard organoid culturing medium


title: Con [9253995035_G]


title: Pro [9253995035_A]


title: High Grade Astrocytoma 9 - Tumour-250Knsp

status: Public on Jul 24 2014

type: genomic

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description: Hybridized to 250K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: primary_data_description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: High Grade Astrocytoma 9 - Tumour

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from snap frozen biopsy and surgical samples from paediatric high grade glioma patients using the acidic phenol-chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: histology

value: anaplastic astrocytoma


title: Con [9253995035_F]


title: High Grade Astrocytoma 8a - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 8a - Tumour

value: glioblastoma


title: Pro [9253995035_B]


title: Pro [9253995035_C]


title: But [9231425044_F]

source_name: But

value: butyrate


title: Ace [9231425044_C]

source_name: Ace

value: acetate


title: But [9231425044_H]


title: But [9231425044_G]


title: But [9231425044_E]


title: Con [9253995035_E]


title: Ace [9231425044_D]


title: Ace [9231425044_B]


title: High Grade Astrocytoma 4 - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 4 - Tumour


title: AM- [9231425047_H]

source_name: AM-

value: A. muciniphila culturing medium


title: High Grade Astrocytoma 1 - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 1 - Tumour


title: High Grade Astrocytoma 3 - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 3 - Tumour


title: High Grade Astrocytoma 7b - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 7b - Tumour


title: Ace [9231425044_A]


title: AM- [9231425047_E]


title: FP+ [9231425057_C]

source_name: FP+

value: F. prausnitzii-conditioned medium


title: AM- [9231425047_F]


title: AM+ [9231425047_D]

source_name: AM+

value: A. muciniphila-conditioned medium


title: FP- [9231425057_G]

source_name: FP-

value: F. prausnitzii-culturing medium


title: FP- [9231425057_E]


title: AM+ [9231425047_A]


title: AM+ [9231425047_B]


title: AM- [9231425047_G]


title: FP- [9231425057_H]


title: AM+ [9231425047_C]


title: FP+ [9231425057_A]


title: FP+ [9231425057_B]


title: FP- [9231425057_F]


title: High Grade Astrocytoma 2 - Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 2 - Tumour


title: GDF8 vs. untreated-3

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description:
US45102927_251486829769_S01_GE2-v5_95_Feb07_1_3
Biological replicate 3 of 4. Control: myoblasts cells, untreated, harvested after 6 days of differentiation.

hyb_protocol: The cRNA was fragmented and hybridized to Agilent-014868 Whole Mouse Genome Oligonucleotide Microarray (4 × 44K slide format) at 37 ºC for 17 hours (Version 5.7, March 2008).

scan_protocol: After washing, the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 9.1.1.1 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE2_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were processed using GeneSpring GX (Agilent).
For identification of genes significantly altered in cell compared with the control normal gene set, total detected entities were filtered by flags (present, marginal) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with GDF8 ([C2C12]-[GDF8]1-4) was used t-test unpaired (p < 0.05) and fold change cutoff over 1.6. Analysis of GO and signaling pathway was carried out using GeneSpring GX 12 (Agilent), KEGG and PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using Panther, a total of 68 cellular pathways were identified.

source_name: C2C12 myoblasts, 6 day of differentiation in [10%HS+20nM GDF8/24h]

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double-stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies Version 5.7, March 2008). US45102927_251486829769_S01_GE2-v5_95_Feb07_1_1.txt and US45102927_251486829769_S01_GE2-v5_95_Feb07_1_4.txt are dye swaps.

growth_protocol: C2C12 myoblasts were conducted in proliferation medium with DMEM/10% FBS (Gibco Invitrogen Co.) till 80% confluence. Next, myoblasts were differentiated during 6 days in DMEM/2% HS (Gibco Invitrogen Co.)

extract_protocol: Total RNA was extracted from the cells with RNeasy (Qiagen). The quality of the total RNA was examined by 2100 Bioanalyzer (Agilent).

treatment_protocol: Differentiating myoblasts were treated every 24h with 20 nM GDF8 (Recombinant Mouse Myostatin; Sigma-Aldrich, Germany) during 6 days. Control cells were untreated.

tag: cell line

tag: cell type

value: myoblasts

tag: days of differentiation

tag: treatment

value: 20nM GDF8/24h/6days

source_name: CTRL C2C12 myoblasts, 6 day of differentiation in [10%HS/24h]


title: GDF8 vs. untreated-2

description:
US45102927_251486829769_S01_GE2-v5_95_Feb07_1_2
Biological replicate 2 of 4. Control: myoblasts cells, untreated, harvested after 6 days of differentiation.


title: FP+ [9231425057_D]

value: male


title: GDF8 vs. untreated-4

description:
US45102927_251486829769_S01_GE2-v5_95_Feb07_1_4
Biological replicate 4 of 4. Control: myoblasts cells, untreated, harvested after 6 days of differentiation. Dye-swap.


title: GDF8 vs. untreated-1

description:
US45102927_251486829769_S01_GE2-v5_95_Feb07_1_1
Biological replicate 1 of 4. Control: myoblasts cells, untreated, harvested after 6 days of differentiation. Dye-swap.


title: High Grade Astrocytoma 5- Tumour-250Knsp

description: Hybridized to 250K

source_name: High Grade Astrocytoma 5- Tumour-


title: Spleen-21dpi-challenged-rep2

city: Yangzhou

first: Teng

last: Ma

state: Jiangsu

address: 88 South University ave.

department: College of Animal Science and technology

country: China

institute: Yangzhou University

description: Gene expression profile of spleen at 21 days post infected with Salmonella pullorum

hyb_protocol: Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent supplied with the Agilent Gene Expression Hybridization Kit, or add 1250 μL of nuclease-free water to the vial containing lyophilized large volume 10X Blocking Agent (Agilent p/n 5188-5281).Mix by gently vortexing. If the pellet does not go into solution completely, heat the mix for 4 to 5 minutes at 37°C.Drive down any material adhering to the tube walls or cap by centrifuging for 5 to 10 seconds.

scan_protocol: Put assembled slide holders with or without the ozone-barrier slide cover into the scanner carousel.In the Scan Control main window, choose the slot number of the first slide for Start Slot and the slot number for the last slide for End Slot.For 4x44K  microarrays, select Profile AgilentG3_GX_1Color. Verify scan settings for one-color scans. Verify that the Scanner status in the main window says Scanner Ready.In the Scan Control main window, click Scan Slot m-n where m is the slot of the first slide, and n is the slot for the last slide.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol G4140-90040_GeneExpression_One-color_v6.5) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Gallus gallus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions:  (complimentary RNA) with a sample input RNA range between 10 ng and  200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for one-color  processing. The method uses T7 RNA polymerase, which simultaneously  amplifies target material and incorporates cyanine 3-labeled CTP.  Amplification is typically at least a 100-fold from total RNA to cRNA with the  use of this kit.

growth_protocol: For this study, one hundred and fifteen Chinese indigenous half-sibling one-day-old Guangxi Yellow chicks were obtained from the Guangdong Poultry Science Institute. All of the chicks were transported in a constant temperature incubator at 32°C. Those chicks were divided into 2 groups and were reared in two separate SPF isolators that were kept sterilized before the chicks entered. Thereafter, the SPF isolators were maintained at temperatures no less than 30°C with 24 hours of light for the first week and temperatures no less than 28°C and 12:12 (light:dark) hours thereafter. The birds were fed sterilized feed (autoclaved) and sterile still water ad libitum without any addition of antibiotics. The chicken manure was cleaned every two days to reduce the chances of re-infection. All of the instruments or tools needed were sterilized (via spraying bromogeramine diluent on the surface) before being sent to the isolators.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: On the first day, the chicks in the SPF isolators were allowed to eat and drink ad libitum to stabilize their physiological status. On the morning of the second day, eighty chicks were assigned to one SPF isolator and thirty-five to the other. The eighty chicks were challenged orally with 0.5 ml bacterial culture containing 2×108 CFU of S. Pullorum, and the remaining thirty five chicks (the control group) were mock-challenged with distilled water, and this process was completed by two technicians within half an hour.   After the last chick was inoculated with bacterial broth, eight challenged chicks and three control chicks were randomly selected. They were weighed, and 0.2 ml-1 ml blood was drawn for testing cytokines and antibodies via ELISA. The chicks were then sacrificed via cervical dislocation immediately after anesthesia with 150 mg/kg sodium pentobarbital. This process was repeated at 2 hours post-infection (hpi), 4 hpi, 8 hpi, 24 hpi, 3 days post-infection (dpi), 5dpi, 7dpi, 12dpi, and 21dpi.

value: Guangxi Yellow

value: Spleen

tag: age

value: 21 days


title: Spleen-12dpi-challenged-rep2

description: Gene expression profile of spleen at 12 days post infected with Salmonella pullorum

value: 13 days


title: Spleen-12dpi-challenged-rep3


title: Spleen-7dpi-control

description: Gene expression profile of spleen at 7 days post infected with Salmonella pullorum

value: 8 days


title: Spleen-21dpi-control-26


title: Spleen-3dpi-challenged-rep3

description: Gene expression profile of spleen at 3 days post infected with Salmonella pullorum

value: 4 days


title: Spleen-1dpi-challenged-rep2

description: Gene expression profile of spleen at 1 day post infected with Salmonella pullorum

value: 2 days


title: Spleen-21dpi-challenged-rep1


title: Spleen-3dpi-challenged-rep1


title: Spleen-5dpi-challenged-rep2

description: Gene expression profile of spleen at 5 days post infected with Salmonella pullorum

value: 6 days


title: Spleen-3dpi-challenged-rep2


title: Spleen-1dpi-control


title: Spleen-12dpi-control


title: Spleen-5dpi-challenged-rep1


title: Spleen-1dpi-challenged-rep1


title: Spleen-7dpi-challenged-rep2


title: Spleen-12dpi-challenged-rep1


title: Spleen-5dpi-challenged-rep3


title: Spleen-5dpi-control


title: Spleen-8hpi-challenged-rep3

description: Gene expression profile of spleen at 8 hours post infected with Salmonella pullorum


title: Spleen-8hpi-control


title: Spleen-21dpi-control-25


title: Spleen-7dpi-challenged-rep3


title: Spleen-8hpi-challenged-rep1


title: Spleen-3dpi-control


title: Spleen-8hpi-challenged-rep2


title: Spleen-1dpi-challenged-rep3


title: Spleen-4hpi-control

description: Gene expression profile of spleen at 4 hours post infected with Salmonella pullorum


title: Spleen-7dpi-challenged-rep1


title: Spleen-2hpi-challenged-rep3

description: Gene expression profile of spleen at 2 hours post infected with Salmonella pullorum


title: Spleen-2hpi-control


title: Spleen-4hpi-challenged-rep2


title: Spleen-2hpi-challenged-rep1


title: Spleen-2hpi-challenged-rep2


title: Spleen-4hpi-challenged-rep1


title: Spleen-4hpi-challenged-rep3


title: TNBS_w5d2_rep1

description: Hy3: Mice were sacrificed 7 days after the fourth cycle (w4d7), representing recovering phase of colitis

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing: image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Annotation is based on miRBASE version 14.0

treatment_protocol: Wild type c57BL/6 mice were sensitized by application of 1% 2-4-6-trinitrobenzenesulphonic acid (TNBS) (Sigma Chemical Co., St. Louis, MO) in 50% ethanol on skin on day -7 (week 1). On day 0 (week 2), mice were given an enema of 5ul/g body weight of 2.5% TNBS in 50% ethanol under anesthesia. Subsequent TNBS enema was repeated on day 7 (week 3) and 14 (week 4). Mice were sacrificed 2 days after the second cycle (w2d2) for the assessment of acute colitis and  2 days after the fourth cycle (w4d2) for the assessment of chronic colitis. A group of mice were sacrificed 7 days after the fourth cycle (w4d7 or w5d2), representing recovering phase of colitis.

value: colon (cross section)

value: wild type

source_name: Total RNA from pooled from individual  samples

value: reference


title: TNBS_w4d2_rep2

description: Hy3: Mice were sacrificed 2 days after the fourth cycle (w4d2) for the assessment of chronic colitis


title: TNBS_w5d2_rep2


title: A9

city: Ningbo

first: Zhisen

last: Shen

address: No.57 Xingning Road

department: Department of Otorhinolaryngology (Head and Neck Surgery)

institute: Lihuili Hospital of Ningbo University

description: Dysplasia,Tis

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used for hybridization. Hybridization was performed in a SureHyb Hybridization Chamber (Agilent) at 65°C for 17 h.

scan_protocol: The slides were scanned with an Agilent DNA Microarray Scanner (Agilent p/n G2565BA)

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies).After quantile normalization of the raw data, LncRNAs and mRNAs that at least 10 out of 14 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Normalization was performed using the Agilent GeneSpring GX v12.0 software

source_name: Laryngeal cancer tissue

label_protocol: An Agilent Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) was used to label 1μg of total RNA according to the manufacturer’s protocol

extract_protocol: Total RNA was extracted by using TRIzol® Reagent (Invitrogen life technologies) according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrohoresis.

value: Laryngeal cancer tissue


title: A3

description: LSCC cancer tissue,well,T2N1M0


title: A4

description: LSCC cancer tissue,poorly,T3N1M0


title: TNBS_w4d2_rep1


title: A5

description: LSCC cancer tissue,moderately,T3N2M0


title: TNBS_w2d2_rep2

description: Hy3: Mice were sacrificed 2 days after the second cycle (w2d2) for the assessment of acute colitis


title: TNBS_w2d2_rep1


title: B3

description: A3 paired adjacent normal tissue

source_name: Paracancerous tissue

value: Paracancerous tissue


title: B7

description: A7 paired adjacent normal tissue


title: B4

description: A4 paired adjacent normal tissue


title: B5

description: A5 paired adjacent normal tissue


title: colon_control_rep2

description: Hy3: Control mouse received H2O enema

value: Control


title: B9

description: A9 paired adjacent normal tissue


title: colon_control_rep1

description: Hy3: Control mouse received H2O enema


title: A2

description: LSCC cancer tissue,moderately,T3N1M0


title: colon_IL10KO_rep2

description:
Hy3: IL10ko mice with colitis, no special treatment.
IL10KO-2

treatment_protocol: Wild type c57BL/6 mice were fed ad libitum with 2.5% (wt/vol) dextran sodium sulfate (DSS, 40KDa, ICN Biochemicals, Aurora, OH) in drinking water for 1, 3 or 5 days to induce acute phase colitis. To induce chronic colitis, C57BL/6 mice were supplied with 2.5% DSS in drinking water for 5 days and switched back to normal drinking water for 9 days before the next cycles. Four cycles of the DSS treatment were used in the study.

value: colon

value: Il10 knockout


title: A7

description: Dysplasia,Tis


title: colon_DSS_c45_rep2

description:
Hy3: Mice were sacrificed 5 days after 4 cycles of DSS treatment
DSS-c4d5_2


title: B2

description: A2 paired adjacent normal tissue


title: colon_IL10KO_rep1

description:
Hy3: IL10ko mice with colitis, no special treatment.
IL10KO-1


title: A10

description: LSCC cancer tissue,moderately,T1N0M0


title: colon_DSS_c45_rep1

description:
Hy3: Mice were sacrificed 5 days after 4 cycles of DSS treatment
DSS-c4d5_1


title: colon_DSS_day3_rep2

description:
Hy3: Mice were sacrificed 3 days post DSS in drinking H2O.
DSS-d3_2


title: colon_DSS_day5_rep2

description:
Hy3: Mice were sacrificed 5 days post DSS in drinking H2O.
DSS-d5_2


title: hESp5-E5

type: SRA

city: San Francisco

first: Michelle

middle: M

last: Chan

state: CA

institute: UCSF

description: RRBS; Raw data not supplied for human subjects due to privacy concerns

library_source: genomic

data_processing:
Alignment using Maq with the following params: maq map -D -s 0 -M c -e 100
Count the number methylated vs unmethylated CpGs (C vs T; G vs A on reverse)
Join the cpg files together
Add the CpG density column (#CpGs +/- 50bp)
Tile the cpg file
Average technical replicates
Supplementary_files_format_and_content: .cpgs: (chromosome,position,seenCount,methylatedCount);hDev100bpMeFinal.txt/mDer100bpMe.txt: (position,100bp methylation value,CpG density)
Genome Build: hg19

Raw data not supplied for human subjects due to privacy concerns

source_name: ESC passage 5

growth_protocol: hESCs were derived and cultured on gamma-irradiated mouse embryonic fibroblasts (MEFs) in derivation media consisting of KO-DMEM (Life Technologies), 15% KO-SR (Life Technologies), 2.5% Fetal Bovine Serum (FBS) (Hyclone), 2mM Glutamax, 1% non-essential amino acids, 50units/ml penicillin and 50μg/ml streptomycin (Life Technologies), 0.055mM β-mercaptoethanol (Life Technologies), 10ng/ml bFGF (Millipore).  mESCs were derived from immunosurgically isolated ICM of E3.5 blastocysts from C57Bl/6 x 129S1/SvIMJ hybrid crosses and propogated on gamma-irradiated MEFs in one of three conditions: mES - 15% Fetal Bovin Serum (Hyclone) supplemented KO-DMEM plus LIF (Millipore); mPD - 15% FBS supplemented KO-DMEM plus LIF and 1 µM PD0325901 (Stemgent), or in N2/B27 supplemented KO-DMEM containing LIF, 1 µM PD0325901 and 3 µM CHIR99021 (Stemgent) (m2i).  All mouse media were additionally supplemented with 2mM Glutamax, 1% non-essential amino acids, 50units/ml penicillin and 50μg/ml streptomycin (Life Technologies), 0.055mM β-mercaptoethanol (Life Technologies).

extract_protocol:
DNA was extracted from all tissue using 14 hour incubation in 300 ug/mL Proteinase K followed by ethanol precipitation and elusion in EB buffer
Reduced representation bisulfite libraries were prepared from Proteinase K treated, MspI digested DNA following ligation with methylated standard adapters, size selection, bisulfite conversion, and amplification of the final libraries. Reduced representation bisulfite sequencing libraries are designed to enrich for a consistent subset of CpGs in the genome using MspI digestion (C'CGG cutting), adapater ligation and bisulfite conversion to generate base resolution maps of cytosine methylation on a consistent genome scale

treatment_protocol: hICM, hTE,mICM and mTE were isolated using standard micromanipulation equipment and a Hamilton Thorne XYClone laser with 300 µs pulsing at 100% intensity. hBlast and 8c embryos were thawed using the Quinn’s Advantage Embryo Thaw Kit (SAGE), screened for morphology, and purified from the Zona Pellucida using Acid Tyrode's solution (Sigma).  Human sperm was purified via centrifugation through a PureCeption gradient solution  (PureCeption 100% Isotonic Solution, Quinn’s Advantage Medium with HEPES, In-Vitro Fertilization Inc) of 90% and 47% in a 15ml conical tube.  C57Bl/6 x 129S1/SvIMJ E6.5 Epi and ExE were dissected from implanted deciduae and purified of visceral endoderm via incubation in 0.5% trypsin/2.5% pancreatin (Sigma) dissolved in PBS for 20 minutes at 4ºC.

tag: developmental stage

value: ESC passage 5

tag: passage

tag: sequenced molecule

value: Msp1 digested bisulfite converted genomic DNA


title: hESp5-E4


title: hESp1-E5

source_name: ESC passage 1

value: ESC passage 1


title: hESp1-E1


title: hESp1-E4


title: colon_DSS_day3_rep1

description:
Hy3: Mice were sacrificed 3 days post DSS in drinking H2O.
DSS-d3_1


title: hESp0-E5

source_name: ESC outgrowth

value: ESC outgrowth


title: hICM-2

source_name: Inner Cell Mass

value: Inner Cell Mass


title: hTE-2

source_name: Trophectoderm

value: Trophectoderm


title: hESp0-E1


title: hTE-1


title: colon_DSS_day1_rep2

description:
Hy3: Mice were sacrificed 1 day post DSS in drinking H2O.
DSS-d1_2


title: colon_H2O_rep1

description:
Hy3: Control mouse received regular drinking H2O
H20-1


title: colon_DSS_day1_rep1

description:
Hy3: Mice were sacrificed 1 day post DSS in drinking H2O.
DSS-d1_1


title: colon_H2O_rep2

description:
Hy3: Control mouse received regular drinking H2O
H20-2


title: hESp0-E4


title: hBlastSingle-5

source_name: Single Blastocyst

value: Single Blastocyst


title: hBlastSingle-2


title: hICM-1


title: hBlast-2

source_name: Blastocyst - pooled

value: Blastocyst - pooled


title: hBlast-1


title: colon_DSS_day5_rep1

description:
Hy3: Mice were sacrificed 5 days post DSS in drinking H2O.
DSS-d5_1


title: h8c-2

source_name: 8 cell embryo

value: 8 cell embryo


title: h8c-1


title: hSperm-534-90

source_name: Sperm

value: Sperm


title: hSperm-533-90


title: hSperm-530-90


title: hSperm-524-90


title: hBlast-3


title: dsho1dmsb2 Parafilm+HDA 12h, biological rep3

city: Marburg

first: Regine

last: Kahmann

address: Karl-von-Frisch Str. 10

department: Organismic Interactions

country: Germany

institute: MPI for Terrestrial Microbiology

description: Gene expression data from U. maydis sho1 msb2 double deletion mutant incubated for 12 on hydrophobic surface with 16-hydroxy hexadecanoic acid

hyb_protocol: 15 ug of fragmented aRNA were hybridized on GeneChip UstilagoA custom arrays and washed with Affymetrix protocols (GeneChip Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)

scan_protocol: GeneChips were scanned using Affymetrix GSC3000G

data_processing: Data was analyzed with GCOS (Affymetrix Microarray Suite 5.9) to create CEL files. Data was normalized with the RMA method using Partek Genomics Suite 6.5

organism: Mycosarcoma maydis

source_name: U. maydis AM1dsho1dmsb2 culture supplemented with 16-hydroxy hexadecanoic acid sprayed on parafilm surface

label_protocol: Biotinylated aRNA was prepared from 100 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix)

growth_protocol: Ustilago maydis strains were grown to mid-log phase (OD600 of 0.8) in liquid YEPSL medium and resuspended in 2% YEPSL (OD600 of 1.0) supplemented with or without 100 uM 16-hydroxy hexadecanoic acid (HDA).

extract_protocol: Cells were harvested from the surfaces using a cell scraper and total RNA was extracted with Aquaphenol/Chloroform.

treatment_protocol: Cell suspensions were sprayed on glass or Parafilm; droplet size on Parafilm did not exceed 2 mm

tag: cellular differentiation

value: filamentous cells

tag: time

value: incubated for 12h on hydrophobic surface with 16-hydroxy hexadecanoic acid


title: dsho1dmsb2 Parafilm+HDA 12h, biological rep2


title: dsho1dmsb2 Parafilm+HDA 12h, biological rep1


title: dsho1dmsb2 Parafilm 12h, biological rep2

description: Gene expression data from U. maydis sho1 msb2 double deletion mutant incubated for 12 on hydrophobic surface

source_name: U. maydis AM1dsho1dmsb2 culture sprayed on parafilm surface

value: incubated for 12h on hydrophobic surface


title: dsho1dmsb2 Parafilm 12h, biological rep3


title: dsho1dmsb2 Parafilm 12h, biological rep1


title: RPMI 8226 myeloma cells expressing cyclin D1-GFP fusion protein (sample 3)

city: Caen Cedex

first: Brigitte

last: Sola

address: CHU Côte de Nacre

department: UFR de médecine

country: France

institute: Université de Caen

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: RPMI 8226, cyclin D1-GFP

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

growth_protocol: RPMI 8226 and LP1 cells were transfected either with the pEGFP-N1 plasmid or an expression plasmid encoding cyclin D1a (long form of cyclin D1) fused to GFP. Cells were cultured in a selective medium containing G418, surviving cells were then cloned by limiting dilution. One clone of each series was maintained in RPMI 1640 medium containing L-glutamine, fetal calf serum and antibiotics.

extract_protocol: Total RNA was extracted from cultured cells withTrizol reagent and clean-up with the RNAeasy Mini kit (Qiagen) according to the supplier. Quality control was performed with a NanoDrop.

value: Multiple myeloma

value: RPMI 8226


title: AM1 Parafilm 12h, biological rep3

description: Gene expression data from U. maydis incubated for 12 on hydrophobic surface

source_name: U. maydis AM1 culture sprayed on parafilm surface


title: AM1 Parafilm+HDA 12h, biological rep2

description: Gene expression data from U. maydis incubated for 12 on hydrophobic surface with 16-hydroxy hexadecanoic acid

source_name: U. maydis AM1 culture supplemented with 16-hydroxy hexadecanoic acid sprayed on parafilm surface


title: AM1 Parafilm 12h, biological rep2


title: AM1 Parafilm+HDA 12h, biological rep3


title: AM1 Parafilm+HDA 12h, biological rep1


title: LP1 myeloma cells expressing GFP protein (sample 1)

source_name: LP1, GFP


title: RPMI 8226 myeloma cells expressing cyclin D1-GFP fusion protein (sample 1)


title: RPMI 8226 myeloma cells expressing GFP  protein (sample 3)

source_name: RPMI 8226, GFP


title: RPMI 8226 myeloma cells expressing GFP  protein (sample 4)


title: LP1 myeloma cells expressing GFP protein (sample 3)


title: RPMI 8226 myeloma cells expressing GFP  protein (sample 1)


title: AM1 Parafilm 12h, biological rep1


title: RPMI 8226 myeloma cells expressing GFP  protein (sample 2)


title: RPMI 8226 myeloma cells expressing cyclin D1-GFP fusion protein (sample 2)


title: AM1 Glass 2h, biological rep3

description: Gene expression data from U. maydis incubated for 2h on hydrophilic surface

source_name: U. maydis AM1 culture sprayed on glass surface

value: yeast-like cells

value: 2 h

value: incubated for 2h on hydrophilic surface


title: LP1 myeloma cells expressing GFP protein (sample 4)


title: RPMI 8226 myeloma cells expressing cyclin D1-GFP fusion protein (sample 4)


title: LP1 myeloma cells expressing cyclin D1-GFP fusion protein (sample 2)

source_name: LP1, cyclin D1-GFP


title: LP1 myeloma cells expressing GFP protein (sample 2)


title: LP1 myeloma cells expressing cyclin D1-GFP fusion protein (sample 1)


title: LP1 myeloma cells expressing cyclin D1-GFP fusion protein (sample 4)


title: LP1 myeloma cells expressing cyclin D1-GFP fusion protein (sample 3)


title: AM1 Glass 2h, biological rep1


title: AM1 Glass 2h, biological rep2


title: Knockout Heart DOX treated, biological rep3

city: beijing

first: zhang

middle: yun

last: long

state: beijing

address: No.10 Xitoutiao, You An Men

department: Department of Physiology and Pathophysiology,

institute: School of Basic Medical Sciences, Capital Medical University

description: Gene expression data from CHIP knockout mouse herat DOX treated for 1dose of 15mg/kg

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

source_name: Mouse heart DOX treated for 1dose of 15mg/kg

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Eight to ten-week-old wild type or CHIP knockout C57BL/6J male mice were kept at least 5 days at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

treatment_protocol: Wild type or CHIP knockout C57BL/6J mice were injected DOX at1dose of 15mg/kg,and the hearts were taken out after 5 days.

value: DOX treated for 1dose of 15mg/kg


title: WT Heart DOX treated, biological rep3

description: Gene expression data from wild type mouse heart DOX treated for 1dose of 15mg/kg


title: WT Heart DOX treated, biological rep2


title: Knockout Heart with no treatment, biological rep3

description: Gene expression data from CHIP knockout mouse heart with no DOX treatmeant

source_name: Mouse heart with no DOX treatmeant

value: no DOX


title: Knockout Heart DOX treated, biological rep1


title: Knockout Heart DOX treated, biological rep2


title: Knockout Heart with no treatment, biological rep1


title: WT Heart DOX treated, biological rep1


title: Ts1Cje P1 hippocampus biological replicate 3

city: UPM Serdang

first: King Hwa

last: Ling

state: Selangor

address: Faculty of Medicine and Health Sciences

department: Department of Biomedical Science

country: Malaysia

institute: Universiti Putra Malaysia

hyb_protocol: Labelled RNA samples were hybridised onto Affymetrix GeneChip Mouse Genome 430 2.0 Arrays according to the AGRFs protocol. Samples were prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that included 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using a GeneChip scanner 3000 with the scanner operating software, GCOS.

data_processing: Normalization with gcRMA using the full (fast=FALSE) algorithm.

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

growth_protocol: All sex matched disomic and trisomic littermates involved in the study were generated by mating Ts1Cje males with C57BL/6 female mice. All mice were kept in a controlled environment of equal light/dark cycle. Unlimited standard pellet diet and water were provided. Genomic DNA was extracted from mouse-tails and genotyped using multiplex PCR primers for neomycin and Grik1 (as an internal control) as described previously (Sago et al., PNA, 95(11): 6256-6261).

extract_protocol: Total RNA was extracted using a Qiagen Rneasy micro kit according to the manufacturer's instructions with a Dnase I digestion step.

value: Female

tag: strain

value: Ts1Cje (Trisomic)

value: Hippocampus


title: B10

description: A10 paired adjacent normal tissue

source_name: Paracancerous tissue

value: Paracancerous tissue


title: Wildtype P15 cerebellum biological replicate 3

tag: gender

value: C57BL/6 (disomic)

value: Cerebellum


title: Wildtype P84 cerebral cortex biological replicate 3

tag: tissue

value: Cerebral cortex


title: Knockout Heart with no treatment, biological rep2


title: Wildtype P30 hippocampus biological replicate 3


title: WT Heart with no treatment, biological rep3

description: Gene expression data from wild type mouse heart with no DOX treatmeant


title: Ts1Cje P30 cerebellum biological replicate 3


title: Wildtype P15 cerebral cortex biological replicate 3


title: WT Heart with no treatment, biological rep1


title: Wildtype P1 cerebellum biological replicate 3


title: Wildtype P15 hippocampus biological replicate 3


title: WT Heart with no treatment, biological rep2


title: Ts1Cje P84 cerebral cortex biological replicate 3


title: Ts1Cje P30 cerebral cortex biological replicate 3


title: Ts1Cje P84 cerebellum biological replicate 3


title: Wildtype P30 cerebral cortex biological replicate 3


title: Ts1Cje P84 hippocampus biological replicate 3


title: Wildtype P84 hippocampus biological replicate 3


title: Ts1Cje P1 cerebral cortex biological replicate 3


title: Ts1Cje P15 cerebral cortex biological replicate 3


title: Wildtype P1 cerebral cortex biological replicate 3


title: Wildtype P1 hippocampus biological replicate 3


title: Ts1Cje P30 cerebral cortex biological replicate 2


title: Wildtype P84 cerebellum biological replicate 3


title: Wildtype P84 cerebral cortex biological replicate 2


title: Ts1Cje P15 hippocampus biological replicate 3


title: Ts1Cje P30 hippocampus biological replicate 3


title: Ts1Cje P15 cerebellum biological replicate 3


title: Wildtype P30 cerebellum biological replicate 2


title: Ts1Cje P15 hippocampus biological replicate 2


title: Ts1Cje P84 cerebellum biological replicate 2


title: Ts1Cje P84 cerebral cortex biological replicate 2


title: Ts1Cje P1 cerebellum biological replicate 3


title: Wildtype P1 cerebellum biological replicate 2


title: Wildtype P15 cerebral cortex biological replicate 2


title: Wildtype P84 cerebellum biological replicate 2


title: Ts1Cje P15 cerebellum biological replicate 2


title: Wildtype P84 hippocampus biological replicate 2


title: Wildtype P30 cerebellum biological replicate 3


title: Ts1Cje P30 hippocampus biological replicate 2


title: Ts1Cje P15 cerebral cortex biological replicate 2


title: Ts1Cje P1 cerebral cortex biological replicate 2


title: Wildtype P1 hippocampus biological replicate 2


title: Wildtype P1 cerebral cortex biological replicate 2


title: Wildtype P15 cerebellum biological replicate 2


title: Wildtype P30 hippocampus biological replicate 2


title: Ts1Cje P1 hippocampus biological replicate 2


title: Wildtype P30 cerebral cortex biological replicate 2


title: Ts1Cje P30 cerebellum biological replicate 2


title: Ts1Cje P84 hippocampus biological replicate 2


title: Wildtype P1 cerebral cortex biological replicate 1


title: Wildtype P15 hippocampus biological replicate 2


title: Wildtype P30 cerebral cortex biological replicate 1


title: Wildtype P15 cerebellum biological replicate 1


title: Ts1Cje P30 cerebellum biological replicate 1


title: Ts1Cje P15 hippocampus biological replicate 1


title: Wildtype P84 cerebellum biological replicate 1


title: Wildtype P15 hippocampus biological replicate 1


title: Ts1Cje P15 cerebellum biological replicate 1


title: Wildtype P30 hippocampus biological replicate 1


title: Ts1Cje P1 cerebellum biological replicate 2


title: Wildtype P30 cerebellum biological replicate 1


title: Ts1Cje P1 cerebral cortex biological replicate 1


title: Wildtype P84 cerebral cortex biological replicate 1


title: ZT16.5_unpulsed2

city: Leicester

first: Eran

last: Tauber

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol

scan_protocol: Affymetrix protocol.

data_processing: R/Bioconductor affylmGUI package (version 1.8.0)

organism: Drosophila melanogaster

source_name: head

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer's protocol

growth_protocol: Flies were maintened at 25deg. C on standard sugar media

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

treatment_protocol: After 4 days in LD 12:12, adult files (age 3-5 d) were exposed to 30 min saturating light pulse at ZT 15 (3 hr after lights off), and were snap frozen after 1 hr (Zt 16.5)

value: Canton-S

tag: treatment protocol

value: control


title: ZT16.5_unpulsed4


title: ZT16.5_pulsed 4

value: light pulse at ZT 15


title: Ts1Cje P84 hippocampus biological replicate 1


title: ZT16.5_unpulsed3


title: Ts1Cje P1 hippocampus biological replicate 1


title: Wildtype P1 cerebellum biological replicate 1


title: Ts1Cje P15 cerebral cortex biological replicate 1


title: ZT16.5_pulsed3


title: ZT16.5_unpulsed1


title: Wildtype P84 hippocampus biological replicate 1


title: Ts1Cje P84 cerebellum biological replicate 1


title: ZT16.5_pulsed2


title: ZT16.5_pulsed1


title: HEK293T cell culture,16h,transfected,biological rep 1

city: Lincoln

first: Timothy

last: Martin

state: NE

address: 32 Chase Hall

department: Biological Systems Engineering

institute: University of Nebraska-Lincoln

description: 16 h gene profile

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R 2.11.1 with Bioconductor 2.4. Arrays were normalised via RMA. Differential expression was obtained from normalized expression data using nonparametric mean-variance smoothing method (see PMID 21611181). For 2h, differential expression is between treated samples and untreated samples. For 8h and 16h, differential expression is between GFP+ and GFP- arrays.

source_name: HEK293T human embryonic epithelial kidney cell culture, transfected_16h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug purified RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: HEK293T cells were grown in T75 in DMEM supplemented with 10% FBS, 1% Pen/Strep, 1% Sodium Pyruvate.

extract_protocol: Total RNA was Trizol extracted and further purified using Qiagen RNeasy Mini kit according to the manufacturer's instructions.

treatment_protocol: Cationic Lipofectamine 2000 was mixed with pEGFP-LUC to form lipoplexes. Cells were treated with lipoplexes 18h after seeding. For 2h arrays, cells were harvested 2h after delivery of lipoplexes. For 8h and 16h arrays, cells were harvested and flow separated 8h or 16h, respectively, after delivery of lipoplexes into fluorescent (GFP positive; GFPP) and non-fluorescent (GFP minus; GFPM) populations. 2h control samples were not treated with lipoplexes.


title: HEK293T cell culture,16h,transfected,biological rep 3

description: 16 h gene profile


title: HEK293T cell culture,16h,untransfected,biological rep 3

description: 16 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, untransfected_16h


title: HEK293T cell culture,8h,transfected,biological rep 1

description: 8 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, transfected_8h


title: Ts1Cje P1 cerebellum biological replicate 1


title: HEK293T cell culture,16h,transfected,biological rep 2

description: 16 h gene profile


title: HEK293T cell culture,8h,untransfected,biological rep 3

description: 8 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, untransfected_8h


title: Ts1Cje P30 hippocampus biological replicate 1


title: Ts1Cje P84 cerebral cortex biological replicate 1


title: Ts1Cje P30 cerebral cortex biological replicate 1


title: Wildtype P15 cerebral cortex biological replicate 1


title: HEK293T cell culture,16h,untransfected,biological rep 2

description: 16 h gene profile


title: HEK293T cell culture,8h,transfected,biological rep 2

description: 8 h gene profile


title: HEK293T cell culture,2h,treated,biological rep 2

description: 2 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, treated_2h


title: Wildtype P1 hippocampus biological replicate 1


title: HEK293T cell culture,2h,treated,biological rep 3

description: 2 h gene profile


title: HEK293T cell culture,8h,untransfected,biological rep 2

description: 8 h gene profile


title: HEK293T cell culture,16h,untransfected,biological rep 1

description: 16 h gene profile


title: HEK293T cell culture,2h,treated,biological rep 1

description: 2 h gene profile


title: HEK293T cell culture,2h,untreated,biological rep 2

description: 2 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, untreated_2h


title: HEK293T cell culture,8h,untransfected,biological rep 1

description: 8 h gene profile


title: HEK293T cell culture,8h,transfected,biological rep 3

description: 8 h gene profile


title: PEI_HEK293T cell culture,16h,untransfected,biological rep 2

description: 16 h gene profile

treatment_protocol: Cationic 25kDa bPEI was mixed with pEGFP-LUC to form polyplexes. Cells were treated with polyplexes 18h after seeding. For 2h arrays, cells were harvested 2h after delivery of polyplexes. For 8h and 16h arrays, cells were harvested and flow separated 8h or 16h, respectively, after delivery of polyplexes into fluorescent (GFP positive; GFPP) and non-fluorescent (GFP minus; GFPM) populations. 2h control samples were not treated with polyplexes.


title: PEI_HEK293T cell culture,16h,transfected,biological rep 2

description: 16 h gene profile

source_name: HEK293T human embryonic epithelial kidney cell culture, transfected


title: PEI_HEK293T cell culture,16h,transfected,biological rep 1

description: 16 h gene profile


title: PEI_HEK293T cell culture,8h,transfected,biological rep 2

description: 8 h gene profile


title: PEI_HEK293T cell culture,8h,transfected,biological rep 3

description: 8 h gene profile


title: HEK293T cell culture,2h,untreated,biological rep 1

description: 2 h gene profile


title: PEI_HEK293T cell culture,8h,transfected,biological rep 1

description: 8 h gene profile


title: PEI_HEK293T cell culture,16h,untransfected,biological rep 1

description: 16 h gene profile


title: PEI_HEK293T cell culture,8h,untransfected,biological rep 3

description: 8 h gene profile


title: PEI_HEK293T cell culture,8h,untransfected,biological rep 1

description: 8 h gene profile


title: PEI_HEK293T cell culture,2h,treated,biological rep 2

description: 2 h gene profile


title: PEI_HEK293T cell culture,2h,treated,biological rep 1

description: 2 h gene profile


title: PEI_HEK293T cell culture,2h,untreated,biological rep 2

description: 2 h gene profile


title: PEI_HEK293T cell culture,2h,untreated,biological rep 1

description: 2 h gene profile


title: PEI_HEK293T cell culture,16h,transfected,biological rep 3

description: 16 h gene profile


title: PEI_HEK293T cell culture,2h,treated,biological rep 3

description: 2 h gene profile


title: PEI_HEK293T cell culture,8h,untransfected,biological rep 2

description: 8 h gene profile


title: PEI_HEK293T cell culture,16h,untransfected,biological rep 3

description: 16 h gene profile


title: Res-Ana (AD) replicate 2

city: Lyon

first: Julie

middle: A

last: Vendrell

state: Select a State or Province

address: 8 avenue Rockefeller

department: INSERM U1052

institute: ISPBL - Faculté de Pharmacie de Lyon

description: miRNA expression data from cell population of MCF-7aro displaying resistance to anastrozole (Res-Ana) treated in the presence of 25 nM of androstenedione, cell culture replicate 2

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: cell population of MCF-7 stably transfected with the human placental aromatase gene resistant to anastrozole (Res-Ana cells)

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cells were grown in DMEM medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA from cell culture was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations and subsequently quantified on a Nanodrop ND1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was checked using the BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Prior to experiment, cells were purged in Dulbecco’s Modified Eagle Medium without phenol red, supplemented with 3% steroid-depleted, dextran-coated and charcoal-treated fetal calf serum (DCC medium) for 4 days. Cells were then grown for 4 days in the presence of 25 nM of androstenedione. Media and treatment were changed every 2 days.

value: Breast cancer


title: NHP3_Anhui01_LL3_d3_3

status: Public on Jul 22 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 8X60K rhesus macaque (Design ID 048534) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were normalized using the quantile normalization method available in GeneData Analyst 7.6.

organism: Macaca fascicularis

source_name: Animal NHP3, Anhui01 infection, lung lesion, day3

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 8 adult cynomolgus macaques (Macaca fascicularis) were infected under anesthesia with 7x10^6 TCID50 A/H7N9/Anhui01/2013 by combined oral, intraocular, intranasal, and intratracheal instillation. Four animals each were humanely sacrificed on days 3 and 6 for necropsy and collection of lung, lung lesion, and trachea samples.

extract_protocol: All lysates were processed simultaneously. Samples were thawed and two additional volumes of RLT buffer with 0.01 volumes of 2-mercaptoethanol were added, followed by an additional two volumes of 70% ethanol. RNA was then extracted using QIAGEN microRNeasy spin columns per the manufacturer's protocol. Low-yield samples were concentrated using the RNA Clean and Concentrator (Zymo Research).

treatment_protocol: Tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC prior to further processing. Tissues were removed from RNAlater, washed in a small volume of RLT buffer, homogenized in 10-20 volumes (w/v) RLT with an equal volume of 70% ethanol and stored at -80°C until RNA isolation.

value: lung lesion

tag: infection

tag: time point

tag: animal id

value: adult

tag: biological replicate


title: NHP2_Anhui01_RLL_d3_2

source_name: Animal NHP2, Anhui01 infection, right lung lower lobe, day3

value: right lung lower lobe


title: NHP6_Anhui01_Trachea_d6_2

source_name: Animal NHP6, Anhui01 infection, trachea, day6

value: trachea


title: Res-Ana (AD) replicate 1

description: miRNA expression data from cell population of MCF-7aro displaying resistance to anastrozole (Res-Ana) treated in the presence of 25 nM of androstenedione, cell culture replicate 1

tag: cell type

tag: cell line


title: NHP6_Anhui01_LL2_d6_2

source_name: Animal NHP6, Anhui01 infection, lung lesion, day6


title: NHP8_Anhui01_RLL_d6_4

source_name: Animal NHP8, Anhui01 infection, right lung lower lobe, day6


title: NHP2_Anhui01_LL2_d3_2

source_name: Animal NHP2, Anhui01 infection, lung lesion, day3


title: NHP4_Anhui01_LL2_d3_4

source_name: Animal NHP4, Anhui01 infection, lung lesion, day3


title: NHP8_Anhui01_Trachea_d6_4

source_name: Animal NHP8, Anhui01 infection, trachea, day6


title: NHP1_Anhui01_LL3_d3_1

source_name: Animal NHP1, Anhui01 infection, lung lesion, day3


title: NHP3_Anhui01_Trachea_d3_3

source_name: Animal NHP3, Anhui01 infection, trachea, day3


title: NHP5_Anhui01_RLL_d6_1

source_name: Animal NHP5, Anhui01 infection, right lung lower lobe, day6


title: NHP4_Anhui01_RLL_d3_4

source_name: Animal NHP4, Anhui01 infection, right lung lower lobe, day3


title: NHP1_Anhui01_RLL_d3_1

source_name: Animal NHP1, Anhui01 infection, right lung lower lobe, day3


title: NHP7_Anhui01_RLL_d6_3

source_name: Animal NHP7, Anhui01 infection, right lung lower lobe, day6


title: NHP8_Anhui01_LL3_d6_4

source_name: Animal NHP8, Anhui01 infection, lung lesion, day6


title: NHP3_Anhui01_RLL_d3_3

source_name: Animal NHP3, Anhui01 infection, right lung lower lobe, day3


title: NHP6_Anhui01_RLL_d6_2

source_name: Animal NHP6, Anhui01 infection, right lung lower lobe, day6


title: NHP2_Anhui01_Trachea_d3_2

source_name: Animal NHP2, Anhui01 infection, trachea, day3


title: NHP5_Anhui01_LL3_d6_1

source_name: Animal NHP5, Anhui01 infection, lung lesion, day6


title: NHP1_Anhui01_Trachea_d3_1

source_name: Animal NHP1, Anhui01 infection, trachea, day3


title: NHP7_Anhui01_LL3_d6_3

source_name: Animal NHP7, Anhui01 infection, lung lesion, day6


title: NHP7_Anhui01_Trachea_d6_3

source_name: Animal NHP7, Anhui01 infection, trachea, day6


title: NHP5_Anhui01_Trachea_d6_1

source_name: Animal NHP5, Anhui01 infection, trachea, day6


title: WT: 1030 min, OD 6.98

first: Aaron

last: Brooks

address: 401 Terry Avenue North

institute: Institute for Systems Biology

hyb_protocol: Scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: RNAs were direct labeled with Alexa547 and Alexa647 dyes (Kreatech). See Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35.

growth_protocol: E. coli K-12 MG1655 inoculated to starting OD = 0.05 in 2L LB in Biflo 110 bioreactor. Growth at 37C, 250 rpm stirring, 2.3 LPM air

extract_protocol: RNA extracted from pellets using hot phenol extraction following Gross lab protocol: http://derisilab.ucsf.edu/microarray/pdfs/Total_RNA_from_Ecoli.pdf

treatment_protocol: Cells collected by centrifugation. Followed by flash freeze of pellets in liquid nitrogen. Storage at -80C.


title: WT: 450 min, OD 4.45


title: WT: 105 min, OD 0.99


title: WT: 135 min, OD 1.41


title: DLBCL_MPI-900

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

description: Tumor_MPI-900; Hybridized to 250K_Sty

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping Console. 4.1.4.840. For further downstream analysis, see corresponding publication.
Results type: Genotyping
Programmatic identifier: GDMTAnalysis.BRMBaseCall.1
Algorithm: Genotypingbrlmm 1.0

source_name: frozen biopsy

extract_protocol: Genomic DNA was extracted using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: lymphoma type

value: diffuse large B cell lymphoma

tag: lymphoma subtype

value: GCB


title: WT: 1500 min, OD 7.30


title: DLBCL_MPI-902

description: Tumor_MPI-902; Hybridized to 250K_Sty

value: unclassified/Type 3


title: NHP4_Anhui01_Trachea_d3_4

source_name: Animal NHP4, Anhui01 infection, trachea, day3

tag: developmental stage


title: DLBCL_MPI-899

description: Tumor_MPI-899; Hybridized to 250K_Sty


title: DLBCL_MPI-857

description: Tumor_MPI-857; Hybridized to 250K_Sty

value: ABC


title: DLBCL_MPI-904

description: Tumor_MPI-904; Hybridized to 250K_Sty


title: WT: 90 min, OD 0.43


title: DLBCL_MPI-875

description: Tumor_MPI-875; Hybridized to 250K_Sty


title: DLBCL_MPI-864

description: Tumor_MPI-864; Hybridized to 250K_Sty


title: DLBCL_MPI-852

description: Tumor_MPI-852; Hybridized to 250K_Sty


title: DLBCL_MPI-874

description: Tumor_MPI-874; Hybridized to 250K_Sty


title: LL34 control shRNA, biological rep3

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

hyb_protocol: cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed.  Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).

source_name: MLE12 cells

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.

growth_protocol: MLE12 cells were cultured in Hams F12, Corning Cellgro, Manassas, VA; 2% FBS, 0.005mg/ml insulin; 0.01mg/ml transferrin; 30nM sodium selenite; 10nM hydrocortisone;10nM beta-estradiol; 10mM HEPES; and, 2mM L-glutamine, to 60% confluency prior to viral infection.

extract_protocol: RNA was extracted using Rneasy mini kit (Qiagene)

treatment_protocol: Lentivirus was produced in HEK-293T cells in 100-mm cell culture dishes were co-transfected with 3 µg psPAX2, 1 µg pMD2.G, and 4 µg pLKO.1 bearing specific shRNAs. Cells were incubated in transfection medium (DMEM; Gibco, Grand Island, NY) for 12 h, followed by incubation in DMEM supplemented with 10% fetal bovine serum, for 36 h. The culture medium containing lentivirus particles was collected, purified using Amicon Ultra-4 100k centrifugal filters (Millipore, Billerica, MA), and reconstituted in an equivalent volume of MLE12 media. MLE12 cells at 60% confluency were infected with lentivirus-bearing specific shRNAs in a 1:4 ratio with fresh MLE12 media containing 8 µg/ml polybrene for 12 hours. Infected MLE12 cells were subcultured for 65 hours prior to sample collection.

tag: treatment

value: Scrambled shRNA


title: DLBCL_MPI-856

description: Tumor_MPI-856; Hybridized to 250K_Sty


title: DLBCL_MPI-873

description: Tumor_MPI-873; Hybridized to 250K_Sty


title: DLBCL_MPI-859

description: Tumor_MPI-859; Hybridized to 250K_Sty


title: LL34 control shRNA, biological rep1


title: DLBCL_MPI-880

description: Tumor_MPI-880; Hybridized to 250K_Sty


title: DLBCL_MPI-901

description: Tumor_MPI-901; Hybridized to 250K_Sty


title: DLBCL_MPI-865

description: Tumor_MPI-865; Hybridized to 250K_Sty


title: DLBCL_MPI-883

description: Tumor_MPI-883; Hybridized to 250K_Sty


title: DLBCL_MPI-851

description: Tumor_MPI-851; Hybridized to 250K_Sty


title: LL34 control shRNA, biological rep2


title: LL34 targeting shRNA, biological rep3

value: LL34 shRNA


title: DLBCL_MPI-855

description: Tumor_MPI-855; Hybridized to 250K_Sty


title: DLBCL_MPI-850

description: Tumor_MPI-850; Hybridized to 250K_Sty


title: LL34 targeting shRNA, biological rep1


title: WT: 45 min, OD 0.25


title: DLBCL_MPI-876

description: Tumor_MPI-876; Hybridized to 250K_Sty


title: NANCI control shRNA, biological rep3


title: DLBCL_MPI-869

description: Tumor_MPI-869; Hybridized to 250K_Sty


title: DLBCL_MPI-881

description: Tumor_MPI-881; Hybridized to 250K_Sty


title: WT: 60 min, OD 0.43


title: DLBCL_MPI-858

description: Tumor_MPI-858; Hybridized to 250K_Sty


title: NANCI control shRNA, biological rep2


title: NANCI targeting shRNA, biological rep2

value: NANCI shRNA


title: NANCI targeting shRNA, biological rep3


title: NANCI control shRNA, biological rep1


title: NANCI targeting shRNA, biological rep1


title: LL34 targeting shRNA, biological rep2


title: DLBCL_MPI-849

description: Tumor_MPI-849; Hybridized to 250K_Sty


title: DLBCL_MPI-844

description: Tumor_MPI-844; Hybridized to 250K_Sty


title: DLBCL_MPI-848

description: Tumor_MPI-848; Hybridized to 250K_Sty


title: DLBCL_MPI-846

description: Tumor_MPI-846; Hybridized to 250K_Sty


title: DLBCL_MPI-842

description: Tumor_MPI-842; Hybridized to 250K_Sty


title: DLBCL_MPI-841

description: Tumor_MPI-841; Hybridized to 250K_Sty


title: DLBCL_MPI-835

description: Tumor_MPI-835; Hybridized to 250K_Sty


title: DLBCL_MPI-840

description: Tumor_MPI-840; Hybridized to 250K_Sty


title: DLBCL_MPI-832

description: Tumor_MPI-832; Hybridized to 250K_Sty


title: DLBCL_MPI-815

description: Tumor_MPI-815; Hybridized to 250K_Sty


title: DLBCL_MPI-810

description: Tumor_MPI-810; Hybridized to 250K_Sty


title: DLBCL_MPI-820

description: Tumor_MPI-820; Hybridized to 250K_Sty


title: DLBCL_MPI-823

description: Tumor_MPI-823; Hybridized to 250K_Sty


title: DLBCL_MPI-843

description: Tumor_MPI-843; Hybridized to 250K_Sty


title: DLBCL_MPI-806

description: Tumor_MPI-806; Hybridized to 250K_Sty


title: DLBCL_MPI-830

description: Tumor_MPI-830; Hybridized to 250K_Sty


title: DLBCL_MPI-821

description: Tumor_MPI-821; Hybridized to 250K_Sty


title: DLBCL_MPI-812

description: Tumor_MPI-812; Hybridized to 250K_Sty


title: DLBCL_MPI-800

description: Tumor_MPI-800; Hybridized to 250K_Sty


title: DLBCL_MPI-813

description: Tumor_MPI-813; Hybridized to 250K_Sty


title: DLBCL_MPI-822

description: Tumor_MPI-822; Hybridized to 250K_Sty


title: DLBCL_MPI-807

description: Tumor_MPI-807; Hybridized to 250K_Sty


title: DLBCL_MPI-802

description: Tumor_MPI-802; Hybridized to 250K_Sty


title: DLBCL_MPI-808

description: Tumor_MPI-808; Hybridized to 250K_Sty


title: DLBCL_MPI-799

description: Tumor_MPI-799; Hybridized to 250K_Sty


title: DLBCL_MPI-796

description: Tumor_MPI-796; Hybridized to 250K_Sty


title: DLBCL_MPI-801

description: Tumor_MPI-801; Hybridized to 250K_Sty


title: DLBCL_MPI-794

description: Tumor_MPI-794; Hybridized to 250K_Sty


title: DLBCL_MPI-792

description: Tumor_MPI-792; Hybridized to 250K_Sty


title: DLBCL_MPI-795

description: Tumor_MPI-795; Hybridized to 250K_Sty


title: DLBCL_MPI-839

description: Tumor_MPI-839; Hybridized to 250K_Sty


title: DLBCL_MPI-781

description: Tumor_MPI-781; Hybridized to 250K_Sty


title: DLBCL_MPI-791

description: Tumor_MPI-791; Hybridized to 250K_Sty


title: DLBCL_MPI-834

description: Tumor_MPI-834; Hybridized to 250K_Sty


title: DLBCL_MPI-780

description: Tumor_MPI-780; Hybridized to 250K_Sty


title: DLBCL_MPI-768

description: Tumor_MPI-768; Hybridized to 250K_Sty


title: DLBCL_MPI-766

description: Tumor_MPI-766; Hybridized to 250K_Sty


title: DLBCL_MPI-769

description: Tumor_MPI-769; Hybridized to 250K_Sty


title: DLBCL_MPI-790

description: Tumor_MPI-790; Hybridized to 250K_Sty


title: DLBCL_MPI-789

description: Tumor_MPI-789; Hybridized to 250K_Sty


title: DLBCL_MPI-761

description: Tumor_MPI-761; Hybridized to 250K_Sty


title: DLBCL_MPI-734

description: Tumor_MPI-734; Hybridized to 250K_Sty


title: DLBCL_MPI-783

description: Tumor_MPI-783; Hybridized to 250K_Sty


title: DLBCL_MPI-746

description: Tumor_MPI-746; Hybridized to 250K_Sty


title: DLBCL_MPI-767

description: Tumor_MPI-767; Hybridized to 250K_Sty


title: DLBCL_MPI-757

description: Tumor_MPI-757; Hybridized to 250K_Sty


title: DLBCL_MPI-762

description: Tumor_MPI-762; Hybridized to 250K_Sty


title: DLBCL_MPI-733

description: Tumor_MPI-733; Hybridized to 250K_Sty


title: DLBCL_MPI-735

description: Tumor_MPI-735; Hybridized to 250K_Sty


title: DLBCL_MPI-714

description: Tumor_MPI-714; Hybridized to 250K_Sty


title: DLBCL_MPI-782

description: Tumor_MPI-782; Hybridized to 250K_Sty


title: DLBCL_MPI-706

description: Tumor_MPI-706; Hybridized to 250K_Sty


title: DLBCL_MPI-745

description: Tumor_MPI-745; Hybridized to 250K_Sty


title: DLBCL_MPI-756

description: Tumor_MPI-756; Hybridized to 250K_Sty


title: DLBCL_MPI-755

description: Tumor_MPI-755; Hybridized to 250K_Sty


title: DLBCL_MPI-731

description: Tumor_MPI-731; Hybridized to 250K_Sty


title: DLBCL_MPI-765

description: Tumor_MPI-765; Hybridized to 250K_Sty


title: DLBCL_MPI-704

description: Tumor_MPI-704; Hybridized to 250K_Sty


title: DLBCL_MPI-702

description: Tumor_MPI-702; Hybridized to 250K_Sty


title: DLBCL_MPI-703

description: Tumor_MPI-703; Hybridized to 250K_Sty


title: DLBCL_MPI-737

description: Tumor_MPI-737; Hybridized to 250K_Sty


title: DLBCL_MPI-732

description: Tumor_MPI-732; Hybridized to 250K_Sty


title: DLBCL_MPI-700

description: Tumor_MPI-700; Hybridized to 250K_Sty


title: DLBCL_MPI-689

description: Tumor_MPI-689; Hybridized to 250K_Sty


title: DLBCL_MPI-730

description: Tumor_MPI-730; Hybridized to 250K_Sty


title: DLBCL_MPI-698

description: Tumor_MPI-698; Hybridized to 250K_Sty


title: DLBCL_MPI-688

description: Tumor_MPI-688; Hybridized to 250K_Sty


title: DLBCL_MPI-701

description: Tumor_MPI-701; Hybridized to 250K_Sty


title: DLBCL_MPI-635

description: Tumor_MPI-635; Hybridized to 250K_Sty


title: DLBCL_MPI-691

description: Tumor_MPI-691; Hybridized to 250K_Sty


title: DLBCL_MPI-407

description: Tumor_MPI-407; Hybridized to 250K_Sty


title: DLBCL_MPI-413

description: Tumor_MPI-413; Hybridized to 250K_Sty


title: DLBCL_MPI-684

description: Tumor_MPI-684; Hybridized to 250K_Sty


title: DLBCL_MPI-694

description: Tumor_MPI-694; Hybridized to 250K_Sty


title: DLBCL_MPI-686

description: Tumor_MPI-686; Hybridized to 250K_Sty


title: DLBCL_MPI-367

description: Tumor_MPI-367; Hybridized to 250K_Sty


title: DLBCL_MPI-404

description: Tumor_MPI-404; Hybridized to 250K_Sty


title: DLBCL_MPI-394

description: Tumor_MPI-394; Hybridized to 250K_Sty


title: DLBCL_MPI-295

description: Tumor_MPI-295; Hybridized to 250K_Sty


title: DLBCL_MPI-410

description: Tumor_MPI-410; Hybridized to 250K_Sty


title: DLBCL_MPI-398

description: Tumor_MPI-398; Hybridized to 250K_Sty


title: DLBCL_MPI-379

description: Tumor_MPI-379; Hybridized to 250K_Sty


title: DLBCL_MPI-199

description: Tumor_MPI-199; Hybridized to 250K_Sty


title: DLBCL_MPI-325

description: Tumor_MPI-325; Hybridized to 250K_Sty


title: DLBCL_MPI-399

description: Tumor_MPI-399; Hybridized to 250K_Sty


title: DLBCL_MPI-319

description: Tumor_MPI-319; Hybridized to 250K_Sty


title: DLBCL_MPI-690

description: Tumor_MPI-690; Hybridized to 250K_Sty


title: DLBCL_MPI-237

description: Tumor_MPI-237; Hybridized to 250K_Sty


title: DLBCL_MPI-250

description: Tumor_MPI-250; Hybridized to 250K_Sty


title: DLBCL_MPI-423

description: Tumor_MPI-423; Hybridized to 250K_Sty


title: DLBCL_MPI-233

description: Tumor_MPI-233; Hybridized to 250K_Sty


title: DLBCL_MPI-194

description: Tumor_MPI-194; Hybridized to 250K_Sty


title: DLBCL_MPI-402

description: Tumor_MPI-402; Hybridized to 250K_Sty


title: DLBCL_MPI-168

description: Tumor_MPI-168; Hybridized to 250K_Sty


title: DLBCL_MPI-176

description: Tumor_MPI-176; Hybridized to 250K_Sty


title: DLBCL_MPI-162

description: Tumor_MPI-162; Hybridized to 250K_Sty


title: DLBCL_MPI-131

description: Tumor_MPI-131; Hybridized to 250K_Sty


title: DLBCL_MPI-192

description: Tumor_MPI-192; Hybridized to 250K_Sty


title: DLBCL_MPI-120

description: Tumor_MPI-120; Hybridized to 250K_Sty


title: DLBCL_MPI-122

description: Tumor_MPI-122; Hybridized to 250K_Sty


title: DLBCL_MPI-115

description: Tumor_MPI-115; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-904

description: tumor RNA hybridized to HGU133A chip

data_processing: Probe intensities were normalized according to a variance-stabilization (vsn) method (Huber et al., Bioinformatics 2002). Gene-expression levels were estimated by fitting an additive model according to Irizarry et al. (Biostatistics 2003).

extract_protocol: RNA was extracted from frozen sections using Qiagen columns.

tag: subgroup


title: RNA_DLBCL_MPI-902

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-110

description: Tumor_MPI-110; Hybridized to 250K_Sty


title: DLBCL_MPI-187

description: Tumor_MPI-187; Hybridized to 250K_Sty


title: DLBCL_MPI-130

description: Tumor_MPI-130; Hybridized to 250K_Sty


title: DLBCL_MPI-113

description: Tumor_MPI-113; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-900

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-104

description: Tumor_MPI-104; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-899

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-901

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-099

description: Tumor_MPI-099; Hybridized to 250K_Sty


title: DLBCL_MPI-036

description: Tumor_MPI-036; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-881

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-046

description: Tumor_MPI-046; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-876

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-880

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-047

description: Tumor_MPI-047; Hybridized to 250K_Sty


title: DLBCL_MPI-133

description: Tumor_MPI-133; Hybridized to 250K_Sty


title: DLBCL_MPI-031

description: Tumor_MPI-031; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-873

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-074

description: Tumor_MPI-074; Hybridized to 250K_Sty


title: DLBCL_MPI-072

description: Tumor_MPI-072; Hybridized to 250K_Sty


title: DLBCL_MPI-024

description: Tumor_MPI-024; Hybridized to 250K_Sty


title: DLBCL_MPI-040

description: Tumor_MPI-040; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-865

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-864

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-858

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-022

description: Tumor_MPI-022; Hybridized to 250K_Sty


title: RNA_DLBCL_MPI-846

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-852

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-848

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-855

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-850

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-869

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-849

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-875

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-857

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-844

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-856

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-851

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-859

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-007

description: Tumor_MPI-007; Hybridized to 250K_Sty


title: DLBCL_MPI-008

description: Tumor_MPI-008; Hybridized to 250K_Sty


title: Miasteczko Śląskie_M5

city: Krakow

first: Hamed

last: Azarbad

address: Gronostajowa 7

institute: Jagiellonian University

description:
M5
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Scanned images were processed using ImaGene version 6.1 (BioDiscovery, El Segundo, CA) by averaging the intensities of every pixel inside the target region (segmentation method). The mean signal intensity was determined for each spot, and the local background signals were subtracted automatically from the hybridization signal of each spot. The spot signals, spot quality, and background fluorescence intensities of scanned images were quantified with ImaGene. After this step all bad spots, which were flagged by the image processing software using predetermined criteria (defined as spots whose signals could not be accurately quantified due to their irregular shapes and/or contaminations) were removed and acceptable spots intensity data were extracted from ImaGene output files. Raw data obtained using ImaGene were uploaded to the laboratory’s microarray data manager and analyzed using a GeoChip 4.2 data analysis pipeline (http://ieg.ou.edu/microarray). Spots with a signal-to-noise ratio [SNR= (signal intensity-background intensity)/standard deviation of the background] greater than 2 were used for further analysis (including potential empty spots and good spots). Normalization was performed as described by He et al. (2007) and Liang et al. (2010). The hybridization signal was normalized by the mean signal intensity across all genes on the array. The across-array mean was calculated based on all intensities on the arrays after the removal of poor spots and outliers. Then, a ratio was calculated for each positive spot by dividing the signal intensity of the spot by the mean signal intensity to obtain the normalized ratio. The average signal intensities across all of the genes were expected to be approximately equal because the same amount of DNA was used for labeling and hybridization. A matrix was then generated from the normalized pixel intensities of all protein-encoding genes.

organism: uncultured bacterium

source_name: Microbial community resilience to metals_Miasteczko Śląskie

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: DNA was extracted from 0.25 g soil using the PowerSoil DNA kit (MoBio Laboratories, Solana Beach, CA) following instructions of the manufacturer. DNA quality was evaluated by the absorbance ratios at A using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE). DNA quality was assessed by UV absorbance ratios of A260/A280 (> 1.8) and A260/A230 (> 1.7), values of 1.7–2.0 predict ‘clean DNA’, using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and DNA concentrations were measured with a PicoGreen method (Ahn et al., 1998).

tag: sample type

value: soil mycrobial communities in metal polluted soils

tag: sample collection area

value: Miasteczko Śląskie transect


title: DLBCL_MPI-026

description: Tumor_MPI-026; Hybridized to 250K_Sty


title: Miasteczko Śląskie_M6

description:
M6
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: RNA_DLBCL_MPI-698

description: tumor RNA hybridized to HGU133A chip


title: Miasteczko Śląskie_M3

description:
M3
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: RNA_DLBCL_MPI-701

description: tumor RNA hybridized to HGU133A chip


title: RNA_DLBCL_MPI-700

description: tumor RNA hybridized to HGU133A chip


title: Miasteczko Śląskie_M2

description:
M2
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: DLBCL_MPI-014

description: Tumor_MPI-014; Hybridized to 250K_Sty


title: KRAS ORF, KRAS not suppressed, rep2

city: Cambridge

first: Diane

last: Shao

state: MA

address: 7 Cambridge Center

institute: Broad

description: KRAS ORF, KRAS not suppressed, rep2

hyb_protocol: Following fragmentation, hybridization was performed overnight at 45C.

scan_protocol: Scanning was performed using

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: KRAS ORF, KRAS not suppressed, rep2

label_protocol: Biotinylated cDNA were prepared according to standard Affymetrix protocol.

growth_protocol: HCTtetK cells expressing the indicated genes were cultured in the RPMI+10%FBS were treated with 500ug/mL doxycyline for 30 hours. Untreated comparison samples were also collected.

extract_protocol: Manufacturer protocol from 5'Prime PerfectPure RNA Cultured Cell Kit.

treatment_protocol: Adherent cells were washed twice with PBS and treated directly with reagents from 5'Prime PerfectPure RNA Cultured Cell Kit.


title: KRAS ORF, KRAS not suppressed, rep1

description: KRAS ORF, KRAS not suppressed, rep1

source_name: KRAS ORF, KRAS not suppressed, rep1


title: Olkusz_O6

description:
O6
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.

source_name: Microbial community resilience to metals_Olkusz

value: Olkusz transect


title: RNA_DLBCL_MPI-407

description: tumor RNA hybridized to HGU133A chip


title: Miasteczko Śląskie_M4

description:
M4
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: Olkusz_O5

description:
O5
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: Olkusz_O2

description:
O2
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: KRAS ORF, KRAS suppression, rep1

description: KRAS ORF, KRAS suppression, rep1

source_name: KRAS ORF, KRAS suppression, rep1


title: YAP1 ORF, KRAS not suppressed, rep2

description: YAP1 ORF, KRAS not suppressed, rep2

source_name: YAP1 ORF, KRAS not suppressed, rep2


title: KRAS ORF, KRAS suppression, rep2

description: KRAS ORF, KRAS suppression, rep2

source_name: KRAS ORF, KRAS suppression, rep2


title: Olkusz_O1

description:
O1
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: Olkusz_O4

description:
O4
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: Olkusz_O3

description:
O3
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.


title: RNA_DLBCL_MPI-883

description: tumor RNA hybridized to HGU133A chip


title: DLBCL_MPI-105

description: Tumor_MPI-105; Hybridized to 250K_Sty


title: DLBCL_MPI-126

description: Tumor_MPI-126; Hybridized to 250K_Sty


title: YAP1 ORF, KRAS suppression, rep1

description: YAP1 ORF, KRAS suppression, rep1

source_name: YAP1 ORF, KRAS suppression, rep1


title: RNA_DLBCL_MPI-874

description: tumor RNA hybridized to HGU133A chip


title: LacZ ORF, KRAS not suppressed, rep2

description: LacZ ORF, KRAS not suppressed, rep2

source_name: LacZ ORF, KRAS not suppressed, rep2


title: Panicle_NIL-GS3/qgl3_rep3

city: Qingdao

first: Xiaojun

last: Zhang

state: Shandong

address: Changcheng road No. 700

institute: QAU

description: changed the qGL3 to qgl3 and gs3 to GS3 in the genetic background of 93-11

hyb_protocol: The pre-hybridization of MOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity.

data_processing: The data processing was processed by Rosetta ResolverÂ® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value. The sample data table values are normalized intensities. The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change|  1 and P < 0.05).

organism: Oryza sativa

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

growth_protocol: In the summer and nomal field condition of Nanjing, Jiangsu province of China.

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: No treatment,  near-isogenic lines in the same genetic background

tag: line

value: NIL-GS3/qgl3 (GS3/qgl3)

value: panicle

tag: development stage

value: primary panicle with 3-6 cm length


title: LacZ ORF, KRAS suppression, rep2

description: LacZ ORF, KRAS suppression, rep2

source_name: LacZ ORF, KRAS suppression, rep2


title: Rhabdomyosarcoma original patient tumor T0

city: Grand Rapids

first: David

last: Cherba

state: MI

address: 333 Bostwick Ave

department: Bioinformatics and Biostatistic Core

institute: Van Andel Institute

description: Gene expression data from original patient tumor

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight  on HG-U133 Plus 2.0 arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station

scan_protocol: scanned using the Affymetrix gene chip scanner 3000 7G

data_processing: Cel files were processed using Affymetrix Gene Expression Console build 1.3.1.187 and MAS 5.0 normalization

source_name: origina patient biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA

growth_protocol: 3 mm cubed tumor portions were implanted subcutaneously in the flank of NU/NU mice.

extract_protocol: For microarray analyses, 5 µm-thick sections of snap frozen tissue were cut and stained with haematoxylin & eosin (H&E). Stained sections were reviewed by a pathologist to identify areas of vital tumor cells and to ensure a tumor content of >50%.  Total RNA was isolated directly from four 50 µm OCT sections using Trizol (Life Technologies), with an initial homogenization for 2 minutes at 40 oscillations/second using the TissueLyser LT (Qiagen), followed by a DNase digestion and RNA clean-up using Qiagen RNeasy Mini Kit.

tag: tumor


title: DLBCL_MPI-039

description: Tumor_MPI-039; Hybridized to 250K_Sty

label_protocol: As per manufacturer (Affymetrix)


title: Rhabdomyosarcoma ICE-T treated tumorgraft F2 #3

description: Gene expression data from ICE-T treated subcutaneous tumorgraft

source_name: subcutaneous mouse tumorgraft


title: HF2303 miR Sox2 3A

data_processing: Data were background corrected and average normalized using GenomeStudio v2011.1

source_name: HF2303 miR Sox2

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.

value: Glioblastoma cells

tag: transfected with

value: miR Sox2 3A

tag: sample group

value: SOX2 knockdown


title: LacZ ORF, KRAS suppression, rep1

description: LacZ ORF, KRAS suppression, rep1

source_name: LacZ ORF, KRAS suppression, rep1


title: Rhabdomyosarcoma ICE-T treated tumorgraft F2 #3 Replicate


title: Panicle_NIL-GS3/qgl3_rep1

tag: tissue


title: Panicle_NIL-qgl3_rep1

description: changed the qGL3 to qgl3 in the genetic background of 93-11

value: NIL-qgl3 (gs3/qgl3)


title: Panicle_NIL-qgl3_rep2


title: YAP1 ORF, KRAS not suppressed, rep1

description: YAP1 ORF, KRAS not suppressed, rep1

source_name: YAP1 ORF, KRAS not suppressed, rep1


title: Panicle_NIL-GS3_rep3

description: changed the gs3 to GS3 in the genetic background of 93-11

value: NIL-GS3 (GS3/qGL3)


title: HF2303 miR Sox2 2B

description: HF2303 Sox2miR_2B.AVG_Signal

value: miR Sox2 2B


title: Panicle_NIL-qgl3_rep3


title: DLBCL_MPI-009

description: Tumor_MPI-009; Hybridized to 250K_Sty

source_name: frozen biopsy

value: diffuse large B cell lymphoma


title: MS_96.2 cell line

description: Gene expression data from cell line

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips scanned with Affymetrix Gene Array Scanner

data_processing: Arrays were analyzed using Affymetrix expression console to generate CEL files process using MAS 5.0

source_name: MPNST cell line

label_protocol: 20ng of total RNA is amplified with Ovation RNA Amplification System V2 (Nugen Technologies, Inc.), and 3.75ug of the resuling amplified cDNA is fragmented and labeled with FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.) and directly used for preparation of hybridization cocktail (please see the Appendix of FL-Ovation cDNA Biotin Module V2 Manual).

growth_protocol: According to ATCC protocols. DMEM culture medium with 10% FBS supplement

extract_protocol: TRIzol (Invitrogen) according to manufacturer's instructions

value: MPNST cell line


title: LacZ ORF, KRAS not suppressed, rep1

description: LacZ ORF, KRAS not suppressed, rep1

source_name: LacZ ORF, KRAS not suppressed, rep1


title: Rhabdomyosarcoma original tumorgraft F0

description: Gene expression data from first generation subcutaneous tumorgraft


title: HF2303 miR scambled control Sox2

description: HF2303miR control.AVG_Signal

source_name: HF2303_miR scrambled controls

value: miR scambled control Sox2

value: miR scambled control


title: Rhabdomyosarcoma ICE-T treated tumorgraft F2 #1


title: Panicle_NIL-GS3_rep1


title: Rhabdomyosarcoma ICE-T treated tumorgraft F2 #2


title: Panicle_93-11_rep2

description: the genetic background


title: HF2303 monolayer early passage

description: HF2303 monolayer early passage.AVG_Signal

source_name: HF2303 monolayer early passage

value: monolayer early passage


title: Panicle_93-11_rep3

description: the genetic background


title: HF2303 shRNA Sox2 32

description: HF2303 SP shRNASox2_32.AVG_Signal

source_name: HF2303 shRNA Sox2

value: shRNA Sox2 32


title: MS_90N adj. normal

description: Gene expression data from adjacent tissue

source_name: adjacent normal tissue

value: adjacent normal tissue


title: HF2303 shRNA scambled control Sox2

description: HF2303 SP NSC.AVG_Signal

source_name: HF2303_shRNA scrambled controls

value: shRNA scambled control Sox2

value: shRNA scambled control


title: MS_90T tumor

description: Gene expression data from tumor

source_name: neurofibroma tumor

value: neurofibroma tumor


title: MS_37T tumor

description: Gene expression data from tumor


title: MS_34T tumor

description: Gene expression data from tumor


title: YAP1 ORF, KRAS suppression, rep2

description: YAP1 ORF, KRAS suppression, rep2

source_name: YAP1 ORF, KRAS suppression, rep2


title: MS_02.2 cell line

description: Gene expression data from cell line


title: GW-1

city: Piscataway

first: Le

last: Zhan

state: NJ

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

description: gene expression data from GW4064 treated WT mouse liver

hyb_protocol: Following fragmentation, cRNA were hybridizedon GeneChip Mouse Gene 1.0 ST Array with standard protocol.

scan_protocol: Not provided.

data_processing: The cel files were analyzed with Expression Cole 1.3.1 from Affymetrix using default analysis settings.

source_name: GW4064 treated WT mouse 4

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

extract_protocol: Total RNA from livers was prepared with TRIzol Reagent (Invitrogen, CA)

treatment_protocol: C57BL/6J mice were treated with GW4064 at 100mg per kg body weight or vehicle control. Mice were treated three times, first dose at 8 am, second dose at 6 pm, third dose at 8 am the second day. Mice were sacrificed 2 hours after the last dose, and liver tissues were harvested for analysis.

tag: strain

tag: genotype/variation

value: wild type

value: liver

value: adult


title: Panicle_NIL-GS3_rep2

value: panicle

value: primary panicle with 3-6 cm length


title: Panicle_93-11_rep1

description: the genetic background


title: MS_37N adj. normal


title: Panicle_NIL-GS3/qgl3_rep2

value: NIL-GS3/qgl3 (GS3/qgl3)


title: RNA_DLBCL_MPI-690

description: tumor RNA hybridized to HGU133A chip

value: GCB


title: HF2303 shRNA Sox2 30

description: HF2303 SP shRNASox2_30.AVG_Signal

tag: cell type

value: Glioblastoma cells

value: shRNA Sox2 30

value: SOX2 knockdown


title: GW-2

source_name: GW4064 treated WT mouse 5


title: GW-3

source_name: GW4064 treated WT mouse 6


title: vehicle-1

description: gene expression data from vehicle treated WT mouse liver

source_name: vehicle treated WT mouse 1


title: vehicle-3

source_name: vehicle treated WT mouse 3


title: HF2303 neurosphere cultured

description: HF2303 SP .AVG_Signal

source_name: HF2303 neurosphere cultured

value: neurosphere cultured


title: Hypertension_HT13

status: Public on Jul 21 2014

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

description: Hypertension patient

data_processing:
We used Excel capabilities to calculate: (a) the average Cq from duplicate wells for each gene; (b) the median values of the three housekeeping genes (B2M, GAPDH and RPL13); (c) RCN as defined below.
Detections were done in duplicate, and the values in Matrix non-normalized worksheet represent the average Cq of the duplicate per each sample. In the rare cases where one of the duplicates was Undetectable ot the dissociatin curve was not appropriate, we used the remaining sample.
Sample data table reports the normalized signal [2^(-ΔCq)] against the median value of the three housekeeping genes: B2M, GAPDH and RPL13.
In our analyses we used the Relative Copy Number [RCN: 2^(–ΔCq) × 100] (instead of calculating 'Fold change')

label: SYBR Green

label_protocol: Reverse transcription was done with Life Technologies Vilo kit (standard protocol), starting from 150 ng total RNA. Quantitative real-time PCR was done in an 7900HT Real-Time PCR System (Life Technologies/ABI) using primer sets and SYBR Green from Qiagen, in 384-well plates, in a final volume of 5 μL and using default cycling parameters of the standard mode.

extract_protocol: Total RNA was extracted with Qiagen RNeasy following the standard protocol, starting from ~10^6 cells

tag: subject group

value: Hypertension patient

tag: gender

value: female

tag: age (yrs)

tag: bmi (kg/m2)

value: Peripheral blood mononuclear cells (PBMCs)


title: Hypertension_HT15

description: Hypertension patient

value: male


title: Hypertension_HT14

description: Hypertension patient


title: Hypertension_HT20

description: Hypertension patient


title: Hypertension_HT18

description: Hypertension patient


title: Hypertension_HT12

description: Hypertension patient


title: Hypertension_HT9

description: Hypertension patient


title: Hypertension_HT11

description: Hypertension patient


title: Hypertension_HT17

description: Hypertension patient


title: Hypertension_HT16

description: Hypertension patient


title: Hypertension_HT19

description: Hypertension patient


title: Hypertension_HT10

description: Hypertension patient


title: Hypertension_HT8

description: Hypertension patient


title: MS_109N adj. normal

value: adjacent normal tissue


title: Hypertension_HT5

description: Hypertension patient


title: vehicle-2

source_name: vehicle treated WT mouse 2

tag: developmental stage


title: Hypertension_HT2

description: Hypertension patient


title: Hypertension_HT3

description: Hypertension patient


title: Hypertension_HT4

description: Hypertension patient


title: Hypertension_HT6

description: Hypertension patient


title: Control_CT26

description: Healthy subject

value: Healthy subject


title: Control_CT25

description: Healthy subject


title: Hypertension_HT7

description: Hypertension patient


title: Control_CT24

description: Healthy subject


title: Control_CT22

description: Healthy subject


title: Hypertension_HT1

description: Hypertension patient


title: Control_CT23

description: Healthy subject


title: Control_CT16

description: Healthy subject


title: Control_CT17

description: Healthy subject


title: Control_CT20

description: Healthy subject


title: Control_CT21

description: Healthy subject


title: Control_CT18

description: Healthy subject


title: Control_CT14

description: Healthy subject


title: Control_CT13

description: Healthy subject


title: Control_CT15

description: Healthy subject


title: Control_CT10

description: Healthy subject


title: Control_CT6

description: Healthy subject


title: Control_CT8

description: Healthy subject


title: Control_CT7

description: Healthy subject


title: Control_CT11

description: Healthy subject


title: Control_CT19

description: Healthy subject


title: Control_CT2

description: Healthy subject


title: Control_CT12

description: Healthy subject


title: Control_CT9

description: Healthy subject


title: Control_CT4

description: Healthy subject


title: Control_CT1

description: Healthy subject


title: Control_CT5

description: Healthy subject


title: Miasteczko Śląskie_M1

description:
M1
GeoChip data for soil sample collected at twelve sites located along two distinct gradients of metal pollution in Southern Poland, replicate 1.

source_name: Microbial community resilience to metals_Miasteczko Śląskie

value: soil mycrobial communities in metal polluted soils

value: Miasteczko Śląskie transect


title: Control_CT3

description: Healthy subject