title: hdac3 cko lung, biological rep5

status: Public on Jun 21 2016

city: Philadelphia

first: Michael

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

description: Hdac3 cko_lung_5

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/).

label: Biotin

source_name: hdac3 cko_embryonic lung at E18.5

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: Female Hdac3 fl/fl mice were plugged by Hdac3 fl/+ ShhCre male mice, and were counted as E0.5 on the day of plugging.

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

treatment_protocol: E18.5 embryonic lungs were dissected from the pregnant females and collected in the RNA later. The genotypes of the embryos were determined by qPCR reactions with specific primers to the Hdac3 flox allele and ShhCre allele.

tag: strain background

tag: genotype/variation

value: Shhcre:Hdac3fl/fl; Hdac3 KO

value: Lung


title: hdac3 cko lung, biological rep3

type: RNA

country: USA

description: Hdac3 cko_lung_3

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue


title: hdac3 cko lung, biological rep2

description: Hdac3 cko_lung_2


title: hdac3 cko lung, biological rep4

description: Hdac3 cko_lung_4


title: Sca1-tomato-Lmo2 thymus cells, biological replicate 8

status: Public on Jun 22 2016

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Gene expression data from leukemic Sca1-TOMATO-Lmo2 thymus cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label: biotin

source_name: leukemic Sca1-TOMATO-Lmo2 thymus cells

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

growth_protocol: Animals were housed in animal facility.

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

value: Thymus

tag: genotype

tag: disease state

value: leukemic


title: shhcre control lung, biological rep 3

source_name: shhcre control_mouse embryonic lung at E18.5

value: Shhcre; control


title: shhcre control lung, biological rep 4


title: shhcre control lung, biological rep 2


title: hdac3 cko lung, biological rep1

description: Hdac3 cko_lung_1


title: shhcre control lung, biological rep 5


title: MCF10A H2A.X-KO_3

city: Bethesda

first: Urbain

middle: S

last: Weyemi

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

hyb_protocol: Five replicates of each group were prepared, labeled, and hybridized to Affymetrix Human Gene 2.0 ST arrays.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip scanner 3000.

data_processing: Affymetrix Expression Console (EC) was used to generate CHP files from CEL files. Then, the CEL files were loaded into Partek Genomics Suite software, version 6.6 for normalization and differential expression analysis.

organism: Homo sapiens

source_name: MCF10A, H2A.X-KO

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 1 ug total RNA. RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled using Affymetrix One Cycle Target Labeling kit following manufacturer's protocol.

growth_protocol: MCF10A parental (WT) or MCF10A cells knockout for H2A.X gene (MCF10A H2A.X-KO) were cultured in special medium consisting of Dulbecco’s minimal essential medium/F-12 (DMEM/F12) (Invitrogen, Carlsbad, CA) supplemented with 5% horse serum (Sigma, St. Louis, MO), 500 ng/ml hydrocortisone (Sigma), 20 ng/ml EGF (R and D Systems, Minneapolis, MN), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma), and 100 mg/ml of penicillin-streptomycin (Invitrogen).

extract_protocol: Total RNAs from MCF10A cells were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer’s instructions.

treatment_protocol: Cells were cultured for 48 hours and harvested for RNA extraction.

tag: cell line

tag: cell type

value: breast cell line

value: H2A.X knockout

tag: group

value: knockout


title: MCF10A H2A.X-KO_4


title: MCF10A H2A.X-KO_1


title: MCF10A H2A.X-KO_2


title: siNF90-treated Huh7 cells rep2

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

country: Japan

institute: Kochi University

description: RMA expression value derived from Expression Console software; RMA-sketch analysis

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with HuGene2.1ST Array Strip (Affymetrix)  and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions.

data_processing: Arrays were summarized and normalized with Expression Console using RMA-sketch.

source_name: siNF90-treated Huh7 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from siNTC- or siNF90-treated Huh7 cells using RNeasy kit (QIAGEN).


title: siNF90-treated Huh7 cells rep1


title: MCF10A WT_5

source_name: MCF10A, WT

value: H2A.X WT

value: parental


title: MCF10A H2A.X-KO_5


title: MCF10A WT_2


title: siNTC-treated Huh7 cells rep1

source_name: siNTC-treated Huh7 cells


title: MCF10A WT_4


title: H1N1 DEE3 Subject 1, Hour 36

city: Ann Arbor

first: Alfred

last: Hero

state: MI

address: 1301 Beal Avenue

institute: University of Michigan

description:
H1N1_DEE3_SAMPLE_7
Gene expression profile from peripheral blood of H1N1 DEE3 subject 1, hour 36.

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133A 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing:
The data were analyzed with robust multi-array average (RMA) normalization using default background adjustment and quantile normalization settings. Then possible batch effect was removed by the parametric and nonparametric empirical Bayes frameworks.
Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENTREZG].

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

extract_protocol: RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3' portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts.

treatment_protocol: 148 human volunteer subjects under 4 different inoculation regimes (HRV, RSV, H1N1, H3N2). During each challenge study, subjects had peripheral blood taken prior to inoculation with virus (baseline), immediately prior to inoculation (pre-challenge) and at set intervals following challenge.

value: peripheral blood

tag: virus

tag: time point

value: hour 36

tag: subject

value: H1N1 DEE3 subject 1


title: Control 12 weeks (1235_2.4)

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4858A), Agilent, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies G2600D SG14324425) using one color scan setting for G3 Microarray format 8x60k (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 12 weeks age matched control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Liver samples from male C57bl/6j submitted to STAMTM protocol were obtained from Stelic Institute Co.

extract_protocol: Total RNA was extracted from liver tissue using miRNeasy Mini kits (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were submitted to STAMTM model. This model has been developed by low-dose streptozotocin injection to induce a diabetic state in mice and high-fat diet feeding to develop steatosis and mild chronic hepatic inflammation from 4 weeks of age onwards. This mouse model progresses from NAFLD to NASH at 8 weeks of age and develops hepatocellular carcinoma at 16 weeks of age.

tag: protocol

value: control

value: 12 weeks

value: liver

tag: strain

tag: gender

value: male


title: MCF10A WT_3


title: Atg7flox/flox; Alb-Cre mice liver #6

city: Niigata-shi

first: Tetsuya

last: Saito

state: Niigata

address: 757, Ichibancho, Asahimachidori, Chuo-ku

department: Biochemistry

institute: Niigata University school of medicine

description: Gene expression of Atg7flox/flox; Alb-Cre mice liver #6

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Mouse Genome Oligo Microarray  (G4846A) using the Agilent Gene Expression Hybridization Kit. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Atg7flox/flox; Alb-Cre mice liver #6

label_protocol: 200 ng of total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol  (Life technologies, Carlsbad CA ) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Liver

value: female


title: H1N1 DEE3 Subject 1, Hour 21

description:
H1N1_DEE3_SAMPLE_5
Gene expression profile from peripheral blood of H1N1 DEE3 subject 1, hour 21.

value: hour 21


description: Gene expression of Atg7flox/flox;Nrf2flox/floxmice liver #2


description: Gene expression of Atg7flox/flox;Nrf2flox/floxmice liver #1


description: Gene expression of Atg7flox/flox;Nrf2flox/flox;Alb-Cre mice liver #7


title: shhcre control lung, biological rep 1

value: Lung


description: Gene expression of Atg7flox/flox;Nrf2flox/floxmice liver #3


description: Gene expression of Atg7flox/flox;Nrf2flox/flox;Alb-Cre mice liver #4


description: Gene expression of Atg7flox/flox;Nrf2flox/flox;Alb-Cre mice liver #12


title: Atg7flox/flox; Alb-Cre mice liver #7

description: Gene expression of Atg7flox/flox; Alb-Cre mice liver #7

source_name: Atg7flox/flox; Alb-Cre mice liver #7


title: H1N1 DEE3 Subject 1, Hour -21

description:
H1N1_DEE3_SAMPLE_1
Gene expression profile from peripheral blood of H1N1 DEE3 subject 1, hour -21.

value: hour -21


title: Atg7flox/flox; Alb-Cre mice liver #4

description: Gene expression of Atg7flox/flox; Alb-Cre mice liver #4

source_name: Atg7flox/flox; Alb-Cre mice liver #4


title: AML_130_Rel_scRNAseq_H12_single cell RNA-seq

type: SRA

city: New York

first: Francine

middle: E.

last: Garrett-Bakelman

state: NY

address: 413 East 69th street, BRB 1426

department: Medicine

institute: Weill Cornell Medicine

description: processed data file: AML_130_Rel_rpkm.txt

library_source: transcriptomic

data_processing:
alignment using STAR aligner (version 2.3.0e; http://code.google.com/p/rna-star/)
Aligned results were annotated using the Refseq gene model and HTSeq union mode
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: text files of normalized expression values (RPKM) from each gene covered in RNA-sequencing results from each subject

source_name: AML_peripheral blood_single cell RNA-seq

growth_protocol: Not applicable; isolated disease cells were used directly in next generation protocols

extract_protocol:
RNA was extracted from cell lysates in trizol; separation into an aqueous phase and organic phase was achieved by the addition of chloroform.  The RNA was recovered from the aqueous phase and purified using silicaN based membrane technology with on column DNase digestion.  RNA molecules < 200 nt are selectively excluded.
Libraries were prepared using the TruSeq RNA-Seq by polyA enrichment kit V2 (Illumina, Inc.; http://www.illumina.com/products/truseq_rna_library_prep_kit_v2.html)

treatment_protocol: Not applicable

tag: subject status

value: Acute Myeloid Leukemia patient

value: Peripheral Blood

tag: processed data column header


title: STAM 6 weeks (1243_2.4)

source_name: STAM model, euthanized after 6 weeks

value: submitted to STAM model

value: 6 weeks

value: steatosis


title: STAM 8 weeks (1243_2.1)

source_name: STAM model, euthanized after 8 weeks

value: 8 weeks

value: steatohepatitis


title: MCF10A WT_1

value: breast cell line

value: H2A.X WT

value: parental


title: AML_130_Rel_scRNAseq_H11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H06_single cell RNA-seq


title: Atg7flox/flox mice liver #2

description: Gene expression of Atg7flox/flox mice liver #2

source_name: Atg7flox/flox mice liver #2


title: AML_130_Rel_scRNAseq_H01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G07_single cell RNA-seq


title: Atg7flox/flox mice liver #1

description: Gene expression of Atg7flox/flox mice liver #1

source_name: Atg7flox/flox mice liver #1


title: AML_130_Rel_scRNAseq_G11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G05_single cell RNA-seq


title: Atg7flox/flox mice liver #3

description: Gene expression of Atg7flox/flox mice liver #3

source_name: Atg7flox/flox mice liver #3


title: AML_130_Rel_scRNAseq_G04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_G02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F05_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_F01_single cell RNA-seq


title: siNTC-treated Huh7 cells rep2

description: RMA expression value derived from Expression Console software; RMA-sketch analysis


title: AML_130_Rel_scRNAseq_E05_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_E01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C05_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_C01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B04_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B03_single cell RNA-seq


title: AML_130_Rel_scRNAseq_D05_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A12_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A11_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A08_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A06_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B05_single cell RNA-seq


title: AML_130_Rel_scRNAseq_H10_single cell RNA-seq


title: AML_130_Rel_scRNAseq_B01_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A07_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A02_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A09_single cell RNA-seq


title: AML_130_Rel_scRNAseq_A04_single cell RNA-seq


title: AML_139_Dx_RNA-sequencing

description: processed data file: Dx_Rel_AML_RNAseq_rpkm.txt

source_name: AML_diagnosis_Bone Marrow_RNA-seq

tag: disease status

value: diagnosis

value: Bone Marrow


title: AML_130_Rel_scRNAseq_A03_single cell RNA-seq


title: AML_133_Rel_RNA-sequencing

source_name: AML_relapse_Bone Marrow_RNA-seq

value: relapse


title: AML_130_Rel_scRNAseq_A10_single cell RNA-seq


title: AML_128_Rel_RNA-sequencing

value: Peripheral Blood pheresis


title: AML_130_Rel_scRNAseq_A05_single cell RNA-seq


title: AML_124_Rel_RNA-sequencing


title: AML_139_Rel_RNA-sequencing

source_name: AML_relapse_Peripheral Blood_RNA-seq


title: AML_125_Dx_RNA-sequencing


title: AML_130_Rel_scRNAseq_A01_single cell RNA-seq


title: AML_133_Dx_RNA-sequencing

source_name: AML_diagnosis_Peripheral Blood_RNA-seq


title: AML_125_Rel_RNA-sequencing


title: AML_128_Dx_RNA-sequencing


title: AML_130_Rel_scRNAseq_B02_single cell RNA-seq


title: AML_124_Dx_RNA-sequencing


title: AML_116_Rel_RNA-sequencing


title: AML_116_Dx_RNA-sequencing


title: AML_117_Rel_RNA-sequencing


title: AML_130_Rel_scRNAseq_C03_single cell RNA-seq


title: AML_109_Dx_RNA-sequencing


title: AML_108_Rel_RNA-sequencing


title: AML_108_Dx_RNA-sequencing


title: AML_103_Rel_RNA-sequencing


title: AML_107_Dx_RNA-sequencing


title: AML_103_Dx_RNA-sequencing


title: AML_064_Dx_RNA-sequencing


title: AML_059_Rel_RNA-sequencing


title: AML_051_Dx_RNA-sequencing


title: AML_049_Dx_RNA-sequencing


title: AML_032_Dx_RNA-sequencing


title: AML_032_Rel_RNA-sequencing


title: AML_028_Rel_RNA-sequencing


title: AML_003_Rel_RNA-sequencing


title: AML_028_Dx_RNA-sequencing


title: AML_015_Dx_RNA-sequencing


title: NBM_14_Sample used for comparisons to tumor samples

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to hg19 using a whole genome using the bismark alignment software with a maximum of 2 mismatches in a directional manner. Only uniquely aligning reads were retained
methylation scores were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base.
Methclone analysis (PMC4242486) to determine epigenetic loci that undergo large shifts between paired patient tumor specimens (AML diagnosis = AML_Dx and AML relapse = AML_Rel) and between tumor samples and control samples (Normal bone marrow CD34+ cells = NBM)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text methclone output files with epiallele designations at genomic loci covered
*Dx_epialleles.tar.gz: Files are gzipped folders of 14 independent comparisons of each diagnosis tumor sample to fourteen normal bone marrow controls; column descriptions are:  | chr | chrosomome | | start | start position | | end | end position | | sample | sample names in the comparison | | distance | length of the genomic locus | | strand | strand information | | loci | the four position of the CpGs in the genomic locus | | entropy | the delta entropy to evaluate the epialellele shift. The low the delta entropy, the higher the epiallele shift | | read1 | number of reads covered this genomic locus in the first sample | | read2 | number of reads covered this genomic locus in the second sample | | meth1 | the average methylation levels of this genomic locus in the first sample | | meth2 | the average methylation levels of this genomic locus in the second sample | | pattern1 | the dominant methylation patterns of this genomic locus in the first sample | | pattern2 | the dominant methylation patterns of this genomic locus in the second sample |; see https://code.google.com/archive/p/methclone/ for additional descriptions

*Rel_epialleles.tar.gz: Gzipped folder containing: 1. epiallele comparison file of relapse sample versus diagnostic sample; 2. gzipped folder of 14 independent comparisons of relapsed tumor sample to fourteen normal bone marrow controls (NBM_01 to NBM_14); column descriptions are:  | chr | chrosomome | | start | start position | | end | end position | | sample | sample names in the comparison | | distance | length of the genomic locus | | strand | strand information | | loci | the four position of the CpGs in the genomic locus | | entropy | the delta entropy to evaluate the epialellele shift. The low the delta entropy, the higher the epiallele shift | | read1 | number of reads covered this genomic locus in the first sample | | read2 | number of reads covered this genomic locus in the second sample | | meth1 | the average methylation levels of this genomic locus in the first sample | | meth2 | the average methylation levels of this genomic locus in the second sample | | pattern1 | the dominant methylation patterns of this genomic locus in the first sample | | pattern2 | the dominant methylation patterns of this genomic locus in the second sample |; see https://code.google.com/archive/p/methclone/ for additional descriptions

molecule: genomic DNA

source_name: NBM_Sample used for comparisons to tumor samples

extract_protocol:
DNA was extracted using Qiagen gentra puregene kit per manufacturer's recommendations.
Enhanced reduced representation of bisulfite sequencing (PMC4354670): High molecular weight genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 75bp single end read reads

value: Normal donor

value: CD34+ bone marrow mononuclear cells


title: AML_003_Dx_RNA-sequencing


title: AML_109_Rel_RNA-sequencing


title: AML_051_Rel_RNA-sequencing


title: NBM_12_Sample used for comparisons to tumor samples


title: NBM_13_Sample used for comparisons to tumor samples


title: NBM_11_Sample used for comparisons to tumor samples


title: NBM_08_Sample used for comparisons to tumor samples


title: NBM_10_Sample used for comparisons to tumor samples


title: AML_064_Rel_RNA-sequencing


title: AML_049_Rel_RNA-sequencing


title: AML_059_Dx_RNA-sequencing


title: NBM_06_Sample used for comparisons to tumor samples


title: NBM_07_Sample used for comparisons to tumor samples


title: AML_015_Rel_RNA-sequencing


title: NBM_04_Sample used for comparisons to tumor samples


title: NBM_03_Sample used for comparisons to tumor samples


title: AML_130_Rel_scRNAseq_H05_single cell RNA-seq


title: AML_140 diagnosis epiallele analysis of ERRBS data

source_name: AML_diagnosis epiallele analysis of ERRBS data

value: Hematopoietic mononuclear cells


title: NBM_02_Sample used for comparisons to tumor samples


title: NBM_01_Sample used for comparisons to tumor samples


title: NBM_09_Sample used for comparisons to tumor samples


title: AML_140 relapse epiallele analysis of ERRBS data

source_name: AML_relapse epiallele analysis of ERRBS data

value: Acute Myeloid Leukemia patient


title: AML_139 relapse epiallele analysis of ERRBS data

value: Peripheral Blood


title: AML_139 diagnosis epiallele analysis of ERRBS data


title: AML_138 diagnosis epiallele analysis of ERRBS data


title: AML_137 diagnosis epiallele analysis of ERRBS data


title: AML_137 relapse epiallele analysis of ERRBS data


title: AML_138 relapse epiallele analysis of ERRBS data


title: AML_134 diagnosis epiallele analysis of ERRBS data


title: AML_133 relapse epiallele analysis of ERRBS data


title: AML_107_Rel_RNA-sequencing


title: AML_136 diagnosis epiallele analysis of ERRBS data


title: AML_132 relapse epiallele analysis of ERRBS data


title: AML_135 diagnosis epiallele analysis of ERRBS data


title: AML_133 diagnosis epiallele analysis of ERRBS data


title: AML_136 relapse epiallele analysis of ERRBS data


title: AML_135 relapse epiallele analysis of ERRBS data


title: AML_134 relapse epiallele analysis of ERRBS data

value: Uknown


title: AML_132 diagnosis epiallele analysis of ERRBS data


title: AML_131 diagnosis epiallele analysis of ERRBS data


title: NBM_05_Sample used for comparisons to tumor samples


title: AML_130_Rel3_epiallele analysis of ERRBS data

source_name: AML_relapse_epiallele analysis of ERRBS data


title: AML_117_Dx_RNA-sequencing


title: AML_130_Rel4_epiallele analysis of ERRBS data


title: AML_130 relapse epiallele analysis of ERRBS data


title: AML_130_Rel2_epiallele analysis of ERRBS data


title: AML_130 diagnosis epiallele analysis of ERRBS data


title: AML_129 relapse epiallele analysis of ERRBS data


title: AML_127 relapse epiallele analysis of ERRBS data


title: AML_128 relapse epiallele analysis of ERRBS data


title: AML_126 relapse epiallele analysis of ERRBS data


title: AML_127 diagnosis epiallele analysis of ERRBS data


title: AML_131 relapse epiallele analysis of ERRBS data


title: AML_128 diagnosis epiallele analysis of ERRBS data


title: AML_125 relapse epiallele analysis of ERRBS data


title: AML_123 relapse epiallele analysis of ERRBS data


title: AML_124 relapse epiallele analysis of ERRBS data


title: AML_123 diagnosis epiallele analysis of ERRBS data


title: AML_125 diagnosis epiallele analysis of ERRBS data


title: AML_122 relapse epiallele analysis of ERRBS data


title: AML_122 diagnosis epiallele analysis of ERRBS data


title: AML_121 relapse epiallele analysis of ERRBS data


title: AML_118 relapse epiallele analysis of ERRBS data


title: AML_118 diagnosis epiallele analysis of ERRBS data


title: AML_121 diagnosis epiallele analysis of ERRBS data


title: AML_120 relapse epiallele analysis of ERRBS data


title: AML_119 relapse epiallele analysis of ERRBS data


title: AML_120 diagnosis epiallele analysis of ERRBS data


title: AML_119 diagnosis epiallele analysis of ERRBS data


title: AML_129 diagnosis epiallele analysis of ERRBS data


title: AML_117 relapse epiallele analysis of ERRBS data


title: AML_116 diagnosis epiallele analysis of ERRBS data


title: AML_115 diagnosis epiallele analysis of ERRBS data


title: AML_126 diagnosis epiallele analysis of ERRBS data


title: AML_114 relapse epiallele analysis of ERRBS data


title: AML_114 diagnosis epiallele analysis of ERRBS data


title: AML_113 relapse epiallele analysis of ERRBS data


title: AML_124 diagnosis epiallele analysis of ERRBS data


title: AML_113 diagnosis epiallele analysis of ERRBS data


title: AML_112 relapse epiallele analysis of ERRBS data


title: AML_112 diagnosis epiallele analysis of ERRBS data


title: AML_111 diagnosis epiallele analysis of ERRBS data


title: AML_110 diagnosis epiallele analysis of ERRBS data


title: AML_110 relapse epiallele analysis of ERRBS data


title: AML_117 diagnosis epiallele analysis of ERRBS data


title: AML_109 relapse epiallele analysis of ERRBS data


title: AML_108 diagnosis epiallele analysis of ERRBS data


title: AML_108 relapse epiallele analysis of ERRBS data


title: AML_116 relapse epiallele analysis of ERRBS data


title: AML_111 relapse epiallele analysis of ERRBS data


title: AML_115 relapse epiallele analysis of ERRBS data


title: AML_109 diagnosis epiallele analysis of ERRBS data


title: AML_107 diagnosis epiallele analysis of ERRBS data


title: AML_107 relapse epiallele analysis of ERRBS data


title: AML_106 diagnosis epiallele analysis of ERRBS data


title: AML_105 relapse epiallele analysis of ERRBS data


title: AML_106 relapse epiallele analysis of ERRBS data


title: AML_104 diagnosis epiallele analysis of ERRBS data


title: AML_103 relapse epiallele analysis of ERRBS data


title: AML_102 relapse epiallele analysis of ERRBS data


title: AML_101 relapse epiallele analysis of ERRBS data


title: AML_102 diagnosis epiallele analysis of ERRBS data


title: AML_101 diagnosis epiallele analysis of ERRBS data


title: AML_100 relapse epiallele analysis of ERRBS data


title: AML_100 diagnosis epiallele analysis of ERRBS data


title: AML_105 diagnosis epiallele analysis of ERRBS data


title: AML_104 relapse epiallele analysis of ERRBS data


title: AML_099 diagnosis epiallele analysis of ERRBS data


title: AML_098 relapse epiallele analysis of ERRBS data


title: AML_098 diagnosis epiallele analysis of ERRBS data


title: AML_099 relapse epiallele analysis of ERRBS data


title: AML_097 relapse epiallele analysis of ERRBS data


title: AML_103 diagnosis epiallele analysis of ERRBS data


title: AML_096 diagnosis epiallele analysis of ERRBS data


title: AML_094 relapse epiallele analysis of ERRBS data


title: AML_095 relapse epiallele analysis of ERRBS data


title: AML_095 diagnosis epiallele analysis of ERRBS data


title: AML_094 diagnosis epiallele analysis of ERRBS data


title: AML_093 relapse epiallele analysis of ERRBS data


title: AML_097 diagnosis epiallele analysis of ERRBS data


title: AML_091 relapse epiallele analysis of ERRBS data


title: AML_092 relapse epiallele analysis of ERRBS data


title: AML_092 diagnosis epiallele analysis of ERRBS data


title: AML_093 diagnosis epiallele analysis of ERRBS data


title: AML_090 diagnosis epiallele analysis of ERRBS data


title: AML_090 relapse epiallele analysis of ERRBS data


title: AML_089 relapse epiallele analysis of ERRBS data


title: AML_087 relapse epiallele analysis of ERRBS data


title: AML_088 diagnosis epiallele analysis of ERRBS data


title: AML_089 diagnosis epiallele analysis of ERRBS data


title: AML_087 diagnosis epiallele analysis of ERRBS data


title: AML_096 relapse epiallele analysis of ERRBS data


title: AML_085 relapse epiallele analysis of ERRBS data


title: AML_085 diagnosis epiallele analysis of ERRBS data


title: AML_086 relapse epiallele analysis of ERRBS data


title: AML_091 diagnosis epiallele analysis of ERRBS data


title: AML_086 diagnosis epiallele analysis of ERRBS data


title: AML_083 relapse epiallele analysis of ERRBS data


title: AML_083 diagnosis epiallele analysis of ERRBS data


title: AML_084 diagnosis epiallele analysis of ERRBS data


title: AML_082 diagnosis epiallele analysis of ERRBS data


title: AML_088 relapse epiallele analysis of ERRBS data


title: AML_079 relapse epiallele analysis of ERRBS data


title: AML_078 diagnosis epiallele analysis of ERRBS data


title: AML_081 diagnosis epiallele analysis of ERRBS data


title: AML_078 relapse epiallele analysis of ERRBS data


title: AML_081 relapse epiallele analysis of ERRBS data


title: AML_082 relapse epiallele analysis of ERRBS data


title: AML_077 diagnosis epiallele analysis of ERRBS data


title: AML_080 relapse epiallele analysis of ERRBS data


title: AML_077 relapse epiallele analysis of ERRBS data


title: AML_076 relapse epiallele analysis of ERRBS data


title: AML_076 diagnosis epiallele analysis of ERRBS data


title: AML_075 relapse epiallele analysis of ERRBS data


title: AML_079 diagnosis epiallele analysis of ERRBS data


title: AML_075 diagnosis epiallele analysis of ERRBS data


title: AML_084 relapse epiallele analysis of ERRBS data


title: AML_074 diagnosis epiallele analysis of ERRBS data


title: AML_073 relapse epiallele analysis of ERRBS data


title: AML_074 relapse epiallele analysis of ERRBS data


title: AML_080 diagnosis epiallele analysis of ERRBS data


title: AML_073 diagnosis epiallele analysis of ERRBS data


title: AML_070 relapse epiallele analysis of ERRBS data


title: AML_071 diagnosis epiallele analysis of ERRBS data


title: AML_072 diagnosis epiallele analysis of ERRBS data


title: AML_070 diagnosis epiallele analysis of ERRBS data


title: AML_071 relapse epiallele analysis of ERRBS data


title: AML_066 relapse epiallele analysis of ERRBS data


title: AML_067 relapse epiallele analysis of ERRBS data


title: AML_072 relapse epiallele analysis of ERRBS data


title: AML_068 diagnosis epiallele analysis of ERRBS data


title: AML_066 diagnosis epiallele analysis of ERRBS data


title: AML_069 diagnosis epiallele analysis of ERRBS data


title: AML_065 diagnosis epiallele analysis of ERRBS data


title: AML_065 relapse epiallele analysis of ERRBS data


title: AML_064 relapse epiallele analysis of ERRBS data


title: AML_064 diagnosis epiallele analysis of ERRBS data


title: AML_063 relapse epiallele analysis of ERRBS data


title: AML_063 diagnosis epiallele analysis of ERRBS data


title: AML_069 relapse epiallele analysis of ERRBS data


title: AML_062 relapse epiallele analysis of ERRBS data


title: AML_068 relapse epiallele analysis of ERRBS data


title: AML_067 diagnosis epiallele analysis of ERRBS data


title: AML_061 relapse epiallele analysis of ERRBS data


title: AML_062 diagnosis epiallele analysis of ERRBS data


title: Calveria_Ctrl_7D

city: Taipei

first: YU-CHIH

last: HUANG

address: No.250, WuXing St,

department: College of Oral Medicine

country: Taiwan

institute: Taipei Medical University

description: Gene expression in unfilled control: Day 7

hyb_protocol: 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rabbit Oligo 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software GeneSpring was used to quantify signal and background intensity for each feature.

organism: Oryctolagus cuniculus

source_name: Unfilled control, calveria, Day7

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: In this study, 24 New Zealand White rabbits, weighing 3.0–3.5 kg, were fed with solid food and water for adaptation in bracket cages at a temperature of 25°C, humidity of 50%. The environment was controlled with a 12-hr light/dark cycle. All rabbits were maintained and used in accordance with the guidelines of The Care and Use of Laboratory Animals of Taipei Medical University.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes differential lysis of newly formed tissue in each group, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Before bone graft implantation surgery, the rabbits were anesthetized with intramuscular Zoletil 50 at a dose of 0.5 mL (Virbac, Carros Cedex, France). Four circular defects (5 mm inner diameter) were made in the parietal bone using a trephine on a slow-speed electric handpiece. The two right defects were grafted with 0.2 g of prepared HPD and the other two were unfilled control.

tag: breed

value: New Zealand White

value: New formed tissue

value: male

value: 4 month


title: Calveria_HPD_7D

description: Gene expression in HPD-filled sample: Day 7

source_name: HPD implantation, calveria, Day7

tag: age


title: Calveria_HPD_3D

description: Gene expression in HPD-filled sample: Day 3

source_name: HPD implantation, calveria, Day3

tag: tissue


title: AML_061 diagnosis epiallele analysis of ERRBS data


title: Calveria_Ctrl_5D

description: Gene expression in unfilled control: Day 5

source_name: Unfilled control, calveria, Day5


title: AML_060 relapse epiallele analysis of ERRBS data


title: AML_059 relapse epiallele analysis of ERRBS data


title: Calveria_Ctrl_3D

description: Gene expression in unfilled control: Day 3

source_name: Unfilled control, calveria, Day3


title: AML_060 diagnosis epiallele analysis of ERRBS data


title: TL112

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

institute: National Health Research Institutes

description: These samples, having names of TLxxx, are the tumor lung counterparts of those previously submitted normal lung samples, which have names like NLxxx. So TL001 is the tumor counterpart of NL001, and TL002 is the tumor counterpart of NL002, and so on.

hyb_protocol: standard Ilumina protocol

scan_protocol: standard Ilumina protocol

data_processing: Data preprocessing of the microarray expression data included standard quality control recommended by Illumina, model based background correction (Ding et al, 2008), and surrogate variable analysis (Leek et al., 2012) to detect and alleviate batch effects33.

label_protocol: standard Ilumina protocol

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to protocol provided in the kit by the manufacturer. Quality control was performed with Agilent Bioanalyser.

value: Female

tag: smoking status

value: Non-smoking


title: Calveria_HPD_5D

description: Gene expression in HPD-filled sample: Day 5

source_name: HPD implantation, calveria, Day5


title: TL111


title: AML_058 relapse epiallele analysis of ERRBS data


title: TL108


title: AML_059 diagnosis epiallele analysis of ERRBS data


title: TL115

value: Male


title: TL109


title: TL113


title: TL114


title: TL110


title: AML_056 relapse epiallele analysis of ERRBS data


title: AML_057 relapse epiallele analysis of ERRBS data


title: AML_058 diagnosis epiallele analysis of ERRBS data

value: diagnosis


title: AML_056 diagnosis epiallele analysis of ERRBS data


title: AML_057 diagnosis epiallele analysis of ERRBS data


title: AML_055 relapse epiallele analysis of ERRBS data

value: Bone Marrow


title: AML_054 relapse epiallele analysis of ERRBS data

value: relapse


title: AML_055 diagnosis epiallele analysis of ERRBS data


title: TL105


title: AML_054 diagnosis epiallele analysis of ERRBS data


title: TL107


title: TL102


title: AML_053 diagnosis epiallele analysis of ERRBS data


title: TL104


title: AML_051 diagnosis epiallele analysis of ERRBS data


title: AML_052 relapse epiallele analysis of ERRBS data


title: AML_052 diagnosis epiallele analysis of ERRBS data


title: AML_051 relapse epiallele analysis of ERRBS data


title: AML_050 relapse epiallele analysis of ERRBS data


title: TL100


title: TL101


title: AML_050 diagnosis epiallele analysis of ERRBS data


title: AML_053 relapse epiallele analysis of ERRBS data


title: TL098


title: TL103


title: AML_049 diagnosis epiallele analysis of ERRBS data


title: TL099


title: AML_047 relapse epiallele analysis of ERRBS data


title: AML_048 diagnosis epiallele analysis of ERRBS data


title: TL097


title: TL096


title: TL028


title: TL076


title: TL022


title: TL106


title: AML_048 relapse epiallele analysis of ERRBS data


title: AML_046 diagnosis epiallele analysis of ERRBS data


title: AML_046 relapse epiallele analysis of ERRBS data


title: AML_047 diagnosis epiallele analysis of ERRBS data


title: AML_045 diagnosis epiallele analysis of ERRBS data


title: AML_044 relapse epiallele analysis of ERRBS data


title: AML_045 relapse epiallele analysis of ERRBS data


title: AML_044 diagnosis epiallele analysis of ERRBS data


title: AML_040 relapse epiallele analysis of ERRBS data


title: AML_042 diagnosis epiallele analysis of ERRBS data


title: AML_040 diagnosis epiallele analysis of ERRBS data


title: AML_041 relapse epiallele analysis of ERRBS data


title: AML_042 relapse epiallele analysis of ERRBS data


title: AML_038 relapse epiallele analysis of ERRBS data


title: AML_037 relapse epiallele analysis of ERRBS data


title: AML_041 diagnosis epiallele analysis of ERRBS data


title: AML_036 relapse epiallele analysis of ERRBS data


title: AML_043 relapse epiallele analysis of ERRBS data


title: AML_049 relapse epiallele analysis of ERRBS data


title: AML_036 diagnosis epiallele analysis of ERRBS data


title: AML_038 diagnosis epiallele analysis of ERRBS data


title: AML_035 diagnosis epiallele analysis of ERRBS data


title: AML_034 relapse epiallele analysis of ERRBS data


title: AML_035 relapse epiallele analysis of ERRBS data


title: AML_034 diagnosis epiallele analysis of ERRBS data


title: AML_033 diagnosis epiallele analysis of ERRBS data


title: AML_032 relapse epiallele analysis of ERRBS data


title: AML_032 diagnosis epiallele analysis of ERRBS data


title: AML_031 relapse epiallele analysis of ERRBS data


title: AML_031 diagnosis epiallele analysis of ERRBS data


title: AML_043 diagnosis epiallele analysis of ERRBS data


title: AML_030 relapse epiallele analysis of ERRBS data


title: AML_029 relapse epiallele analysis of ERRBS data


title: AML_029 diagnosis epiallele analysis of ERRBS data


title: AML_037 diagnosis epiallele analysis of ERRBS data


title: AML_030 diagnosis epiallele analysis of ERRBS data


title: AML_028 relapse epiallele analysis of ERRBS data


title: AML_028 diagnosis epiallele analysis of ERRBS data


title: AML_027 relapse epiallele analysis of ERRBS data


title: AML_026 relapse epiallele analysis of ERRBS data


title: AML_033 relapse epiallele analysis of ERRBS data


title: AML_026 diagnosis epiallele analysis of ERRBS data


title: AML_027 diagnosis epiallele analysis of ERRBS data


title: AML_025 relapse epiallele analysis of ERRBS data


title: AML_025 diagnosis epiallele analysis of ERRBS data


title: TL094


title: TL085


title: TL090


title: AML_024 relapse epiallele analysis of ERRBS data


title: TL080


title: TL088


title: TL084


title: TL078


title: TL083


title: TL079


title: TL082


title: TL081


title: TL089


title: TL091


title: TL087


title: TL093


title: TL086


title: TL092


title: AML_024 diagnosis epiallele analysis of ERRBS data


title: AML_023 relapse epiallele analysis of ERRBS data


title: AML_022 relapse epiallele analysis of ERRBS data


title: TL075


title: TL073


title: AML_022 diagnosis epiallele analysis of ERRBS data


title: TL070


title: TL074


title: TL077


title: AML_023 diagnosis epiallele analysis of ERRBS data


title: TL072


title: AML_021 diagnosis epiallele analysis of ERRBS data


title: AML_021 relapse epiallele analysis of ERRBS data


title: TL071


title: TL068


title: TL067


title: TL064


title: TL063


title: TL065


title: TL066


title: TL060


title: TL057


title: TL062


title: TL061


title: AML_020 relapse epiallele analysis of ERRBS data


title: Huh1 K67 #4

description: Gene expression of Huh1 K67 #4

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarray  (G4845A) using the Agilent Gene Expression Hybridization Kit. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

tag: treatment


title: TL069


title: TL059


title: AML_019 diagnosis epiallele analysis of ERRBS data


title: TL058


title: AML_017 diagnosis epiallele analysis of ERRBS data


title: AML_019 relapse epiallele analysis of ERRBS data


title: Huh1 DMSO #3

description: Gene expression of Huh1 DMSO #3

source_name: Huh1 DMSO #3

tag: cell line

value: DMSO


title: AML_016 relapse epiallele analysis of ERRBS data

tag: cell type


title: Huh1 K67 #1

description: Gene expression of Huh1 K67 #1


title: Huh1 K67 #3

description: Gene expression of Huh1 K67 #3


title: keratinocyte_MT-HGF_AG1478 treated_rep1

first: Christophe

last: Cataisson

state: Maryland

address: 37 Covent drive

institute: National Cancer Institute

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw gene expression data (.CEL files) were processed with the Robust Multichip Average algorithm (RMA) and quantile normalization (Irizarry, 2003 #27) implemented in the BRB-ArrayTools version 4.3.2 (software developed by Dr. Richard Simon and BRB‑ArrayTools Development Team; http://linus.nci.nih.gov/BRB‑ArrayTools.html)

source_name: primary keratinocytes MT-HGF transgenic mock transduced AG1478 treated

label_protocol: Gene expression profiling was done using Affymetrix Mouse Gene 1.0 ST array platform. RNA quality testing, microarray hybridization and processing were done by the CCR Laboratory of Molecular Technology in Frederick, MD.

growth_protocol: cells are grown in 8% FBS throughout the experiment

extract_protocol: Total RNA were extracted using Trizol according to manusfacturer protocol

treatment_protocol: Treatment with AG1478 or vehicle control were conducted for 24 hours

value: FVB/N


title: TL056


title: Huh1 K67 #2

description: Gene expression of Huh1 K67 #2


title: keratinocyte_MT-HGF_AG1478 treated_rep3


title: MT-HGF keratinocyte control, biological replicate 3

hyb_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov

source_name: MT-HGF

growth_protocol: Keratinocyte grown in regular media (no starvation)

extract_protocol: Trizol + Qiagen column purification

treatment_protocol: RAS transduction for 3 days

tag: genotype/variation

value: MT-HGF

value: primary mouse keratinocytes in culture


title: MT-HGF keratinocyte control, biological replicate 2

scan_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov


title: Huh1 DMSO #1

description: Gene expression of Huh1 DMSO #1

source_name: Huh1 DMSO #1


title: TL046


title: Huh1 DMSO #4

description: Gene expression of Huh1 DMSO #4

source_name: Huh1 DMSO #4


title: keratinocyte_MT-HGF_AG1478 treated_rep2


title: TL054


title: TL055


title: TL045


title: AML_020 diagnosis epiallele analysis of ERRBS data

value: Acute Myeloid Leukemia patient

value: Hematopoietic mononuclear cells


title: AML_018 relapse epiallele analysis of ERRBS data


title: AML_018 diagnosis epiallele analysis of ERRBS data


title: AML_017 relapse epiallele analysis of ERRBS data


title: smith-00014: dap069

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

description: target extract_L_20070910_12-03-49-27_dap069-u133v2

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: acute lymphoblastic leukemia

value: acute lymphoblastic leukemia


title: smith-00014: dap102

description: target extract_L_20070911_16-35-21-301_dap102-u133v2

scan_protocol: See mage-tab files linked to series entry for additional details


title: AML_012 relapse epiallele analysis of ERRBS data


title: AML_015 diagnosis epiallele analysis of ERRBS data


title: AML_014 diagnosis epiallele analysis of ERRBS data


title: AML_016 diagnosis epiallele analysis of ERRBS data

value: Peripheral Blood


title: AML_014 relapse epiallele analysis of ERRBS data


title: AML_011 relapse epiallele analysis of ERRBS data


title: AML_015 relapse epiallele analysis of ERRBS data


title: AML_012 diagnosis epiallele analysis of ERRBS data


title: wildtype keratinocyte v-rasHa transduced, biological replicate 3

source_name: wild-type RAS

label_protocol: procedure performed by Genomics Laboratory  Cancer Research Technology Program  Frederick National Laboratory for Cancer Research  http://atp.ncifcrf.gov

value: wild-type RAS


title: AML_011 diagnosis epiallele analysis of ERRBS data


title: TL048


title: smith-00014: dap200

description: target extract dap200-u133v2

data_processing: See mage-tab files linked to series entry for additional details


title: TL051


title: wildtype keratinocyte control, biological replicate 2

source_name: wild-type

value: wild-type


title: TL049


title: smith-00014: dap198

description: target extract dap198-u133v2

label_protocol: See mage-tab files linked to series entry for additional details


title: TL050


title: TL043


title: MT-HGF keratinocyte control, biological replicate 1


title: smith-00014: dap108

description: target extract_L_20070911_16-35-21-301_dap108-u133v2

extract_protocol: See mage-tab files linked to series entry for additional details


title: wildtype keratinocyte control, biological replicate 3


title: AML_010 relapse epiallele analysis of ERRBS data


title: TL044


title: smith-00014: dap208

description: target extract dap208-u133v2


title: TL042


title: AML_010 diagnosis epiallele analysis of ERRBS data

source_name: AML_diagnosis epiallele analysis of ERRBS data


title: TL037


title: TL039


title: smith-00014: dap203

description: target extract dap203-u133v2


title: wildtype keratinocyte v-rasHa transduced, biological replicate 1


title: AML_009 diagnosis epiallele analysis of ERRBS data


title: TL034


title: TL040


title: smith-00014: dap100

description: target extract_L_20070911_16-35-21-301_dap100-u133v2


title: AML_009 relapse epiallele analysis of ERRBS data

source_name: AML_relapse epiallele analysis of ERRBS data


title: TL035


title: 4Cont

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

description:
Biological replicate 4 mock control.
4655469061_D

hyb_protocol: Hybridized to the Illumina MouseWG-6 v2.0 expression BeadChip following the standard Illumina hybridization protocol.

scan_protocol: The BeadChips were scanned on the Illumina Iscan.

data_processing: Scanned files were loaded into BeadStudio software for analysis.

source_name: thioglycollate-elicited peritoneal macrophages, control

label_protocol: Labeled cRNA for hybridization onto Illumina BeadChips following the recommended Illumina protocol using a TotalPrep RNA Amplification kit (Applied Biosystems). Purification of the cRNA will follow and integrity of the cRNA will be assessed by running aliquots on the Bioanalyzer prior to hybridization.

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.

treatment_protocol: Thioglycollate-elicited peritoneal macrophages were incubated in the presence of Ac-LDL (120 μg/ml) or mock treated for 24 h.

tag: strain/background

value: 8 weeks

value: mock


title: wildtype keratinocyte v-rasHa transduced, biological replicate 2


title: TL036

value: Female

value: Non-smoking


title: smith-00014: dap079

description: target extract_L_20070910_12-03-49-27_dap079-u133v2


title: wildtype keratinocyte control, biological replicate 1


title: 3Cont

description:
Biological replicate 3 mock control.
4655469061_A


title: TL041


title: Huh1 DMSO #2

description: Gene expression of Huh1 DMSO #2

source_name: Huh1 DMSO #2


title: 3AcLDL

description:
Biological replicate 3 Ac-LDL.
4655469061_B

source_name: thioglycollate-elicited peritoneal macrophages, AcLDL

value: acetylated low density lipoprotein (Ac-LDL)


title: TL033

value: Male


title: 1Cont

description:
Biological replicate 1 mock control.
4655469036_A


title: 2AcLDL

description:
Biological replicate 2 Ac-LDL.
4655469036_E


title: smith-00014: dap104

description: target extract_L_20070911_16-35-21-301_dap104-u133v2


title: 4AcLDL

description:
Biological replicate 4 Ac-LDL.
4655469061_E


title: 2Cont

description:
Biological replicate 2 mock control.
4655469036_D


title: AML_008 relapse epiallele analysis of ERRBS data

value: relapse

value: Bone Marrow


title: smith-00014: dap205

description: target extract dap205-u133v2


title: smith-00014: dap122

description: target extract dap122-u133v2


title: AML_008 diagnosis epiallele analysis of ERRBS data

value: diagnosis


title: AML_007 relapse epiallele analysis of ERRBS data


title: smith-00014: dap106

description: target extract_L_20070911_16-35-21-301_dap106-u133v2


title: smith-00014: dap210

description: target extract dap210-u133v2


title: 1AcLDL

description:
Biological replicate 1 Ac-LDL.
4655469036_B


title: smith-00014: dap098

description: target extract_L_20070911_16-35-21-301_dap098-u133v2


title: AML_007 diagnosis epiallele analysis of ERRBS data


title: AML_005 relapse epiallele analysis of ERRBS data


title: smith-00014: dap084

description: target extract_L_20070911_13-46-01-249_dap084-u133v2


title: TL031

description: These samples, having names of TLxxx, are the tumor lung counterparts of those previously submitted normal lung samples, which have names like NLxxx. So TL001 is the tumor counterpart of NL001, and TL002 is the tumor counterpart of NL002, and so on.


title: AML_006 diagnosis epiallele analysis of ERRBS data


title: smith-00014: dap214

description: target extract dap214-u133v2


title: AML_006 relapse epiallele analysis of ERRBS data


title: TL030


title: TL026


title: TL029


title: smith-00014: dap083

description: target extract_L_20070911_13-46-01-249_dap083-u133v2


title: AML_004 diagnosis epiallele analysis of ERRBS data


title: TL025


title: AML_004 relapse epiallele analysis of ERRBS data


title: smith-00014: dap094

description: target extract_L_20070911_13-46-01-249_dap094-u133v2


title: AML_005 diagnosis epiallele analysis of ERRBS data


title: smith-00014: dap206

description: target extract dap206-u133v2


title: smith-00014: dap105

description: target extract_L_20070911_16-35-21-301_dap105-u133v2


title: AML_003 relapse epiallele analysis of ERRBS data


title: AML_002 relapse epiallele analysis of ERRBS data


title: AML_003 diagnosis epiallele analysis of ERRBS data


title: TL023


title: smith-00014: dap101

description: target extract_L_20070911_16-35-21-301_dap101-u133v2


title: TL095


title: smith-00014: dap075

description: target extract_L_20070910_12-03-49-27_dap075-u133v2


title: AML_002 diagnosis epiallele analysis of ERRBS data


title: TL018


title: smith-00014: dap123

description: target extract dap123-u133v2


title: smith-00014: dap090

description: target extract_L_20070911_13-46-01-249_dap090-u133v2


title: TL027


title: TL019


title: TL021


title: smith-00014: dap074

description: target extract_L_20070910_12-03-49-27_dap074-u133v2


title: smith-00014: dap121

description: target extract dap121-u133v2


title: TL017


title: smith-00014: dap195

description: target extract dap195-u133v2


title: smith-00014: dap120

description: target extract dap120-u133v2


title: AML_001 relapse epiallele analysis of ERRBS data


title: smith-00014: dap082

description: target extract_L_20070910_12-03-49-27_dap082-u133v2


title: smith-00014: dap237

description: target extract dap237-u133v2


title: smith-00014: dap091

description: target extract_L_20070911_13-46-01-249_dap091-u133v2


title: smith-00014: dap202

description: target extract dap202-u133v2


title: AML_001 diagnosis epiallele analysis of ERRBS data


title: TL024


title: TL020


title: TL014


title: TL013


title: TL010


title: TL016


title: smith-00014: dap236

description: target extract dap236-u133v2


title: TL012


title: smith-00014: dap132

description: target extract dap132-u133v2


title: TL015


title: TL009


title: TL008


title: TL011


title: TL004


title: smith-00014: dap241

description: target extract dap241-u133v2


title: smith-00014: dap068

description: target extract_L_20070910_12-03-49-27_dap068-u133v2


title: smith-00014: dap095

description: target extract_L_20070911_13-46-01-249_dap095-u133v2


title: TL007


title: TL006


title: smith-00014: dap196

description: target extract dap196-u133v2


title: smith-00014: dap073

description: target extract_L_20070910_12-03-49-27_dap073-u133v2


title: smith-00014: dap207

description: target extract dap207-u133v2


title: TL003


title: smith-00014: dap204

description: target extract dap204-u133v2


title: TL052


title: TL053


title: TL002


title: smith-00014: dap078

description: target extract_L_20070910_12-03-49-27_dap078-u133v2


title: smith-00014: dap201

description: target extract dap201-u133v2


title: smith-00014: dap118

description: target labeled extract dap118-u133v4


title: smith-00014: dap128

description: target extract dap128-u133v2


title: smith-00014: dap089

description: target extract_L_20070911_13-46-01-249_dap089-u133v2


title: smith-00014: dap215

description: target extract dap215-u133v2


title: TL001


title: TL038


title: smith-00014: dap225

description: target extract dap225-u133v2


title: TL047


title: TL005


title: smith-00014: dap197

description: target extract dap197-u133v2


title: TL032


title: smith-00014: dap211

description: target extract dap211-u133v2


title: smith-00014: dap085

description: target extract_L_20070911_13-46-01-249_dap085-u133v2


title: smith-00014: dap093

description: target extract_L_20070911_13-46-01-249_dap093-u133v2


title: smith-00014: dap096

description: target extract_L_20070911_13-46-01-249_dap096-u133v2


title: smith-00014: dap114

description: target extract_L_20070911_16-38-39-383_dap114-u133v2


title: smith-00014: dap107

description: target extract_L_20070911_16-35-21-301_dap107-u133v2


title: smith-00014: dap080

description: target extract_L_20070910_12-03-49-27_dap080-u133v2


title: smith-00014: dap099

description: target extract_L_20070911_16-35-21-301_dap099-u133v2


title: Primary AML patient 94

city: Padova

first: Matteo

last: Zampini

state: PD

address: corso stati uniti 4

country: Italy

institute: Istituto di Ricerca Pediatrica (IRP)  Città della Speranza

description: Gene expression data from pediatric AML patient according to C/EBPδ expression level (gene-level)

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The Genechips were scanned with an Affymetrix 7G scanner according to manifacturer guidelines.

data_processing: The CEL files generated were analyzed through Affymetrix Expression Console Software (version 1.3) which normalizes array signals using a robust multiarray averaging (RMA) algorithm. Normalized data were analyzed using Transcriptome Analysis Console (TAC) 3.0 Software (Affymetrix). An unpaired t-test was applied to identify differentially expressed transcript genes between sample pairs and probes with P-values less than 0.01 and fold-change >2 were declared significant.

source_name: AML BM

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

extract_protocol: Total bone marrow RNA was extracted using TRIzol reagent (Invitrogen) according to manufacturer guidelines, quantified using UV spectroscopy (Nanodrop Technologies), and qualitatively assessed using an Agilent2100 Bioanalyzer (Agilent Technologies).

tag: fab

tag: c/ebpsigma quartile

tag: karyotypic aberration

value: NEG


title: Primary AML patient 95


title: smith-00014: dap076

description: target extract_L_20070910_12-03-49-27_dap076-u133v2


title: Primary AML patient 89


title: smith-00014: dap139

description: target extract dap139-u133v2


title: Primary AML patient 86


title: Primary AML patient 93


title: smith-00014: dap117

description: target labeled extract dap117-u133v3


title: Primary AML patient 88


title: Cells transfected with SRSF1 siRNA sample 3 replicate 3

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

data_processing: Summarization was performed using RMA

source_name: A549 Lung Adenocarcinoma Cell Line

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter


title: Primary AML patient 78


title: Primary AML patient 82


title: smith-00014: dap137

description: target extract dap137-u133v2


title: Primary AML patient 80


title: smith-00014: dap199

description: target extract dap199-u133v2


title: Primary AML patient 73


title: smith-00014: dap138

description: target extract dap138-u133v2


title: Cells transfected with SRSF1 siRNA sample 2 replicate 2


title: Cells transfected with SRSF1 siRNA sample 3 replicate 1


title: Cells treated with scrambled RNA sample 3 replicate 3


title: Cells transfected with SRSF1 siRNA sample 2 replicate 3


title: Cells transfected with SRSF1 siRNA sample 1 replicate 1


title: Cells transfected with SRSF1 siRNA sample 2 replicate 1


title: Primary AML patient 72


title: smith-00014: dap212

description: target extract dap212-u133v2


title: Cells transfected with SRSF1 siRNA sample 1 replicate 2


title: Cells transfected with SRSF1 siRNA sample 3 replicate 2


title: smith-00014: dap077

description: target extract_L_20070910_12-03-49-27_dap077-u133v2


title: Cells transfected with SRSF1 siRNA sample 1 replicate 3


title: smith-00014: dap070

description: target extract_L_20070910_12-03-49-27_dap070-u133v2


title: smith-00014: dap213

description: target extract dap213-u133v2


title: Primary AML patient 71


title: Primary AML patient 69

value: inv(16) CBFB/MYH11


title: Primary AML patient 68


title: smith-00014: dap071

description: target extract_L_20070910_12-03-49-27_dap071-u133v2


title: Primary AML patient 70


title: Cells treated with scrambled RNA sample 3 replicate 1


title: Cells treated with scrambled RNA sample 3 replicate 2


title: smith-00014: dap115

description: target extract_L_20070911_16-38-39-383_dap115-u133v2


title: Primary AML patient 60


title: Primary AML patient 67


title: Cells treated with scrambled RNA sample 2 replicate 1


title: smith-00014: dap127

description: target extract dap127-u133v2


title: Cells treated with scrambled RNA sample 2 replicate 2


title: Wowe tumor

type: genomic

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: 200 µl hybridization mix was hybridized to genotyping microarrays for 16 h at 50°C.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were processed with R v3.0.1 and Bioconductor extension packages; microarray CDF and CEL files were read with affxparser, non-polymorphic probes were retained for analysis; the limma package was used to perform between-sample loess normalization of log2-transformed signal values.

source_name: Wowe2 MCC tumor cell line

label_protocol: 500 ng total genomic DNA was precessed with the Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Tumor cells and WoWe1 cells were cultured in RPMI 1640 supplemented with 10% FCS, 100 U/ml penicillin and 0.1 mg/ml streptomycin

extract_protocol: genomic DNA was isolated using qia amp DNA Mini Kit (Qiagen)

treatment_protocol: PBLs were isolated by Ficoll  gradient centrifugation; CD3+T cells were isolated by MACS cell separation (Miltenyi)

value: Wowe2 MCC tumor cell line

tag: group

value: tumor


title: Primary AML patient 48

value: MLL-t


title: Primary AML patient 49


title: Cells treated with scrambled RNA sample 1 replicate 2


title: Cells treated with scrambled RNA sample 2 replicate 3


title: miR-130b anti-miR expressing cell 48h rep3

city: Houston

first: Jason

last: Yustein

state: Texas

address: 1102 Bates Street Suite 1025.07

department: Cancer Center Hemotology/Oncology

institute: Texas Children's Hospital

description:
replicate3
SH-130b-3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGenome Studio

source_name: Ewing Sarcoma

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Norgen Biotek RNA cleanup and concentration kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: TC71 cells


title: smith-00014: dap145

description: target extract dap145-u133v2

value: acute lymphoblastic leukemia


title: Cells treated with scrambled RNA sample 1 replicate 1


title: BroLi control

source_name: Broli T-cells

value: BroLi T-cells

value: control


title: miR-130b anti-miR expressing cell 48h rep1

description:
replicate1
SH-130b-1


title: Cells treated with scrambled RNA sample 1 replicate 3


title: Cells trated with Lipofectamine sample 3 replicate 3


title: smith-00014: dap116

description: target labeled extract dap116-u133v2


title: miR-130b anti-miR expressing cell 48h rep4

description:
replicate4
SH-130b-4


title: miR-130b anti-miR expressing cell 48h rep2

description:
replicate2
SH-130b-2


title: miR-130b mimic expressing cell 48hl rep4

description:
replicate4
130B-4


title: smith-00014: dap072

description: target extract_L_20070910_12-03-49-27_dap072-u133v2


title: Cells trated with Lipofectamines sample 3 replicate 2


title: Primary AML patient 45


title: smith-00014: dap129

description: target extract dap129-u133v2


title: Cells trated with Lipofectamine sample 3 replicate 1


title: smith-00014: dap235

description: target extract dap235-u133v2


title: LoKe  tumor

source_name: Loke4 MCC tumor cell line

value: LoKe4 MCC tumor cell line


title: Cells trated with Lipofectamine sample 2 replicate 3


title: Primary AML patient 46


title: smith-00014: dap144

description: target extract dap144-u133v2


title: Wowe control

source_name: Wowe1 non-MCC cell line

value: Wowe1 non-MCC cell line


title: LoKe  control

source_name: Loke4 lymphocytes

value: LoKe4 lymphocytes


title: miR-130b mimic expressing cell 48hl rep2

description:
replicate2
130B-2


title: miR-130b mimic expressing cell 48hl rep3

description:
replicate3
130B-3


title: Primary AML patient 52


title: AlDo tumor

source_name: Aldo MCC tumor cell line

value: AlDo MCC tumor cell line


title: Primary AML patient 87


title: Cells trated with Lipofectamine sample 2 replicate 2


title: Primary AML patient 44


title: scramble expressing cell 48h rep3

description:
replicate 3
scr-3


title: AlDo control

source_name: Aldo lymphocytes

value: AlDo lymphocytes


title: smith-00014: dap240

description: target extract dap240-u133v2

source_name: acute lymphoblastic leukemia


title: scramble expressing cell 48h rep4

description:
replicate 4
scr-4


title: Cells trated with Lipofectamine sample 2 replicate 1


title: smith-00014: dap103

description: target extract_L_20070911_16-35-21-301_dap103-u133v2


title: smith-00014: dap216

description: target extract dap216-u133v2


title: Cells trated with Lipofectamine sample 1 replicate 2


title: BroLi tumor

source_name: Broli MCC tumor cell line

value: BroLi MCC tumor cell line


title: smith-00014: dap092

description: target extract_L_20070911_13-46-01-249_dap092-u133v2


title: smith-00014: dap217

description: target extract dap217-u133v2


title: smith-00014: dap131

description: target extract dap131-u133v2


title: Cells trated with Lipofectamine sample 1 replicate 1


title: Primary AML patient 63

value: Bone Marrow


title: Primary AML patient 62


title: miR-130b mimic expressing cell 48hl rep1

description:
replicate1
130B-1


title: scramble expressing cell 48h rep1

description:
replicate 1
scr-1


title: T5

city: Shanghai

first: Weijie

last: Min

state: Yangpu

address: Changhai road NO.168

department: Neurosurgery

country: China

institute: Changhai Hospital,Second Military Medical University

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: glioblastoma tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: tissues were cut off immediately after glioma operation, put into and stored in liquid nitrogen before total RNA extration

tag: pair

value: glioblastoma tissue


title: scramble expressing cell 48h rep2

description:
replicate 2
scr-2


title: Primary AML patient 47


title: T2


title: T3


title: Primary AML patient 34

value: NEG


title: Primary AML patient 55


title: smith-00014: dap097

description: target extract_L_20070911_16-35-21-301_dap097-u133v2


title: N4

source_name: paired adjacent normal glioblastoma tissue


title: smith-00014: dap119

description: target extract dap119-u133v2


title: T4


title: N5

value: paired adjacent normal glioblastoma tissue


title: Primary AML patient 35


title: Primary AML patient 41


title: N3


title: Primary AML patient 66


title: smith-00014: dap081

description: target extract_L_20070910_12-03-49-27_dap081-u133v2


title: smith-00014: dap109

description: target extract_L_20070911_16-38-39-383_dap109-u133v2


title: Glioblastoma xenograft + bevacizumab at nine generations, replicate 3

city: San Francisco

first: Garima

last: Yagnik

institute: UCSF

description: replicate 3

data_processing:
Array files are Illumina .idat files from platform HumanHT-12 v4.0 Gene Expression BeadChip
Annotation files for this chip were downloaded from http://support.illumina.com/downloads/humanht-12_v4_product_file.html on Sept 9, 2014
Specifically:
* HumanHT-12 v4.0 Manifest File (BGX Format) BGX (13 MB)  05/23/2013
* HumanHT-12 v4.0 Manifest File (TXT Format) ZIP (13 MB)  05/23/2013
* HumanHT-12 Sample Sheet (CSV Format)       CSV (< 1 MB) 12/13/2013
The annotation file used was the above-downloaded humanht-12_v4_0_r2_15002873_b.bgx file.
Processing of the arrays was handled via the R Bioconductor package illuminaio (Illumina IO)
Numeric expression values are Illumina expression values, with no units. Note that they are NOT on a log scale. Values range from ~30000 to ~80

label_protocol: Biotinylated cRNA were prepared with the TargetAmp-Nano Labelling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen), following manufacturers protocol, followed by quality control testing using Agilent Bioanalyzer with a RIn score > 8.

value: Glioblastoma xenograft

tag: xenograft host

value: Mus musculus

tag: host strain

value: Athymic nude mice

tag: host age

value: 6-8 weeks old


title: Glioblastoma xenograft + bevacizumab at four generations, replicate 3

description: replicate 3


title: N2


title: U937-B8 rep2

city: Montreal

first: Koren

last: Mann

state: Quebec

address: 3755 Cote Ste Catherine

country: Canada

institute: Lady Davis Institute

hyb_protocol: The labeled cRNA was then normalized at 600ng, fragmented and hybridized on Human GE Microarray 8X60K. The arrays were incubated in an Agilent Hybridization oven at 650C for 17 hours at 10 rpm.

scan_protocol: They were washed and scanned on an Agilent DNA Microarray Scanner C.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: U937-B8 cells grown in vorinostat replicate 2

label_protocol: Cyanine 3-labeled CTP cRNA was produced with 25ng of total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc)

growth_protocol: All cells were grown in RPMI 10% FBS

extract_protocol: RNA was extracted with the Qiagen extraction kit

tag: resistance

value: yes


title: Primary AML patient 31


title: Glioblastoma xenograft + bevacizumab at four generations, replicate 1

description: replicate 1


title: Glioblastoma xenograft + bevacizumab at four generations, replicate 2

description: replicate 2


title: Glioblastoma xenograft + bevacizumab at one generation, replicate 2

description: replicate 2


title: Primary AML patient 33


title: Primary AML patient 24


title: smith-00014: dap209

description: target extract dap209-u133v2

value: acute lymphoblastic leukemia


title: U937-B8 rep1

source_name: U937-B8 cells grown in vorinostat replicate 1


title: U937B8 wash off rep1

source_name: U937-B8 cells grown without vorinostat for 1 week replicate 1

value: no


title: Glioblastoma xenograft + bevacizumab at one generation, replicate 1

description: replicate 1


title: Glioblastoma xenograft + bevacizumab at one generation, replicate 3

description: replicate 3


title: Primary AML patient 23

source_name: AML BM


title: Primary AML patient 22


title: Cells trated with Lipofectamine sample 1 replicate 3

source_name: A549 Lung Adenocarcinoma Cell Line


title: Primary AML patient 43

value: MLL-t


title: Glioblastoma xenograft + bevacizumab at nine generations, replicate 1

description: replicate 1


title: Glioblastoma xenograft - bevacizumab, replicate 2

description: replicate 2

source_name: Glioblastoma xenograft_control


title: U937 2µM vor 12h rep2

source_name: U937 cells treated 12h 2µM vorinostat replicate 2


title: Glioblastoma xenograft + bevacizumab at nine generations, replicate 2

description: replicate 2


title: Primary AML patient 21


title: Glioblastoma xenograft - bevacizumab, replicate 1

description: replicate 1


title: U937 2µM vor 12h rep1

source_name: U937 cells treated 12h 2µM vorinostat replicate 1


title: U937 ctl rep2

source_name: U937 cells non treated replicate 2


title: Glioblastoma xenograft - bevacizumab, replicate 3

description: replicate 3


title: U937-B8 wash off rep2

source_name: U937-B8 cells grown without vorinostat for 1 week replicate 2


title: U937 ctl rep1

source_name: U937 cells non treated replicate 1


title: Meningioma Grade II  [MG_Grade_II_CJ 15753_2000153802.gpr]

type: protein

city: Mumbai

first: Sanjeeva

last: Srivastava

address: Powai

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Bombay

description: Recombinantly expressed proteins with GST fusion tag

hyb_protocol: The proteome array was blocked with 3% BSA in SuperBlock (Thermo Fisher Scientific) for 2 hours on a gentle shaker. Then the microarray was incubated with serum sample (diluted 1:500 in 2% BSA in TBST (tris buffered saline with 0.1% tween20) and anti-GST rabbit antibody (EMD Millipore, catalogue number AB3282) (diluted 1:500 in TBST) for 2 hours on shaker at RT. For detection, we used 1:1000 dilution of anti-human IgG conjugated with Cy5 (JacksonImmunoResearch, catalogue number 109-175-064) and 1:5000 dilution anti-rabbit antibody conjugated with Cy3 (Invitrogen, catalogue number A21429) and incubated for 1 hour at RT. Both these antibodies were diluted in the blocking buffer. After each incubation step, the array was rinsed and washed four times for 5 min each with TBST. Then the array was rinsed in distilled water and dried at 900 rpm for 2 minutes.

scan_protocol: The microarrays were scanned GenePix 4000B Microarray Scanner (Molecular Devices)

data_processing: The background correction was made using 'nec' method present in the limma package.For normalization, we used ‘normalizebetweenarrays’ method with the ‘quantile normalization’ function in limma.

molecule: protein

source_name: Serum

tag: age

tag: Sex

value: Female


title: Meningioma Grade II  [MG_Grade_II_CK 7710_2000153907.gpr]

label_protocol: For detection, we used 1:1000 dilution of anti-human IgG conjugated with Cy5 (JacksonImmunoResearch, catalogue number 109-175-064) and 1:5000 dilution anti-rabbit antibody conjugated with Cy3 (Invitrogen, catalogue number A21429) and incubated for 1 hour at RT.


title: Meningioma Grade II  [MG_Grade_II_CJ 15491_2000153803.gpr]

value: Male


title: Primary AML patient 84

tag: tissue

value: inv(11) NUP98/DDX10


title: Primary AML patient 83


title: Meningioma Grade II  [MG_Grade_II_CH 17967_2000153914.gpr]


title: Skeletal muscle cells differentiated from GEN058 BMD hESCs rep B

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description:
GEN058B Skeletal Muscle Disease 2
9463775051_L_Grn.idat

hyb_protocol: 750ng of cRNA from each sample was hybridized to Human HT-12 beadchip microarrays (Illumina) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina) at scan factor 1 as per manufacturer specifications.

data_processing:
Probe intensities were background subtracted using Beadstudio (Illumina) and normalized using the cross-correlation method (Chua et al., 2006) with MATLAB scripts. Gene probe sets with minimum 1.5- fold change (on a Log2 scale) and t-test significance P<0.05 over the average of the unaffected controls were identified.
Background subtracted cross-correlation method normalized intensity values generated using MATLAB scripts
[references] Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: Skeletal muscle, differentiated BMD hECS, GEN058, replicate B

label_protocol: 250ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed to biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, Life Technologies).

growth_protocol: Undifferentiated hESC lines were maintained and expanded feeder-free, on collagen I-coated plates (Biocoat, BD Bioscience) and in serum-free M2 Medium (Genea Biocells).

extract_protocol: Total RNA was harvested from myotube cultures using the Axyprep Multisource total RNA kit (Axygen Bioscience).

treatment_protocol: Cells were plated at 2500 cells/cm2 onto collagen I-coated plates and maintained for 10 days in Skeletal Muscle Induction medium. At day 10, cells were dissociated with 0.05% trypsin and replated at 2500 cells/cm2 onto collagen I-coated plates and maintained for 8 days in Skeletal Myoblast medium. After 18 days differentiation, cells were incubated in Myotube medium v1.0 and myotubes were maintained for 7 days.

value: skeletal muscle cell (SkMC)

tag: origin

value: GEN058 hESCs

tag: disease type

value: BMD

tag: replicate

value: B


title: Skeletal muscle cells differentiated from GEN096 FSHD1 hESCs rep B

description:
GEN096B Skeletal Muscle Disease 1
9463775051_J_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN096, replicate B

tag: cell type

value: GEN096 hESCs


title: Skeletal muscle cells differentiated from GEN058 BMD hESCs rep A

description:
GEN058A Skeletal Muscle Disease 2
9463775051_K_Grn.idat

source_name: Skeletal muscle, differentiated BMD hECS, GEN058, replicate A

value: A


title: Primary AML patient 42

value: Bone Marrow


title: Meningioma Grade I  [MG_Grade_I_CJ 29822_2000153909.gpr]


title: Primary AML patient 85


title: Skeletal muscle cells differentiated from GEN096 FSHD1 hESCs rep C

description:
GEN096C Skeletal Muscle Disease 1
9463775057_H_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN096, replicate C

value: C


title: Primary AML patient 40

description: Gene expression data from pediatric AML patient according to C/EBPδ expression level (gene-level)


title: Skeletal muscle cells differentiated from GEN058 BMD hESCs rep C

description:
GEN058C Skeletal Muscle Disease 2
9463775057_I_Grn.idat

source_name: Skeletal muscle, differentiated BMD hECS, GEN058, replicate C


title: Skeletal muscle cells differentiated from GEN096 FSHD1 hESCs rep A

description:
GEN096A Skeletal Muscle Disease 1
9463775051_I_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN096, replicate A


title: Skeletal muscle cells differentiated from GEN050 FSHD1 hESCs rep C

description:
GEN050C Skeletal Muscle Disease 1
9463775057_G_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN050, replicate C

value: GEN050 hESCs


title: Meningioma Grade II  [MG_Grade_II_CJ 3577_2000153910.gpr]


title: Primary AML patient 36


title: Meningioma Grade I  [MG_Grade_I_CJ 26538_2000153915.gpr]


title: Primary AML patient 39


title: Meningioma Grade I  [MG_Grade_I_CJ 29583_2000153908.gpr]


title: Primary AML patient 32


title: Primary AML patient 29


title: Skeletal muscle cells differentiated from GEN050 FSHD1 hESCs rep B

description:
GEN050B Skeletal Muscle Disease 1
9463775051_H_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN050, replicate B


title: Skeletal muscle cells differentiated from GEN050 FSHD1 hESCs rep A

description:
GEN050A Skeletal Muscle Disease 1
9463775051_G_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN050, replicate A


title: Meningioma Grade I  [MG_Grade_I_CJ 14742_2000153789.gpr]


title: Primary AML patient 20

source_name: AML BM

value: NEG


title: Meningioma Grade I  [MG_Grade_I_CJ 20619_2000153788.gpr]


title: Meningioma Grade I  [MG_Grade_I_CJ 29452_2000153786.gpr]


title: Primary AML patient 28


title: Meningioma Grade I  [MG_Grade_I_CJ 9179_2000153906.gpr]


title: Primary AML patient 96


title: Skeletal muscle cells differentiated from GEN049 FSHD1 hESCs rep C

description:
GEN049C Skeletal Muscle Disease 1
9463775057_F_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN049, replicate C

value: GEN049 hESCs


title: Primary AML patient 26


title: Skeletal muscle cells differentiated from GEN019 normal hESCs rep B

description:
GEN019B Skeletal Muscle unaffected
9463775051_B_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN019, replicate B

value: GEN019 hESCs

value: Normal


title: Primary AML patient 18


title: Meningioma Grade I  [MG_Grade_I_CJ 4231_2000153790.gpr]


title: Skeletal muscle cells differentiated from GEN049 FSHD1 hESCs rep B

description:
GEN049B Skeletal Muscle Disease 1
9463775051_F_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN049, replicate B


title: Primary AML patient 17


title: Primary AML patient 27


title: Healthy control [Control_HV-71_2000144458.gpr]


title: Skeletal muscle cells differentiated from GEN049 FSHD1 hESCs rep A

description:
GEN049A Skeletal Muscle Disease 1
9463775051_E_Grn.idat

source_name: Skeletal muscle, differentiated FSHD1 hECS, GEN049, replicate A


title: Healthy control [Control_HV-70_2000144457.gpr]


title: Meningioma Grade I  [MG_Grade_I_CF 4450_2000153801.gpr]


title: Skeletal muscle cells differentiated from GEN015 normal hESCs rep C

description:
GEN015C Skeletal Muscle unaffected
9463775057_E_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN015, replicate C

value: GEN015 hESCs


title: Meningioma Grade I  [MG_Grade_I_CH 24953_2000153787.gpr]

value: Female


title: Skeletal muscle cells differentiated from GEN019 normal hESCs rep C

description:
GEN019C Skeletal Muscle unaffected
9463775057_A_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN019, replicate C


title: Skeletal muscle cells differentiated from GEN019 normal hESCs rep A

description:
GEN019A Skeletal Muscle unaffected
9463775051_A_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN019, replicate A


title: Healthy control [Control_HV-59_2000155740.gpr]

description: Recombinantly expressed proteins with GST fusion tag

source_name: Serum

value: Male


title: Skeletal muscle cells differentiated from GEN015 normal hESCs rep B

description:
GEN015B Skeletal Muscle unaffected
9463775057_D_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN015, replicate B


title: Primary AML patient 14

value: t(8;21) RUNX1/RUNX1T1


title: Healthy control [Control_HV-56_2000155735.gpr]


title: Skeletal muscle cells differentiated from GEN015 normal hESCs rep A

description:
GEN015A Skeletal Muscle unaffected
9463775057_C_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN015, replicate A

value: skeletal muscle cell (SkMC)


title: Primary AML patient 16


title: Skeletal muscle cells differentiated from GEN002 normal hESCs rep B

description:
GEN002B Skeletal Muscle unaffected
9463775051_D_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN002, replicate B

value: GEN002 hESCs


title: Healthy control [Control_HV-64_2000144456.gpr]


title: Skeletal muscle cells differentiated from GEN002 normal hESCs rep C

description:
GEN002C Skeletal Muscle unaffected
9463775057_B_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN002, replicate C


title: Healthy control [Control_HC-25_2000153932.gpr]


title: Primary AML patient 13

description: Gene expression data from pediatric AML patient according to C/EBPδ expression level (gene-level)


title: Primary AML patient 12


title: Primary AML patient 15


title: Primary AML patient 11


title: Skeletal muscle cells differentiated from GEN002 normal hESCs rep A

description:
GEN002A Skeletal Muscle unaffected
9463775051_C_Grn.idat

source_name: Skeletal muscle, differentiated normal hECS, GEN002, replicate A


title: Healthy control [Control_H-58_2000153935.gpr]


title: Healthy control [Control_H-35_2000153942.gpr]


title: Healthy control [Control_H-59_2000154016.gpr]


title: Primary AML patient 07


title: Healthy control [Control_H-25_2000153952.gpr]


title: Primary AML patient 09


title: WNT11_DMZ_2

city: Karlsruhe

first: Dietmar

last: Gradl

address: Fritz Haber Weg 2

institute: Karlsruhe Institute of Technology

description: Stage 12 dorsal marginal zone explants, WNT11MO injected

hyb_protocol: at least 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the Gene Expression Hybridization Kit (Agilent). The probes were hybridized to a Xenopus 4x44K gene expression chip (Agilent) for 17 h at 65°C.  After hybridization, the chips were washed.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software (Version 10.7.3.1, Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 023448_D_F_20130122) to obtain background and spatially detrended processed signal intensities. The raw data were quantile normalized and afterwards log2-transformed with the aid of the Bioconductor R software.

organism: Xenopus laevis

source_name: Dorsal marginal zone explants, WNT11MO injected

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit, One Colour (Agilent) according to the manufacturer's instructions, purification by RNAeasy Mini Kit (Qiagen, Germany).  Dye incorporation and cRNA yield were checked with a Spectrophotometer.

growth_protocol: Xeopus laevis were injected in both dorsal blastomeres at 8-cell stage (COMO, WNT5AMO, WNT11MO) and cultivated until stage 10.25

extract_protocol: Total RNA was isolated from 30 DMZ explants via TRIzol Plus RNA Purification Kit (Life Technologies GmbH, Germany) according to manufactur's instructions. Total RNA was concentrated by Rneasy MinElute Cleanup Kit (Qiagen, Germany). Only probes with a RIN-value over 8 were used for the analysis (Agilent 2100 Bioanalyzer)

treatment_protocol: DMZ explants were dissected at stage 10.25 and cultivated until their siblings reach stage 12

value: Dorsal marginal zone explants

tag: developmental stage

value: Stage 12


title: WNT11_DMZ_3


title: WNT5A_DMZ_3

description: Stage 12 dorsal marginal zone explants, WNT5AMO injected

source_name: Dorsal marginal zone explants, WNT5AMO injected


title: Healthy control [Control_H-23_2000154009.gpr]


title: WNT11_DMZ_1


title: Healthy control [Control_H-19_2000154008.gpr]


title: Healthy control [Control_H-02_2000153953.gpr]


title: Healthy control [Control_H-41_2000154026.gpr]


title: Primary AML patient 06

tag: fab


title: WNT5A_DMZ_2


title: Primary AML patient 04

tag: c/ebpsigma quartile


title: CoMO_DMZ_3

description: Stage 12 dorsal marginal zone explants, CoMO injected

source_name: Dorsal marginal zone explants, CoMO injected


title: Primary AML patient 03

source_name: AML BM

tag: karyotypic aberration


title: Control of Proband 33

status: Public on Jun 20 2016

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: healthy control of proband 33, peripheral whole blood

hyb_protocol: For each array, 750 ng of each Cy5- (human universal control) and Cy3-labeled sample cRNA were hybridized using the Agilent in situ hybridization kit. Hybridizations were performed for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent scanner. Images were quantified using Agilent Feature Extraction Software(v 11.0)

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and LOWESS normalization.

source_name: whole blood sample from control of proband 33

label_protocol: A total of 500ng RNA was amplified and labeled using the Agilent fluorescent linear amplification kit following the manufacturer’s standard protocol.

extract_protocol: Total RNA extracted using the PAXgene RNA isolation kit in accordance with the manufacturer’s recommendations

value: whole blood

source_name: Universal Reference RNA (Agilent, catalogue number: 740000)

tag: reference

value: 10 cell lines for human


title: Primary AML patient 01

value: Bone Marrow


title: Primary AML patient 02


title: CoMO_DMZ_2


title: Primary AML patient 05


title: Healthy control [Control_H-03_2000153943.gpr]


title: CoMO_DMZ_1


title: WNT5A_DMZ_1


title: Control of Proband 29

description: healthy control of proband 29, peripheral whole blood

source_name: whole blood sample from control of proband 29


title: Control of Proband 17

description: healthy control of proband 17, peripheral whole blood

source_name: whole blood sample from control of proband 17


title: Control of Proband 28

description: healthy control of proband 28, peripheral whole blood

source_name: whole blood sample from control of proband 28


title: Control of Proband 30

description: healthy control of proband 30, peripheral whole blood

source_name: whole blood sample from control of proband 30