title: P60 Wild-type Mouse Control Incisor Dental Mesenchyme 3

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of lower incisor dental mesenchyme from postnatal day 60 wild-type mouse following two weeks after unilateral resection of the inferior alveolar nerve on the contralateral side.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from murine adult incisor dental mesenchyme.

treatment_protocol: Mice were maintained under standard IACUC protocols.

tag: genotype/variation

value: wild-type

tag: denervation

value: contralateral

value: Incisor Dental Mesenchyme

value: Not determined


title: CD34+/CD1a- technical replicate 2

status: Public on Dec 30 2014

type: RNA

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing: Raw data were decoded by GenomeStudio Illumina Inc. And normalization was done (1) forcePositive background correction, (2) log2 transformation and (3) quantile normalization

molecule: total RNA

organism: Homo sapiens

source_name: thymus biopsy

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

extract_protocol: Normal human postnatal thymocytes were isolated by Ficoll-Hypaque centrifugation and magnetic cell sorting from thymus fragments removed during corrective cardiac surgery

tag: Sex

value: mixed

tag: age

value: 1-24 months

tag: cell type


title: P60 Wild-type Mouse Control Incisor Dental Mesenchyme 2

country: USA

label: biotin

organism: Mus musculus

tag: strain

tag: tissue

tag: gender


title: P60 Wild-type Mouse Control Incisor Dental Mesenchyme 4


title: CD34+/CD1a+ technical replicate 1


title: CD34+/CD1a+ technical replicate 2


title: Pre-TCR+ technical replicate 1

value: Pre-TCR+


title: P60 Wild-type Mouse Control Incisor Dental Mesenchyme 5


title: CD34+/CD1a- technical replicate 1


title: P60 Wild-type Mouse Control Incisor Dental Mesenchyme 1


title: Neurons overexpressing Hes1 and GFP, biological rep2

city: Seville

first: Pedro

middle: Jose

last: Chacon

state: Seville

address: Americo Vespucio s/n

department: Cell Signaling

institute: Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER).

description: Gene expression data from neuron overexpressing GFP and Hes-1

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004

scan_protocol: Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix

data_processing:
CEL files were processed using the Robust Multichip Average (RMA) normalization
Fold-change (log2) values (M) and their FDR-adjusted p-values were calculated with LIMMA (Linear Models for Microarray Analysis) using the affylmGUI interface. All the statistical analysis was performed using R language and the packages freely available from the “Bioconductor Project” (http://www.bioconductor.org)

source_name: Neurons overexpressing Hes1 and GFP

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.

growth_protocol: Neurons were plated for 6 days on 60mm-diameter dishes plates coated with poly-L-lysine at a density of 350,000 neurons/cm2, and they were cultured in Neurobasal supplemented with B-27 and GlutaMAX I.

extract_protocol: Cells were lysed and total RNA was extracted using illustra RNAspin Mini RNA isolation kit from GE Healthcare. RNA quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Neurons were transduced at 6 DIV using Sindbis virus expressing myc-tagged Hes1 and GFP or GFP alone as control. After 6h viral particles were removed and proteins were allowed to express during 16h.

value: FVB

value: 6 DIV cultured hippocampal neurons

tag: transfected with


title: Xenopus laevis testis 90days 100ug/L (XL03)

city: jinan

first: sai

middle: lin

last: lin

state: shandong

address: 18877Jingshi Road

department: Toxicology

country: China

institute: Shandong Academy of Occupational Health and Occupational Medicine

description: Gene expression of male Xenopus laevis testis after 90 days exposure of 100 ug/L simazine

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

scan_protocol: After hybridization and washing, the chips were scanned with the Axon GenePix 4000B microarray Scanner.

data_processing: Original fluorescent datas were readed by GenePix pro V6.0 software and the datas were standardized by the Agilent GeneSpring GX v11.5.1 Software for further analysis. Differentially expressed genes were identified by determining the fold-change (FC) and p values of the t-test. Genes with an FC of ≧2 and a p value of <0.05 between 2 groups were identified as differentially expressed genes

organism: Xenopus laevis

source_name: testis 90days 100ug/L

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Average water temperature was 22 ± 2℃ in all treatments over the entire course of the experiment, and the photoperiod was 12 h light: 12 h dark. Experiment water was renewed every three days to maintain the appropriate concentration of simazine and to maintain water quality. Young tadpoles were fed fairy shrimp, and when the tadpoles grew older, they were fed pork liver three times per week ad libitum.

extract_protocol: RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. The RNA integrity was evaluated by Nano Drop ND-1000 spectrophotometer. 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Testis from the  male Xenopus laevis were flash-frozen in liquid nitrogen, and stored at −80 ◦C for microarray expression analysis.

value: testis

tag: concentration


title: P60 Wild-type Mouse Denerved Incisor Dental Mesenchyme 5

description: Whole genome transcriptome profile of denerved lower incisor dental mesenchyme from postnatal day 60 wild-type mouse following two weeks after unilateral resection of the inferior alveolar nerve.

value: ipsilateral


title: PCR2

status: Public on Dec 29 2014

city: Xi'an

last: Zhao

address: Xiwu Road

department: Orthopaedic Surgery

institute: Xi'an Jiaotong University

hyb_protocol: The total mixture with hybridization buffer was hybridized to the microarray in a 12-Bay Hybridization System (Hybridization System, NimbleGen Systems, Inc., Madison, WI, USA), which provides an active mixing action and a constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were washed several times using the wash buffer kit (Exiqon), and finally dried by centrifugation. The slides were then scanned with the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

data_processing: For each spot, verify the signal by subtracting background intensity (B) from foreground intensity (F). Verified signal value= F - B. The spots, of which verified signal values are less than 50, and the control spots are filtered. For verified signal values of the left spots, perform median normalization.

source_name: nucleus pulposus

label_protocol: After RNA isolation from the samples, the miRCURY  Hy3/Hy5 Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer's guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase. After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual.

extract_protocol: Total RNA from each sample was isolated individually using the TRIzol (Invitrogen, Carlsbad, CA, USA) and miRNeasy mini kit (QLAGEN, Valencia, CA, USA) according to manufacture's instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies, Wilmington, DE, USA) and RNA integrity was determined by gel electrophoresis.

value: LIDH patients(EG)

value: Male

value: 63 years

tag: segment

tag: mri grade

value: V


title: Xenopus laevis testis 90days 100ug/L (XL04)


title: Xenopus laevis testis 90days 100ug/L (XL05)


title: PCR6

value: Female

value: 55 years

value: IV


title: Xenopus laevis testis 90days 0ug/L (XL02)

description: Gene expression of male Xenopus laevis testis after 90 days exposure of 0 ug/L simazine

source_name: testis 90days 0ug/L


title: NPCR2

value: Trauma patients(CG)

value: 56 years

value: II


title: PCR4

value: 70 years


title: NPCR6

value: 58 years


title: NPCR3

value: 51 years


title: P60 Wild-type Mouse Denerved Incisor Dental Mesenchyme 3

value: wild-type

value: Incisor Dental Mesenchyme

value: Not determined


title: P60 Wild-type Mouse Denerved Incisor Dental Mesenchyme 2

value: ipsilateral


title: P60 Wild-type Mouse Denerved Incisor Dental Mesenchyme 4


title: Scid.adh, pool vs Scid.adh EGR1 transduced

city: Boston

first: Julja

last: Burchard

state: MA

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description: Gradations in ERK signaling have been implicated in essentially every developmental checkpoint or differentiation process encountered by lymphocytes. Yet, despite intensive effort, the molecular basis by which differences in ERK activation specify alternative cell fates remains poorly understood. We report here that differential ERK signaling controls lymphoid fate specification through an alternative mode of action. While ERK phosphorylates most substrates, such as Rsk, by targeting them through its D-domain, this well-studied mode of ERK action was dispensable for development of gamma-delta T cells. Instead, development of gamma-delta T cells was dependent upon an alternative mode of action mediated by the DEF-binding pocket (DBP) of ERK. This domain enabled ERK to bind a distinct and select set of proteins required for specification of the gamma-delta fate. These data provide the first in vivo demonstration for the role of DBP-mediated interactions in orchestrating alternate ERK-dependent developmental outcomes.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Scid mouse lymphoma, Scid.adh

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: conditions

value: Scid.adh, pool

value: Scid.adh EGR1 transduced


title: Xenopus laevis testis 90days 0ug/L (XL01)

value: testis


title: P60 Wild-type Mouse Denerved Incisor Dental Mesenchyme 1


title: 40A

city: Manchester

first: Kim

last: Linton

address: Department of Haemato-oncology, The Christie NHS Foundation Trust, Wilmslow Road

department: Faculty of Medical and Human Sciences

country: United Kingdom

institute: The University of Manchester

hyb_protocol: Samples were hybridized to Affymetrix HG U133 Plus 2.0 arrays following the manufacturer’s instructions throughout. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with AGCC software

data_processing: Raw signal intensity data were extracted using Expression Console (Affymetrix). Scatter plots and Pearson’s correlation coefficients were used to assess data reproducibility and the strength of association between FT and FFPE-processed tissues. At probe set level, present and absent calls in the first 20 paired FT/FFPE arrays (8 ABC and 12 GCB tumors) were used to calculate the sensitivity and specificity of gene detection in FFPE relative to FT. Probe sets detected exclusively in either FT or FFPE were characterized by relative signal intensity and examined for bias in microarray probe set position. A t-test was used to calculate the proportion of exclusive FT probe sets differentially regulated in ABC and GCB tumors.

source_name: activated B cell-like diffuse large B-cell lymphoma, diagnostic FFPE tissue

label_protocol: One hundred nanograms of total RNA was amplified and labeled using a combined oligo(dT) and random hexamer priming approach (NuGEN WT-Ovation FFPE v2) coupled with the NuGEN FL-Ovation cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

growth_protocol: Two to three 1-mm FFPE cores were removed using a tissue microarrayer under strict RNase-free conditions

extract_protocol: RNA was extracted and DNase treated using an in-house optimization of the RNeasy FFPE protocol (Qiagen, Hilden, Germany). Manufacturer's instructions were followed apart from increasing the length of proteinase K digestion from 15 to 60 minutes at the recommended concentration (10µg), and doubling the heating step to 30 minutes.

value: diffuse large B-cell lymphoma

tag: sample type

value: diagnostic FFPE tissue

tag: dlbcl previous classification

value: activated B cell-like

tag: dlbcl re-classification


title: SP CD8+ 1

type: genomic

description: Bisulfite-converted DNA

hyb_protocol: Illumina’s Infinium HD Assay Methylation Protocol

data_processing: Raw data were decoded by GenomeStudio Illumina Inc. And normalization was done (1) forcePositive background correction, (2) log2 transformation, (3) quantile adjusted for color balance and (4) quantile normalization

molecule: genomic DNA

value: mixed

value: 1-24 months

value: SP CD8+


title: SP CD4+ 2

description: Bisulfite-converted DNA

label_protocol: Illumina’s Infinium HD Assay Methylation Protocol

value: SP CD4+


title: 35A


title: SP CD4+ 1

description: Bisulfite-converted DNA


title: 29A

source_name: germinal center B cell-like diffuse large B-cell lymphoma, diagnostic FFPE tissue

value: germinal center B cell-like


title: 28A


title: 39A


title: Neu E2F3 Het_1465

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

description: Neu E2F3 Het_1465

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Normalization was with Affymetrix Expression Console using build 1.2.1.20.

source_name: breast cancer

label_protocol: standard affymetrix protocol

growth_protocol: MMTV-Neu tumors were induced in the indicated E2F wildtype or knockout background.

extract_protocol: Rneasy was used to extract RNA following manufacturer guidelines.

treatment_protocol: Tumors were extracted at endpoint and were flash frozen.

value: breast cancer

value: FVB

value: Neu E2F3 Het


title: SP CD8+ 2

description: Bisulfite-converted DNA


title: 37A


title: 36A


title: Neu E2F3 Het_2164

description: Neu E2F3 Het_2164


title: 38A


title: 34A


title: 31A


title: 26A


title: 33A


title: Neu E2F3 Het_1462

description: Neu E2F3 Het_1462


title: DP TCR α/β+ 2

description: Bisulfite-converted DNA

value: DP TCR α/β+


title: 30A


title: 32A


title: 27A


title: CD34+/CD1a- 2

description: Bisulfite-converted DNA


title: Neu E2F3 Het_1461

description: Neu E2F3 Het_1461


title: Neu E2F3 Het_1419

description: Neu E2F3 Het_1419


title: Pre-TCR+ 1

description: Bisulfite-converted DNA

value: Pre-TCR+


title: CD34+/CD1a+

description: Bisulfite-converted DNA


title: 25A


title: Neu E2F3 Het_1417

description: Neu E2F3 Het_1417


title: Pre-TCR+ 2

description: Bisulfite-converted DNA


title: 23A


title: Neu E2F3 Het_1418

description: Neu E2F3 Het_1418


title: EC, Terminal Effector memory CD8+ sample C

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description:
Replicate 3
5786065146_K

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization

source_name: PBMC, Rosette-Sep CD8+ negative enrichment, followed by CD45RO and CCR7 magnetic depletion

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

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

tag: step 1 response

tag: mutation type


title: Neu E2F3 Het_1365

description: Neu E2F3 Het_1365

tag: genotype/variation


title: 21A


title: 22A


title: Neu E2F3 Het_1356

description: Neu E2F3 Het_1356


title: 20A


title: EA, Terminal Effector memory CD8+ sample A

description:
Replicate 1
5786049054_K


title: Neu E2F3 Het_1360

description: Neu E2F3 Het_1360


title: Neu E2F3 Het_1421

description: Neu E2F3 Het_1421


title: 19A


title: Neu E2F3 Het_1364

description: Neu E2F3 Het_1364


title: 24A


title: CD8C

description:
Replicate 4
5786065100_L

source_name: PBMC, Rosette-Sep CD8+ negative enrichment


title: Neu E2F3 Het_1135

description: Neu E2F3 Het_1135


title: EB, Terminal Effector memory CD8+ sample B

description:
Replicate 2
5786065100_K


title: CD34+/CD1a- 1

description: Bisulfite-converted DNA

tag: Sex


title: Neu E2F3 Het_1012

description: Neu E2F3 Het_1012


title: DP TCR α/β+ 1

description: Bisulfite-converted DNA

tag: age


title: CD8D

description:
Replicate 5
5786065146_L


title: CD8B

description:
Replicate 3
5786049054_L


title: Neu E2F3 Het_1459

description: Neu E2F3 Het_1459


title: 18A


title: 17A


title: Neu E2F2 KO_2501

description: Neu E2F2 KO_2501

value: Neu E2F2 KO


title: Oga_KO_MEF_E7_rep3

city: Bethesda

first: Chithra

middle: N

last: Keembiyehetty

state: MD

address: 8 Center Dr.

department: NIDDK

institute: NIH

hyb_protocol: Affymetrix Mouse Gene 430.2  arrays were hybridized with fragmented and labelled cRNA for 18 h at 45C using Affymetrix hybridization oven

scan_protocol: Hybridized chips were processed using affymetrix 450 Fluidic station, using GeneChip hyb, Wash and Stain kit according to the instructions and scan using affymetrix GeneChip scanner 3000

data_processing: .CEL files were generated using GCOS software and data anlyzed using Partek software to identify 1.5 fold changed transcripts in Het, and KO compared to WT, as well as Het versus KO.

source_name: MEF cells from female  Oga knock out embryo (D12.5)

label_protocol: Biotin labelling according to Standard Affymetrix  protocol using 20ug of  cRNA

growth_protocol: MEF cells culture in DMEM media

extract_protocol: Trizol extraction followed by DNAase digestion

tag: genotype

value: Oga knockout

value: Female

tag: cell type

value: MEF


title: 16A

tag: tissue

value: diffuse large B-cell lymphoma


title: Oga_KO_MEF_E7_rep1

tag: gender


title: 14A

value: diagnostic FFPE tissue


title: Oga_Het_MEF_E4_rep3

source_name: MEF cells from female  Oga Heterozygous embryo (D12.5)

value: Oga heterozygous


title: Neu E2F2 KO_2491

description: Neu E2F2 KO_2491

tag: strain


title: 59041

source_name: PBMC

value: stable disease


title: Oga_Het_MEF_E4_rep1


title: Oga_Het_MEF_E4_rep2


title: 11A


title: Oga_WT_MEF_E8_rep3

source_name: MEF cells from female  WT embryo (D12.5)

value: WT


title: CD8E

description:
Replicate 2
5786049014_L


title: Neu E2F2 KO_2366

description: Neu E2F2 KO_2366


title: 12A


title: 13E


title: 59019


title: Oga_KO_MEF_E7_rep2


title: Neu E2F2 KO_2306

description: Neu E2F2 KO_2306


title: 59048


title: 59046

value: progression


title: Neu E2F2 KO_2241

description: Neu E2F2 KO_2241


title: Oga_WT_MEF_E8_rep2


title: Neu E2F2 KO_2236

description: Neu E2F2 KO_2236


title: 15A


title: Neu E2F2 KO_2307

description: Neu E2F2 KO_2307


title: 59014


title: 10A


title: 9A


title: 7A

value: activated B cell-like


title: 6A


title: 8A

value: germinal center B cell-like


title: Neu E2F2 KO_2494

description: Neu E2F2 KO_2494

value: breast cancer


title: Neu E2F2 KO_1295

description: Neu E2F2 KO_1295

value: FVB


title: Oga_WT_MEF_E8_rep1


title: 59018


title: Neu E2F2 KO_1007

description: Neu E2F2 KO_1007


title: 5A


title: Neu E2F1 KO_2546

description: Neu E2F1 KO_2546

value: Neu E2F1 KO


title: Neu E2F2 KO_2184

description: Neu E2F2 KO_2184


title: Neu E2F2 KO_1960

description: Neu E2F2 KO_1960


title: 59059


title: Neu E2F2 KO_1183

description: Neu E2F2 KO_1183


title: 59012

description:
Replicate 6
5786049054_F


title: Neu E2F2 KO_2183

description: Neu E2F2 KO_2183


title: 59013


title: 59024

description:
Replicate 8
5786049054_H


title: 59032


title: 59052

description:
Replicate 5
5786049014_I


title: 3D


title: 4A


title: 2D


title: 59045

description:
Replicate 9
5786049054_I


title: Neu E2F2 KO_2186

description: Neu E2F2 KO_2186


title: 59016

description:
Replicate 7
5786049054_G


title: 1A


title: CD8A

description:
Replicate 1
5786049014_K


title: WT_17

city: Vienna

first: Sabine

last: Strehl

address: Zimmermannplatz 10

department: CCRI, CHILDREN'S CANCER RESEARCH INSTITUTE

country: Austria

institute: St. Anna Kinderkrebsforschung e.V.

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the Affymetrix GeneChip Command Console Software (AGCC).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the fRMA algorithm and the summarization method robust_weighted_average

source_name: bone marrow sample from child with acute lymphoblastic leukemia

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 500ng total RNA was processed to generate a biotinylated hybridization target using the Affymetrix GeneChip 3’ IVT Express kit and the Affymetrix GeneChip Hybridization, Wash, and Stain kit . All procedures were performed according to the manufacturer's protocols.

extract_protocol: Total RNA was isolated out of leukemic cells using Trizol reagent (Invitrogen). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

value: PAX5 wild type

value: Bone marrow

tag: disease state

value: B-cell precursor acute lymphoblastic leukemia

tag: diagnosis

value: sample collected at diagnosis B ALL


title: Neu E2F1 KO_2323

description: Neu E2F1 KO_2323


title: WT_15


title: 59022

description:
Replicate 3
5786049014_G

value: NOT TESTED


title: WT_16


title: 59002

description:
Replicate 1
5786049014_E


title: WT_12


title: Neu E2F1 KO_2363

description: Neu E2F1 KO_2363


title: Neu E2F1 KO_2453

description: Neu E2F1 KO_2453


title: WT_14


title: 59029

description:
Replicate 16
5786065146_B

value: complete response


title: 59043

description:
Replicate 4
5786049014_H


title: Neu E2F1 KO_2179

description: Neu E2F1 KO_2179


title: Neu E2F1 KO_2488

description: Neu E2F1 KO_2488


title: WT_10


title: WT_13


title: 59051

description:
Replicate 18
5786065146_D


title: Neu E2F1 KO_2174

description: Neu E2F1 KO_2174


title: Neu E2F1 KO_2180

description: Neu E2F1 KO_2180


title: Neu E2F1 KO_2358

description: Neu E2F1 KO_2358


title: 59040

description:
Replicate 17
5786065146_C

value: partial response


title: 59008

description:
Replicate 15
5786065146_A


title: Neu E2F1 KO_2070

description: Neu E2F1 KO_2070


title: 59015

description:
Replicate 2
5786049014_F


title: WT_9


title: WT_8


title: 59058

description:
Replicate 19
5786065146_E


title: WT_11


title: 59057

description:
Replicate 14
5786065100_E


title: Neu E2F1 KO_2017

description: Neu E2F1 KO_2017


title: WT_3


title: WT_6


title: Neu E2F1 KO_2069

description: Neu E2F1 KO_2069


title: 59038

description:
Replicate 12
5786065100_C


title: 59050

description:
Replicate 13
5786065100_D


title: Neu_2191

value: Neu


title: WT_4


title: Neu E2F1 KO_1636

description: Neu E2F1 KO_1636


title: 59049

description:
Replicate 8
5786049054_D


title: Neu E2F1 KO_1630

description: Neu E2F1 KO_1630


title: Neu_2188


title: WT_5


title: WT_2


title: 59025

description:
Replicate 11
5786065100_B


title: 59056

description:
Replicate 9
5786049054_E


title: Neu_2178


title: Neu_2297


title: PAX5JAK2_5

value: PAX5-JAK2 fusion


title: 59037

description:
Replicate 7
5786049054_C


title: Neu_2182


title: WT_1


title: PAX5JAK2_4


title: 59017

description:
Replicate 6
5786049054_B


title: 59006

description:
Replicate 10
5786065100_A


title: 59003

description:
Replicate 5
5786049054_A.


title: Neu_2187


title: 59054

description:
Replicate 4
5786049014_D


title: PAX5JAK2_3


title: Neu_1906


title: 59042

description:
Replicate 3
5786049014_C


title: Neu_1894


title: PAX5ETV6_4

value: PAX5-ETV6 fusion


title: 59034

description:
Replicate 2
5786049014_B


title: PAX5ETV6_3


title: PAX5ETV6_2


title: PAX5JAK2_1


title: Neu_1358


title: PAX5JAK2_2


title: Neu_1357


title: PAX5C20orf112_3

value: PAX5-C20orf112 fusion


title: Neu_1414


title: 59009

description:
Replicate 1
5786049014_A


title: Neu_1132


title: PAX5C20orf112_5


title: PAX5C20orf112_6


title: Neu_1753


title: eHBs Passage 5

city: Shanghai

first: Wenlin

last: Li

address: 800 Xiangyin Road

institute: Second Military Medical University

description: Gene expression of cultured hepatoblasts at early passage

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Signals were calculated by the Agilent Gene Spring Software 11.0 and automatically underwent Quantile algorithm normalization.

source_name: Cultured hepatoblasts passage 5

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

growth_protocol: Expandable hepatoblasts (eHBs) were routinely cultured in basal medium (DMEM/F12 medium supplemented with insulin-transferrin-sodium selenite, 5 mM nicotinamide, 30 μg/ml 2-phospho-L-ascorbic acid and 50 μg/ml bovine serum albumin human recombinant albumin and 1% penicillin/streptomycin including 10 ng/ml EGF, 3 μM CHIR99021, 2 μM E-616452, 5 μM LPA and 0.5 μM S1P, on Matrigel or laminin-coated surface. The culture was split 1:6 using Accutase.

extract_protocol: Total RNA was prepared from passage 5 and passage 20 of eHBs (passage 5 and passage 20 of eHBs were derived from two independent experiments) using the RNeasy Plus Mini Kit.

value: Liver


title: Neu_1363


title: eHBs Passage 20

description: Gene expression of cultured hepatoblasts at late passage

source_name: Cultured hepatoblasts passage 20


title: PAX5C20orf112_2


title: Neu_1131


title: Spneumoniae_ R6_DNA_rep_2

city: Majadahonda

first: Antonio

middle: J.

last: Martin-Galiano

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Bacterial genetics

institute: Instituto de Salud Carlos III

description: Genomic DNA extracted from S. pneumoniae R6 in exponential growth (OD620=0.4)

hyb_protocol: Hybridization mix including labeled DNA was prepared following the Agilent array-based CGH Genomic DNA analysis. Arrays were hybridized at 65ºC for 40 hours.

scan_protocol: Scanning was done on a Roche MS200 scanner

data_processing: Raw data were extracted and normalized using Agilent Feature extraction 11.5.1.1 software

organism: Streptococcus pneumoniae R6

source_name: Spn R6 DNA

label_protocol: 10ng of genomic DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma; reference WGA2) and subsequently Cy3 labeled using Agilent Genomic DNA ULS Labeling kit according to manufacturer's instructions.

growth_protocol: Bacteria were grown in Todd-Hewitt medium + 0.5% yeast extract until OD620=0.4

extract_protocol: The genomic DNA was extracted by cesium chloride density gradient centrifugation

tag: growth phase

value: Exponential growth


title: PAX5C20orf112_4


title: Neu E2F1 KO_2543

description: Neu E2F1 KO_2543


title: PAX5ETV6_1


title: P493_Mismatch_rep1

status: Public on Dec 27 2014

city: Chiba

first: Hiroki

last: Nagase

address: 666-2 Nitona, Chuo-ku

country: Japan

institute: Chiba Cancer Center Research Institute

description:
Gene expression of human P493 cells treated with mismatch-MYC5
MYC5_015

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint Human GE Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um and Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-v6.5 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: P493, Mismatch, replicate-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low RNA Input Quick-Amp labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human Burkitt's lymphoma model cell line, P493.6, carrying an inducible MYC repression system and K562 (human chronic myelogenous leukaemia, obtained from RIKEN, Japan) cells were used. Cells were maintained in an RPMI 1640 medium with 10% fetal bovine serum (GIBCO/BRL) and 1% streptomycin and penicillin (Invitrogen).

extract_protocol: RNA was prepared using the RNA easy plus mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: K562 and P493 cells were treated with 10uM of PI polyamides for 72 hours and RNAs were prepared.

tag: cell line

tag: tissue origin

value: human Burkitt's lymphoma

tag: agent

value: Mismatch PI polyamides


title: P493_DMSO_rep3

description:
Gene expression of human P493 cells treated with DMSO
MYC5_011

source_name: P493, DMSO, replicate-3

value: DMSO


title: P493_DMSO_rep2

description:
Gene expression of human P493 cells treated with DMSO
MYC5_010

source_name: P493, DMSO, replicate-2


title: K562_MYC5_rep2

description:
Gene expression of human K562 cells treated with MYC5
MYC5_006

source_name: K562, MYC5, replicate-2

value: human chronic myelogenous leukemia


title: PIM153_PP

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Digestive gland  RNA of Mytilus galloprovincialis

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v10.7.3.1 and normalized by quantile normalization using R statistical software

label: Cyanine 3

organism: Mytilus galloprovincialis

source_name: Digestive gland of Mytilus galloprovincialis exposed to polystyrene contaminated with pyrene (PS-PYR)

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Total RNA was isolated using Extract-all (Eurobio) procedure.

tag: condition

value: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 6L- glass-beakers and exposed to rcontaminated plastics (PS-PYR) for 7 days


title: K562_DMSO_rep4

description:
Gene expression of human K562 cells treated with DMSO
MYC5_004

source_name: K562, DMSO, replicate-4


title: P493_DMSO_rep1

description:
Gene expression of human P493 cells treated with DMSO
MYC5_009

source_name: P493, DMSO, replicate-1


title: PIM151_PP


title: PAX5C20orf112_1

value: Bone marrow


title: PIM152_PP


title: K562_MYC5_rep1

description:
Gene expression of human K562 cells treated with MYC5
MYC5_005

source_name: K562, MYC5, replicate-1


title: P493_Mismatch_rep2

description:
Gene expression of human P493 cells treated with mismatch-MYC5
MYC5_016

source_name: P493, Mismatch, replicate-2


title: K562_Mismatch_rep1

description:
Gene expression of human K562 cells treated with mismatch-MYC5
MYC5_007

source_name: K562, Mismatch, replicate-1


title: P493_MYC5_rep1

description:
Gene expression of human P493 cells treated with MYC5
MYC5_013

source_name: P493, MYC5, replicate-1


title: Spneumoniae_ R6_DNA_rep_1


title: P493_DMSO_rep4

description:
Gene expression of human P493 cells treated with DMSO
MYC5_012

source_name: P493, DMSO, replicate-4


title: PIM134_POL

source_name: Digestive gland of Mytilus galloprovincialis exposed to polystyrene (PS)

value: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 6L- glass-beakers and exposed to vPS for 7 days


title: K562_Mismatch_rep2

description:
Gene expression of human K562 cells treated with mismatch-MYC5
MYC5_008

source_name: K562, Mismatch, replicate-2


title: P493_MYC5_rep2

description:
Gene expression of human P493 cells treated with MYC5
MYC5_014

source_name: P493, MYC5, replicate-2


title: PIM133_POL


title: PIM154_PP


title: PIM104_CTRL

source_name: Digestive gland of Mytilus galloprovincialis control group

value: Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater and 18± 1 °C, salinity at 28–30 ‰.  Mussels were distributed into 6L- glass-beakers for 7 days.


title: PIM132_POL


title: K562_DMSO_rep3

description:
Gene expression of human K562 cells treated with DMSO
MYC5_003

source_name: K562, DMSO, replicate-3


title: K562_DMSO_rep2

description:
Gene expression of human K562 cells treated with DMSO
MYC5_002

source_name: K562, DMSO, replicate-2


title: MPTP and nonacupoints acupuncture-treated mouse 2 substantia nigral regions

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from substantia nigral regions following nonacupoints-acupuncture-treatment to MPTP-intoxicated mouse

hyb_protocol: Following labeling, each cDNA was hybridized for 17 hr at 45℃ at 60 rpm on Affymetrix MouseGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The mean signal intensities of all genes (35,557 probes (28,853 genes) in a platform) were obtained from 2 chips of each experimental group.

source_name: MPTP and nonacupoints acupuncture-treated mouse substantia nigral regions

label_protocol: Fragmented and biotinylated cDNA were prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual from 300 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay manual, Affymetrix).

growth_protocol: Six-week old male inbred C57BL/6 mice (20-22 g) were grown up.

extract_protocol: The total RNA in the bilateral substantia nigral tissues of each group (n=2 per each group) was extracted using an RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

treatment_protocol: While mice in the control group (n=9) were intraperitoneally injected with saline 0.9% (100 µl) once daily for four weeks, the mice in the MPTP group (n=9) were intraperitoneally injected with MPTP-HCl (20 mg/kg of free base) dissolved in saline 0.9% (100 µl) at twenty-four hr intervals for four weeks to produce the sustained chronic model of parkinsonism. Acupuncture was performed by hand two hr after the first MPTP injection and then at forty-eight hr intervals (fourteen total sessions). The acupuncture procedure (acupoint GB34 (Yanglingquan) and acupoint LR3 (Taichong) for acupoints; both sides of the hips for non-acupoints) was performed as previously reported. Mice in the acupoints group were immobilized by hand two hr after MPTP administration. Acupuncture needles were inserted bilaterally to depths of 1 mm at acupoint LR3 and 3 mm at acupoint GB34, and then turned at a rate of two spins per sec for fifteen sec as reported in a previous study. For the non-acupoints group, the needles were inserted to depths of 3 mm at both sides of the hips rather than at the acupoints GB34 and LR3 for the acupoints group, and then the same procedures were performed as with the acupoints.

value: Male

value: substantia nigral tissues

tag: developmental stage

value: Adult

tag: treatment


title: PIM102_CTRL


title: MPTP and acupoints acupuncture-treated mouse 2 substantia nigral regions

description: Gene expression data from substantia nigral regions following acupoints-acupuncture-treatment to MPTP-intoxicated mouse

source_name: MPTP and acupoints acupuncture-treated mouse substantia nigral regions

value: MPTP and acupoints acupuncture-treated


title: MPTP-treated mouse 2 substantia nigral regions

description: Gene expression data from substantia nigral regions of MPTP-intoxicated mouse

source_name: MPTP-treated C57BL/6 mouse substantia nigral regions

value: MPTP-treated


title: MPTP and nonacupoints acupuncture-treated mouse 1 substantia nigral regions


title: PIM103_CTRL


title: MPTP and acupoints acupuncture-treated mouse 1 substantia nigral regions


title: ALDH+ Huh7 cells

status: Public on Dec 26 2014

city: Guangzhou

first: Qiu-Zhong

last: Pan

address: 651 Dongfeng Road East

institute: Sun Yat-Sen University Cancer Center

description: Gene expression data from ALDH+ Huh7 cells

hyb_protocol: The labeled cRNA was hybridized to Human Gene 1.0 ST microarray.

scan_protocol: Genechips were scanned using the Affymetrix Model 3000 Scanner.

data_processing: Data were normalized and analyzed with RMA using Affymetrix default analysis settings

source_name: ALDH+ cells isolated from Huh7 cells by flow cytometry

label_protocol: Total cRNA was labeled with biotin according to the standard Affymetrix protocol.

extract_protocol: Total RNA was prepared with Trizol reagent according to the manufacturer's instructions.

tag: cell marker

value: ALDH+


title: Control mouse 1 substantia nigral regions

description: Gene expression data from normal substantia nigral regions

source_name: Control C57BL/6 mouse substantia nigral regions

value: Control


title: Control mouse 2 substantia nigral regions


title: CD133+ Huh7 cells

description: Gene expression data from CD133+ Huh7 cells

source_name: CD133+ cells isolated from Huh7 cells by flow cytometry


title: MPTP-treated mouse 1 substantia nigral regions


title: ALDH- Huh7 cells

description: Gene expression data from ALDH- Huh7 cells

source_name: ALDH- cells isolated from Huh7 cells by flow cytometry

value: ALDH-


title: TKO

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Gene expression from triple KO mutant

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Signal intensity and call for each probe was obtained using MAS5.0 algorithm provided by Affymetrix with default settings.

source_name: thymocytes

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: Mutant thymocytes were cultured in standard medium.

extract_protocol: RNA of Lin- cells from DKO and TKO mice were extracted by RNeasy tissue kit Qiagen).

treatment_protocol: Lineage marker (Lin) negative cells of thymocytes from LckCre(-)Cdkn2a-/-Ring1A-/-Ring1Bfl/fl and LckCre(+)Cdkn2a-/-Ring1A-/-Ring1Bfl/fl mice were purified using Dynabeads-based depletion.

value: thymocytes

tag: genotype/variation

value: Ring1A, Ring1B and Cdkn2a triple KO


title: K562_DMSO_rep1

description:
Gene expression of human K562 cells treated with DMSO
MYC5_001

source_name: K562, DMSO, replicate-1


title: PIM101_CTRL

description: Digestive gland  RNA of Mytilus galloprovincialis


title: Mammary tumor animal #14809

status: Public on Dec 25 2014

first: Kent

last: Hunter

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

hyb_protocol: Hybridization performed according to Affymetrix recommended protocol.

scan_protocol: Scanning performed according to Affymetrix recommended protocol.

data_processing: Data was imported into BRB ArrayTools using the ST array import tool. Data was normalized using the median array as a reference. No further filtering was performed. Log intensity data was extracted from BRB ArrayTools for the Sample data tables.

source_name: mammary tumor, DO x PyMT

label_protocol: Labelling protocol performed according to Affymetrix recommended protocol.

growth_protocol: DO x PyMT tumors spontaneously developed and were permitted to grow until animals reached approximately 100 days of age. Tumors were harvested, snap frozen in LN2 and stored at -80oC until RNA preparation.

extract_protocol: Total RNA was extracted by Trizol, following manufacturer's recommended protocol.

treatment_protocol: No treatment.

tag: strain/background

value: Diversity Outcross x PyMT

value: mammary tumor

value: female

tag: age

value: 100 days

tag: animal #


title: Mammary tumor animal #14550

tag: tissue


title: Mammary tumor animal #14812

tag: gender


title: Mammary tumor animal #14808


title: WT_7

source_name: bone marrow sample from child with acute lymphoblastic leukemia

tag: genotype

value: PAX5 wild type

value: Bone marrow

value: B-cell precursor acute lymphoblastic leukemia

value: sample collected at diagnosis B ALL


title: Mammary tumor animal #14799


title: Mammary tumor animal #14800


title: Mammary tumor animal #14803


title: H3K4me3 1of2

description: H3K4me3 ChIP-chip 1 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Cy5/Cy3 ratios were calculated and assigned to TSS (from 4kb upstream to 4kb downstream) of all genes using our in-house program. Means of log ratio were approximated with two Gaussian curves and marked genes were classified as FDR (false discovery ratio) was 0.05.
Processed data contain Yes/No classification of analysis described above.

source_name: Thymus

label_protocol: Purified immunoprecipitated and input DNA were subjected to blunt ligation with linker oligo DNA, linker-mediated PCR (LM-PCR), labeling, hybridization and washing following the Agilent mammalian ChIP-on-chip protocol.

growth_protocol: Thymocytes were cultured in standard medium.

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

treatment_protocol: Thymocytes were subjected to ChIP assay using anti-trimethyl-Histone H3 (Lys4) (07-473, Millipore), anti-trimethyl-Histone H3 (Lys27) (07-449, Millipore), and anti-Ring1B  (D139-3, MBL) antibodies.

tag: strain

tag: cell type

tag: antibody

value: none (input)


title: H3K27me3 2of2

description: H3K27me3 ChIP-chip 2 of 2

value: anti-trimethyl-Histone H3 (Lys27) (07-449, Millipore)


title: Mammary tumor animal #14795


title: H3K4me3 2of2

description: H3K4me3 ChIP-chip 2 of 2

value: anti-trimethyl-Histone H3 (Lys4) (07-473, Millipore)


title: Mammary tumor animal #14775


title: Mammary tumor animal #14788


title: Mammary tumor animal #14789


title: Mammary tumor animal #14790


title: Ring1B 1of2

description: Ring1B ChIP-chip 1 of 2

value: anti-Ring1B  (D139-3, MBL)


title: DKO

description: Gene expression from double KO mutant

value: Ring1A and Ring1B double KO


title: H3K27me3 1of2

description: H3K27me3 ChIP-chip 1 of 2


title: Mammary tumor animal #14794


title: Mammary tumor animal #14776


title: Mammary tumor animal #14783


title: Ring1B 2of2

description: Ring1B ChIP-chip 2 of 2


title: Mammary tumor animal #14797


title: Mammary tumor animal #14780


title: Mammary tumor animal #14548


title: Mammary tumor animal #14769


title: Mammary tumor animal #14771


title: Mammary tumor animal #14768


title: Mammary tumor animal #14547


title: Mammary tumor animal #14770


title: Mammary tumor animal #14760


title: Mammary tumor animal #14762


title: Mammary tumor animal #14767


title: Mammary tumor animal #14763


title: Mammary tumor animal #14752


title: Mammary tumor animal #14546


title: Mammary tumor animal #14766


title: Mammary tumor animal #14741


title: Mammary tumor animal #14756


title: Mammary tumor animal #14745


title: Mammary tumor animal #14723


title: Mammary tumor animal #14755


title: Mammary tumor animal #14730


title: Mammary tumor animal #14750


title: Mammary tumor animal #14739


title: Mammary tumor animal #14736


title: Mammary tumor animal #14728


title: Mammary tumor animal #14753


title: Mammary tumor animal #14744


title: Mammary tumor animal #14764


title: Mammary tumor animal #14729


title: Mammary tumor animal #14544


title: Mammary tumor animal #14746


title: Mammary tumor animal #14747


title: Mammary tumor animal #14735


title: Mammary tumor animal #14759


title: Mammary tumor animal #14632


title: Mammary tumor animal #14635


title: Mammary tumor animal #14543


title: Mammary tumor animal #14633


title: Mammary tumor animal #14630


title: Mammary tumor animal #14637


title: Mammary tumor animal #14620


title: Mammary tumor animal #14623


title: Mammary tumor animal #14631


title: Mammary tumor animal #14624


title: Mammary tumor animal #14629


title: Mammary tumor animal #14613


title: Mammary tumor animal #14628


title: Mammary tumor animal #14618


title: Mammary tumor animal #14617


title: Mammary tumor animal #14625


title: Mammary tumor animal #14611R


title: Mammary tumor animal #14612


title: Mammary tumor animal #14542


title: Mammary tumor animal #14619


title: Mammary tumor animal #14616


title: Mammary tumor animal #14608R


title: Mammary tumor animal #14603


title: Mammary tumor animal #14606


title: Mammary tumor animal #14541


title: Mammary tumor animal #14607


title: Mammary tumor animal #14602


title: Mammary tumor animal #14596


title: Mammary tumor animal #14597


title: Mammary tumor animal #14591


title: Mammary tumor animal #14601


title: Mammary tumor animal #14590


title: Mammary tumor animal #14595


title: Mammary tumor animal #14576


title: Mammary tumor animal #14587


title: Mammary tumor animal #14558


title: Mammary tumor animal #14593


title: Mammary tumor animal #14578


title: Mammary tumor animal #14562


title: Mammary tumor animal #15025


title: Mammary tumor animal #14580


title: Mammary tumor animal #15002


title: Mammary tumor animal #15007


title: Mammary tumor animal #14540


title: Mammary tumor animal #15026


title: Mammary tumor animal #14956


title: Mammary tumor animal #14958


title: Mammary tumor animal #14556


title: Mammary tumor animal #14959


title: Mammary tumor animal #15029


title: Mammary tumor animal #14957


title: Mammary tumor animal #14954


title: Mammary tumor animal #14579


title: Mammary tumor animal #14951


title: Mammary tumor animal #14948


title: Mammary tumor animal #14946


title: Mammary tumor animal #14944


title: Mammary tumor animal #14945


title: Mammary tumor animal #14947


title: Mammary tumor animal #14939


title: Mammary tumor animal #14554


title: Mammary tumor animal #14928


title: Mammary tumor animal #14929


title: Mammary tumor animal #14941


title: Mammary tumor animal #14936


title: Mammary tumor animal #14938


title: Mammary tumor animal #14924


title: Mammary tumor animal #14922


title: Mammary tumor animal #14930


title: Mammary tumor animal #14919


title: Mammary tumor animal #14908


title: Mammary tumor animal #14553


title: Mammary tumor animal #14926


title: Mammary tumor animal #14721


title: Mammary tumor animal #14917


title: Mammary tumor animal #14911


title: Mammary tumor animal #14909


title: Mammary tumor animal #14904


title: Mammary tumor animal #14907


title: Mammary tumor animal #14903


title: Mammary tumor animal #14896


title: Mammary tumor animal #14902


title: Mammary tumor animal #14913


title: Mammary tumor animal #14894


title: Mammary tumor animal #14914


title: Mammary tumor animal #14648


title: Mammary tumor animal #14897


title: Mammary tumor animal #14718


title: Mammary tumor animal #14888


title: Mammary tumor animal #14891


title: Mammary tumor animal #14884


title: Mammary tumor animal #14552


title: Mammary tumor animal #14863


title: Mammary tumor animal #14879


title: Mammary tumor animal #14864


title: Mammary tumor animal #14551


title: Mammary tumor animal #14887


title: Mammary tumor animal #14857


title: Mammary tumor animal #14877


title: Mammary tumor animal #14880


title: Mammary tumor animal #14852


title: Mammary tumor animal #14893


title: Mammary tumor animal #14873


title: Mammary tumor animal #14823


title: Mammary tumor animal #14815


title: Mammary tumor animal #14819


title: Mammary tumor animal #14826


title: Mammary tumor animal #14825


title: Mammary tumor animal #14824


title: Surgical sample of intestinal-type gastric cancer 16

city: Chuo-ku

last: Sasaki

state: Tokyo

institute: National Cancer Center Reseach Institute

description: Gene expression data using Human Expression Array U95AV2

hyb_protocol: We used human U95A oligonucleotide probe arrays (Affymetrix, Santa Clara, CA) for analysis of mRNA expression levels corresponding to 12,626 transcripts.  Ten micrograms of fragmented cRNA were hybridized to the microarrays in 200 ul of a hybridization cocktail at 45 ℃ for 16 h in a rotisserie oven set at 60 rpm.  The arrays were then washed with nonstringent wash buffer (6xSSPE) at 25 ℃, followed by stringent wash buffer (100 mM MES (pH6.7), 0.1 M NaCl, and 0.01% Tween 20) at 50 ℃, stained with streptavidin phycoerythrin (Molecular Probes), washed again with 6xSSPE, stained with biotinylated anti-streptavidin IgG, followed by a second staining with streptavidin phycoerythrin and a third wash with 6xSSPE.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix) at 3-um resolution.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.

label: Biotin

source_name: Gastric cancer

label_protocol: cRNA derived from 5 ug of total RNA was used to generate a byotinylated cRNA probe by T7-transcription. The procedures were conducted according to the supplier’s protocols.

growth_protocol: All gastric cancer tissues were provided by the National Cancer Center Hospital after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.

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

treatment_protocol: All surgical samples were obtained from gastric cancer patients without neoadjuvant therapy. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. The samples were immediately frozen at -80 ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenised befor total RNA extraction.

value: Intestinal-type gastric cancer tumor


title: Surgical sample of intestinal-type gastric cancer 17


title: Surgical sample of intestinal-type gastric cancer 18


title: Surgical sample of intestinal-type gastric cancer 14


title: Surgical sample of intestinal-type gastric cancer 15


title: Mammary tumor animal #14859


title: Surgical sample of intestinal-type gastric cancer 12


title: Surgical sample of intestinal-type gastric cancer 11


title: Surgical sample of intestinal-type gastric cancer 13


title: Surgical sample of intestinal-type gastric cancer 05


title: Surgical sample of intestinal-type gastric cancer 04


title: Surgical sample of intestinal-type gastric cancer 09


title: Surgical sample of intestinal-type gastric cancer 10


title: Surgical sample of intestinal-type gastric cancer 02


title: Surgical sample of diffuse-type gastric cancer 09

value: Diffuse-type gastric cancer tumor


title: Surgical sample of intestinal-type gastric cancer 03


title: Surgical sample of diffuse-type gastric cancer 07


title: Surgical sample of diffuse-type gastric cancer 08


title: Surgical sample of intestinal-type gastric cancer 07


title: Surgical sample of intestinal-type gastric cancer 06


title: Surgical sample of intestinal-type gastric cancer 08


title: Surgical sample of diffuse-type gastric cancer 12


title: Surgical sample of diffuse-type gastric cancer 06


title: Surgical sample of intestinal-type gastric cancer 01


title: Surgical sample of diffuse-type gastric cancer 04


title: Surgical sample of diffuse-type gastric cancer 05


title: Surgical sample of diffuse-type gastric cancer 10


title: Surgical sample of diffuse-type gastric cancer 11


title: Surgical sample of diffuse-type gastric cancer 01


title: Larynx squamous cell carcinoma  (AT2_361_869)

city: Ribeirao Preto

first: Wilson

middle: Araújo

last: Silva Jr

state: Sao Paulo

address: Rua Catao Roxo, 2501

department: Genetics

country: Brazil

institute: University of Sao Paulo

description: Tumor sample in advanced stage obtained from a not cured patient

hyb_protocol: RNA hybridization to Whole Human Genome Oligo Microarray chips (Agilent Technologies, G4112F) was performed in a Fluidics Station 450 system (Affymetrix) using the Quick Amp Labeling One-Color kit (5190-0442; Agilent, US)

scan_protocol: CEL files from scanned microarrays were produced with the GenePix 4000B scanner (Axon Instruments, US) together with the GenePix Pro 6.0 and Agilent Feature Extraction 9.5.3.1 softwares. Agi4x44PreProcess Bioconductor package (Agilent, US) was used for loading probe signals

data_processing: Data analysis was performed with R packages from the Bioconductor project (www.bioconductor.org). Spearman Rank Coefficient-based correlation metric together with Average Linkage methods were applied for hierarchical clustering and exclusion of masked spots from microarray dataset. Statistical significance was determined with a nonpaired-T test analysis. False Discovery Rate (FDR) was used to verify p-values (q-values).

source_name: larynx

label_protocol: Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

extract_protocol: Total RNA was extracted with TRIZOL® (Life Technologies, US) according to manufactures’ guidelines

value: larynx

value: male

value: advanced

value: not cured


title: Surgical sample of diffuse-type gastric cancer 03


title: DP265-CD

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

description: Gene expression in cells from MSCGM-CD culture condition

hyb_protocol: Following labeling and clean up, the amplified RNA and dye incorporation were quantified using a ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE) and hybridized to Agilent whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies). After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Each sample was analyzed once.

data_processing: Agilent gProcessed signal intensities are uploaded.

label_protocol: After RNA was qualified by the Agilent 2100 Bioanalyzer, 250 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3-labeled CTP using the Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the protocol supplied by the manufacturer.

growth_protocol: Dental pulp cells were cultured in MSCGM or MSCGM-CD medium (LONZA).

extract_protocol: RNA extraction (RNeasy Plus Mini Kit; Qiagen, Valencia, CA, USA)

value: dental pulp cells

value: female


title: Surgical sample of diffuse-type gastric cancer 02


title: Larynx squamous cell carcinoma  (AT2_344_867)

source_name: supraglottis

value: supraglottis


title: DP264-M

institute: Gifu University Graduate School of Medicine

description: Gene expression in cells from MSCGM culture condition


title: Larynx squamous cell carcinoma  (AT1_388_869)

description: Tumor sample in advanced stage obtained from a cured patient

value: cured


title: DP265-M


title: Larynx squamous cell carcinoma  (AT2_243_325)

source_name: glottis

value: glottis


title: Larynx squamous cell carcinoma  (AT2_335_325)


title: DP264-CD


title: DP245-CD


title: Larynx squamous cell carcinoma  (AT1_407_869)


title: Larynx squamous cell carcinoma  (AT2_393_869)


title: Larynx squamous cell carcinoma  (AT1_368_867)


title: Larynx squamous cell carcinoma  (AT1_226_322)


title: Larynx squamous cell carcinoma  (BT2_205_323)

description: Tumor sample in beginning stage obtained from a not cured patient

value: beginning


title: Larynx squamous cell carcinoma  (AT1_371_867)


title: Larynx squamous cell carcinoma  (AT1_209_322)

source_name: glottis&supraglottis

value: glottis&supraglottis


title: Larynx squamous cell carcinoma  (AT1_185_322)


title: Larynx squamous cell carcinoma  (AT1_327_325)


title: Larynx squamous cell carcinoma  (AT1_380_867)


title: Larynx squamous cell carcinoma  (BT2_297_326)

source_name: laryngopharynx

value: laryngopharynx


title: Larynx squamous cell carcinoma  (BT2_186_323)


title: Larynx squamous cell carcinoma  (BT2_213_323)


title: Larynx squamous cell carcinoma  (BT2_252_326)

source_name: subglottis&oropharynx

value: subglottis&oropharynx


title: Larynx squamous cell carcinoma  (BT2_224_326)


title: Larynx squamous cell carcinoma  (BT2_287_326)


title: Larynx squamous cell carcinoma  (AT2_332_325)


title: DP245-M


title: Larynx squamous cell carcinoma  (BT1_333_870)

description: Tumor sample in beginning stage obtained from a cured patient


title: Larynx squamous cell carcinoma  (BT1_383_739)


title: Larynx squamous cell carcinoma  (BT1_247_323)


title: Larynx squamous cell carcinoma  (BT1_358_868)


title: Larynx squamous cell carcinoma  (BT1_394_870)


title: Surgical safety border  (AM1_371_737)

description: Tumor margin sample in advanced stage tumor obtained from a cured patient

value: margin


title: Surgical safety border  (AM1_226_737)


title: Surgical safety border  (AM1_209_738)


title: Surgical safety border  (AM1_388_871)


title: DP193

description: Gene expression in cells from mature teeth

growth_protocol: Dental pulp cells were cultured in MSCGM medium (LONZA).

treatment_protocol: No treatment


title: Surgical safety border  (BM2_297_871)

description: Tumor margin sample in beginning stage tumor obtained from a not cured patient


title: Larynx squamous cell carcinoma  (BT1_400_870)

source_name: epiglottis

value: epiglottis


title: Surgical safety border  (AM2_393_324)

description: Tumor margin sample in advanced stage tumor obtained from a not cured patient


title: Surgical safety border  (AM2_201_324)


title: Surgical safety border  (AM2_332_871)


title: Larynx squamous cell carcinoma  (BT1_336_868)


title: Surgical safety border  (BM1_394_324)


title: Surgical safety border  (BM2_205_324)


title: DP101

description: Gene expression in cells from immature teeth


title: Surgical safety border  (BM1_247_737)

description: Tumor margin sample in beginning stage tumor obtained from a cured patient


title: DP75


title: Surgical safety border  (BM2_331_871)


title: DP1


title: DP133


title: DP159


title: 4SL3 SB203580 + LPS 4h

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
replicate_3
5455178007_L

data_processing: The data were filtered for p< 0.05 and normalised using quantile normalisation with GeneSpring, and log2 transformed.

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

growth_protocol: Human mononuclear THP-1 cells, a model for monocyte lineage cells, including microglia and macrophages [1-3], were maintained in medium containing 90 % RPMI (Gibco), 10 % FBS (Hyclone), 2 mM L-glutamine (Sigma), and a combination of 100 U/ml penicillin with 100 µg/ml streptomycin (P/S, Sigma) at 37°C with 5 % CO2 and are usually split 1:3 to 1:4 once to twice a week after reaching approximately 1 x 106 cells per milliliter.

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

tag: cell line

tag: time


title: Surgical safety border  (BM1_336_737)


title: DP28


title: CD133- Huh7 cells

description: Gene expression data from CD133- Huh7 cells

source_name: CD133- cells isolated from Huh7 cells by flow cytometry


title: 4SH1 SB203580 + gp120 4h

description:
replicate_1
5455178007_G


title: 4SL1 SB203580 + LPS 4h

description:
replicate_1
5455178007_J


title: 4S2 SB203580 4h

description:
replicate_2
5455178007_E


title: 4L1 LPS 4h

description:
replicate_1
5455178007_A

source_name: LPS

value: LPS


title: 4SL2 SB203580 + LPS 4h

description:
replicate_2
5455178007_K


title: 4C1 control 4h

description:
replicate_1
5374255058_G

source_name: control

value: control


title: 4H2 gp120 4h

description:
replicate_2
5374255058_K


title: 4S3 SB203580 4h

description:
replicate_3
5455178007_F


title: 4SH2 SB203580 + gp120 4h

description:
replicate_2
5455178007_H


title: 4L3 LPS 4h

description:
replicate_3
5455178007_C


title: 24SL2 SB203580 + LPS 24h

description:
replicate_2
5374255058_E


title: 4C3 control 4h

description:
replicate_3
5374255058_I


title: 24SL3 SB203580 + LPS 24h

description:
replicate_3
5374255058_F


title: 4H3 gp120 4h

description:
replicate_3
5374255058_L


title: 24SH2 SB203580 + gp120 24h

description:
replicate_2
5374255058_B


title: 24S2 SB203580 24h

description:
replicate_2
5374255018_K


title: 24S3 SB203580 24h

description:
replicate_3
5374255018_L


title: 4S1 SB203580 4h

description:
replicate_1
5455178007_D


title: 24SH3 SB203580 + gp120 24h

description:
replicate_3
5374255058_C


title: 4H1 gp120 4h

description:
replicate_1
5374255058_J


title: 4SH3 SB203580 + gp120 4h

description:
replicate_3
5455178007_I


title: 4C2 control 4h

description:
replicate_2
5374255058_H


title: 24SL1 SB203580 + LPS 24h

description:
replicate_1
5374255058_D


title: 24SH1 SB203580 + gp120 24h

description:
replicate_1
5374255058_A


title: 24S1 SB203580 24h

description:
replicate_1
5374255018_J


title: 24L2 LPS 24h

description:
replicate_2
5374255018_H


title: 24L1 LPS 24h

description:
replicate_1
5374255018_G


title: 24H3 gp120 24h

description:
replicate_3
5374255018_F


title: Serum 092B

type: other

city: stanford

first: Jacob

last: Rosenberg

state: Ca

address: 269 Campus Drive, CCSR 2240

institute: Stanford University

hyb_protocol: Arrays were first blocked in 5% milk (Bio-Rad) in phosphate-buffered saline (PBS) plus 0.1% Tween (Sigma-Aldrich) (PBST) for one hour, then washed three times in PBST. Arrays were probed with serum diluted 1:150 in 10% fetal calf serum (FCS) 1% PBST. Arrays were subjected to three five minute washes in 1% PBST. Serum reactivity was detected using an Alexafluor 647-conjugated goat anti-human IgG secondary antibody (Jackson) diluted to 0.375μg/ml in 1% PBST for 45 minutes. Arrays were washed three times in PBST and dried under negative pressure.

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing:
Local background was subtracted from feature mean fluorescence intensity. Means were calculated across replicates, and these values were used for analysis.
processed using GenePix 6 software

molecule: other

source_name: serum

label_protocol: Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA)

growth_protocol: Serum was collected by centrifuging whole blood, stored at -80C, and thawed for analysis.

treatment_protocol: Serum was diluted into probing buffer as described

tag: sample type

value: serum

tag: phenotype

value: immunodeficient


title: Serum 562T


title: 24L3 LPS 24h

description:
replicate_3
5374255018_I


title: Serum 562B


title: Serum 561T


title: Serum 561B


title: 24H2 gp120 24h

description:
replicate_2
5374255018_E


title: Serum 560T


title: 24C1 control 24h

description:
replicate_1
5374255018_A


title: 24C2 control 24h

description:
replicate_2
5374255018_B


title: Serum 560B


title: Serum 559T


title: Ji_Batch5_13Baseline (day 0)

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

description:
Whole blood transcripts.
STANSUB_SLVP015-120-2012
Ji_Batch5_13
Protocol manuals are available on the Series record.

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

source_name: blood, female, Fluzone single-dose syringe, day0

value: whole blood

tag: Sex

tag: age (years)

tag: stanford internal vaccine reference id


title: Serum 2ary


title: Ji_Batch5_50Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-118-2012
Ji_Batch5_50
Protocol manuals are available on the Series record.

source_name: blood, male, Fluzone single-dose syringe, day0

value: male


title: Ji_Batch5_33Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-115-2012
Ji_Batch5_33
Protocol manuals are available on the Series record.


title: Serum 559B


title: 24C3 control 24h

description:
replicate_3
5374255018_C

tag: treatment


title: Ji_Batch5_51Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-119-2012
Ji_Batch5_51
Protocol manuals are available on the Series record.


title: Ji_Batch5_17Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-114-2012
Ji_Batch5_17
Protocol manuals are available on the Series record.


title: Ji_Batch5_52Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-123-2012
Ji_Batch5_52
Protocol manuals are available on the Series record.


title: Serum 554B


title: Ji_Batch5_14Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-112-2012
Ji_Batch5_14
Protocol manuals are available on the Series record.


title: Serum 553T


title: Ji_Batch5_62Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-106-2012
Ji_Batch5_62
Protocol manuals are available on the Series record.


title: Serum 552T


title: Serum 553B


title: Serum 519B


title: Ji_Batch5_71Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-107-2012
Ji_Batch5_71
Protocol manuals are available on the Series record.


title: Serum 519T


title: Serum 552B


title: Ji_Batch5_45Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-110-2012
Ji_Batch5_45
Protocol manuals are available on the Series record.


title: Ji_Batch5_54Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-108-2012
Ji_Batch5_54
Protocol manuals are available on the Series record.


title: Serum 518B


title: Ji_Batch5_38Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-100-2012
Ji_Batch5_38
Protocol manuals are available on the Series record.


title: Ji_Batch5_56Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-105-2012
Ji_Batch5_56
Protocol manuals are available on the Series record.


title: Ji_Batch5_20Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-099-2012
Ji_Batch5_20
Protocol manuals are available on the Series record.


title: Ji_Batch5_7Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-103-2012
Ji_Batch5_7
Protocol manuals are available on the Series record.


title: 24H1 gp120 24h

description:
replicate_1
5374255018_D


title: Ji_Batch5_58Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-104-2012
Ji_Batch5_58
Protocol manuals are available on the Series record.


title: Serum 516T


title: Serum 516B


title: Serum 515B


title: Ji_Batch5_68Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-094-2012
Ji_Batch5_68
Protocol manuals are available on the Series record.


title: Ji_Batch5_53Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-097-2012
Ji_Batch5_53
Protocol manuals are available on the Series record.


title: Serum 515T


title: Ji_Batch5_46Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-093-2012
Ji_Batch5_46
Protocol manuals are available on the Series record.


title: Serum 514T


title: Ji_Batch5_10Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-092-2012
Ji_Batch5_10
Protocol manuals are available on the Series record.


title: Serum 514B


title: Serum 518T


title: Ji_Batch5_1Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-090-2012
Ji_Batch5_1
Protocol manuals are available on the Series record.


title: Serum 512T


title: Serum 510T


title: Serum 512B


title: Serum 509T


title: Ji_Batch5_30Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-087-2012
Ji_Batch5_30
Protocol manuals are available on the Series record.


title: Ji_Batch5_44Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-082-2012
Ji_Batch5_44
Protocol manuals are available on the Series record.


title: Ji_Batch5_64Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-084-2012
Ji_Batch5_64
Protocol manuals are available on the Series record.


title: Ji_Batch5_69Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-080-2012
Ji_Batch5_69
Protocol manuals are available on the Series record.


title: Serum 508T


title: Ji_Batch5_61Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-089-2012
Ji_Batch5_61
Protocol manuals are available on the Series record.


title: Ji_Batch5_5Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-070-2012
Ji_Batch5_5
Protocol manuals are available on the Series record.


title: Ji_Batch5_22Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-073-2012
Ji_Batch5_22
Protocol manuals are available on the Series record.


title: Serum 508B


title: Ji_Batch5_43Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-079-2012
Ji_Batch5_43
Protocol manuals are available on the Series record.


title: Ji_Batch5_2Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-072-2012
Ji_Batch5_2
Protocol manuals are available on the Series record.


title: 4L2 LPS 4h

description:
replicate_2
5455178007_B


title: Serum 507T


title: Serum 507B


title: Ji_Batch5_3Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-069-2012
Ji_Batch5_3
Protocol manuals are available on the Series record.


title: Ji_Batch5_36Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-067-2012
Ji_Batch5_36
Protocol manuals are available on the Series record.


title: Ji_Batch5_40Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-065-2012
Ji_Batch5_40
Protocol manuals are available on the Series record.


title: Serum 184T


title: Serum 184B


title: Ji_Batch5_57Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-064-2012
Ji_Batch5_57
Protocol manuals are available on the Series record.


title: Serum 509B


title: Ji_Batch5_35Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-066-2012
Ji_Batch5_35
Protocol manuals are available on the Series record.


title: Serum 182B


title: Serum 182T


title: Serum 101T


title: Serum 101B


title: Serum 099T


title: Serum 100B


title: Ji_Batch5_42Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-053-2012
Ji_Batch5_42
Protocol manuals are available on the Series record.


title: Serum 098T


title: Ji_Batch5_28Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-061-2012
Ji_Batch5_28
Protocol manuals are available on the Series record.


title: Ji_Batch5_9Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-058-2012
Ji_Batch5_9
Protocol manuals are available on the Series record.


title: Serum 181T


title: Serum 099B


title: Ji_Batch5_41Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-054-2012
Ji_Batch5_41
Protocol manuals are available on the Series record.


title: Serum 098B


title: Serum 097T


title: Ji_Batch5_59Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-060-2012
Ji_Batch5_59
Protocol manuals are available on the Series record.


title: Ji_Batch5_66Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-050-2012
Ji_Batch5_66
Protocol manuals are available on the Series record.


title: Serum 097B


title: Ji_Batch5_26Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-052-2012
Ji_Batch5_26
Protocol manuals are available on the Series record.


title: Ji_Batch5_34Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-048-2012
Ji_Batch5_34
Protocol manuals are available on the Series record.


title: Ji_Batch5_15Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-051-2012
Ji_Batch5_15
Protocol manuals are available on the Series record.


title: Ji_Batch5_70Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-044-2012
Ji_Batch5_70
Protocol manuals are available on the Series record.


title: Serum 096B


title: Serum 094T


title: Serum 094B


title: Serum 095B


title: Serum 093T


title: Serum 093B


title: Serum 092T


title: Serum 096T


title: Serum 095T


title: Ji_Batch5_55Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-041-2012
Ji_Batch5_55
Protocol manuals are available on the Series record.


title: Ji_Batch5_37Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-045-2012
Ji_Batch5_37
Protocol manuals are available on the Series record.


title: Ji_Batch5_32Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-038-2012
Ji_Batch5_32
Protocol manuals are available on the Series record.


title: Ji_Batch5_39Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-037-2012
Ji_Batch5_39
Protocol manuals are available on the Series record.


title: Gonad_SS_rep5

city: Barcelona

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

description: Fish that exhibited a slow growing rate and through a reduction of the feeding were forced to slow down growth even more

hyb_protocol: Each sample (1.65 μg) was hybridized to D. labrax array (Agilent ID 023790) at 65 °C for 17 h using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. The microarray platform GPL13443 has been validated and uploaded to the Gene Expression Omnibus (GEO)-NCBI database.

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp (Ritchie et al., 2007) method. To assure comparability across samples quantile normalization (Bolstad, 2001) was used. A probe was considered reliable if its raw foreground intensity was at least two times higher than the respective background intensity and if it was neither saturated nor flagged by the Feature Extraction software. On our custom array design, most probes (78%) were represented in two (or in some cases more) identical copies. Median intensities of respective probe replicates were taken in order to yield only one expression value per probe. A probe was considered reliable if at least half of its replicates were reliable, as defined above. Differential expression analysis was carried out on all non-control probes with an empirical Bayes approach on linear models (limma) (Smyth, 2004). Results were corrected for multiple testing according to the False Discovery Rate (FDR) method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed if they had adjusted P-value < 0.05, absolute fold change > 1.2 and were reliable in all samples.  All statistical analyses were performed with the Bioconductor project (http://www.bioconductor.org/) in the R statistical environment (http://cran.rproject.org/) (Gentleman et al., 2004).

organism: Dicentrarchus labrax

source_name: Whole gonad,  332 days post fertilization, Slow growing-Slow growing fish from the population

label_protocol: RNA labelling, hybridizations, and scanning were performed according to manufacturer’s instructions. Briefly, total RNA (100 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen), quantified with the Nanodrop ND- 1000 and verified using the Bioanalyzer 2100.

growth_protocol: Rearing conditions and handling methods were as described at (Díaz et al., 2013). At the beginning of the experiment both experimental groups (F and S) followed the same feeding protocol; larvae were fed three times a day with Artemia AF and then with amino acid enriched Artemia EG (INVE Aquaculture, Belgium). Juveniles and adults were fed following each specific group feeding regime with dry food (ProAqua S.A., Spain) of different diameters according to fish size.

extract_protocol: Total RNA was purified from 170 dph European sea bass isolated gonads by homogenizing the tissue with Trizol reagent (Invitrogen- Live Technologies, Scotland, UK). Briefly, samples were then separated into phases by chloroform, precipitated with isopropanol and washed in 75% Ethanol. The quality and concentration of the RNA were assessed by ND-1000 spectrophotometer (NanoDrop Technologies) based on A260 absorbance and checked on a 1% agarose/formaldehyde gel. Integrity of the total RNA was then verified analyzing 1 µl/sample with a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent, Spain) before processing for microarrays to assure consistency across samples. RNA samples of 100-200 ng/µl and RINs higher than 7 were used to perform the hybridizations. Two hundred nanograms of total RNA were treated with E.coli RNAse H in order to remove complementary RNA. From this RNA 100 ng were used for the cDNA synthesis using SuperScript III RNase Transcriptase (Invitrogen, Spain) and Random hexamer (Invitrogen, Spain) following manufacturer’s instructions.

treatment_protocol: Larvae were divided in two tanks and maintained at 17ºC, a temperature known to avoid temperature effects on sex ratio (Piferrer et al., 2005; Navarro-Martín et al., 2009), for the first 20 dph and then raised and maintained at 21ºC to allow growth from the whole experiment until fall, when temperature followed natural fluctuations to allow gonad maturation. Different feeding regimes are described elsewhere (Díaz et al., 2013; Experiment 2).

value: Testis


title: Ji_Batch5_47Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-032-2012
Ji_Batch5_47
Protocol manuals are available on the Series record.

value: female


title: Gonad_SS_rep2


title: Ji_Batch5_49Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-033-2012
Ji_Batch5_49
Protocol manuals are available on the Series record.


title: Ji_Batch5_48Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-031-2012
Ji_Batch5_48
Protocol manuals are available on the Series record.


title: Ji_Batch5_23Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-046-2012
Ji_Batch5_23
Protocol manuals are available on the Series record.


title: Ji_Batch5_25Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-036-2012
Ji_Batch5_25
Protocol manuals are available on the Series record.


title: Gonad_SS_rep3


title: Ji_Batch5_16Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-026-2012
Ji_Batch5_16
Protocol manuals are available on the Series record.


title: Gonad_SS_rep1


title: Ji_Batch5_19Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-035-2012
Ji_Batch5_19
Protocol manuals are available on the Series record.


title: Gonad_SS_rep4


title: Ji_Batch5_18Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-034-2012
Ji_Batch5_18
Protocol manuals are available on the Series record.


title: Ji_Batch5_67Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-028-2012
Ji_Batch5_67
Protocol manuals are available on the Series record.


title: Gonad_SF_rep5

description: Fish that exhibited a slow growing rate and through overfeeding were forced to accelerate growth rate

source_name: Whole gonad,  332 days post fertilization, Slow growing-Fast growing fish from the population


title: Ji_Batch5_63Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-016-2012
Ji_Batch5_63
Protocol manuals are available on the Series record.


title: Gonad_SF_rep4


title: Ji_Batch5_21Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-024-2012
Ji_Batch5_21
Protocol manuals are available on the Series record.


title: Ji_Batch5_12Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-025-2012
Ji_Batch5_12
Protocol manuals are available on the Series record.


title: Gonad_FS_rep5

description: Fish that exhibited a fast growing rate and through a reduction of the feeding were forced to slow down growth

source_name: Whole gonad,  332 days post fertilization, Fast growing-Slow growing  fish from the population


title: Gonad_SF_rep2


title: Gonad_SF_rep1


title: Ji_Batch5_29Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-029-2012
Ji_Batch5_29
Protocol manuals are available on the Series record.


title: Ji_Batch5_4Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-020-2012
Ji_Batch5_4
Protocol manuals are available on the Series record.


title: Gonad_SF_rep3


title: Ji_Batch5_27Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-023-2012
Ji_Batch5_27
Protocol manuals are available on the Series record.


title: Ji_Batch5_8Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-015-2012
Ji_Batch5_8
Protocol manuals are available on the Series record.


title: Ji_Batch5_6Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-022-2012
Ji_Batch5_6
Protocol manuals are available on the Series record.


title: Pdyn ob F Hypo Input3

city: New York

first: Zhiying

state: NY

address: 1230 York ave.

institute: Rockefeller University

description:
total RNA
transcriptome data from total hypothalamic RNA of ob/ob mice

hyb_protocol: 20ug of cRNA for each sample was fragmented according to manufacturer's instruction and hybridized to room temperature-equilibriated arrays according to kit instruction (Affymetrix 900720) in Hybridizatoin Oven 640 (Affymetrix 800138), following which the arrays were washed and stained according to manufacturer's instruction using GeneChip Fluidic Station 450 (Affymetrix, 00-0079).

scan_protocol: Mouse Genome 430 2.0 arrays were scanned using the GeneChip Sanner 3000 (Affymetrix, 00-00212).

data_processing: Data were processed using GeneSpring GX software. GC-RMA was used for normalization. Probesets with a minimum hybridization intensity of 100 in all sample of at least one condition were deemed expressed. Averaged values for each condition were used for further analyses.

source_name: ob/ob hypothalamic Input sample 3

label_protocol: Biotinylated cRNA was prepared according to manufacturer's instructions (Affymetrix, 901230)

growth_protocol: Mice were housed under 12hr light-dark cycle at room temperature 68-72 °F and fed ad lib with regular rodent chow until 3-4 month of age.

extract_protocol: BAC TRAP procedure: pooled hypothalami were hypogenized, polysomal RNA was immuno-precipitated using antibodies against GFP after an aliquote for Input RNA was saved separately.

treatment_protocol: No treatment other than routine feeding and cleaning were done when mice were growing up. On the day of experiment, hypothalami were dissected on ice and immediately processed for IP and Input RNA purification

value: hypothalamus

value: ob/ob

tag: developmental stage

value: adult

value: none (input)

tag: antibody source

value: The Rockefeller University Monoclonal Antibody Resource Center, HtzGFP-19F7 and HtzGFP-19C8


title: Pdyn ob M Hypo Input2

source_name: ob/ob hypothalamic Input sample 2


title: Pdyn ob M Hypo Input1

source_name: ob/ob hypothalamic Input sample 1


title: Gonad_FS_rep4


title: Pdyn ob F Hypo IP3

description:
immunoprecipitated polysomal RNA
transcriptome data from hypothalamic Pdyn neurons-specific polysomal RNA of ob/ob mice

source_name: ob/ob hypothalamic IP sample 3

value: anti-GFP


title: Ji_Batch5_11Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-012-2012
Ji_Batch5_11
Protocol manuals are available on the Series record.


title: Pdyn ob M Hypo IP2

source_name: ob/ob hypothalamic IP sample 2


title: Pdyn wt F Hypo Input3

description:
total RNA
transcriptome data from total hypothalamic RNA of wild-type mice

source_name: wild-type hypothalamic Input sample 3

value: wildtype


title: Pdyn wt M Hypo IP1

description:
immunoprecipitated polysomal RNA
transcriptome data from hypothalamic Pdyn neurons-specific polysomal RNA of wild-type mice
Sample was removed from analysis due to significant differences from remaining wt IP samples. No processed data provided for this record.

source_name: wild-type hypothalamic IP sample 1


title: Unc93b TKO 1

type: protein

city: Worcester

first: Rebecca

last: Baum

address: 55 N Lake Ave LRB 240D

department: Medicine

institute: University of Massachusetts Medical School

description:
Serum samples pretreated with DNAse I were diluted 1:100 and incubated with autoantigen arrays bearing 125 autoantigens
raw data in: Slide 2.gpr

hyb_protocol: Autoantigen array protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX).

scan_protocol: Genepix Pro 7.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: Heatmap was generated using Cluster and treeview software (http://rana.lbl.gov/EisenSoftware.htm)

label: cy3-labeled anti-mouse IgG

molecule: protein

source_name: Sera

label_protocol: Autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG)

growth_protocol: not applicable

extract_protocol: Sera was isolated from blood that was centrifuged at 6000rpm for 10 minutes.

treatment_protocol: not applicable

tag: age

value: 10 months

tag: mouse strain

value: Female

value: Unc93b TKO


title: Unc93b TKO 2

tag: gender

value: Male


title: Unc93b TKO 3

tag: genotype


title: Ji_Batch5_60Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-010-2012
Ji_Batch5_60
Protocol manuals are available on the Series record.

tag: tissue


title: Gonad_FS_rep1


title: Pdyn ob M Hypo IP1

source_name: ob/ob hypothalamic IP sample 1

tag: strain


title: Ji_Batch5_31Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-006-2012
Ji_Batch5_31
Protocol manuals are available on the Series record.


title: Ji_Batch5_24Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-004-2012
Ji_Batch5_24
Protocol manuals are available on the Series record.


title: AIM2 TKO 3

value: AIM2 TKO


title: Gonad_FS_rep3


title: Pdyn wt F Hypo IP3

description:
immunoprecipitated polysomal RNA
transcriptome data from hypothalamic Pdyn neurons-specific polysomal RNA of wild-type mice

source_name: wild-type hypothalamic IP sample 3

tag: antibody


title: Gonad_FS_rep2


title: Ji_Batch5_65Baseline (day 0)

description:
Whole blood transcripts.
STANSUB_SLVP015-011-2012
Ji_Batch5_65
Protocol manuals are available on the Series record.


title: Gonad_FF_rep5

description: Fish that exhibited a fast growing rate and through overfeeding were forced to maintain a fast growing rate

source_name: Whole gonad,  332 days post fertilization, Fast growing-Fast growing fish from the population


title: Gonad_FF_rep4