title: CSCC_CT-ID1_W40-1-1-J.03

description:
Cellular Tumor sampled by high expression of gene ID1
305272990


title: CSCC_CThbv-TGFBR2_W22-1-1-F.03

status: Public on Dec 01 2017

type: SRA

city: Seattle

first: Ralph

middle: B.

last: Puchalski

state: WA

address: 550 17th Ave., Suite 570

country: USA

institute: Swedish Neuroscience Institute

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
304950302

library_source: transcriptomic

data_processing:
(RNA-Seq Data Alignment) The data generation, collection, alignment, and normalization is described in detail online at glioblastoma.alleninstitute.org  in the Documentation tab.  Raw read (fastq) files were aligned to the hg19 human genome sequence (Meyer et al., 2013) with the RefSeq transcriptome version 54 (downloaded 8/25/2012 and updated by removing duplicate gene entries from the gtf reference file for consistency with the LIMS). For alignment, Illumina sequencing adapters were clipped from the reads using the fastqMCF program (Aronesty, 2011).
After clipping, the paired-end reads were mapped using RNA-Seq by Expectation-Maximization (RSEM) (Li et al., 2010) using default settings except for two mismatch parameters: bowtie-e (set to 500) and bowtie-m (set to 100). RSEM aligns reads to known isoforms and then calculates gene expression as the sum of isoform expression for a given gene, assigning ambiguous reads to multiple isoforms using a maximum likelihood statistical model. Reads that did not map to the transcriptome were then aligned to the hg19 genome sequence using Bowtie with default settings (Langmead et al., 2009). Reads that mapped to neither the transcriptome with RSEM nor to the genome with Bowtie were mapped against the ERCC sequences (in this project as a negative control).
The final results files included quantification of the mapped reads (raw read counts, FPKM, and TPM values for the transcriptome-mapped reads, chromosome-wide counts for the genomic-mapped reads), BAM files including both transcriptome and genome-mapped reads, and fastq files for the unmapped reads. Anonymized BAM files (where sequence-level information has been removed) and gene-level quantification (TPM, FPKM, and number of reads) are available as part of the resource (see Download tab).  Resulting FPKM values (normalized for gene length and sequencing depth) used for the analyses of this paper were further adjusted for the total transcript count using TbT normalization as described below.
(RNA-Seq Data Normalization) In the Allen Human Brain Atlas, analysis of the RNA-Seq data showed minimal process batch effects but improvements in variability after normalization could be made (Miller et al., 2014), and therefore a comparable post-hoc data normalization strategy was used for this project. Gene expression values were summarized as transcripts per million (TPM) and fragments per kilobase per million (FPKM), as described above, both of which normalize read counts by gene length and for the total number of reads in slightly different ways.
In the manuscript (as well as for the heatmaps shown on the website), the FPKM data matrix was further adjusted for the total transcript count using TbT normalization (Kadota et al., 2012), which scales each sample based on the summed expression of all genes that are not differentially expressed. FPKM values were TbT normalized in linear space, with the differential expression vector defined as TRUE if a sample was from cellular tumor and FALSE otherwise.
Sample data was then scaled such that the total log2(FPKM) across the entire data set remained unchanged after normalization. The result of this step was that expression levels for all genes in a particular sample were multiplied by a scalar value close to 1 (in most cases between 0.7-1.3).
Genome_build: GRCh37.p5
Supplementary_files_format_and_content: fpkm_table.csv contains the (row, column) matrix of fpkm values obtained for each (gene, sample).  The first row contains the sample unique identifiers (rna_well_id).  The first column contains the gene unique identifiers (gene_id).
Supplementary_files_format_and_content: columns-samples.csv  contains information about the samples profiled with RNA sequencing:  (1) tumor_id, block_id, specimen_id and corresponding names:  Specimen from which the sample was dissected and the specimen's parent block and tumor.  (2) rna_well_id:  Unique identifier of the sample.  (3) polygon_id:  Unique identifier of an avg_graphic_object that outlines where the sample was cut from.  (4) structure_id, structure_abbreviation, structure_color, structure_name:  Label that groups samples obtained from laser micro-dissected anatomic structures or putative cancer stem cell clusters.
Supplementary_files_format_and_content: rows-genes.csv contains information about the genes for which fpkm values were calculated. (1) gene_id:  Unique identifier for the gene. (2) chromosome:  Chromosome associated with the gene.  (3) gene_entrez_id, gene_symbol, gene_name:  entrez_id, NCBI symbol, and name of the gene.

molecule: total RNA

organism: Homo sapiens

source_name: glioblastoma

extract_protocol:
(Laser Microdissection)  In preparation for laser microdissection, PEN slides were removed from -80°C and quickly processed through cresyl violet and Eosin to lightly stain the tissue. Sections were fixed in ice-cold 70% ethanol for 30 seconds, washed for 15 seconds in nuclease-free water, stained with 0.7% cresyl violet in 0.05% NaOAc, pH 3.4 for 4 minutes, rinsed in nuclease-free water for 10 seconds, 15 seconds in 70% ethanol, followed by 2 dips in 0.25% Eosin, and 20 seconds each in 95%, 100%, and 100% ethanol rinses. Slides were air-dried for 2 minutes and desiccated by vacuum for 1 hour at room temperature, then frozen at -80°C until microdissection. For both RNA-Seq studies, cresyl violet/Eosin-stained sections mounted on PEN membranes were microdissected while visually referring to H&E-stained sections that had been curated to identify matched target regions. For the Cancer Stem Cells RNA-Seq study, ISH reference gene expression patterns informed the curation of the H&E-stained sections. A Leica LMD6000 (Leica Microsystems, Inc., Bannockburn, IL) was used for microdissection, and the system included an upright research microscope fitted with a diode laser and a CCD camera to acquire live images of slides. The scope and laser were controlled via a dedicated computer running Leica LMD software (v.6.6.2.3552).  (RNA Isolation and RNA Integrity)  Microdissected tissue was collected directly into RLT buffer from the RNeasy Micro PLUS kit (Qiagen Inc., Valencia, CA) with 1:100 beta-mercaptoethanol diluation, per manufacturer’s instructions. Samples were volume-adjusted with water to 75μl, vortexed, centrifuged, and frozen at -80°C. RNA samples, after following the manufacturer’s directions, were eluted in 14μl, and 1μl was run on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) using the Pico assay. Due to low sample volume and incompatibility of the eluent with the Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE), samples were quantitated using the Bioanalyzer concentration output. This was done by running a 1ng/μl RNA standard on the same Pico chip and then dividing the sample concentration output by the output of the standard concentration. The average RNA Integrity Number (RIN) of all passed samples was 7.1. Samples were failed when the Bioanalyzer traces showed degraded 18S and 28S bands, with RINs typically lower than 4.5 failing.
In most cases, 5ng of total RNA was used as the input amount for the library prep.  5ng total RNA was used as input into CloneTech SMARTer Ultra Low Input RNA Kit for Illumina Sequencing-HV (# 634820). 12 PCR cycles were used for amplification as suggested in the manufacturer’s instructions (ClonTech SMARTer Kit Manual 120213). The Modified Nextera DNA sample preparation was used after step V.B of the CloneTech SMARTer kit, instead of Covaris shearing and instead of step VI in the CloneTech SMARTer kit. RNA Sequencing was done on Illumina HiSeq 2000, producing approximately 30M 50bp paired-end clusters per sample. In most cases, 5 samples per lane were run.  RNA-Seq libraries were assessed for quality by yield and visual inspection of the presence, quality, and size of cDNA product on a Bioanalyzer.  Initially, 11 samples failed (7 for no product and 4 for majority of product <500bp) the quality control criteria.  However, upon a second attempt at synthesis, all 275 samples passed.  One of the 275 samples was failed for low inter-array-correlation (IAC) and was excluded from the data set.  The average concentration of samples that passed the criteria was 1582 pM.

tag: study

value: cancer stem cell clusters

tag: structure acronym

tag: rin

tag: gene-level raw fpkm profile  file_download_link


title: CSCC_CThbv-TGFBR2_W19-1-1-B.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
304357567


title: CSCC_CThbv-TGFBR2_W1-1-2-E.1.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
304950324


title: CSCC_CThbv-TGFBR2_W16-1-1-F.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
303748336


title: CSCC_CThbv-POSTN_W3-1-1-C.2.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
304357597

value: CThbv-POSTN


title: CSCC_CThbv-POSTN_W40-1-1-J.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
305272992


title: CSCC_CThbv-POSTN_W53-1-1-E.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
306124416


title: CSCC_CThbv-POSTN_W29-1-1-B.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
304950336


title: CSCC_CThbv-POSTN_W9-1-1-C.2.04

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
306124448


title: CSCC_CThbv-POSTN_W13-1-1-A.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
305405290


title: CSCC_CThbv-POSTN_W10-1-1-E.2.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene POSTN
306124454


title: CSCC_CThbv-ITGA6_W33-1-1-F.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene ITGA6
305952570


title: CSCC_CThbv-DANCR_W33-1-1-L.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene DANCR
304477583

value: CThbv-DANCR


title: CSCC_CThbv-CD44_W38-1-1-I.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene CD44
306124462


title: CSCC_CThbv-IGFBP2_W43-1-1-I.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene IGFBP2
305405302


title: CSCC_CT-DANCR_W54-1-1-C.03

description:
Cellular Tumor sampled by high expression of gene DANCR
304950411

value: CT-DANCR


title: CSCC_CThbv-ITGA6_W38-1-1-I.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene ITGA6
306124484


title: CSCC_CThbv-IGFBP2_W13-1-1-A.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene IGFBP2
305461084


title: CSCC_CThbv-TGFBR2_W6-1-1-C.2.06

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene TGFBR2
305461068


title: CSCC_CT-control-TNFAIP3_W39-1-1-O.03

description:
Cellular Tumor sampled by low expression of gene TNFAIP3
304703655


title: CSCC_CT-control-TNFAIP3_W4-1-1-C.2.03

description:
Cellular Tumor sampled by low expression of gene TNFAIP3
304357599


title: CSCC_CT-DANCR_W42-1-1-G.03

description:
Cellular Tumor sampled by high expression of gene DANCR
304703661


title: CSCC_CT-control-TNFAIP3_W3-1-1-B.2.03

description:
Cellular Tumor sampled by low expression of gene TNFAIP3
306124486


title: CSCC_CThbv-HIF1A_W54-1-1-F.03

description:
Hyperplastic blood vessels in cellular tumor sampled by high expression of gene HIF1A
305461074


title: CSCC_CT-control-TGFBR2_W22-1-1-F.03

description:
Cellular Tumor sampled by low expression of gene TGFBR2
304950300


title: CSCC_CT-control-TGFBR2_W9-1-1-I.2.03

description:
Cellular Tumor sampled by low expression of gene TGFBR2
303748330


title: CSCC_CT-control-TNFAIP3_W36-1-1-E.03

description:
Cellular Tumor sampled by low expression of gene TNFAIP3
303748342


title: CSCC_CT-control-TNFAIP3_W11-1-1-E.2.03

description:
Cellular Tumor sampled by low expression of gene TNFAIP3
303748264


title: CSCC_CT-control-TGFBR2_W19-1-1-B.03

description:
Cellular Tumor sampled by low expression of gene TGFBR2
304357565


title: CSCC_CT-control-PROM1-TNFAIP3-POSTN_W10-1-1-E.2.03

description:
Cellular Tumor sampled by low expression of genes PROM1, TNFAIP3 and POSTN
306124452


title: CSCC_CT-control-PROM1-POSTN_W9-1-1-C.2.04

description:
Cellular Tumor sampled by low expression of genes PROM1 and POSTN
306124422


title: CSCC_CT-control-PROM1-HIF1A_W54-1-1-F.03

description:
Cellular Tumor sampled by low expression of genes PROM1 and HIF1A
305461070


title: CSCC_CT-control-POSTN-TGFBR2_W34-1-1-G.03

description:
Cellular Tumor sampled by low expression of genes POSTN and TGFBR2
305272792


title: CSCC_CT-control-POSTN-TGFBR2_W29-1-1-B.03

description:
Cellular Tumor sampled by low expression of genes POSTN and TGFBR2
304357589


title: CSCC_CT-control-POSTN-PI3_W43-1-1-J.03

description:
Cellular Tumor sampled by low expression of genes POSTN and PI3
304950261


title: CSCC_CT-control-POSTN_W53-1-1-E.03

description:
Cellular Tumor sampled by low expression of gene POSTN
306124414

value: CT-control-POSTN


title: CSCC_CT-control-PI3-TGFBR2_W6-1-1-C.2.06

description:
Cellular Tumor sampled by low expression of genes PI3 and TGFBR2
305273040


title: CSCC_CT-control-POSTN_W20-2-1-L.03

description:
Cellular Tumor sampled by low expression of gene POSTN
304950405


title: CSCC_CT-control-PI3-NOS2-TNFAIP3_W34-1-1-D.03

description:
Cellular Tumor sampled by low expression of genes PI3, NOS2 and TNFAIP3
305273032


title: CSCC_CT-control-POSTN-IGFBP2_W13-1-1-A.03

description:
Cellular Tumor sampled by low expression of genes POSTN and IGFBP2
305461082


title: CSCC_CT-control-PI3-ID2_W12-1-1-D.2.05

description:
Cellular Tumor sampled by low expression of genes PI3 and ID2
304950249


title: CSCC_CT-control-POSTN_W3-1-1-C.2.03

description:
Cellular Tumor sampled by low expression of gene POSTN
304357595


title: CSCC_CT-control-PI3-IGFBP2_W10-1-1-I.2.03

description:
Cellular Tumor sampled by low expression of genes PI3 and IGFBP2
305461107


title: CSCC_CT-control-PROM1_W29-1-1-F.03

description:
Cellular Tumor sampled by low expression of gene PROM1
304477577


title: CSCC_CT-control-PDPN_W40-1-1-I.03

description:
Cellular Tumor sampled by low expression of gene PDPN
304357561

value: CT-control-PDPN


title: CSCC_CT-control-PI3_W4-1-1-A.1.03

description:
Cellular Tumor sampled by low expression of gene PI3
305952554


title: CSCC_CT-control-PDPN-TGFBR2_W1-1-2-E.1.03

description:
Cellular Tumor sampled by low expression of genes PDPN and TGFBR2
304950326


title: CSCC_CT-control-PI3_W21-1-1-B.06

description:
Cellular Tumor sampled by low expression of gene PI3
305461103


title: CSCC_CT-control-PDPN-HIF1A_W27-2-1-I.03

description:
Cellular Tumor sampled by low expression of genes PDPN and HIF1A
304950380


title: CSCC_CT-control-PDPN_W2-1-1-K.2.03

description:
Cellular Tumor sampled by low expression of gene PDPN
304357591


title: CSCC_CT-control-PDPN-PI3_W22-2-1-A.03

description:
Cellular Tumor sampled by low expression of genes PDPN and PI3
305461076


title: CSCC_CT-control-NOS2_W53-1-1-C.03

description:
Cellular Tumor sampled by low expression of gene NOS2
305405304


title: CSCC_CT-control-TGFBR2_W16-1-1-F.03

description:
Cellular Tumor sampled by low expression of gene TGFBR2
303748334


title: CSCC_CT-control-PI3_W16-1-1-B.03

description:
Cellular Tumor sampled by low expression of gene PI3
304357512


title: CSCC_CT-control-PDGFRA_W20-2-1-H.03

description:
Cellular Tumor sampled by low expression of gene PDGFRA
304950370

value: CT-control-PDGFRA


title: CSCC_CT-control-PROM1_W20-2-1-I.03

description:
Cellular Tumor sampled by low expression of gene PROM1
304950374


title: CSCC_CT-control-MYC_W27-2-1-D.03

description:
Cellular Tumor sampled by low expression of gene MYC
305272988

value: CT-control-MYC


title: CSCC_CT-control-IGFBP2-CD44-TGFBR2_W31-1-1-E.03

description:
Cellular Tumor sampled by low expression of genes IGFBP2, CD44 and TGFBR2
305273000


title: CSCC_CT-control-MET-ID2_W53-1-1-B.03

description:
Cellular Tumor sampled by low expression of genes MET and ID2
304357518


title: CSCC_CT-control-IGFBP2_W21-1-1-E.03

description:
Cellular Tumor sampled by low expression of gene IGFBP2
303748338


title: CSCC_CT-control-ITGA6_W16-1-1-D.03

description:
Cellular Tumor sampled by low expression of gene ITGA6
304357603


title: CSCC_CT-control-MET-TGFBR2_W53-1-1-A.03

description:
Cellular Tumor sampled by low expression of genes MET and TGFBR2
304703663


title: CSCC_CT-control-PI3-MYC_W22-1-1-H.03

description:
Cellular Tumor sampled by low expression of genes PI3 and MYC
305272994


title: CSCC_CT-control-PDPN_W3-1-1-E.1.04

description:
Cellular Tumor sampled by low expression of gene PDPN
306124418


title: CSCC_CT-control-ID1-POSTN_W40-1-1-J.03

description:
Cellular Tumor sampled by low expression of genes ID1 and POSTN
305272798


title: CSCC_CT-control-ID1-TGFBR2_W48-1-1-M.03

description:
Cellular Tumor sampled by low expression of genes ID1 and TGFBR2
306124488


title: CSCC_CT-control-ID2_W32-1-1-E.04

description:
Cellular Tumor sampled by low expression of gene ID2
306124511


title: CSCC_CT-control-PDPN-PI3_W42-1-1-J.03

description:
Cellular Tumor sampled by low expression of genes PDPN and PI3
305272986


title: CSCC_CT-control-ID1-PDPN_W7-1-1-A.2.03

description:
Cellular Tumor sampled by low expression of genes ID1 and PDPN
305461119


title: CSCC_CT-control-HIF1A_W28-1-1-N.03

description:
Cellular Tumor sampled by low expression of gene HIF1A
306124406


title: CSCC_CT-control-DANCR-IGFBP2_W43-1-1-I.03

description:
Cellular Tumor sampled by low expression of genes DANCR and IGFBP2
305405298


title: CSCC_CT-control-ID1_W28-1-1-A.03

description:
Cellular Tumor sampled by low expression of gene ID1
304477573


title: CSCC_CT-control-DANCR_W42-1-1-G.03

description:
Cellular Tumor sampled by low expression of gene DANCR
305461115

value: CT-control-DANCR


title: CSCC_CT-CD44_W4-1-1-B.1.03

description:
Cellular Tumor sampled by high expression of gene CD44
305952560


title: CSCC_CT-control-CD44-MYC_W29-1-1-G.03

description:
Cellular Tumor sampled by low expression of genes CD44 and MYC
305405292


title: CSCC_CT-control-ID2_W8-1-1-A.1.03

description:
Cellular Tumor sampled by low expression of gene ID2
303748260


title: CSCC_CT-control-CD44-PROM1-ITGA6_W38-1-1-I.03

description:
Cellular Tumor sampled by low expression of genes CD44, PROM1 and ITGA6
306124460


title: CSCC_CT-control-DANCR_W54-1-1-C.03

description:
Cellular Tumor sampled by low expression of gene DANCR
304950409


title: ASTR_LE-reference-histology_W8-1-1-H.1.01

description:
Leading Edge sampled by reference histology
302264004

value: anatomic structures

value: LE-reference-histology


title: CSCC_CT-control-CD44_W4-1-1-B.1.03

description:
Cellular Tumor sampled by low expression of gene CD44
305952558


title: ASTR_LE-reference-histology_W55-1-1-E.03

description:
Leading Edge sampled by reference histology
303748317


title: ASTR_LE-reference-histology_W55-1-1-D.03

description:
Leading Edge sampled by reference histology
303748311


title: ASTR_LE-reference-histology_W9-1-1-D.1.01

description:
Leading Edge sampled by reference histology
302262284


title: ASTR_LE-reference-histology_W55-1-1-C.03

description:
Leading Edge sampled by reference histology
303748307


title: ASTR_LE-reference-histology_W8-1-1-F.1.01

description:
Leading Edge sampled by reference histology
301626601


title: ASTR_LE-reference-histology_W5-1-1-K.2.06

description:
Leading Edge sampled by reference histology
300629407


title: CSCC_CT-control-ID1-ITGA6_W33-1-1-F.03

description:
Cellular Tumor sampled by low expression of genes ID1 and ITGA6
305952566


title: ASTR_LE-reference-histology_W1-1-2-N.1.01

description:
Leading Edge sampled by reference histology
300629386


title: ASTR_LE-reference-histology_W1-1-2-H.2.01

description:
Leading Edge sampled by reference histology
300173638


title: ASTR_LE-reference-histology_W31-1-1-A.01

description:
Leading Edge sampled by reference histology
301626695


title: ASTR_LE-reference-histology_W31-1-1-G.03

description:
Leading Edge sampled by reference histology
301287706


title: ASTR_LE-reference-histology_W2-1-1-F.1.01

description:
Leading Edge sampled by reference histology
300629352


title: CSCC_CT-CD44_W31-1-1-E.03

description:
Cellular Tumor sampled by high expression of gene CD44
305273026


title: CSCC_CT-control-DANCR_W33-1-1-L.03

description:
Cellular Tumor sampled by low expression of gene DANCR
304477581


title: ASTR_LE-reference-histology_W8-1-1-G.2.01

description:
Leading Edge sampled by reference histology
302263996


title: ASTR_LE-reference-histology_W11-1-1-B.1.01

description:
Leading Edge sampled by reference histology
301287609


title: ASTR_IT-reference-histology_W9-1-1-D.1.01

description:
Infiltrating Tumor sampled by reference histology
301287584

value: IT-reference-histology


title: ASTR_LE-reference-histology_W11-1-1-F.1.01

description:
Leading Edge sampled by reference histology
301287640


title: ASTR_IT-reference-histology_W9-1-1-C.2.03 #1

description:
Infiltrating Tumor sampled by reference histology
301287599


title: ASTR_LE-reference-histology_W5-1-1-K.1.01

description:
Leading Edge sampled by reference histology
300629399


title: ASTR_IT-reference-histology_W9-1-1-C.2.03 #2

description:
Infiltrating Tumor sampled by reference histology
301287601


title: ASTR_IT-reference-histology_W8-1-1-G.1.01

description:
Infiltrating Tumor sampled by reference histology
301626609


title: ASTR_IT-reference-histology_W55-1-1-F.03

description:
Infiltrating Tumor sampled by reference histology
303748195


title: ASTR_LE-reference-histology_W31-1-1-H.06

description:
Leading Edge sampled by reference histology
301287730


title: ASTR_IT-reference-histology_W8-1-1-G.2.01

description:
Infiltrating Tumor sampled by reference histology
302263998


title: ASTR_LE-reference-histology_W2-1-1-N.1.01

description:
Leading Edge sampled by reference histology
300629372


title: ASTR_IT-reference-histology_W8-1-1-F.1.01

description:
Infiltrating Tumor sampled by reference histology
301626603


title: ASTR_IT-reference-histology_W55-1-1-E.03

description:
Infiltrating Tumor sampled by reference histology
303748315


title: ASTR_IT-reference-histology_W5-1-1-K.1.01

description:
Infiltrating Tumor sampled by reference histology
300629401


title: ASTR_IT-reference-histology_W55-1-1-C.03

description:
Infiltrating Tumor sampled by reference histology
303748305


title: ASTR_IT-reference-histology_W31-1-1-H.06

description:
Infiltrating Tumor sampled by reference histology
301287728


title: ASTR_IT-reference-histology_W5-1-1-K.2.06

description:
Infiltrating Tumor sampled by reference histology
300629409


title: ASTR_IT-reference-histology_W5-1-1-O.1.03

description:
Infiltrating Tumor sampled by reference histology
300629430


title: ASTR_LE-reference-histology_W1-1-2-D.2.01

description:
Leading Edge sampled by reference histology
300629325


title: ASTR_IT-reference-histology_W31-1-1-J.01

description:
Infiltrating Tumor sampled by reference histology
301287734


title: ASTR_IT-reference-histology_W31-1-1-G.03

description:
Infiltrating Tumor sampled by reference histology
301287704


title: ASTR_IT-reference-histology_W2-1-1-N.2.01

description:
Infiltrating Tumor sampled by reference histology
300629382


title: ASTR_IT-reference-histology_W2-1-1-N.1.01

description:
Infiltrating Tumor sampled by reference histology
300629374


title: ASTR_IT-reference-histology_W1-1-2-H.2.01

description:
Infiltrating Tumor sampled by reference histology
300173640


title: ASTR_IT-reference-histology_W2-1-1-M.2.01

description:
Infiltrating Tumor sampled by reference histology
300629356


title: ASTR_IT-reference-histology_W11-1-1-F.1.01

description:
Infiltrating Tumor sampled by reference histology
301287638


title: ASTR_IT-reference-histology_W1-1-2-V.1.01

description:
Infiltrating Tumor sampled by reference histology
300629323


title: ASTR_IT-reference-histology_W11-1-1-B.1.01

description:
Infiltrating Tumor sampled by reference histology
301287607


title: ASTR_IT-reference-histology_W9-1-1-B.2.01

description:
Infiltrating Tumor sampled by reference histology
301287572


title: ASTR_CT-reference-histology_W9-1-1-D.1.01

description:
Cellular Tumor sampled by reference histology
301287582

value: CT-reference-histology


title: ASTR_CT-reference-histology_W8-1-1-H.1.01

description:
Cellular Tumor sampled by reference histology
302264000


title: ASTR_CT-reference-histology_W8-1-1-F.1.01

description:
Cellular Tumor sampled by reference histology
301626597


title: ASTR_CT-reference-histology_W8-1-1-G.1.01

description:
Cellular Tumor sampled by reference histology
301626605


title: ASTR_CT-reference-histology_W9-1-1-K.2.01

description:
Cellular Tumor sampled by reference histology
302262300


title: ASTR_CT-reference-histology_W9-1-1-B.2.01

description:
Cellular Tumor sampled by reference histology
301287570


title: ASTR_CT-reference-histology_W55-1-1-G.03

description:
Cellular Tumor sampled by reference histology
303748328


title: ASTR_CT-reference-histology_W5-1-1-K.2.06

description:
Cellular Tumor sampled by reference histology
300629403


title: ASTR_CT-reference-histology_W55-1-1-D.03

description:
Cellular Tumor sampled by reference histology
303748309


title: ASTR_CT-reference-histology_W55-1-1-C.03

description:
Cellular Tumor sampled by reference histology
303748303


title: ASTR_CT-reference-histology_W5-1-1-O.2.03

description:
Cellular Tumor sampled by reference histology
300629432


title: ASTR_CT-reference-histology_W32-1-1-E.03

description:
Cellular Tumor sampled by reference histology
304357555


title: ASTR_CT-reference-histology_W5-1-1-N.2.01

description:
Cellular Tumor sampled by reference histology
300629424


title: ASTR_IT-reference-histology_W1-1-2-N.1.01

description:
Infiltrating Tumor sampled by reference histology
300173644


title: ASTR_CT-reference-histology_W31-1-1-H.06

description:
Cellular Tumor sampled by reference histology
301287708


title: ASTR_CT-reference-histology_W26-1-1-I.03

description:
Cellular Tumor sampled by reference histology
301626689


title: ASTR_CT-reference-histology_W31-1-1-F.03

description:
Cellular Tumor sampled by reference histology
301287698


title: ASTR_CT-reference-histology_W31-1-1-A.01

description:
Cellular Tumor sampled by reference histology
301626693


title: ASTR_CT-reference-histology_W32-1-1-B.01

description:
Cellular Tumor sampled by reference histology
304950292


title: ASTR_CT-reference-histology_W26-1-1-E.03

description:
Cellular Tumor sampled by reference histology
301626681


title: ASTR_CT-reference-histology_W26-1-1-F.03

description:
Cellular Tumor sampled by reference histology
301626685


title: ASTR_CT-reference-histology_W2-1-1-D.1.01

description:
Cellular Tumor sampled by reference histology
300629344


title: ASTR_CT-reference-histology_W1-1-2-D.2.01

description:
Cellular Tumor sampled by reference histology
300173630


title: ASTR_CT-reference-histology_W1-1-2-Q.1.01

description:
Cellular Tumor sampled by reference histology
300629315


title: ASTR_CT-reference-histology_W1-1-2-H.2.01

description:
Cellular Tumor sampled by reference histology
300173636


title: ASTR_CT-reference-histology_W2-1-1-F.1.01

description:
Cellular Tumor sampled by reference histology
300629350


title: ASTR_CT-reference-histology_W11-1-1-F.1.01

description:
Cellular Tumor sampled by reference histology
301287636


title: ASTR_CT-reference-histology_W11-1-1-D.1.01

description:
Cellular Tumor sampled by reference histology
301287630


title: ASTR_CTpan-reference-histology_W9-1-1-K.2.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301287740

value: CTpan-reference-histology


title: ASTR_CT-reference-histology_W32-1-1-A.01

description:
Cellular Tumor sampled by reference histology
304950286


title: ASTR_CTpan-reference-histology_W9-1-1-H.2.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
302262292


title: ASTR_CTpan-reference-histology_W9-1-1-J.2.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
302262298


title: ASTR_CTpan-reference-histology_W5-1-1-K.2.06

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629405


title: ASTR_CTpan-reference-histology_W32-1-1-E.03

description:
Pseudopalisading cells around necrosis sampled by reference histology
304357557


title: ASTR_CTpan-reference-histology_W8-1-1-F.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301626599


title: ASTR_CTpan-reference-histology_W8-1-1-H.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
302264002


title: ASTR_CT-reference-histology_W11-1-1-C.1.01

description:
Cellular Tumor sampled by reference histology
301287613


title: ASTR_CTpan-reference-histology_W32-1-1-B.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
304950294


title: ASTR_CTpan-reference-histology_W8-1-1-G.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301626607


title: ASTR_CT-reference-histology_W2-1-1-N.1.01

description:
Cellular Tumor sampled by reference histology
300629358


title: ASTR_CTpan-reference-histology_W26-1-1-F.03

description:
Pseudopalisading cells around necrosis sampled by reference histology
301626687


title: ASTR_CTpan-reference-histology_W26-1-1-E.03

description:
Pseudopalisading cells around necrosis sampled by reference histology
301626683


title: ASTR_CTpan-reference-histology_W26-1-1-I.03

description:
Pseudopalisading cells around necrosis sampled by reference histology
301626595


title: ASTR_CTpan-reference-histology_W2-1-1-F.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629370


title: ASTR_CTpan-reference-histology_W32-1-1-A.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
304950288


title: ASTR_CTpan-reference-histology_W1-1-2-V.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629321


title: ASTR_CTpan-reference-histology_W2-1-1-D.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629346


title: ASTR_CTpan-reference-histology_W1-1-2-H.2.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300173642


title: ASTR_CTpan-reference-histology_W1-1-2-Q.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629317


title: ASTR_CTpan-reference-histology_W2-1-1-N.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629360


title: ASTR_CTpan-reference-histology_W11-1-1-B.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301287611


title: ASTR_CTpan-reference-histology_W11-1-1-D.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301287634


title: ASTR_CTpan-reference-histology_W11-1-1-C.1.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
301287615


title: ASTR_CTmvp-reference-histology_W9-1-1-K.2.01

description:
Microvascular proliferation sampled by reference histology
301287738

value: CTmvp-reference-histology


title: ASTR_CTmvp-reference-histology_W9-1-1-J.2.01

description:
Microvascular proliferation sampled by reference histology
303748201


title: ASTR_CTpan-reference-histology_W5-1-1-O.2.03

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629434


title: ASTR_CTmvp-reference-histology_W8-1-1-H.1.01

description:
Microvascular proliferation sampled by reference histology
302264006


title: ASTR_CTpan-reference-histology_W5-1-1-N.2.01

description:
Pseudopalisading cells around necrosis sampled by reference histology
300629426


title: ASTR_CTmvp-reference-histology_W55-1-1-G.03

description:
Microvascular proliferation sampled by reference histology
303748199


title: ASTR_CTmvp-reference-histology_W55-1-1-F.03

description:
Microvascular proliferation sampled by reference histology
302264010


title: ASTR_CTmvp-reference-histology_W5-1-1-K.1.01

description:
Microvascular proliferation sampled by reference histology
301287568


title: ASTR_CTmvp-reference-histology_W5-1-1-K.2.06

description:
Microvascular proliferation sampled by reference histology
300629422


title: ASTR_CTmvp-reference-histology_W31-1-1-F.03

description:
Microvascular proliferation sampled by reference histology
301287700


title: ASTR_CTmvp-reference-histology_W9-1-1-H.2.01

description:
Microvascular proliferation sampled by reference histology
302262290


title: ASTR_CTmvp-reference-histology_W32-1-1-E.03

description:
Microvascular proliferation sampled by reference histology
304357559


title: ASTR_CTmvp-reference-histology_W31-1-1-J.01

description:
Microvascular proliferation sampled by reference histology
301287736


title: ASTR_CTmvp-reference-histology_W31-1-1-A.01

description:
Microvascular proliferation sampled by reference histology
301287692


title: ASTR_CTmvp-reference-histology_W32-1-1-A.01

description:
Microvascular proliferation sampled by reference histology
304950290


title: ASTR_CTmvp-reference-histology_W2-1-1-N.1.01

description:
Microvascular proliferation sampled by reference histology
300629376


title: ASTR_CTmvp-reference-histology_W2-1-1-N.2.01

description:
Microvascular proliferation sampled by reference histology
300629384


title: ASTR_CTmvp-reference-histology_W5-1-1-O.2.03

description:
Microvascular proliferation sampled by reference histology
300629436


title: ASTR_CTmvp-reference-histology_W2-1-1-D.1.01

description:
Microvascular proliferation sampled by reference histology
300629348


title: ASTR_CTmvp-reference-histology_W32-1-1-B.01

description:
Microvascular proliferation sampled by reference histology
304950296


title: ASTR_CTmvp-reference-histology_W11-1-1-M.1.01

description:
Microvascular proliferation sampled by reference histology
301626679


title: ASTR_CTmvp-reference-histology_W1-1-2-N.1.01

description:
Microvascular proliferation sampled by reference histology
300173646


title: ASTR_CTmvp-reference-histology_W1-1-2-H.2.01

description:
Microvascular proliferation sampled by reference histology
300629309


title: ASTR_CTmvp-reference-histology_W11-1-1-G.2.01

description:
Microvascular proliferation sampled by reference histology
301287644


title: ASTR_CTmvp-reference-histology_W1-1-2-D.2.01

description:
Microvascular proliferation sampled by reference histology
300173634


title: ASTR_CTmvp-reference-histology_W11-1-1-D.1.01

description:
Microvascular proliferation sampled by reference histology
301287632


title: ASTR_CTmvp-reference-histology_W55-1-1-E.03

description:
Microvascular proliferation sampled by reference histology
302264008


title: normal pulp tissue C8(CONTROL 4)

type: RNA

city: Guangzhou

first: Xin

last: Huang

address: No.9 Jinsui Road

country: China

institute: Guangzhou Women and Children’s Medical Center

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. The hybridized arrays were washed, fixed and scanned.

scan_protocol: The arrays were scanned with using the Agilent DNA Microarray Scanner. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 7 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: normal, non-pulpitis

label_protocol: each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: All samples were immediately placed in liquid nitrogen and subsequently frozen at -80℃.

extract_protocol: TRIzol Reagent was used to extract total RNA from the normal and inflamed pulp tissue samples.mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

tag: tissue

value: normal pulp tissue from healty teeth

tag: age

value: 24 years


title: normal pulp tissue C2(CONTROL 1)

value: 25 years


title: normal pulp tissue C3(CONTROL 2)


title: normal pulp tissue C9(CONTROL 5)


title: inflamed pulp tissue 15(TEST 2)

source_name: pulpitis

value: inflamed pulp tissue from the teeth of pulpitis

value: 27 years


title: normal pulp tissue C5(CONTROL 3)

value: 22 years


title: inflamed pulp tissue 20(TEST 4)


title: inflamed pulp tissue 13(TEST 1)

value: 26 years


title: Lymph node, Control rat C9

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

description: Gene expression data from lymph

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.  Washed and stained with phycoerytrin conjugated streptavidin using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned in the Affymetrix GeneArray 3000 7G scanner. Cell intensity files were generated in the GeneChip Command Console Software (AGCC; Affymetrix).

data_processing: Raw .CEL files were pre-processed by quantile normalization, and gene summaries were extracted via robust multi-array average (RMA) in Affymetrix Expression Console v.1.4.46.

label: biotin

organism: Rattus norvegicus

source_name: Right popliteal lymph node, control knee

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

extract_protocol: A 5 mm stainless steel bead was placed together with tissue (max 30 mg/tube) in 2 ml of RTL buffer (Qiagen) with 1% β-mercaptoethanol and homogenized twice for 2 min at 25 Hz. RNA was purified using the RNeasy® Mini Kit (Qiagen) and eluted in 20 µl RNase-free water.

treatment_protocol: Intra-articular knee tissue and popliteal lymph nodes were stored in RNAlater until tissue homogenization. Maximum 4 weeks from tissue collection to RNA purification

value: lymph node


title: Lymph node, Control rat C7

description: Gene expression data from lymph


title: Knee tissue, Control rat C7

description: Gene expression data from synovial tissue

source_name: Synovial tissue, right knee, control knee

value: synovial tissue


title: Knee tissue, Control rat C5


title: Knee tissue, Control rat C3


title: Knee tissue, Control rat C2


title: Lymph node, Control rat C8

description: Gene expression data from lymph


title: inflamed pulp tissue 21(TEST 5)


title: inflamed pulp tissue 18(TEST 3)

value: 29 years


title: Knee tissue, Control rat C6


title: Knee tissue, Control rat C1


title: Knee tissue, Control rat C9


title: Lymph node, Control rat C3

description: Gene expression data from lymph


title: Lymph node, Control rat C5

description: Gene expression data from lymph


title: inflamed pulp tissue 9(TEST 7)


title: inflamed pulp tissue 23(TEST 6)


title: Lymph node, Control rat C6

description: Gene expression data from lymph


title: Lymph node, Control rat C4

description: Gene expression data from lymph


title: Lymph node, Control rat C1

description: Gene expression data from lymph


title: Injured knee, Knee tissue, rat K9

source_name: Synovial tissue, left injured knee


title: Injured knee, Knee tissue, rat K6


title: Injured knee, Knee tissue, rat K2


title: Injured knee, Knee tissue, rat K8


title: Lymph node, Control rat C2

description: Gene expression data from lymph


title: Contralateral knee, Knee tissue, rat K10

source_name: Synovial tissue, right knee, contralateral knee


title: Injured knee, Knee tissue, rat K5


title: Injured knee, Knee tissue, rat K11


title: Contralateral knee, Knee tissue, rat K7


title: Contralateral knee, Knee tissue, rat K8


title: Contralateral knee, Knee tissue, rat K11


title: Contralateral knee, Knee tissue, rat K5


title: Injured knee, Knee tissue, rat K10


title: Contralateral knee, Knee tissue, rat K9


title: Injured knee, Knee tissue, rat K1


title: Contralateral knee, Knee tissue, rat K6


title: Injured knee, Knee tissue, rat K4


title: Injured knee, Knee tissue, rat K3


title: Contralateral knee, Knee tissue, rat K3


title: Injured knee, Knee tissue, rat K7


title: Contralateral knee, Knee tissue, rat K4


title: Blood-1.50Gy_6hr_rep5

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Leukocytes treated with 1.50 Gy radiation, measured 6 hr post-exposure.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45oC to Affymetrix® GeneChip® PrimeViewTM Human arrays (GEO platform GPL15207) according to the GeneChip® 3' array Hybridization User Manual from Affymetrix®. The arrays were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix) and the GeneChip® Command Console® software version 4.0 (Affymetrix®).

data_processing: All data analysis was performed in R using bioconductor packages.  CEL files were preprocessed and normalized using robust multichip averaging (RMA).  Differential expression was performed using Limma.

source_name: blood, isolated leukocytes, 1.50 Gy radiation, 6 hr post-exposure

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix® 3' IVT Express Reagent Kit (Affymetrix® Inc., Santa Clara, CA) from 100 ng total RNA.

growth_protocol: Whole blood was drawn from ten (10) volunteers in 2-ml green topped vacutainer tubes containing 30 USP units of sodium heparain.  Blood samples were then subsequently stored at 37oC in an Engel MHD13F-DM portable incubator (Engel USA, Jupiter, FL).

extract_protocol: At the end of the incubation period, blood samples were transferred to 50ml conical tubes containing 30ml of NH4Cl red blood cell (RBC) lysis buffer (1:15 v/v dilution), pre-warmed at 37oC in order to isolate leukocytes.  The tubes were agitated 5 minutes on a rocker platform and centrifuged for 5 minutes at 1,500 RPM at room temperature.  Cells were suspended in 10 ml of phosphate-buffered saline (PBS) and centrifuged again twice for 5 minutes at 1,500 RPM.  White blood cells (WBC) were suspended in 2 ml PBS, equivalent to the initial volume of the whole blood.  WBC were centrifuged 5 min at 1,500 RPM.  Supernatant was discarded and cell pellets were suspended in 600µl RLT lysis buffer (Qiagen, Venlo, The Netherlands) and tubes were vortexed vigorously and stored at -70oC until RNA purification. Purification of total RNA was performed using the RNAeasy Mini Kit (Qiagen).  Optional on-column DNase digestion was performed to eliminate genomic DNA contamination.  Total RNA was eluted in 50 µl of RNase-free water. The quantity analysis of the total RNA was performed with a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE).  The quality of the total RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, Santa Clara, CA).

treatment_protocol: Whole blood samples were radiated at the Kentucky Lion Eye Center using a Gammacell 1000 Elite (Cs-137) (Best Theratronics Ltd., Ottawa, Canada) for 0 seconds (control), 1.5 seconds (0.15 Gy exposure), 3 seconds (0.30 Gy exposure), or 16 seconds (1.5 Gy exposure).  Vacutainer tubes containing whole blood were incubated at 37oC for either 1 hr, 2 hr, or 6 hr after being radiated.

tag: volunteer

value: blood

tag: radiation dose

tag: time

value: 6 hr

tag: cell type

value: isolated leukocytes


title: Blood-1.50Gy_6hr_rep2


title: Blood-1.50Gy_6hr_rep4


title: Contralateral knee, Knee tissue, rat K2


title: Contralateral knee, Knee tissue, rat K1


title: Injured knee, Lymph node, rat K11

description: Gene expression data from lymph

source_name: Left popliteal lymph node, injured knee


title: U937 cells transduced with pCDH-MSCV-puro lentivirus vector_methylation

type: genomic

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC BeadChip microarray using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human promyelocytic leukemia cell line_U937_empty_vector

label_protocol: Standard Illumina labelling protocol

growth_protocol: The human promyelocytic leukemia cells, U937 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 1× antibiotic-antimycotic (Gibco by Life Technologies) in a humidified chamber with 5% CO2 atmosphere at 37°C

extract_protocol: Total DNA was isolated by standard procedures

treatment_protocol: Cultured U937 cells were infected with lentivirus in the presence of 8 µg/ml polybrene (Sigma) and cultured for 72 hours. The infected cells were selected with 2 µg/mL puromycin for 2-weeks to obtain stable clones. DNMT3A WT/mutants expression was checked by immunoblot analysis and stable cells used for DNA extraction for methylation microarray analysis.

tag: cell line

value: Human promyelocytic leukemia cell line

value: Blood


title: Blood-1.50Gy_6hr_rep1


title: Injured knee, Lymph node, rat K10

description: Gene expression data from lymph


title: Blood-1.50Gy_2hr_rep10

description: Leukocytes treated with 1.50 Gy radiation, measured 2 hr post-exposure.

source_name: blood, isolated leukocytes, 1.50 Gy radiation, 2 hr post-exposure

value: 2 hr


title: Injured knee, Lymph node, rat K7

description: Gene expression data from lymph


title: Injured knee, Lymph node, rat K8

description: Gene expression data from lymph


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-R882H lentivirus vector_methylation

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A_R882H


title: Injured knee, Lymph node, rat K9

description: Gene expression data from lymph


title: Blood-1.50Gy_2hr_rep6


title: Blood-1.50Gy_2hr_rep5


title: Blood-1.50Gy_2hr_rep8


title: Blood-1.50Gy_2hr_rep2


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-WT lentivirus vector_methylation

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A_wildtype


title: Injured knee, Lymph node, rat K3

description: Gene expression data from lymph


title: Injured knee, Lymph node, rat K6

description: Gene expression data from lymph


title: Injured knee, Lymph node, rat K4

description: Gene expression data from lymph


title: Injured knee, Lymph node, rat K5

description: Gene expression data from lymph


title: Blood-1.50Gy_2hr_rep3


title: Blood-1.50Gy_2hr_rep7


title: Blood-1.50Gy_2hr_rep1


title: Blood-1.50Gy_1hr_rep10

description: Leukocytes treated with 1.50 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 1.50 Gy radiation, 1 hr post-exposure

value: 1 hr


title: Blood-1.50Gy_2hr_rep4


title: U937 cells transduced with pCDH-MSCV-puro-DNMT3A-R882C lentivirus vector_methylation

source_name: Human promyelocytic leukemia cell line_U937_DNMT3A_R882C


title: Injured knee, Lymph node, rat K2

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K9

description: Gene expression data from lymph

source_name: Right popliteal lymph node, contralateral knee


title: Blood-1.50Gy_1hr_rep8


title: Contralateral knee, Lymph node, rat K11

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K6

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K7

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K8

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K10

description: Gene expression data from lymph


title: Injured knee, Lymph node, rat K1

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K4

description: Gene expression data from lymph


title: Contralateral knee, Lymph node, rat K5

description: Gene expression data from lymph


title: Blood-1.50Gy_1hr_rep7


title: Blood-1.50Gy_1hr_rep1


title: Contralateral knee, Lymph node, rat K3

description: Gene expression data from lymph


title: Blood-1.50Gy_1hr_rep4


title: Blood-0.30Gy_6hr_rep4

description: Leukocytes treated with 0.30 Gy radiation, measured 6 hr post-exposure.

source_name: blood, isolated leukocytes, 0.30 Gy radiation, 6 hr post-exposure


title: Blood-1.50Gy_1hr_rep3


title: Contralateral knee, Lymph node, rat K2

description: Gene expression data from lymph


title: Blood-1.50Gy_1hr_rep5


title: Blood-1.50Gy_1hr_rep9


title: Blood-1.50Gy_1hr_rep2


title: Contralateral knee, Lymph node, rat K1

description: Gene expression data from lymph


title: Blood-0.30Gy_6hr_rep1


title: Blood-0.30Gy_6hr_rep2


title: Blood-1.50Gy_1hr_rep6


title: Blood-1.50Gy_6hr_rep3


title: Blood-0.30Gy_6hr_rep5


title: Blood-0.30Gy_2hr_rep10

description: Leukocytes treated with 0.30 Gy radiation, measured 2 hr post-exposure.

source_name: blood, isolated leukocytes, 0.30 Gy radiation, 2 hr post-exposure


title: Blood-0.30Gy_2hr_rep6


title: Blood-0.30Gy_1hr_rep9

description: Leukocytes treated with 0.30 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 0.30 Gy radiation, 1 hr post-exposure


title: Blood-0.30Gy_2hr_rep9


title: Blood-0.30Gy_2hr_rep7


title: Blood-0.30Gy_2hr_rep2


title: Blood-0.30Gy_2hr_rep5


title: Blood-0.30Gy_2hr_rep3


title: x14

city: New York

first: Thomas

middle: W

last: Battaglia

state: NY

address: 423 E 23rd Street

department: Medicine

institute: NYU School of Medicine

hyb_protocol: Hydridized according to the manufacturer's protocol. the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. Data Collection is carried out in the nCounter‘ Digital Analyzer. At the highest standard data resolution, 555_1155 fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format. (http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf)

data_processing: Probe set summarization and normalization was performed by Probe-level background correction using the R/Bioconductor package NanoStringNorm

label: Nanostring fluorescence oligonucleotide probe (3'-biotin)

organism: Mus musculus

source_name: Terminal Ileum

label_protocol: Labeled according to the manufacturer's protocol.  The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on the 3' end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to target and yet still be individually resolved and identified during data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

tag: genotype/variation

tag: treatment

value: STAT

tag: gender

value: Female


title: r22

value: CON


title: r21


title: r24


title: x02


title: x08


title: Blood-0.30Gy_1hr_rep10


title: Blood-1.50Gy_2hr_rep9


title: Blood-0.30Gy_2hr_rep1


title: Blood-0.30Gy_1hr_rep6


title: Blood-0.30Gy_1hr_rep4


title: Blood-0.30Gy_1hr_rep1


title: Blood-0.15Gy_6hr_rep5

description: Leukocytes treated with 0.15 Gy radiation, measured 6 hr post-exposure.

source_name: blood, isolated leukocytes, 0.15 Gy radiation, 6 hr post-exposure


title: Blood-0.30Gy_2hr_rep8


title: Blood-0.15Gy_6hr_rep4


title: n62


title: Blood-0.30Gy_1hr_rep2


title: Blood-0.30Gy_1hr_rep7


title: Blood-0.30Gy_1hr_rep5


title: Blood-0.30Gy_1hr_rep3


title: Blood-0.30Gy_1hr_rep8


title: Blood-0.30Gy_2hr_rep4


title: n58


title: n59


title: a69


title: a67


title: a64


title: Blood-0.15Gy_2hr_rep8

description: Leukocytes treated with 0.15 Gy radiation, measured 2 hr post-exposure.

source_name: blood, isolated leukocytes, 0.15 Gy radiation, 2 hr post-exposure


title: Blood-0.15Gy_2hr_rep10


title: Blood-0.15Gy_6hr_rep3


title: Blood-0.15Gy_6hr_rep1


title: Blood-0.15Gy_2hr_rep5


title: Blood-0.15Gy_6hr_rep2


title: Blood-0.15Gy_2hr_rep7


title: Blood-0.15Gy_2hr_rep6


title: Blood-0.15Gy_2hr_rep1


title: Blood-0.30Gy_6hr_rep3


title: Blood-0.15Gy-1hr-rep8

description: Leukocytes treated with 0.15 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 0.15 Gy radiation, 1 hr post-exposure


title: Blood-0.15Gy-1hr-rep9


title: Blood-0.15Gy-1hr-rep7


title: Blood-0.00Gy-6hr-rep4

description: Leukocytes treated with 0 Gy radiation, measured 6 hr post-exposure.

source_name: blood, isolated leukocytes, 0 Gy radiation, 6hr post-exposure

value: 0 Gy


title: Blood-0.15Gy_2hr_rep2


title: Blood-0.15Gy_2hr_rep9


title: Blood-0.15Gy_2hr_rep4


title: Blood-0.15Gy_2hr_rep3


title: Blood-0.15Gy-1hr-rep10


title: Blood-0.15Gy-1hr-rep2


title: Blood-0.15Gy-1hr-rep6


title: Blood-0.15Gy-1hr-rep3


title: Blood-0.15Gy-1hr-rep4


title: Blood-0.15Gy-1hr-rep5


title: Blood-0.15Gy-1hr-rep1


title: Blood-0.00Gy-6hr-rep2


title: Blood-0.00Gy-2hr-rep10

description: Leukocytes treated with 0 Gy radiation, measured 2 hr post-exposure.

source_name: blood, isolated leukocytes, 0 Gy radiation, 2hr post-exposure


title: Blood-0.00Gy-6hr-rep3


title: Blood-0.00Gy-2hr-rep6


title: Blood-0.00Gy-2hr-rep9


title: Blood-0.00Gy-2hr-rep3


title: Blood-0.00Gy-6hr-rep1


title: Blood-0.00Gy-2hr-rep5


title: Blood-0.00Gy-2hr-rep2


title: Blood-0.00Gy-2hr-rep1


title: Blood-0.00Gy-2hr-rep8


title: Blood-0.00Gy-2hr-rep4


title: Blood-0.00Gy-1hr-rep10

description: Leukocytes treated with 0 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 0 Gy radiation, 1hr post-exposure


title: Blood-0.00Gy-1hr-rep7


title: Blood-0.00Gy-2hr-rep7


title: Blood-0.00Gy-1hr-rep6


title: Blood-0.00Gy-1hr-rep3


title: U937_Pu27_72hr_rep2

description: Gene expression data with PU27 treatment at 72hr

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC to Affymetrix® GeneChip® PrimeViewTM Human arrays (GEO platform GPL15207) according to the GeneChip® 3' array Hybridization User Manual from Affymetrix®.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix) and the GeneChip® Command Console® software version 3.1 (Affymetrix®).

data_processing: All data analysis was performed in R using bioconductor packages.  CEL files were normalized using robust multichip averaging (RMA).  Differential expression was performed using Limma.

source_name: U937_Pu27 treatment_72hr

growth_protocol: U937 (Histiocytic Lymphoma) were obtained from American Type Culture Collection (ATCC, Manassas, VA). The cell lines were maintained in culture in RPMI-1640/10%FBS/penicillin-streptomycin (all from HyCloneTM, Thermo ScientificTM, Logan, Utah) at 37C/5%CO2 in humid atmosphere.

extract_protocol: At each time point cells were collected, spun down, the pellets were resuspended in 5ml TRIzol® reagent (Ambion®/Invitrogen, Thermo Fisher Scientific Inc.) and stored at -80oC until all the time points for 3 repeat experiments were collected. Total RNA extraction was performed following the instruction manual. RNA concentration was measured by NanoDrop (Thermo Scientific) at 260/280nm, then on Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) for RNA integrity.

treatment_protocol: U937 at exponential growth were cultured at 5x106cells/10ml in T25 flask in the presence of 10µM Pu27 (oligonucleotide sequence TGGGGAGGGTGGGGAGGGTGGGGAAGG), Pu5- (oligonucleotide TGGGGAGGGTGGGGAGGGTGGTGAGGGTGGGGAGGGGGAAGG) or Pu9- (oligonucleotide GGGTGGGGAGGGTGGGGAAG) compared to untreated. Three time points were evaluated 24, 48 and 72 h culture compared to the T0.

value: histiocytic lymphoma

tag: treated with

tag: time point


title: U937_Pu27_72hr_rep1


title: Blood-0.00Gy-6hr-rep5


title: Blood-0.00Gy-1hr-rep1


title: Res TGFB3 7d

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Gene expression data of induced chondrocyte derived from induced mesenchymal stromal cells (iMSCs)

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA16 algorithm.

source_name: resFOP-iMSCs

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: iMSCs were induced and maintained in a minimum essential medium alpha modification supplemented with 10% FBS, 5 ng/mL FGF2 and 0.5% penicillin and streptomycin

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: iMSCs were chondrogenic differentiated  for 6, 24 ,48 hours, or 7 days with 100 ng/mL Activin-A, 100 ng/mL BMP-7 or 10 ng/mL TGF-B3

value: induced chondrocyte


title: Blood-0.00Gy-1hr-rep5


title: Blood-0.00Gy-1hr-rep8


title: Blood-0.00Gy-1hr-rep4


title: U937_Pu27_48hr_rep1

description: Gene expression data with PU27 treatment at 48hr

source_name: U937_Pu27 treatment_48hr


title: Res TGFB3 48h


title: Blood-0.00Gy-1hr-rep9


title: U937_Pu27_48hr_rep2


title: Blood-0.00Gy-1hr-rep2


title: U937_Pu27_72hr_rep3


title: U937_Pu27_48hr_rep3


title: Res TGFB3 24h


title: Res TGFB3 6h


title: Res BMP7 24h


title: Res BMP7 7d


title: PDAC_Short survival_Sample 11

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX2948

hyb_protocol: Hybridization and staining to the HumanHT-12 v4 Expression BeadChip (Illumina, San Diego, CA) was performed using 750ng of Biotin-aRNA product following protocols outlined in Illumina’s Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: Scanning of the BeadChip was performed using the iScan Microarray Scanner (Illumina, San Diego, CA).

data_processing: Gene expression data were imported into Illumina’s Genome Studio. They were imported with cubic spline normalization. Quality control was performed in Genome Studio. The Partek Report Plug-in from Illumina’s Genome Studio was used to export the gene expression data for import into Partek’s Genomics Suite (version 6.15.1207).

label_protocol: Total RNA was amplified and labeled using the TargetAmp-Nano Labeling Kit (epicenter, Madison, WI) which enables amplification and target preparation compatible with the Direct Hybridization Assay (Illumina, San Diego, CA). Amplification was performed with 500ng of total RNA input following procedures described in the TargetAmp-Nano Labeling Kit user guide.

extract_protocol: Frozen pancreatic adenocarcinoma tissue specimens were stored at -80°C in RNAlater Stabilization Solution (Life Technolo¬gies, Carlsbad, CA) prior to homogenization in lysis buffer using the gentleMACS dissociator’s (Miltenyi Biotec Inc., Auburn, CA) “Homogenization of tissue for total RNA isolation” protocol. Total RNA was purified using the E.Z.N.A. Total RNA Kit I (Omega, Norcross, GA), quantified (Nanodrop 8000, Thermo Scientific), and stored at –80°C.

treatment_protocol: Patients undergoing pancreatic resection at William Beaumont Hospital (Royal Oak, MI) were consented prior to surgery with local IRB oversight. Samples were collected at time of surgery and stored at -80°C according to CAP (College of American Pathologist)-accredited standard operating procedures.

value: pancreatic ductal adenocarcinoma

tag: surival group

value: Short survival

tag: survival, months

value: < 10 months

tag: patient id


title: U937_Pu27_24hr_rep3

description: Gene expression data with PU27 treatment at 24hr

source_name: U937_Pu27 treatment_24hr


title: PDAC_Short survival_Sample 12

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX2980


title: Res ActA 6h


title: PDAC_Short survival_Sample 10

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX2898


title: U937_Pu9-_72hr_rep2

description: Gene expression data with PU9- treatment at 72hr

source_name: U937_Pu9- treatment_72hr


title: PDAC_Short survival_Sample 13

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX3310


title: Res BMP7 48h


title: Res (-) 7d


title: U937_Pu9-_48hr_rep3

description: Gene expression data with PU9- treatment at 48hr

source_name: U937_Pu9- treatment_48hr


title: U937_Pu9-_72hr_rep3


title: U937_Pu27_24hr_rep1


title: U937_Pu9-_48hr_rep2


title: Res ActA 7d


title: U937_Pu9-_72hr_rep1


title: Res BMP7 6h


title: Res ActA 48h


title: PDAC_Short survival_Sample 9

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX2066


title: PDAC_Short survival_Sample 7

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX1538


title: U937_Pu9-_48hr_rep1


title: U937_Pu9-_24hr_rep3

description: Gene expression data with PU9- treatment at 24hr

source_name: U937_Pu9- treatment_24hr


title: U937_Pu9-_24hr_rep2


title: Res ActA 24h


title: PDAC_Short survival_Sample 6

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX1249


title: Res (-) 6h


title: PDAC_Long-term survival_Sample 11

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX2057

value: Long-term survival

value: > 20 months


title: Res (-) 0h


title: PDAC_Short survival_Sample 3

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX0380


title: PDAC_Short survival_Sample 2

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX0349


title: FOP TGFB3 24h

source_name: FOP-iMSCs


title: FOP TGFB3 7d


title: PDAC_Short survival_Sample 1

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX0209


title: U937_Pu5-_72hr_rep3

description: Gene expression data with PU5- treatment at 72hr

source_name: U937_Pu5- treatment_72hr


title: U937_Pu5-_48hr_rep2

description: Gene expression data with PU5- treatment at 48hr

source_name: U937_Pu5- treatment_48hr


title: U937_Pu5-_24hr_rep2

description: Gene expression data with PU5- treatment at 24hr

source_name: U937_Pu5- treatment_24hr


title: PDAC_Short survival_Sample 5

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX0524


title: PDAC_Short survival_Sample 4

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX0513


title: U937_Pu5-_72hr_rep1


title: U937_Pu9-_24hr_rep1


title: FOP TGFB3 48h

description: Gene expression data of induced chondrocyte derived from induced mesenchymal stromal cells (iMSCs)


title: U937_Pu5-_72hr_rep2


title: U937_Pu5-_24hr_rep3


title: PDAC_Long-term survival_Sample 10

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1997


title: FOP TGFB3 6h


title: Res (-) 48h


title: Res (-) 24h


title: FOP BMP7 7d


title: U937_Pu5-_48hr_rep3


title: PDAC_Long-term survival_Sample 9

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1944


title: U937_Pu5-_48hr_rep1


title: U937_Pu5-_24hr_rep1


title: FOP BMP7 6h


title: PDAC_Long-term survival_Sample 6

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1411

value: > 37 months


title: PDAC_Long-term survival_Sample 8

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1801


title: PDAC_Long-term survival_Sample 7

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1581


title: FOP ActA 48h


title: PDAC_Long-term survival_Sample 5

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX1017


title: FOP ActA 7d


title: FOP BMP7 24h


title: FOP ActA 24h


title: FOP ActA 6h


title: U937_WildType_72hr_rep3

description: Gene expression data with no treatment at 72hr

source_name: U937_no treatment_72hr

value: none (untreated control)


title: U937_WildType_72hr_rep2


title: U937_WildType_24hr_rep3

description: Gene expression data with no treatment at 24hr

source_name: U937_no treatment_24hr


title: PDAC_Long-term survival_Sample 1

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX0204


title: U937_WildType_48hr_rep3

description: Gene expression data with no treatment at 48hr

source_name: U937_no treatment_48hr


title: U937_WildType_48hr_rep2


title: U937_WildType_72hr_rep1


title: U937_WildType_48hr_rep1


title: FOP (-) 48h


title: FOP (-) 24h


title: FOP BMP7 48h


title: FOP (-) 7d


title: U937_WildType_24hr_rep2


title: PDAC_Long-term survival_Sample 2

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX0235


title: PDAC_Long-term survival_Sample 4

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX0887


title: U937_Pu27_24hr_rep2

description: Gene expression data with PU27 treatment at 24hr


title: PDAC_Long-term survival_Sample 3

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with long-term survival
PDAC_Long-term survival_AX0739


title: U937_WildType_24hr_rep1


title: U937_WildType_0hr_rep3

description: Gene expression data with no treatment at 0hr

source_name: U937_no treatment_0hr


title: U937_WildType_0hr_rep1


title: K562 cells_AF1q_rep 2

city: Jinan

first: Wei

last: Li

state: Shandong

address: #44,West Wenhua Road

institute: Shandong University

description: Gene expression data from AF1q-overexpressing K562 cells, 2

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) algorithm as normalization method.

source_name: K562 cells, overexpressing AF1q

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit.

growth_protocol: K562 cells are cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

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

treatment_protocol: K562 cells infected with lentiviruses harboring AF1q and negative control are selected separately to be AF1q-1,2,3 and RFP-1,2,3.

value: chronic myeloid leukemia cell line


title: U937_WildType_0hr_rep2


title: K562 cells_NC_rep 1

description: Gene expression data from negative-control K562 cells, 1

source_name: K562 cells, negative control


title: 2-C1N miRNA

city: Callaghan

first: Murray

middle: J

last: Cairns

state: NSW

address: University Drive

country: Australia

institute: University of Newcastle

description: miRNA expression data from undifferentiated SH-SY5Y cells

hyb_protocol: Standard Affymetrix hybridisation protocol.

scan_protocol: Standard Affymetrix scan protocol.

data_processing: Raw expression data were exported from Genespring GX for further analysis in Excel.

source_name: SH-SY5Y cells Nucleus, biological replicate 1

label_protocol: miRNA HSR FlashTag Biotin labelling kit (Genisphere)

growth_protocol: Cells were grown in high-glucose DMEM with 10% FCS under standard conditions

extract_protocol: TRIzol extraction with addition of 2ul glycogen during precipitation step, and overnight precipitation.

treatment_protocol: Nucleus and Cytoplasm were fractionated by hypotonic lysis.

value: undifferentiated SH-SY5Y cells


title: 8-C2N miRNA

source_name: SH-SY5Y cells Nucleus, biological replicate 2


title: 14-C3N miRNA

source_name: SH-SY5Y cells Nucleus, biological replicate 3


title: 15-C3C miRNA

source_name: SH-SY5Y cells Cytoplasm, biological replicate 3


title: 9-C2C miRNA

source_name: SH-SY5Y cells Cytoplasm, biological replicate 2


title: FOP (-) 6h

description: Gene expression data of induced chondrocyte derived from induced mesenchymal stromal cells (iMSCs)


title: K562 cells_NC_rep 2

description: Gene expression data from negative-control K562 cells, 2


title: PDAC_Short survival_Sample 8

description:
Gene expression data from pancreatic ductal adenocarcinoma from patient with short survival
PDAC_Short survival_AX2017


title: K562 cells_AF1q_rep 1

description: Gene expression data from AF1q-overexpressing K562 cells, 1


title: 3-C1C miRNA

source_name: SH-SY5Y cells Cytoplasm, biological replicate 1


title: CFC1_overexpressed_NGPcells_sample1

city: Kitaadachi-gun Ina town

first: Takehiko

last: Kamijo

state: Saitama

address: 780, Komuro

institute: Saitama Cancer Center

description: Gene expression of CFC1-overexpressed NGP cells (CFC1)

hyb_protocol: Purified labeled RNA was hybridized to SurePrint G3 Human Gene Expression 8x60K Microarray Kit ver2.0 (Agilent Technologies).

scan_protocol: the scanning of microarrays, and data extraction from scanned images were conducted according to the Agilent protocol version 6.9.

data_processing: Data signal values were transformed to the log base and normalized with the 75% percentile shift method by GeneSpringGX (Agilent). Differentially expressed genes were selected based on the up-regulation of expression by more than 2-fold (moderate t-test, p<0.05).

label_protocol: 200 ng of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Cell culture was performed using RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using IsogenII according to the manufacturer's instructions.

treatment_protocol: Mock and CFC1 cDNA were transducted to NGP cells using lentiviral system. Puromycin (Invitrogen) selection was performed after transfection.

value: NGP

value: neuroblastoma cell line


title: FOP (-) 0h


title: CFC1_overexpressed_NGPcells_sample3


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 24)

city: Chapel Hill

first: Di

last: Wu

state: North Carolina

address: 385 S. Columbia Street, CB#7455

institute: University of North Carolina

description:
SAMPLE 24
mRNA gene expression

hyb_protocol: illumina array follow the manufacturer's instructions.

data_processing:
neqc for background correction and normalization
Normalized data was obtained as follow.   Raw intensities were normalized by using the neqc function in limma package, which performs normexp background correction and quantile normalization by using control probes then log2-transformed.

source_name: mouse antrum, gp130F/F

growth_protocol: no

treatment_protocol: no

tag: genotype

value: FF

tag: strain

tag: condition

value: GF

value: 4 weeks old

value: antrum


title: K562 cells_NC_rep 3

description: Gene expression data from negative-control K562 cells, 3


title: CFC1_overexpressed_NGPcells_sample2


title: CFC1_overexpressed_NGPcells_sample4


title: Mock_infected_NGPcells_sample3

description: Gene expression of mock-infected NGP cells (mock)


title: Mock_infected_NGPcells_sample4


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 20)

description:
SAMPLE 20
mRNA gene expression

scan_protocol: illumina array follow the manufacturer's instructions.

value: mixed

tag: age

tag: tissue


title: K562 cells_AF1q_rep 3

description: Gene expression data from AF1q-overexpressing K562 cells, 3


title: Mock_infected_NGPcells_sample1


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 21)

description:
SAMPLE 21
mRNA gene expression

label_protocol: illumina array follow the manufacturer's instructions.


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 22)

description:
SAMPLE 22
mRNA gene expression


title: Mock_infected_NGPcells_sample2


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 23)

description:
SAMPLE 23
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free, BL6 (SAMPLE 12)

description:
SAMPLE 12
mRNA gene expression

value: SPF


title: gp130F/F mouse antrum at 4 weeks old  at germ free condition (SAMPLE 19)

description:
SAMPLE 19
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 11)

description:
SAMPLE 11
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at germ free condition (SAMPLE 16)

description:
SAMPLE 16
mRNA gene expression

source_name: mouse antrum, WT

value: WT


title: wildtype mouse antrum at 4 weeks old at germ free condition, BL6 (SAMPLE 18)

description:
SAMPLE 18
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 10)

description:
SAMPLE 10
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at germ free condition (SAMPLE 13)

description:
SAMPLE 13
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free, BL6 (SAMPLE 6)

description:
SAMPLE 6
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at germ free condition, BL6 (SAMPLE 17)

description:
SAMPLE 17
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 2)

description:
SAMPLE 2
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 9)

description:
SAMPLE 9
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 8)

description:
SAMPLE 8
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at germ free condition (SAMPLE 14)

description:
SAMPLE 14
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at germ free condition (SAMPLE 15)

description:
SAMPLE 15
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 5)

description:
SAMPLE 5
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 3)

description:
SAMPLE 3
mRNA gene expression


title: gp130F/F mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 7)

description:
SAMPLE 7
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 1)

description:
SAMPLE 1
mRNA gene expression


title: wildtype mouse antrum at 4 weeks old at specific pathogen free (SAMPLE 4)

description:
SAMPLE 4
mRNA gene expression


title: 1972 A

city: Philadelphia

first: Jianglan

last: Liu

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

description:
s101
Melanoma cells (WM1972_A)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: melanomaA

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

growth_protocol: Human melanocytes were grown in 254CF medium before they reach the 70% confluency. Melanoma cells in MelanomaA subgroup were grown in Tumor 2% medium before they reach the 70% confluency. Melanoma cells in MelanomaF subgroup were grown in StemPro medium. NCSC were maintained in StemPro medium.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

value: melanoma cells cultured in 2% Tumor medium


title: 1976A 5_4

description:
s64
Melanoma cells (WM1976_A)


title: 115A 1.19

description:
s54
Melanoma cells (WM115_A)


title: Col-0 vs pfd4-2

city: Boston

first: Carlos

last: Perea Resa

address: 185 Cambridge St

institute: MGH-HMS

description: Biological replicate 1 of 3. 2-week-old Arabidopsis plants exposed 1 day at 4ºC.

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization). Limma software was used for the normalization.

organism: Arabidopsis thaliana

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Plants were grown on a 3:1 mix of substrate and vermiculite at 22C with a 16h/8h day/night photoperiod for two weeks

extract_protocol: Total RNA was extracted with Trizol and subsequently purified using Quiagen columns

treatment_protocol: Plants were conveniently trasnferrered to a growth chamber at 4C for 24h


title: 3734A 7_16

description:
s76
Melanoma cells (WM3734_A)


title: 115 A

description:
s103
Melanoma cells (WM115_A)


title: Col-0 vs pfd4-1


title: Col-0 vs pfd4-3


title: 3523A 38

description:
s19
Melanoma cells (WM3523_A)


title: 2_3734 A 3_31

description:
s38
Melanoma cells (WM3734_A)


title: 3523A 1.19

description:
s49
Melanoma cells (WM3523_A)


title: 1972A 1.19

description:
s44
Melanoma cells (WM1972_A)


title: 1976A 1.19

description:
s52
Melanoma cells (WM1976_A)


title: 1972A 38

description:
s13
Melanoma cells (WM1972_A)


title: 115 F

description:
s105
Melanoma cells (WM115_F)

source_name: melanomaF

value: melanoma cells cultured in stem cell medium


title: 115A 38

description:
s15
Melanoma cells (WM115_A)


title: 3130A 7_19

description:
s73
Melanoma cells (WM3130_A)


title: 3130 F

description:
s97
Melanoma cells (WM3130_F)


title: 3523A 2.5

description:
s46
Melanoma cells (WM3523_A)


title: 1972 F

description:
s104
Melanoma cells (WM1972_F)


title: 1976 F

description:
s102
Melanoma cells (WM1976_F)


title: RUNX1_b_2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 3 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing: Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma packages of Bioconductor.

source_name: K562 cells transduced with shRUNX1 vector

label_protocol: Microarrays were done using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the SurePrint G3 Human Gene Expression 8x60K v2 Microarray Kit, Product number G4851B, (Agilent Microarray Design ID 039494). 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: K562 cells were grown under standard conditions (ATCC). Human CD34+ cells were purified from mobilised apharesis samples with magnetic CD34+ antibody beads (Miltenyi). Cells were maintained and transduced in serum free expansion medium (StemSpan, StemCell Technologies)

extract_protocol: Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies). mRNA was reverse-transcribed using oligo-dT and random hexameric primers and was quantified via qRT-PCR analysis using SYBR Green (Invitrogen/Life Technologies).

treatment_protocol: Cells were lentivirally transduced with specific shvectors or a control shvector targeted against LacZ. Transduction was monitored by GFP, only cells with more than 95% GFP positiv cells were further processed. Cells were harvested 5 days after transduction.

value: K562 CML cell line


title: 1976A 38

description:
s17
Melanoma cells (WM1976_A)


title: Tal1_b_1

source_name: K562 cells transduced with shTAL1 vector


title: 3130A

description:
s22
Melanoma cells (WM3130_A)


title: 3734F 7_16

description:
s75
Melanoma cells (WM3734_F)


title: 3130F 7_19

description:
s74
Melanoma cells (WM3130_F)


title: 1_3734 F 5_31

description:
s37
Melanoma cells (WM3734_F)


title: 1976F

description:
s53
Melanoma cells (WM1976_F)


title: RUNX1_b_1


title: PRMT3_a_1

source_name: K562 cells transduced with shPRMT3 vector


title: 3130F 31207

description:
s23
Melanoma cells (WM3130_F)


title: PRMT6_a_2

source_name: K562 cells transduced with shPRMT6 vector


title: Tal1_b_2


title: LacZ_b_2

source_name: K562 cells transduced with shLacZ control vector


title: 115F 1.19

description:
s43
Melanoma cells (WM115_F)


title: 115F 38

description:
s16
Melanoma cells (WM115_F)


title: LacZ_a_2


title: 1972F 1.19

description:
s45
Melanoma cells (WM1972_F)


title: SC-D26 D14

description:
s32
Neural crest stem cells

source_name: stem

value: Neural crest stem cells derived from human skin


title: SC-D19 P0

description:
s10
Neural crest stem cells


title: PRMT3_a_2


title: SC-D18 P0 D15

description:
s11
Neural crest stem cells


title: PRMT6_a_1


title: 1972F 38

description:
s14
Melanoma cells (WM1972_F)


title: SC-D11

description:
s31
Neural crest stem cells


title: CD34_Tal1_1

source_name: human primary CD34 cells transduced with shTAL1 vector

value: primary CD34+ cells


title: SC-D13

description:
s8
Neural crest stem cells


title: CD34_RUNX1_1

source_name: human primary CD34 cells transduced with shRUNX vector


title: CD34_Tal1_2


title: FOM 173_1

description:
s98
Melanocytes

source_name: melanocyte

value: Parental melanocyte


title: 1976F 38

description:
s18
Melanoma cells (WM1976_F)


title: SC-D15 P3

description:
s9
Neural crest stem cells


title: LacZ_a_1


title: Form 173 p6

description:
s95
Melanocytes


title: FOM178-1 P5

description:
s56
Melanocytes


title: CD34_RUNX1_2


title: FOM136 1020

description:
s24
Melanocytes


title: CD34_LacZ_2

source_name: human primary CD34 cells transduced with shLacZ control vector


title: FOM 136-1 P9

description:
s55
Melanocytes


title: CD34_PRMT6_2

source_name: human primary CD34 cells transduced with shPRMT6 vector


title: LacZ_b_1


title: CD34_LacZ_1


title: FOM 173 5_4

description:
s63
Melanocytes


title: Neonatal male NHR heart 1_miRNA

city: Melbourne

first: Francine

last: Marques

state: VIC

address: Level 3, 75 Commercial Rd

institute: Baker IDI Heart and Diabetes

description:
NOM1
microRNA expression from neonatal male NHR heart

hyb_protocol: After fragmentation, samples were hybridized for 20 hr at 55°C to Agilent Rat miRNA Microarrays (V3, release 16.0). Chips were washed and stained in the Agilent Microarray Hybridization Chamber SureHyb. The Agilent’s miRNA Complete Labeling and Hyb Kit was used according to Agilent's manual.

scan_protocol: The chips were scanned on an Agilent G2565BA scanner.

data_processing: The samples were between array normalized so that expression intensities were similar across all arrays using the quantile method, in the R application (version 2.11.1). Differentially expressed miRNAs were identified using the moderated two-sample t-test in the Limma package.

source_name: Neonatal male NHR heart

label_protocol: 100ng of total RNA was prepared for hybridisation according to the standard Agilent protocol (microRNA Labeling & Hybridization Kit Manual, Agilent, Version 1.7, October 2009).

growth_protocol: The whole heart from neonatal animals was obtained immediately after euthanasia.

extract_protocol: miRNeasy kit (Qiagen) was used for extraction of total RNA and microRNA according to the manufacturer's instructions.

treatment_protocol: Tissue was transferred either into microtubes and immediately frozen with liquid nitrogen. It was then preserved at -80°C before RNA extraction.

value: Male

value: heart

value: NHR

value: 2 days old

tag: heart size

value: Normal


title: Neonatal male NHR heart 2_miRNA

description:
NOM2
microRNA expression from neonatal male NHR heart


title: Neonatal female NHR heart 4_miRNA

description:
NOF4
microRNA expression from neonatal female NHR heart

source_name: Neonatal female NHR heart

value: Female


title: GFP-2

city: Wako

first: Kota

last: Tamada

address: Hirosawa 2-1

department: BSI

institute: RIKEN

description: raw data file: 2nd.txt

hyb_protocol: 10 ug of digoxigenin-labeled cRNA samples were fragmented for 30 min at 60℃ and hybridized for 16h to Mouse Genome Survey Microarrays (Applied Biosystems) at a temperature of 55℃. After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.

scan_protocol: Chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure.

data_processing: Detectable probes were determined by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool. Global median normalization method was used for calculating the normalized value for each array.

label: Digoxigenin

source_name: GFP-

label_protocol: 500 ng total RNA were introduced into an RT-IVT reaction: the RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides (Roche).

growth_protocol: No growth. Sorted cells were immediately used for total RNA extraction.

extract_protocol: Total RNA was isolated from FACS-sorted cortical cells using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The purity and integrity of the RNAs were assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies) and the quantities were determined by NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Sorted cells from GAD67-EGFP +/- P0 pup by flow cytometory

value: Cells from cerebral cortex

tag: cell gfp status

value: GFP-

tag: replicate


title: GFP+3

description: raw data file: 3rd.txt

source_name: GFP+

tag: cell type

value: GFP+


title: GFP-3

description: raw data file: 3rd.txt

tag: genotype/variation


title: Neonatal male NHR heart 3_miRNA

description:
NOM3
microRNA expression from neonatal male NHR heart


title: β-catenin ChIP 3

city: Berne

first: Christian

last: Strauss

address: Laengassstrasse 122

country: Switzerland

institute: Institute of Animal Pathology

description: ChIP-chip mouse keratinocytes at onset of terminal differentiation using β-catenin antibodies

hyb_protocol: according to NimbleGen standart protocol, performed by NimbleGen

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Publication conclusions based on MEAN scaled, log2 (ChIP/Input) ratios.
Supplementary processed data files: "mean".txt and "peaks".txt.

source_name: β-catenin (bCat) ChIP DNA from mouse keratinocytes

growth_protocol: keratinocytes were grown till confluency, then four days in high calcium medium and harvested

extract_protocol: Four days after calcium switch, keratinocytes grown in 4x75cm2 flasks were washed with PBS(+) and proteins cross-linked with 2mM di-succinimidyl-glutarate(5) for 45min at RT followed by 1% formaldehyde for 15min at RT. Cells were scraped into 3ml PBS(+), centrifuged at 1,000rpm for 10min at RT and cell pellets lysed with 500μl lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0). To shear DNA, lysates were sonicated in a Covaris S2 water bath sonicator (Covaris; Raublingen, Germany) with settings for 500bp DNA fragment length, confirmed by BioAnalyzer©. Samples were diluted 1:1 with 70mM HEPES, pH 7.5, 2.5mM NaCl, 1.5mM EDTA, 1.5% Triton-X100, 0.6% Deoxycholate (DOC) and centrifuged for 30min at 14,000rpm (Centrifuge 5417R, Eppendorf). The supernatant was pre-cleared with tRNA blocked Dynabeads® (Invitrogen Switzerland) for 2h at 4°C by rotation (Input). Immunoprecipitation was performed by rotating with 5µg antibody (PG, β-catenin (BD Biosciences)) per 1ml lysate at 4°C overnight, and 30µl Dynabeads® (pre-blocked with 1mg/ml tRNA for 1h at 4°C rotating) were added the next day for 3h at 4°C. Beads were washed twice with 1ml mixed micelle washing buffer (150mM NaCl, 100mM Tris-HCl, pH 8.1, 100mM EDTA, pH 8.0, 5% w/v sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with 1ml buffer 500 (0.1% DOC, 1mM EDTA, pH 8.0, 50mM HEPES, pH 7.5, 500mM NaCl, 1% Triton X-100, 0.2% NaN3), twice with 1ml LiCl buffer (0.5% DOC, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris-HCl, pH 8.0, 0.2% NaN3) and once with 1ml TE buffer. Protein-DNA complexes were eluted with 100µl elution buffer (1% SDS, 1mM NaHCO3) for 2x30min at 60°C. Samples were diluted 1:1 with TE buffer and NaCl (0.5M final concentration), reverse cross-linked overnight at 65°C followed by 100ng/µl proteinase K and 100ng/µl RNase A treatment for 1h at 55°C. A tenth volume 4M LiCl was added and proteins extracted with phenol:chloroform:isoamyl alcohol. DNA was precipitated with 100% ice cold ethanol and washed with 70% ethanol before resuspending in 50µl dH2O. The input sample was treated in the same way. The DNA amount was determined using NanoDrop

treatment_protocol: at confluency, terminal differentiation was initiated with high calcium medium

value: keratinocytes

tag: chip antibody

value: β-catenin

tag: chip antibody vendor

value: BD Biosciences

tag: chip antibody catalog#

source_name: Input DNA from mouse keratinocytes

value: none, input DNA


title: GFP+4

description: raw data file: 4th.txt


title: Neonatal female NHR heart 3_miRNA

description:
NOF3
microRNA expression from neonatal female NHR heart

tag: gender


title: β-catenin ChIP 2

label_protocol: according to NimbleGen standart protocol, performed by NimbleGen


title: CD34_PRMT6_1


title: Neonatal male NHR heart 4_miRNA

description:
NOM4
microRNA expression from neonatal male NHR heart


title: Fom 174-1 P3

description:
s2
Melanocytes


title: β-catenin ChIP 1


title: GFP+1

description: raw data file: 1st.txt


title: Plakoglobin ChIP 2

description: ChIP-chip mouse keratinocytes at onset of terminal differentiation using Plakoglobin antibodies

source_name: Plakoglobin (PG) ChIP DNA from mouse keratinocytes

value: Plakoglobin


title: Plakoglobin ChIP 3


title: GFP+2

description: raw data file: 2nd.txt


title: Neonatal female NHR heart 1_miRNA

description:
NOF1
microRNA expression from neonatal female NHR heart


title: Neonatal female NHR heart 2_miRNA

description:
NOF2
microRNA expression from neonatal female NHR heart


title: Neonatal male HHR heart 4_miRNA

description:
BHM4
microRNA expression from neonatal male HHR heart

source_name: Neonatal male HHR heart

value: HHR

value: Hypetrophic


title: GFP-4

description: raw data file: 4th.txt


title: GFP-1

description: raw data file: 1st.txt


title: Neonatal female HHR heart 3_miRNA

description:
BHF3
microRNA expression from neonatal female HHR heart

source_name: Neonatal female HHR heart


title: iPSC_2

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

description: Human induced Pluripotent Stem cells, replicate 2

hyb_protocol: Manufature's protocol

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

data_processing: GeneSpring GX. Signals were normalized to percentile.

label_protocol: Manufature's protocol

growth_protocol: Somatic cell lines were maintained in appropriate conditions according to manufacturer's recommendation.   TRA-1-60 (+) cells and iPSCs were maintained on SNL feeders in Primate ESC medium (ReproCELL) supplemented with 4 ng/ml basic fibroblast growth factor at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: The samples on day3 were EGFP (+) cells collected by flow cytometry. TRA-1-60 (+) cells on days 7-28 were collected by magnetic activated cell sorting.

value: induced Pluripotent Stem cell line


title: iPSC_1

description: Human induced Pluripotent Stem cells, replicate 1


title: Neonatal female HHR heart 2_miRNA

description:
BHF2
microRNA expression from neonatal female HHR heart


title: iPSC_3

description: Human induced Pluripotent Stem cells, replicate 3


title: Mock_2

description: Human dermal fibroblasts introduced empty vector (Mock), replicate 2

value: Reprogramming cells


title: DPC

description: Human dental pulp-derived fibroblastic cells

value: Somatic cell line


title: Neonatal male HHR heart 3_miRNA

description:
BHM3
microRNA expression from neonatal male HHR heart

value: Male

value: heart


title: OSKM_3

description: Human dermal fibroblasts expressing OSKM, replicate 3