title: Ji_Batch2_5__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-060-2011
protocol manuals are available on the series record


title: Ji_Batch2_62_day0

status: Public on Dec 01 2016

type: RNA

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

country: USA

institute: stanford

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-079-2011
protocol manuals are available on the series record

data_processing: Genespring GX 12.6., RMA normalization: median of all samples

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: whole blood

tag: time point

value: day 0 (before vaccination)

tag: Sex

value: male

tag: age (years)


title: Ji_Batch2_57_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-108-2011
protocol manuals are available on the series record


title: Ji_Batch2_61_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-051-2011
protocol manuals are available on the series record

value: female


title: Ji_Batch2_53_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-119-2011
protocol manuals are available on the series record


title: Ji_Batch2_52_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-103-2011
protocol manuals are available on the series record


title: Ji_Batch2_58_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-041-2011
protocol manuals are available on the series record


title: Ji_Batch2_66_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-053-2011
protocol manuals are available on the series record


title: Ji_Batch2_49_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-044-2011
protocol manuals are available on the series record


title: Ji_Batch2_54_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-011-2011
protocol manuals are available on the series record


title: Ji_Batch2_6__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-055-2011
protocol manuals are available on the series record

value: Fluzone multi-dose vial|49281-388-15


title: Ji_Batch2_47_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-070-2011
protocol manuals are available on the series record


title: Ji_Batch2_43_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-006-2011
protocol manuals are available on the series record


title: Ji_Batch2_46_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-075-2011
protocol manuals are available on the series record


title: Ji_Batch2_41_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-025-2011
protocol manuals are available on the series record


title: Ji_Batch2_4__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-013-2011
protocol manuals are available on the series record


title: Ji_Batch2_40_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-104-2011
protocol manuals are available on the series record


title: Ji_Batch2_39_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-097-2011
protocol manuals are available on the series record


title: Ji_Batch2_37_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-111-2011
protocol manuals are available on the series record


title: Ji_Batch2_44_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-090-2011
protocol manuals are available on the series record


title: Ji_Batch2_31_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-115-2011
protocol manuals are available on the series record


title: Ji_Batch2_36_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-036-2011
protocol manuals are available on the series record


title: Ji_Batch2_33_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-092-2011
protocol manuals are available on the series record


title: Ji_Batch2_42_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-118-2011
protocol manuals are available on the series record


title: Ji_Batch2_35_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-122-2011
protocol manuals are available on the series record


title: Ji_Batch2_45_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-067-2011
protocol manuals are available on the series record


title: Ji_Batch2_34_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-084-2011
protocol manuals are available on the series record


title: Ji_Batch2_29_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-095-2011
protocol manuals are available on the series record


title: Ji_Batch2_28_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-029-2011
protocol manuals are available on the series record


title: Ji_Batch2_27_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-106-2011
protocol manuals are available on the series record


title: Ji_Batch2_3__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-100-2011
protocol manuals are available on the series record


title: Ji_Batch2_25_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-102-2011
protocol manuals are available on the series record


title: Ji_Batch2_26_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-061-2011
protocol manuals are available on the series record


title: H3K9ac-NE-plusDox-Rep3

type: genomic

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

hyb_protocol: ChIP samples and corresponding input chromatin samples were hybridized to Nimblegen HD2 2.1M feature tiled arrays after linear amplification (using the Sigma WGA kit (#WGA2)) and labelling as described above. MOgene performed ChIP-chip hybridizations using a NimbleGen Hybridization System and Kit, as recommended by the manufacturer.

scan_protocol: MOgene performed scanning, using the NimbleGen MS 200 Microarray Scanner for two color microarrays

data_processing:
Data analysis was performed by MOgene, using Nimblegen platform software (Nimblescan/Signal Map).  The Nimblescan FindPeak software generated scaled log2-ratio data (ratio of IP vs input for individual probes) peak files containing regions of significant factor binding/histone modification.
Peaks with fdr>0.2 were filtered from the list by Nimblescan. For Geminin ChIP, we set a cutoff of fdr<0.05 for each peak list and truncated peaks that did not meet this criteria. Peak intersection analysis for the three independent biological replicates for each sample type above was performed using Bedtools, peaks present in at least two of the three replicates were defined in ENSEMBL Build 67 (mm9), using Liftover, and the nearest transcription start site was defined with Peak Annotator, defining reproducible regions of peak overlap between the three experimental replicates. To define Geminin-dependent  H3K9ac peaks, we performed the same analysis as above to define H3K9ac peaks found in 2 of 3 independent experiments, but retained the default cut-off of fdr>0.2 (which also indicates high quality peaks), to maintain all significantly enriched regions for comparisons with Gem binding.  This analysis was done for three independent experimental samples in 2.5 day neuroectoderm both under wild type conditions (no Dox) and under conditions of Geminin knockdown (+Dox).  Peaks remaining under conditions of Geminin knockdown were then subtracted from the no Dox sample, so define the “no Dox-specific” peaks that were lost upon Geminin knockdown.

molecule: genomic DNA

organism: Mus musculus

source_name: Plus Dox-Gmnn knockdown-H3K9ac ChIP in neuroectoderm, using an ESC line for Doxycycline-inducible Gmnn knockdown, no Dox added control

label_protocol: Cy3 nad Cy5 labeling of experimental (IP) and control (input) samples was performed by Mogene, LC, using the NimbleGen DualColor DNA Labeling Kit

growth_protocol: Monolayer neural differentiation of ES cells was done as previously described (Ying and Smith, Methods in Enzymology 2003, 365: 327-41). Briefly, ES cells cultured on feeder cells were dissociated and plated at 1x105/cm2 for one day on 0.1% gelatin-coated tissue culture dishes. After 24 hours, cells were plated onto 0.1% gelatin-coated tissue culture dishes at low density (1x104 cells/cm2) in N2B27 medium and cultured for 2.5 days.

extract_protocol: Quantitative ChIP was done with modifications to a standard protocol (Upstate/Millipore) as follows. For each ChIP reaction, sheared chromatin (sonicated to 200-500 bp) from 2-5x10^6 mES cells fixed in 1% Formaldehyde (Sigma) in DMEM+5% FBS was incubated with 5µg antibody using Dynabeads (Invitrogen) as per the manufacturers instructions. Antibodies used for ChIP were Gmnn (N-18;Santa Cruz sc-8449) and H3K9ac (Abcam; Ab10812). After washing, elution and cross-link reversal, DNA from each ChIP sample and the corresponding input sample was purified. ChIP enrichement for positive control amplicons was analyzed further using qPCR as follows: each ChIP sample and a range of dilutions of the corresponding input sample (0.01%-5% input) were quantitatively analyzed with gene specific primers using the 7500 FAST Real-time PCR Detection System (ABI) and SYBR Advantage qPCR Premix (Clontech).

treatment_protocol: 500ng Dox treatment during ESC to neuroectoderm specification

tag: cell type

value: mouse ESC-derived neuroectoderm

source_name: Input for ES cell-derived neuroectoderm

treatment_protocol: no treatment


title: H3K9ac-NE-plusDox-Rep2


title: H3K9ac-NE-plusDox-Rep1


title: Ji_Batch2_20_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-123-2011
protocol manuals are available on the series record


title: Ji_Batch2_22_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-007-2011
protocol manuals are available on the series record


title: H3K9ac-NE-noDox-Rep2

source_name: No Dox control-H3K9ac ChIP in neuroectoderm, using an ESC line for Doxycycline-inducible Gmnn knockdown, no Dox added control


title: H3K9ac-NE-noDox-Rep3


title: H3K9ac-NE-noDox-Rep1


title: Ji_Batch2_19_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-037-2011
protocol manuals are available on the series record


title: Ji_Batch2_23_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-082-2011
protocol manuals are available on the series record


title: Ji_Batch2_24_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-065-2011
protocol manuals are available on the series record


title: Ji_Batch2_16_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-107-2011
protocol manuals are available on the series record


title: Ji_Batch2_21_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-071-2011
protocol manuals are available on the series record


title: Ji_Batch2_17_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-066-2011
protocol manuals are available on the series record


title: Gmnn-NE-Rep3

source_name: Gmnn ChIP in ESC-derived neuroectoderm


title: Ji_Batch2_18_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-048-2011
protocol manuals are available on the series record


title: Ji_Batch2_11_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-040-2011
protocol manuals are available on the series record


title: Gmnn-NE-Rep2


title: Ji_Batch2_12_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-072-2011
protocol manuals are available on the series record


title: Ji_Batch2_15_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-022-2011
protocol manuals are available on the series record


title: Gmnn-ESC-Rep3

source_name: Gmnn ChIP in ESCs

growth_protocol: The A2lox mouse ES cell line (Iacovino et al., Stem Cells 2011, 29(10): 1580-88) and a clonal derivative engineered for Doxycycline-dependent Gmnn shRNA.expression (Yellajoshyula et al., PNAS 2011, 108(8): 3294-99) were routinely propagated on feeder cells (mouse embryonic fibroblast cells, Chemicon) in DMEM (Invitrogen) supplemented with 15% fetal calf serum (Hyclone), 1 mM sodium pyruvate, 1 mM Non-Essential amino acids, 1mM L-Glutamine (Invitrogen), 10−4 M 2-mercaptoethanol (Sigma) and 103 units per ml of leukemia inhibitory factor (ESGRO, Chemicon).

value: mouse embryonic stem cells (ESCs)

source_name: Input for ES cells


title: Ji_Batch2_2__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-062-2011
protocol manuals are available on the series record


title: Ji_Batch2_10_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-050-2011
protocol manuals are available on the series record


title: Ji_Batch2_13_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-014-2011
protocol manuals are available on the series record


title: Gmnn-ESC-Rep1


title: Gmnn-ESC-Rep2


title: Ji_Batch2_14_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-089-2011
protocol manuals are available on the series record


title: Ji_Batch2_1__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-035-2011
protocol manuals are available on the series record


title: Gmnn-NE-Rep1


title: A17-16hpi-repeat2

city: Cambridge

first: Thomas

middle: Robert

last: Rey

address: Bateman street

country: United Kingdom

institute: Sainsbury Laboratory Cambridge University

description:
Gene expression data from pooled roots of germinated seedlings
20 pooled seedling roots

hyb_protocol: The labeled and fragmented aRNA was spiked with cDNA hybridization controls (GeneChip® Hybridization Control Kit, Affymetrix), which serve as an internal control for sensitivity and accuracy of the hybridization reaction as well as of the wash and stain procedure. The spiked aRNA samples were hybridized at 45°C for 16 hrs on separate Affymetrix GeneChip® Medi-cago Genome Arrays.After hybridization, microarrays were stained in two binding cycles using anti-Biotin antibodys and Streptavidin, R-phycoerythrin conjugate

scan_protocol: Fluorescent signal intensities were detected with the Affymetrix GeneChip® 3000 Scanner and AGCC Scan Control Software v3.2.3.1515 (Affymetrix). Automatic grid was arranged and raw data (*.DAT files) were processed to gen-erate image and intensity files (*:CEL, *.JPG) by the AGCC Scan Control Software.

data_processing: The software tools AGCC Viewer v3.2.0.1515 and Expression Console v1.3.1.187 (both Affymetrix Inc.) were used for quality control and visualization of the performance of microarray analysis.The software tool GeneSpring GX 12.6.1 (Agilent Technologies) was used for visualization and normalization. The RMA algorithm was applied for summarization quantile normalization of the data set.

organism: Medicago truncatula

source_name: A17 seedlings 16hpi

label_protocol: 200 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the RNA samples were spiked with polyadenylated transcripts (Gene Chip® Poly-A Control Kit, Affymetrix Inc.) which serve as an internal labeling control for linearity, sensitivity and accu-racy.  The spiked total RNA was reversely transcribed into double-stranded cDNA and then con-verted into Biotin-labeled aRNA by 16 hrs in-vitro transcription (3´IVT Expression Kit, Affy-metrix Inc.). The generated single stranded aRNA was purified and fragmented.

growth_protocol: Growth protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186)

extract_protocol: RNA extraction protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186)

treatment_protocol: Treatment protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186)

tag: genotype

value: A17 (wildtype)

value: root

tag: developmental stage

value: seedling

tag: pathogen

value: Phytophthora palmivora


title: case3_R_RNA

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

country: Japan

institute: KYUSHUUNIVERSItY

hyb_protocol: Hybridization was carried out using the conditions specified in the Agilent Human Whole Genome Expression system.

scan_protocol: Fluorescence intensities were determined with an Agilent DNA Microarray Scanner.

data_processing: The gene expression profiles obtained from microarray data were quantile normalized.

source_name: Primary colorectal tumor tissue

label_protocol: not provided

extract_protocol:
Laser micro-dissection
Total RNA was isolated by standard procedures

tag: case id

tag: gender

value: Male

tag: age

tag: tissue type

value: Primary colorectal tumor tissue

tag: primary tumor defferentiation

value: well to moderately differentiated

tag: tumor or normal colon location

value: descending colon


title: A17-16hpi-repeat3

description:
Gene expression data from pooled roots of germinated seedlings
21 pooled seedling roots


title: case3_Liver_RNA

source_name: Liver metastasis tumor tissue

value: Liver metastasis tumor tissue

value: liver


title: case3_G1_RNA


title: A17-Mock-repeat2

description:
Gene expression data from pooled roots of germinated seedlings
14 pooled seedling roots

source_name: A17 seedlings Mock

value: none (mock)


title: api-16hpi-repeat3

description:
Gene expression data from pooled roots of germinated seedlings
18 pooled seedling roots

source_name: api seedlings 16hpi

value: api


title: case3_Q_RNA


title: case3_C_RNA


title: api-Mock-repeat3

description:
Gene expression data from pooled roots of germinated seedlings
12 pooled seedling roots

source_name: api seedlings Mock


title: case3_G2_RNA


title: A17-Mock-repeat3

description:
Gene expression data from pooled roots of germinated seedlings
15 pooled seedling roots


title: api-16hpi-repeat1

description:
Gene expression data from pooled roots of germinated seedlings
16 pooled seedling roots


title: Chick-BP-48hr-Gentamicin-Biological-rep1

city: Boston

first: Zheng-Yi

last: Chen

state: MA

address: 243 Charles Street

department: Otolaryngology

institute: MEEI

description: Gene expression data from chick basilar papilla basal halves 48 hrs after gentamicin

hyb_protocol: Following the Affymetrix gene chip standard protocol of hybridization Wash and stain. 15 ug of fragmented cRNA were hybridized on GeneChip Chicken Genome Array. The arrays were placed in Affymetrix Genechip Hybridization Oven 640, incubated for 16 hours at 45C, 60rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene chip Scanner 3000 7G.

data_processing: The data were analyzed with dChip, normalized using Invariant set normalization method. The expression values of Model-based expression indexes (MBEI) were created with PM/MM difference model using the default settings. The data were also analyzed with MAS 5.0 to obtain Present/Absent calls.

organism: Gallus gallus

source_name: chick basilar papilla 48 hrs after gentamicin, Pooled, Biological rep2

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Small Sample Target Labeling Assay Version II protocol from 0.3-2 ug total RNA.

growth_protocol: Chicks were maintained in Boston Children's Hospital animal facility.

extract_protocol: Total RNA was extracted with Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: 12-16-day-old chicks were treated with gentamicin. Basilar papilla samples at different time points after gentamicin treatment were dissected and the basal halves were collected in RNA Later solution for RNA extraction.

value: dissected basilar papilla, basal halves

value: wild type


title: case3_F1_RNA


title: case3_po3_RNA


title: Chick-BP-72hr-Gentamicin-Biological-rep1

description: Gene expression data from chick basilar papilla basal halves 72 hrs after gentamicin

source_name: chick basilar papilla 72 hrs after gentamicin, Pooled, Biological rep1


title: case3_J_RNA


title: case3_D_RNA


title: A17-Mock-repeat1

description:
Gene expression data from pooled roots of germinated seedlings
13 pooled seedling roots


title: Chick-BP-48hr-Gentamicin-Biological-rep2


title: api-Mock-repeat2

description:
Gene expression data from pooled roots of germinated seedlings
11 pooled seedling roots


title: api-Mock-repeat1

description:
Gene expression data from pooled roots of germinated seedlings
10 pooled seedling roots


title: A17-16hpi-repeat1

description:
Gene expression data from pooled roots of germinated seedlings
19 pooled seedling roots


title: case3_H_RNA


title: api-16hpi-repeat2

description:
Gene expression data from pooled roots of germinated seedlings
17 pooled seedling roots


title: case3_normal_RNA

source_name: Normal colon tissue tissue

value: Normal colon tissue tissue


title: Chick-BP-72hr-Gentamicin-Biological-rep2

source_name: chick basilar papilla 72 hrs after gentamicin, Pooled, Biological rep2


title: case3_E3_RNA


title: Chick-BP-Ctrl-0hr-Biological-rep2

description: Gene expression data from control chick basilar papilla basal halves

source_name: chick basilar papilla control, Pooled, Biological rep2


title: case3_M_RNA


title: case3_po2_RNA


title: case3_B_RNA


title: case3_O_RNA


title: Chick-BP-Ctrl-0hr-Biological-rep1


title: case3_S_RNA


title: case3_E1_RNA


title: case3_F2_RNA


title: OvarianCarcinoma_16_04-0187

city: Oslo

first: Marianne

middle: Lislerud

last: Smebye

address: Postboks 4953 Nydalen

country: Norway

institute: Oslo University Hospital

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

hyb_protocol: Samples were hybridized 16 - 18h onto GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and were washed, stained, and scanned according to manufacturer's protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Cell intensity (CEL)-files from the 19 tumor samples were background corrected, inter-chip quantile normalized, and summarized at gene level by the robust multi-array average (RMA) approach (Irizarry et al., 2003) implemented in the Affymetrix Expression Console 1.1 software. Annotation files: the HuEx-1_0-st-v2.r2 core library files and the annotation files HuEx-1_0-st-v2.na35.hg19.probeset.csv and HuEx-1_0-st-v2.na35.hg19.transcript.csv, available from the Affymetrix web page (www.affymetrix.com).

source_name: Ovarian carcinoma

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

growth_protocol: Tumor tissue adjacent to that used for cytogenetic analysis and histologic examination had been frozen and stored at −80°C.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and miRNAeasy spin columns (Qiagen GmbH, Hilden, Germany). First, tumor tissue was homogenized in TRIzol and the aqueous phase was removed and processed with the Qiagen miRNeasy Mini kit according to the manufacturer's protocol. Total RNA was quantified and the purity was assessed using a NanoVue spectrophotometer (GE Healthcare, Little Chalfont, UK). RNA quality was checked by the Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA). All 12 samples had RQI (RNA quality indicator) value 6.7 or higher.

value: Ovarian carcinoma

tag: histologic subtype

value: High-grade serous carcinoma


title: OvarianCarcinoma_17_04-0349

tag: karyotype aberration with structural rearrangement of chromosome 19 (der(19)).


title: case3_I_RNA


title: KP1019 treated_3h_rep2

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

description: Gene expression data from yeast cells (exponential phase) treated with KP1019 (50μg/ml) for 3h.

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G.

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

organism: Saccharomyces cerevisiae

source_name: Yeast cells (exponential phase) treated with 50μg/ml of KP1019 for 3h

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

growth_protocol: Saccharomyces cerevisiae strain (W1588-4c) was grown in standard Synthetic Complete liquid media (contain 2% glucose) at 30oC with orbital shaking.

extract_protocol: Total RNAs were extracted immediately after harvesting yeast cells by using heat/freeze RNA isolation method as previously described in [Schmitt ME, Brown TA, Trumpower BL. A Rapid and Simple Method for Preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Research, 1990; 18 (10): 3091–92.]. The quality of RNA was high as assessed by absorbance (260 and 280nm), by Formaldehyde Agarose-Gel electrophoresis, and by Agilent 2100 Bioanalyzer.

treatment_protocol: The yeast cells (W1588-4c) were grown to exponential phase (OD600: 0.8-1) and then treated with either DMSO solvent (Untreated Control) or a sub-lethal dose of 50µg/ml KP1019 (freshly prepared 40mg/ml stock in DMSO) for 3h at 30oC with shaking.

tag: strain

tag: growth phase

value: exponential


title: case3_po1_RNA


title: OvarianCarcinoma_12_03-751

tag: tissue

value: Undifferentiated carcinoma


title: OvarianCarcinoma_14_03-1004


title: DMSO_Control_rep2

description: Gene expression data from DMSO treated yeast cells (exponential phase)


title: DMSO_Control_rep1

source_name: DMSO treated yeast cells (exponential phase)


title: SW620_6_H_COMPOUND_1 2

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

institute: The Institute of Cancer Research

hyb_protocol: Cy 3 labelled cRNA was co-hybridised with Cy5 labelled Universal Human Reference RNA

scan_protocol: The arrays were scanned using an Agilent Technologies Scanner G2505C US84300231, using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.7.3.1 and extraction protocol GE2_107_Sep09 and grid file 028004_D_F_20110708.  Lowess normalization was applied to the samples.

data_processing: Background subtracted data for sample and reference were entered in the Genespring analysis software (Agilent).

source_name: SW620 xenografts harvested 6  hours after the final dose of COMPOUND_1

label_protocol: Quick Amp Labeling protocol

growth_protocol: All cell lines were purchased from the American Type Culture Collection and grown in their recommended culture medium, which was supplemented with 10% fetal bovine serum (FBS) at 37°C in an atmosphere of 5% CO2 and passaged for less than six months. Three million SW620 human colorectal carcinoma cells were injected s.c. in the right flanks of female NCr athymic mice 6–8 weeks of age.

extract_protocol: MagNA Pure LC RNA Isolation Tissue buffer (Roche) was added to the tumours and were homogenized using the Precellys homogenizer. RNA was purified on the MagNA Pure 96 System (Roche) according to the manufacturers instructions.

treatment_protocol: Therapy was initiated when established tumors reached a mean volume of 60 mm (day 13). Animals were randomly assigned to two cohorts. Control mice received vehicle (10% DMSO, 5% Tween 20, 85% saline) and treated animals compound 1 at 70 mg/kg orally twice a day with a 2-day break after 1 week's dosing. Animals were treated on day 1-7 and day 10 -14. Tumor volumes and body weights were measured three times weekly and the study was terminated on day 14. Tumour sample were collected 2 and 6 hours after the final dose. Tumours were snap frozen and stored at minus 80 degrees celcius.

tag: xenografted cell line

tag: treatment

tag: time (h)

source_name: Stratagene Universal Human Reference RNA

tag: sample type

value: Reference


title: OvarianCarcinoma_19_04-1096


title: SW620_6_H_COMPOUND_1 4


title: SW620_6_H_COMPOUND_1 5


title: OvarianCarcinoma_08_02-363


title: SW620_6_H_COMPOUND_1 3


title: Yeast BY4742 rep2

city: Fukui

first: kazuma

last: kamata

address: 3-9-1 Bunkyo

department: Applied Chemistry Biotechnology

institute: University of Fukui

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Wild type yeast strain

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (GeneChip®  3’ IVT Express Kit user Manual, 2010, Affymetrix).

growth_protocol: Yeast cells were grown in 5ml YPD until exponential phase (optimal density of 0.7).

extract_protocol: Total RNA was extracted by acid phenol-chloroform extraction.

treatment_protocol: Deletion strains were constructed by homologous recombination utilizing a KanMX gene.

tag: genotype/variation

value: Wild tyoe


title: OvarianCarcinoma_18_04-919

value: Serous carcinoma not graded due to neoadjuvant chemotherapy


title: OvarianCarcinoma_15_04-0186


title: OvarianCarcinoma_11_02-814


title: OvarianCarcinoma_13_03-819


title: Yeast gcn5 deletion

source_name: gcn5 deleted yeast strain

value: gcn5 deletion


title: Yeast BY4742 rep1

value: Wild type


title: Yeast ada1 deletion

source_name: ada1 deleted yeast strain

value: ada1 deletion


title: SW620_6_H_COMPOUND_1 1


title: OvarianCarcinoma_09_02-489


title: OvarianCarcinoma_07_02-233


title: OvarianCarcinoma_05_01-837


title: OvarianCarcinoma_10_02-781


title: OvarianCarcinoma_01_00-1002


title: KP1019 treated_3h_rep1

tag: genotype


title: OvarianCarcinoma_02_00-1012


title: SW620_6_H_VEHICLE 3

source_name: SW620 xenografts harvested 6  hours after the final dose of VEHICLE

value: VEHICLE


title: OvarianCarcinoma_03_01-805


title: OvarianCarcinoma_06_01-838


title: SW620_6_H_VEHICLE 5


title: SW620_2_H_COMPOUND_1 3

source_name: SW620 xenografts harvested 2  hours after the final dose of COMPOUND_1


title: SW620_2_H_VEHICLE 4

source_name: SW620 xenografts harvested 2  hours after the final dose of VEHICLE


title: SW620_2_H_VEHICLE 2


title: SW620_2_H_COMPOUND_1 4


title: OvarianCarcinoma_04_01-806


title: Smad4 KO mice arteries, biological rep1

city: Beijing

first: Xiao

last: Yang

address: 20 Dongdajie

country: China

institute: Beijing Institute of Biotechnology

description: Gene expression data from Smad4-KO mice artery at 6 weeks old

hyb_protocol: Following fragmentation,2 ug of cRNA were hybridized for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Scanner 7G.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and global scaling as normalization method. RMA analysis was employed to evaluate the gene expression

source_name: mice aortas

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA

growth_protocol: The mice were exposed to a 12-h light/dark cycle with controlled temperature and humidity. Food and water were provided ad libitum.

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

treatment_protocol: The aortic arteries were collected at 6 weeks old and were immediately put in RNAlatter reagent.


title: SW620_2_H_COMPOUND_1 5


title: SW620_6_H_VEHICLE 1


title: SW620_2_H_COMPOUND_1 1


title: SW620_6_H_VEHICLE 2


title: SW620_2_H_VEHICLE 3


title: Smad4 KO mice arteries, biological rep2


title: SW620_2_H_VEHICLE 5


title: SW620_2_H_VEHICLE 1


title: Colo205_6_H_VEHICLE 4

source_name: Colo205 xenografts harvested 6 hours after the final dose of VEHICLE

growth_protocol: All cell lines were purchased from the American Type Culture Collection and grown in their recommended culture medium, which was supplemented with 10% fetal bovine serum (FBS) at 37°C in an atmosphere of 5% CO2 and passaged for less than six months. Three million Colo205 human colorectal carcinoma cells were injected s.c. in the right flanks of female NCr athymic mice 6–8 weeks of age.

treatment_protocol: Therapy was initiated when established tumors reached a mean volume of 60 mm (day 5). Animals were randomly assigned to three cohorts. Control mice received vehicle (10% DMSO, 5% Tween 20, 85% saline) and treated animals compound 1 at 70 mg/kg and Compound 3 at 20 mg/kg orally twice a day. Animals were treated on day 1-8. Tumor volumes and body weights were measured on day 0, 4 and 8, and the study was terminated on day 8. Tumour samples were collected 2 and 6 hours after the final dose. Tumours were snap frozen and stored at minus 80 degrees celcius.


title: Colo205_6_H_COMPOUND_1 3

source_name: Colo205 xenografts harvested 6 hours after the final dose of COMPOUND_1


title: Colo205_6_H_COMPOUND_3 4

source_name: Colo205 xenografts harvested 6 hours after the final dose of COMPOUND_3


title: Colo205_6_H_COMPOUND_1 1


title: WT mice arteries, biological rep2

description: Gene expression data from WT mice aortic arteries at 6 weeks old

value: WT


title: Colo205_6_H_COMPOUND_3 2


title: Colo205_6_H_COMPOUND_3 1


title: Colo205_6_H_COMPOUND_3 3


title: Colo205_6_H_VEHICLE 2


title: Colo205_6_H_VEHICLE 1


title: Colo205_6_H_COMPOUND_1 2


title: Colo205_6_H_VEHICLE 3


title: Colo205_2_H_COMPOUND_3 4

source_name: Colo205 xenografts harvested 2 hours after the final dose of COMPOUND_3


title: SW620_2_H_COMPOUND_1 2


title: pDCIS22

city: Duesseldorf

first: Silke

last: Schultz

address: Merowingerplatz 1A

department: Department of Obstetrics and Gynaecology

country: Germany

institute: University Hospital Duesseldorf

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadStation 500 scanner protocol

data_processing: normalized by Illumina GenomeStudio software procedure

source_name: breast cancer

label_protocol: Standard Illumina labelling protocol

extract_protocol: total RNA was extracted using the Roche High Pure miRNA isolation Kit. Quality control was performed with Agilent Bioanalyser.

tag: diagnosis

value: breast cancer

value: FFPE

tag: subtype

value: ductal carcinoma in situ

tag: tissue donor

value: Patient 38


title: pDCIS21

value: Patient 37


title: pDCIS23

value: Patient 39


title: pDCIS19

value: Patient 35


title: pDCIS20

value: Patient 36


title: Colo205_2_H_COMPOUND_3 3


title: pDCIS24

value: Patient 40


title: Colo205_2_H_COMPOUND_1 4

source_name: Colo205 xenografts harvested 2 hours after the final dose of COMPOUND_1

value: Reference


title: Colo205_2_H_COMPOUND_1 2


title: pDCIS18

value: Patient 34


title: Colo205_2_H_COMPOUND_1 1


title: Colo205_2_H_COMPOUND_1 3


title: pDCIS15

value: Patient 31


title: Colo205_2_H_VEHICLE 3

source_name: Colo205 xenografts harvested 2 hours after the final dose of VEHICLE


title: Colo205_2_H_COMPOUND_3 2


title: pDCIS16

value: Patient 32


title: pDCIS17

value: Patient 33


title: WT mice arteries, biological rep1


title: pDCIS14

value: Patient 30


title: pDCIS13

value: Patient 29


title: Colo205_2_H_VEHICLE 4

value: VEHICLE


title: Colo205_2_H_VEHICLE 1


title: Colo205_2_H_COMPOUND_3 1


title: Colo205_2_H_VEHICLE 2


title: pDCIS11

value: breast cancer

value: Patient 27


title: pDCIS12

value: FFPE

value: ductal carcinoma in situ

value: Patient 28


title: pDCIS10

value: Patient 26


title: pDCIS9

value: Patient 25


title: pDCIS7

value: Patient 23


title: pDCIS6

value: Patient 22


title: pDCIS5

value: Patient 21


title: SW620_6_H_VEHICLE 4

value: Reference


title: DU145 prostate cancer cells, scrambled shRNA, rep2

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: Gene expression data from DU145 prostate cancer cells, transfected with scrambled shRNA

hyb_protocol: The cDNA was hybridized onto Affymetrix Human Gene 2.0 ST Arrays and the Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize and wash the cartridges. Control Oligonucleotide B2 and 20X Eukaryotic Hybridization Controls were added to the hybridization cocktail containing the labeled sample and injected into the cartridge. The Incubation lasted 16 hr at 45°C with a rotation at 60 rpm. Then, the Fluidics Station 450/250 was used to wash and stain the Affymetrix GeneChip Human Gene 2.0 ST probe arrays.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) for images and intensities.

data_processing: The data was processed using R/bioconductor and GC-RMA with default parameters.

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA was used for fragmentation and labeling.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen # 74106) and treated with DNaseI (Qiagen #79254).

treatment_protocol: DU145 prostate cancer cells were transfected with shRNA constructs for the knockdown of USP9X/Y and USP9X using the Lipofectamine 2000 transfection reagent (control samples included a scrambled RNA control, a transfection reagent control, and an unperturbed control)

value: DU145 prostate cancer cells

value: scrambled shRNA


title: DU145 prostate cancer cells, scrambled shRNA, rep3


title: DU145 prostate cancer cells, scrambled shRNA, rep1


title: DU145 prostate cancer cells, Usp9X shRNA, rep3

description: Gene expression data from DU145 prostate cancer cells transfected with Usp9X shRNA

value: Usp9X shRNA


title: DU145 prostate cancer cells, transfection control, rep3

description: Gene expression data from DU145 prostate cancer cells, transfection reagent without shRNA construct

value: transfection control


title: pDCIS4

value: Patient 20


title: pDCIS8

value: Patient 24


title: IDC15

value: breast cancer

value: invasive duct carcinoma

value: Patient 15


title: DCIS16

value: FFPE

value: ductal carcinoma in situ

value: Patient 16


title: IDC16


title: DCIS14

value: Patient 14


title: IDC13

value: Patient 13


title: DCIS13


title: DCIS15


title: pDCIS1

value: Patient 17


title: pDCIS3

value: Patient 19


title: pDCIS2

value: Patient 18


title: IDC12

value: Patient 12


title: IDC14


title: DU145 prostate cancer cells, unperturbed, rep3

description: Gene expression data from DU145 prostate cancer cells, unperturbed

value: DU145 prostate cancer cells

value: unperturbed


title: DU145 prostate cancer cells, unperturbed, rep2


title: DU145 prostate cancer cells, Usp9X shRNA, rep2

value: Usp9X shRNA


title: IDC8

value: Patient 8


title: IDC9

value: Patient 9


title: DCIS9

value: breast cancer


title: IDC10

value: invasive duct carcinoma

value: Patient 10


title: DCIS11

value: FFPE

value: Patient 11


title: DCIS10

value: ductal carcinoma in situ


title: DCIS8


title: DCIS7

value: Patient 7


title: IDC7


title: IDC6

value: Patient 6


title: DCIS6


title: DU145 prostate cancer cells, Usp9XY shRNA, rep1

description: Gene expression data from DU145 prostate cancer cells transfected with Usp9XY shRNA

value: Usp9XY shRNA


title: DU145 prostate cancer cells, transfection control, rep2

value: transfection control


title: DU145 prostate cancer cells, Usp9X shRNA, rep1


title: IDC5

value: Patient 5


title: DCIS5


title: IDC4

value: Patient 4


title: IDC11


title: DU145 prostate cancer cells, transfection control, rep1

value: DU145 prostate cancer cells


title: DU145 prostate cancer cells, Usp9XY shRNA, rep2


title: DU145 prostate cancer cells, Usp9XY shRNA, rep3


title: DU145 prostate cancer cells, unperturbed, rep1

value: unperturbed


title: DCIS4


title: IDC3

value: Patient 3


title: DCIS2

value: Patient 2


title: IDC2


title: DCIS3


title: Apc tumor organoid 5AZA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: organoids derived from intestinal tumors after treatment with 5-Aza-CdR

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

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

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

source_name: tumors of ApcMin mice

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Organoid culture was performed in matrigel with serum-free medium including R-spondin 1, EGF and Noggin.

extract_protocol: RNA samples were extracted from cells using mirVana isolation kit (Thermo Fisher Scientific).

treatment_protocol: Tumor organoids were treated with 1 uM of 5-Aza-CdR.

value: ApcMin mouse

tag: tissue source

value: intestinal tumor

value: organoids

tag: treated with

value: 1 uM of 5-Aza-CdR


title: IDC1

value: breast cancer

value: FFPE

value: invasive duct carcinoma

value: Patient 1


title: Wild-type organoid

description: organoids derived from normal epithelia

source_name: intestinal epitehlia of wild-type mice

value: wild type

value: normal epithelium


title: Apc tumor organoid

description: organoids derived from intestinal tumors


title: DCIS1

value: ductal carcinoma in situ


title: right kidney tissue

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: mouse right kidney

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Kidney

tag: Sex

value: Male


title: Nkx2-5 delta/+ heart (apex), 15 weks, replicate 2

city: Bar Harbor

first: Mauro

middle: W

last: Costa

address: 600 Main Street

institute: The Jackson Laboratory

description: Nkx2-5 delta/+ rep.2

hyb_protocol: For chip hybridization, 600 ng of Cy3 labelled cRNAs were fragmented at 60 °C for 30 min in a reaction volume of 25 μl containing 1× Agilent Fragmentation buffer and 2 × Agilent Gene Expression Blocking agent. Specific activities ranging between 16–18 pmol Cy3/μg cRNA were used for each sample. On completion, 25 μl of 2 × HI-RPM Gene Expression buffer (Agilent) was added. 40 μl of samples were hybridised on SurePrint G3 Mouse GE 8 × 60 K microarrays (Agilent) for 17 h at 65 °C in a rotating hybridisation oven (Agilent). Following hybridisation, microarrays were washed with GE wash buffer 1 (Agilent) for 1 min at room temperature and with GE wash buffer 2 at 37 °C for 1 min.

scan_protocol: Microarrays were scanned with an Agilent C, DNA microarray scanner at 3 μm resolution (scan area 61 × 21.6 mm), dye channel set to green, 20 bit tiff. The scanned images were analysed with Agilent Feature Extraction Software 11.0.1.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw single-channel signals provided by the Agilent Feature Extraction image analysis software was used for data analysis. Log-2 transformation and quantile normalisation was done in R scripts using public Bioconductor packages. Differential analysis was performed using the Bioconductor Limma package, which fits a linear model of gene expression. Differentially expressed genes (p-value<0.01) were retained for fold-change calculation.

source_name: 15 week whole heart (apex)

label_protocol: Samples showed RNA integrity numbers (RINs) ranging between 9–10, as determined by the 2100 Bioanalyser (Agilent) were used. 0.1 μg of total RNA was used to prepare Cyanine-3 (Cy3) labelled cRNA for hybridization. For labelling, the One-Color Low input Quick Amp labelling Kit (Agilent) was used according to the manufacturer's instructions, after which labelled RNA was cleaned using by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were determined with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana kit (Invitrogen) folowed by DNAseI digestion following the manufacturer's recommendations. RNA was quantified and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Triplicate samples from 15-week adult male hearts

value: Nkx2-5 delta/+

value: heart

tag: background strain

tag: age

value: 15 week adult

tag: gender

value: male


title: left kidney tissue

source_name: mouse left kidney


title: Nkx2-5 I183P/+ heart (apex), 15 weeks, replicate 3

description: Nkx2-5 183P/+ rep.3


title: Nkx2-5 I183P/+ heart (apex), 15 weeks, replicate 1

description: Nkx2-5 183P/+ rep.1


title: MEF (control)_Mm

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description:
raw data file: MES.txt
Normalized gProcessed value is used

hyb_protocol: The mixed labelled cRNAs were hybridized overnight to each array at 65 °C under constant rotation in the hybridization buffer supplied with the Gene Expression Hybridization Kit (Agilent).

scan_protocol: Arrays were washed by using a Gene Expression Wash Pack (Agilent) and scanned with a G2505B DNA microarray scanner (Agilent) in accordance with the manufacturer’s protocol.

data_processing: Linear and LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent Feature Extraction Software was used.  Normalized gProcessed or rProcessed value is reported in data table.

source_name: Mouse embryonic fibroblast

label_protocol: Each total RNA (400 ng) was used to synthesize fluorescence-labelled complementary RNA (cRNA) by using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) in accordance with the manufacturer’s protocol. Total RNAs of MES and MEF were labelled with cyanine-5 (Cy5) and cyanine-3 (Cy3), respectively. The labelled cRNA was purified by using a QIAGEN RNeasy Mini Kit (Qiagen).

growth_protocol: Cells were grown in a 5% CO2 humidified incubator at 37degreeC in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from the cells by using Fast pure RNA kit (Takara) in accordance with the manufacturer's protocol.

tag: cell line

value: Mouse embryonic fibroblast (control)


title: Control ESCs vs HDAC6-OE ESCs rep1

city: Tian Jin

first: Yu

last: Yin

address: 94 Wei Jin Road

institute: Nankai University

description: Biological replicate 1 of 2

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: WT ES cells at passage 26

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: ESCs were maintained on mitomycin C treated mouse embryonic fibroblasts (feeders) in ESCs medium containing knockout Dulbecco’s modified Eagle medium (KO-DMEM) (Invitrogen) added with 20% fetal bovine serum (Hyclone), 1000 U/ml LIF (Chemicon), 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, 0.1 mM non-essential amino acids, 100 units/ml penicillin and 100 μg/ml streptomycin.

tag: strain

tag: cell type

value: ESC

value: WT

tag: passage

source_name: OE ES cells at passage 26

value: HDAC6 overexpression


title: Nkx2-5 I183M/+ heart (apex), 15 weeks, replicate 1

description: Nkx2-5 183M/+ rep.1

tag: tissue


title: Nkx2-5 delta/+ heart (apex), 15 weks, replicate 1

description: Nkx2-5 delta/+ rep.1


title: VP control and OBP treatment

description: RNAs were obtained from ventral prostate of TRAP rats

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Rattus norvegicus

source_name: VP-control

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

growth_protocol: TRAP rats were fed a control diet during experimental periods.

extract_protocol: Total RNA was isolated from prostate tissue samples using miRNeasy kit (QIAGEN).

treatment_protocol: TRAP rats were intravenously injected with OBP-801 (1mg/kg) or saline 2 times a week.

value: ventral prostate cancer tissue

value: Six week-old

tag: agent

value: saline

source_name: VP-OBP-801 treated

value: 1mg of OBP-801


title: Nkx2-5 I183M/+ heart (apex), 15 weeks, replicate 3

description: Nkx2-5 183M/+ rep.3


title: LP control and OBP treatment

description: RNAs were obtained from lateral prostate of TRAP rats

source_name: LP-control

value: lateral prostate cancer tissue

source_name: LP-OBP-801 treated


title: Nkx2-5 delta/+ heart (apex), 15 weks, replicate 3

description: Nkx2-5 delta/+ rep.3


title: control cornea pool #3

city: ann arbor

first: philip

last: gage

state: mi

address: 1000 wall street

institute: university of michigan

description: gene expression at E12.5 in mouse cornea

hyb_protocol: 600ng of Alexa 555 labeled aminoallyl-aRNA was used to hybridize on the Agilent 60-mer oligo array (Mouse Gene Expression V.2, 8X60K) for 17 hours at 65°C at 10 rpm in the hybridization oven.  After hybridization the slides were washed with Agilent GE Wash Buffers following the Agilent’s protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner with extended dynamic range (XDR) at 5 micron resolution.

data_processing: Tiff images were analyzed with Agilent's feature extraction software (v11.0.1.1). Data were analyzed in GeneSpring v12. Data on each microarray were quantile normalized.

source_name: cornea ,E12.5, control, pool 3

label_protocol: Amplification and Alexa 555 labeling of RNA was performed using 200 pg of total RNA for each pooled sample and the TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (Epicentre, Madison, WI)

extract_protocol: RNA was prepared using a Qiagen RNAeasy micro kit.

treatment_protocol: Corneal tissue from flash frozen  e12.5 mouse embryos of the indicated genotypes was isolated by laser microdissection.

tag: genotype/variation

tag: development stage

value: cornea


title: mutant cornea pool #9

source_name: cornea, E12.5, mutant, pool 9


title: Nkx2-5 I183M/+ heart (apex), 15 weeks, replicate 2

description: Nkx2-5 183M/+ rep.2

tag: genotype


title: Nkx2-5 control/+ heart (apex), 15 weeks, replicate 3

description: Nkx2-5 Ctr/+ rep.3

value: Nkx2-5 control/+


title: mutant cornea pool #11

source_name: cornea, E12.5, mutant, pool 11


title: Control ESCs vs HDAC6-OE ESCs rep2

description: Biological replicate 2 of 2


title: MES (control)_Mm

description:
raw data file: MES.txt
Normalized rProcessed value is used

source_name: Mouse embryonic stem cell

value: Mouse embryonic stem cell (control)


title: plasma at 6 hour

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

source_name: plasma of heathy and young males

tag: time point

value: 6 hour

value: Male


title: mutant cornea pool #12

source_name: cornea, E12.5, mutant, pool 12


title: control cornea pool #1

source_name: cornea, E12.5, control, pool 1


title: Nkx2-5 control/+ heart (apex), 15 weeks, replicate 2

description: Nkx2-5 Ctr/+ rep.2

value: heart


title: plasma at 3 hour

value: 3 hour


title: ko

city: Fukuoka

first: Takehito

last: Uruno

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Mouse Gene Expression Microarray 4x44K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: CD4+T cells, DOCK8-/-

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using Isogen (Nippon Gene).

treatment_protocol: For antigen stimulation, CD4+ T cells (3 x 10(5) cells/ml) were cultured in a 24-well plate with T cell–depleted, irradiated spleen cells (5 x 10(6) cells/ml) in the presence of the following peptides: MCC88-103 (ANERADLIAYLKQATK, 3 μg/ml) for 24 hr.

value: spleen and lymph nodes

value: male


title: control cornea pool #2

source_name: cornea, E12.5, control, pool 2


title: plasma at 2 hour

value: 2 hour


title: mutant cornea pool #10

source_name: cornea, E12.5, mutant, pool 10


title: Nkx2-5 I183P/+ heart (apex), 15 weeks, replicate 2

description: Nkx2-5 183P/+ rep.2

source_name: 15 week whole heart (apex)

value: 15 week adult


title: plasma at 1 hour

value: 1 hour


title: control cornea pool #4

source_name: cornea, E12.5, control, pool 4


title: plasma at 0 hour

value: 0 hour


title: Nkx2-5 control/+ heart (apex), 15 weeks, replicate 1

description: Nkx2-5 Ctr/+ rep.1


title: plasma at 0.5 hour

value: 0.5 hour


title: Control (non-induced) ASCs culture from donor C (female, age 28) on day 21, biological rep 3

city: Pretoria

first: Melvin

middle: Anyasi

last: Ambele

state: Gauteng

address: 5 Bophelo Road

department: Immunology

country: South Africa

institute: University of Pretoria

hyb_protocol: Following fragmentation and labelling, 3.5 μg single-stranded DNA together with the affymetrix hybridization cocktail was hybridised to Affymetrix GeneChip® Human Gene 2.0 ST array. The array was placed in an Affymetrix GeneChip® Hybridisation Oven- 645 rotating at 60 rpm at 45°C for 17 h, after which the chip was washed and stained in an Affymetrix GeneChip® Fluidics Station-450Dx

scan_protocol: All chips were scanned using Affymetrix GeneChip® Scanner-7G.

data_processing: The output Affymetrix CEL files from scanned chip which have intensity values for all probes present on the scanned chips was used for further analysis. Using the default settings, Robust Multiarray Analysis algorithm in Affymetrix Expression ConsoleTM was used to perform background correction, summarisation, normalisation and calculation of probe set expression values from CEL files, giving the resultant output in a CHP file format. Affymetrix Transcription Analysis ConsoleTM was used to calculate fold change of each probe set or transcript cluster identifier number from CHP file and mapped it onto the corresponding gene.

molecule: cytoplasmic RNA

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 21 days (control)

label_protocol: Fragmented single-stranded DNA were labelled with DNA Labeling Reagent provided in the Affymetrix GeneChip® WT PLUS Reagent Kit according to standard affymetrix protocol provided with kit

growth_protocol: ASCs were cultured in complete culture medium consisting of α-MEM (GIBCO, Life Technologies™, New York, USA) supplemented with 10% foetal bovine serum (FBS; Biochrom), 2% (v/v) penicillin [10 000 U/mL]-streptomycin [10 000 µg/mL] (p/s; GIBCO, Life Technologies™, New York, USA) in 80 cm2 culture flasks (NUNCTM, Roskilde Site, Kamstrupvej, Denmark) at 37oC in a 5% CO2 incubator (Thermo Forma CO2 water jacketed incubator, 3111TF). The cells used in this study had been cryopreserved and were thawed just prior to use. When the cultures reached 80% confluence, they were washed twice with 4 mL PBS containing 2% (v/v) p/s and detached from the bottom of culture flask by adding 3 mL trypsin (GIBCO, Life Technologies™, New York, USA) followed by incubation at 37oC in 5% CO2 for about 7-10 min to ensure the cells were dislodged. Trypsin was neutralised by adding equal amounts of complete medium and the suspension was centrifuged at 184 g for 5 min to pellet the cells. Immunophenotypic characterisation was previously performed on fresh cells at each passage and on frozen cells prior to adipogenic induction using flow cytometry.

extract_protocol: Total RNA was isolated from controls (non-treated) and adipogenic induced (treated) cells on days 1, 7, 14 and 21 following adipogenic induction using the RNeasy Minikit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and integrity of the RNA was determined using the Agilent Tape station 2000 and corresponding kit (Agilent Technologies, California, USA) according to the  manufacturer’s instructions.

treatment_protocol: For adipogenic differentiation, cells were seeded at a density of 5 000 cells/cm2 in complete culture medium and grown to confluence. The cell cultures were washed twice with 4 mL PBS containing 2% (v/v) p/s and differentiation was induced by adding adipogenic induction cocktail to the cell cultures, while control cultures (non-induced cultures) received only complete culture medium. The adipogenic induction cocktail used consisted of Dulbecco’s Modified Eagle’s Medium (GIBCO, Life Technologies™, New York, USA) supplemented with 10% FBS, 2% (v/v) p/s, insulin (10 μg/mL), dexamethasone (1 μM), isobutylmethylxanthine (0.5 M) and indomethacin (200 μM). Differentiation was allowed to proceed over a period of 21 days and cells from both adipogenic induced cultures and their respective controls were harvested on days 1, 7, 14 and 21 for RNA isolation.

value: abdominal subcutaneous adipose tissue

value: adipose-derived stromal cells

tag: induction

value: control

tag: donor

value: donor C

value: female

tag: age (years)

tag: culture time

value: day 21


title: Adipogenic induced ASCs culture from donor D (female, age 20) on day 21, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 21 days (post-adipogenic induced)

value: post-adipogenic induction

value: donor D


title: Control (non-induced) ASCs culture from donor D (female, age 20) on day 21, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 21 days (control)


title: Adipogenic induced ASCs culture from donor D (female, age 20) on day 14, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 14 days (post-adipogenic induced)

value: day 14


title: Adipogenic induced ASCs culture from donor D (female, age 20) on day 1, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for one day (post-adipogenic induced)

value: day 1


title: Control (non-induced) ASCs culture from donor C (female, age 28) on day 7, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 7 days (control)

value: day 7


title: Adipogenic induced ASCs culture from donor B (male, age 32) on day 21, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 21 days (post-adipogenic induced)

value: donor B

value: male


title: Control (non-induced) ASCs culture from donor D (female, age 20) on day 7, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 7 days (control)


title: Adipogenic induced ASCs culture from donor C (female, age 28) on day 21, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 21 days (post-adipogenic induced)


title: Control (non-induced) ASCs culture from donor B (male, age 32) on day 21, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 21 days (control)


title: Control (non-induced) ASCs culture from donor D (female, age 20) on day 14, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 14 days (control)


title: Adipogenic induced ASCs culture from donor C (female, age 28) on day 14, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 14 days (post-adipogenic induced)


title: Control (non-induced) ASCs culture from donor D (female, age 20) on day 1, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for one day (control)


title: DCIS12

source_name: breast cancer

tag: diagnosis

value: breast cancer

value: FFPE

tag: subtype

value: ductal carcinoma in situ

tag: tissue donor

value: Patient 12


title: Control (non-induced) ASCs culture from donor C (female, age 28) on day 14, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 14 days (control)

value: abdominal subcutaneous adipose tissue

tag: gender


title: Adipogenic induced ASCs culture from donor D (female, age 20) on day 7, biological rep 4

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor D cultured for 7 days (post-adipogenic induced)

value: adipose-derived stromal cells


title: Adipogenic induced ASCs culture from donor B (male, age 32) on day 7, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 7 days (post-adipogenic induced)


title: Control (non-induced) ASCs culture from donor C (female, age 28) on day 1, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for one day (control)

value: control


title: Control (non-induced) ASCs culture from donor B (male, age 32) on day 14, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 14 days (control)


title: Control (non-induced) ASCs culture from donor B (male, age 32) on day 1, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for one days (control)


title: Adipogenic induced ASCs culture from donor B (male, age 32) on day 1, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for one day (post-adipogenic induced)


title: Adipogenic induced ASCs culture from donor A (female, age 19) on day 14, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 14 days (post-adipogenic induction)

value: donor A


title: Adipogenic induced ASCs culture from donor C (female, age 28) on day 7, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for 7 days (post-adipogenic induced)

value: donor C

value: female


title: Control (non-induced) ASCs culture from donor A (female, age 19) on day 21, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 21 days (control)

value: day 21


title: Adipogenic induced ASCs culture from donor B (male, age 32) on day 14, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 14 days (post-adipogenic induced)

value: post-adipogenic induction


title: Adipogenic induced ASCs culture from donor C (female, age 28) on day 1, biological rep 3

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor C cultured for one day (post-adipogenic induced)


title: Control (non-induced) ASCs culture from donor B (male, age 32) on day 7, biological rep 2

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor B cultured for 7 days (control)


title: Adipogenic induced ASCs culture from donor A (female, age 19) on day 21, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 21 days (post-adipogenic induction)


title: Control (non-induced) ASCs culture from donor A (female, age 19) on day 14, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 14 days (control)

value: day 14


title: adrenal cortex-at slaughter 30

city: Dummerstorf

first: Bodo

last: Brand

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute of Farm Animal Biology

hyb_protocol: The fragmented cDNA was hybridized to the microarray using the Affymetrix Hyb-WashStain Kit and Affymetrix standard protocols

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 (Affymetrix, St. Clara, USA)

data_processing:
Gene-level analysis and RMA normalization was performed using Affymetrix Expression Console software based on 147 Microarrays. Filtering of Probesets was performed using the detection above background algorithm. Probe sets that were present in 75% of all samples and transcripts with at least 50% of all probe sets present were included in the final analyses. Two samples (30 and 89) were excluded due to misssing phenotypic data.
BovGene-1_0-v1.pgf
BovGene-1_0-v1.mps

organism: Bos taurus

source_name: adrenal cortex

label_protocol: 5.5 µg of  cDNA was fragmented and labeled using the Affymetrix Terminal Labeling Kit  and Affymetrix standard protocols

extract_protocol: Total RNA was isolated from the adrenal cortex of 147 animals using TRI Reagent (Sigma, Taufkirchen, Germany). After DNaseI treatment the RNA was further purified with the RNeasy Kit (QIAGEN, Hilden, Germany) following the manufacturers recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (Peqlab, Erlangen, Germany). Integrity of RNA was checked by running 1 μg of RNA on a 1% agarose gel. Absence of DNA contamination was verified by PCR amplifying fragments of GAPDH with RNA as a template.

value: adrenal cortex


title: Adipogenic induced ASCs culture from donor A (female, age 19) on day 7, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 7 days (post-adipogenic induction)

value: day 7


title: Control (non-induced) ASCs culture from donor A (female, age 19) on day 7, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for 7 days (control)


title: Ctrl_shScr_UT-SCC-24B Replicate 2

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Department of Biomedicine

country: Finland

institute: University of Helsinki

description:
shScr-24B_2
NT2_(HuGene-2_0-st).CEL

hyb_protocol: A hybridization cocktail was prepared including the labeled, fragmented target and hybridization controls. The target was then hybridized to GeneChip array in cartridge format during 16-hour incubation at 45˚C.

scan_protocol: Immediately following hybridization, the array was washed and stained with streptavidin phycoerytherin conjugate using an automated protocol on the GeneChip Fluidics 450, followed by scanning on an Affymetrix Gene Scanner 3000 7G.

data_processing: Data was normalized using Affymetrix Gene Expression Console and prosessed using Chipster software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and quantile normalized.

source_name: UT-SCC-24B_ctrl/shScramble (plKO.1)

label_protocol: DNA was labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin.

growth_protocol: Cells were grown on Dulbecco's Modified Eagles Medium, supplemented with fetal bovine serum (10%), non essential amino acids, penicillin and streptomycin and L-glutamin.

extract_protocol: RNA was extracted according to miRNA easy Minikit from Qiagen.

treatment_protocol: Cells were transduced with lentiviral particles carrying shScr, shPPFIA1, PPFIA1 ORF or empty vector constructs, selected with puromycin or blastidicin after which cells were harvested and RNA extracted.

tag: tissue source

value: neck metastasis

tag: cell line

value: head and neck squamous cell carcinoma

tag: transduced with

value: scramble shRNA


title: adrenal cortex-at slaughter 89

tag: tissue


title: shPPFIA1_UT-SCC-24B Replicate 3

description:
shPPFIA1_24B_3
KD3_(HuGene-2_0-st).CEL

source_name: UT-SCC-24B_shPPFIA1 (plKO.1)

tag: cell type

value: PPFIA1 shRNA


title: Adipogenic induced ASCs culture from donor A (female, age 19) on day 1, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for one day (post-adipogenic induction)

value: day 1


title: shPPFIA1_UT-SCC-24B Replicate 1

description:
shPPFIA1_24B_1
KD1_(HuGene-2_0-st).CEL


title: Ctrl_shScr_UT-SCC-24B Replicate 3

description:
shScr-24B_3
NT3_(HuGene-2_0-st).CEL


title: shPPFIA1_UT-SCC-24B Replicate 2

description:
shPPFIA1_24B_2
KD2_(HuGene-2_0-st).CEL


title: adrenal cortex-at slaughter 147

tag: age at slaughter in days

tag: year-season of slaughter


title: adrenal cortex-at slaughter 144


title: adrenal cortex-at slaughter 143


title: Control (non-induced) ASCs culture from donor A (female, age 19) on day 1, biological rep 1

source_name: ASCs isolated from subcutaneous adipose tissue lipospirate from donor A cultured for one day (control)


title: adrenal cortex-at slaughter 146


title: parthenogenetic LLC6P ESCs

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description: embryonic uniparental stem cells derived from LLC6P

hyb_protocol: 130µl hybridization mix prepared from labeled ssDNA was hybridized for 17h at 45°C to GeneChip Human Gene 2.0 ST arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_002.

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

data_processing: Data were preprocessed with the Expression Console v1.2.1.20 software (Affymetrix); background correction, nomalization and gene-level probeset summary were performed with the RMA sketch workflow using default parameter settings.

source_name: uniparental hESCs

label_protocol: 100ng of total RNA were amplified with the WT Expression Kit (Ambion), followed by ssDNA labeling with the WT Terminal Labeling Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: hESC lines were cultured on mitomycin-C (Sigma-Aldrich) treated human foreskin fibroblasts (ATCC-LGC Standards, Wesel, Germany).

extract_protocol: Total RNA was extracted with the mirVana miRNA isolation kit (Ambion) following the manufacturer's protocol for total RNA isolation.

treatment_protocol: Cells were differentiated into the neural lineage as described (Ahmad et al., 2012).

tag: parental state

value: uniparental

tag: stem cell type

value: embryonic


title: adrenal cortex-at slaughter 145


title: biparental HS401 ESCs

description: embryonic biparental stem cells derived from HS401

source_name: biparental hESCs

value: biparental


title: K562, PMA

city: New Delhi

first: Alok

last: Bhattacharya

address: JNU

department: School of Life Sciences

institute: Jawaharlal Nehru University

description: Gene Expression after 20nM PMA treatment of K562 cells

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (GPL10487) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (genepix 4000B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: K562 CELLS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick-amp labelling kit (Agilent, part no 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, cat no 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% FBS and 1X-Pen-Strep.

extract_protocol: RNA was extracted using miRvana total RNA isolation kit.

treatment_protocol: K562 cells were treated with 20nM PMA for 48 hours. Control cells were treated with equal amount of solvent (PMA was dissolved in DMSO).

value: Chronic myeloid leukemia


title: K562, Control (DMSO)

description: Gene Expression as a control for PMA treated K562 cells.


title: parthenogenetic LLC9P NSCs

description: neural uniparental stem cells derived from LLC9P

source_name: uniparental NSCs

value: neural


title: biparental HS401 NSCs

description: neural biparental stem cells derived from HS401

source_name: biparental NSCs


title: parthenogenetic LLC9P ESCs

description: embryonic uniparental stem cells derived from LLC9P


title: Ctrl_shScr_UT-SCC-24B Replicate 1

description:
shScr-24B_1
NT1_(HuGene-2_0-st).CEL


title: parthenogenetic LLC6P NSCs

description: neural uniparental stem cells derived from LLC6P


title: adrenal cortex-at slaughter 142


title: adrenal cortex-at slaughter 141


title: adrenal cortex-at slaughter 139


title: adrenal cortex-at slaughter 140


title: adrenal cortex-at slaughter 126


title: adrenal cortex-at slaughter 130


title: adrenal cortex-at slaughter 135


title: adrenal cortex-at slaughter 136


title: adrenal cortex-at slaughter 127


title: adrenal cortex-at slaughter 138


title: adrenal cortex-at slaughter 137


title: adrenal cortex-at slaughter 131


title: adrenal cortex-at slaughter 129


title: adrenal cortex-at slaughter 133


title: adrenal cortex-at slaughter 134


title: adrenal cortex-at slaughter 128


title: adrenal cortex-at slaughter 132


title: het

description: Isolation by magnetic sorting with Dynabeads Mouse CD4 followed by treatment with DETACHaBEAD Mouse CD4 (Invitrogen)

source_name: CD4+T cells, DOCK8+/-

value: spleen and lymph nodes

tag: strain

value: male

tag: genotype/variation


title: adrenal cortex-at slaughter 125

value: female


title: adrenal cortex-at slaughter 119


title: adrenal cortex-at slaughter 120


title: adrenal cortex-at slaughter 122


title: adrenal cortex-at slaughter 123


title: adrenal cortex-at slaughter 118


title: adrenal cortex-at slaughter 116


title: adrenal cortex-at slaughter 115


title: adrenal cortex-at slaughter 117


title: D2

city: FuZhou

first: Guo

last: Zheng

state: FuJian

address: No.1 Xue Yuan Road

department: Department of Bioinformatics

institute: Fujian Medical University

description: DNA methylation analysis of lung adenocarcinoma and adjacent non-tumor tissues

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Processed methylation chips were scanned using an iScan reader (Illumina)

data_processing: Infinium Methylation data were processed using the Methylation Module of the GenomeStudio software package (v. 2011.1)

label: Cy5 and Cy3

source_name: non-tumor lung tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from frozen tissue samples using the Qiagen® Genomic DNA Mini Kit

tag: disease state

value: non-tumor

tag: subject

value: Patient 6


title: adrenal cortex-at slaughter 121

value: adrenal cortex


title: D1

value: Patient 5


title: D3

value: Patient 7


title: adrenal cortex-at slaughter 114


title: B4

value: Patient 4


title: adrenal cortex-at slaughter 113


title: adrenal cortex-at slaughter 112


title: adrenal cortex-at slaughter 110


title: adrenal cortex-at slaughter 109


title: adrenal cortex-at slaughter 106


title: adrenal cortex-at slaughter 107


title: adrenal cortex-at slaughter 124


title: adrenal cortex-at slaughter 111


title: adrenal cortex-at slaughter 105


title: C2

source_name: lung adenocarcinoma tissue

value: lung adenocarcinoma


title: B2

value: Patient 2


title: D4

value: Patient 8


title: C1


title: B3

value: Patient 3


title: adrenal cortex-at slaughter 104


title: C4


title: A1

value: Patient 1


title: adrenal cortex-at slaughter 103


title: C3


title: A4


title: B1


title: UPN2-post

city: bei jing

first: Jing

last: Nie

state: bei jing

address: 28 fuxing road

institute: PLA General Hospital

description: immune

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

data_processing: BeadStudio software v3.2

source_name: UPN2 2 cycles following decitabhine therapy

growth_protocol: PBLs were isolated from heparinized blood by Ficoll-Hypaque density gradient centrifugation.

extract_protocol: Genomic DNA was extracted according to the manufacturer's instructions.

treatment_protocol: Solid tumor patients were given decitabine therapy as 10 mg per day for 5 days/28 day cycle, and the blood samples were collected before and after 2 cycles of decitabine therapy.

value: PBMC


title: adrenal cortex-at slaughter 101


title: adrenal cortex-at slaughter 102


title: adrenal cortex-at slaughter 100


title: UPN2-pre

description: immune

source_name: UPN2 baseline


title: UPN1-post

description: immune

source_name: UPN1 2 cycles following decitabhine therapy


title: adrenal cortex-at slaughter 108

source_name: adrenal cortex


title: adrenal cortex-at slaughter 99


title: A2


title: adrenal cortex-at slaughter 97


title: adrenal cortex-at slaughter 95


title: adrenal cortex-at slaughter 98


title: adrenal cortex-at slaughter 94


title: adrenal cortex-at slaughter 96


title: adrenal cortex-at slaughter 93


title: adrenal cortex-at slaughter 92


title: genomic DNA from intracranial aneurysm 9 matched superficial temporal artery

first: Jia

last: Wang

address: Tian Tan Xili 6#

department: Neurosurgery

institute: Beijing Tian Tan Hospital, Capital Medical University

description: FDF-NQ

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 BeadChip using standard Illumina protocol

data_processing:
GenomeStudio software (Illumina)
Significant differentially methylated sites were screened between two groups using the criterion of differences ∆β≥0.2 and diffscore≥13. Data included in supplementary file Significant differentially methylated sites.txt

label_protocol: Standard Illumina manufacturer’s instructions.

extract_protocol: Genomic DNA of intracranial aneurysm and matched superficial temporal_from same patient (n=9) was extracted  with QIAamp DNA Mini Kit (Qiagen, Valencia, CA).

value: superficial temporal artery

tag: individual


title: genomic DNA from intracranial aneurysm 8

description: WPF-DML

source_name: intracranial aneurysm 8

value: intracranial aneurysm


title: adrenal cortex-at slaughter 91


title: genomic DNA from intracranial aneurysm 9

description: FDF-DML

source_name: intracranial aneurysm 9


title: genomic DNA from intracranial aneurysm 8 matched superficial temporal artery

description: WPF-NQ


title: adrenal cortex-at slaughter 90


title: adrenal cortex-at slaughter 87


title: genomic DNA from intracranial aneurysm 7 matched superficial temporal artery

description: TRY-NQ


title: genomic DNA from intracranial aneurysm 7

description: TRY-DML

source_name: intracranial aneurysm 7


title: adrenal cortex-at slaughter 83


title: adrenal cortex-at slaughter 82


title: adrenal cortex-at slaughter 86


title: adrenal cortex-at slaughter 88


title: UPN1-pre

description: immune

source_name: UPN1 baseline


title: adrenal cortex-at slaughter 84


title: adrenal cortex-at slaughter 81


title: adrenal cortex-at slaughter 85


title: adrenal cortex-at slaughter 80


title: adrenal cortex-at slaughter 77


title: adrenal cortex-at slaughter 78


title: adrenal cortex-at slaughter 79


title: adrenal cortex-at slaughter 76


title: genomic DNA from intracranial aneurysm 5

description: MZA-DML

source_name: intracranial aneurysm 5


title: adrenal cortex-at slaughter 72


title: adrenal cortex-at slaughter 69


title: adrenal cortex-at slaughter 73


title: adrenal cortex-at slaughter 70


title: genomic DNA from intracranial aneurysm 6 matched superficial temporal artery

description: SYS-NQ


title: adrenal cortex-at slaughter 74


title: adrenal cortex-at slaughter 75


title: genomic DNA from intracranial aneurysm 6

description: SYS-DML

source_name: intracranial aneurysm 6


title: adrenal cortex-at slaughter 68


title: adrenal cortex-at slaughter 66


title: adrenal cortex-at slaughter 71


title: adrenal cortex-at slaughter 67


title: adrenal cortex-at slaughter 64


title: genomic DNA from intracranial aneurysm 5 matched superficial temporal artery

description: MZA-NQ


title: A3


title: adrenal cortex-at slaughter 65


title: adrenal cortex-at slaughter 63


title: adrenal cortex-at slaughter 62


title: adrenal cortex-at slaughter 60


title: adrenal cortex-at slaughter 59


title: genomic DNA from intracranial aneurysm 2

description: YFX-DML

source_name: intracranial aneurysm 2


title: genomic DNA from intracranial aneurysm 4

description: ZSF-DML

source_name: intracranial aneurysm 4


title: genomic DNA from intracranial aneurysm 4 matched superficial temporal artery

description: ZSF-NQ


title: adrenal cortex-at slaughter 61


title: genomic DNA from intracranial aneurysm 1 matched superficial temporal artery

description: ZSY-NQ


title: adrenal cortex-at slaughter 57


title: adrenal cortex-at slaughter 56


title: genomic DNA from intracranial aneurysm 2 matched superficial temporal artery

description: YFX-NQ


title: adrenal cortex-at slaughter 58


title: adrenal cortex-at slaughter 55


title: GSY124-Rep2-Inoc

city: Stanford

first: Barbara

last: Dunn

state: CA

department: Genetics

institute: Stanford University

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82544.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505C

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: GSY124-Rep2-Inoc-MB2-68genomic DNA, Hae III cut, 450 ng

tag: genotype

value: whole genome

tag: developmental stage

tag: replicate


title: GSY122-Rep1-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82528.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY122-Rep1-Inoc-MB2-1genomic DNA, Hae III cut, 450 ng


title: genomic DNA from intracranial aneurysm 3 matched superficial temporal artery

city: Beijing

description: BJX-NQ


title: adrenal cortex-at slaughter 53

tag: gender

value: female


title: GSY124-Rep1-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83531.gif

source_name: GSY124-Rep1-Inoc-MB2-68genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 54


title: genomic DNA from intracranial aneurysm 1

description: ZSY-DML

source_name: ntracranial aneurysm 1


title: adrenal cortex-at slaughter 51


title: adrenal cortex-at slaughter 52


title: GSY31-Rep2-200a

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82532.gif

source_name: GSY31-Rep2-200a-MB1-44genomic DNA, Hae III cut, 450 ng


title: GSY144-Rep3-200a

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82542.gif

source_name: GSY144-Rep3-200a-MB1-26genomic DNA, Hae III cut, 450 ng


title: genomic DNA from intracranial aneurysm 3

description: BJX-DML

source_name: intracranial aneurysm 3


title: adrenal cortex-at slaughter 50

source_name: adrenal cortex


title: adrenal cortex-at slaughter 49


title: GSY123-Rep1-200b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82555.gif

source_name: GSY123-Rep1-200b-MB2-39genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 48


title: GSY144-Rep2-g200-FRY976

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82535.gif

source_name: GSY144-Rep2-g200-FRY976-MB1-17genomic DNA, Hae III cut, 450 ng


title: GSY144-Rep1-3-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82536.gif

source_name: GSY144-Rep1-3-Inoc-MB1-1genomic DNA, Hae III cut, 450 ng


title: GSY144-Rep1-g200-FRY923

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82531.gif

source_name: GSY144-Rep1-g200-FRY923-MB1-8genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 44


title: adrenal cortex-at slaughter 47


title: adrenal cortex-at slaughter 45


title: adrenal cortex-at slaughter 46


title: GSY123-Rep1-200j

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82525.gif

source_name: GSY123-Rep1-200j-MB2-40genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 40


title: adrenal cortex-at slaughter 41


title: adrenal cortex-at slaughter 39


title: adrenal cortex-at slaughter 42


title: GSY31-Rep1-3-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82538.gif

source_name: GSY31-Rep1-3-Inoc-MB1-28genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 43


title: adrenal cortex-at slaughter 36


title: adrenal cortex-at slaughter 31


title: adrenal cortex-at slaughter 34


title: adrenal cortex-at slaughter 35


title: adrenal cortex-at slaughter 29


title: adrenal cortex-at slaughter 33


title: adrenal cortex-at slaughter 26


title: GSY31-Rep3-g200-FRY970

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82546.gif

source_name: GSY31-Rep3-g200-FRY970-MB1-54genomic DNA, Hae III cut, 450 ng


title: GSY124-Rep2-200b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82553.gif

source_name: GSY124-Rep2-200b-MB2-78genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 37


title: adrenal cortex-at slaughter 28


title: adrenal cortex-at slaughter 32


title: adrenal cortex-at slaughter 27


title: adrenal cortex-at slaughter 38


title: GSY122-Rep2-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82545.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY122-Rep2-Inoc-MB2-14genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 25


title: adrenal cortex-at slaughter 24


title: GSY123-Rep1-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82522.gif

source_name: GSY123-Rep1-Inoc-MB2-28 genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 23


title: GSY31-Rep3-g200-FRY969

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82539.gif

source_name: GSY31-Rep3-g200-FRY969-MB1-53genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 21


title: GSY122-Rep1-g200-FRY891

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82548.gif

source_name: GSY122-Rep1-g200-FRY891-MB2-11genomic DNA, Hae III cut, 450 ng


title: GSY123-Rep2-200d

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82524.gif

source_name: GSY123-Rep2-200d-MB2-53genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 17


title: adrenal cortex-at slaughter 18


title: adrenal cortex-at slaughter 19


title: adrenal cortex-at slaughter 16


title: adrenal cortex-at slaughter 22


title: adrenal cortex-at slaughter 15


title: adrenal cortex-at slaughter 20


title: adrenal cortex-at slaughter 13


title: adrenal cortex-at slaughter 12


title: adrenal cortex-at slaughter 14


title: GSY122-Rep2-g200-FRY992

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82549.gif

source_name: GSY122-Rep2-g200-FRY992-MB2-24genomic DNA, Hae III cut, 450 ng


title: GSY31-Rep1-g200-FRY974

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82540.gif

source_name: GSY31-Rep1-g200-FRY974-MB1-36genomic DNA, Hae III cut, 450 ng


title: GSY124-Rep2-g50-FRY1016

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82584.gif

source_name: GSY124-Rep2-g50-FRY1016-MB2-70 genomic DNA, Hae III cut, 450 ng


title: GSY124-Rep1-g200-FRY997

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82554.gif

source_name: GSY124-Rep1-g200-FRY997-MB2-66genomic DNA, Hae III cut, 450 ng


title: GSY123-Rep2-200b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82541.gif

source_name: GSY123-Rep2-200b-MB2-52genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 11

source_name: adrenal cortex


title: GSY124-Rep2-g200-F06-IX-D-200c

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82951.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY124-Rep2-g200-F06-IX-D-200c, genomic DNA, Hae III cut, 500 ng


title: adrenal cortex-at slaughter 8


title: GSY122-Rep2-100c

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82603.gif

source_name: GSY122-Rep2-100c-MB2-18 genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 9


title: GSY31-Rep1-g200-FRY973

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82533.gif

source_name: GSY31-Rep1-g200-FRY973-MB1-35genomic DNA, Hae III cut, 450 ng


title: FRY891-CHEFBand6-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83627.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY891-CHEFBand6-b, 15 ng, HaeIII-cut

value: CHEF


title: adrenal cortex-at slaughter 10


title: GSY123-Rep2-g50-FRY1007

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82595.gif

source_name: S cerevisiae + S bayanus genomic DNA sonicated, 300 ng each

source_name: GSY123-Rep2-g50-FRY1007-MB2-43 genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 7


title: adrenal cortex-at slaughter 3


title: GSY122-Rep2-g150-FRY983

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82600.gif

source_name: GSY122-Rep2-g150-FRY983-MB2-23 genomic DNA, Hae III cut, 450 ng


title: adrenal cortex-at slaughter 2


title: adrenal cortex-at slaughter 4


title: adrenal cortex-at slaughter 6


title: adrenal cortex-at slaughter 5


title: FRY892-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83470.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 100 ng each

source_name: FRY892-CHEFBand2-b, 15 ng, HaeIII-cut


title: GSY123-Rep2-Inoc

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-01/82523.gif

source_name: GSY123-Rep2-Inoc-MB2-41genomic DNA, Hae III cut, 450 ng


title: GSY122-Rep1-g200-FRY893

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82944.gif

value: S cerevisiae + S bayanus genomic DNA sonicated, 350 ng each

source_name: GSY122-Rep1-g200-FRY893-MB2-13, genomic DNA, Hae III cut, 500 ng


title: GSY123-Rep2-g100-F06-IX-B-100b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-02/82936.gif

source_name: GSY123-Rep2-g100-F06-IX-B-100b-MB2-46, genomic DNA, Hae III cut, 500 ng


title: FRY891-CHEFBand4-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-05/83623.gif

source_name: FRY891-CHEFBand4-b, 15 ng, HaeIII-cut


title: FRY992-CHEFBand2-b

description:
Simple annotation: Interspecific Hybrid, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2009-04/83468.gif

source_name: FRY992-CHEFBand2-b, 15 ng, HaeIII-cut